scholarly journals Ecological Factors and Diversification among Neotropical Characiforms

2012 ◽  
Vol 2012 ◽  
pp. 1-20 ◽  
Author(s):  
Cástor Guisande ◽  
Patricia Pelayo-Villamil ◽  
Manuel Vera ◽  
Ana Manjarrés-Hernández ◽  
Mónica R. Carvalho ◽  
...  
Keyword(s):  
Sequence Data ◽  
Phylogenetic Reconstruction ◽  
Ecological Factors ◽  
Trophic Niche ◽  
Large Item ◽  
Dna Sequence Data ◽  
Dorsal Fin ◽  
Niche Differences ◽  
Early Diversification ◽  
Morphological Differences

Morphological and DNA sequence data has been used to propose hypotheses of relationships within the Characiformes with minimal comparative discussion of causes underpinning the major intraordinal diversification patterns. We explore potential primary morphological factors controlling the early diversification process in some Neotropical characiforms as the first step to identifying factors contributing to the pronounced intraordinal morphological and species diversity. A phylogenetic reconstruction based on 16S rDNA (mitochondrial) and 18S rDNA (nuclear) genes provided the framework for the identification of the main morphological differences among the Acestrorhynchidae, Anostomidae, Characidae, Ctenoluciidae, Curimatidae, Cynodontidae, Gasteropelecidae, Prochilodontidae and Serrasalmidae. Results indicate an initial split into two major groupings: (i) species with long dorsal-fin bases relative to the size of other fins (Curimatidae, Prochilodontidae, Anostomidae, Serrasalmidae) which primarily inhabit lakes, swamps, and rivers (lineage I); and (ii) species with short dorsal-fin bases (Acestrorhynchidae, Gasteropelecidae, Characidae) which primarily inhabit creeks and streams (lineage II). The second diversification stage in lineage I involved substantial morphological diversification associated with trophic niche differences among the monophyletic families which range from detritivores to large item predators. Nonmonophyly of the Characidae complicated within lineage II analyzes but yielded groupings based on differences in pectoral and anal fin sizes correlated with life style differences.

scholarly journals Song and Molecular Data Identify Congruent but Novel Affinities of the Green Oropendola (Psarocolius Viridis)

The Auk ◽  
2004 ◽  
Vol 121 (1) ◽  
pp. 224-229
Author(s):  
J. Jordan Price ◽  
Scott M. Lanyon
Keyword(s):  
Sequence Data ◽  
Phylogenetic Reconstruction ◽  
Molecular Data ◽  
Phylogenetic Position ◽  
Data Sets ◽  
Dna Sequence Data ◽  
Close Relationship ◽  
Morphological Differences ◽  
Vocal Evolution ◽  
Avian Song

Abstract The accuracy with which avian song features indicate phylogenetic relationships has rarely been investigated. In a previous study of vocal evolution in oropendolas (Price and Lanyon 2002a), we estimated the phylogenetic position of the Green Oropendola (Psarocolius viridis) using characters derived from oropendolas' elaborate courtship songs. Here, we test that estimate using mitochondrial DNA sequence data. The position of the Green Oropendola determined from molecular data is remarkably close to that based solely on song characters; both data sets support a close relationship between P. viridis and members of the genus Gymnostinops. Numerous morphological differences yet low genetic divergence among the species in question suggest that rapid diversification has occurred in the group. The fact that this position has not been proposed previously for P. viridis underscores the effectiveness of song characters for phylogenetic reconstruction.

scholarly journals A new species of penzigioid Xylaria (Xylariaceae) from the cloud forest in eastern Mexico revealed through morphological and phylogenetic analyses

Botany ◽  
2019 ◽  
Vol 97 (7) ◽  
pp. 381-389
Author(s):  
Santiago Chacón ◽  
Dolores González
Keyword(s):  
Sequence Data ◽  
Novel Species ◽  
Cloud Forest ◽  
Phylogenetic Analyses ◽  
Phylogenetic Reconstruction ◽  
Morphological Characteristics ◽  
Its Sequences ◽  
Dna Sequence Data ◽  
Morphological Differences ◽  
Morphological Transformations

Xylaria subtropicalis, a species new to science, was collected from a montane cloud forest in eastern Mexico. It is described and illustrated, based on detailed macro- and microscopic morphological characteristics, habitat, and DNA sequence data. The distinctive morphological differences between X. subtropicalis and other Xylaria species include: the stromata being significantly erumpent, the size of the ascospores being 23–28 μm × 13–15 μm, and a straight germ slit as long as the spore. To determine whether this was a novel species, ITS sequences were generated and compared with 2478 sequences available for the genus from GenBank, using the software USEARCH. Additionally, a phylogenetic reconstruction was performed with Parsimony Ratchet, Maximum Likelihood, and Bayesian Inference, using 122 concatenated ITS sequences, and segments from the 28S rDNA and RPB2. Sequences of this novel species form a strongly supported lineage, clearly separated from other species of Xylaria. Phylogenetic relationships indicate that there have been numerous morphological transformations within the genus.

