hmmmmmm argue.....maybe you might see it that way....putting out what I believe to be truth....that's how I look at it....I have tried to let it die.....but there are just to many questions not answered on the side of evolution.....want to give the evolutionist a fair chance.

This is from someone who doesn't care one way or another:

You put out what you believe and they put out what they believe and nobody gets anywhere.

We all know what you and they believe now, so I think the thread, as far as what people believe about evolution... should logically be dead.

Is anybody logical?

Well except for new people that come in.....that I still get e-mails from. I would really like someone to show me something ligit that has evolved....I know they say that it happens according to them over billions of years...so something in the past 500 years has to have evolved....otherwise I would say that the point of evolution has not been proved it is still a theory and creation has more credability.

Here is a article on the evolution of a platypus

Genome analysis of the platypus reveals unique signatures of evolution


We present a draft genome sequence of the platypus, Ornithorhynchus anatinus. This monotreme exhibits a fascinating combination of reptilian and mammalian characters. For example, platypuses have a coat of fur adapted to an aquatic lifestyle; platypus females lactate, yet lay eggs; and males are equipped with venom similar to that of reptiles. Analysis of the first monotreme genome aligned these features with genetic innovations. We find that reptile and platypus venom proteins have been co-opted independently from the same gene families; milk protein genes are conserved despite platypuses laying eggs; and immune gene family expansions are directly related to platypus biology. Expansions of protein, non-protein-coding RNA and microRNA families, as well as repeat elements, are identified. Sequencing of this genome now provides a valuable resource for deep mammalian comparative analyses, as well as for monotreme biology and conservation.

The platypus (Ornithorhynchus anatinus) has always elicited excitement and controversy in the zoological world1. Some initially considered it to be a true mammal despite its duck-bill and webbed feet. The platypus was placed with the echidnas into a new taxon called the Monotremata (meaning 'single hole' because of their common external opening for urogenital and digestive systems). Traditionally, the Monotremata are considered to belong to the mammalian subclass Prototheria, which diverged from the therapsid line that led to the Theria and subsequently split into the marsupials (Marsupialia) and eutherians (Placentalia). The divergence of monotremes and therians falls into the large gap in the amniote phylogeny between the eutherian radiation about 90 million years (Myr) ago and the divergence of mammals from the sauropsid lineage around 315 Myr ago (Fig. 1). Estimates of the monotreme–theria divergence time range between 160 and 210 Myr ago; here we will use 166 Myr ago, recently estimated from fossil and molecular data2.

Figure 1: Emergence of traits along the mammalian lineage.
Amniotes split into the sauropsids (leading to birds and reptiles) and synapsids (leading to mammal-like reptiles). These small early mammals developed hair, homeothermy and lactation (red lines). Monotremes diverged from the therian mammal lineage 166 Myr ago2 and developed a unique suite of characters (dark-red text). Therian mammals with common characters split into marsupials and eutherians around 148 Myr ago2 (dark-red text). Geological eras and periods with relative times (Myr ago) are indicated on the left. Mammal lineages are in red; diapsid reptiles, shown as archosaurs (birds, crocodilians and dinosaurs), are in blue; and lepidosaurs (snakes, lizards and relatives) are in green.

High resolution image and legend (192K)


The most extraordinary and controversial aspect of platypus biology was initially whether or not they lay eggs like birds and reptiles. In 1884, William Caldwell's concise telegram to the British Association announced "Monotremes oviparous, ovum meroblastic", not holoblastic as in the other two mammalian groups3, 4. The egg is laid in an earthen nesting burrow after about 21 days and hatches 11 days later5, 6. For about 4 months, when most organ systems differentiate, the young depend on milk sucked directly from the abdominal skin, as females lack nipples. Platypus milk changes in protein composition during lactation (as it does in marsupials, but not in most eutherians5). The anatomy of the monotreme reproductive system reflects its reptilian origins, but shows features typical of mammals7, as well as unique specialized characteristics. Spermatozoa are filiform, like those of birds and reptiles, but, uniquely among amniotes, form bundles of 100 during passage through the epididymis. Chromosomes are arranged in defined order in sperm8 as they are in therians, but not birds9. The testes synthesize testosterone and dihydrotestosterone, as in therians, but there is no scrotum and testes are abdominal10.

Other special features of the platypus are its gastrointestinal system, neuroanatomy (electro-reception) and a venom delivery system, unique among mammals11. Platypus is an obligate aquatic feeder that relies on its thick pelage to maintain its low (31–32 °C) body temperature during feeding in often icy waters. With its eyes, ears and nostrils closed while foraging underwater, it uses an electro-sensory system in the bill to help locate aquatic invertebrates and other prey12, 13. Interestingly, adult monotremes lack teeth.

The platypus genome, as well as the animal, is an amalgam of ancestral reptilian and derived mammalian characteristics. The platypus karyotype comprises 52 chromosomes in both sexes14, 15, with a few large and many small chromosomes, reminiscent of reptilian macro- and microchromosomes. Platypuses have multiple sex chromosomes with some homology to the bird Z chromosome16. Males have five X and five Y chromosomes, which form a chain at meiosis and segregate into 5X and 5Y sperm17, 18. Sex determination and sex chromosome dosage compensation remain unclear.

Platypuses live in the waterways of eastern and southern Australia, including Tasmania. Its secretive lifestyle hampers understanding of its population dynamics and the social and family structure. Platypuses are still relatively common in the wild, but were recently reclassified as 'vulnerable' because of their reliance on an aquatic environment that is under stress from climate change and degradation by human activities. Water quality, erosion, destruction of habitat and food resources, and disease now threaten populations. Because the platypus has rarely bred in captivity and is the last of a long line of ornithorhynchid monotremes, their continued survival is of great importance. Here we describe the platypus genome sequence and compare it to the genomes of other mammals, and of the chicken.

Top of pageSequencing and assembly

All sequencing libraries were prepared from DNA of a single female platypus (Glennie; Glenrock Station, New South Wales, Australia) and were sequenced using established whole-genome shotgun (WGS) methods19. A draft assembly was produced from 6 coverage of whole-genome plasmid, fosmid and bacterial artificial chromosome (BAC) reads (Supplementary Table 1) using the assembly program PCAP20 (Supplementary Notes 1). A BAC-based physical map was developed in parallel with the sequence assembly and subsequently integrated with the WGS assembly to provide the primary means of scaffolding the assembly into larger ordered and oriented groupings (ultracontigs; Supplementary Notes 2 and 3 and Supplementary Table 2). Because there were no platypus linkage maps available, we used fluorescent in situ hybridization (FISH) to localize a subset of the sequence scaffolds to chromosomes following the agreed nomenclature21. Of the 1.84 gigabases (Gb) of assembled sequence, 437 megabases (Mb) were ordered and oriented along 20 of the platypus chromosomes. We analysed numerous metrics of assembly quality (Supplementary Notes 4–11) and we conclude that despite the adverse contiguity, the existing platypus assembly, given its structural and nucleotide accuracy, provides a reasonable substrate for the analyses presented here.

Top of pageNon-protein-coding genes

In general, the platypus genome contains fewer computationally predicted non-protein-coding (nc)RNAs (1,220 cases excluded high repetitive small nucleolar RNA (snoRNA) copies; see below) than do other mammalian species (for example, human with 4,421 Rfam hits), similar to observations in chicken19 (655 Rfam-based ncRNAs). This is probably because of the extensive retrotransposition of ncRNAs in therian mammals and the apparent lack of L1-mediated retrotransposition in chicken and platypus. The exception to this is the platypus family of snoRNAs, which is markedly expanded (2,000 matches to the Rfam covariant models) compared to that for therian mammals (200). snoRNAs are involved in RNA modifications, in particular of ribosomal RNA, and are often located in introns of protein-coding genes22. Our investigations revealed a novel short-interspersed-element (SINE)-like, snoRNA-related retrotransposon—which we have labelled snoRTEs—that has duplicated in platypus to 40,000 full-length or truncated copies. It is retrotransposed by means of retrotransposon-like non-LTR (long terminal repeat) transposable elements (RTE) as opposed to the L1-mediated transposition mechanism in therians23. We constructed a complementary DNA library of small, ncRNAs and identified 371 consensus sequences of small RNAs that included 166 snoRNAs23 (Supplementary Table 3). Ninety-nine of these cloned snoRNAs are found in paralogous families, and 21 of them belong to the snoRTE class. The presence of both the structural requirements known to be important in snoRNA function24 and evidence of their expression are consistent with these snoRTE elements being functional in the platypus. Similar to other unrelated ncRNAs that have proliferated in therian mammals (for example, 7SL RNA-derived primate Alu elements, tRNA-derived rodent identifier (ID) elements), this recent SINE-like expansion is probably due to chance events. However, given the RNA modification activity of snoRNAs, and our increasing awareness of the cellular importance of RNA molecules, it might be that some of the retrotranspositionally duplicated RNAs were exapted into new functions in this species.

Other small RNAs

Overall, we found commonalities with small RNA (sRNA) pathways of other mammals, but also features that are unique to monotremes. Components of the RNA interference machinery are conserved in platypus, including elements of biogenesis pathways (Dicer and Drosha) and RNA-interference effector complexes (argonaute proteins; Supplementary Table 4). Of 20,924,799 platypus and echidna sRNA reads derived from liver, kidney, brain, lung, heart and testis, 67% could be assigned to known microRNA (miRNA) families. Established patterns of miRNA expression were generally recapitulated in monotremes.

To determine the conservation patterns of miRNAs in platypus, we identified platypus miRNAs sharing at least 16-nucleotide identity with miRNAs in eutherian mammals (mouse/human) and chicken. Although most conserved miRNAs were identified across these vertebrate lineages (137 miRNAs), 10 miRNAs were shared only with eutherians (mouse/human) and 4 only with chicken (Fig. 2a). miRNAs can be classified into families based on identity of the functional 'seed' region at position 2–8 of the mature miRNA strand. We identified miRNA families that were shared between platypus and eutherians but not chicken (40 families), or between platypus and chicken but not eutherians (8 families), suggesting that for some miRNAs only the seed region may have been selectively conserved (Fig. 2a). Conserved miRNAs tended to be more robustly expressed in the platypus tissues analysed than lineage-restricted miRNAs (Fig. 2b).

Figure 2: Platypus miRNAs.

a, Platypus has miRNAs shared with eutherians and chickens, and a set that is platypus-specific. miRNAs cloned from six platypus tissues were assigned to families based on seed conservation. Platypus miRNAs and families were divided into classes (indicated) based on their conservation patterns with eutherian mammals (mouse/human) and with chicken. b, Expression of platypus miRNAs. The cloning frequency of each platypus mature miRNA sequenced more than once is represented by a vertical bar and clustered by conservation pattern. miRNAs from a set of monotreme-specific miRNA clusters that are expressed in testis are shaded in red.

High resolution image and legend (82K)



To identify miRNAs unique to monotremes we used a heuristic search that identifies miRNA candidates in deep-sequencing data sets25. This method predicted 183 novel miRNAs in platypus and echidna (Fig. 2a). Notably, 92 of these lay in 9 large clusters, on platypus chromosome X1 and contigs 1754, 7160, 7359, 8388, 11344, 22847, 198872 and 191065. Physical mapping confirmed that at least five of these contigs are linked to the long arm of chromosome X1 (ref. 25). These abundantly expressed clusters were sequenced almost exclusively from platypus and echidna testis (Fig. 2b). The expansion of this unique miRNA class and its expression domain suggest possible roles in monotreme reproductive biology25.

