Davide Pisani
Research interests
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InterestsPhylogeny, Evolution, Evo-Devo, Comparative Genomics, Evolutionary Bioinformatics, Systematics, Genetic Analysis
Publications
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29.75Impact points
The Cambrian conundrum: early divergence and later ecological success in the early history of animals.
Science (New York, N.Y.). 11/2011; 334(6059):1091-7.
Diverse bilaterian clades emerged apparently within a few million years during the early Cambrian, and various environmental, developmental, and ecological causes have been proposed to explain this abrupt appearance. A compilation of the patterns of fossil and molecular diversification, comparative ... [more] Diverse bilaterian clades emerged apparently within a few million years during the early Cambrian, and various environmental, developmental, and ecological causes have been proposed to explain this abrupt appearance. A compilation of the patterns of fossil and molecular diversification, comparative developmental data, and information on ecological feeding strategies indicate that the major animal clades diverged many tens of millions of years before their first appearance in the fossil record, demonstrating a macroevolutionary lag between the establishment of their developmental toolkits during the Cryogenian [(850 to 635 million years ago (Ma)], and the later ecological success of metazoans during the Ediacaran (635 to 541 Ma) and Cambrian (541 to 488 Ma) periods. We argue that this diversification involved new forms of developmental regulation, as well as innovations in networks of ecological interaction within the context of permissive environmental circumstances.
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3.56Impact points
Resolving phylogenetic signal from noise when divergence is rapid: a new look at the old problem of echinoderm class relationships.
Molecular phylogenetics and evolution. 09/2011; 62(1):27-34.
Resolving evolutionary relationships in groups that underwent fast radiation in deep time is a problem for molecular phylogeny, as the scant phylogenetic signal that characterises short internal branches is generally swamped by more recent substitutions. We implement an approach, that maps how the s... [more] Resolving evolutionary relationships in groups that underwent fast radiation in deep time is a problem for molecular phylogeny, as the scant phylogenetic signal that characterises short internal branches is generally swamped by more recent substitutions. We implement an approach, that maps how the support for rival phylogenies changes when analysing subsets of sites with either faster and more heterogeneous rates or slower and more homogeneous rates, to address a long-standing problem in deuterostome phylogeny - the interrelationships of the eleutherozoan echinoderm classes. We show that miRNA genes are phylogenetically uninformative as to the relationships of asteroids, echinoids and ophiuroids, consistent with a rapid radiation of these groups as suggested by their fossil record. Using three nuclear rRNAs and seven nuclear housekeeping genes, we map the support for the three possible phylogenetic arrangements of asteroids, ophiuroids and echinoids when moving between subsets of the data with very similar or very different rates of evolution. Only one of the three possible topologies (asteroids (ophiuroids+echinoids)) strengthens when the most rate-homogeneous subset of data are analysed. The other two possible pairings become stronger in a less reliable data subset, which includes the fastest and thus homoplasy-rich data in our alignment. Thus, while superficial analysis of our concatenated alignment identifies asteroids and ophiuroids as sister taxa, more thorough analyses suggest that ophiuroids may be more closely related to echinoids. Divergence of these echinoderm groups, using a relaxed molecular clock, is estimated to have occurred within ≈ 5 million years. Our results illustrate that the analytic approach of phylogenetic signal dissection can be a powerful tool to investigate rapid radiations in deep geologic time.
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9.43Impact points
MicroRNAs and phylogenomics resolve the relationships of Tardigrada and suggest that velvet worms are the sister group of Arthropoda.
Proceedings of the National Academy of Sciences of the United States of America. 09/2011; 108(38):15920-4.
