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PubMed1999

Phylogenetic analyses reveal ancient duplication of estrogen receptor isoforms.

To determine the origin and evolutionary significance of a recently discovered isoform of the estrogen receptor (ERbeta), we examined the phylogenetic relationship of ERbeta to the well-known alpha isoform (ERalpha) and other steroid receptors. Our phylogenetic analyses traced the origin of ERbeta to a single duplication event at least 450 million years ago. Since this duplication, the evolution of both ER isoforms has apparently been constrained such that 80% of the amino acid positions in the DNA binding domain (DBD) and 53% of the ligand binding domain (LBD) have remained unchanged. Using the phylogenetic tree, we determined the amount of evolutionary change that had occurred in two ER isoforms. The DBD and the LBD had lower rates of evolutionary change compared to the NH(2) terminal domain. However, even with strong selective constraints on the DBD and LBD, our phylogenetic analyses demonstrate two clearly separate phylogenetic histories for ERalpha and ERbeta dating back several hundred million years. The ancient duplication of ER and the parallel evolution of the two ER isoforms suggest that, although ERalpha and ERbeta share a substantial degree of sequence identity, they play unique roles in vertebrate physiology and reproduction.

Animals↗

PubMed1997

Molecular phylogenetic information on the identity of the closest living relative(s) of land vertebrates.

The phylogenetic position of tetrapods relative to the other two living sarcopterygian lineages (lungfishes and the coelacanth) has been subject to debate for many decades, yet remains unresolved. There are three possible alternatives for the phylogenetic relationships among these three living lineages of sarcopterygians, i.e., lungfish as living sister group of tetrapods, the coelacanth as closest living relative of tetrapods, and lungfish and coelacanth equally closely related to tetrapods. To resolve this important evolutionary question several molecular data sets have been collected in recent years, the largest being the almost complete 28S rRNA gene sequences (about 3500 bp) and the complete mitochondrial genomes of the coelacanth and a lungfish (about 16,500 bp each). Phylogenetic analyses of several molecular data sets had not provided unequivocal support for any of the three hypotheses. However, a lungfish + tetrapod or a lungfish + coelacanth clade were predominantly favored over a coelacanth + tetrapod grouping when the entire mitochondrial genomes alone or in combination with the nuclear 28S rRNA gene data were analyzed with maximum parsimony, neighbor-joining, and maximum likelihood phylogenetic methods. Also, current paleontological and morphological data seem to concur with these molecular results. Therefore the currently available molecular data seems to rule out a coelacanth + tetrapod relationship, the traditional textbook hypothesis. These tentative molecular phylogenetic results point to the inherent difficulty in resolving relationships among lineages which apparently originated in rapid succession during the Devonian.

Animals↗

PubMed2004

Phylogenetic analysis of Asian Symplocos (Symplocaceae) based on nuclear and chloroplast DNA sequences.

Thirty species and one variety of Symplocos (Symplocaceae), including all taxa distributed in Japan, were phylogenetically analyzed with DNA sequence data. The evolution of morphological characters is discussed on the basis of the phylogenetic relationships obtained. All species were Asian, except one, S. austromexicana, from Mexico. The nuclear ribosomal internal transcribed spacer (ITS) region and two intergenic spacer regions, between trnL and trnF, and between trnH and psbA of chloroplast DNA were used. The topologies of trees obtained from ITS and the chloroplast intergenic spacers are largely congruent. S. sonoharae, the representative of the subgenus Symplocos in Asia, was sister to all other species. The position of the American species, S. austromexicana, which also belongs to the subgenus Symplocos, was not well resolved. The phylogenetic tree based on combined sequence data largely supports the monophyletic origin of the infrageneric sections proposed earlier. However, the phylogenetic relationship between them is not well resolved, probably due to rapid diversification. The section Palura, a deciduous group, is well defined in the DNA analysis, suggesting its independent status in the genus Symplocos. In spite of their morphological divergence, the three endemic species of the Bonin Islands are monophyletic. The occurrence of curved seeds seems to be homoplastic, scattered over the phylogenetic tree without showing a particular infrageneric relationship.

Asia↗

PubMed2006

Phylogenetic relationships of Steinernema Travassos, 1927 (Nematoda: Cephalobina: Steinernematidae) based on nuclear, mitochondrial and morphological data.

