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Bones, molecules...or both?
Abstract
Evolutionary trees constructed by studying biological molecules
often don't resemble those drawn up from morphology. Can the two ever be reconciled,
asks Trisha Gura
... Debate surrounding the use of different types of data for phylogenetic analysis often circulates around the supremacy of molecular data over morphological data (e.g., Gura 2000;Wood 2000, 2001;Scotland et al. 2003) or the utility of morphological data for understanding relationships between fossil taxa (e.g., Wiens 2004;Strait and Grine 2004) and character evolution (e.g., Assis and de Carvalho 2010). Other analyses of congruence have focused on assumptions made about character behavior as possible reasons for incongruence between data sets (e.g., Masters and Brothers 2002). ...
... In this case, the use of Colobus to root the tree results in a spurious assignment of character polarity. This is clearly visible in Gura's (2000) review of the morphology-molecule debate, where, on page 232, the molecular and morphological views of great ape-human relationships differ only in the placement of the root. ...
When molecules and morphology produce incongruent hypotheses of primate interrelationships, the data are typically viewed as incompatible, and molecular hypotheses are often considered to be better indicators of phylogenetic history. However, it has been demonstrated that the choice of which taxa to include in cladistic analysis as well as assumptions about character weighting, character state transformation order, and outgroup choice all influence hypotheses of relationships and may positively influence tree topology, so that relationships between extant taxa are consistent with those found using molecular data. Thus, the source of incongruence between morphological and molecular trees may lie not in the morphological data themselves but in assumptions surrounding the ways characters evolve and their impact on cladistic analysis. In this study, we investigate the role that assumptions about character polarity and transformation order play in creating incongruence between primate phylogenies based on morphological data and those supported by multiple lines of molecular data. By releasing constraints imposed on published morphological analyses of primates from disparate clades and subjecting those data to parsimony analysis, we test the hypothesis that incongruence between morphology and molecules results from inherent flaws in morphological data. To quantify the difference between incongruent trees, we introduce a new method called branch slide distance (BSD). BSD mitigates many of the limitations attributed to other tree comparison methods, thus allowing for a more accurate measure of topological similarity. We find that releasing a priori constraints on character behavior often produces trees that are consistent with molecular trees. Case studies are presented that illustrate how congruence between molecules and unconstrained morphological data may provide insight into issues of polarity, transformation order, homology, and homoplasy.
... Although the exact interpretation of methylation patterns may be problematic [21], sequences are increasing used to infer ancestral relationships, especially when (like in human colon) few other alternatives exist. Ancestry may potentially be completely inferred from sequences, although a synthesis with morphologic markers will likely yield a better understanding of evolutionary relationships [24]. Molecular species phylogenies are continuously refined with more sequences and better analytic methods. ...
... Most crypts appear to be long-lived structures, consistent with an ability to observe clonal patches established before birth in adult colons [9]. Of note, ancestries based on sequences are inherently controversial [24], and the same general objections to species phylogenetic studies likely apply to our somatic cell trees. Although the exact interpretation of methylation patterns may be problematic [21], sequences are increasing used to infer ancestral relationships, especially when (like in human colon) few other alternatives exist. ...
The ability to discern ancestral relationships between individual human colon crypts is limited. Widely separated crypts likely trace their common ancestors to a time around birth, but closely spaced adult crypts may share more recent common ancestors if they frequently divide by fission to form clonal patches. Alternatively, adult crypts may be long-lived structures that infrequently divide or die.
Methylation patterns (the 5' to 3' order of methylation) at CpG sites that exhibit random changes with aging were measured from isolated crypts by bisulfite genomic sequencing. This epigenetic drift may be used to infer ancestry because recently related crypts should have similar methylation patterns.
Methylation patterns were different between widely separated ("unrelated") crypts greater than 15 cm apart. Evidence for a more recent relationship between directly adjacent or branched crypts could not be found because their methylation pattern distances were not significantly different than widely separated crypt pairs. Methylation patterns are essentially equally different between two adult human crypts regardless of their relative locations.
Methylation patterns appear to record somatic cell trees. Starting from a single cell at conception, sequences replicate and may drift apart. Most adult human colon crypts appear to be long-lived structures that become mosaic with respect to methylation during aging.
... Both the resulting maximum likelihood tree, and the TNFα and IAPP indels provided independent sources of information to get more insight in rodent and Glires phylogeny. The data may help restore the morphologists' confidence in the potential of molecular evidence (Gura, 2000). ...
... Our approach is to perform a total-evidence analysis; that is, to incorporate both DNA and phenotypic data in the same analysis, without imposing any a priori hypotheses about the phylogenetic relationships among hominids. The potential usefulness of a total-evidence analysis for solving the apparent conflict between molecular and morphological data in hominid phylogenetics was recognized several years ago (Gura, 2000), but such an analysis has, to our knowledge, not yet been carried out. In an early study, Andrews & Martin (1987) combined morphological and molecular data in one analysis, but they were limited by the relatively simple analytical methods available at the time, and in addition had access to only a rather small data set in comparison to those available at present. ...