New genetic lineages within Moroccan day geckos Quedenfeldtia (Sphaerodactylidae) revealed by mitochondrial and nuclear DNA sequence data

2017 ◽  
Vol 38 (1) ◽  
pp. 97-101 ◽  
Author(s):  
David James Harris ◽  
Daniela Rosado ◽  
Raquel Xavier ◽  
Daniele Salvi
Keyword(s):  
Nuclear Dna ◽  
Sequence Data ◽  
Phylogenetic Reconstruction ◽  
Taxonomic Revision ◽  
Substantial Portion ◽  
Genetic Lineages ◽  
Mountainous Regions ◽  
Dna Sequence Data ◽  
Atlas Mountains ◽  
Morphological Assessment

The genus Quedenfeldtia is composed of two species, Q. moerens and Q. trachyblepharus, both endemic to the Atlas Mountains region of Morocco. Previous studies recovered two main genetic lineages within each Quedenfeldtia species, although sampling did not cover a substantial portion of their known distribution. In this study we collected individuals from previously unsampled localities of Quedenfeldtia and carried out genetic analyses in order to assess the range of previously identified lineages and the occurrence of additional lineages. Phylogenetic reconstruction based on both mitochondrial (12S and ND4 + tRNA) and nuclear (MC1R) markers revealed that while the new individuals of Q. moerens belong to previously described lineages, two new lineages of Q. trachyblepharus were uncovered from the northern and southern parts of the range. Genetic divergence of these new lineages (8-9% ND4 + tRNA p-distance) was higher than values observed between other lizard sister species. In the future a thorough morphological assessment is needed to complement this study and allow a taxonomic revision of these taxa. The results of this study highlight the importance of biodiversity assessments in mountainous regions characterized by high endemicity but which are difficult to access.

Towards rectifying limitations on species delineation in dusky salamanders (Desmognathus: Plethodontidae): An ecoregion-drainage sampling grid reveals additional cryptic clades

Zootaxa ◽  
2020 ◽  
Vol 4734 (1) ◽  
pp. 1-61 ◽  
Author(s):  
DAVID A. BEAMER ◽  
TRIP LAMB
Keyword(s):  
Sequence Data ◽  
Phylogenetic Reconstruction ◽  
Large Species ◽  
Eastern United States ◽  
Species Delineation ◽  
Molecular Systematic ◽  
Dna Sequence Data ◽  
Species Complexes ◽  
Sampling Regime ◽  
Comprehensive Recovery

Dusky salamanders (Desmognathus) constitute a large, species-rich group within the family Plethodontidae, and though their systematic relationships have been addressed extensively, most studies have centered on particular species complexes and therefore offer only piecemeal phylogenetic perspective on the genus. Recent work has revealed Desmognathus to be far more clade rich—35 reciprocally monophyletic clades versus 22 recognized species—than previously imagined, results that, in turn, provide impetus for additional survey effort within clades and across geographic areas thus far sparsely sampled. We conceived and implemented a sampling regime combining level IV ecoregions and independent river drainages to yield a geographic grid for comprehensive recovery of all genealogically exclusive clades. We sampled over 550 populations throughout the distribution of Desmognathus in the eastern United States of America and generated mitochondrial DNA sequence data (mtDNA; 1,991 bp) for 536 specimens. A Bayesian phylogenetic reconstruction of the resulting haplotypes revealed forty-five reciprocally monophyletic clades, eleven of which have never been included in a comprehensive phylogenetic reconstruction, and an additional three not represented in any molecular systematic survey. Although general limitations associated with mtDNA data preclude new species delineation, we profile each of the 45 clades and assign names to 10 new clades (following a protocol for previous clade nomenclature). We also redefine several species complexes and erect new informal species complexes. Our dataset, which contains topotypic samples for nearly every currently recognized species and most synonymies, will offer a robust framework for future efforts to delimit species within Desmognathus. 

