scholarly journals Distribution of Endogenous Retroviruses in Crocodilians

2009 ◽  
Vol 83 (19) ◽  
pp. 10305-10308 ◽  
Author(s):  
Weerachai Jaratlerdsiri ◽  
Clara J. Rodríguez-Zárate ◽  
Sally R. Isberg ◽  
Chandramaya Siska Damayanti ◽  
Lee G. Miles ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Sister Group ◽  
Endogenous Retroviruses ◽  
Future Studies ◽  
Extant Species

ABSTRACT Knowledge of endogenous retroviruses (ERVs) in crocodilians (Crocodylia) is limited, and their distribution among extant species is unclear. Here we analyzed the phylogenetic relationships of these retroelements in 20 species of crocodilians by studying the pro-pol gene. The results showed that crocodilian ERVs (CERVs) cluster into two major clades (CERV 1 and CERV 2). CERV 1 clustered as a sister group of the genus Gammaretrovirus, while CERV 2 clustered distantly with respect to all known ERVs. Interestingly, CERV 1 was found only in crocodiles (Crocodylidae). The data generated here could assist future studies aimed at identifying orthologous and paralogous ERVs among crocodilians.

A new species of Protopsychoda Azar et al., 1999 from the Lower Cretaceous Lebanese amber (Diptera: Psychodidae)

2020 ◽  
Vol 3 (4) ◽  
pp. 352-356
Author(s):  
DANY AZAR ◽  
SIBELLE MAKSOUD
Keyword(s):  
New Species ◽  
Phylogenetic Relationships ◽  
Lower Cretaceous ◽  
Large Family ◽  
Sister Group ◽  
Sister Group Relationship ◽  
Separate Family ◽  
Extant Species ◽  
A New Species

Psychodidae Newman, 1834 is a large family of small, hairy nematoceran dipterans, comprising more than 2,600 described extant species. It is currently subdivided into seven subfamilies: Bruchomyiinae Alexander, 1920, Horaiellinae Enderlein, 1936, Phlebotominae Rondani, 1840, Psychodinae Newman, 1834, Sycoracinae Jung, 1954, Trichomyiinae Tonnoir, 1922, and the fossil subfamily Protopsychodinae Stebner et al., 2015. Some authors consider the group to consist of two families, i.e., Psychodidae and Phlebotomidae (Williams, 1993; Azar et al., 1999). This fact is founded only on the hematophagous and medically important aspects of the phlebotomines, nevertheless this arrangement is unfounded, because the phylogenetic relationships between the psychodid subfamilies remain unresolved, even if there is a possible sister-group relationship between the Phlebotominae and Psychodinae (Curler & Moulton, 2012). We consider recognizing phlebotomines as a separate family would necessitate also giving separate familial status to all the currently recognized subfamilies, which is not adopted here.

Review of Eohiodon (Teleostei: Osteoglossomorpha) from western North America, with a phylogenetic reassessment of Hiodontidae

1997 ◽  
Vol 71 (6) ◽  
pp. 1109-1124 ◽  
Author(s):  
Li Guo-Qing ◽  
Mark V. H. Wilson ◽  
Lance Grande
Keyword(s):  
North America ◽  
Sister Group ◽  
Sensu Stricto ◽  
Valid Species ◽  
Western North America ◽  
Extant Species ◽  
The Family ◽  
Fossil Records ◽  
Fossil Genus ◽  
Freshwater Teleosts

Review of recently collected material of Eohiodon from North America suggests that there are two valid species, E. rosei (Hussakof) and E. woodroffi Wilson. Eohiodon falcatus Grande is identical to E. woodruffi in known skeletal features and nearly all meristic features and is treated as a junior synonym of the latter. The fossil genus Eohiodon Cavender differs from Hiodon Lesueur, which is known from both fossil and extant species, in numerous meristic and osteological features. The caudal skeleton in Eohiodon is nearly identical to that in Hiodon.The traditionally accepted Notopteroidei, containing Lycopteridae, Hiodontidae, and Notopteridae, is a polypheletic group. The Asian fossil family Lycopteridae is not more closely related to Hiodontidae than it is to other taxa in the Osteoglossomorpha, but is sister to all other Osteoglossomorpha. The Hiodontiformes sensu stricto, including only the family Hiodontidae, is the sister-group of the Osteoglossiformes. This family is not more closely related to notopterids than to other taxa in Osteoglossiformes. The Notopteridae are most closely related to the Mormyroidea; together they and the fossil family Ostariostomidae constitute the sister-group of the Osteoglossoidei.Fossil records of Hiodontiformes sensu stricto and Notopteroidei indicate a widespread pre-Neogene biogeographic range of these freshwater teleosts, suggesting that extinction must have been involved in the Cenozoic evolution of these two osteoglossomorph sublineages.