Morphological data traditionally group Tardigrada (water bears), Onychophora (velvet worms), and Arthropoda (e.g., spiders, insects, and their allies) into a monophyletic group of invertebrates with walking appendages known as the Panarthropoda. However, molecular data generally do not support the i... [more] Morphological data traditionally group Tardigrada (water bears), Onychophora (velvet worms), and Arthropoda (e.g., spiders, insects, and their allies) into a monophyletic group of invertebrates with walking appendages known as the Panarthropoda. However, molecular data generally do not support the inclusion of tardigrades within the Panarthropoda, but instead place them closer to Nematoda (roundworms). Here we present results from the analyses of two independent genomic datasets, expressed sequence tags (ESTs) and microRNAs (miRNAs), which congruently resolve the phylogenetic relationships of Tardigrada. Our EST analyses, based on 49,023 amino acid sites from 255 proteins, significantly support a monophyletic Panarthropoda including Tardigrada and suggest a sister group relationship between Arthropoda and Onychophora. Using careful experimental manipulations--comparisons of model fit, signal dissection, and taxonomic pruning--we show that support for a Tardigrada + Nematoda group derives from the phylogenetic artifact of long-branch attraction. Our small RNA libraries fully support our EST results; no miRNAs were found to link Tardigrada and Nematoda, whereas all panarthropods were found to share one unique miRNA (miR-276). In addition, Onychophora and Arthropoda were found to share a second miRNA (miR-305). Our study confirms the monophyly of the legged ecdysozoans, shows that past support for a Tardigrada + Nematoda group was due to long-branch attraction, and suggests that the velvet worms are the sister group to the arthropods.
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3.32Impact points
The Public Goods Hypothesis for the evolution of life on Earth.
Biology direct. 08/2011; 6:41.
It is becoming increasingly difficult to reconcile the observed extent of horizontal gene transfers with the central metaphor of a great tree uniting all evolving entities on the planet. In this manuscript we describe the Public Goods Hypothesis and show that it is appropriate in order to describe b... [more] It is becoming increasingly difficult to reconcile the observed extent of horizontal gene transfers with the central metaphor of a great tree uniting all evolving entities on the planet. In this manuscript we describe the Public Goods Hypothesis and show that it is appropriate in order to describe biological evolution on the planet. According to this hypothesis, nucleotide sequences (genes, promoters, exons, etc.) are simply seen as goods, passed from organism to organism through both vertical and horizontal transfer. Public goods sequences are defined by having the properties of being largely non-excludable (no organism can be effectively prevented from accessing these sequences) and non-rival (while such a sequence is being used by one organism it is also available for use by another organism). The universal nature of genetic systems ensures that such non-excludable sequences exist and non-excludability explains why we see a myriad of genes in different combinations in sequenced genomes. There are three features of the public goods hypothesis. Firstly, segments of DNA are seen as public goods, available for all organisms to integrate into their genomes. Secondly, we expect the evolution of mechanisms for DNA sharing and of defense mechanisms against DNA intrusion in genomes. Thirdly, we expect that we do not see a global tree-like pattern. Instead, we expect local tree-like patterns to emerge from the combination of a commonage of genes and vertical inheritance of genomes by cell division. Indeed, while genes are theoretically public goods, in reality, some genes are excludable, particularly, though not only, when they have variant genetic codes or behave as coalition or club goods, available for all organisms of a coalition to integrate into their genomes, and non-rival within the club. We view the Tree of Life hypothesis as a regionalized instance of the Public Goods hypothesis, just like classical mechanics and euclidean geometry are seen as regionalized instances of quantum mechanics and Riemannian geometry respectively. We argue for this change using an axiomatic approach that shows that the Public Goods hypothesis is a better accommodation of the observed data than the Tree of Life hypothesis.
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4.11Impact points
A congruent solution to arthropod phylogeny: phylogenomics, microRNAs and morphology support monophyletic Mandibulata.
Proceedings. Biological sciences / The Royal Society. 01/2011; 278(1703):298-306.
While a unique origin of the euarthropods is well established, relationships between the four euarthropod classes-chelicerates, myriapods, crustaceans and hexapods-are less clear. Unsolved questions include the position of myriapods, the monophyletic origin of chelicerates, and the validity of the c... [more] While a unique origin of the euarthropods is well established, relationships between the four euarthropod classes-chelicerates, myriapods, crustaceans and hexapods-are less clear. Unsolved questions include the position of myriapods, the monophyletic origin of chelicerates, and the validity of the close relationship of euarthropods to tardigrades and onychophorans. Morphology predicts that myriapods, insects and crustaceans form a monophyletic group, the Mandibulata, which has been contradicted by many molecular studies that support an alternative Myriochelata hypothesis (Myriapoda plus Chelicerata). Because of the conflicting insights from published molecular datasets, evidence from nuclear-coding genes needs corroboration from independent data to define the relationships among major nodes in the euarthropod tree. Here, we address this issue by analysing two independent molecular datasets: a phylogenomic dataset of 198 protein-coding genes including new sequences for myriapods, and novel microRNA complements sampled from all major arthropod lineages. Our phylogenomic analyses strongly support Mandibulata, and show that Myriochelata is a tree-reconstruction artefact caused by saturation and long-branch attraction. The analysis of the microRNA dataset corroborates the Mandibulata, showing that the microRNAs miR-965 and miR-282 are present and expressed in all mandibulate species sampled, but not in the chelicerates. Mandibulata is further supported by the phylogenetic analysis of a comprehensive morphological dataset covering living and fossil arthropods, and including recently proposed, putative apomorphies of Myriochelata. Our phylogenomic analyses also provide strong support for the inclusion of pycnogonids in a monophyletic Chelicerata, a paraphyletic Cycloneuralia, and a common origin of Arthropoda (tardigrades, onychophorans and arthropods), suggesting that previous phylogenies grouping tardigrades and nematodes may also have been subject to tree-reconstruction artefacts.