Australia's wasp-pollinated flying duck orchids revised (Paracaleana: Orchidaceae)

2006 ◽  
Vol 19 (3) ◽  
pp. 211 ◽  
Author(s):  
Stephen D. Hopper ◽  
Andrew P. Brown
Keyword(s):  
Sequence Data ◽  
South Australia ◽  
Pollination Syndrome ◽  
The South ◽  
Geographical Differences ◽  
Sexual Deception ◽  
Dna Sequence Data ◽  
South West ◽  
Morphological Differences ◽  
Putative Hybrids

We uphold the generic rank of Paracaleana on the basis of its divergent pollination syndrome (sexual deception of male thynnid wasps compared with pollination of Caleana by male sawflies), recent DNA sequence data demonstrating monophyly, and nomenclatural stability. Ten of the 13 species recognised herein are new, all endemic to the South-west Australian Floristic Region: Paracaleana alcockii, P. brockmanii, P. dixonii, P. gracilicordata, P. granitica, P. hortiorum, P. lyonsii, P. parvula, P. terminalis and P. triens. Although some of these taxa have subtle morphological differences, primarily of labellum morphology, evidence from other Australian orchid genera whose flowers sexually deceive wasp pollinators indicates that reproductive isolation is probable among close sister taxa in Paracaleana. Moreover, phenological, ecological and geographical differences help separate morphologically close sister taxa. P. disjuncta D.L. Jones is considered to extend from Victoria and South Australia west into the South-west Australian Floristic Region, where James Drummond first collected the species, probably in 1838. Additional research is needed on pollinators, molecular phylogeny, possibly undescribed taxa within P. nigrita and on the few putative hybrids identified in the genus.

Is Ronnbergia (Bromeliaceae, Bromelioideae) a geographically disjunct genus? Evidence from morphology and chloroplast DNA sequence data

Phytotaxa ◽  
2015 ◽  
Vol 219 (3) ◽  
pp. 261 ◽  
Author(s):  
Julian Aguirre-Santoro ◽  
Julio Betancur ◽  
Gregory K. Brown ◽  
Timothy M. Evans ◽  
Fabiano Salgueiro ◽  
...  
Keyword(s):  
Chloroplast Dna ◽  
Dna Sequence ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Phylogenetic Reconstruction ◽  
Morphological Data ◽  
Phylogenetic Study ◽  
Geographic Ranges ◽  
Dna Sequence Data ◽  
Disjunct Genus

A phylogenetic study testing the monophyly of the geographically disjunct genus Ronnbergia (Bromeliaceae, Bromelioideae) is presented. The phylogenetic analyses were based on taxon sampling that included all but one species of Ronnbergia, and representative lineages across the subfamily Bromelioideae. Three chloroplast DNA sequence markers (matK, psbA-trnH, and trnL-trnF) and morphological data were used for the phylogenetic reconstruction. Both the molecular and morphological datasets supported the polyphyly of Ronnbergia, either independently or in combination. These findings suggest that the geographic disjunction of this genus is most likely a product of taxonomic misinterpretation. The results also indicate that the species currently circumscribed in Ronnbergia are closely related to species in the genus Aechmea with similar geographic ranges. The datasets do not have enough resolution power to reconstruct a deep phylogenetic history that involves all the species of Ronnbergia. Nevertheless, this study provides clues for future approaches that should focus on a larger species sampling and the use of multi-locus DNA sequence data.

scholarly journals On the Species Delimitation of the Maddenia Group of Prunus (Rosaceae): Evidence From Plastome and Nuclear Sequences and Morphology

2021 ◽  
Vol 12 ◽  
Author(s):  
Na Su ◽  
Bin-bin Liu ◽  
Jun-ru Wang ◽  
Ru-chang Tong ◽  
Chen Ren ◽  
...  
Keyword(s):  
Species Delimitation ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Phylogenetic Reconstruction ◽  
Phylogenetic Network ◽  
Single Copy ◽  
Morphological Evidence ◽  
Molecular Evidence ◽  
Variable Regions ◽  
Dna Sequence Data

