scholarly journals Phylogeny and divergence times of suckers (Cypriniformes: Catostomidae) inferred from Bayesian total-evidence analyses of molecules, morphology, and fossils

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5168 ◽  
Author(s):  
Justin C. Bagley ◽  
Richard L. Mayden ◽  
Phillip M. Harris
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Fossil Record ◽  
Total Evidence ◽  
Morphological Data ◽  
Divergence Times ◽  
Data Types ◽  
Multiple Data ◽  
Phylogenetic Informativeness ◽  
Divergence Dating

Catostomidae (“suckers”) is a diverse (76 species) and broadly distributed family of Holarctic freshwater fishes with a rich fossil record and a considerable number (∼35%) of threatened and imperiled species. We integrate DNA sequences (three mitochondrial genes, three nuclear genes), morphological data, and fossil information to infer sucker phylogenetic relationships and divergence times using Bayesian “total-evidence” methods, and then test hypotheses about the temporal diversification of the group. Our analyses resolved many nodes within subfamilies and clarified Catostominae relationships to be of the form ((Thoburniini, Moxostomatini), (Erimyzonini, Catostomini)). Patterns of subfamily relationships were incongruent, but mainly supported two placements of the Myxocyprininae; distinguishing these using Bayes factors lent strongest support to a model with Myxocyprininae sister to all remaining sucker lineages. We improved our Bayesian total-evidence dating analysis by excluding problematic characters, using a clock-partitioning scheme identified by Bayesian model selection, and employing a fossilized birth-death tree prior accommodating morphological data and fossils. The resulting chronogram showed that suckers evolved since the Late Cretaceous–Eocene, and that the Catostomini and Moxostomatini clades have accumulated species diversity since the early to mid-Miocene. These results agree with the fossil record and confirm previous hypotheses about dates for the origins of Catostomide and catostomine diversification, but reject previous molecular hypotheses about the timing of divergence of ictiobines, and between Asian–North American lineages. Overall, our findings from a synthesis of multiple data types enhance understanding of the phylogenetic relationships, taxonomic classification, and temporal diversification of suckers, while also highlighting practical methods for improving Bayesian divergence dating models by coupling phylogenetic informativeness profiling with relaxed-clock partitioning.

Morphological and molecular evidence of some Minuartia species (Caryophyllaceae) from Turkey, with a desciption of a new species

Phytotaxa ◽  
2019 ◽  
Vol 391 (2) ◽  
pp. 122 ◽  
Author(s):  
MURAT KOÇ ◽  
ERGIN HAMZAOĞLU ◽  
AHMET AKSOY
Keyword(s):  
New Species ◽  
Dna Sequences ◽  
Related Species ◽  
Phylogenetic Relationships ◽  
Morphological Data ◽  
Molecular Evidence ◽  
A New Species

The genus Minuartia is represented in Turkey by 34 taxa. Some interesting specimens were collected from Antalya province, and examined. These specimens resemble Minuartia meyeri, and M. multinervis from which differ by characters (macro-, and micromorphological) of inflorescence, alar pedicels, petals, sepals, capsules and seeds. Moreover, by using the DNA sequences of the ITS genes, phylogenetic relationships between this collected species, and the related species were investigated. As a result of the evaluation of molecular, and morphological data, we proposed to described the population from Antalya as a new species for the science. A description, pictures, distribution, habitat, and IUCN category are given.

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

Zootaxa ◽  
2012 ◽  
Vol 3315 (1) ◽  
pp. 1 ◽  
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 relationships and classification of the Malagasy pseudoxyrhophiine snake genera Geodipsas and Compsophis based on morphological and molecular data

Zootaxa ◽  
2007 ◽  
Vol 1517 (1) ◽  
pp. 53-62 ◽  
Author(s):  
FRANK GLAW ◽  
ZOLTÁN T. NAGY ◽  
MIGUEL VENCES
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Close Relationships ◽  
Original Description ◽  
Molecular Data ◽  
Morphological Data ◽  
Molecular Phylogenetic ◽  
Species Groups ◽  
Morphological And Molecular Data