J. R. Grehan & J. H. Schwartz (Journal of Biogeography, 2009, 36, 1823–1844) argued that humans (Homo) are more closely related to orangutans (Pongo) than to chimpanzees (Pan), and used this scenario to draw biogeographical conclusions about human origins. They discussed a contradiction between phenotypical and molecular results that has led to a debate about the reliability of genetic versus phenotypic data. The main aim of our study is to test the conflicting phylogenetic hypotheses by a total-evidence analysis based on simultaneous optimization of extensive phenotypic and molecular data sets. Our results supported the human–chimpanzee clade, without any phenotypical–molecular data conflict, as the same phylogeny emerged both from the total analysis and when the molecular and phenotypic data were analysed separately. Sensitivity analyses showed that the result was not dependent on the parameters chosen for character weighting.
... The relative importance of molecular and morphological data has been a subject of controversy within the systematics community for a number of years (Gura, 2000;Hillis & Wiens, 2000). In particular, some authors have claimed that molecular data either has, or soon will, completely supersede morphological evidence for phylogenetic inference (Scotland & al, 2003), a claim wholly rejected by others (Wiens, 2004). ...
There has been a long history of interest in measuring the information conveyed by phylogenetic data. In one application, recent studies have attempted to compare the informativeness of morphological and molecular data, and of nucleotide and amino acid sequence alignments. While a variety of measures have been proposed to quantify phylogenetic information, most measures are rather unsatisfactory, failing to capture every aspect of the informativeness of a character. One measure, cladistic information content (CIC) is a natural measure of phylogenetic information. We show why CIC is preferable to other, recently introduced, measures, and, as an example, use CIC to compare the information of recent morphological and molecular datasets. This provides new empirical data relevant to the debate about the relative utility of morphology and molecules in phylogenetic inference, a subject of significant interest.
... Substantiation of the Theria hypothesis would implicate a more parsimonious single origin for these features. The incongruent mammalian family trees resulting from mitochondrial sequence analysis and morphological characters have contributed to a divisive debate over their utilities in phylogenetic inference (Gura 2000). Thus far, only small nuclear genes have been applied to the Theria/Marsupionta question (i.e., <1.5 kb open reading frame; Kullander et al. 1997; Toyosawa et al. 1999), and they have failed to convincingly validate either hypothesis. ...
The three living monophyletic divisions of Class Mammalia are the Prototheria (monotremes), Metatheria (marsupials), and
Eutheria (`placental' mammals). Determining the sister relationships among these three groups is the most fundamental question
in mammalian evolution. Phylogenetic comparison of these mammals by either anatomy or mitochondrial DNA has resulted in two
conflicting hypotheses, Theria and Marsupionta, and has fueled a ``genes versus morphology'' controversy. We have cloned and
analyzed a large nuclear gene, the mannose 6-phosphate/insulin-like growth factor II receptor (M6P/IGF2R), from representatives of all three mammalian groups, including platypus, echidna, opossum, wallaby, hedgehog, mouse, rat,
rabbit, cow, pig, bat, tree shrew, colugo, ringtail lemur, and human. Statistical analysis of this nuclear gene unambiguously
supports the morphology-based Theria hypothesis that excludes monotremes from a clade of marsupials and eutherians. The M6P/IGF2R was also able to resolve the finer structure of the eutherian mammalian family tree. In particular, our analyses support
sister group relationships between lagomorphs and rodents, and between the primates and Dermoptera. Statistical support for
the grouping of the hedgehog with Feruungulata and Chiroptera was also strong.
... Despite the currently popular focus on mechanisms of variation generation, there are still open challenges regarding the assessment of particular homologies. Well-confirmed phylogenies are a precondition for any account of novelty, yet in some cases classical and molecular data lead to conflicting phylogenies, and there are currently no generally agreed upon methods of combining both kinds of data (Gura 2000). Claims about actual patterns of structural transformation and whether or not structures in a descendant are homologous to some ancestral features can also be controversial in many cases. ...
This article reviews the recent reissuing of Richard Owen’s On the Nature of Limbs and its three novel, introductory essays. These essays make Owen’s 1849 text very accessible by discussing the historical context of his work and explaining how Owen’s ideas relate to his larger intellectual framework. In addition to the ways in which the essays point to Owen’s relevance for contemporary biology, I discuss how Owen’s unity of type theory and his homology claims about fins and limbs compare with modern views. While the phenomena studied by Owen are nowadays of major interest to evolutionary developmental biology, research in evo-devo has largely shifted from homology (which was Owen’s concern) towards evolutionary novelty, e.g., accounting for fins as a novelty. Still, I argue that questions about homology are important and raise challenges even for explanations of novelty.
Up to now, we have presented key chemical processes in our environment. Biochemical processes fashioned by different organisms, and the biogeochemical cycles of key elements and water, are also of paramount importance. We proceed now to discuss them.
Vor allem im englischen Sprachraum hat es sich eingebürgert, von einer Darwinschen Revolution (Darwinian Revolution) zu sprechen, deren weltanschauliche Wirkung durchaus mit der wissenschaftlichen Revolution des 17. Jahrhunderts vergleichbar sei. Demnach befreite Darwin die Lebenswissenschaften aus einer jahrtausendealten, religiös und metaphysisch motivierten Umklammerung durch typologische und teleologische Denkfiguren (vgl. Ruse 1979; Mayr 1982/2002; Junker/Hoßfeld 2009). Vor der Veröffentlichung von Darwins Über die Entstehung der Arten im Jahr 1859, so der kleinste gemeinsame Nenner, schien eine Transformation der Arten durch Akkumulation individueller und ungerichteter Variationen unmöglich, entweder weil individuelle Variationen als bloße Abweichungen betrachtet wurden, die das Wesen oder die »Essenz« einer Art grundsätzlich nicht berührten (Essentialismus), oder weil man der Überzeugung war, dass jede produktive Variation im Einklang mit den Bedürfnissen von Lebewesen stehen müsse und daher nicht ungerichtet sein könne (Teleologie).
