scholarly journals Morphological and molecular differences between the Amphiamerican populations of Antillesoma (Sipuncula: Antillesomatidae), with the description of a new species

2019 ◽  
Vol 67 (S5) ◽  
pp. S101-S109
Author(s):  
Itzahí Silva-Morales ◽  
Mónica J. López-Aquino ◽  
Valentina Islas-Villanueva ◽  
Fernando Ruiz-Escobar ◽  
J. Rolando Bastida-Zavala
Keyword(s):  
Marine Invertebrates ◽  
Phylogenetic Reconstruction ◽  
Sister Group ◽  
Molecular Data ◽  
Sensu Stricto ◽  
Genetic Distances ◽  
Likelihood Method ◽  
Tropical Eastern Pacific ◽  
Mexican Pacific ◽  
The Caribbean

Introduction: The sipunculans are a group of marine invertebrates that have been little studied in the tropical eastern Pacific (TEP). Antillesoma antillarum is a species belonging to the monospecific family Antillesomatidae, considered widely distributed in tropical and subtropical localities across the globe. Objective: The main objective of this work was to examine the morphological and molecular differences between specimens from both coasts of tropical America to clarify the taxonomy of this species. Methods: We examined the morphology with material from the Mexican Caribbean and southern Mexican Pacific. To perform molecular analyses, two sequences of the COI molecular marker were obtained from specimens collected in Panteón Beach, Oaxaca, southern Mexican Pacific, and compared with four sequences identified as A. antillarum in GenBank, all of them from different localities. A phylogenetic reconstruction was performed with the maximum likelihood method and genetic distances were calculated with the Kimura 2P model and compared to reference values. Results: The phylogenetic analysis revealed three different lineages of Antillesoma that are well supported by bootstrap values: Antillesoma antillarum sensu stricto from the Caribbean Sea and Florida; a sister group to the one represented by our samples from the Mexican Pacific; and a third group from Thailand. Conclusion: Based on morphological traits and molecular data, Antillesoma mexicanum sp. nov. is described from the Mexican Pacific, differing from A. antillarum in the trunk papillae, color patterns and, additionally, the specimens from the Caribbean attain significantly bigger trunk sizes than the ones Pacific.

Revision of theAlpheus cristulifronsspecies complex (Crustacea: Decapoda: Alpheidae), with description of a new species from the tropical eastern Atlantic

2008 ◽  
Vol 88 (3) ◽  
pp. 543-562 ◽  
Author(s):  
Arthur Anker ◽  
Carla Hurt ◽  
Nancy Knowlton
Keyword(s):  
Gulf Of California ◽  
Molecular Data ◽  
Sensu Stricto ◽  
Eastern Pacific ◽  
Gulf Of Guinea ◽  
Western Atlantic ◽  
Sister Clade ◽  
The Caribbean ◽  
Colour Patterns ◽  
A New Species

The taxonomy of the snapping shrimpAlpheus cristulifronsRathbun, 1900, previously reported from the eastern Pacific and western and eastern Atlantic, is reviewed based on molecular data (COI), morphology and colour patterns. Three species are recognized in theA. cristulifronsspecies complex.Alpheus cristulifrons sensu strictois restricted to the western Atlantic, ranging from Florida and the Caribbean Sea to southern Brazil. The eastern PacificA. cristulifrons sensuKim & Abele, 1988 corresponds toA. utriensisRamos & Von Prahl, 1989, ranging from the Gulf of California to Colombia; this species can be separated fromA. cristulifronsby the absence of balaeniceps setae on the male minor chela and the presence of bands on the antennular and antennal flagella. The eastern AtlanticA. cristulifronssensuCrosnier & Forest, 1966 is described asA. xanthocarpussp. nov. based on recently collected material from the island of São Tomé in the Gulf of Guinea; this species differs fromA. cristulifronsby the posteriorly more extending rostral carina and the presence of conspicuous yellow spots on the carpus and chela of the second pereiopod. Molecular data suggest thatA. utriensisis the eastern Pacific sister clade to the amphi-Atlntic clade that includesA. cristulifronsandA. xanthocarpussp. nov.