Based on a specimen found at Montagne d'Ambre in northern Madagascar morphologically agreeing with Compsophis albiventris Mocquard, 1894, we report on the rediscovery of this enigmatic snake genus and species and its molecular phylogenetic relationships. Compsophis albiventris, considered to be the only representative of its genus and unreported since its original description, bears strong morphological similarities to species of Geodipsas Boulenger, 1896. A molecular phylogeny based on DNA sequences of three mitochondrial and nuclear genes (complete cytochrome b, fragments of 16S rRNA and c-mos) in Compsophis albiventris and three Geodipsas species corroborated close relationships between C. albiventris and Geodipsas boulengeri, and showed that the genera Compsophis and Geodipsas together form a monophyletic unit. Despite the general similarities, morphological data and chromatic features support the existence of two species groups, corresponding to Compsophis and Geodipsas. We consequently consider Geodipsas as a subgenus of Compsophis and transfer all species currently in Geodipsas into the genus Compsophis.

Phylogenetic relationships and divergence times of the family Araucariaceae based on the DNA sequences of eight genes

2009 ◽  
Vol 54 (15) ◽  
pp. 2648-2655 ◽  
Author(s):  
Nian Liu ◽  
Yong Zhu ◽  
ZongXian Wei ◽  
Jie Chen ◽  
QingBiao Wang ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Divergence Times ◽  
The Family

scholarly journals Using more than the oldest fossils: Dating Osmundaceae by three Bayesian clock approaches

2014 ◽  
Author(s):  
Guido Grimm ◽  
Pashalia Kapli ◽  
Benjamin Bomfleur ◽  
Stephen McLoughlin ◽  
Susanne S Renner
Keyword(s):  
Dna Sequences ◽  
Fossil Record ◽  
Morphological Characters ◽  
Genetic Distances ◽  
Total Evidence ◽  
Extinction Rates ◽  
Sister Clade ◽  
Extant Species ◽  
Dating Methods ◽  
Divergence Dates

A major concern in molecular clock dating is how to use information from the fossil record to calibrate genetic distances from DNA sequences. Here we apply three Bayesian dating methods that differ in how calibration is achieved--"node dating" (ND) in BEAST, "total evidence" (TE) dating in MrBayes, and the "fossilized birth-death" (FBD) in FDPPDiv--to infer divergence times in the Osmundaceae or royal ferns. Osmundaceae have 13 species in four genera, two mainly in the Northern Hemisphere and two in South Africa and Australasia; they are the sister clade to the remaining leptosporangiate ferns. Their fossil record consists of at least 150 species in ~17 genera and three extinct families. For ND, we used the five oldest fossils, while for TE and FBD dating, which do not require forcing fossils to nodes and thus can use more fossils, we included up to 36 rhizome and frond compression/impression fossils, which for TE dating were scored for 33 morphological characters. We also subsampled 10%, 25%, and 50% of the 36 fossils to assess model sensitivity. FBD-derived divergence dates were generally greater than ages inferred from ND dating; two of seven TE-derived ages agreed with FBD-obtained ages, the others were much younger or much older than ND or FBD ages. We favour the FBD-derived ages because they best match the Osmundales fossil record (including Triassic fossils not used in our study). Under the preferred model, the clade encompassing extant Osmundaceae (and many fossils) dates to the latest Palaeozoic to Early Triassic; divergences of the extant species occurred during the Neogene. Under the assumption of constant speciation and extinction rates, FBD yielded 0.0299 (0.0099--0.0549) and 0.0240 (0.0039--0.0495) for these rates, whereas neontological data yielded 0.0314 and 0.0339. However, FBD estimates of speciation and extinction are sensitive to violations in the assumption of continuous fossil sampling, therefore these estimates should be treated with caution.

scholarly journals Craniodental morphology and phylogeny of marsupials

2021 ◽  
Author(s):  
Robin M. D. Beck ◽  
Robert Voss ◽  
Sharon Jansa
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Sequences ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Future Research ◽  
Data Types ◽  
Wide Range ◽  
Morphological And Molecular Data ◽  
Dense Sampling