The Battle Lines are Drawn You would not know there is a war going on in evolutionary circles, but there is. This war is not the war that pits evolutionists against creationism and design. This war is being waged among the evolutionists themselves and the battle lines are clearly drawn. On one side of the battle lines are the traditionalists, those who use morphology, cranial shape, dentition, and skeletal clues to build evolutionary and phylogenic trees. Squarely opposed to them and on the other side of the battlefield are the geneticists that say the best way to understand the evolutionary history of an organism is with genetic studies. These genetic studies involve mitochondrial DNA and other molecular molecules (1). Many evolutionary scientists find themselves somewhere in the middle of this evolutionary battle. From an evolutionary point of view they find that both sides of the data provide useful information. What is interesting is that the adamant supporter of the opposing scenario feels that the other side is standing on very weak scientific grounds. Figure 1. DNA removed from cellular mitochondria shown above is known as mtDNA. Before looking at the result of this battle let's go back a few decades. Back to a time before the genetic studies came to the forefront. Many scientists believed the fossil record revealed modern humans and the Neanderthals had evolved from Homo erectus. Homo erectus had descended from the Australopithecines and had moved out of Africa about 2 million years ago and had interbred with various regional hominids and gave rise to the diverse Homo branches. These branches included Homo sapiens or modern man, and Homo neanderthalensis or Neanderthal man. This was often called the "multiregional theory" since the erectus genes were scattered through many regions and all human ancestors, including modern humans and the Neanderthal, were more or less related. Many scientists felt and still feel very comfortable with the idea of the inter-relatedness of the various fossil men. Recently in about the last 10-15 years genetic studies have supposedly shown that the multiregional picture was not correct. In 1987 the research of Mark Stoneking, Rebecca Cann, and Allan Wilson (2) traced all modern humans to an evolutionary "Eve." This Eve's genes had migrated out of Africa about 200,000 years ago and had given rise to Homo sapiens with no interbreeding with various other hominids. This became known as the mitochondrial Eve theory, since the DNA material that was analyzed had been gathered from the fossil mitochondria (3) in the fossil substrate. This type of DNA is commonly called mtDNA (fig1).
Our Earth is a remarkable reaction vessel. It is of paramount importance that students grow in their understanding and awareness of the astounding effects that chemistry and biochemistry have on our environment. The first book in the field to encompass theory and practice, Environmental Chemistry: Fundamentals covers the chemical and biochemical processes that take place in air, water, soil, and living systems. The text is written with advanced college students in mind; nevertheless, issues are frequently presented in such a way that graduate students and professionals can find subjects of interest. Available separately, an experimental companion book, Environmental Chemistry: Microscale Laboratory Experiments, provides students with a thorough practical introduction to environmental experimentation. By using literature data in many of the examples and problems, both Environmental Chemistry: Fundamentals and Environmental Chemistry: Microscale Laboratory Experiments help students expand their problem solving skills and practice with real situations. © 2007 Springer Science-Business Med ia, LLC. All right s reserved.
The linewidth enhancement factor of a 5 μm distributed feedback (DFB) quantum cascade laser above the threshold current detuned from the gain peak was investigated. This laser oscillates in two DFB modes located on either side of the gain peak. Using the optical feedback self-mixing method, we have observed variations in the linewidth enhancement factor, deviating from zero. The signs of the two DFB modes are both negative, which was verified by comparing their waveforms with that of conventional 1.55 μm laser diodes, suggesting that the gain curve is asymmetric with respect to the gain peak.
Snakes are one of the most extraordinary groups of terrestrial vertebrates, with numerous specializations distinguishing them from other squamates (lizards and their allies). Their musculoskeletal system allows creeping, burrowing, swimming and even gliding, and their predatory habits are aided by chemo- and thermoreceptors, an extraordinary degree of cranial kinesis and, sometimes, powerful venoms. Recent discoveries of indisputable early fossil snakes with posterior legs are generating intense debate about the evolutionary origin of these reptiles. New cladistic analyses dispute the precise significance and phylogenetic placement of these fossils. These conflicting hypotheses imply radically different scenarios of snake origins and relationships with wide biological implications.
The history of a tumour is currently inferred from its morphology. However, progression may be variable between similar appearing tumours, and some critical events may be difficult to see. It has become increasingly apparent that histories are also written within sequences. Every tumour likely records its own progression within its genome. In the future, it may be possible to read the past based on these sequences. A critical issue is whether these autobiographies will recapitulate morphology or whether they reveal unexpected ghosts.