Phylogenetic patterns and diversification in the caesalpinioid legumesThis paper is one of a selection of papers published in the Special Issue on Systematics Research.

Botany ◽  
2008 ◽  
Vol 86 (7) ◽  
pp. 697-718 ◽  
Author(s):  
Anne Bruneau ◽  
Marjorie Mercure ◽  
Gwilym P. Lewis ◽  
Patrick S. Herendeen
Keyword(s):  
Cross Validation ◽  
Phylogenetic Analyses ◽  
Sister Group ◽  
Molecular Data ◽  
Likelihood Method ◽  
Matk Gene ◽  
Penalised Likelihood ◽  
Chloroplast Dna Evolution ◽  
Selection Of ◽  
Age Estimates

Subfamily Caesalpinioideae is a paraphyletic grade of 171 genera that comprises the first branches of the Leguminosae and from which are derived the monophyletic subfamilies Mimosoideae and Papilionoideae. We have sequenced the chloroplast matK gene, and the trnL and 3′-trnK introns for 153 genera of caesalpinioid legumes. Parsimony and Bayesian phylogenetic analyses of these data support the monophyly of several major groups within the caesalpinioid legumes: the Cercideae, Detarieae, Detarieae s. str., Prioria , Amherstieae, Dialiinae, Cassia , Caesalpinia , Peltophorum , and Tachigali clades. Relationships among the first branching lineages of the legumes are not well supported, with Cercideae, Detarieae, and the genus Duparquetia alternatively resolved as sister group to all of the legumes. The division of certain large genera (e.g., Caesalpinia s. l., Bauhinia s. l.) into segregate genera generally is supported by our molecular data. Using 18 well-documented fossils as calibration points, fixing the stem node of the legumes at 65 Ma, and using the Penalised Likelihood method, we estimate the crown node of the Leguminosae at 64 Ma and the crown age of each of the major caesalpinioid lineages varying from 34 to 56 Ma. Fossil cross-validation suggests that none of the 18 fossil calibrations is internally inconsistent. Analyses done without fossil calibrations yield much younger divergence times. The age estimates for the Detarieae clade are more sensitive to the presence of calibration points than other caesalpinioid clades, a situation which we attribute to the slow rate of chloroplast DNA evolution in this group.

Redescriptions of Eunice filamentosa and E. denticulata and description of E. tovarae n. sp. (Polychaeta: Eunicidae), highlighted with morphological and molecular data

Zootaxa ◽  
2011 ◽  
Vol 2880 (1) ◽  
pp. 51 ◽  
Author(s):  
LUIS F. CARRERA-PARRA ◽  
SERGIO I. SALAZAR-VALLEJO
Keyword(s):  
Genetic Divergence ◽  
Sequence Variation ◽  
Molecular Data ◽  
Morphological Data ◽  
Valid Species ◽  
Caribbean Region ◽  
Tropical Eastern Pacific ◽  
Mexican Pacific ◽  
Nucleotide Sequence Variation ◽  
Morphological And Molecular Data

In a series of studies on eunicids, three Grand Caribbean species Eunice filamentosa, E. denticulata, and E. conglomerans were regarded as synonyms, or part of a species complex with an amphiamerican distribution. The revision of type and additional materials collected in the Grand Caribbean Region (GCR) and along the Mexican Pacific coasts, allowed us to clarify that E. conglomerans is a junior synonym of E. denticulata. Thus, E. filamentosa and E. denticulata are valid species in the GCR; while the specimens from the Tropical Eastern Pacific belong to a newly described species, E. tovarae n.sp. Herein we describe these three species, and some morphological features described in previous studies are reevaluated. Additionally, we found an important genetic divergence in nucleotide sequence variation of COI, which supported the morphological data. E. filamentosa and E. denticulata have a genetic divergence of 19.6%; whereas E. tovarae n. sp. has a genetic divergence of 20.7% from E. denticulata, and a 12.9% divergence from E. filamentosa.

scholarly journals Less is more stable: arguing for few names in turtle’s taxonomy

