A nine-family classification of caecilians (Amphibia: Gymnophiona)

Zootaxa ◽  
2011 ◽  
Vol 2874 (1) ◽  
pp. 41 ◽  
Author(s):  
MARK WILKINSON ◽  
DIEGO SAN MAURO ◽  
EMMA SHERRATT ◽  
DAVID J. GOWER
Keyword(s):  
Phylogenetic Relationships ◽  
Phylogenetic Analyses ◽  
Current Understanding ◽  
Taxon Sampling ◽  
New Family ◽  
Family Level ◽  
Family Classification

We propose a new family-level classification of caecilians that is based on current understanding of phylogenetic relationships and diversity. The 34 currently recognised genera of caecilians are diagnosed and partitioned into nine family-level taxa. Each family is an hypothesised monophylum, that, subject to limitations of taxon sampling, is well-supported by phylogenetic analyses and is of ancient (Mesozoic) origin. Each family is diagnosed and also defined phylogenetically. The proposed classification provides an alternative to an exclusive reliance upon synonymy in solving the longstanding problem of paraphyly of the Caeciliidae.

scholarly journals A revised classification of the fluvicoline tyrant flycatchers (Passeriformes, Tyrannidae, Fluvicolinae)

Zootaxa ◽  
2020 ◽  
Vol 4747 (1) ◽  
pp. 167-176 ◽  
Author(s):  
JAN I. OHLSON ◽  
MARTIN IRESTEDT ◽  
HENRIQUE BATALHA FILHO ◽  
PER G. P. ERICSON ◽  
JON FJELDSÅ
Keyword(s):  
Phylogenetic Relationships ◽  
New World ◽  
Current Understanding ◽  
New Classification ◽  
New Family ◽  
Family Level ◽  
Tyrant Flycatchers

A new classification is proposed for the subfamily Fluvicolinae in the New World Flycatchers (Tyrannidae), based on the results of a previously published phylogeny including more than 90% of the species. In this classification we propose one new family level name (Ochthoecini) and one new generic name (Scotomyias). We also resurrect three genera (Heteroxolmis, Pyrope and Nengetus) and subsume five (Tumbezia, Lathrotriccus, Polioxolmis, Neoxolmis and Myiotheretes) into other genera to align the classification with the current understanding of phylogenetic relationships in Fluvicolinae. 

Back to the Future? Molecules Take Us Back to the 1925 Classification of the Lembophyllaceae (Bryopsida)

2009 ◽  
Vol 34 (3) ◽  
pp. 443-454 ◽  
Author(s):  
Dietmar Quandt ◽  
Sanna Huttunen ◽  
Ray Tangney ◽  
Michael Stech
Keyword(s):  
Single Species ◽  
Molecular Data ◽  
Nuclear Ribosomal Dna ◽  
New Family ◽  
Morphological Studies ◽  
The Family ◽  
Family Level ◽  
Plastid Markers ◽  
Pleurocarpous Moss

Although the Lembophyllaceae has undergone considerable revision during the last century, the generic and familial level relationships of this pleurocarpous moss family are still poorly understood. To address this problem, a generic revision of the Lembophyllaceae based on molecular data was undertaken. We analyzed two plastid markers, the trnL-trnF and the psbT-psbH region in combination with the ITS2 of nuclear ribosomal DNA. The molecular data reveal that the current circumscription of the family is too narrow and that several genera previously placed in the Lembophyllaceae should be reincluded. The family includes: Bestia, Camptochaete, Dolichomitra, Dolichomitriopsis, Fallaciella, Fifea, Isothecium, Lembophyllum, Looseria stat. nov., Pilotrichella, Rigodium, Tripterocladium, and Weymouthia. Looseria contains a single species: Looseria orbiculata comb. nov. Acrocladium is excluded and provisionally accommodated in the Lepyrodontaceae. Generic limits supported by the molecular data support a return to the early twentieth century family concept of Brotherus. The analyses indicate that the segregate genus Orthostichella is distinct from its parent genus Pilotrichella, probably at the family level. Whereas Pilotrichella is resolved within the Lembophyllaceae, Orthostichella clusters with Porotrichum and Porothamnium forming a clade (OPP-clade) sister to the remaining Neckeraceae and Lembophyllaceae. Hence, the Neckeraceae is paraphyletic. Recognition of the OPP-clade as a new family is desirable but awaits the results of detailed ongoing morphological studies.