Phylogenetic relationships in the monocot order Commelinales, with a focus on PhilydraceaeThis paper is one of a selection of papers published in the Special Issue on Systematics Research.

Botany ◽  
2008 ◽  
Vol 86 (7) ◽  
pp. 719-731 ◽  
Author(s):  
Jeffery M. Saarela ◽  
Peter J. Prentis ◽  
Hardeep S. Rai ◽  
Sean W. Graham
Keyword(s):  
Phylogenetic Relationships ◽  
Strong Support ◽  
Sister Group ◽  
Higher Order ◽  
Special Issue ◽  
Likelihood Methods ◽  
The Family ◽  
Selection Of

To characterize higher-order phylogenetic relationships among the five families of Commelinales, we surveyed multiple plastid loci from exemplar taxa sampled broadly from the order, and from other major monocot lineages. Phylogenetic inferences in Commelinales using parsimony and likelihood methods are congruent, and we find strong support for most aspects of higher-order relationship in the order. We obtain moderately strong support for the local placement of Philydraceae, a family whose position has proven particularly difficult to infer in previous studies. Commelinaceae and Hanguanaceae are sister taxa, and together they are the sister group of a clade consisting of Haemodoraceae, Philydraceae, and Pontederiaceae; Haemodoraceae and Pontederiaceae are also sister taxa. Our sampling of Philydraceae includes all three or four genera in the family; we identify Philydrella as the sister group of a Helmholtzia–Philydrum clade, a resolution that is potentially consistent with several aspects of morphology.

scholarly journals Taxonomic revision and phylogenetic relationships of Dasyloricaria Isbrücker & Nijssen, 1979 (Siluriformes: Loricariidae), with description of a new species

2016 ◽  
Vol 14 (1) ◽  
Author(s):  
Alejandro Londoño-Burbano ◽  
Roberto E. Reis
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Phylogenetic Relationships ◽  
Taxonomic Revision ◽  
Sister Group ◽  
Valid Species ◽  
Maracaibo Basin ◽  
New Synonyms ◽  
Branchial Arches ◽  
A New Species

ABSTRACT A taxonomic revision and phylogenetic analysis were completed for Dasyloricaria . The genus includes three valid species: D . filamentosa and D . latiura previously included in the genus, and a new species described herein. Dasyloricaria have a restricted trans-Andean distribution, with D . filamentosa occurring at the lower and middle Magdalena, lower Cauca, and Sinu in Colombia, and lago Maracaibo basin in Colombia and Venezuela; D . latiura in the Atrato and the Tuyra basins in Colombia and Panama, respectively; and the new species in the upper and middle Magdalena basin in Colombia. New synonyms for D . filamentosa and D . latiura are proposed, and a lectotype is designated for the latter. Dasyloricaria is herein recognized as monophyletic, with D . filamentosa as the sister group of D . latiura , and the new speciesas sister to that clade. Spatuloricaria is hypothesized to be the sister group of Dasyloricaria based on synapomorphies of the neurocranium, branchial arches and external morphology features. The subtribe Rineloricariina was partially corroborated through the phylogenetic analysis. An identification key for the species of Dasyloricaria is provided.

Phylogenetic relationships of the African genera Alestes and Brycinus (Teleostei, Characiformes, Alestidae)

2002 ◽  
Vol 80 (11) ◽  
pp. 1887-1899 ◽  
Author(s):  
Alison M Murray ◽  
Kathlyn M Stewart
Keyword(s):  
Phylogenetic Relationships ◽  
Cladistic Analysis ◽  
Sister Group ◽  
Monophyletic Group ◽  
The Family ◽  
The Subject

The family Alestidae (also referred to as the African Characidae) comprises the African dwarf forms ("Petersiini") and the genera Alestes, Brycinus, Bryconaethiops, and Hydrocynus. Although several authors have presented characters to support the monophyly of the family, a cladistic analysis of the group has not been published. Furthermore, the interrelationships of the constituent groups are the subject of some controversy. A cladistic analysis of the Alestidae is presented, including characters to support the monophyly of the family. The results of this study indicate that several species should be removed from the genus Brycinus, that Hydrocynus is the sister group of Alestes s.str. (containing only five species), and that the dwarf alestids ("Petersiini") do not form a monophyletic group.