2015 ◽  
Author(s):  
Pedro S. R. Romano
Keyword(s):  
Phylogenetic Reconstruction ◽  
Sister Group ◽  
Sensu Stricto ◽  
Botanical Nomenclature ◽  
Crown Group ◽  
Diagnostic Characters ◽  
Less Is More ◽  
Phylogenetic Reconstructions ◽  
Stem Species ◽  
Phylogenetic Nomenclature

Background. Beyond the International Codes of Zoological (ICZN) and Botanical Nomenclature and the PhyloCode, there is an alternative taxonomic system for phylogenetic systematics proposed. This phylogenetic nomenclature suggests the elimination of suprageneric names and the use of negative indexes instead of it. This system of nomenclature has a basic principle to identify clades: the presence of nominal heterobathmy, which is analogous to Hennig's "heterobathmy of characters", but applied to taxa names. Here I argue for an extensive use of heterobathmy as basic criteria to determinate “good” nodes to identify higher level taxa names. Methods. I used a previews published dataset (doi:10.5061/dryad.f2h6r) and ran several searches for Most Parsimonious Trees (MPT) using different search algorithms and assumptions in TNT. After that, I compared the results of different searches, mapped the characters transformations, and calculate the Bremer supports. The results were then compared with the current taxonomy proposed for Pelomedusoides, with emphasis on Bothremydidae. Results. The remarkable divergences with the current taxonomy of Bothremydidae are: (1) Kurmademydini and Bothremydini need to be redefined; (2) Cearachelyini and Galianemys lack diagnostic characters and, therefore, are not monophyletic; and (3) Bothremydidae do not possess common diagnostic characters in all MPT, thus, lacks a well supported heterobathmy with its sister-group, Podocnemidinura (=Pan-Podocnemididae). Moreover, the Infrafamily Bothremydodda has Bremer support of 3. However, given that all bothremydids are extinct, it is impossible to define a panstem clade based on a crown group. The result is an unstable nomenclature with more names than necessary. Discussion. The use of heterobathmy is a center point in Hennig's argumentation for phylogenetic reconstruction. Indeed, it implies the zero length collapsing rule applied to cladistic reconstruction (which is the TNT default option). Nonetheless, ambiguous characters or several equal MPT can imply on phylogenetic reconstructions that lack a consistent heterobathmy (i.e.: a common diagnostic character in the ancestor eidophoront of a given node in all MPT; as is the case of Bothremydidae). A possible solution is to use the suffix “formes” to designate extinct lineages with stem-species when some nodes are not well supported in a given phylogeny. In the example presented here, it would consist on naming ICZN’s Bothremydodda as “Bothremydidae” (sensu stricto) and ICZN’s Bothremydidae (sensu lato, i.e.: including stem-Bothremydidae) as “Bothremydidiformes” and avoid naming each node of the consensus tree unless it has high Bremer support. By taking into account this delimitation criterion, we can propose a more stable and clean taxonomy.

Molecular data sheds light on the classification of long-legged flies (Diptera:Dolichopodidae)

2011 ◽  
Vol 25 (4) ◽  
pp. 303 ◽  
Author(s):  
Christoph Germann ◽  
Corinne Wimmer ◽  
Marco Valerio Bernasconi
Keyword(s):  
New World ◽  
Sister Group ◽  
Molecular Data ◽  
Sensu Stricto ◽  
Nuclear Marker ◽  
Mitochondrial Markers ◽  
Traditional Classification ◽  
Molecular Phylogenetic ◽  
Early Radiation