Phylogeny and classification of the New World suboscines (Aves, Passeriformes)

Zootaxa ◽  
2013 ◽  
Vol 3613 (1) ◽  
pp. 1-35 ◽  
Author(s):  
JAN I. OHLSON ◽  
MARTIN IRESTEDT ◽  
PER G. P. ERICSON ◽  
JON FJELDSÅ
Keyword(s):  
Molecular Markers ◽  
Phylogenetic Relationships ◽  
New World ◽  
Remarkable Difference ◽  
Phylogenetic Hypothesis ◽  
New Family ◽  
Climatic Optimum

Here we present a phylogenetic hypothesis for the New World suboscine radiation, based on a dataset comprising of 219 terminal taxa and five nuclear molecular markers (ca. 6300 bp). We also estimate ages of the main clades in this radiation. This study corroborates many of the recent insights into the phylogenetic relationships of New World suboscines. It further clarifies a number of cases for which previous studies have been inconclusive, such as the relationships of Conopophagidae, Melanopareiidae and Tityridae. We find a remarkable difference in age of the initial divergence events in Furnariida and Tyrannida. The deepest branches in Furnariida are of Eocene age, whereas the extant lineages of Tyrannida have their origin in the Oligocene. Approximately half of the New World suboscine species are harboured in 5 large clades that started to diversify around the Mid Miocene Climatic Optimum (16–12 Mya). Based on our phylogenetic results we propose a revised classification of the New World suboscines. We also erect new family or subfamily level taxa for four small and isolated clades: Berlepschiinae, Pipritidae, Tachurididae and Muscigrallinae.

Delving deeper into the phylogenetics of the herbaceous bamboos (Poaceae, Bambusoideae, Olyreae): evaluation of generic boundaries within the Parodiolyra/Raddiella clade uncovers a new genus

2019 ◽  
Vol 192 (1) ◽  
pp. 61-81 ◽  
Author(s):  
Iasmin L C Oliveira ◽  
Andreza O Matos ◽  
Christian Silva ◽  
Maria Luiza S Carvalho ◽  
Christopher D Tyrrell ◽  
...  
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Phylogenetic Relationships ◽  
New Genus ◽  
Phylogenetic Analyses ◽  
Taxonomic Status ◽  
Morphological Evidence ◽  
Taxon Sampling ◽  
Plastid Genomes ◽  
Herbaceous Bamboos

Abstract The present study aims to expand the knowledge of phylogenetic relationships in Olyrinae, a subtribe of herbaceous bamboos (Poaceae: Bambusoideae: Olyreae). Our focus is on Parodiolyra and Raddiella, two historically related genera that, with their sister Diandrolyra, form one of the four main lineages in the subtribe. Previous phylogenetic analyses suggested that Parodiolyra is not monophyletic, but its taxonomic boundaries and its relationship with Raddiella remain uncertain due to low sampling. We increased the taxon sampling and sequenced five regions of the nuclear and plastid genomes for this lineage and other representatives of Olyreae. We used maximum parsimony, maximum likelihood, Bayesian inference and coalescence analysis. Our results corroborate the paraphyly of Parodiolyra, with P. micrantha sister to a clade including the remaining Parodiolyra and Raddiella. All remaining Parodiolyra form a well-supported clade, but Raddiella had conflicting resolutions, being either monophyletic or not. Thus, based on phylogenetic and morphological evidence, we here recircumscribe Parodiolyra, transferring P. micrantha and P. colombiensis to the new genus Taquara (described here). Regarding Raddiella, sampling is still not comprehensive and does not allow a decision on to its taxonomic status to be made at this time. Inclusion of other phreatophytic species may be crucial to resolve the problem of conflicting topologies.

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.

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.

Phylogenetics of scolopendromorph centipedes: can denser taxon sampling improve an artificial classification?

2013 ◽  
Vol 27 (5) ◽  
pp. 578 ◽  
Author(s):  
Varpu Vahtera ◽  
Gregory D. Edgecombe ◽  
Gonzalo Giribet
Keyword(s):  
Bayesian Inference ◽  
New World ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Taxon Sampling ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Multiple Sequence Alignments ◽  
Artificial Classification

Previous phylogenetic analyses of the centipede order Scolopendromorpha indicated a fundamental division into blind and ocellate clades. These analyses corroborated the monophyly of most families and tribes but suggested that several species-rich, cosmopolitan genera in traditional and current classifications are polyphyletic. Denser taxon sampling is applied to a dataset of 122 morphological characters and sequences for four nuclear and mitochondrial loci. Phylogenetic analyses including 98 species and subspecies of Scolopendromorpha employ parsimony under dynamic and static homology schemes as well as maximum likelihood and Bayesian inference of multiple sequence alignments. The monotypic Australian genera Notiasemus and Kanparka nest within Cormocephalus and Scolopendra, respectively, and the New Caledonian Campylostigmus is likewise a clade within Cormocephalus. New World Scolopendra are more closely related to Hemiscolopendra and Arthrorhabdus than to Scolopendra s.s., which is instead closely allied to Asanada; the tribe Asanadini nests within Scolopendrini for molecular and combined datasets. The generic classification of Otostigmini has a poor fit to phylogenetic relationships, although nodal support within this tribe is weak. New synonymies are proposed for Ectonocryptopinae Shelley & Mercurio, 2005 (= Newportiinae Pocock, 1896), Asanadini Verhoeff, 1907 (= Scolopendrini Leach, 1814), and Kanparka Waldock & Edgecombe, 2012 (= Scolopendra Linnaeus, 1758). Scolopendrid systematics largely depicts incongruence between phylogeny and classification rather than between morphology and molecules.

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.

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