Comparison of mammalian brain parts has often focused on differences in absolute size, revealing only a general tendency for all parts to grow together. Attempts to find size-independent effects using body weight as a reference variable obscure size relationships owing to independent variation of body size and give phylogenies of questionable significance. Here we use the brain itself as a size reference to define the cerebrotype, a species-by-species measure of brain composition. With this measure, across many mammalian taxa the cerebellum occupies a constant fraction of the total brain volume (0.13 +/- 0.02), arguing against the hypothesis that the cerebellum acts as a computational engine principally serving the neocortex. Mammalian taxa can be well separated by cerebrotype, thus allowing the use of quantitative neuroanatomical data to test evolutionary relationships. Primate cerebrotypes have progressively shifted and neocortical volume fractions have become successively larger in lemurs and lorises, New World monkeys, Old World monkeys, and hominoids, lending support to the idea that primate brain architecture has been driven by directed selection pressure. At the same time, absolute brain size can vary over 100-fold within a taxon, while maintaining a relatively uniform cerebrotype. Brains therefore constitute a scalable architecture.
Recent advances in mathematics and sequencing have revolutionised the analysis of evolution. Modern phylogeny is molecular phylogeny, or histories reconstructed from sequences. The same quantitative sequence approaches have not been fully translated to colorectal cancer. Molecular tumour clocks provide opportunities to reconstruct individual tumour histories. Phenotypic and genetic progression are usually thought to be synonymous, but many mutations may accumulate in normal appearing cells. Although such occult genetic progression is essentially invisible, molecular tumour clocks offer the somewhat magical ability to reconstruct what may never be seen. Potentially much of colorectal cancer progression is unseen and unexplored because tumours usually appear late in life.
When phylogenetic trees constructed from morphological and molecular evidence disagree (i.e. are incongruent) it has been suggested that the differences are spurious or that the molecular results should be preferred a priori. Comparing trees can increase confidence (congruence), or demonstrate that at least one tree is incorrect (incongruence). Statistical analyses of 181 molecular and 49 morphological trees shows that incongruence is greater between than within the morphological and molecular partitions, and this difference is significant for the molecular partition. Because the level of incongruence between a pair of trees gives a minimum bound on how much error is present in the two trees, our results indicate that the level of error may be underestimated by congruence within partitions. Thus comparisons between morphological and molecular trees are particularly useful for detecting this incongruence (spurious or otherwise). Molecular trees have higher average congruence than morphological trees, but the difference is not significant, and both within- and between-partition incongruence is much lower than expected by chance alone. Our results suggest that both molecular and morphological trees are, in general, useful approximations of a common underlying phylogeny and thus, when molecules and morphology clash, molecular phylogenies should not be considered more reliable a priori.
Recent research has shown that genetic drift may have produced many cranial differences between Neandertals and modern humans. If this is the case, then it should be possible to estimate population genetic parameters from Neandertal and modern human cranial measurements in a manner analogous to how estimates are made from DNA sequences. Building on previous work in evolutionary quantitative genetics and on microsatellites, we present a divergence time estimator for neutrally evolving morphological measurements. We then apply this estimator to 37 standard cranial measurements collected on 2,524 modern humans from 30 globally distributed populations and 20 Neandertal specimens. We calculate that the lineages leading to Neandertals and modern humans split ≈311,000 (95% C.I.: 182,000 to 466,000) or 435,000 (95% C.I.: 308,000 to 592,000) years ago, depending on assumptions about changes in within-population variation. These dates are quite similar to those recently derived from ancient Neandertal and extant human DNA sequences. Close correspondence between cranial and DNA-sequence results implies that both datasets largely, although not necessarily exclusively, reflect neutral divergence, causing them to track population history or phylogeny rather than the action of diversifying natural selection. The cranial dataset covers only aspects of cranial anatomy that can be readily quantified with standard osteometric tools, so future research will be needed to determine whether these results are representative. Nonetheless, for the measurements we consider here, we find no conflict between molecules and morphology.
• craniometrics
• evolutionary quantitative genetics
• microsatellites
• population genetics
• human evolution
Which mammals are the closest relatives to cetaceans (dolphins, porpoises and whales)? That is, which mammalian group is their 'sister taxon'? There is a wide gulf between the morphological and molecular evolutionary studies on the question, for they give conflicting answers. In a paper in Systematic Biology, O'Leary and Geisler1 highlight the importance of the early divergent lineages, or extinct fossil taxonomic groups, in resolving this intriguing problem.
Abstract — Arguments for and against combined analysis of multiple data sets in phylogenetic inference are reviewed. Simultaneous analysis of combined data better maximizes cladistic parsimony than separate analyses, hence is to be preferred. Simultaneous analysis can allow “secondary signals” to emerge because it measures strength of evidence supporting disparate results. Separate analyses are useful and of interest to understanding the differences among data sets, but simultaneous analysis provides the greatest possible explanatory power, and should always be evaluated when possible. The mechanics of simultaneous analysis are discussed.