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4.37Impact points
The environmental affinities of marine higher taxa and possible biases in their first appearances in the fossil record
Geology. 01/2011; 39:971-974.
Relative to epicontinental seas, shallow, open-ocean settings are underrepresented in the Paleozoic record, and it is possible that higher taxa associated with these environments that appeared to diversify in the post-Paleozoic may have unpreserved Paleozoic histories. As an initial test of this pos... [more] Relative to epicontinental seas, shallow, open-ocean settings are underrepresented in the Paleozoic record, and it is possible that higher taxa associated with these environments that appeared to diversify in the post-Paleozoic may have unpreserved Paleozoic histories. As an initial test of this possibility, we evaluated the statistical affinity for open-ocean–facing environments of two elements of the modern fauna that appear to diversify in the middle Mesozoic, the veneroid bivalves and the buccinoid gastropods, and showed that, indeed, Mesozoic genera in both groups had statistical propensities to occur in ocean-facing settings. In contrast, two groups with extensive Paleozoic fossil records had either an affinity for epicontinental seas (the terebratulid brachiopods), or showed no statistical preference for either setting (the mytilid bivalves). We conducted molecular clock analyses to estimate the divergence times of these taxa, and found that our estimates for the origin of terebratulids and mytilids in the Paleozoic were concordant with their known geological records. While our molecular estimate for the origin of the buccinoids was also concordant with their known record, with an estimated origin in the Jurassic, molecular data indicate that the veneroids originated in the Paleozoic, more than 200 m.y. before their first fossil appearance in the Mesozoic. This intriguing result raises the possibility that additional elements of the modern fauna with preferences for open-ocean–facing settings may have had more extensive Paleozoic histories than heretofore appreciated.
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2.72Impact points
Identification and characterization of visual pigments in caecilians (Amphibia: Gymnophiona), an order of limbless vertebrates with rudimentary eyes.
The Journal of experimental biology. 10/2010; 213(Pt 20):3586-92.
In comparison with the other amphibian orders, the Anura (frogs) and Urodela (salamanders), knowledge of the visual system of the snake-like Gymnophiona (caecilians) is relatively sparse. Most caecilians are fossorial with, as far as is known any surface activity occurring mainly at night. They have... [more] In comparison with the other amphibian orders, the Anura (frogs) and Urodela (salamanders), knowledge of the visual system of the snake-like Gymnophiona (caecilians) is relatively sparse. Most caecilians are fossorial with, as far as is known any surface activity occurring mainly at night. They have relatively small, poorly developed eyes and might be expected to possess detectable changes in the spectral sensitivity of their visual pigments. Microspectrophotometry was used to determine the spectral sensitivities of the photoreceptors in three species of caecilian, Rhinatrema bivittatum, Geotrypetes seraphini and Typhlonectes natans. Only rod opsin visual pigment, which may be associated with scotopic (dim light) vision when accompanied by other 'rod-specific' components of the phototransduction cascade, was found to be present. Opsin sequences were obtained from the eyes of two species of caecilian, Ichthyophis cf. kohtaoensis and T. natans. These rod opsins were regenerated in vitro with 11-cis retinal to give pigments with spectral sensitivity peaks close to 500 nm. No evidence for cone photoreception, associated with diurnal and colour vision, was detected using molecular and physiological methods. Additionally, visual pigments are short-wavelength shifted in terms of the maximum absorption of light when compared with other amphibian lineages.
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Deep genomic-scale analyses of the metazoa reject Coelomata: evidence from single- and multigene families analyzed under a supertree and supermatrix paradigm.