Entomopathogenic nematodes of the genus Steinernema are lethal parasites of insects that are used as biological control agents of several lepidopteran, dipteran and coleopteran pests. Phylogenetic relationships among 25 Steinernema species were estimated using nucleotide sequences from three genes and 22 morphological characters. Parsimony analysis of 28S (LSU) sequences yielded a well-resolved phylogenetic hypothesis with reliable bootstrap support for 13 clades. Parsimony analysis of mitochondrial DNA sequences (12S rDNA and cox 1 genes) yielded phylogenetic trees with a lower consistency index than for LSU sequences, and with fewer reliably supported clades. Combined phylogenetic analysis of the 3-gene dataset by parsimony and Bayesian methods yielded well-resolved and highly similar trees. Bayesian posterior probabilities were high for most clades; bootstrap (parsimony) support was reliable for approximately half of the internal nodes. Parsimony analysis of the morphological dataset yielded a poorly resolved tree, whereas total evidence analysis (molecular plus morphological data) yielded a phylogenetic hypothesis consistent with, but less resolved than trees inferred from combined molecular data. Parsimony mapping of morphological characters on the 3-gene trees showed that most structural features of steinernematids are highly homoplastic. The distribution of nematode foraging strategies on these trees predicts that S. hermaphroditum, S. diaprepesi and S. longicaudum (US isolate) have cruise forager behaviours.

Amino Acid Sequence↗

PubMed2005

Reconstruction of large phylogenetic trees: a parallel approach.

Reconstruction of phylogenetic trees for very large datasets is a known example of a computationally hard problem. In this paper, we present a parallel computing model for the widely used Multiple Instruction Multiple Data (MIMD) architecture. Following the idea of divide-and-conquer, our model adapts the recursive-DCM3 decomposition method [Roshan, U., Moret, B.M.E., Williams, T.L., Warnow, T, 2004a. Performance of suptertree methods on various dataset decompositions. In: Binida-Emonds, O.R.P. (Eds.), Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life, vol. 3 of Computational Biology, Kluwer Academics, pp. 301-328; Roshan, U., Moret, B.M.E., Williams, T.L., Warnow, T., 2004b. Rec-I-DCM3: A Fast Algorithmic Technique for reconstructing large phylogenetic trees, Proceedings of the IEEE Computational Systems Bioinformatics Conference (ICSB)] to divide datasets into smaller subproblems. It distributes computation load over multiple processors so that each processor constructs subtrees on each subproblem within a batch in parallel. It finally collects the resulting trees and merges them into a supertree. The proposed model is flexible as far as methods for dividing and merging datasets are concerned. We show that our method greatly reduces the computational time of the sequential version of the program. As a case study, our parallel approach only takes 22.1h on four processors to outperform the best score to date (Found at 123.7h by the Rec-I-DCM3 program [Roshan, U., Moret, B.M.E., Williams, T.L., Warnow, T, 2004a. Performance of suptertree methods on various dataset decompositions. In: Binida-Emonds, O.R.P. (Eds.), Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life, vol. 3 of Computational Biology, Kluwer Academics, pp. 301-328; Roshan, U., Moret, B.M.E., Williams, T.L., Warnow, T., 2004b. Rec-I-DCM3: A Fast Algorithmic Technique for reconstructing large phylogenetic trees, Proceedings of the IEEE Computational Systems Bioinformatics Conference (ICSB)] on one dataset. Developed with the standard message-passing library, MPI, the program can be recompiled and run on any MIMD systems.

Journal Article↗

PubMed2006

Identification and phylogenetic analysis of hepatitis C virus in forensic blood samples obtained from injecting drug users.

Injecting drug users (IDUs) are a high-risk group for contracting hepatitis B virus (HBV), hepatitis C virus (HCV), and human immunodeficiency virus (HIV) infections. In Japan, data on the prevalence of those blood-borne viruses among IDUs are very limited. Blood samples were obtained from 12 cadavers of IDUs sent to Nagoya City University for the purpose of judicious autopsy and two alive IDUs with hepatitis C referred to a local hospital at the same period. The viruses were detected by polymerase chain reaction and phylogenetic analysis was performed. Two (16.6%) of the 12 autopsy cases were positive for HCV, but no case was positive for either HBV or HIV. Phylogenetic analysis of the two HCV isolates revealed that one was classified into genotype 1b and another was genotype 2b. Furthermore, nucleotide sequences of two isolates recovered from IDUs with hepatitis C were identical, that indicated the transmission of HCV between them, and those HCV were phylogenetically classified into genotype 2a. The prevalence of HCV infection among IDUs in Japan, despite the case of judicious autopsy, seems to be high, but HIV infection seems to be rare. The transmission of HCV between IDUs was demonstrated, and this indicates that phylogenetic analysis would applicable to also forensic analysis. HCV isolates identified in this study did not phylogenetically segregate, thus multiple transmission route of HCV among IDUs seems be exist in Japan.