Phylogenetic relationships among the holometabolous insect orders were inferred from cladistic analysis of nucleotide sequences of 18S ribosomal DNA (rDNA) (85 exemplars) and 28S rDNA (52 exemplars) and morphological characters. Exemplar outgroup taxa were Collembola (1 sequence), Archaeognatha (1), Ephemerida (1), Odonata (2), Plecoptera (2), Blattodea (1), Mantodea (1), Dermaptera (1), Orthoptera (1), Phasmatodea (1), Embioptera (1), Psocoptera (1), Phthiraptera (1), Hemiptera (4), and Thysanoptera (1). Exemplar ingroup taxa were Coleoptera: Archostemata (1), Adephaga (2), and Polyphaga (7); Megaloptera (1); Raphidioptera (1); Neuroptera (sensu stricto = Planipennia): Mantispoidea (2), Hemerobioidea (2), and Myrmeleontoidea (2); Hymenoptera: Symphyta (4) and Apocrita (19); Trichoptera: Hydropsychoidea (1) and Limnephiloidea (2); Lepidoptera: Ditrysia (3); Siphonaptera: Pulicoidea (1) and Ceratophylloidea (2); Mecoptera: Meropeidae (1), Boreidae (1), Panorpidae (1), and Bittacidae (2); Diptera: Nematocera (1), Brachycera (2), and Cyclorrhapha (1); and Strepsiptera: Corioxenidae (1), Myrmecolacidae (1), Elenchidae (1), and Stylopidae (3). We analyzed ∼1 kilobase of 18S rDNA, starting 398 nucleotides downstream of the 5′ end, and ∼400 bp of 28S rDNA in expansion segment D3. Multiple alignment of the 18S and 28S sequences resulted in 1,116 nucleotide positions with 24 insert regions and 398 positions with 14 insert regions, respectively. All Strepsiptera and Neuroptera have large insert regions in 18S and 28S. The secondary structure of 18S insert 23 is composed of long stems that are GC rich in the basal Strepsiptera and AT rich in the more derived Strepsiptera. A matrix of 176 morphological characters was analyzed for holometabolous orders. Incongruence length difference tests indicate that the 28S + morphological data sets are incongruent but that 28S + 18S, 18S + morphology, and 28S + 18S + morphology fail to reject the hypothesis of congruence. Phylogenetic trees were generated by parsimony analysis, and clade robustness was evaluated by branch length, Bremer support, percentage of extra steps required to force paraphyly, and sensitivity analysis using the following parameters: gap weights, morphological character weights, methods of data set combination, removal of key taxa, and alignment region. The following are monophyletic under most or all combinations of parameter values: Holometabola, Polyphaga, Megaloptera + Raphidioptera, Neuroptera, Hymenoptera, Trichoptera, Lepidoptera, Amphiesmenoptera (Trichoptera + Lepidoptera), Siphonaptera, Siphonaptera + Mecoptera, Strepsiptera, Diptera, and Strepsiptera + Diptera (Halteria). Antliophora (Mecoptera + Diptera + Siphonaptera + Strepsiptera), Mecopterida (Antliophora + Amphiesmenoptera), and Hymenoptera + Mecopterida are supported in the majority of total evidence analyses. Mecoptera may be paraphyletic because Boreus is often placed as sister group to the fleas; hence, Siphonaptera may be subordinate within Mecoptera. The 18S sequences for Priacma (Coleoptera: Archostemata), Colpocaccus (Coleoptera: Adephaga), Agulla (Raphidioptera), and Corydalus (Megaloptera) are nearly identical, and Neuropterida are monophyletic only when those two beetle sequences are removed from the analysis. Goleoptera are therefore paraphyletic under almost all combinations of parameter values. Halteria and Amphiesmenoptera have high Bremer support values and long branch lengths. The data do not support placement of Strepsiptera outside of Holometabola nor as sister group to Coleoptera. We reject the notion that the monophyly of Halteria is due to long branch attraction because Strepsiptera and Diptera do not have the longest branches and there is phylogenetic congruence between molecules, across the entire parameter space, and between morphological and molecular data.
Taxonomic congruence and total evidence are competing paradigms in phylogenetic inference. Taxonomic congruence focuses on deriving a consensus from the results obtained from separately analyzed data sets, whereas total evidence uses character congruence in the search for the best-fitting hypothesis for all of the available character evidence. Explicit or implicit use of taxonomic congruence is usually employed when an investigator either has both molecular and morphological data sets or has different gene-, rRNA-, or protein-sequence data sets available. Indeed, a taxonomic congruence rationale is frequently used as the basis for exploring classes of data, thus allowing comparison between the phylogenetic signal emerging from a particular data set and those of other such classes. Problematic aspects of employing the taxonomic congruence approach include the potentially misleading and arbitrary choices of both a consensus method and the division of characters into subsets. If the goal of an analysis is to provide the best estimate of genealogy afforded by the available character evidence, then taxonomic congruence is substantially more arbitrary than a total evidence approach. The theoretical advantages of phylogenetic estimates based on total evidence are argued in the present study and are illustrated with an example of amniote relationships. We report conflicting results from total evidence and taxonomic congruence approaches, with analyses of previously reported data from both fossil and living amniotes and from both morphology and molecules, the latter including available 18S rRNA, 28S rRNA, and protein sequences. We conclude that a more highly resolved and robust phylogenetic hypothesis of amniotes, the traditional one, emerges when a total evidence approach is employed.