Genome biology and evolution. 01/2010; 2:310-24.
Solving the phylogeny of the animals with bilateral symmetry has proven difficult. Morphological studies have suggested a variety of alternative hypotheses, of which, Hyman's Coelomata hypothesis has become the most established. Studies based on 18S rRNA have failed to endorse Coelomata, support... [more] Solving the phylogeny of the animals with bilateral symmetry has proven difficult. Morphological studies have suggested a variety of alternative hypotheses, of which, Hyman's Coelomata hypothesis has become the most established. Studies based on 18S rRNA have failed to endorse Coelomata, supporting instead the rearrangement of the protostomes into two new clades: the Lophotrochozoa (including, e.g., the molluscs and the annelids) and the Ecdysozoa (including the Panarthropoda and most pseudocoelomates, such as the nematodes and priapulids). Support for this new animal phylogeny has been attained from expressed sequence tag studies, although these generally have a limited gene sampling. In contrast, deep genomic-scale analyses have often supported Coelomata. However, these studies are problematic due to their limited taxonomic sampling, which could exacerbate tree reconstruction artifacts. Here, we address both of these sampling limitations; we study the effect of long-branch attraction (LBA) in deep genomic-scale analyses and provide convincing evidence, using both single- and multigene families, that Coelomata is an artifact. We show that optimal outgroup selection is key in avoiding LBA and identify the use of inadequate outgroups as the reason previous deep genomic-scale analyses found strong support for Coelomata.
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Ecdysozoan mitogenomics: evidence for a common origin of the legged invertebrates, the Panarthropoda.
Genome biology and evolution. 01/2010; 2:425-40.
Ecdysozoa is the recently recognized clade of molting animals that comprises the vast majority of extant animal species and the most important invertebrate model organisms--the fruit fly and the nematode worm. Evolutionary relationships within the ecdysozoans remain, however, unresolved, impairing t... [more] Ecdysozoa is the recently recognized clade of molting animals that comprises the vast majority of extant animal species and the most important invertebrate model organisms--the fruit fly and the nematode worm. Evolutionary relationships within the ecdysozoans remain, however, unresolved, impairing the correct interpretation of comparative genomic studies. In particular, the affinities of the three Panarthropoda phyla (Arthropoda, Onychophora, and Tardigrada) and the position of Myriapoda within Arthropoda (Mandibulata vs. Myriochelata hypothesis) are among the most contentious issues in animal phylogenetics. To elucidate these relationships, we have determined and analyzed complete or nearly complete mitochondrial genome sequences of two Tardigrada, Hypsibius dujardini and Thulinia sp. (the first genomes to date for this phylum); one Priapulida, Halicryptus spinulosus; and two Onychophora, Peripatoides sp. and Epiperipatus biolleyi; and a partial mitochondrial genome sequence of the Onychophora Euperipatoides kanagrensis. Tardigrada mitochondrial genomes resemble those of the arthropods in term of the gene order and strand asymmetry, whereas Onychophora genomes are characterized by numerous gene order rearrangements and strand asymmetry variations. In addition, Onychophora genomes are extremely enriched in A and T nucleotides, whereas Priapulida and Tardigrada are more balanced. Phylogenetic analyses based on concatenated amino acid coding sequences support a monophyletic origin of the Ecdysozoa and the position of Priapulida as the sister group of a monophyletic Panarthropoda (Tardigrada plus Onychophora plus Arthropoda). The position of Tardigrada is more problematic, most likely because of long branch attraction (LBA). However, experiments designed to reduce LBA suggest that the most likely placement of Tardigrada is as a sister group of Onychophora. The same analyses also recover monophyly of traditionally recognized arthropod lineages such as Arachnida and of the highly debated clade Mandibulata.
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2.60Impact points
Where's the glass? Biomarkers, molecular clocks, and microRNAs suggest a 200-Myr missing Precambrian fossil record of siliceous sponge spicules.