Adult↗

PubMed2004

Phylogenetic relationships of discoglossid frogs (Amphibia:Anura:Discoglossidae) based on complete mitochondrial genomes and nuclear genes.

The complete nucleotide sequence of the mitochondrial (mt) genome was determined for three species of discoglossid frogs (Amphibia:Anura:Discoglossidae), representing three of the four recognized genera: Alytes obstetricans, Bombina orientalis, and Discoglossus galganoi. The organization and size of these newly determined mt genomes are similar to those previously reported for other vertebrates. Phylogenetic analyses (maximum likelihood, Bayesian inference, minimum evolution, and maximum parsimony) of mt protein-coding genes at the amino acid level were performed in combination with already published mt genome sequence data of three species of Neobatrachia, one of Pipoidea, and four of Caudata. Phylogenetic analyses based on the deduced amino acid sequences of all mt protein-coding genes arrived at the same topology. The monophyly of Discoglossidae is strongly supported. Within the Discoglossidae, Alytes is consistently recovered as sister group of Discoglossus, to the exclusion of Bombina. The three species representing Neobatrachia exhibited extremely long branches irrespective of the phylogenetic inference method used, and hence their relative position with respect to Discoglossidae and Xenopus may be artefactual due to a severe long branch attraction effect. To further investigate the phylogenetic intrarelationships of discoglossids, nucleotide sequences of four nuclear protein-coding genes (CXCR4, RAG1, RAG2, and Rhodopsin) with sequences available for the three discoglossid genera and Xenopus were retrieved from GenBank, and together with a concatenated nucleotide sequence data set containing all mt protein-coding genes except ND6 were subjected to separate and combined phylogenetic analyses. In all cases, a sister group relationship between Alytes and Discoglossus was recovered with high statistical support.

Amino Acid Sequence↗

PubMed2005

Mitochondrial phylogeny of Anura (Amphibia): a case study of congruent phylogenetic reconstruction using amino acid and nucleotide characters.

We explore whether phylogenetic analyses of the same sequence data set at the amino acid and nucleotide level are able to recover congruent topologies, as well as the advantages and limitations of both alternative approaches. As a case study, mitochondrial protein-coding genes were used to discern among competing hypotheses on the phylogenetic relationships of major anuran amphibian lineages. To properly address this phylogenetic question, the complete nucleotide sequences of the mitochondrial genomes of two archaeobatrachian species, Ascaphus truei and Pelobates cultripes, were determined anew. Bayesian and maximum likelihood phylogenetic inferences of the same sequence data set were performed based on both amino acid and nucleotide characters, with the latter analysed either as codons or as a reduced data set of first+second (P12) codon positions. In addition, likelihood-based ratio tests were performed to evaluate the support of alternative topologies. The different data sets arrived at congruent and highly supported topologies, suggesting a similar phylogenetic resolving power of the two character types provided that correctly selected sites and appropriate evolutionary models are used. The reconstructed anuran mitochondrial phylogeny supports the paraphyly of Archaeobatrachia, with Ascaphus as sister group to all the remaining anurans, and Pelobates as sister group of Neobatrachia. However, the employed tree reconstruction methods and likelihood-based ratio tests seemed to be negatively affected by the fast evolving sequences of neobatrachians, suggesting that the phylogeny of Anura here presented is not definitive, and needs further investigation using an extended taxon sampling.

Amphibian Proteins↗

PubMed2006

On the phylogenetic position of a rare Iberian endemic mammal, the Pyrenean desman (Galemys pyrenaicus).