Piwi-interacting RNAs (piRNAs) associate with a germline-expressed clade of argonaute proteins, known as Piwis26, and have a role in transposon silencing and genome methylation26. Monotreme piRNAs bear strong structural similarity to those in eutherians. They are 29 nucleotides in length and arise from large testis-specific genomic clusters with distinct genomic strand asymmetry, often with a typical 'bidirectional' organization. We identified 50 major platypus piRNA clusters as well as numerous smaller clusters25. In contrast to piRNAs in mouse, platypus piRNAs are repeat-rich and bear strong signatures of active transposon defence.

Top of pageGene evolution

We set out to define the protein-coding gene content of platypus to illuminate both the specific biology of the monotreme clade and for comparisons to eutherians and marsupials, or to chicken, the representative sauropsid. Protein-coding genes were predicted using the established Ensembl pipeline27 suitably modified for platypus (Supplementary Notes 14), with a greater emphasis placed on similarity matches to mammalian genes. Overall this resulted in 18,527 protein-coding genes being predicted from the current platypus assembly. The number of platypus protein-coding genes thus is similar to estimates (18,600–20,800) for human and opossum28, 29.

We were interested first in identifying platypus genes that contribute most to core biological functions that are conserved across the mammals. These will typically be 'simple' 1:1 orthologues, genes that have remained as single copies without duplication or deletion in platypus, in Eutheria (specifically, in dog, human and mouse) and in opossum, a representative marsupial. Subsequently, we considered genes that have been duplicated or deleted in the monotreme lineage, or that have been lost in eutherian and/or marsupial lineages. Such genes are proposed to contribute most to the lineage-specific biological functions that distinguish individual mammals30. These studies required the use of an outgroup species, here chicken, a representative of the sauropsids.

As expected, the majority of platypus genes (82%; 15,312 out of 18,596) have orthologues in these five other amniotes (Supplementary Table 5). The remaining 'orphan' genes are expected to primarily reflect rapidly evolving genes, for which no other homologues are discernible, erroneous predictions, and true lineage-specific genes that have been lost in each of the other five species under consideration. Simple 1:1 orthologues, which have been conserved without duplication, deletion or non-functionalization across the five mammalian species, were greatly enriched in housekeeping functions, such as metabolism, DNA replication and mRNA splicing (Supplementary Table 6).

We then identified evolutionary lineages that experienced the most stringent purifying selection. The mouse terminal lineage exhibited a significantly higher degree of purifying selection (the ratio of amino acid replacement to silent substitution rates, dN/dS = 0.105, P < 0.001) than dog, opossum and chicken terminal branches (values of 0.123–0.128); human and platypus terminal lineages showed significantly reduced purifying selection (both 0.132, P < 0.03). These values probably reflect the increased efficiency of purifying selection in populations of larger effective size, such as that of mouse31. We find that at least one nucleotide substitution has occurred, on average, in synonymous sites of platypus and human orthologues since their last common ancestor (Supplementary Notes 17 and Supplementary Fig. 1). This means that most neutral sequence cannot be aligned accurately between monotreme and eutherian genomes.

Next, we determined the genetic distance of echidna (Tachyglossus aculeatus) from platypus. The median dS value of 0.125 for the orthologues of echidna and platypus, when compared to the value for the monotreme lineage, predicts that platypus and echidna last shared a common ancestor 21.2 Myr ago. Although similar to previous estimates32, this value seems to be at odds with fossil evidence, perhaps owing to relatively recent reductions of mutational rates in the monotreme lineage33.

Top of pageMonotreme biology

We next investigated whether the ancestral reptilian characters of monotremes are reflected in the set of genes that have been retained in platypus, sauropsids and other vertebrates from outside of the amniote clade (such as frogs and fish), but have been lost from eutherian and marsupial lineages (Fig. 1). These ancestral, sauropsid-like, characters of platypus include oviparity (egg laying) and the outward appearances of its spermatozoa and retina. Simultaneously, we sought genetic evidence within the platypus genome both for characteristics peculiar to monotremes, such as venom production and electro-reception, and for characteristics unique to mammals, in particular lactation. By investigating platypus homologues of genes already known to be involved in specific physiological processes (see Methods), we highlight those platypus genes for which evolution exemplifies the ancestral or derived physiological characters of monotremes.

Chemoreception

The semi-aquatic platypus was expected to sense its terrestrial, but not aquatic, environment by detecting airborne odorants using olfactory receptors and vomeronasal receptors (types 1 and 2: V1Rs, V2Rs). Nevertheless large numbers of odorant receptor, V1R and V2R homologues (approximately 700, 950 and 80, respectively) are apparent in the platypus genome assembly, although for each family only a minority lack frame disruptions (approximately 333, 270 and 15, respectively)34. Many of these platypus genes and pseudogenes are monophyletic, having arisen by duplication in the 166 Myr since the last common ancestor of monotremes and therians. Although mouse and rat genomes possess greater numbers of odorant receptors and V2Rs than the platypus genome35, 36, the platypus repertoire of V1Rs, showing undisrupted reading frames, is the largest yet seen, 50% more than for mouse (Fig. 3b). This is particularly noteworthy as the Anolis carolinensis lizard (sequence data used with the permission of the Broad Institute) and the chicken19 seem to possess no such receptors. The large expansion of the platypus V1R gene family might reflect sensory adaptations for pheromonal communication or, more generally, for the detection of water-soluble, non-volatile odorants, during underwater foraging.

Figure 3: The platypus chemosensory receptor gene repertoire.
a, b, The platypus genome contains only few olfactory receptor genes from olfactory receptor families that are greatly expanded among therians (three other mammals and a reptile shown), but many genes in olfactory receptor family 14 (a), and relatively numerous vomeronasal type 1 (V1R) receptors (b). These schematic phylogenetic trees show relative family sizes and pseudogene contents of different gene families (enumerated beside internal branches) and the V1R repertoire in platypus. Pie charts illustrate the proportions of intact genes (heavily shaded) versus disrupted pseudogenes (lightly shaded).

High resolution image and legend (132K)



The platypus odorant receptor gene repertoire is roughly one-half as large as those in other mammals37. Nevertheless, platypus odorant receptors fall into class, family and subfamily structures that are well represented from across the mammals, with a few notable exceptions such as family 14 (Fig. 3a). Together with the finding that lizard contains only 200 odorant receptor genes and pseudogenes, this indicates that the platypus olfactory repertoire is, as expected, more akin to other mammals than it is to sauropsids.

Eggs

Fertilization in the platypus exhibits both sauropsid and therian characteristics. Platypus ova are small (4 mm diameter) relative to comparably sized reptiles and birds, and eggs hatch at an early stage of development so that most growth of the embryo and infant is dependent on lactation, as in marsupials. Like all mammals and many other amniotes, when fertilization occurs the ovum is invested with a zona pellucida. The platypus genome encodes each of the four proteins of the human zona pellucida38, as well as two ZPAX genes (Table 1) that previously were observed only in birds, amphibians and fish. The aspartyl-protease nothepsin is present in platypus, but has been lost from marsupial and eutherian genomes (Table 1). In zebrafish, this gene is specifically expressed in the liver of females under the action of oestrogens, and accumulates in the ovary39. These are the same characteristics as of the vitellogenins, indicating that nothepsin may be involved in processing vitellogenin or other egg-yolk proteins. We find that platypus has retained a single vitellogenin gene and pseudogene, whereas sauropsids such as chicken have three and the viviparous marsupials and eutherians have none.

Table 1: Platypus genes that have been lost from the eutherian lineage

Spermatozoa

Orthologues of many of the eutherian sperm membrane proteins related to fertilization40 are present in platypus (and marsupial) genomes. These include the genes for a number of putative zona pellucida receptors and proteins implicated in sperm–oolemma fusion. Testis-specific proteases, which in eutherians participate in degradation of the zona pellucida during fertilization, are all absent from the platypus genome assembly.

Monotreme spermatozoa undergo some post-testicular maturational changes, including the acquisition of progressive motility, loss of cytoplasmic droplets and aggregation of single spermatozoa into bundles during passage through the epididymis11. Nevertheless, maturational changes in the sperm surface that are both unique and essential in other mammals for fertilization of the ovum have yet to be identified. Also, the epididymis of monotremes is not highly adapted for sperm storage as in most marsupial and eutherian mammals. Consistent with these findings is the absence of platypus genes for the epididymal-specific proteins that have been implicated in sperm maturation and storage in other mammals. The most abundant secreted protein in the platypus epididymis is a lipocalin, the homologues of which are the most secreted proteins in the reptilian epididymis41. Notably, ADAM7, a protease that is secreted in the epididymis of eutherians, has an orthologue in the platypus. This is a bona fide protease with a characteristic Zn2+-coordinating sequence HExxH in the platypus, in the opossum and the tree shrew (Tupaia belangeri). However, loss of its proteolytic activity is predicted in eutherians42 owing to a single point mutation within its active site (E to Q).

Lactation and dentition

Lactation is an ancient reproductive trait whose origin predates the origin of mammals. It has been proposed that early lactation evolved as a water source to protect porous parchment-shelled eggs from desiccation during incubation43 or as a protection against microbial infection. Parchment-shelled egg-laying monotremes also exhibit a more ancestral glandular mammary patch or areola without a nipple that may still possess roles in egg protection. However, in common with all mammals, the milk of monotremes has evolved beyond primitive egg protection into a true milk that is a rich secretion containing sugars, lipids and milk proteins with nutritional, anti-microbial and bioactive functions. In a reflection of this eutherian similarity platypus casein genes are tightly clustered together in the genome, as they are in other mammals, although platypus contains a recently duplicated -casein gene (Supplementary Fig. 2).

Mammalian casein genes are thought to have originally arisen by duplication of either enamelin or ameloblastin44, both of which are tooth enamel matrix protein genes that are located adjacent to the casein gene cluster in eutherians and, we find, also in platypus. Adult platypuses, as well as echidnas, lack teeth but the conservation of these enamel protein genes is consistent with the presence of teeth and enamel in the juvenile, as well as the fossil platypuses45.

Venom

Only a handful of mammals are venomous, but the male platypus is unique among them in delivering its poison not via a bite but from hind-leg spurs. Despite the obvious difficulties in obtaining samples, it is now known that platypus venom is a cocktail of at least 19 different substances46 including defensin-like peptides (vDLPs), C-type natriuretic peptide (vCNP) and nerve growth factor (vNGF). When analysed phylogenetically and mapped to the platypus genome assembly, these sequences are revealed to have arisen from local duplications of genes possessing very different functions (Fig. 4). Notably, duplications in each of the -defensin, C-type natriuretic peptide and nerve growth factor gene families have also occurred independently in reptiles during the evolution of their venom47. Convergent evolution has thus clearly occurred during the independent evolution of reptilian and monotreme venom48.

Figure 4: The evolution of -defensin peptides in platypus venom gland.
The diagram illustrates separate gene duplications in different parts of the phylogeny for platypus venom defensin-like peptides (vDLPs), for lizard venom crotamine-like peptides (vCLPs) and for snake venom crotamines. These venom proteins have thus been co-opted from pre-existing non-toxin homologues independently in platypus and in lizards and snakes48.

High resolution image and legend (136K)



Immunity

Although the major organs of the monotreme immune system are similar to those of other mammals49, the repertoire of immunity molecules shows some important differences from those of other mammals. In particular, the platypus genome contains at least 214 natural killer receptor genes (Supplementary Notes 18) within the natural killer complex, a far larger number than for human (15 genes50), rat (45 genes50) or opossum (9 genes51).

