An integrated phylogenetic analysis of turtles

Background. Testudines is a reptilian order with unique morphological features among vertebrates. This order is currently divided into two suborders: Pleurodira and Cryptodira; which comprises approimately 14 extant families with 95 genera, about 320 species. Phylogenetic affinities below the family level remain largely unresolved. The main discrepancies among previous studies concern the position of the superfamily Trionychoidea and the families Chelydridae and Platystenidae. The recent improvement in combined phylogenetic inference and divergence time estimates, as well as the increased taxon sampling available in databases, prompted us to investigate their evolutionary relationships. Methods. In order to clarify the phylogenetic relatioships of Testudines, we inferred phylogenies from two datasets: (1) molecular dataset based on 12 genes, including 294 species; and (2) total evidence based on 12 genes plus 235 morphologic caracteres from the matrix of Sterli et al. (2013), including 28 extant and 69 extinct taxa. Maximum likelihood phylogenetic inference was performed with the data set partitioned into: (1) molecular nuclear data under GTR model of substitution, and (2) morphological data under Mk model. Statistical support for clades was assessed with 2000 nonparametric bootstrap replicates (BT). Results. Our results supported a split between Pleurodira and Cryptodira (BT > 97). In Cryptodira, we inferred an early split between Trionychoidea and all other Cryptodira, known as Durocryptodira (BT = 100). The monophyly of all families and superfamilies were recovered with high support (BT=100), except for the family Podocnemididae (BT=59). In both analyses, Chelydridae was recovered as sister-group to the superfamily Kinosternoidae (BT=99). With regard to Platysternidae, this monotypic asian family would split from Emydidae in the molecular phylogeny (BT = 81), whereas in the total analysis this split was between Emydidae and all remaining Testudinoidea: Emydidae + Geomydidae + Testudinidae. Discussion. All 14 families were represented in both analyses, although the molecular analysis contains 294 species-level taxa and total-evidence one has only 29 genus-level taxa. Pleurodira and Cryptodira were recovered as monophyletic as in most previous works. Trionychoidea was recovered as a clade within Cryptodira, in contrast to previous hypotheses, which placed this superfamily either as sister to Pleurodira or Cryptodira, or as sister group of all Testudines altogether. Chelydridae was recovered as sister-group of Kinosternoidae, whereas Platysternidae, a monotypic Asian family, was recovered as a member of Testudinoidae; although his position within the group was conflicting. This position of Platysternidae was the only conflict between crown groups found between our datasets.

An integrated phylogenetic analysis of turtles

10.7287/peerj.preprints.948v1 ◽

2015 ◽

Author(s):

Anieli Pereira ◽

Carlos Schrago

Keyword(s):

Divergence Time ◽

Nuclear Data ◽

Phylogenetic Inference ◽

Sister Group ◽

Total Evidence ◽

Morphological Data ◽

Nonparametric Bootstrap ◽

Data Set ◽

Molecular phylogeny and divergence time estimates of Penaeid Shrimp Lineages (Decapoda: Penaeidae)

Zootaxa ◽

10.11646/zootaxa.2107.1.2 ◽

2009 ◽

Vol 2107 (1) ◽

pp. 41-52 ◽

Cited By ~ 5

Author(s):

CAROLINA M VOLOCH ◽

PABLO R FREIRE ◽

CLAUDIA A M RUSSO

Keyword(s):

Fossil Record ◽

Divergence Time ◽

Penaeid Shrimp ◽

Time Estimates ◽

Global Clock ◽

Late Tertiary ◽

The Family ◽

Molecular Studies ◽

Triassic Period

Fossil record of penaeids indicates that the family exists since the Triassic period, but extant genera appeared only recently in Tertiary strata. Molecular based divergence time estimates on the matter of penaeid radiation were never properly addressed, due to shortcomings of the global molecular clock assumptions. Here, we studied the diversification patterns of the family, uncovering, more specifically, a correlation between fossil and extant Penaeid fauna. For this, we have used a Bayesian framework that does not assume a global clock. Our results suggest that Penaeid genera originated between 20 million years ago and 43 million years ago, much earlier than expected by previous molecular studies. Altogether, these results promptly discard late Tertiary or even Quaternary hypotheses that presumed a major glaciations influence on the diversification patterns of the family.