Dolichopodidae (long-legged flies) is the world’s fourth largest dipteran family, but a phylogeny based on a broad global taxon sample is still lacking. We present here a first molecular phylogenetic hypothesis for Dolichopodidae, based on 157 dolichopodid species in 68 genera and 15 subfamilies from the Old and New World, and seven empidoid species (Empididae, Hybotidae) as outgroups. Both relatively fast-evolving mitochondrial markers (COI, 12S, 16S) and a more conserved nuclear marker (18S) were used, the latter being widely employed to study the phylogeny at higher taxonomic levels. We present strong evidence for Microphorinae as sister group to Dolichopodidae sensu stricto, and for the monophyletic Parathalassiinae as part of Dolichopodidae sensu stricto. Monophyly of Achalcinae, Dolichopodinae, and Sciapodinae is supported and Stolidosomatinae are placed within Sympycninae. Diaphorinae, Medeterinae, Neurigoninae, Rhaphiinae, and Sympycninae are paraphyletic, and Hydrophorinae and Peloropeodinae polyphyletic. Our broad taxon sample allows us to gain new insights into the complex systematics of Dolichopodidae. Our results highlight several problems with the traditional classification, which have considerable consequences for the systematic status of some taxa. The poor resolution observed in deep divergences supports previous hypotheses suggesting a rapid early radiation of Dolichopodidae.

scholarly journals Taxonomic revision and phylogenetic position of the flying squirrel genus Biswamoyopterus (Mammalia, Rodentia, Sciuridae, Pteromyini) on the northern Indo-China peninsula

ZooKeys ◽  
2020 ◽  
Vol 939 ◽  
pp. 65-85
Author(s):  
Guogang Li ◽  
Ye Htet Lwin ◽  
Bin Yang ◽  
Tao Qin ◽  
Phouthong Phothisath ◽  
...  
Keyword(s):  
Nuclear Dna ◽  
Phylogenetic Analyses ◽  
Morphological Characteristics ◽  
Taxonomic Revision ◽  
Sister Group ◽  
Molecular Data ◽  
Genetic Distances ◽  
Phylogenetic Position ◽  
Flying Squirrel ◽  
Two Samples

The flying squirrel genus Biswamoyopterus (Rodentia: Sciuridae: Pteromyini) was once considered to contain three species, Biswamoyopterus biswasi from northeastern India, B. laoensis from central Laos and B. gaoligongensis from southwest China, all identified from morphological characteristics of one or two specimens. However, based on similar morphological characteristics of two samples of the genus Biswamoyopterus collected recently from northern Laos and northern Myanmar, and the small genetic distances on mitochondrial DNA and nuclear DNA between them, the results strongly support these two samples as representatives of the same species. The phylogenetic analyses strongly support Biswamoyopterus as an independent genus of Pteromyini, as a sister group to Aeromys. Biswamoyopterus biswasi is distributed in the northern Indo-China peninsula, where it is exposed to a series of threats, such as intense hunting activity, illegal trade, and rapid habitat loss; this should warrant its classification as critically endangered according to the International Union for Conservation of Nature (IUCN) Red List criteria. Here, the molecular data for genus Biswamoyopterus and two new specimen records from northern Laos and northern Myanmar are presented.

scholarly journals Phylogenetic relationships of heteroscleromorph demosponges and the affinity of the genus Myceliospongia (Demospongiae incertae sedis)

2019 ◽  
Author(s):  
Dennis V. Lavrov ◽  
Manuel Maldonado ◽  
Thierry Perez ◽  
Christine Morrow
Keyword(s):  
Molecular Clock ◽  
Phylogenetic Relationships ◽  
Sister Group ◽  
Molecular Data ◽  
Sensu Stricto ◽  
Rrna Genes ◽  
Phylogenetic Position ◽  
Incertae Sedis ◽  
Middle Paleozoic ◽  
Clade 1