The inferred transition from terrestrial hoofed mammal to fully aquatic cetacean has been intensively studied with fossil
evidence. However, large sections of this remarkable evolutionary sequence are missing. Phylogenetic analysis of extant taxa
may help to fill in some of these gaps. In this report, kappa-casein (exon 4) and beta-casein (exon 7) milk protein genes
from cetaceans and other placental mammals were PCR-amplified, sequenced, and aligned to previously published sequences. Phylogenetic
analyses of the casein data suggest that hippopotamid artiodactyls are more closely related to cetaceans than to other artiodactyls
(even-toed hoofed mammals). An analysis of the nuclear casein sequences combined with published mitochondrial cytochrome b
DNA sequences also supports the Cetacea/Hippopotamidae sister group. This affinity implies that some of the aquatic traits
of cetaceans were derived in the common ancestor of Cetacea and Hippopotamidae. An extant "missing link" to Cetacea may have
been overlooked by science since the description of the semiaquatic Hippopotamus in 1758. Paleontological information is grossly
inconsistent with this hypothesis. If the casein phylogeny is accurate, large gaps in the fossil record as well as extensive
morphological reversals and convergences must be acknowledged.
Insertion analysis of short and long interspersed elements is a powerful method for phylogenetic inference. In a previous study of short interspersed element data, it was found that cetaceans, hippopotamuses, and ruminants form a monophyletic group. To further resolve the relationships among these taxa, we now have isolated and characterized 10 additional loci. A phylogenetic analysis of these data was able to resolve relationships among the major cetartiodactyl groups, thereby shedding light on the origin of whales. The results indicated (i) that cetaceans are deeply nested within Artiodactyla, (ii) that cetaceans and hippopotamuses form a monophyletic group, (iii) that pigs and peccaries form a monophyletic group to the exclusion of hippopotamuses, (iv) that chevrotains diverged first among ruminants, and (v) that camels diverged first among cetartiodactyls. These findings lead us to conclude that cetaceans evolved from an immediate artiodactyl, not mesonychian, ancestor.
In their quest to reconstruct the tree of life, evolutionary biologists are constantly looking for new sources of data. Morphological data have been applied to the phylogeny problem since the 1800s, and morphology continues to be the only source of available data on relationships for the vast majority of species on Earth, past and present. However, since the 1960s, molecular data have contributed an increasing fraction of the new information used to reconstruct phylogenetic history (1). Each new source of molecular information has provided a new perspective on evolutionary history, and each technique has a set of advantages and disadvantages. As with morphological approaches, most of these molecular techniques continue to be useful for specific kinds of problems. Nonetheless, almost every new molecular approach to phylogenetic inference has been ballyhooed as capable of ''rev-olutionizing'' the field. In truth, no one technique is a perfect solution for all phylogenetic problems, even though each provides us with a new perspective on evolution. Even the oft-perceived superiority of molecular data is largely a matter of timing. As Avise (2) has noted, imagine if we had studied the DNA sequences of organisms for decades without ever seeing a phenotype , and then someone suddenly discovered the morphologies and behaviors that DNA sequences specify! The sense that we were finally making real progress in our understanding of evolution would be at least as great as the sense of wonder and excitement that has accompanied advances in molecular biology.
The expansion of premodern humans into western and eastern Europe approximately 40,000 years before the present led to the eventual replacement of the Neanderthals by modern humans approximately 28,000 years ago. Here we report the second mitochondrial DNA (mtDNA) analysis of a Neanderthal, and the first such analysis on clearly dated Neanderthal remains. The specimen is from one of the eastern-most Neanderthal populations, recovered from Mezmaiskaya Cave in the northern Caucasus. Radiocarbon dating estimated the specimen to be approximately 29,000 years old and therefore from one of the latest living Neanderthals. The sequence shows 3.48% divergence from the Feldhofer Neanderthal. Phylogenetic analysis places the two Neanderthals from the Caucasus and western Germany together in a clade that is distinct from modern humans, suggesting that their mtDNA types have not contributed to the modern human mtDNA pool. Comparison with modern populations provides no evidence for the multiregional hypothesis of modern human evolution.
Relationships among representatives of the five major Hawaiian Drosophila species groups were examined using data from eight different gene regions. A simultaneous analysis of these data resulted in a single most-parsimonious tree that (1) places the adiastola picture-winged subgroup as sister taxon to the other picture-winged subgroups, (2) unites the modified-tarsus species group with flies from the Antopocerus species group, and (3) places the white-tip scutellum species group as the most basal taxon. Because of the different gene sources used in this study, numerous process partitions can be erected within this data set. We examined the incongruence among these various partitions and the ramifications of these data for the taxonomic consensus, prior agreement, and simultaneous analysis approaches to phylogenetic reconstruction. Separate analyses and taxonomic consensus appear to be inadequate methods for dealing with the partitions in this study. Although detection of incongruence is possible and helps elucidate particular areas of disagreement among data sets, separation of partitions on the basis of incongruence is problematic for many reasons. First, analyzing all genes separately and then either presenting them all as possible hypotheses or taking their consensus provides virtually no information concerning the relationships among these flies. Second, despite some evidence of incongruence, there are no clear delineations among the various gene partitions that separate only heterogeneous data. Third, to the extent that problematic genes can be identified, these genes have nearly the same information content, within a combined analysis framework, as the remaining nonproblematic genes. Our data suggest that significant incongruence among data partitions may be isolated to specific relationships and the "false" signal creating this incongruence is most likely to be overcome by a simultaneous analysis. We present a new method, partitioned Bremer support, for examining the contribution of a particular data partition to the topological support of the simultaneous analysis tree.