Both platypus and opossum genomes contain gene expansions in the cathelicidin antimicrobial peptide gene family (Supplementary Fig. 3). Among eutherians, primates and rodents have a single cathelicidin gene52, 53, whereas sheep and cows have numerous genes that have been duplicated only recently54. The expanded repertoire of cathelicidin genes in both marsupials and monotremes may arm their immunologically naive young with a diverse arsenal of innate immune responses. In eutherians, with their increases in length of gestation and advances in development in utero of their immune systems, the diversity of antimicrobial peptide genes may have become less critical. The platypus genome also contains an expansion in the macrophage differentiation antigen CD163 gene family (Supplementary Notes 18).

Top of pageGenome landscape

First, we analyse the phylogenetic position of platypus and confirm that marsupials and eutherians are more closely related than either is to monotremes (Supplementary Notes 19). We then describe platypus chromosomes and observe some properties of platypus interspersed and tandem repeats. We also discuss a potential relationship between interspersed repeats and genomic imprinting and investigate how the extremely high G+C fraction in platypus affects the strong association seen in eutherians between CpG islands and gene promoters.

Platypus chromosomes

Platypus chromosomes provide clues to the relationship between mammal and reptile chromosomes, and to the origins of mammal sex chromosomes and dosage compensation. Our analysis provides further insight with the following findings: the 52 platypus chromosomes show no correlation between the position of orthologous genes on the small platypus chromosomes and chicken microchromosomes; for the unique 5X chromosomes of platypus we reveal considerable sequence alignment similarity to chicken Z and no orthologous gene alignments to human X, implying that the platypus X chromosome evolved directly from a bird-like ancestral reptilian system55; and the genes on the five platypus X chromosomes appear to be partially dosage compensated (Supplementary Fig. 5), perhaps parallel to the incomplete dosage compensation recently described in birds56.

Repeat elements

About one-half of the platypus genome consists of interspersed repeats derived from transposable elements. The most abundant and still active repeats are (severely truncated) copies of the 5-kb long-interspersed-element (LINE2) and its non-autonomous SINE-companion mammalian-wide interspersed repeat (MIR, Mon-1 in monotremes) that became extinct in marsupials and in eutherians 60–100 Myr ago. We estimate that there are 1.9 and 2.75 million copies of LINE2 and MIR/Mon-1, respectively, in the 2.3-Gb platypus genome. DNA transposons and LTR retroelements are quite rare in platypus, but there are thousands of copies of an ancient gypsy-class LTR element (all LTR elements previously identified in mammals, birds, or reptiles belong to the retrovirus clade). Overall, the frequency of interspersed repeats (over 2 repeats per kb) is higher than in any previously characterized metazoan genome. Population analysis using LINE2/Mon-1 elements distinguished the Tasmanian population from three other mainland clusters (Supplementary Fig. 4a, b), in good agreement with tree-based analysis, physical proximity and previous knowledge of platypus population relationships57.

Cluster analysis of all LINE2 copies revealed a phylogenetic relationship lacking branches, as if a single-locus, fast-evolving gene has steadily spread an exceptional number of pseudogenes over time (Supplementary Fig. 6). This 'master gene' appearance is, to a lesser degree, also observed for LINE1 in eutherians58, but not to the same extent for MIR/Mon-1 or other retrotransposons in mammals. The phylogeny of LINE2 and Mon-1 was also supported by a genome-wide transposition-in-transposition (TinT) analysis59 (Supplementary Tables 7 and 8). LINE2 density is similar on all chromosomes (Supplementary Fig. 7); it does not correlate with chromosome length (and recombination rate) as the CR1 LINE density does in the chicken genome19, nor is it higher on sex chromosomes than on autosomes, as LINE1 density is in eutherians (which has led to postulations on a function in dosage compensation)60.

We compared microsatellites in the platypus genome with those of representative vertebrates (Supplementary Notes 22). The mean microsatellite coverage of platypus genomic sequences assembled into chromosomes is 2.67 0.34%; significantly lower than all other mammalian genomes sequenced so far and most similar to that observed in chicken (Supplementary Fig. 8). Microsatellites are on average shorter in platypus than in other genomes (Supplementary Table 9), but microsatellite coverage surpasses chicken owing to very long tri- and tetranucleotide repeats (Supplementary Fig. 9). The platypus has a higher proportion of microsatellites with high A+T content, in comparison to the other vertebrates examined, an abundance distribution that has more in common with reptiles than with mammals (Supplementary Fig. 10).

Genomic imprinting

Genomic imprinting is an epigenetic phenomenon that results in monoallelic gene expression. In the vertebrates, imprinting seems to have evolved recently and has only been confirmed in marsupials and eutherian mammals61, 62. The autosomal localization of some imprinted orthologues in platypus is known63. However, we examined the conservation of synteny and the distribution of retrotransposed elements in all orthologous eutherian-imprinted clustered and non-clustered genes in the platypus genome. A representative cluster is shown in Fig. 5 (see also Supplementary Fig. 12).

Figure 5: Comparative mammalian analysis for a representative eutherian imprinted gene cluster (PEG1/MEST).

a, The gene arrangement is conserved between mammals. However, non-coding regions are expanded in therians. Arrows indicate genes and the direction of transcription; the scale shows base pairs. b, Summary of repeat distribution for the PEG1/MEST cluster. Histograms represent the sequence (%) masked by each repeat element within the MEST cluster; black bars represent repeat distribution across the entire genome. With the exception of SINEs, platypus has fewer repeats of LINEs, LTRs, DNA and simple repeats (Simple) than eutherian mammals. Low comp., low complexity; sRNAs, small RNAs.

High resolution image and legend (193K)


Clusters that became imprinted in therians (with the exception of the Prader–Willi–Angelman locus64) have not been assembled recently and reside in ancient syntenic mammalian groups, although some regions have expanded by mechanisms such as gene duplication or transposition. There were significantly fewer LTR and DNA elements across all platypus orthologous regions relative to eutherian imprinted genes (P < 0.04 and 0.04, respectively), whereas there was a significant increase in the sequences masked by SINEs (P < 0.03). The chicken had fewer total repeats and no SINEs or sRNAs. Comparison of all regions in the platypus with the orthologous regions in opossum, mouse, dog and human demonstrates that accumulation of LTR, DNA elements, and simple and low complexity repeats coincides with, and may be a driving force in, the acquisition of imprinting in these regions in therian mammals.

The CpG fraction

The eutherian and chicken genomes generally average around 41% G+C content, although many intervals differ substantially from the average, particularly in humans (Supplementary Notes 23). In contrast, the platypus genome averages 45.5% G+C content and rarely deviates far from the average. The opossum genome averages only 38% G+C content and also has a narrow distribution (Supplementary Fig. 13). The source of the elevated G+C fraction in platypus remains unclear. It is explained only in part by monotreme interspersed repeat elements, as platypus DNA outside of known interspersed repeats is 44.7% G+C. Furthermore, tandem repeats of short DNA motifs (microsatellites) in platypus show an A+T bias, as with other mammals. Recombination-driven biased gene conversion may be a factor, in agreement with what has been shown for eutherians65 and marsupials66. This is suggested by the observation that the six platypus chromosomes where the currently mapped DNA sequence averages over 45% G+C content (that is, 17, 20, 15, 14, 10 and 11 in order of decreasing G+C fraction) are among the 10 shortest (Supplementary Fig. 14), because short chromosomes have a higher recombination rate67. However, a direct test is currently lacking because platypus recombination rates have not been measured. A further examination of the CpG fraction, that associated with promoter elements, is found in Supplementary Notes 24 and Supplementary Fig. 15.

Top of page Conclusions

The egg-laying platypus is a remarkable species with many biological features unique among mammals. Our sequencing of the platypus genome now enables us to compare its sequence characteristics and organization with those of birds and therian mammals in order to address the questions of platypus biology and to date the emergence of mammalian traits. We report here that sequence characteristics of the platypus genome show features of reptiles as well as mammals.

Platypus contains a largely standard repertoire of non-protein-coding, ncRNAs, except for the snoRNAs, which exhibit a marked expansion associated with at least one retrotransposed subfamily. Some of these retrotransposed snoRNAs are expressed and thus may have functional roles. The platypus has fully elaborated piRNA and miRNA pathways, the latter including many monotreme-specific miRNAs and miRNAs that are shared with either mammals or chickens. Many functional assessments of these novel miRNAs remain to be carried out and will surely add to our knowledge of mammalian miRNA evolution.

The 18,527 protein-coding genes predicted from the platypus assembly fall within the range for therian genomes. Of particular interest are families of genes involved in biology that links monotremes to reptiles, such as egg-laying, vision and envenomation, as well as mammal-specific characters such as lactation, characters shared with marsupials such as antibacterial proteins, and platypus-specific characters such as venom delivery and underwater foraging. For instance, anatomical adaptations for chemoreception during underwater foraging are reflected in an unusually large repertoire of vomeronasal type 1 receptor genes. However, the repertoire of milk protein genes is typically mammalian, and the arrangement of milk protein genes seems to have been preserved since the last common ancestor of monotremes and therian mammals.

Since its initial description, the platypus has stood out as a species with a blend of reptilian and mammalian features, which is a characteristic that penetrates to the level of the genome sequence. The density and distribution of repetitive sequence, for example, reflects this fact. The high frequency of interspersed repeats in the platypus genome, although typical for mammalian genomes, is in contrast with the observed mean microsatellite coverage, which appears more reptilian. Additionally, the correlation of parent-of-origin-specific expression patterns in regions of reduced interspersed repeats in the platypus suggests that the evolution of imprinting in therians is linked to the accumulation of repetitive elements.

We find that the mixture of reptilian, mammalian and unique characteristics of the platypus genome provides many clues to the function and evolution of all mammalian genomes. The wealth of new findings and confirmation of existing knowledge immediately evident from the release of these data promise that the availability of the platypus genome sequence will provide the critically needed background to inspire rapid advances in other investigations of mammalian biology and evolution.


http://www.nature.com/nature/journal/v453/n7192/full/nature06936.html

How do you convince a creationist that a fossil is a transitional fossil? Give up? It is a trick question. You cannot do it. There is no convincing someone who has his mind made up already. But sometimes, it is even worse. Sometimes, when you point out a fossil that falls into the middle of a gap and is a superb morphological and chronological intermediate, you are met with the response: "Well, now you have two gaps where you only had one before! You are losing ground!"

One of the favorite anti-evolutionist challenges to the existence of transitional fossils is the supposed lack of transitional forms in the evolution of the whales. Duane Gish of the Institute for Creation Research (ICR) regularly trots out the "bossie-to-blowhole" transition to ridicule the idea that whales could have evolved from terrestrial, hooved ancestors.


There simply are no transitional forms in the fossil record between the marine mammals and their supposed land mammal ancestors . . . It is quite entertaining, starting with cows, pigs, or buffaloes, to attempt to visualize what the intermediates may have looked life. Starting with a cow, one could even imagine one line of descent which prematurely became extinct, due to what might be called an “udder failure” (Gish 1985: 78-9).


Of course, for many years the fossil record for the whales was quite spotty, but now there are numerous transitional forms that illustrate the pathway of whale evolution.

Recent discoveries of fossil whales provide the evidence that will convince an honest skeptic. However, evolutionary biology predicts more than just the existence of fossil ancestors with certain characteristics - it also predicts that all other biological disciplines should also reveals patterns of similarity among whales, their ancestors, and other mammals correlated with evolutionary relatedness between groups. It should be no surprise that this is what we find, and since the findings in one biological discipline, say biochemistry, is derived without reference to the findings in another, say comparative anatomy, scientists consider these different fields to provide independent evidence of the evolution of whales. As expected, these independent lines of evidence all confirm the pattern of whale evolution that we would anticipate in the fossil record.

To illustrate this approach, I will present the evidence from multiple fields for the origin of the whales from terrestrial mammals. This paper will examine mutually reinforcing evidence from nine independent areas of research. Of course, as a starting point, we need to describe what makes a whale a whale.