Phylogenetic Position of the New World Quail (Odontophoridae): Eight Nuclear Loci and Three Mitochondrial Regions Contradict Morphology and the Sibley-Ahlquist Tapestry

The Auk ◽

10.1093/auk/124.1.71 ◽

2007 ◽

Vol 124 (1) ◽

pp. 71-84 ◽

Cited By ~ 5

Author(s):

W. Andrew Cox ◽

Rebecca T. Kimball ◽

Edward L. Braun

Keyword(s):

New World ◽

Sequence Data ◽

Evolutionary Relationship ◽

Strong Support ◽

Nuclear Data ◽

Morphological Data ◽

Phylogenetic Position ◽

Data Set ◽

Mitochondrial Data ◽

Nuclear Loci

Abstract The evolutionary relationship between the New World quail (Odontophoridae) and other groups of Galliformes has been an area of debate. In particular, the relationship between the New World quail and guineafowl (Numidinae) has been difficult to resolve. We analyzed >8 kb of DNA sequence data from 16 taxa that represent all major lineages of Galliformes to resolve the phylogenetic position of New World quail. A combined data set of eight nuclear loci and three mitochondrial regions analyzed with maximum parsimony, maximum likelihood, and Bayesian methods provide congruent and strong support for New World quail being basal members of a phasianid clade that excludes guineafowl. By contrast, the three mitochondrial regions exhibit modest incongruence with each other. This is reflected in the combined mitochondrial analyses that weakly support the Sibley-Ahlquist topology that placed the New World quail basal in relation to guineafowl and led to the placement of New World quail in its own family, sister to the Phasianidae. However, simulation-based topology tests using the mitochondrial data were unable to reject the topology suggested by our combined (mitochondrial and nuclear) data set. By contrast, similar tests using our most likely topology and our combined nuclear and mitochondrial data allow us to strongly reject the Sibley-Ahlquist topology and a topology based on morphological data that unites Old and New World quail. Posición Filogenética de las Codornices del Nuevo Mundo (Odontophoridae): Ocho Loci Nucleares y Tres Regiones Mitocondriales Contradicen la Morfología y la Filogenia de Sibley y Ahlquist

Towards a phylogeny of the Metazoa: evaluating alternative phylogenetic positions of Platyhelminthes, Nemertea, and Gnathostomulida, with a critical reappraisal of cladistic characters

Contributions to Zoology ◽

10.1163/18759866-0730102001 ◽

2004 ◽

Vol 73 (1-2) ◽

pp. 3-163 ◽

Cited By ~ 36

Author(s):

Ronald A. Jenner

Keyword(s):

Sister Group ◽

Morphological Characters ◽

Total Evidence ◽

Morphological Data ◽

Future Research ◽

Sister Group Relationship ◽

Cladistic Analyses ◽

Phylogenetic Hypotheses ◽

Data Matrices

This paper critically assesses all morphological cladistic analyses of the Metazoa that were published during the last one and a half decades. Molecular and total evidence analyses are also critically reviewed. This study focuses on evaluating alternative phylogenetic positions of the ‘acoelomate’ worms: Platyhelminthes, Nemertea, and Gnathostomulida. This paper consists of two parts. In Part I, all recently proposed sister group hypotheses and the supporting synapomorphies for these phyla are evaluated. Discrepancies in the treatment of corresponding characters in different cladistic analyses are identified, and where possible, resolved. In Part II, the overall phylogenetic significance across the Metazoa of all characters relevant for placing the ‘acoelomate’ worms is examined. The coding and scoring of these characters for other phyla are evaluated, and uncertainties in our understanding are pointed out in order to guide future research. The characters discussed in this paper are broadly categorized as follows: epidermis and cuticle, reproduction and sexual condition, development, larval forms, coeloms and mesoderm source, nervous system and sensory organs, nephridia, musculature, digestive system, and miscellaneous characters. Competing phylogenetic hypotheses are compared in terms of several criteria: 1) taxon sampling and the fulfillment of domain of definition for each character; 2) character sampling; 3) character coding; 4) character scoring and quality of primary homology; 5) quality of the proposed diagnostic synapomorphies as secondary homologies. On the basis of this study I conclude that a sister group for the Platyhelminthes has not yet been unambiguously established. A clade minimally composed of Neotrochozoa (Mollusca, Sipuncula, Echiura, Annelida) emerges as the most likely sister group of the Nemertea on the basis of morphological and total evidence analyses. Finally, morphological data currrently favor a sister group relationship of Gnathostomulida and Syndermata (probably plus Micrognathozoa). In contrast, molecular or total evidence analyses have not identified a reliable sister group of Gnathostomulida.Further progress in our understanding of metazoan phylogeny crucially depends on the improvement of the quality of currently adopted cladistic data matrices. A thorough reassessment of many of the more than 70 morphological characters discussed here is necessary. Despite the recent compilation of comprehensive data matrices, the power to test competing hypotheses of higher-level metazoan relationships is critically compromised due to uncritical data selection and poor character study in even the most recently published cladistic analyses.

