scholarly journals Phylogenetic taxonomy and classification of the Crinoidea (Echinodermata)

2017 ◽  
Vol 91 (4) ◽  
pp. 829-846 ◽  
Author(s):  
David F. Wright ◽  
William I. Ausich ◽  
Selina R. Cole ◽  
Mark E. Peter ◽  
Elizabeth C. Rhenberg
Keyword(s):  
Phylogenetic Relationships ◽  
Fossil Record ◽  
Phylogenetic Analyses ◽  
Major Goal ◽  
Evolutionary Patterns ◽  
Phylogenetic Taxonomy ◽  
Phylogenetic Perspective ◽  
Phylogenetic Hypotheses ◽  
Patterns And Processes

AbstractA major goal of biological classification is to provide a system that conveys phylogenetic relationships while facilitating lucid communication among researchers. Phylogenetic taxonomy is a useful framework for defining clades and delineating their taxonomic content according to well-supported phylogenetic hypotheses. The Crinoidea (Echinodermata) is one of the five major clades of living echinoderms and has a rich fossil record spanning nearly a half billion years. Using principles of phylogenetic taxonomy and recent phylogenetic analyses, we provide the first phylogeny-based definition for the Clade Crinoidea and its constituent subclades. A series of stem- and node-based definitions are provided for all major taxa traditionally recognized within the Crinoidea, including the Camerata, Disparida, Hybocrinida, Cladida, Flexibilia, and Articulata. Following recommendations proposed in recent revisions, we recognize several new clades, including the Eucamerata Cole 2017, Porocrinoidea Wright 2017, and Eucladida Wright 2017. In addition, recent phylogenetic analyses support the resurrection of two names previously abandoned in the crinoid taxonomic literature: the Pentacrinoidea Jaekel, 1918 and Inadunata Wachsmuth and Springer, 1885. Last, a phylogenetic perspective is used to inform a comprehensive revision of the traditional rank-based classification. Although an attempt was made to minimize changes to the rank-based system, numerous changes were necessary in some cases to achieve monophyly. These phylogeny-based classifications provide a useful template for paleontologists, biologists, and non-experts alike to better explore evolutionary patterns and processes with fossil and living crinoids.

scholarly journals A revised global biogeography of turtles

2015 ◽  
Author(s):  
Walter G. Joyce ◽  
Márton Rabi
Keyword(s):  
Middle Jurassic ◽  
Fossil Record ◽  
Phylogenetic Analyses ◽  
Sensu Stricto ◽  
Early History ◽  
Marine Turtles ◽  
Biogeographic History ◽  
Global Presence ◽  
History Of ◽  
Phylogenetic Hypotheses

Background. Over the course of the last decades, much effort has gone into unraveling the biogeographic history of turtles, but while much progress has been achieved in resolving post- Jurassic dispersal events, traditional phylogenetic hypotheses have yielded incongruous results in regards to the early history of the group. Methods. We re-evaluate the fossil record of turtles in context of recent phylogenetic analyses and fossil finds, including the extensive record of fragmentary but diagnostic remains. Given that near-coastal and marine turtles readily disperse across aquatic barriers, a broad set of neritic to pelagic groups were disregarded from consideration. Significant disagreement still exists among current phylogenetic hypotheses and we therefore place much effort into tracing the fossil record of unambiguously monophyletic groups. We finally employed molecular backbone constraints, given that the molecular phylogenies are more consistent with the fossil record than current, morphological phylogenies. Results. Among derived, aquatic turtles, we recognize four clades that can be traced back to discrete biogeographic centers: Paracryptodira in North America and Europe, Pan- Cryptodira in Asia, Pan-Pelomedusoides in northern Gondwanan landmasses and Pan- Chelidae in southern Gondwanan landmasses. This pattern is partially mirrored by three clades of primarily terrestrial, basal turtles: Solemydidae in North American and Europe, Sichuanchelyidae in Asia, and Meiolaniformes sensu stricto in southern Gondwanan landmasses. Although the exact interrelationships of these clades remain unclear, most can be traced back to the Middle Jurassic. Discussion. The conclusion that the two primary lineages of pleurodires and paracryptodires can be traced back to mutually exclusive land masses is not novel, but the realization that the early history of pan-cryptodires is restricted to Asia has not been realized previously, because traditional phylogenies implied an early, global presence of pan-cryptodires. The timing of the origin of the three primary clades of derived turtles (i.e., Pan-Pleurodira, Pan-Cryptodira, and Paracryptodira) correlates with the opening of the central Atlantic and the formation of the Turgai Strait in the Middle Jurassic, somewhat later than predicted by molecular calibration studies. The primary diversity of extant turtles therefore appears to have been driven by vicariance. A similar hypothesis could also be formulated for the three clades of basal turtles that survive at least into the Late Cretaceous, but given that their combined monophyly remains uncertain, it is unclear if their diversity was also driven by vicariance, or if they emulate a vicariance-like pattern. Although most groups remained within their primary geographic range throughout their evolutionary history, the dominant vicariance signal was thoroughly obfuscated by rich dispersal from littoral to marine turtles and crown cryptodires.