Although morphological data have historically favored a basal position for the Indian gharial (Gavialis gangeticus) within Crocodylia and a Mesozoic divergence between Gavialis and all other crocodylians, several recent molecular data sets have argued for a sister-group relationship between Gavialis and the Indonesian false gharial (Tomistoma schlegelii) and a divergence between them no earlier than the Late Tertiary. Fossils were added to a matrix of 164 discrete morphological characters and subjected to parsimony analysis. When morphology was analyzed alone, Gavialis was the sister taxon of all other extant crocodylians whether or not fossil ingroup taxa were included, and a sister-group relationship between Gavialis and Tomistoma was significantly less parsimonious. In combination with published sequence and restriction site fragment data, Gavialis was the sister taxon of all other living crocodylians, but the position of Tomistoma depended on the inclusion of fossil ingroup taxa; with or without fossils, preferred morphological and molecular topologies were not significantly different. Fossils closer to Gavialis than to Tomistoma can be recognized in the Late Cretaceous, and fossil relatives of Tomistoma are known from the basal Eocene, strongly indicating a divergence long before the Late Tertiary. Comparison of minimum divergence time from the fossil record with different measures of molecular distance indicates evolutionary rate heterogeneity within Crocodylia. Fossils strongly contradict a post-Oligocene divergence between Gavialis and any other living crocodylian, but the phylogenetic placement of Gavialis is best viewed as unresolved.
The DNA sequences of the mitochondrial cytochromeb gene of marine mammals (Cetacea, Pinnipedia, Sirenia) were compared with cytochromeb genes of terrestrial mammals including the semiaquatic hippopotamus. The comparison included 28 sequences, representing 22 families and 10 orders. The dugong (order Sirenia) sequence associated with that of the elephant, supporting the Tethytheria clade. The fin whale and dolphin (order Cetacea) sequences are more closely related to those of the artiodactyls, and the comparison suggests that the hippopotamus may be the extant artiodactyl species that is most closely related to the cetaceans. The seal sequence may be more closely related to those of artiodactyls, cetaceans, and perissodactyls than to tethytheres, rodents, lagomorphs, or primates. The cytochromeb proteins of mammals do not evolve at a uniform rate. Human and elephant cytochromeb amino acid sequences were found to evolve the most rapidly, while those of myomorph rodents evolved slowest. The cytochromeb of marine mammals evolves at an intermediate rate. The pattern of amino acid substitutions in marine mammals is similar to that of terrestrial mammals.
DNA was extracted from the Neandertal-type specimen found in 1856 in western Germany. By sequencing clones from short overlapping PCR products, a hitherto unknown mitochondrial (mt) DNA sequence was determined. Multiple controls indicate that this sequence is endogenous to the fossil. Sequence comparisons with human mtDNA sequences, as well as phylogenetic analyses, show that the Neandertal sequence falls outside the variation of modern humans. Furthermore, the age of the common ancestor of the Neandertal and modern human mtDNAs is estimated to be four times greater than that of the common ancestor of human mtDNAs. This suggests that Neandertals went extinct without contributing mtDNA to modern humans.
The origin of whales and their transition from terrestrial life to a fully aquatic existence has been studied in depth. Palaeontological, morphological and molecular studies suggest that the order Cetacea (whales, dolphins and porpoises) is more closely related to the order Artiodactyla (even-toed ungulates, including cows, camels and pigs) than to other ungulate orders. The traditional view that the order Artiodactyla is monophyletic has been challenged by molecular analyses of variations in mitochondrial and nuclear DNA. We have characterized two families of short interspersed elements (SINEs) that were present exclusively in the genomes of whales, ruminants and hippopotamuses, but not in those of camels and pigs. We made an extensive survey of retropositional events that might have occurred during the divergence of whales and even-toed ungulates. We have characterized nine retropositional events of a SINE unit, each of which provides phylogenetic resolution of the relationships among whales, ruminants, hippopotamuses and pigs. Our data provide evidence that whales, ruminants and hippopotamuses form a monophyletic group.
The proposal that all mitochondrial DNA (mtDNA) types in contemporary humans stem from a common ancestor present in an African
population some 200,000 years ago has attracted much attention. To study this proposal further, two hypervariable segments
of mtDNA were sequenced from 189 people of diverse geographic origin, including 121 native Africans. Geographic specificity
was observed in that identical mtDNA types are shared within but not between populations. A tree relating these mtDNA sequences
to one another and to a chimpanzee sequence has many deep branches leading exclusively to African mtDNAs. An African origin
for human mtDNA is supported by two statistical tests. With the use of the chimpanzee and human sequences to calibrate the
rate of mtDNA evolution, the age of the common human mtDNA ancestor is placed between 166,000 and 249,000 years. These results
thus support and extend the African origin hypothesis of human mtDNA evolution.
Mitochondrial DNAs from 147 people, drawn from five geographic populations have been analysed by restriction mapping. All these mitochondrial DNAs stem from one woman who is postulated to have lived about 200,000 years ago, probably in Africa. All the populations examined except the African population have multiple origins, implying that each area was colonised repeatedly.