The current literature on marsupial phylogenetics includes numerous studies based on analyses of morphological data with relatively limited sampling of Recent and fossil taxa, and many studies based on analyses of molecular data that include a dense sampling of Recent taxa, but relatively few that combine both data types. Another dichotomy in the marsupial phylogenetic literature is between studies that focus on New World taxa, others that focus on Sahulian taxa. To date, there has been no attempt to assess the phylogenetic relationships of the global marsupial fauna, based on combined analyses of morphology and molecular sequences, for a dense sampling of Recent and fossil taxa. For this report, we compiled morphological and molecular data from an unprecedented number of Recent and fossil marsupials. Our morphological data consist of 180 craniodental characters that we scored for 97 species representing every currently recognized Recent genus, 42 additional ingroup (crown-clade marsupial) taxa represented by well-preserved fossils, and 5 outgroups (non-marsupial metatherians). Our molecular data comprise 24.5 kb of DNA sequences from whole-mitochondrial genomes and six nuclear loci (APOB, BRCA1, GHR, RAG1, RBP3 and VWF) for 97 marsupial terminals (the same Recent taxa scored for craniodental morphology) and several placental and monotreme outgroups. The results of separate and combined analyses of these data using a wide range of phylogenetic methods support many currently accepted hypotheses of ingroup (marsupial) relationships, but they also underscore the difficulty of placing fossils with key missing data (e.g., †Evolestes), and the unique difficulty of placing others that exhibit mosaics of plesiomorphic and autapomorphic traits (e.g., †Yalkaparidon). Unique contributions of our study are (1) critical discussions and illustrations of marsupial craniodental morphology, including descriptions and illustrations of some features never previously coded for phylogenetic analysis; (2) critical assessments of relative support for many suprageneric clades; (3) estimates of divergence times derived from tip-and-node dating based on uniquely taxon-dense analyses; and (4) a revised, higher-order classification of marsupials accompanied by lists of supporting craniodental synapomorphies. Far from the last word on these topics, this report lays the foundation for future research that may be enabled by the discovery of new fossil taxa, better-preserved material of previously described taxa, novel morphological characters, and improved methods of phylogenetic analysis.

scholarly journals Synergistic effects of combining morphological and molecular data in resolving the phylogeny of butterflies and skippers

2005 ◽  
Vol 272 (1572) ◽  
pp. 1577-1586 ◽  
Author(s):  
Niklas Wahlberg ◽  
Michael F Braby ◽  
Andrew V.Z Brower ◽  
Rienk de Jong ◽  
Ming-Min Lee ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Synergistic Effects ◽  
Strong Support ◽  
Sister Group ◽  
Morphological Characters ◽  
Molecular Data ◽  
Total Evidence ◽  
Data Matrix ◽  
Morphological Data ◽  
Combined Analysis

Phylogenetic relationships among major clades of butterflies and skippers have long been controversial, with no general consensus even today. Such lack of resolution is a substantial impediment to using the otherwise well studied butterflies as a model group in biology. Here we report the results of a combined analysis of DNA sequences from three genes and a morphological data matrix for 57 taxa (3258 characters, 1290 parsimony informative) representing all major lineages from the three putative butterfly super-families (Hedyloidea, Hesperioidea and Papilionoidea), plus out-groups representing other ditrysian Lepidoptera families. Recently, the utility of morphological data as a source of phylogenetic evidence has been debated. We present the first well supported phylogenetic hypothesis for the butterflies and skippers based on a total-evidence analysis of both traditional morphological characters and new molecular characters from three gene regions ( COI , EF-1α and wingless ). All four data partitions show substantial hidden support for the deeper nodes, which emerges only in a combined analysis in which the addition of morphological data plays a crucial role. With the exception of Nymphalidae, the traditionally recognized families are found to be strongly supported monophyletic clades with the following relationships: (Hesperiidae+(Papilionidae+(Pieridae+(Nymphalidae+(Lycaenidae+Riodinidae))))). Nymphalidae is recovered as a monophyletic clade but this clade does not have strong support. Lycaenidae and Riodinidae are sister groups with strong support and we suggest that the latter be given family rank. The position of Pieridae as the sister taxon to nymphalids, lycaenids and riodinids is supported by morphology and the EF-1α data but conflicted by the COI and wingless data. Hedylidae are more likely to be related to butterflies and skippers than geometrid moths and appear to be the sister group to Papilionoidea+Hesperioidea.