What is a whale?
A whale is first and foremost, a mammal - a warm-blooded vertebrate that uses its high metabolism to generate heat and regulate its internal temperature. Female whales bear live young, which they nurse from mammary glands. Although adult whales have no covering of body hair, they acquire body hair temporarily as fetuses, and some adult whales have sensory bristles around their mouths. These features are unequivocally mammalian.

But a whale is a very specialized mammal with many unique characters that are not shared with other mammals - many of these are not even shared with other marine mammals such as sirenians (manatees and dugongs) and pinnipeds (seals, sea lions, and walruses). For example, whales have streamlined bodies that are thick and rounded, unlike the generally slim, elongated bodies of fishes. A whale's tail has horizontal flukes, which are its sole means of propulsion through the water. The dorsal fin is stiffened by connective tissue, but is fleshy and entirely without supporting bones.

The neck vertebrae of the whale are shortened and at least partly fused into a single bony mass. The vertebrae behind the neck are numerous and very similar to one another; the bony processes that connect the vertebrae are greatly reduced, allowing the back to be very flexible and to produce powerful thrusts from the tail flukes. The flippers that allow the whale to steer are composed of flattened and shortened arm bones, flat, disk-like wrist bones, and multiple elongated fingers. The elbow joint is virtually immobile, making the flipper rigid. In the shoulder girdle, the shoulder blade is flattened, and there is no clavicle. A few species of whales still possess a vestigial pelvis, and some have greatly reduced and nonfunctional hindlimbs.

The rib cage is very mobile - in some species, the ribs are entirely separated from the vertebral column - which allows the chest to expand greatly when the whale is breathing in and allows the thorax to compress at depth when the whale is diving deeply.

The skull also has a set of features unique among mammals. The jaws extend forward, giving whales their characteristically long head, and the two front-most bones of the upper jaw (the maxillary and premaxillary) are "telescoped" rearward, sometimes entirely covering the top of the skull. The rearward migration of these bones is the process by which the nasal openings have moved to the top of the skull, creating blowholes and shifting the brain and the auditory apparatus to the back of the skull. The odontocetes (toothed whales) have a single blowhole, while the mysticetes (baleen whales) have paired blowholes.

In the odontocetes, there is a pronounced asymmetry in the telescoped bones and the blowhole that provides a natural means of classification. Although teeth often occur in fetal mysticetes, only odontocetes exhibit teeth as adults. These teeth are always simple cones or pegs; they are not differentiated by region or function as teeth are in other mammals. (Whales cannot chew their food; it is ground up instead in a forestomach, or muscular crop, containing stones.)

Unlike the rest of the mammals, whales have no tear glands, no skin glands, and no olfactory sense. Their hearing is acute but the ear has no external opening. Hearing occurs via vibrations transmitted to a heavy, shell-like bone formed by fusion of skull bones (the periotic and auditory bullae).

These, then, are the major features of whales. Some clearly show the distinctive adaptations imposed on whales by their commitment to marine living; others clearly link the whales to their terrestrial ancestors. Others show the traces of descent from a terrestrial ancestor in common with several ancient and modern species. From all these features together, we can reconstruct the pathway that whale evolution took from a terrestrial ancestor to a modern whale confined to deep oceans.

Thinking about the ancestry of the whale
In 1693, John Ray recorded his realization that whales are mammals based on the similarity of whales to terrestrial mammals (Barnes 1984). The pre-Darwinian scientific discussion revolved around whether whales were descended from or ancestral to terrestrial mammals. Darwin (1859) suggested that whales arose from bears, sketching a scenario in which selective pressures might cause bears to evolve into whales; embarrassed by criticism, he removed his hypothetical swimming bears from later editions of the Origin (Gould 1995).

Later, Flower (1883) recognized that the whales have persistent rudimentary and vestigial features characteristic of terrestrial mammals, thus confirming that the direction of descent was from terrestrial to marine species. On the basis of morphology, Flower also linked whales with the ungulates; he seems to have been the first person to do so.

Early in the 20th century, Eberhard Fraas and Charles Andrews suggested that creodonts (primitive carnivores, now extinct) were the ancestors of whales (Barnes 1984). Later, WD Matthew of the American Museum of Natural History postulated that whales descended from insectivores, but his idea never gained much support (Barnes 1984). Later still, Everhard Johannes Slijper tried to combine the two ideas, claiming that whales descended from what Barnes aptly called "creodonts-cum-insectivores". However, no such animal has ever been found. More recently, Van Valen (1966) and Szalay (1969) associated early whales with mesonychid condylarths (a now-extinct group of primitive carnivorous ungulates, none bigger than a wolf) on the basis of dental characters. More recent evidence confirms their assessment. Thus Flower was basically right.

The evidence
The evidence that whales descended from terrestrial mammals is here divided into nine independent parts: paleontological, morphological, molecular biological, vestigial, embryological, geochemical, paleoenvironmental, paleobiogeographical, and chronological. Although my summary of the evidence is not exhaustive, it shows that the current view of whale evolution is supported by scientific research in several distinct disciplines.

1. Paleontological evidence
The paleontological evidence comes from studying the fossil sequence from terrestrial mammals through more and more whale-like forms until the appearance of modern whales. Although the early whales (Archaeocetes) exhibit greater diversity than I have space to discuss here, the examples in this section represent the trends that we see in this taxon. Although there are two modern suborders of whales (Odontocetes and Mysticetes), this discussion will focus on the origin of the whales as an order of mammals, and set aside the issues related to the diversification into suborders.

Sinonyx
We start with Sinonyx, a wolf-sized mesonychid (a primitive ungulate from the order Condylarthra, which gave rise to artiodactyls, perissodactyls, proboscideans, and so on) from the late Paleocene, about 60 million years ago. The characters that link Sinonyx to the whales, thus indicating that they are relatives, include an elongated muzzle, an enlarged jugular foramen, and a short basicranium (Zhou and others 1995). The tooth count was the primitive mammalian number (44); the teeth were differentiated as are the heterodont teeth of today's mammals. The molars were very narrow shearing teeth, especially in the lower jaw, but possessed multiple cusps. The elongation of the muzzle is often associated with hunting fish - all fish-hunting whales, as well as dolphins, have elongated muzzles. These features were atypical of mesonychids, indicating that Sinonyx was already developing the adaptations that later became the basis of the whales' specialized way of life.

Pakicetus
The next fossil in the sequence, Pakicetus, is the oldest cetacean, and the first known archaeocete. It is from the early Eocene of Pakistan, about 52 million years ago (Gingerich and others 1983). Although it is known only from fragmentary skull remains, those remains are very diagnostic, and they are definitely intermediate between Sinonyxand later whales. This is especially the case for the teeth. The upper and lower molars, which have multiple cusps, are still similar to those of Sinonyx, but the premolars have become simple triangular teeth composed of a single cusp serrated on its front and back edges. The teeth of later whales show even more simplification into simple serrated triangles, like those of carnivorous sharks, indicating that Pakicetus's teeth were adapted to hunting fish.

Gingrich and others (1983) published this reconstruction of the skull of
Pakicetus inachus (redrawn for RNCSE by Janet Dreyer).


A well-preserved cranium shows that Pakicetus was definitely a cetacean with a narrow braincase, a high, narrow sagittal crest, and prominent lambdoidal crests. Gingerich and others (1983) reconstructed a composite skull that was about 35 centimeters long. Pakicetus did not hear well underwater. Its skull had neither dense tympanic bullae nor sinuses isolating the left auditory area from the right one - an adaptation of later whales that allows directional hearing under water and prevents transmission of sounds through the skull (Gingerich and others 1983). All living whales have foam-filled sinuses along with dense tympanic bullae that create an impedance contrast so they can separate sounds arriving from different directions. There is also no evidence in Pakicetus of vascularization of the middle ear, which is necessary to regulate the pressure within the middle ear during diving (Gingerich and others 1983). Therefore, Pakicetus was probably incapable of achieving dives of any significant depth. This paleontological assessment of the ecological niche of Pakicetus is entirely consistent with the geochemical and paleoenvironmental evidence. When it came to hearing, Pakicetus was more terrestrial than aquatic, but the shape of its skull was definitely cetacean, and its teeth were between the ancestral and modern states.



Zhou and others (1995) published this reconstruction of the skull of
Sinonyx jiashanensis (redrawn for RNCSE by Janet Dreyer).


Ambulocetus
In the same area that Pakicetus was found, but in sediments about 120 meters higher, Thewissen and colleagues (1994) discovered Ambulocetus natans, "the walking whale that swims", in 1992. Dating from the early to middle Eocene, about 50 million years ago, Ambulocetus is a truly amazing fossil. It was clearly a cetacean, but it also had functional legs and a skeleton that still allowed some degree of terrestrial walking. The conclusion that Ambulocetus could walk by using the hind limbs is supported by its having a large, stout femur. However, because the femur did not have the requisite large attachment points for walking muscles, it could not have been a very efficient walker. Probably it could walk only in the way that modern sea lions can walk - by rotating the hind feet forward and waddling along the ground with the assistance of their forefeet and spinal flexion. When walking, its huge front feet must have pointed laterally to a fair degree since, if they had pointed forward, they would have interfered with each other.

The forelimbs were also intermediate in both structure and function. The ulna and the radius were strong and capable of carrying the weight of the animal on land. The strong elbow was strong but it was inclined rearward, making possible rearward thrusts of the forearm for swimming. However, the wrists, unlike those of modern whales, were flexible.

It is obvious from the anatomy of the spinal column that Ambulocetus must have swum with its spine swaying up and down, propelled by its back feet, oriented to the rear. As with other aquatic mammals using this method of swimming, the back feet were quite large. Unusually, the toes of the back feet terminated in hooves, thus advertising the ungulate ancestry of the animal. The only tail vertebra found is long, making it likely that the tail was also long. The cervical vertebrae were relatively long, compared to those of modern whales; Ambulocetus must have had a flexible neck.

Ambulocetus's skull was quite cetacean (Novacek 1994). It had a long muzzle, teeth that were very similar to later archaeocetes, a reduced zygomatic arch, and a tympanic bulla (which supports the eardrum) that was poorly attached to the skull. Although Ambulocetus apparently lacked a blowhole, the other skull features qualify Ambulocetus as a cetacean. The post-cranial features are clearly in transitional adaptation to the aquatic environment. Thus Ambulocetus is best described as an amphibious, sea-lion-sized fish-eater that was not yet totally disconnected from the terrestrial life of its ancestors.

Rodhocetus
In the middle Eocene (46-7 million years ago) Rodhocetus took all of these changes even further, yet still retained a number of primitive terrestrial features (Gingerich and others 1994). It is the earliest archaeocete of which all of the thoracic, lumbar, and sacral vertebrae have been preserved. The lumbar vertebrae had higher neural spines than in earlier whales. The size of these extensions on the top of the vertebrae where muscles are attached indicate that Rodhocetus had developed a powerful tail for swimming.



Gingrich and others (1994) published this reconstruction of the skeleton of
Rodhocetus kasrani (redrawn for RNCSE by Janet Dreyer).


Elsewhere along the spine, the four large sacral vertebrae were unfused. This gave the spine more flexibility and allowed a more powerful thrust while swimming. It is also likely that Rodhocetus had a tail fluke, although such a feature is not preserved in the known fossils: it possessed features - shortened cervical vertebrae, heavy and robust proximal tail vertebrae, and large dorsal spines on the lumbar vertebrae for large tail and other axial muscle attachments - that are associated in modern whales with the development and use of tail flukes. All in all, Rodhocetus must have been a very good tail-swimmer, and it is the earliest fossil whale committed to this manner of swimming.