scholarly journals Phylogenetic relationships among extinct and extant turtles: the position of Pleurodira and the effects of the fossils on rooting crown-group turtles

2010 ◽  
Vol 79 (3) ◽  
pp. 93-106 ◽  
Author(s):  
Juliana Sterli
Keyword(s):  
Phylogenetic Relationships ◽  
Sister Group ◽  
Molecular Data ◽  
Morphological Data ◽  
Phylogenetic Position ◽  
Separate Analysis ◽  
Crown Group ◽  
Rapid Radiation ◽  
Present Contribution ◽  
Origin And Evolution

The origin and evolution of the crown-group of turtles (Cryptodira + Pleurodira) is one of the most interesting topics in turtle evolution, second perhaps only to the phylogenetic position of turtles among amniotes. The present contribution focuses on the former problem, exploring the phylogenetic relationships of extant and extinct turtles based on the most comprehensive phylogenetic dataset of morphological and molecular data analyzed to date. Parsimony analyses were conducted for different partitions of data (molecular and morphological) and for the combined dataset. In the present analysis, separate analyses of the molecular data always retrieve Pleurodira allied to Trionychia. Separate analysis of the morphological dataset, by contrast, depicts a more traditional arrangement of taxa, with Pleurodira as the sister group of Cryptodira, being Chelonioidea the most basal cryptodiran clade. The simultaneous analysis of all available data retrieves all major extant clades as monophyletic, except for Cryptodira given that Pleurodira is retrieved as the sister group of Trionychia. The paraphyly of Cryptodira is an unorthodox result, and is mainly caused by the combination of two factors. First, the molecular signal allies Pleurodira and Trionychia. Second, the morphological data with extinct taxa locates the position of the root of crown-group Testudines in the branch leading to Chelonioidea. This study highlights major but poorly explored topics of turtle evolution: the alternate position of Pleurodira and the root of crown turtles. The diversification of crown turtles is characterized by the presence of long external branches and short internal branches (with low support for the internal nodes separating the major clades of crown turtles), suggesting a rapid radiation of this clade. This rapid radiation is also supported by the fossil record, because soon after the appearance of the oldest crown-group turtles (Middle-Late Jurassic of Asia) the number and diversity of turtles increases remarkably. This evolutionary scenario of a rapid diversification of modern turtles into the major modern lineages is likely the reason for the difficulty in determining the interrelationships and the position of the root of crown-group turtles.

The phylogenetic relationships of Paramesotriton (Caudata: Salamandridae) based on partial mitochondrial DNA gene sequences

Zootaxa ◽  
2012 ◽  
Vol 3150 (1) ◽  
pp. 59
Author(s):  
XIAOMING GU ◽  
HUI WANG ◽  
RONGRONG CHEN ◽  
YINGZHOU TIAN ◽  
SONG LI
Keyword(s):  
Mitochondrial Dna ◽  
Bayesian Inference ◽  
Maximum Likelihood ◽  
16S Rdna ◽  
Phylogenetic Relationships ◽  
Maximum Parsimony ◽  
Mitochondrial Gene ◽  
Sister Group ◽  
Species Group ◽  
Close Phylogenetic Relationship

We examined phylogenetic relationships among newst of the genus Paramesotriton using partial mitochondrial gene se-quences, including the ND2-tRNATyr region (1415 bp) and the 12S rDNA-tRNAVal -16S rDNA region (1774 bp), from 42individuals of 10 recognized Paramesotriton species and outgroups by Bayesian inference (BI), Maximum likelihood(ML) and Maximum Parsimony (MP) methods. We found that, (1) Laotriton laoensis is the sister group of Paramesotri-ton, (2) the genus Paramesotriton is monophyletic, composed of either the P. caudopunctatus species group and the P.chinensis species group, or the subgenera Allomesotriton and Paramesotriton (3) P. longliensis and P. zhijinensis shouldbe placed in the P. caudopunctatus species group or subgenus Allomesotriton; (4) P. fuzhongensis is not a junior synonym of P. chinensis, and there is a close phylogenetic relationship between P. fuzhongensis and P. guangxiensis.

scholarly journals Highly Resolved Phylogenetic Relationships within Order Acipenseriformes According to Novel Nuclear Markers

Genes ◽  
2019 ◽  
Vol 10 (1) ◽  
pp. 38 ◽  
Author(s):  
Dehuai Luo ◽  
Yanping Li ◽  
Qingyuan Zhao ◽  
Lianpeng Zhao ◽  
Arne Ludwig ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Single Copy ◽  
Species Trees ◽  
Degenerate Primers ◽  
Nuclear Markers ◽  
Gene Markers ◽  
Fossil Species ◽  
Living Fossil ◽  
Molecular Clock Model ◽  
Extant Species