AbstractClass Demospongiae – the largest in the phylum Porifera (Sponges) – encompasses 7,581 accepted species across the three recognized subclasses: Keratosa, Verongimorpha, and Heteroscleromorpha. The latter subclass contains the majority of demosponge species and was previously subdivided into subclasses Heteroscleromorpha sensu stricto and Haploscleromorpha. The current classification of demosponges is the result of nearly three decades of molecular studies that culminated in a formal proposal of a revised taxonomy (Morrow and Cardenas, 2015). However, because most of the molecular work utilized partial sequences of nuclear rRNA genes, this classification scheme needs to be tested by additional molecular markers. Here we used sequences and gene order data from complete or nearly complete mitochondrial genomes of 117 demosponges (including 60 new sequences determined for this study and 6 assembled from public sources) and three additional partial mt-genomes to test the phylogenetic relationships within demosponges in general and Heteroscleromorpha sensu stricto in particular. We also investigated the phylogenetic position of Myceliospongia araneosa – a highly unusual demosponge without spicules and spongin fibers, currently classified as Demospongiae incertae sedis.Our results support the sub-class relationship within demosponges and reveal four main clades in Heteroscleromorpha sensu stricto: Clade 1 composed of Spongillida, Sphaerocladina, and Scopalinida; Clade 2 composed of Axinellida, Biemnida, Bubarida; Clade 3 composed of Tetractinellida and “Rhizomorina” lithistids; and Clade 4 composed of Agelasida, Polymastida, Clionaida, Suberitida, Poecilosclerida, and Tethyida. The four clades appear to be natural lineages that unite previously defined taxonomic orders. Therefore, if those clades are to be systematically interpreted, they will have the rank of superorders (hence S1-S4). We inferred the following relationships among the newly defined clades: (S1(S2(S3+S4))). Analysis of molecular data from Myceliospongia araneosa – first from this species/genus – placed it in S3 as a sister group to Microscleroderma sp. and Leiodermatium sp. (“Rhizomorina”).Molecular clock analysis indicated that the origin of the Heteroscleromorpha sensu stricto as well as the basal split in this group between S1 and the rest of the superorder go back to Cambrian, while the divergences among the three other superorders occurred in Ordovician (with the 95% standard variation from Late Cambrian to Early Silurian). Furthermore most of the proposed orders within Heteroscleromorpha appear to have middle Paleozoic origin, while crown groups within order date mostly to Paleozoic to Mesozoic transition. We propose that these molecular clock estimates can be used to readjust ranks for some of the higher taxa within Heteroscleromorpha.In addition to phylogenetic information, we found several unusual mtgenomic features among the sampled species, broadening our understanding of mitochondrial genome evolution in this group and animals in general. In particular, we found mitochondrial introns within cox2 (first in animals) and rnl (first in sponges).

scholarly journals The phylogeny and taxonomic status of the Chlorocystini (sensu stricto) (Homoptera, Tibicinidae)

1995 ◽  
Vol 65 (4) ◽  
pp. 201-231 ◽  
Author(s):  
A.J. de Boer
Keyword(s):  
Computer Program ◽  
Computer Analysis ◽  
Phylogenetic Reconstruction ◽  
Taxonomic Status ◽  
Sister Group ◽  
Sensu Stricto ◽  
Complete Data ◽  
Data Matrix ◽  
A Posteriori

The “Baeturia and related genera complex”, as defined earlier (De Boer, 1990) by shared aedeagal characters, is identified as the tribe Chlorocystini (sensu stricto). The Prasiini (sensu stricto) are identified as the sister group of the Chlorocystini (sensu stricto), while the genus Muda is recognized as the nearest outgroup. The phylogeny and biogeography of the sister group and outgroup is briefly discussed. Baeturia kuroiwae Matsumura is transferred to the genus Muda. A phylogenetic reconstruction of all 147 species of the Chlorocystini (sensu stricto) is presented, based on 154 characters and 409 character states. The computer program PAUP 3.1.1 (Swofford, 1993) was used for analysing the data; the genera Prasia and Muda were used as outgroups in this analysis. The results obtained from the computer analysis were slightly modified a posteriori, favouring some presumably phylogenetically important characters over strongly fluctuating ones. These final modifications were carried out with the aid of the computer program MacClade 3.0 (Maddison & Maddison, 1992). A complete data matrix and a list of characters and character states are given in an appendix; for descriptions and illustrations of these characters one is referred to previous publications.

scholarly journals About the specific status of Baiomys musculus and B. brunneus

Therya ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 291-301
Author(s):  
Giovani Hernández-Canchola ◽  
Livia León Paniagua
Keyword(s):  
Molecular Data ◽  
Genetic Distances ◽  
Central American ◽  
Complex Topography ◽  
Future Studies ◽  
Western Mexico ◽  
Geographic Boundaries ◽  
The Caribbean ◽  
Tropical Lowlands ◽  
Arid And Semiarid