The nucleotide sequences of the complete mitochondrial genome and nine partial nuclear genes of the Pyrenean desman (Galemys pyrenaicus) were determined in order to establish the relative phylogenetic position of this species at different taxonomic levels within the placental tree. Phylogenetic relationships of desman within the family Talpidae were inferred based on complete mitochondrial cytochrome b gene nucleotide sequence data. The Pyrenean desman was unambiguously recovered as sister group of the Russian desman (Desmana moschata) confirming the monophyly of the subfamily Desmaninae. However, phylogenetic relationships among major lineages within the Talpidae could not be confidently resolved. Phylogenetic analyses based on mitochondrial (at the amino acid level) and nuclear (at the nucleotide level) sequence data sets confidently placed desman within the Eulipotyphla (that also included moles, shrews, and hedgehogs), and partially recovered placental interordinal relationships. The monophyly of Laurasiatheria (including Eulipotyphla, Chiroptera, Carnivora, Pholidota, Perissodactyla, and Cetartiodactyla) was strongly supported. Mitochondrial amino acid sequences of Pholidota (pangolins) were found to bias phylogenetic inferences due to long-branch attraction effects. A Bayesian inference based on a combined mitochondrial and nuclear data set without Pholidota arrived at an almost fully resolved tree that supported the basal position of Eulipotyphla within Laurasiatheria.

Animals↗

PubMed2006

Phylogenetic relationships among clonal groups of extraintestinal pathogenic Escherichia coli as assessed by multi-locus sequence analysis.

The evolutionary origins of extraintestinal pathogenic Escherichia coli (ExPEC) remain uncertain despite these organisms' relevance to human disease. A valid understanding of ExPEC phylogeny is needed as a framework against which the observed distribution of virulence factors and clinical associations can be analyzed. Accordingly, phylogenetic relationships were defined by multi-locus sequence analysis among 44 representatives of selected ExPEC clonal groups and the E. coli Reference (ECOR) collection. Recombination, which significantly obscured the phylogenetic signal for several strains, was dealt with by excluding strains or specific sequences. Conflicting overall phylogenies, and internal phylogenies for virulence-associated phylogenetic group B2, were inferred depending on the specific dataset (i.e., how extensively purged of recombination), outgroup (Salmonella enterica and/or Escherichia fergusonii), and analysis method (neighbor joining, maximum parsimony, maximum likelihood, or Bayesian likelihood). Nonetheless, the major E. coli phylogenetic groups A, B1, and B2 were consistently well resolved, as was a major sub-component of group D and an ECOR 37-O157:H7 clade. Moreover, nine important ExPEC clonal groups within groups B2 and D, characterized by serotypes O6:K2:H1, O18:K1:H7, O6:H31, and O4:K+:H+ (from group B2), and O1:K1:H-, O7:K1:H-, O157:K+:H (non-7), O15:K52:H1, and O11/17/77:K52:H18 ("clonal group A") (from group D), were consistently well resolved, regardless of clinical background (cystitis, pyelonephritis, neonatal meningitis, sepsis, or fecal), host group, geographical origin, and virulence profile. Among the group B2-derived clonal groups the O6:K2:H1 clade appeared basal. Within group D, "clonal group A" and the O15:K52:H1 clonal group were consistently placed with ECOR 47 and ECOR 44, respectively, as nearest neighbors. These findings clarify phylogenetic relationships among key ExPEC clonal groups but also emphasize that recombination appears to obscure the oldest evolutionary relationships, despite extensive targeted sequencing and use of a wide range of analysis techniques.

Animals↗

PubMed2005

Metabolic profiling and phylogenetic analysis of medicinal Zingiber species: Tools for authentication of ginger (Zingiber officinale Rosc).

Phylogenetic analysis and metabolic profiling were used to investigate the diversity of plant material within the ginger species and between ginger and closely related species in the genus Zingiber (Zingiberaceae). In addition, anti-inflammatory data were obtained for the investigated species. Phylogenetic analysis demonstrated that all Zingiber officinale samples from different geographical origins were genetically indistinguishable. In contrast, other Zingiber species were significantly divergent, allowing all species to be clearly distinguished using this analysis. In the metabolic profiling analysis, the Z. officinale samples derived from different origins showed no qualitative differences in major volatile compounds, although they did show some significant quantitative differences in non-volatile composition, particularly regarding the content of [6]-, [8]-, and [10]-gingerols, the most active anti-inflammatory components in this species. The differences in gingerol content were verified by HPLC. The metabolic profiles of other Zingiber species were very different, both qualitatively and quantitatively, when compared to Z. officinale and to each other. Comparative DNA sequence/chemotaxonomic phylogenetic trees showed that the chemical characters of the investigated species were able to generate essentially the same phylogenetic relationships as the DNA sequences. This supports the contention that chemical characters can be used effectively to identify relationships between plant species. Anti-inflammatory in vitro assays to evaluate the ability of all extracts from the Zingiber species examined to inhibit LPS-induced PGE(2) and TNF-alpha production suggested that bioactivity may not be easily predicted by either phylogenetic analysis or gross metabolic profiling. Therefore, identification and quantification of the actual bioactive compounds are required to guarantee the bioactivity of a particular Zingiber sample even after performing authentication by molecular and/or chemical markers.