The pelvis of Rodhocetus was smaller than that of its predecessors, but it was still connected to the sacral vertebrae, meaning that Rodhocetus could still walk on land to some degree. However, the ilium of the pelvis was short compared to that of the mesonychids, making for a less powerful muscular thrust from the hip during walking, and the femur was about 1/3 shorter than Ambulocetus’s, so Rodhocetus probably could not get around as well on land as its predecessors (Gingerich and others 1994).

Rodhocetus's skull was rather large compared to the rest of the skeleton. The premaxillae and dentaries had extended forward even more than its predecessors’, elongating the skull and making it even more cetacean. The molars have higher crowns than in earlier whales and are greatly simplified. The lower molars are higher than they are wide. There is a reduced differentiation among the teeth. For the first time, the nostrils have moved back along the snout and are located above the canine teeth, showing blowhole evolution. The auditory bullae are large and made of dense bone (characteristics unique to cetaceans), but they apparently did not contain the sinuses typical of later whales, making it questionable whether Rodhocetus possessed directional hearing underwater.

Overall, Rodhocetus showed improvements over earlier whales by virtue of its deep, slim thorax, longer head, greater vertebral flexibility, and expanded tail-related musculature. The increase in flexibility and strength in the back and tail with the accompanying decrease in the strength and size of the limbs indicated that it was a good tail-swimmer with a reduced ability to walk on land.

Basilosaurus
The particularly well-known fossil whale Basilosaurus represents the next evolutionary grade in whale evolution (Gingerich 1994). It lived during the late Eocene and latest part of the middle Eocene (35-45 million years ago). Basilosaurus was a long, thin, serpentine animal that was originally thought to have been the remains of a sea serpent (hence it is name, which actually means "king lizard"). Its extreme body length (about 15 meters) appears to be due to a feature unique among whales; its 67 vertebrae are so long compared to other whales of the time and to modern whales that it probably represents a specialization that sets it apart from the lineage that gave rise to modern whales.

What makes Basilosaurus a particularly interesting whale, however, is the distinctive anatomy of its hind limbs (Gingerich and others 1990). It had a nearly complete pelvic girdle and set of hindlimb bones. The limbs were too small for effective propulsion, less than 60 cm long on this 15-meter-long animal, and the pelvic girdle was completely isolated from the spine so that weight-bearing was impossible. Reconstructions of the animal have placed its legs external to the body - a configuration that would represent an important intermediate form in whale evolution.

Although no tail fluke has ever been found (since tail flukes contain no bones and are unlikely to fossilize), Gingerich and others (1990) noted that Basilosaurus's vertebral column shares characteristics of whales that do have tail flukes. The tail and cervical vertebrae are shorter than those of the thoracic and lumbar regions, and Gingerich and others (1990) take these vertebral proportions as evidence that Basilosaurus probably also had a tail fluke.

Further evidence that Basilosaurus spent most of its time in the water comes from another important change in the skull. This animal had a large single nostril that had migrated a short distance back to a point corresponding to the back third of the dental array. The movement from the forward extreme of the snout to the a position nearer the top of the head is characteristic of only those mammals that live in marine or aquatic environments.

Dorudon
Dorudon was a contemporary of Basilosaurus in the late Eocene (about 40 million years ago) and probably represents the group most likely to be ancestral to modern whales (Gingerich 1994). Dorudon lacked the elongated vertebrae of Basilosaurus and was much smaller (about 4-5 meters in length). Dorudon’s dentition was similar to Basilosaurus’s; its cranium, compared to the skulls of Basilosaurus and the previous whales, was somewhat vaulted (Kellogg 1936). Dorudon also did not yet have the skull anatomy that indicates the presence of the apparatus necessary for echolocation (Barnes 1984).



Gingrich and Uhen (1996) published this reconstruction of the skeleton of
Dorudon atrox (redrawn for RNCSE by Janet Dreyer).




Basilosaurus and Dorudon were fully aquatic whales (like Basilosaurus, Dorudon had very small hind limbs that may have projected slightly beyond the body wall). They were no longer tied to the land; in fact, they would not have been able to move around on land at all. Their size and their lack of limbs that could support their weight made them obligate aquatic mammals, a trend that is elaborated and reinforced by subsequent whale taxa.

Clearly, even if we look only at the paleontological evidence, the creationist claim of "No fossil intermediates!" is wrong. In fact, in the case of whales, we have several, beautifully arranged in morphological and chronological order.

In summarizing the paleontological evidence, we have noted the consistent changes that indicate a series of adaptations from more terrestrial to more aquatic environments as we move from the most ancestral to the most recent species. These changes affect the shape of the skull, the shape of the teeth, the position of the nostrils, the size and structure of both the forelimbs and the hindlimbs, the size and shape of the tail, and the structure of the middle ear as it relates to directional hearing underwater and diving. The paleontological evidence records a history of increasing adaptation to life in the water - not just to any way of life in the water, but to life as lived by contemporary whales.

2. Morphological evidence
The examination of the morphological characteristics shared by the fossil whales and living ungulates makes their common ancestry even clearer. For example, the anatomy of the foot of Basilosaurus allies whales with artiodactyls (Gingerich and others 1990). The axis of foot symmetry in these fossil whales falls between the 3rd and 4th digits. This arrangement is called paraxonic and is characteristic of the artiodactyls, whales, and condylarths, and is rarely found in other groups (Wyss 1990).

Another example involves the incus (the "anvil" of the middle ear). The incus of Pakicetus, preserved in at least one specimen, is morphologically intermediate in all characters between the incus of modern whales and that of modern artiodactyls (Thewissen and Hussain 1993). Additionally, the joint between the malleus (hammer) and incus of most mammals is oriented at an angle between the middle and the front of the animal (rostromedially), while in modern whales and in ungulates, it is oriented at an angle between the side and the front (rostrolaterally). In Pakicetus, the first fossil cetacean, the joint is oriented rostrally (intermediate in position between the ancestral and derived conditions). Thus the joint has clearly rotated toward the middle from the ancestral condition in terrestrial mammals (Thewissen and Hussain 1993); Pakicetus provides us with a snapshot of the transition.

3. Molecular biological evidence
The hypothesis that whales are descended from terrestrial mammals predicts that living whales and closely related living terrestrial mammals should show similarities in their molecular biology roughly in proportion to the recency of their common ancestor. That is, whales should be more similar in their molecular biology to groups of animals with which they share a more recent common ancestor than to other animals that exhibit convergent similarities in morphology, ecology, or behavior. In contrast, creationism lacks any scientific basis for predicting what the patterns of similarity should be, for there is no scientific way to predict how the creator decided to distribute molecular similarities among species.

Molecular studies by Goodman and others (1985) show that whales are more closely related to the ungulates than they are to all other mammals - a result consistent with evolutionary expectations. These studies examined myoglobin, lens alpha-crystallin A, and cytochrome c in a study of 46 different species of mammals. Miyamoto and Goodman (1986) later expanded the number of protein sequences by including alpha- and beta- hemoglobins and ribonuclease; they also increased the number of mammals included in the study to 72. The results were the same: the whales clearly are included among the ungulates. Other molecular studies on a variety of genes, proteins, and enzymes by Irwin and others (1991), Irwin and Arnason (1994), Milinkovitch (1992), Graur and Higgins (1994), Gatesy and others (1996), and Shimamura and others (1997) also identified the whales as closely related to the artiodactyls, although there are differences in the details among the studies.

By placing whales close to, and even firmly within, the Artiodactyls, these molecular studies confirm the predictions made by evolutionary theory. This pattern of biochemical similarities must be present if the whales and the ungulates, especially the Artiodactyls, share a close common ancestor. The fact that these similarities are present is therefore strong evidence for the common ancestry of whales and ungulates.

4. Vestigial evidence
The vestigial features of whales tell us two things. They tell us that whales, like so many other organisms, have features that make no sense from a design perspective - they have no current function, they require energy to produce and maintain, and they may be deleterious to the organism. They also tell us that whales carry a piece of their evolutionary past with them, highlighting a history of a terrestrial ancestry.

Modern whales often retain rod-like vestiges of pelvic bones, femora, and tibiae, all embedded within the musculature of their body walls. These bones are more pronounced in earlier species and less pronounced in later species. As the example of Basilosaurus shows, whales of intermediate age have intermediate-sized vestigial pelves and rear limb bones.

Whales also retain a number of vestigial structures in their organs of sensation. Modern whales have only vestigial olfactory nerves. Furthermore, in modern whales the auditory meatus (the exterior opening of the ear canal) is closed. In many, it is merely the size of a thin piece of string, about 1 mm in diameter, and often pinched off about midway. All whales have a number of small muscles devoted to nonexistent external ears, which are apparently a vestige of a time when they were able to move their ears - a behavior typically used by land animals for directional hearing.

The diaphragm in whales is vestigial and has very little muscle. Whales use the outward movement of the ribs to fill their lungs with air. Finally, Gould (1983) reported several occurrences of captured sperm whales with visible, protruding hind limbs. Similarly, dolphins have been spotted with tiny pelvic fins, although they probably were not supported by limb bones as in those rare sperm whales. And some whales, such as belugas, possess rudimentary ear pinnae - a feature that can serve no purpose in an animal with no external ear and that can reduce the animal's swimming efficiency by increasing hydrodynamic drag while swimming.

Although this list is by no means exhaustive, it is nonetheless clear that the whales have a wealth of vestigial features left over from their terrestrial ancestors.

5. Embryological evidence
Like the vestigial features, the embryological features also tells us two things. First, the whale embryo develops a number of features that it later abandons before it attains its final form. How can creationism explain such seemingly nonsensical process, building structures only to abandon them or to destroy them later? Darwin (1859) asked the same question. Would it not make more sense to have embryos attain their adult forms quickly and directly? It seems unreasonable for a perfect designer or creator to send the embryo along such a tortuous pathway, but evolution requires that new features are built on the foundation of previous features that it would modify or discard later.

Second, the embryology of the whale, examined in detail, also provides evidence for its terrestrial ancestry. As embryos no less than as adult animals, whales are junkyards, as it were, of old, discarded features that are of no further use to them. Many whales, while still in the womb, begin to develop body hair. Yet no modern whales retain any body hair after birth, except for some snout hairs and hairs around their blowholes used as sensory bristles in a few species. The fact that whales possess the genes for producing body hair shows that their ancestors had body hair. In other words, their ancestors were ordinary mammals.

In many embryonic whales, external hind limb buds are visible for a time but thendisappear as the whale grows larger. Also visible in the embryo are rudimentary ear pinnae, which disappear before birth (except in those that carry them as rare atavisms). And, in some whales, the olfactory lobes of the brain exist only in the fetus. The whale embryo starts off with its nostrils in the usual place for mammals, at the tip of the snout. But during development, the nostrils migrate to their final place at the top of the head to form the blowhole (or blowholes).

We can also understand evolution within the whales via their embryology. We know that the baleen whales evolved from the toothed whales: some embryos of the baleen whales begin to develop teeth. As with body hair, the teeth disappear before birth. Since there is no use for teeth in the womb, only inheritance from a common ancestor makes any sense; there is no reason for the intelligent designer or special creator to provide embryonic whales with teeth. So we have yet another independent field in complete accord with the overall thesis - that whales possess features that connect them with terrestrial mammalian ancestors, in particular the hoofed mammals.

6. Geochemical evidence
The earliest whales lived in freshwater habitats, but the ancestors of modern whales moved into saltwater habitats and thus had to adapt to drinking salt water. Since fresh water and salt water have somewhat different isotopic ratios of oxygen, we can predict that the transition will be recorded in the whales' skeletal remains - the most enduring of which are the teeth. Sure enough, fossil teeth from the earliest whales have lower ratios of heavy oxygen to light oxygen, indicating that the animals drank fresh water (Thewissen and others 1996). Later fossil whale teeth have higher ratios of heavy oxygen to light oxygen, indicating that they drank salt water. This absolutely reinforces the inference drawn from all the other evidence discussed here: the ancestors of modern whales adapted from terrestrial habitats to saltwater habitats by way of freshwater habitats.