To what extent is cranial vault thickness (CVT) a character that is strongly linked to the genome, or to what extent does it reflect the activity of an individual prior to skeletal maturity? Experimental data from pigs and armadillos indicate that CVT increases more rapidly in exercised juveniles than in genetically similar controls, despite the low levels of strain generated by chewing or locomotion in the neurocranium. CVT increases in these individuals appear to be a consequence of systemic cortical bone growth induced by exercise. In addition, an analysis of the variability in vault thickness in the genus Homo demonstrates that, until the Holocene, there has been only a slight, general decrease in vault thickness over time with no consistent significant differences between archaic and early anatomically modern humans from the Late Pleistocene. Although there may be some genetic component to variation in CVT, exercise-related, non-genetically heritable stimuli appear to account for most of the variance between individuals. The thick cranial vaults of most hunter-gatherers and early agriculturalists suggests that they may have experienced higher levels of sustained exercise relative to body mass than the majority of recent, post-industrial humans.
Recent phylogenetic analyses of DNA sequences suggest that cetaceans (whales) and hippopotamid artiodactyls (hippos) are extant sister taxa. Consequently, the shared aquatic specializations of these taxa may be synapomorphies. This molecular view is contradicted by paleontological data that overwhelmingly support a monophyletic Artiodactyla (even-toed ungulates) and a close relationship between Cetacea and extinct mesonychian ungulates. According to the fossil evidence, molecular, behavioral, and anatomical resemblances between hippos and whales are interpreted as convergences or primitive retentions. In this report, competing interpretations of whale origins are tested through phylogenetic analyses of the blood-clotting protein gene gamma-fibrinogen from cetaceans, artiodactyls, perissodactyls (odd-toed ungulates), and carnivores (cats, dogs, and kin). In combination with published DNA sequences, the gamma-fibrinogen data unambiguously support a hippo/whale clade and are inconsistent with the paleontological perspective. If the phylogeny favored by fossil evidence is accepted, the convergence at the DNA level between Cetacea and Hippopotamidae is remarkable in its distribution across three genetic loci: gamma-fibrinogen, the linked milk casein genes, and mitochondrial cytochrome b.
Although the sister-group relationship between Cetacea and Artiodactyla is widely accepted, the actual artiodactyl group which is closest to Cetacea has not been conclusively identified. In the present study, we have sequenced the complete mitochondrial genome of the hippopotamus, Hippopotamus amphibius, and included it in phylogenetic analyses together with 15 other placental mammals. These analyses separated the hippopotamus from the other suiform included, the pig, and identified the hippopotamus as the artiodactyl sister group of the cetaceans, thereby making both. Artiodactyla and the suborder. Suiformes paraphyletic. The divergence between the hippopotamid and cetacean lineages was calculated using this molecular data and was estimated at ca. 54 Ma BP.
The DNA sequence of the second hypervariable region of the mitochondrial control region of the Neandertal type specimen, found in 1856 in central Europe, has been determined from 92 clones derived from eight overlapping amplifications performed from four independent extracts. When the reconstructed sequence is analyzed together with the previously determined DNA sequence from the first hypervariable region, the Neandertal mtDNA is found to fall outside a phylogenetic tree relating the mtDNAs of contemporary humans. The date of divergence between the mtDNAs of the Neandertal and contemporary humans is estimated to 465,000 years before the present, with confidence limits of 317,000 and 741,000 years. Taken together, the results support the concept that the Neandertal mtDNA evolved separately from that of modern humans for a substantial amount of time and lends no support to the idea that they contributed mtDNA to contemporary modern humans.
Cladistic analysis of cranial and dental evidence has been widely used to generate phylogenetic hypotheses about humans and their fossil relatives. However, the reliability of these hypotheses has never been subjected to external validation. To rectify this, we applied identical methods to equivalent evidence from two groups of extant higher primates for whom reliable molecular phylogenies are available, the hominoids and papionins. We found that the phylogenetic hypotheses based on the craniodental data were incompatible with the molecular phylogenies for the groups. Given the robustness of the molecular phylogenies, these results indicate that little confidence can be placed in phylogenies generated solely from higher primate craniodental evidence. The corollary of this is that existing phylogenetic hypotheses about human evolution are unlikely to be reliable. Accordingly, new approaches are required to address the problem of hominin phylogeny.
Recent phylogenetic analyses of cetacean relationships based on DNA sequence data have challenged the traditional view that baleen whales (Mysticeti) and toothed whales (Odontoceti) are each monophyletic, arguing instead that baleen whales are the sister group of the odontocete family Physeteridae (sperm whales). We reexamined this issue in light of a morphological data set composed of 207 characters and molecular data sets of published 12S, 16S, and cytochrome b mitochondrial DNA sequences. We reach four primary conclusions: (1) Our morphological data set strongly supports the traditional view of odontocete monophyly; (2) the unrooted molecular and morphological trees are very similar, and most of the conflict results from alternative rooting positions; (3) the rooting position of the molecular tree is sensitive to choice of artiodactyls outgroup taxa and the treatment of two small but ambiguously aligned regions of the 12S and 16S sequences, whereas the morphological root is strongly supported; and (4) combined analyses of the morphological and molecular data provide a well-supported phylogenetic estimate consistent with that based on the morphological data alone (and the traditional view of toothed-whale monophyly) but with increased bootstrap support at nearly every node of the tree.
- W C Wheeler
- C Hayashi
- WC Wheeler
- C A Brochu
- CA Brochu
- A G Kluge
- AG Kluge