A molecular phylogeny of Callianassidae and related families (Crustacea : Decapoda : Axiidea) with morphological support

Invertebrate Systematics ◽

10.1071/is19021 ◽

2020 ◽

Vol 34 (2) ◽

pp. 113 ◽

Cited By ~ 3

Author(s):

Rafael Robles ◽

Peter C. Dworschak ◽

Darryl L. Felder ◽

Gary C. B. Poore ◽

Fernando L. Mantelatto

Keyword(s):

Bayesian Analysis ◽

Molecular Analysis ◽

Single Species ◽

Molecular Data ◽

Total Evidence ◽

Morphological Data ◽

12S Rrna ◽

New Genera ◽

Key Species ◽

The axiidean families Callianassidae and Ctenochelidae, sometimes treated together as Callianassoidea, are shown to represent a monophyletic taxon. It comprises 265 accepted species in 74 genera, twice this number of species if fossil taxa are included. The higher taxonomy of the group has proved difficult and fluid. In a molecular phylogenetic approach, we inferred evolutionary relationships from a maximum-likelihood (ML) and Bayesian analysis of four genes, mitochondrial 16S rRNA and 12S rRNA along with nuclear histone H3 and 18S rRNA. Our sample consisted of 298 specimens representing 123 species plus two species each of Axiidae and Callianideidae serving as outgroups. This number represented about half of all known species, but included 26 species undescribed or not confidently identified, 9% of all known. In a parallel morphological approach, the published descriptions of all species were examined and detailed observations made on about two-thirds of the known fauna in museum collections. A DELTA (Description Language for Taxonomy), database of 135 characters was made for 195 putative species, 18 of which were undescribed. A PAUP analysis found small clades coincident with the terminal clades found in the molecular treatment. Bayesian analysis of a total-evidence dataset combined elements of both molecular and morphological analyses. Clades were interpreted as seven families and 53 genera. Seventeen new genera are required to reflect the molecular and morphological phylograms. Relationships between the families and genera inferred from the two analyses differed between the two strategies in spite of retrospective searches for morphological features supporting intermediate clades. The family Ctenochelidae was recovered in both analyses but the monophyly of Paragourretia was not supported by molecular data. The hitherto well recognised family Eucalliacidae was found to be polyphyletic in the molecular analysis, but the family and its genera were well defined by morphological synapomorphies. The phylogram for Callianassidae suggested the isolation of several species from the genera to which they had traditionally been assigned and necessitated 12 new generic names. The same was true for Callichiridae, with stronger ML than Bayesian support, and five new genera are proposed. Morphological data did not reliably reflect generic relationships inferred from the molecular analysis though they did diagnose terminal taxa treated as genera. We conclude that discrepancies between molecular and morphological analyses are due at least in part to missing sequences for key species, but no less to our inability to recognise unambiguously informative morphological synapomorphies. The ML analysis revealed the presence of at least 10 complexes wherein 2–4 cryptic species masquerade under single species names.