7. Paleoenvironmental evidence
Evolution makes other predictions about the history of taxa based on the "big-picture" view of the fossils in a larger, environmental, context. The sequence of whale fossils and their changes should also relate to changes observed in the fossil records of other organisms at the same time and in similar environments. The fossils of other organisms associated with the whale fossils indicate the environment that the whales lived in. Furthermore, this evidence should be consistent with the evidence from the other areas of study. We should expect to find evidence for a series of transitional environments, from fully terrestrial to fully marine, occupied by the series of whale species in the fossil record.

The morphology of Sinonyx indicates that it was fully terrestrial. It should be no surprise, therefore, that its fossils are found associated with the fossils of other terrestrial animals. Pakicetus probably spent a lot of time in the water in search of food. Although the mammalian fauna found with Pakicetus consists of rodents, bats, various artiodactyls, perissodactyls and probiscideans, and even a primate (Gingerich and others 1983), there are also aquatic animals such as snails, fish, turtles and crocodilians. Moreover, the sediment associated with Pakicetus shows evidence of streaming or flowing, usually associated with soils that are carried by water. The paleoenvironmental evidence thus clearly shows that Pakicetus lived in the low-lying wet terrestrial environment, making occasional excursions into fresh water. Interestingly, both deciduous and permanent teeth of the animal are found in these sediments with about the same frequency, supporting the idea that Pakicetus gave birth on the land.

The sediments in which Ambulocetus was found contain leaf impressions as well as fossils of the turret-snail Turritella and other marine mollusks. Clearly, the presence of such fossils must mean that the Ambulocetus fossil was found in what was once a shallow sea - although leaves can be washed into the sea and fossilize there, marine mollusks would not be found on the land.

Rodhocetus is found in green shales deposited in the deep-neritic zone (equivalent to the outer part of the continental shelf). Because green shales are associated with fairly low-oxygen bottom waters, Rodhocetus must have lived at a greater water depth than any previous cetacean. The fact that it is found in association with planktonic foraminiferans and other microfossils agrees with this determination of water depth. Basilosaurus and Dorudon have been found in a variety of sediment types (Kellogg 1936), indicating that they were wide-ranging and capable of living in deep as well as shallow water.

From the paleoenvironmental evidence, we can clearly see that, as whales evolved, they made their way into deeper water and became progressively liberated from the terrestrial and near-shore environments.

8. Paleobiogeographic evidence
The geographic evidence is also consistent with the expected distributional patterns for the whale’s first appearance and later geographic expansion. We would expect terrestrial species to have a more restricted geographic distribution than marine species, which have essentially the whole ocean as their geographic range. The range of Sinonyx is restricted to central Asia. Specimens of Pakicetus have only been found in Pakistan; Ambulocetus and Rodhocetus seem to be similarly restricted. In contrast, Basilosaurus and Dorudon, representing the whales more adapted to living in the open sea, are found in a much wider area. Their fossils have been found as far away from southern Asia as Georgia, Louisiana, and British Columbia.

During the Eocene, most of the areas in which fossils of the later whales have been found were fairly close to one another. In fact, most of them are along the outer margin of an ancient sea called the Tethys, the remnants of which today are the Mediterranean, the Caspian, the Black, and the Aral Seas. The biogeographic distribution of fossil whales matches the pattern predicted by evolution: whales are initially found in a rather small geographic area and did not become distributed throughout the world until after they evolved into fully aquatic animals that were no longer tied to the land.

9. Chronological evidence
The final strand of evidence in our mutually consistent picture of whale origins comes from a consideration of why the whales originated when they did. Evolution is a response to environmental challenges and opportunities. During the early Cenozoic, mammals were presented with a new set of opportunities for radiation and diversification due, in part, to the vacuum left by mass extinctions at the close of the Cretaceous Period. Because the reptiles no longer predominated, there were new ways in which mammals could make a living.

In the specific case of whales, the swimming reptiles of the world's oceans could no longer keep the mammals at bay. Before the late-Cretaceous extinctions, the Mesozoic marine reptiles such as the plesiosaurs, ichthyosaurs, mosasaurs, and marine crocodiles might well have feasted upon any mammal that strayed off shore in search of food. Once those predators were gone, the evolution quickly produced mammals, including whales, that were as at home in the seas as they once were on land. The transition took some 10-15 million years to produce fully aquatic, deep-diving whales with directional underwater hearing. Evolution predicts that whales could not have successfully appeared and radiated before the Eocene, and that mammals should have radiated into marine environments as they did into a wide variety of other environments vacated by the reptiles at the end of the Cretaceous.

Conclusion Taken together, all of this evidence points to only one conclusion - that whales evolved from terrestrial mammals. We have seen that there are nine independent areas of study that provide evidence that whales share a common ancestor with hoofed mammals. The power of evidence from independent areas of study that support the same conclusion makes refutation by special creation scenarios, personal incredulity, the argument from ignorance, or "intelligent design" scenarious entirely unreasonable. The only plausible scientific conclusion is that whales did evolve from terrestrial mammals. So no matter how much anti-evolutionists rant about how impossible it is for land-dwelling, furry mammals to evolve into fully aquatic whales, the evidence itself shouts them down. This is the power of using mutually reinforcing, independent lines of evidence. I hope that it will become a major weapon to strike down groundless anti-evolutionist objections and to support evolutionary thinking in the general public. This is how real science works, and we must emphasize the process of scientific inference as we point out the conclusions that scientists draw from the evidence - that the concordant predictions from independent fields of scientific study confirm the same pattern of whale ancestry.

http://www.talkorigins.org/features/whales/

29 + evidences of Macroevolution

http://www.talkorigins.org/faqs/comdesc/section1.html

The problem with evolution is that one cannot just explain it in five simple words! This is why many don't even touch the subject.

The Evolution of Extraordinary Eyes: The Cases of Flatfishes and Stalk-eyed Flies

The history of life is an unbroken stream of evolution stretching over 3.5 billion years. In order to study it--and in order to describe it--it must be carved into episodes. If scientists want to understand the origin, say, of bats, they do not run experiments to test a hypothesis about how DNA first evolved on the early Earth. They do not do research on the transition from single-celled protozoans to the first animals 600 million years ago. Likewise, they do not get bogged down with bat evolution after bats first evolved--how, for example, bats spread around the world and how they coevolved with their prey. There is only so much time in the day. Science writers follow the same rules to describe evolution. A newspaper article on the evolution of bats must focus only on that brief episode of life’s history. Let its scope grow too large, and it will be too big for a book--or a shelf of books.

This simple necessity can, unfortunately, give people the wrong impression about evolution. We tend to picture evolution as a series of isolated milestones. Once some particular trait evolves, we may assume that evolution simply stops.

The history of eyes is particularly vulnerable to this illusion. Consider, for example, a masterful paper entitled, “Evolution of the vertebrate eye: opsins, photoreceptors, retina, and eye cup,” published by Trevor Lamb of Australian National University and his colleagues in the December 2007 issue of Nature Reviews Neuroscience (Lamb et al. 2007). “Here,” Lamb and his co-authors announce, “we review a wide range of findings that capture glimpses of the gradations that appear to have occurred during eye evolution, and provide a scenario for the unseen steps that have led to the emergence of the vertebrate eye.” They end their review with the emergence of the vertebrate eye. Of course, Lamb et al. (2007) do not mean to imply that the evolution of vertebrate eyes ceased after they first emerged. But their focus is not on what happened afterwards.

Figuring out how a patch of light-sensitive receptors evolved into a camera-like imaging system shared by 40,000-odd species of vertebrates is certainly an important thing to do, and it is a job that will fill many scientists’ entire careers. But when the first full-blown vertebrate eyes emerged in some primitive fishes half a billion years ago, the evolution of the vertebrate eye did not stop. The eyes of every vertebrate alive today are different in some important ways from those early eyes. In some cases, the transformation has been exquisitely subtle. But in others, it has been so extreme as to be quite striking.

In this essay, I will look at two animals in which evolution has radically reworked a “standard” kind of eye: flatfishes and stalk-eyed flies. In both cases, eyes have moved far from their original position on the head. But flatfishes and stalk-eyed flies are not just freakish codas on the symphony of evolution. Instead, they are remarkable illustrations of some of the most powerful forces shaping all life, weird or otherwise.

Flatfishes--such as flounder, turbot, and plaice--are among the most striking animals in the sea. They spend much of their adult life sideways, hugging the sea floor where they lie in wait to ambush smaller fish. Their anatomy and DNA both reveal that they belong to the most diverse radiation of vertebrates today, known as the teleosts. Teleosts include most of the fishes we are most familiar with, such as goldfish and trout. In many respects, flatfishes have a standard teleost body plan. But as they have adapted to life on the sea floor, some new traits have evolved. All vertebrates, ourselves included, use hair cells in the inner ear to keep ourselves balanced. In most flatfish species, the hairs have changed orientation to match the orientation of their bodies. (Schrieber 2006). Many flatfishes can camouflage the upward-facing side of their body. The underside is pale, and in many species the fin on the underside is tiny.

And then, of course, there are the eyes.

On a typical teleost, such as a goldfish, the eyes face out from either side of the head. On a flounder, both eyes sit on one side, gazing upwards. It takes time for this Picasso-esque anatomy to emerge: flatfishes are born with eyes in the normal position, but as they grow, one eye moves across its head to join its partner. To accommodate this migrant, the bones of the flatfish head twist and turn to make room.
When Charles Darwin published the Origin of Species in 1859, a number of critics took him on, but none more seriously than a British zoologist named St. George Jackson Mivart. In 1871, Mivart published a full-scale challenge to evolution by natural selection, called On the Genesis of Species. In one of his attacks, Mivart wielded the flatfish:

In all these fishes the two eyes, which in the young are situated as usual one on each side, come to be placed, in the adult, both on the same side of the head. If this condition had appeared at once, if in the hypothetically fortunate common ancestor of these fishes an eye had suddenly become thus transferred, then the perpetuation of such a transformation by the action of “Natural Selection” is conceivable enough. Such sudden changes, however, are not those favoured by the Darwinian theory, and indeed the accidental occurrence of such a spontaneous transformation is hardly conceivable. But if this is not so, if the transit was gradual, then how such transit of one eye a minute fraction of the journey towards the other side of the head could benefit the individual is indeed far from clear. It seems, even, that such an incipient transformation must rather have been injurious. (Mivart 1871)

How exactly a transitional flatfish eye would have hurt the animal, Mivart did not say. In general, Mivart was more interested in the fact that intermediate forms of traits did not seem to be useful. What good was half a wing to a bird, he wondered. What good was an eye that had not made it all the way around a flatfish’s head?