Order Acipenseriformes contains 27 extant species distributed across the northern hemisphere, including so-called “living fossil” species of garfish and sturgeons. Previous studies have focused on their mitochondrial genetics and have rarely used nuclear genetic data, leaving questions as to their phylogenetic relationships. This study aimed to utilize a bioinformatics approach to screen for candidate single-copy nuclear genes, using transcriptomic data from sturgeon species and genomic data from the spotted gar, Lepisosteus oculatus. We utilized nested polymerase chain reaction (PCR) and degenerate primers to identify nuclear protein-coding (NPC) gene markers to determine phylogenetic relationships among the Acipenseriformes. We identified 193 nuclear single-copy genes, selected from 1850 candidate genes with at least one exon larger than 700 bp. Forty-three of these genes were used for primer design and development of 30 NPC markers, which were sequenced for at least 14 Acipenseriformes species. Twenty-seven NPC markers were found completely in 16 species. Gene trees according to Bayesian inference (BI) and maximum likelihood (ML) were calculated based on the 30 NPC markers (20,946 bp total). Both gene and species trees produced very similar topologies. A molecular clock model estimated the divergence time between sturgeon and paddlefish at 204.1 Mya, approximately 10% later than previous estimates based on cytochrome b data (184.4 Mya). The successful development and application of NPC markers provides a new perspective and insight for the phylogenetic relationships of Acipenseriformes. Furthermore, the newly developed nuclear markers may be useful in further studies on the conservation, evolution, and genomic biology of this group.

scholarly journals Preliminary Analysis of Phylogenetic Relationships Among Palaearctic Simuliinae (Diptera, Simuliidae) Inferred From Morphological Characters

2012 ◽  
Vol 46 (6) ◽  
pp. 31-48
Author(s):  
K. B. Sukhomlin
Keyword(s):  
Phylogenetic Relationships ◽  
Preliminary Analysis ◽  
Sister Group ◽  
Morphological Characters ◽  
Consensus Trees ◽  
The Matrix ◽  
Group Relationships

Abstract Phylogenetic relationships among the Palaearctic genera of the subfamily Simuliinae are analyzed based on the matrix of 100 morphological characters and 37 taxa, including 6 outgroups. Parsimonic analysis was resulted in 3 consensus trees (weighting based on CI, RI and RC indices) of slightly different topology, which show monophyly of the subfamily Simuliinae, tribes Stegopternini, Nevermanniini, Wilhelmiini and Simuliini, and a possible sister-group relationships between the latter two tribes. Tribe Ectemniini is apparently a paraphyletic formation. The analysis also supports transferring of the Stegopternini and Nevermanniini from Prosimuliinae to Simuliinae.

scholarly journals Cretaceous origin and repeated tertiary diversification of the redefined butterflies

2011 ◽  
Vol 279 (1731) ◽  
pp. 1093-1099 ◽  
Author(s):  
Maria Heikkilä ◽  
Lauri Kaila ◽  
Marko Mutanen ◽  
Carlos Peña ◽  
Niklas Wahlberg
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Evolutionary History ◽  
Sister Group ◽  
Morphological Characters ◽  
Molecular Data ◽  
Bayesian Approaches ◽  
The Family ◽  
Family Level ◽  
Morphological And Molecular Data

Although the taxonomy of the ca 18 000 species of butterflies and skippers is well known, the family-level relationships are still debated. Here, we present, to our knowledge, the most comprehensive phylogenetic analysis of the superfamilies Papilionoidea, Hesperioidea and Hedyloidea to date based on morphological and molecular data. We reconstructed their phylogenetic relationships using parsimony and Bayesian approaches. We estimated times and rates of diversification along lineages in order to reconstruct their evolutionary history. Our results suggest that the butterflies, as traditionally understood, are paraphyletic, with Papilionidae being the sister-group to Hesperioidea, Hedyloidea and all other butterflies. Hence, the families in the current three superfamilies should be placed in a single superfamily Papilionoidea. In addition, we find that Hedylidae is sister to Hesperiidae, and this novel relationship is supported by two morphological characters. The families diverged in the Early Cretaceous but diversified after the Cretaceous–Palaeogene event. The diversification of butterflies is characterized by a slow speciation rate in the lineage leading to Baronia brevicornis , a period of stasis by the skippers after divergence and a burst of diversification in the lineages leading to Nymphalidae, Riodinidae and Lycaenidae.

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