Geobiology. 11/2009;
The earliest evidence for animal life comes from the fossil record of 24-isopropylcholestane, a sterane found in Cryogenian deposits, and whose precursors are found in modern demosponges, but not choanoflagellates, calcareans, hexactinellids, or eumetazoans. However, many modern demosponges are also... [more] The earliest evidence for animal life comes from the fossil record of 24-isopropylcholestane, a sterane found in Cryogenian deposits, and whose precursors are found in modern demosponges, but not choanoflagellates, calcareans, hexactinellids, or eumetazoans. However, many modern demosponges are also characterized by the presence of siliceous spicules, and there are no convincing demosponge spicules in strata older than the Cambrian. This temporal disparity highlights a problem with our understanding of the Precambrian fossil record - either these supposed demosponge-specific biomarkers were derived from the sterols of some other organism and are simply retained in modern demosponges, or spicules do not primitively characterize crown-group demosponges. Resolving this issue requires resolving the phylogenetic placement of another group of sponges, the hexactinellids, which not only make a spicule thought to be homologous to the spicules of demosponges, but also make their first appearance near the Precambrian/Cambrian boundary. Using two independent analytical approaches and data sets - traditional molecular phylogenetic analyses and the presence or absence of specific microRNA genes - we show that demosponges are monophyletic, and that hexactinellids are their sister group (together forming the Silicea). Thus, spicules must have evolved before the last common ancestor of all living siliceans, suggesting the presence of a significant gap in the silicean spicule fossil record. Molecular divergence estimates date the origin of this last common ancestor well within the Cryogenian, consistent with the biomarker record, and strongly suggests that siliceous spicules were present during the Precambrian but were not preserved.
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9.87Impact points
Phylogenetic-signal dissection of nuclear housekeeping genes supports the paraphyly of sponges and the monophyly of Eumetazoa.
Molecular biology and evolution. 08/2009;
The relationships at the base of the metazoan tree have been difficult to robustly resolve, and there are several different hypotheses regarding the interrelationships amongst sponges, cnidarians, ctenophores, placozoans and bilaterians, with each hypothesis having different implications for the bod... [more] The relationships at the base of the metazoan tree have been difficult to robustly resolve, and there are several different hypotheses regarding the interrelationships amongst sponges, cnidarians, ctenophores, placozoans and bilaterians, with each hypothesis having different implications for the body plan of the last common ancestor of animals and the paleoecology of the late precambrian. We have sequenced seven nuclear housekeeping genes from 17 new sponges, bringing the total to 29 species analyzed, including multiple representatives of the Demospongiae, Calcarea, Hexactinellida and Homoscleromorpha, and analyzed a data set also including six non-metazoan outgroups and 36 eumetazoans using a variety of phylogenetic methods and evolutionary models. We used leaf stability to identify rogue taxa and to investigate their effect on the support of the nodes in our trees, and we identified clades most likely to represent phylogenetic artifacts through the comparison of trees derived using different methods (and models) and through site-stripping analyses. Further, we investigated compositional heterogeneity and tested whether amino acid composition bias affected our results. Finally, we used Bayes factors to compare our results against previously published phylogenies. All our maximum likelihood and Bayesian analyses find sponges to be paraphyletic, with all analyses finding three extant paraphyletic sponge lineages, Demospongiae plus Hexactinellida, Calcarea and Homoscleromorpha. All but one of our Maximum likelihood and Bayesian analyses support the monophyly of Eumetazoa (here Cnidaria + Bilateria) and a sister group relationship between Placozoa (here Trichoplax adhaerens) and Eumetazoa. Bayes factors invariably provide decisive support in favor of poriferan paraphyly when compared against either a sister group relationship between Porifera and Cnidaria, or to a monophyletic Porifera with respect to a monophyletic Eumetazoa. Although we were able to recover sponge monophyly using our data set, this was only possible under unrealistic evolutionary models, if poorly performing phylogenetic methods were used, or in situations where the potential for the generation of tree reconstruction artifacts was artificially exacerbated. Everything considered, our data set does not provide any support for a monophyletic Diploblastica (here Placozoa + Cnidaria + Porifera) and suggests that a monophyletic Porifera may be better seen as a phylogenetic artifact.
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4.11Impact points
Dinosaurs and the Cretaceous Terrestrial Revolution.
Proceedings. Biological sciences / The Royal Society. 11/2008; 275(1650):2483-90.