Anti-Inflammatory Agents↗

PubMed2003

A decade of progress in plant molecular phylogenetics.

Over the past decade, botanists have produced several thousand phylogenetic analyses based on molecular data, with particular emphasis on sequencing rbcL, the plastid gene encoding the large subunit of Rubisco (ribulose bisphosphate carboxylase). Because phylogenetic trees retrieved from the three plant genomes (plastid, nuclear and mitochondrial) have been highly congruent, the "Angiosperm Phylogeny Group" has used these DNA-based phylogenetic trees to reclassify all families of flowering plants. However, in addition to taxonomy, these major phylogenetic efforts have also helped to define strategies to reconstruct the "tree of life", and have revealed the size of the ancestral plant genome, uncovered potential candidates for the ancestral flower, identified molecular living fossils, and linked the rate of neutral substitutions with species diversity. With an increased interest in DNA sequencing programmes in non-model organisms, the next decade will hopefully see these phylogenetic findings integrated into new genetic syntheses, from genomes to taxa.

DNA, Plant↗

PubMed2004

A phylogenetic approach to cultural evolution.

There has been a rapid increase in the use of phylogenetic methods to study the evolution of languages and culture. Languages fit a tree model of evolution well, at least in their basic vocabulary, challenging the view that blending, or admixture among neighbouring groups, was predominant in cultural history. Here, we argue that we can use language trees to test hypotheses about not only cultural history and diversification, but also bio-cultural adaptation. Phylogenetic comparative methods take account of the non-independence of cultures (Galton's problem), which can cause spurious statistical associations in comparative analyses. Advances in phylogenetic methods offer new possibilities for the analysis of cultural evolution, including estimating the rate of evolution and the direction of coevolutionary change of traits on the tree. They also enable phylogenetic uncertainty to be incorporated into the analyses, so that one does not have to treat phylogenetic trees as if they were known without error.

Journal Article↗

PubMed2006

Conflicting phylogenetic position of Schizosaccharomyces pombe.

The phylogenetic position of the fission yeast Schizosaccharomyces pombe in the fungal Tree of Life is still controversial. Three alternative phylogenetic positions have been proposed in the literature, namely (1) a position basal to the Hemiascomycetes and Euascomycetes, (2) a position as a sister group to the Euascomycetes with the Hemiascomycetes as a basal branch, or (3) a sister group to the Hemiascomycetes with Euascomycetes as a basal branch. Here we compared 91 clusters of orthologous proteins containing a single orthologue that are shared by 19 eukaryote genomes. The major part of these 91 orthologues supports a phylogenetic position of S. pombe as a basal lineage among the Ascomycota, thus supporting the second proposition. Interestingly, part of the orthologous proteins supported a fourth, not yet described alternative, in which S. pombe is basal to both Basidiomycota and Ascomycota. Both topologies of phylogenetic trees are well supported. We believe that both reflect correctly the phylogenetic history of the species concerned. This apparent paradox may point to a heterogeneous nuclear genome of the fungi. Importantly, this needs to be taken in consideration for a correct understanding of the fungal Tree of Life.

Genetic Speciation↗

PubMed2004

Phylogenetic comparison of metabolic capacities of organisms at genome level.

Horizontal gene transfer (HGT) has been shown to widely spread in organisms by comparative genomic studies. However, its effect on the phylogenetic relationship of organisms, especially at a system level of different cellular functions, is still not well understood. In this work, we have constructed phylogenetic trees based on the enzyme, reaction, and gene contents of metabolic networks reconstructed from annotated genome information of 82 sequenced organisms. Results from different phylogenetic distance definitions and based on three different functional subsystems (i.e., metabolism, cellular processes, information storage and processing) were compared. Results based on the three different functional subsystems give different pictures on the phylogenetic relationship of organisms, reflecting the different extents of HGT in the different functional systems. In general, horizontal transfer is prevailing in genes for metabolism, but less in genes for information processing. Nevertheless, the major results of metabolic network-based phylogenetic trees are in good agreement with the tree based on 16S rRNA and genome trees, confirming the three domain classification and the close relationship between eukaryotes and archaea at the level of metabolic networks. These results strongly support the hypothesis that although HGT is widely distributed, it is nevertheless constrained by certain pre-existing metabolic organization principle(s) during the evolution. Further research is needed to identify the organization principle and constraints of metabolic network on HGT which have large impacts on understanding the evolution of life and in purposefully manipulating cellular metabolism.