A new predatory leech from Vietnam (Hirudinida : Arhynchobdellida : Salifidae): its phylogenetic position with comments on the classification of the family

2015 ◽  
Vol 29 (5) ◽  
pp. 473 ◽  
Author(s):  
Takafumi Nakano ◽  
Son Truong Nguyen
Keyword(s):  
Phylogenetic Relationships ◽  
Phylogenetic Analyses ◽  
Morphological Characteristics ◽  
Molecular Data ◽  
Phylogenetic Position ◽  
12S Rrna ◽  
The Family ◽  
Morphological And Molecular Data ◽  
First Time

The family Salifidae is a predaceous leech taxon in the suborder Erpobdelliformes. Although Salifidae is widely distributed in the African, Oriental, Indo-Malayan, Sino-Japanese and Australasian regions, the phylogenetic relationships of the family Salifidae have never been tested using molecular data obtained from leeches collected from the family distributional range. A salifid species was collected for the first time in Vietnam, and relevant morphological and molecular data are presented here. Because the Vietnamese salifid species possesses unique morphological characteristics among the known salifid species, this species is herein described as a new species, Salifa motokawai, sp. nov. Phylogenetic analyses based on nuclear 18S rRNA and histone H3, as well as mitochondrial cytochrome c oxidase subunit I, tRNACys, tRNAMet, 12S rRNA, tRNAVal, 16S rRNA, tRNALeu and NADH dehydrogenase subunit 1 markers demonstrate that the Vietnamese salifid species is a close congener with the African Salifa perspicax and the Malagasy Linta be. Furthermore, molecular data revealed non-monophyly of the Asian salifid leeches. According to the observed phylogenetic relationships and morphological characteristics of the Vietnamese Salifa motokawai, sp. nov., the current classification of salifid taxa should be revised.

Phylogenetic uncertainties and sensitivity analyses in comparative biology

1996 ◽  
Vol 351 (1345) ◽  
pp. 1241-1249 ◽  
Keyword(s):  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Sensitivity Analyses ◽  
Comparative Biology ◽  
Sensitivity Tests ◽  
Alternative Hypotheses ◽  
Phylogenetic Hypotheses ◽  
Combine Information ◽  
Character Correlations

Phylogenetic comparative analyses combine information on character states and phylogenetic relationships of taxa to test hypotheses regarding character evolution. These studies encounter uncertainties at various steps, including uncertainty in the topology of phylogenetic trees, the scoring of characters, and the addition of taxa that have not explicitly been included in phylogenetic analyses. Here we highlight a variety of sensitivity tests designed to explore the robustness of comparative conclusions to changes in underlying assumptions. These include the examination of character correlations on a set of plausible phylogenetic hypotheses (including alternative rootings and ‘neighbouring’ trees), as well as under alternative character codings. TreeBASE -a prototype relational database of phylogenetic data - should prove useful in accessing alternative hypotheses.

scholarly journals Phylogenomic analyses support traditional relationships within Cnidaria

2015 ◽  
Author(s):  
Felipe Zapata ◽  
Freya E Goetz ◽  
Stephen A Smith ◽  
Mark Howison ◽  
Stefan Siebert ◽  
...  
Keyword(s):  
Molecular Evolution ◽  
Phylogenetic Relationships ◽  
Phylogenetic Analyses ◽  
Sister Group ◽  
Diverse Group ◽  
Transcriptome Data ◽  
Evolutionary Processes ◽  
Phylogenetic Hypotheses ◽  
Phylogenomic Analyses