The southern pygmy mouse, Baiomys musculus, is distributed in arid and semiarid lowlands, from southern Nayarit and central Veracruz in México to northwestern Nicaragua, excluding the Yucatán Peninsula and the Caribbean tropical lowlands.  Previous reports suggest that B. musculus includes two clades that may be eligible for specific status, although this remains uncertain.  We used mitochondrial DNA (cytochrome b) and morphometric data to test whether two lineages exist within the species.  Molecular data support the existence of two monophyletic groups with genetic distances of 6.69 % between them: clade I, a western clade found in Colima, Jalisco, and Michoacán; and clade II, an eastern clade found in Guerrero, Morelos, Oaxaca, and Veracruz.  Morphologically, clade I individuals are larger than clade II.  Moreover, these clades seem to be allopatric, and their geographic boundaries are located in the complex topography of western México.  Examination of previous reviews in addition to the data from this study suggest that it may be appropriate to recognize each clade as a species: clade I as B. musculus (Merriam, 1892) and clade II as B. brunneus (Allen and Chapman, 1897).  Future studies with nuclear or genomic data, including Central American populations, would verify this taxonomic hypothesis.

scholarly journals Less is more stable: arguing for few names in turtle’s taxonomy

2015 ◽  
Author(s):  
Pedro S. R. Romano
Keyword(s):  
Phylogenetic Reconstruction ◽  
Sister Group ◽  
Sensu Stricto ◽  
Botanical Nomenclature ◽  
Crown Group ◽  
Diagnostic Characters ◽  
Less Is More ◽  
Phylogenetic Reconstructions ◽  
Stem Species ◽  
Phylogenetic Nomenclature

Background. Beyond the International Codes of Zoological (ICZN) and Botanical Nomenclature and the PhyloCode, there is an alternative taxonomic system for phylogenetic systematics proposed. This phylogenetic nomenclature suggests the elimination of suprageneric names and the use of negative indexes instead of it. This system of nomenclature has a basic principle to identify clades: the presence of nominal heterobathmy, which is analogous to Hennig's "heterobathmy of characters", but applied to taxa names. Here I argue for an extensive use of heterobathmy as basic criteria to determinate “good” nodes to identify higher level taxa names. Methods. I used a previews published dataset (doi:10.5061/dryad.f2h6r) and ran several searches for Most Parsimonious Trees (MPT) using different search algorithms and assumptions in TNT. After that, I compared the results of different searches, mapped the characters transformations, and calculate the Bremer supports. The results were then compared with the current taxonomy proposed for Pelomedusoides, with emphasis on Bothremydidae. Results. The remarkable divergences with the current taxonomy of Bothremydidae are: (1) Kurmademydini and Bothremydini need to be redefined; (2) Cearachelyini and Galianemys lack diagnostic characters and, therefore, are not monophyletic; and (3) Bothremydidae do not possess common diagnostic characters in all MPT, thus, lacks a well supported heterobathmy with its sister-group, Podocnemidinura (=Pan-Podocnemididae). Moreover, the Infrafamily Bothremydodda has Bremer support of 3. However, given that all bothremydids are extinct, it is impossible to define a panstem clade based on a crown group. The result is an unstable nomenclature with more names than necessary. Discussion. The use of heterobathmy is a center point in Hennig's argumentation for phylogenetic reconstruction. Indeed, it implies the zero length collapsing rule applied to cladistic reconstruction (which is the TNT default option). Nonetheless, ambiguous characters or several equal MPT can imply on phylogenetic reconstructions that lack a consistent heterobathmy (i.e.: a common diagnostic character in the ancestor eidophoront of a given node in all MPT; as is the case of Bothremydidae). A possible solution is to use the suffix “formes” to designate extinct lineages with stem-species when some nodes are not well supported in a given phylogeny. In the example presented here, it would consist on naming ICZN’s Bothremydodda as “Bothremydidae” (sensu stricto) and ICZN’s Bothremydidae (sensu lato, i.e.: including stem-Bothremydidae) as “Bothremydidiformes” and avoid naming each node of the consensus tree unless it has high Bremer support. By taking into account this delimitation criterion, we can propose a more stable and clean taxonomy.

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