Darwin took Mivart very seriously, and in 1872--the year after On the Genesis of Species came out--he took on Mivart’s arguments in the sixth edition of the Origin of Species. Mivart, Darwin argued, was not thinking carefully enough about what could or could not evolve by gradual evolution. Darwin agreed that flatfishes did not evolve in a sudden change. But he could envision a way in which the fish could have evolved in a series of steps. He had read how young flatfishes--with normal eyes--sometimes fall to the sea floor and then twist their lower eye upward to see above them. They seem to strain their lower eye, twisting it as far as possible.
At this point in his life, Darwin was warming to Jean Lamarck, the French naturalist who had proposed an earlier theory of evolution in 1800. Lamarck had argued that an animal’s body changed through its experiences, and that those changes could be passed down to its offspring. Natural selection, Darwin’s great discovery, depended instead on pure inheritance. Nothing we do in our lives changes the inherited traits we pass down to our offspring. But Darwin struggled with the mystery of heredity. Over time, he became more open to Lamarck. And so he offered a surprisingly Lamarckian explanation of creeping flatfishes’ eyes. The more the young flatfishes strained their lower eyes, he suggested, the more it migrated during its development towards the other side. He wrote,

We thus see that the first stages of the transit of the eye from one side of the head to the other, which Mr. Mivart considers would be injurious, may be attributed to the habit, no doubt beneficial to the individual and to the species, of endeavouring to look upward with both eyes, while resting on one side at the bottom. (Darwin 1872)

Natural selection had driven the eye further, Darwin proposed. “For all spontaneous variations in the right direction will thus be preserved; as will those individuals which inherit in the highest degree the effects of the increased and beneficial use of any part. How much to attribute in each particular case to the effects of use, and how much to natural selection, it seems impossible to decide.”

By the early 1900s, as scientists began to understand how genes work, they realized that mutations could fuel natural selection. But some biologists still argued that evolution might proceed by giant leaps. In the 1930s, the German biologist Richard Goldschmidt pointed to rare cases in which animals were produced with dramatic changes to their bodies. He called them “hopeful monsters,” and suggested that in some cases they might happen to be well suited to their environment. For Goldschmidt, flatfishes looked like promising candidates for hopeful monsters (Goldschmidt 1933). After all, he pointed out, no one had found a transition between ordinary fishes and flatfishes. Perhaps, Goldschmidt suggested, it had only taken a single mutation to launch a fish eye on its journey across the skull, and the basic flatfish anatomy emerged in a flash.

In 2008, a graduate student at the University of Chicago named Matt Friedman discovered compelling evidence that the flatfish eye evolved not in a single jump, but in a series of steps. He discovered a fossil that Mivart claimed could not exist--a proto-flatfish with a transitional eye (Friedman 2008).

Friedman made the discovery while researching his dissertation on the diversity of teleosts. One day, as he paged through a book on fish fossils, he noticed a 50-million-year-old specimen called Amphistium. Like many fish fossils, this one only showed the bones from one side of the animal. It was generally agreed that Amphistium belonged to some ordinary group of teleosts, although biologists argued over which one. But Friedman saw something different. To him it looked like a flounder. He was struck not by its eyes (the fossil was not preserved well enough for Friedman to see clearly what its eyes were like). Instead, he noticed subtler traits on Amphistium found only on flatfishes. All flatfishes, for instance, have spines on some of their vertebrae that bow forward in a peculiar and distinctive way. So does Amphistium.
To see if he was right, Friedman began traveling to museums around Europe to look at their Amphistium fossils. When he found an intriguing specimen still encased in rock, he had it run through a CT scanner so that he could see its skull. He discovered that Amphistium shares many traits with flatfishes found in no other fish. Most striking of all Amphistium’s anatomy was its pair of eyes. On one side, the eye sat in its normal teleost position. But on the other side, the eye sat high on the fish’s head. In other words, this was a fish Mivart had said could not have existed

This was not a freakish deformity, Friedman realized as he looked at more and more Amphistium fossils. And since they were adult fish, not juveniles, the fossils could not be showing developing eyes still drifting from one side to the other. Intriguingly, though, some Amphistium had a higher left eye, while others had a higher right eye. In most living flatfishes, each species only develops its eyes on one side or the other.

Friedman also wondered if Amphistium was not a transitional early flatfish, but instead a flatfish that had evolved an eye that had moved back to its original side. But he was able to reject that possibility when he traveled to Vienna to look at another Amphistium fossil. It turned out not to be Amphistium at all, but a separate species altogether. He named it Heteronectes (meaning “different swimmer”).

Heteronectes lived around the time of Amphistium, and it also had many traits shared only by flatfishes. It also had one eye sitting high on its head. But a careful comparison of Heteronectes to living and fossil fish revealed that it was missing some traits found only in Amphistium and living flatfishes. In other words, Heteronectes, Amphistium, and living flatfishes all share a close common ancestor. Heteronectes belongs to the first lineage to branch off from that ancestor. Later, the ancestors of Amphistium and living flatfishes split. That is, the two oldest branches of flatfish relatives had the same intermediate eyes.

In a common ancestor of Heteronectes, Amphistium, and living flatfishes, Friedman argues, one eye began to move upward. Friedman proposes that at this early stage, proto-flatfishes were lying on the sea floor at least some of the time. They propped themselves up a bit with their downward-facing fins, so that they could see a little with their downward-facing eye. Mutations arose that produced eyes sitting higher on their heads. Natural selection might have favored them because they gave the fish better vision. Even with one eye midway up their head, the early flatfishes thrived as predators. (Friedman found one fossil of Amphistium with the skeleton of another fish in its gut.)

A fish in Lake Malawi in Africa called Nimbochromis livingstonii may offer a clue to this early stage of flatfish evolution. To catch its prey, it lies on one side on the lake bottom pretending to be dead. White blotches on its flank add to the illusion, because they look like fungi feeding on a dead fish. Unsuspecting fish swim by, whereupon Nimbochromis bursts from the lake bottom to engulf them (McKaye 1981).

But flatfish evolution did not grind to a halt once both eyes ended up on the same side of the head. It turns out there is a living fossil flatfish on Earth today, known as Psettodes. (There are three species in this genus, found in the Atlantic, Indian, and Pacific Oceans.) The ancestors of Psettodes branched off from all other living flatfishes long ago. Intriguingly, some Psettodes put both eyes on their left side and some on their right--the same loose variations found in fossil flatfishes. They even swim vertically like other teleosts, because they have fins on both sides of their bodies. Friedman argues that the full-blown flatfish body did not emerge until after Psettodes branched off--more evidence of the steps by which this weird kind of creature evolved.

The lesson of the flatfish is the same kind of lesson emerging from research on other evolutionary transitions. Fish did not suddenly leap onto land, equipped with legs and toes and other adaptations to life out of the water. A lineage of fish gradually evolved parts of the tetrapod body plan, initially while they were still aquatic vertebrates (Shubin 2008). And after tetrapods began to walk on land, new adaptations continued to emerge for many millions of years, such as the amniote egg that allowed one lineage of tetrapods to lay their eggs on dry land. Whales evolved between 50 and 40 million years ago, but they did not leap back in the water, shedding their legs and sprouting flukes in a sudden evolutionary jolt. Instead, a lineage of mammals gradually became more and more adapted to life in the water. Ten million years after whales first shifted to the water, when they reached 50 ft long and never returned to land in their lives, whales still had tiny rear legs complete with toes (Zimmer 1998).

Flatfish eyes also offer a lesson in convergent evolution--the way in which separate lineages independently arrive at similar solutions to the same biological problem. Convergent evolution is a striking combination of similarities and differences. Organisms are often prevented from evolving into identical forms by developmental constraints and by the contingencies of their evolutionary history. Flatfishes are not the only fish that have evolved flat bodies for swimming on the sea floor. Rays have as well, and like flatfishes, they have eyes on the upper surface of their bodies. But rays do not have migrating eyes. Instead, they evolved a flat body by expanding their pectoral fins, which they use to “fly” underwater much like birds use their wings to fly in the air. Their eyes simply tilted upwards from the sides of their heads.

Flatfishes, on the other hand, did not have that option. Their teleost ancestors were flattened from side to side. The easiest path to a flattened lifestyle was to flop over on one of their sides. As a result, the only way to get both eyes looking upward was for one of them to migrate (Dawkins 1986).

Vertebrate eyes are, of course, not the only kind of eye in the animal kingdom. The millions of insects, crustaceans, and other arthropods on Earth share a very different kind of organ for capturing light to detect objects. From one species to the next, the basic anatomy of the arthropod eye is pretty much the same. Hundreds or thousands of columns develop into a tightly packed grid on either side of an arthropod’s head. Each column can only detect light from a narrow portion of an arthropod’s field of vision. But the arthropod brain can combine the signals from all of them to perceive large-scale patterns--like an oncoming fly swatter.
Once the arthropod eye evolved roughly 530 million years ago, it also took on some weird forms. In several lineages of insects, for example, an eyestalk evolved. The best-studied case of insect eyestalks can be found in a family of flies called Diopsidae, or the stalk-eyed flies (Chapman et al. 2005). There are hundreds of species of stalk-eyed flies, mostly in the tropics of the Old World, and if you ignore their heads, they look like relatively ordinary flies, with six legs and folding wings. But ignoring their heads is impossible. Their eyes sit on wand-like appendages, in some cases stretching out longer than the animal’s entire body.

Like the flounder, the stalk-eyed fly starts out life looking a lot like its ordinary relatives (Warren and Smith 2007). It hatches from an egg and develops as a larva. The larva then becomes a pupa, encasing itself in a shell inside of which it will develop into its adult form. Two patches of cells at the front end of the pupa begin to express a distinctive set of eye-building genes--the same kinds of genes that switch on in other flies, such as Drosophilia melanogaster. Eye cells begin to develop on these patches, and neurons begin to link them to the brain--again in a process much like that in a Drosophila head.

But in stalk-eyed flies, these neurons begin to grow rapidly, while surrounding cells form a sleeve of cuticle that will become the stalk. Trapped inside the puparium, the lengthening eye stalks are forced to grow into tight coils (Buschbeck and Hoy 2005). When the fly finally emerges, it begins to pump fluid into its stalks, unfolding them to their full extent over the course of about 15 min.

The eyes of stalk-eyed flies are more like spheres than the bulging disks of typical insects. They are covered with facets that can receive light from all directions (stalk-eyed flies have 2,000 facets on their eyes, almost three times more than on Drosophila’s). Stalk-eyed flies have some binocular vision where the fields of their two eyes overlap. But the longer the stalks, the smaller that field becomes. Experiments also show that long eyestalks make it harder for the flies to maneuver in flight. You do not see a lot of fighter jets with enormous bendable beams sticking from either side of the cockpit. Studies at the University of North Dakota have shown that stalk-eyed flies can only turn about 860 degrees per second. Other flies can turn 2,000 degrees (Ribak and Swallow 2007).

Stalk-eyed flies have eyes as strangely transformed as flatfishes’. The question naturally arises, how did stalk eyes evolve? The flies have had them for a long time--stalk-eyed flies trapped in amber date back about 50 million years. Some scientists have proposed that the eyes first began to stretch out from the head because natural selection favored flies with better peripheral vision. But it is clear that another force soon came into play: sexual selection.

Stalk-eyed flies typically flit around moist undergrowth during the day, but at night they congregate in roosts on rootlets and leaves. As they gather, fights break out. Males try to eject one another from the groups. They rear up and spread their front legs out alongside their eyestalks, kicking each other to try to knock them over. Males with bigger eyestalks tend to win these fights; some evidence even suggests that males measure each other up by comparing eyestalks, and the male with the smaller eyestalks backs down. Before dawn, the remaining males mate with the females in a group. At this point, the eyestalks play another role in the sex life of stalk-eyed flies: it turns out that females prefer to mate with males with longer eyestalks.

Both lines of evidence suggest that stalk eyes evolved in the same way Darwin argued antlers on deer and bright plumage on birds had evolved. They are the result of competition for mates, rather than a competition to survive. Since male flies with longer eye stalks reproduce more offspring than other males, they pass down their genes, making the average eye stalks longer in the next generation.

But why should a female favor long eye stalks in the first place? Three potential explanations look promising, based on the evidence scientists have gathered so far. The ultimate answer may turn out to be a combination of some of these explanations or even all three.