Morphological diversity and phylogenetic relationships within a South-American clade of iguanian lizards (Liolaemidae: Phymaturus)

Zootaxa ◽

10.11646/zootaxa.3315.1.1 ◽

2012 ◽

Vol 3315 (1) ◽

pp. 1 ◽

Cited By ~ 18

Author(s):

FERNANDO LOBO ◽

CRISTIAN ABDALA ◽

SOLEDAD VALDECANTOS

Keyword(s):

Phylogenetic Relationships ◽

Morphological Diversity ◽

Color Pattern ◽

Total Evidence ◽

Morphological Data ◽

Data Set ◽

The North ◽

South Central ◽

Evidence Analysis ◽

La Rioja

With 36 species and at least nine potentially independent lineages (not formally described yet) occurring mostly in theAndes and adjacent Patagonia and Puna plateau areas, Phymaturus lizards represent one of the most endemic vertebrategroups of the arid southwestern region of South America. Phylogenetic relationships among species of Phymaturus areinferred using mainly a morphological data set of 206 characters. Also available sequences of mitochondrial DNA for sev-en terminals were added for a total evidence analysis. Most information is included in the discrete characters block; mostcharacters involve color pattern, osteology and squamation. Continuous characters were taken from body proportions,squamation and skeletons. Among morphological data, binary polymorphic characters were analyzed applying the scaledcoding criteria. Continuous characters were entered in the analysis using standardized ranges, a method that allows a sim-ple optimization to estimate distances/costs avoiding the arbitrary coding as discrete characters. For our parsimony anal-yses we chose the implied weights method, which underweights homoplastic characters. Several runs were madeanalyzing all the information combined and also separating morphological from molecular datasets. Binary polymor-phisms were also analyzed as missing data. All characters affected by sexual dimorphism were analyzed separating thesexes; female information was more congruent with the total evidence analysis. Characters involving continuous and poly-morphic information are relevant for searching and building phylogenetic hypotheses in Phymaturus. There exists signif-icant congruence between the molecular information analyzed in this study and previous published analyses. Within bothmain clades of Phymaturus, northern subgroups are those more recently originated during the genus diversification. Spe-cies belonging to the puna subclade of the palluma group are arranged in two natural groups, one distributed in the north(Catamarca and La Rioja provinces), and the other in the south, La Rioja and San Juan provinces. Within the patagonicusgroup, the majority of the species are arranged in a south-central Chubut clade, eastern-central Chubut clade, central Rio Negro clade and a Payunia clade.

Phylogenetic interrelationships in the order Primulales, with special emphasis on the family circumscriptions

Canadian Journal of Botany ◽

10.1139/b95-184 ◽

1995 ◽

Vol 73 (11) ◽

pp. 1699-1730 ◽

Cited By ~ 57

Author(s):

Arne A. Anderberg ◽

Bertil Ståhl

Keyword(s):

Key Words ◽

Sister Group ◽

Monophyletic Group ◽

Morphological Data ◽

Cladistic parsimony analyses, based on morphological data, have been undertaken with the purpose of identifying major monophyletic groups and phylogenetic interrelationships within the Primulales. Actinidia (Actinidiaceae, Ericales) and three genera from two families of the Ebenales (Diospyros of the Ebenaceae and Manilkara and Monotheca of the Sapotaceae) were used as outgroups in the analyses. The results indicate that the Primulaceae, Theophrastaceae, and Myrsinaceae (excluding Maesa) represent three major monophyletic groups. The Myrsinaceae were found to be paraphyletic, with the majority of taxa forming a monophyletic group but with the genus Maesa constituting the sister group of the Primulaceae. It is proposed that Maesa should be raised to the rank of family to obtain strictly monophyletic groups in the Primulales. The genera Aegiceras and Coris, for which family affinities have been controversial, are well nested within the families Myrsinaceae and Primulaceae, respectively. Key words: Primulales, Theophrastaceae, Myrsinaceae, Primulaceae, morphology, taxonomy, phylogeny, cladistics, classification.

The greenhouse thrips, Heliothrips haemorrhoidalis, and its generic relationships within the subfamily Panchaetothripinae (Thysanoptera: Thripidae)

Insect Systematics & Evolution ◽

10.1163/187631201x00164 ◽

2001 ◽

Vol 32 (2) ◽

pp. 205-216 ◽

Cited By ~ 2

Author(s):

John W.H. Trueman ◽

Rita Marullo ◽

Laurence A. Mound

Keyword(s):