The observed diversity of dinosaurs reached its highest peak during the mid- and Late Cretaceous, the 50 Myr that preceded their extinction, and yet this explosion of dinosaur diversity may be explained largely by sampling bias. It has long been debated whether dinosaurs were part of the Cretaceous ... [more] The observed diversity of dinosaurs reached its highest peak during the mid- and Late Cretaceous, the 50 Myr that preceded their extinction, and yet this explosion of dinosaur diversity may be explained largely by sampling bias. It has long been debated whether dinosaurs were part of the Cretaceous Terrestrial Revolution (KTR), from 125-80 Myr ago, when flowering plants, herbivorous and social insects, squamates, birds and mammals all underwent a rapid expansion. Although an apparent explosion of dinosaur diversity occurred in the mid-Cretaceous, coinciding with the emergence of new groups (e.g. neoceratopsians, ankylosaurid ankylosaurs, hadrosaurids and pachycephalosaurs), results from the first quantitative study of diversification applied to a new supertree of dinosaurs show that this apparent burst in dinosaurian diversity in the last 18 Myr of the Cretaceous is a sampling artefact. Indeed, major diversification shifts occurred largely in the first one-third of the group's history. Despite the appearance of new clades of medium to large herbivores and carnivores later in dinosaur history, these new originations do not correspond to significant diversification shifts. Instead, the overall geometry of the Cretaceous part of the dinosaur tree does not depart from the null hypothesis of an equal rates model of lineage branching. Furthermore, we conclude that dinosaurs did not experience a progressive decline at the end of the Cretaceous, nor was their evolution driven directly by the KTR.
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11.56Impact points
The prokaryotic tree of life: past, present... and future?
Trends in ecology & evolution (Personal edition). 06/2008; 23(5):276-81.
No accepted phylogenetic scheme for prokaryotes emerged until the late 1970s. Prior to that, it was assumed that there was a phylogenetic tree uniting all prokaryotes, but no suitable data were available for its construction. For 20 years, through the 1980s and 1990s, rRNA phylogenies were the gold ... [more] No accepted phylogenetic scheme for prokaryotes emerged until the late 1970s. Prior to that, it was assumed that there was a phylogenetic tree uniting all prokaryotes, but no suitable data were available for its construction. For 20 years, through the 1980s and 1990s, rRNA phylogenies were the gold standard. However, beginning in the last decade, findings from genomic data have challenged this new consensus. Gene trees can conflict greatly, and strains of the same species can differ enormously in genome content. Horizontal gene transfer is now known to be a significant influence on genome evolution. The next decade is likely to resolve whether or not we retain the centuries-old metaphor of the tree for all of life.
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5.12Impact points
The Ediacaran emergence of bilaterians: congruence between the genetic and the geological fossil records.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences. 05/2008; 363(1496):1435-43.
Unravelling the timing of the metazoan radiation is crucial for elucidating the macroevolutionary processes associated with the Cambrian explosion. Because estimates of metazoan divergence times derived from molecular clocks range from quite shallow (Ediacaran) to very deep (Mesoproterozoic), it has... [more] Unravelling the timing of the metazoan radiation is crucial for elucidating the macroevolutionary processes associated with the Cambrian explosion. Because estimates of metazoan divergence times derived from molecular clocks range from quite shallow (Ediacaran) to very deep (Mesoproterozoic), it has been difficult to ascertain whether there is concordance or quite dramatic discordance between the genetic and geological fossil records. Here, we show using a range of molecular clock methods that the major pulse of metazoan divergence times was during the Ediacaran, which is consistent with a synoptic reading of the Ediacaran macrobiota. These estimates are robust to changes in priors, and are returned with or without the inclusion of a palaeontologically derived maximal calibration point. Therefore, the two historical records of life both suggest that although the cradle of Metazoa lies in the Cryogenian, and despite the explosion of ecology that occurs in the Cambrian, it is the emergence of bilaterian taxa in the Ediacaran that sets the tempo and mode of macroevolution for the remainder of geological time.
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4.11Impact points
A supertree of temnospondyli: cladogenetic patterns in the most species-rich group of early tetrapods.
Proceedings. Biological sciences / The Royal Society. 01/2008; 274(1629):3087-95.