Cnidaria, the sister group to Bilateria, is a highly diverse group of animals in terms of morphology, lifecycles, ecology, and development. How this diversity originated and evolved is not well understood because phylogenetic relationships among major cnidarian lineages are unclear, and recent studies present contrasting phylogenetic hypotheses. Here, we use transcriptome data from 15 newly-sequenced species in combination with 26 publicly available genomes and transcriptomes to assess phylogenetic relationships among major cnidarian lineages. Phylogenetic analyses using different partition schemes and models of molecular evolution, as well as topology tests for alternative phylogenetic relationships, support the monophyly of Medusozoa, Anthozoa, Octocorallia, Hydrozoa, and a clade consisting of Staurozoa, Cubozoa, and Scyphozoa. Support for the monophyly of Hexacorallia is weak due to the equivocal position of Ceriantharia. Taken together, these results further resolve deep cnidarian relationships, largely support traditional phylogenetic views on relationships, and provide a historical framework for studying the evolutionary processes involved in one of the most ancient animal radiations.

scholarly journals Phylogeny and classification of the genus-group taxa of Loxandrina (Coleoptera, Carabidae, Abacetini)

2020 ◽  
Vol 67 (2) ◽  
pp. 151-182
Author(s):  
Kipling Will
Keyword(s):  
North American ◽  
Phylogenetic Relationships ◽  
Phylogenetic Analyses ◽  
Morphological Characteristics ◽  
Historical Biogeography ◽  
North American Species ◽  
Diagnostic Features ◽  
Genus Level

Bayesian and parsimony phylogenetic analyses of combined and partitioned datasets of molecular (partial sequences of 28S, wg, COI, and CAD) and morphological (51 characters of adults) data for exemplar taxa of five outgroup and 76 ingroup abacetine carabids resulted in a monophyletic Loxandrina Erwin & Sims, 1984 that is split into Australian and American clades. The genus Loxandrus LeConte, 1853 as previously delimited is not monophyletic relative to numerous genus-level taxa in Abacetini Chaudoir, 1873 and is restricted to a subgenus of North American species. A reclassification and nomenclatural changes for the subtribe that are consistent with the phylogeny are provided. Three genera are removed from Loxandrina: Aulacopodus Britton, 1940 moved to Pterostichini Bonelli, 1810; Cosmodiscus Sloane, 1907 and Tiferonia Darlington, 1962 moved to Abacetina. Based on the phylogenetic relationships and nomenclatural priority only four genera are recognized in Loxandrina: Cerabilia Laporte, 1867, Zeodera Laporte, 1867, Pediomorphus Chaudoir, 1878, and Oxycrepis Reiche, 1843. All other previously recognized genera are treated as subgenera. The classification change created eight secondary homonyms that are resolved by the proposal of the following: Oxycrepis gebi, replacement name for O. balli (Straneo, 1993); O. amatona, replacement name for O. matoana (Straneo, 1993); O. xiproma, replacement name for O. proxima (Straneo, 1993); O. rasutulis, replacement name for O. suturalis (Straneo, 1993); O. laevinota, replacement name for O. laevicollis (Bates, 1871); O. arvulap, replacement name for O. parvula (Straneo, 1951); O. noaffine, replacement name for O. affinis (Straneo, 1991); O. alutona, replacement name for O. notula (Tschitschérine, 1901). An overview of the morphological characteristics and diagnostic features of Loxandrina taxa is provided. A key and habitus images are provided for identification of genera and subgenera. The possible historical biogeography of the group is discussed in light of their phylogenetic relationships and past geological events.

scholarly journals A Phylogenetic Investigation of the New Zealand  Pteridaceae Ferns

2021 ◽  
Author(s):  
◽  
Whitney L M Bouma
Keyword(s):  
New Zealand ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Native Species ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Taxonomic Confusion ◽  
Species Specific