The first possibility is that eye stalks give females a reliable signal of a male’s genetic quality. It takes a lot of energy to build eye stalks, and when male flies with small eye stalks starve, they can only make tiny ones. Male flies with long stalks barely shrink their stalks at all. If females evolve an attraction to males with long eye stalks, they will be more likely to endow their offspring with stress-resistant genes from their father--ensuring the long-term success of her own genes.

The second possibility is that males are advertising another kind of gift: a way to fight against parasites. These parasites are not tapeworms or viruses or other organisms you might be familiar with. They are parasitic genes in stalk-eyed fly DNA. Female stalk-eyed flies in some populations carry a peculiar segment of DNA on their X chromosomes known as a sex-ratio distorter. The flies pass this DNA on to their offspring, and in their sons, the sex-ratio distorter genes kill off sperm cells with Y chromosomes in them. All that remain are sperm with X chromosomes carrying the sex-ratio distorter. When these males mate, they only produce daughters, which also carry the sex-ratio distorter. The sperm-killing ability of sex-ratio distorters means that, over a few generations, a population of stalk-eyed flies can become made up mostly of females, most of which carry sex-ratio distorters.

It turns out that males with long eyestalks also carry DNA on their X chromosomes that can suppress sex-ratio distorters. Females that choose a long-stalked male will also be choosing sperm that can produce both males and females. In a population dominated by females, males have an evolutionary edge, because each male can mate more often and leave more offspring. So it pays for the female flies to choose mates that will give them sons. Having long eye stalks and suppressor genes might not seem to have much in common. But it turns out that the DNA for both traits sit very close to each other on the male stalk-eyed fly X chromosome. If you get one, you get the other (Presgraves et al. 1997; Johns et al. 2005).

The third possibility is that long eye stalks signal fertility to females. When females mate with long-stalked males, they tend to produce more offspring than when they mate with other males. Another intriguing clue is the fact that males with long eye stalks also have long sperm (Johns and Wilkinson 2007). Female flies that mate with several males may be able not only to select which males to mate with but which male’s sperm to fertilize their eggs. Long-stalked eyes may just be one of many signals the females use to boost their reproductive success.

In both flatfishes and stalk-eyed flies, an ancient kind of eye has been transformed in recent evolutionary history. In both cases, the eye’s evolution has not been driven simply by the benefits of better vision. The eye has been dragged, stretched, and otherwise altered to accommodate other changes to the lives of fishes and flies. As marvelous as these eyes may be in their intricacy and power, in these recent transitions, they have just been along for the ride.

See this is the thing for me though......yes the scientist have fossils of teeth and skulls...Which of course have changed within this unique animal.

As like before when this was brought to me I countered with creations version of the Platypus.

"Evolutionists insist that the duck-billed platypus is an evolutionary link between mammals and birds."

Anyone who reads any evolutionary literature, even at a basic level, will quickly find out that birds are thought to have evolved from dinosaurs in the Jurassic about 150 million years ago, and that mammals are thought to have evolved from a reptile-like group of animals called the therapsids in the Triassic about 220 million years ago. No competent evolutionist has ever claimed that platypuses are a link between birds and mammals. Theory

This is thought to be a link between mammals and birds because of its "duckbill". In fact, scientists have always known that the bill has nothing in common with that of a duck except for the shape. The bill of a duck is a hard keratin structure, while that of the platypus is a soft flexible organ packed with electrical and touch sensors. While underwater, the bill is used to explore the environment and find food. (Thus Huse also gets it wrong when he says the the platypus "uses echo location like dolphins"; it does not.)

Platypus fossils are exactly the same as modern forms." minus the teeth and size.


As for the rest of the body, it is totally unsupported. It would be reasonable to guess that fossil and modern forms might have differed elsewhere in the body, and later finds have confirmed this, at least for the head.

The complex structures of the egg and milk glands are always fully developed and offer no solution as to the origin and development of the womb or milk glands."

Fossil platypuses were not as old as many other more modern mammals, but this was hardly a problem for evolution. The obvious explanation, that older fossil platypuses existed but had not yet been found, turned out to be the correct one.

Doolan et al. (1986) make the following statements about the platypus:

"What about the history of the platypus? Where did it come from? Why is it only found in Australia? All fossils found of it are essentially the same as today's living creatures. It certainly shows no signs of evolution. Its only significant change seems to have been to lose some teeth and shrink in size." (Doolan, Mackay, Snelling, & Hallby, 1986)

Not true; there are other differences between the modern platypus and the skull of Obdurodon ****soni than size. Archer et al.(1992) list over 20 differences between them. Also, it would be more accurate to say "all teeth" than "some teeth", since the modern form has no teeth as an adult.

"Indeed, evolutionary scientists are baffled about the ancestry of the platypus."

This is not a problem for evolution, since it is clear that any bafflement is due mainly to a shortage of evidence. Actually, similarities with other fossil mammals do give at least some hints to the ancestry of monotremes. "They openly admit that nothing is known about its history that can explain its geographical distribution."


The skull mentioned above must be the Riversleigh skull, which was found in 1985, after the fossil they are about to introduce, and is a much more complete and informative fossil (although not nearly as old).

"In 1984, however, a platypus jaw with three large teeth was found among a collection of opalised bones at Lightning Ridge in northern New South Wales, and pronounced to be at least 110 million years old. Naturally, evolutionist scientists were excited. It seemed that they had now established the platypus's great antiquity.

"But this platypus jaw did not help the evolutionists discover how the platypus had evolved. The new jaw was bigger than that of the present-day platypus and had larger teeth. If anything, it showed that today's platypus has degenerated since the time of its ancestor."

The new fossils do give important information about platypus evolution, indicating that it evolved from a larger toothed form. The statement about "larger teeth" is misleading, since the modern platypus has no teeth at all as an adult. That modern platypuses are smaller than their ancestors is no evidence of degeneration, since small creatures can be just as complex as large ones.

Because the monotremes are so different from other mammals, most evolutionary authorities realize that the alleged evolutionary ancestry of echidnas and platypuses is unexplainable. All they have come up with by way of a suggested explanation is that the monotremes must have originated from a line of mammal-like reptiles different from that which gave rise to the other mammals.

No one has a clue what those mammal-like reptiles could have been, of course, because no “mammal-like reptile” comes close to looking like a common ancestor for the echidna and platypus.

Echidnas and platypuses are unique in their biology, lifestyle, and habitat compared with other mammals, reptiles, and birds. Therefore there is no reason to think that their ancestors were significantly different from today's monotremes.

With no clear evidence from fossils or anywhere else to indicate that echidnas and platypuses have evolved from non-monotremes, it is surely more logical to deduce that they never evolved at all. We believe that God created them as egg-laying echidnas and platypuses right from the beginning, and they have always been that way.

So this is the point.....if this is what your bringing me as evidence of evolution that the platypus was anything but a platypus...I say no try again.

And see this is the point...because most that believe in evolution bring the same evidence which has already been proven wrong.....

And yes smiles manybe you are right and this could be argued until we change hmmmmmm back in monkeys....gigglesnort......

The bible and evolution don't get along. The majority of christians believe in evolution, so please don't say otherwise. The Roman Catholic, Eastern Orthodox, and Protestant(Main and Liberal) all teach evoltion and make up over 2/3 of the Christian population.

And every time someone brings forth such evidence, we get a response out of you like:



Which is why a number of us have given up. You're not being objective, what you are looking for is an answer that fits with YOUR definition of evolution, and as it has been stated by a number of different people, the "proof" you are looking for, that would prove your definition of evolution, would actually disprove the whole theory of evolution.

This should have dies a long time ago

hmmmmm maybe you should read before you speak....I never said I don't believe in evolution...to the contrary. Do I believe even the platypus evolved...sure I do....But it was never anything but a platypus......

Well what would you like me to do.....say yippy skippy to the answers that to me have not proved evolution....but more have proved the awesomeness of the God that created the platypus or other such creatures. It's not a matter of being objective here....it's a matter of give me something that is crediblle. I do believe in evolving within a species, but like I said so many times when your only evidence is that of teeth and skull that onlyy prove my point that the platypus has evolved within itself and gotten smaller and has no teeth......I would just say you have not proved evolution in the sense that you people are talking about....

I quote your original post.
Can You Believe in Both Evolution and Christianity?

“Christ died for our sins.” As you probably know, that is one of the basic teachings of Christianity. (1 Corinthians 15:3; 1 Peter 3:18) To see why evolution is incompatible with that statement, we first need to understand why the Bible calls us sinners and what sin does to us

I Debbie.

My point is that these two populations started out as the same species . . . . it can literally be a single change, a single adaptation to one group that can make it impossible for the two groups to interbreed. Once its impossible for genes to be passed between these two groups, the single adaptations that each group gains from there on out will accumulate. They will become more and more different as time goes by . . . . this is micro evolution becoming macro evolution.

For ANYONE to say macro evolution cannot happen, they would need to provide a mechanism by which these changes would be limited, a way in which a single protein change within a gamete would not happen, and thus not allow this kind of separation of species.

Retro viruses can insert DNA into a gamete. This single event can create an impasse between two populations of the same species and create two groups that cannot interbreed.

Feral macro evolution is real. It happens, you can choose to believe this has been guided by god for the purpose of creating humans, when and where he wanted, but please understand that technology, science, knowledge has moved on . . . this is old news. It may be time for your group to actually allow this new knowledge to guide you to the truth . . .

Well on the contrary if you read the article the scientists(which are at least 100 of them if you go to the link) of the document claim they evolved from a different species millions of years ago.

So here we have another example of how two different views will always dispute about the subject of evolution or not.

In the end I think it is a good thing for it makes both sides work harder in finding the truth behind how we as a species evolved or for that matter how other species evolved (as the same species as you indicate) or as (a different species as others indicate).

I am sure that more will be discovered in time regardless who will claim to be right or not.


I also don't see that it is a competition of anykind. I am sure the scientists don't see it this way either, yet they do like the hard questions so they can work harder in finding out what could have been and we should admire them for trying regardless in what their viewpoint is.

I personally think evolution exists and that it is very possible that a species has changed complete form or even cross gendered to survive the perils or harsh environments of the past. Why couldn't it be absolutely impossible?

I also think it is a slow transition and not something quick like 500 years only. The planet wasn't much different 500 years ago concerning ecological change, yet millions of years ago we can see that the planet was different.

So to tackle this would require many years of study and evaluation and you would probably get a much better answer from those who do study this for a living.

I am sure they have emails to be contacted. Try Richard Dawkin's or Carl Zimmer. Who knows they may email you back and show you what they have discovered. If you believe them that is up to you.

Weather one believes in writen word of God or not, ... it is obvious ...

Starting here at this point in history.

Neanderthals ... no longer exist after they evolved to Cro Magnon.
Cro-Magnon ... no longer exists after the evolution to Homo Sapeins.

if man evolved from apes ... then there would be no apes. But, there are still apes, So, for apes to evolve and become man... then that would mean there would be no apes. And besides, Apes in the wild are no evolving... why not?

Reguardless of who post what, there are some folks who stick firmly behind their beliefs ... no matter how wrong they are or aren't.

This is a good question. If man evolved from a ape then why are there still apes today?

So here are some conclusions I can come up with

Perhaps we come from a ape(primate) that doesn't exist anymore and branched off from other ape families

Perhaps we never came from apes, but have similiar characteristics from ape or primate and evolved through the times in gradual changes

Perhaps evolutionists are missing a small key in finding out what we come from

and perhaps

like creationists always say we come as humans and never changed much, but just adapted to the changes from time

and then we have adam and eve. Bare naked with no hair on our bodies, just a little on the head and armpits.


Whatever it is worth many are studying, researching, and exploring the possiblities in the best of their ability today.