As the most diverse group of early tetrapods, temnospondyls provide a unique opportunity to investigate cladogenetic patterns among basal limbed vertebrates. We present five species-level supertrees for temnospondyls, built using a variety of methods. The standard MRP majority rule consensus includi... [more] As the most diverse group of early tetrapods, temnospondyls provide a unique opportunity to investigate cladogenetic patterns among basal limbed vertebrates. We present five species-level supertrees for temnospondyls, built using a variety of methods. The standard MRP majority rule consensus including minority components shows slightly greater resolution than other supertrees, and its shape matches well several currently accepted hypotheses of higher-level phylogeny for temnospondyls as a whole. Also, its node support is higher than those of other supertrees (except the combined standard plus Purvis MRP supertree). We explore the distribution of significant as well as informative changes (shifts) in branch splitting employing the standard MRP supertree as a reference, and discuss the temporal distribution of changes in time-sliced, pruned trees derived from this supertree. Also, we analyse those shifts that are most relevant to the end-Permian mass extinction. For the Palaeozoic, shifts occur almost invariably along branches that connect major Palaeozoic groups. By contrast, shifts in the Mesozoic occur predominantly within major groups. Numerous shifts bracket narrowly the end-Permian extinction, indicating not only rapid recovery and extensive diversification of temnospondyls over a short time period after the extinction event (possibly less than half a million years), but also the role of intense cladogenesis in the late part of the Permian (although this was counteracted by numerous 'background' extinctions).
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29.75Impact points
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3.52Impact points
Relative time scales reveal multiple origins of parallel disjunct distributions of African caecilian amphibians.
Biology letters. 11/2007; 3(5):505-8.
Parallel patterns of distribution in different lineages suggest a common cause. Explanations in terms of a single biogeographic event often imply contemporaneous diversifications. Phylogenies with absolute time scales provide the most obvious means of testing temporal components of biogeographic hyp... [more] Parallel patterns of distribution in different lineages suggest a common cause. Explanations in terms of a single biogeographic event often imply contemporaneous diversifications. Phylogenies with absolute time scales provide the most obvious means of testing temporal components of biogeographic hypotheses but, in their absence, the sequence of diversification events and whether any could have been contemporaneous can be tested with relative date estimates. Tests using relative time scales have been largely overlooked, but because they do not require the calibration upon which absolute time scales depend, they make a large amount of existing molecular data of use to historical biogeography and may also be helpful when calibration is possible but uncertain. We illustrate the use of relative dating by testing the hypothesis that parallel, disjunct east/west distributions in three independent lineages of African caecilians have a common cause. We demonstrate that at least two biogeographic events are implied by molecular data. Relative dating analysis reveals the potential complexity of causes of parallel distributions and cautions against inferring common cause from common spatial patterns without considering the temporal dimension.
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9.87Impact points
Supertrees disentangle the chimerical origin of eukaryotic genomes.
Molecular biology and evolution. 09/2007; 24(8):1752-60.
Eukaryotes are traditionally considered to be one of the three natural divisions of the tree of life and the sister group of the Archaebacteria. However, eukaryotic genomes are replete with genes of eubacterial ancestry, and more than 20 mutually incompatible hypotheses have been proposed to account... [more] Eukaryotes are traditionally considered to be one of the three natural divisions of the tree of life and the sister group of the Archaebacteria. However, eukaryotic genomes are replete with genes of eubacterial ancestry, and more than 20 mutually incompatible hypotheses have been proposed to account for eukaryote origins. Here we test the predictions of these hypotheses using a novel supertree-based phylogenetic signal-stripping method, and recover supertrees of life based on phylogenies for up to 5,741 single gene families distributed across 185 genomes. Using our signal-stripping method, we show that there are three distinct phylogenetic signals in eukaryotic genomes. In order of strength, these link eukaryotes with the Cyanobacteria, the Proteobacteria, and the Thermoplasmatales, an archaebacterial (euryarchaeotes) group. These signals correspond to distinct symbiotic partners involved in eukaryote evolution: plastids, mitochondria, and the elusive host lineage. According to our whole-genome data, eukaryotes are hardly the sister group of the Archaebacteria, because up to 83% of eukaryotic genes with a prokaryotic homolog have eubacterial, not archaebacterial, origins. The results reject all but two of the current hypotheses for the origin of eukaryotes: those assuming a sulfur-dependent or hydrogen-dependent syntrophy for the origin of mitochondria.
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8.48Impact points
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8.48Impact points
Investigating stagnation in morphological phylogenetics using consensus data.
Systematic biology. 03/2007; 56(1):125-9.
Following (12)
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David Alvarez-Ponce
National University of Ireland, Maynooth -
James A Cotton
Wellcome Trust Sanger Institute -
Brendan Anderson
University of Kansas -
James Mcinerney
National University of Ireland, Maynooth -
Chris Creevey
TEAGASC - The Agriculture and Food Development Authority
Topics (6)