<p>The fern family Pteridaceae is among the largest fern families in New Zealand. It comprises 17 native species among five genera. Traditionally the classification of Pteridaceae was based on morphological characters. The advent of molecular technology, now makes is possible to test these morphology-based classifications. The Pteridaceae has previously been subjected to phylogenetic analyses; however representatives from New Zealand and the South Pacific have never been well represented in these studies. This thesis research aimed to investigate the phylogenetic relationships of the New Zealand Pteridaceae, as well as, the phylogenetic relationships of the New Zealand species to their overseas relatives. The DNA sequences of several Chloroplast loci (e.g. trnL-trnF locus, rps4 and rps4-trnS IGS, atpB, and rbcL) were determined and the phylogenetic relationships of the New Zealand Pteridaceae and several species-specific question within the genus Pellaea and Adiantum were investigated. Results presented in this thesis confirm previously published phylogenetics of the Pteridaceae, which show the resolution of five major clades, i.e.,cryptogrammoids, ceratopteridoids, pteridoids, cheilanthoids, and the adiantoids. The addition of the New Zealand species revealed a possible South West Pacific groups formed by the respective genera, where New Zealand species were generally more related to one another than to overseas relatives. Within the New Zealand Pellaea, the analysis of the trnL-trnF locus sequence data showed that the morphologically-intermediate plants P. aff. falcata, responsible for taxonomic confusion, were more closely related to P. rotundifolia than to P. falcata. Furthermore, the species collected on the Kermadec Islands, previously thought to be P. falcata, are genetically distinct from the Australian P. falcata and they could constitute a new species. Adiantum hispidulum, which is polymorphic for two different hair types being used to distinguish them as different species, was also reinvestigated morphologically and molecularly. Morphological inspection of hairs revealed three hair types as opposed to the previous thought two, and furthermore, they correspond to three different trnL-trnF sequences haplotypes.</p>

Molecular phylogeny and divergence time estimates in pennatulaceans (Cnidaria: Octocorallia: Pennatulacea)

2020 ◽  
Vol 84 (4) ◽  
pp. 317-330
Author(s):  
Francisco J. García-Cárdenas ◽  
Mónica Núñez-Flores ◽  
Pablo J. López-González
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Morphological Characters ◽  
Nuclear Markers ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Soft Bottoms

Pennatulaceans are an important component of benthic marine communities usually related to soft bottoms. Despite their important ecological role, as yet little is known about their origin and divergence time. The first attempts to establish phylogenetic relationships among genera date from the early 20th century, when only morphological characters were available. In the last decade, phylogenetic analyses based on mitochondrial DNA sequences from a selected number of species have proposed a different hypothetical ancestor for this group, but their intergeneric relationships remain obscure. The present study is based on a combination of mitochondrial and nuclear markers (mtMutS, Cox1 and 28S rDNA), adding new molecular information about the phylogenetic relationships among the pennatulacean genera, including 38 new sequences belonging to 13 different species. Some of the phylogenetic relationships inferred in the present study question the current classification of sea pens based on morphology (at different taxonomic levels), clearly indicating that the two main groups Sessiliflorae and Subselliflorae, some of their main families (e.g. Pennatulidae, Umbellulidae, Virgulariidae) and some genera (e.g. Umbellula, Veretillum) are non-monophyletic. In addition, the veretillids, traditionally considered the most primitive pennatulaceans, are not shown as the earliest-diverging taxon. Moreover, an analysis of divergence time performed here suggested that the origin of the pennatulaceans dates from the Lower Cretaceous (Berriasian, ~144 Ma), in agreement with their sparsely known fossil record, while the initial divergence of most extant genera occurred in the Oligocene and Miocene times.

scholarly journals Early Tetrapodomorph Biogeography: Controlling for Fossil Record Bias in Macroevolutionary Analyses

2019 ◽  
Author(s):  
Jacob D. Gardner ◽  
Kevin Surya ◽  
Chris L. Organ
Keyword(s):  
Fossil Record ◽  
Regression Models ◽  
Phylogenetic Analyses ◽  
Sampling Bias ◽  
Data Sampling ◽  
Species Dispersal ◽  
Geographic Context ◽  
Adaptive Radiations ◽  
Patterns And Processes

ABSTRACTThe fossil record provides direct empirical data for understanding macroevolutionary patterns and processes. Inherent biases in the fossil record are well known to confound analyses of this data. Sampling bias proxies have been used as covariates in regression models to test for such biases. Proxies, such as formation count, are associated with paleobiodiversity, but are insufficient for explaining species dispersal owing to a lack of geographic context. Here, we develop a sampling bias proxy that incorporates geographic information and test it with a case study on early tetrapodomorph biogeography. We use recently-developed Bayesian phylogeographic models and a new supertree of early tetrapodomorphs to estimate dispersal rates and ancestral habitat locations. We find strong evidence that geographic sampling bias explains supposed radiations in dispersal rate (potential adaptive radiations). Our study highlights the necessity of accounting for geographic sampling bias in macroevolutionary and phylogenetic analyses and provides an approach to test for its effect.