Animals↗

PubMed2004

Relative character-state space, amount of potential phylogenetic information, and heterogeneity of nucleotide and amino acid characters.

We examined a broad selection of protein-coding loci from a diverse array of clades and genomes to quantify three factors that determine whether nucleotide or amino acid characters should be preferred for phylogenetic inference. First, we quantified the difference in observed character-state space between nucleotides and amino acids. Second, we quantified the loss of potential phylogenetic signal from silent substitutions when amino acids are used. Third, we used the disparity index to quantify the relative compositional heterogeneity of nucleotides and amino acids and then determined how commonly convergent (rather than unique) shifts in nucleotide and amino acid composition occur in a phylogenetic context. The greater potential phylogenetic signal for nucleotide characters was found to be enormous (on average 440% that of amino acids), whereas the greater observed character-state space for amino acids was less impressive (on average 150.4% that of nucleotides). While matrices of amino acid sequences had less compositional heterogeneity than their corresponding nucleotide sequences, heterogeneity in amino acid composition may be more homoplasious than heterogeneity in nucleotide composition. Given the ability of increased taxon sampling to better utilize the greater potential phylogenetic signal of nucleotide characters and decrease the potential for artifacts caused by heterogeneous nucleotide composition among taxa, we suggest that increased taxon sampling be performed whenever possible instead of restricting analyses to amino acid characters.

Amino Acids↗

PubMed2004

Intragenomic variation of the rDNA internal transcribed spacers in sponges (Phylum Porifera): implications for phylogenetic studies.

The internal transcribed spacer regions (ITS1 and ITS2) of the tandemly repeated nuclear ribosomal DNA clusters are frequently used as markers for fine scale analyses in diverse animals. In certain taxa, ITS is nearly exclusively used for population level or inter-specific studies, despite the frequent presence of divergent paralogs within individual genomes that can be phylogenetically misleading. For the first time we survey diverse marine sponges to determine the extent and phylogenetic implications of intragenomic polymorphisms (IGPs) exhibited at their ITS loci. We discover that the extent of IGP varies greatly between taxa (with most taxa exhibiting very few) and cannot be predicted by taxonomy. Furthermore, we demonstrate that ITS can be phylogenetically informative between species when moderate levels of IGPs are detected, but that ITS paralogy can interfere with population level studies. We caution against the routine use of ITS in phylogenetic studies of sponges without (1) screening for IGPs in specimens from every population sampled; (2) including all divergent paralogs in phylogenetic analyses; (3) testing ITS data using other single-copy, unlinked loci (such as nuclear introns).

Animals↗

PubMed2005

Molecular phylogenetics and evolution of turtles.

Turtles are one of Earth's most instantly recognizable life forms, distinguished for over 200 million years in the fossil record. Even so, key nodes in the phylogeny of turtles remain uncertain. To address this issue, we sequenced >90% of the nuclear recombination activase gene 1 (RAG-1) for 24 species representing all modern turtle families. RAG-1 exhibited negligible saturation and base composition bias, and extensive base composition homogeneity. Most of the relationships suggested by prior phylogenetic analyses were also supported by RAG-1 and, for at least two critical nodes, with a much higher level of support. RAG-1 also indicates that the enigmatic Platysternidae and Chelydridae, often considered sister taxa based on morphological evidence, are not closely related, although their precise phylogenetic placement in the turtle tree is still unresolved. Although RAG-1 is phylogenetically informative, our research revealed fundamental conflicts among analytical methods for estimating phylogenetic hypotheses. Maximum parsimony analyses of RAG-1 alone and in combination with two mitochondrial genes suggest the earliest phylogenetic splits separating into three basal branches, the pig-nosed turtles (Carettochelyidae), the softshell turtles (Trionychidae), and a clade comprising all remaining extant turtles. Maximum likelihood and Bayesian analyses group Carettochelyidae and Trionychidae (=Trionychoidae) in their more traditional location as the sister taxon to all other hidden-necked turtles, collectively forming the Cryptodira. Our research highlights the utility of molecular data in identifying issues of character homology in morphological datasets, while shedding valuable light on the biodiversity of a globally imperiled taxon.

Animals↗