Sister Group ◽

Morphological Characters ◽

Molecular Data ◽

Morphological Data ◽

Sister Group Relationship ◽

Pest Species ◽

Data Set ◽

Weak Support ◽

Heliothrips Haemorrhoidalis ◽

Generic Relationships

AbstractThe subfamily Panchaetothripinae, comprising 35 genera and 98 species, includes several pest species of which the most notorious is the greenhouse thrips, Heliothrips haemorrhoidalis. In an attempt to establish the sister-group of Heliothrips, the relationships of this genus to 31 of the other genera in the subfamily were examined cladistically, using 35 parsimony-informative morphological characters. The analysis indicated that there was no support for two of the three tribes into which this subfamily is customarily arranged, the Monilothripini and the Panchaetothripini, but weak support for the tribe Tryphactothripini. No clear sister-group relationship could be identified for the New World genus Heliothrips, although it grouped with three old world genera Australothrips, Retithrips and Rhipiphorothrips. It is concluded that a morphological data set is not capable of producing a robust phylogeny of the Panchaetothripinae, and that the subject requires re-examination using molecular data.

Synonymization of the male-based ant genus Phaulomyrma (Hymenoptera, Formicidae) with Leptanilla based upon Bayesian total-evidence phylogenetic inference

10.1101/2020.08.28.272799 ◽

2020 ◽

Author(s):

Zachary H. Griebenow

Keyword(s):

Sequence Data ◽

Phylogenetic Inference ◽

Morphological Characters ◽

Molecular Data ◽

Total Evidence ◽

Morphological Data ◽

Systematic Revision ◽

Dna Sequence Data ◽

Evidence Framework ◽

Nuclear Loci

Abstract.Although molecular data have proven indispensable in confidently resolving the phylogeny of many clades across the tree of life, these data may be inaccessible for certain taxa. The resolution of taxonomy in the ant subfamily Leptanillinae is made problematic by the absence of DNA sequence data for leptanilline taxa that are known only from male specimens, including the monotypic genus Phaulomyrma Wheeler & Wheeler. Focusing upon the considerable diversity of undescribed male leptanilline morphospecies, the phylogeny of 35 putative morphospecies sampled from across the Leptanillinae, plus an outgroup, is inferred from 11 nuclear loci and 41 discrete male morphological characters using a Bayesian total-evidence framework, with Phaulomyrma represented by morphological data only. Based upon the results of this analysis Phaulomyrma is synonymized with Leptanilla Emery, and male-based diagnoses for Leptanilla that are grounded in phylogeny are provided, under both broad and narrow circumscriptions of that genus. This demonstrates the potential utility of a total-evidence approach in inferring the phylogeny of rare extant taxa for which molecular data are unavailable and begins a long-overdue systematic revision of the Leptanillinae that is focused on male material.

The Implications of Lineage-Specific Rates for Divergence Time Estimation

Systematic Biology ◽

10.1093/sysbio/syz080 ◽

2019 ◽

Vol 69 (4) ◽

pp. 660-670 ◽

Cited By ~ 1

Author(s):

Tom Carruthers ◽

Michael J Sanderson ◽

Robert W Scotland

Keyword(s):

Estimation Error ◽

Divergence Time ◽

Time Estimation ◽

Rate Variation ◽

Data Set ◽

Divergence Time Estimation ◽

Time Estimates ◽

The Impact ◽

Highest Posterior Density

Abstract Rate variation adds considerable complexity to divergence time estimation in molecular phylogenies. Here, we evaluate the impact of lineage-specific rates—which we define as among-branch-rate-variation that acts consistently across the entire genome. We compare its impact to residual rates—defined as among-branch-rate-variation that shows a different pattern of rate variation at each sampled locus, and gene-specific rates—defined as variation in the average rate across all branches at each sampled locus. We show that lineage-specific rates lead to erroneous divergence time estimates, regardless of how many loci are sampled. Further, we show that stronger lineage-specific rates lead to increasing error. This contrasts to residual rates and gene-specific rates, where sampling more loci significantly reduces error. If divergence times are inferred in a Bayesian framework, we highlight that error caused by lineage-specific rates significantly reduces the probability that the 95% highest posterior density includes the correct value, and leads to sensitivity to the prior. Use of a more complex rate prior—which has recently been proposed to model rate variation more accurately—does not affect these conclusions. Finally, we show that the scale of lineage-specific rates used in our simulation experiments is comparable to that of an empirical data set for the angiosperm genus Ipomoea. Taken together, our findings demonstrate that lineage-specific rates cause error in divergence time estimates, and that this error is not overcome by analyzing genomic scale multilocus data sets. [Divergence time estimation; error; rate variation.]