scholarly journals A revised global biogeography of turtles

2015 ◽  
Author(s):  
Walter G. Joyce ◽  
Márton Rabi
Keyword(s):  
Middle Jurassic ◽  
Fossil Record ◽  
Phylogenetic Analyses ◽  
Sensu Stricto ◽  
Early History ◽  
Marine Turtles ◽  
Biogeographic History ◽  
Global Presence ◽  
History Of ◽  
Phylogenetic Hypotheses

Background. Over the course of the last decades, much effort has gone into unraveling the biogeographic history of turtles, but while much progress has been achieved in resolving post- Jurassic dispersal events, traditional phylogenetic hypotheses have yielded incongruous results in regards to the early history of the group. Methods. We re-evaluate the fossil record of turtles in context of recent phylogenetic analyses and fossil finds, including the extensive record of fragmentary but diagnostic remains. Given that near-coastal and marine turtles readily disperse across aquatic barriers, a broad set of neritic to pelagic groups were disregarded from consideration. Significant disagreement still exists among current phylogenetic hypotheses and we therefore place much effort into tracing the fossil record of unambiguously monophyletic groups. We finally employed molecular backbone constraints, given that the molecular phylogenies are more consistent with the fossil record than current, morphological phylogenies. Results. Among derived, aquatic turtles, we recognize four clades that can be traced back to discrete biogeographic centers: Paracryptodira in North America and Europe, Pan- Cryptodira in Asia, Pan-Pelomedusoides in northern Gondwanan landmasses and Pan- Chelidae in southern Gondwanan landmasses. This pattern is partially mirrored by three clades of primarily terrestrial, basal turtles: Solemydidae in North American and Europe, Sichuanchelyidae in Asia, and Meiolaniformes sensu stricto in southern Gondwanan landmasses. Although the exact interrelationships of these clades remain unclear, most can be traced back to the Middle Jurassic. Discussion. The conclusion that the two primary lineages of pleurodires and paracryptodires can be traced back to mutually exclusive land masses is not novel, but the realization that the early history of pan-cryptodires is restricted to Asia has not been realized previously, because traditional phylogenies implied an early, global presence of pan-cryptodires. The timing of the origin of the three primary clades of derived turtles (i.e., Pan-Pleurodira, Pan-Cryptodira, and Paracryptodira) correlates with the opening of the central Atlantic and the formation of the Turgai Strait in the Middle Jurassic, somewhat later than predicted by molecular calibration studies. The primary diversity of extant turtles therefore appears to have been driven by vicariance. A similar hypothesis could also be formulated for the three clades of basal turtles that survive at least into the Late Cretaceous, but given that their combined monophyly remains uncertain, it is unclear if their diversity was also driven by vicariance, or if they emulate a vicariance-like pattern. Although most groups remained within their primary geographic range throughout their evolutionary history, the dominant vicariance signal was thoroughly obfuscated by rich dispersal from littoral to marine turtles and crown cryptodires.

scholarly journals Mitochondrial DNA Phylogeny of Babblers (Timaliidae)

The Auk ◽  
2003 ◽  
Vol 120 (1) ◽  
pp. 35-54
Author(s):  
Alice Cibois
Keyword(s):  
Mitochondrial Dna ◽  
Maximum Likelihood ◽  
Molecular Phylogeny ◽  
Phylogenetic Relationships ◽  
Molecular Data ◽  
Mitochondrial Genes ◽  
Dna Phylogeny ◽  
Traditional Classification ◽  
Phylogenetic Hypotheses

Abstract The systematics of the babblers (Timaliidae) and related members of the Old World insectivorous passerines have been particularly difficult. To clarify our understanding of this group, phylogenetic relationships were constructed using sequences of three mitochondrial genes (cytochrome b, rRNA 12S and 16S). The results indicated that several species traditionally placed among babblers, the shrike babblers (Pteruthius) and the Gray-chested Thrush Babbler (Kakamega poliothorax), are not related to the Timaliidae, but belong to other passerine groups. Furthermore, the phylogenetic hypotheses inferred from molecular data suggest that the babblers assemblage includes two other oscine taxa traditionally considered to be distantly related, Sylvia (Sylviidae) and Zosterops (Zosteropidae). The polyphyly of several babbler genera is discussed, with particular attention to the laughingthrushes (genera Garrulax and Babax) for which the phylogeny is compared to previous hypotheses of relationships. Results from different tests under the maximum-parsimony and maximum-likelihood criteria indicate the rejection of the hypothesis of monophyly for the laughingthrushes group. Thus, the molecular phylogeny challenges the traditional classification of the Timaliidae.

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