scholarly journals Testing alternative phylogenetic hypotheses for the tent tortoise species complex (Reptilia, Testudinidae) using multiple data types and methods

2020 ◽  
Author(s):  
Zhongning Zhao ◽  
Neil Heideman ◽  
Jaco Oosthuizen ◽  
Margaretha D. Hofmeyr
Keyword(s):  
Species Complex ◽  
Approximate Bayesian Computation ◽  
Morphological Data ◽  
Southern Population ◽  
Data Types ◽  
Bottleneck Effect ◽  
Dna Evidence ◽  
Multiple Data ◽  
Phylogenetic Hypotheses ◽  
Approximate Bayesian

AbstractWe examined genetic differentiation in the highly polymorphic and taxonomically confusing tent tortoise (Psammobates tentorius) species complex in southern Africa, using three types of molecular markers (nDNA, mtDNA and microsatellite DNA) and morphological data. The Approximate Bayesian Computation based simulation analyses advocated an alternative phylogenetic hypothesis for the tent tortoise species complex, which was better and more inclusive in explaining its genealogical history. Based on the evidence derived from the sequence, microsatellite and morphology data, a four species scheme (among the seven mtDNA clades) appears to be the best taxonomic solution for the systematic puzzle of the P. tentorius species complex, namely, “C1+C4+C5+C7”, “C3”, “C2” and “C6”. The microsatellite datasets yielded similar genetic structure and gene flow patterns among the seven mtDNA clades in comparison to the sequence DNA. Evidence was found of possible hybridization between C1 and C2 in their intergradation zone, but not between C2 and C4. Results of the inbreeding analyses provided strong evidence of inbreeding in the eastern population of C1 and southern population of C2, which may be indicative of a bottleneck effect.

Combining morphological and molecular data resolves the phylogeny of Squilloidea (Crustacea : Malacostraca)

2019 ◽  
Author(s):  
Cara Van Der Wal ◽  
Shane T. Ahyong ◽  
Simon Y. W. Ho ◽  
Luana S. F. Lins ◽  
Nathan Lo
Keyword(s):  
Phylogenetic Analysis ◽  
Adaptive Radiation ◽  
Phylogenetic Relationships ◽  
Morphological Characters ◽  
Molecular Data ◽  
Total Evidence ◽  
Morphological Data ◽  
Mantis Shrimp ◽  
Generic Groups ◽  
Morphological And Molecular Data

The mantis shrimp superfamily Squilloidea, with over 185 described species, is the largest superfamily in the crustacean order Stomatopoda. To date, phylogenetic relationships within this superfamily have been comprehensively analysed using morphological data, with six major generic groupings being recovered. Here, we infer the phylogeny of Squilloidea using a combined dataset comprising 75 somatic morphological characters and four molecular markers. Nodal support is low when the morphological and molecular datasets are analysed separately but improves substantially when combined in a total-evidence phylogenetic analysis. We obtain a well resolved and strongly supported phylogeny that is largely congruent with previous estimates except that the Anchisquilloides-group, rather than the Meiosquilla-group, is the earliest-branching lineage in Squilloidea. The splits among the Anchisquilloides- and Meiosquilla-groups are followed by those of the Clorida-, Harpiosquilla-, Squilla- and Oratosquilla-groups. Most of the generic groups are recovered as monophyletic, with the exception of the Squilla- and Oratosquilla-groups. However, many genera within the Oratosquilla-group are not recovered as monophyletic. Further exploration with more extensive molecular sampling will be needed to resolve relationships within the Oratosquilla-group and to investigate the adaptive radiation of squilloids. Overall, our results demonstrate the merit of combining morphological and molecular datasets for resolving phylogenetic relationships.

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