The recognition, identification, and differentiation of closely related plant species present significant and notorious challenges to taxonomists. The Maddenia group of Prunus, which comprises four to seven species, is an example of a group in which species delimitation and phylogenetic reconstruction have been difficult, due to the lack of clear morphological distinctions, limited sampling, and low informativeness of molecular evidence. Thus, the precise number of species in the group and the relationships among them remain unclear. Here, we used genome skimming to generate the DNA sequence data for 22 samples, including 17 Maddenia individuals and five outgroups in Amygdaloideae of Rosaceae, from which we assembled the plastome and 446 single-copy nuclear (SCN) genes for each sample. The phylogenetic relationships of the Maddenia group were then reconstructed using both concatenated and coalescent-based methods. We also identified eight highly variable regions and detected simple sequence repeats (SSRs) and repeat sequences in the Maddenia species plastomes. The phylogenetic analysis based on the complete plastomes strongly supported three main subclades in the Maddenia group of Prunus, while five subclades were recognized based on the nuclear tree. The phylogenetic network analysis detected six hybridization events. Integrating the nuclear and morphological evidence, we proposed to recognize five species within the Maddenia group, i.e., Prunus fujianensis, P. himalayana, P. gongshanensis, P. hypoleuca, and P. hypoxantha. Within this group, the first three species are well-supported, while the gene flow occurring throughout the Maddenia group seems to be especially frequent between P. hypoleuca and P. hypoxantha, eroding the barrier between them. The phylogenetic trees based on eight concatenated hypervariable regions had a similar topology with the complete plastomes, showing their potential as molecular markers and effective barcodes for further phylogeographic studies on Maddenia.

Systematics and biogeography of the family Scorpionidae (Chelicerata : Scorpiones), with a discussion on phylogenetic methods

2003 ◽  
Vol 17 (2) ◽  
pp. 185 ◽  
Author(s):  
Lorenzo Prendini ◽  
Timothy M. Crowe ◽  
Ward C. Wheeler
Keyword(s):  
Mitochondrial Genome ◽  
Sequence Data ◽  
Conservation Status ◽  
Phylogenetic Reconstruction ◽  
Cladistic Analysis ◽  
Nuclear Genome ◽  
Sister Group ◽  
Dna Sequence Data ◽  
Phylogenetic Methods ◽  
The Family

A cladistic analysis of relationships among the genera of Scorpionidae Latreille, 1802—Heterometrus Ehrenberg, 1828; Opistophthalmus C. L. Koch, 1837; Pandinus Thorell, 1876; and Scorpio Linnaeus, 1758—based on morphology and DNA sequence data from loci of three genes in the mitochondrial genome (12S ribosomal DNA (rDNA), 16S rDNA and cytochrome oxidase I) and one gene in the nuclear genome (28S rDNA) is presented. The analysis makes use of exemplar species, specifically selected to test the monophyly of the genera, rather than supraspecific terminal taxa. Other methods used in the analysis are justified in the context of a discussion of current methods for phylogenetic reconstruction. Relationships among the scorpionid genera are demonstrated to be as follows: (Opistophthalmus (Scorpio (Heterometrus + Pandinus))). This reconstruction identifies Opistophthalmus as the basal lineage of the Scorpionidae, rather than the sister-group of Scorpio. Revised descriptions, diagnoses and a key to identification of the four scorpionid genera are provided, together with a summary of what is known about their ecology, distribution and conservation status.

scholarly journals Insight into the Systematics of Novel Entomopathogenic Fungi Associated with Armored Scale Insect, Kuwanaspis howardi (Hemiptera: Diaspididae) in China

2021 ◽  
Vol 7 (8) ◽  
pp. 628
Author(s):  
Xiu-Lan Xu ◽  
Qian Zeng ◽  
Yi-Cong Lv ◽  
Rajesh Jeewon ◽  
Sajeewa S. N. Maharachchikumbura ◽  
...  
Keyword(s):  
New Species ◽  
Entomopathogenic Fungi ◽  
Sequence Data ◽  
Scale Insect ◽  
Dna Sequence Data ◽  
Extant Species ◽  
Armored Scale ◽  
Morphological Differences ◽  
His3 Gene ◽  
Insight Into

This study led to the discovery of three entomopathogenic fungi associated with Kuwanaspis howardi, a scale insect on Phyllostachys heteroclada (fishscale bamboo) and Pleioblastus amarus (bitter bamboo) in China. Two of these species belong to Podonectria: P. kuwanaspidis X.L. Xu & C.L. Yang sp. nov. and P. novae-zelandiae Dingley. The new species P. kuwanaspidis has wider and thicker setae, longer and wider asci, longer ascospores, and more septa as compared with similar Podonectria species. The morphs of extant species P. novae-zelandiae is confirmed based on sexual and asexual morphologies. Maximum likelihood and Bayesian inference analyses of ITS, LSU, SSU, tef1-α, and rpb2 sequence data provide further evidence for the validity of the two species and their placement in Podonectriaceae (Pleosporales). The second new species, Microcera kuwanaspidis X.L. Xu & C.L. Yang sp. nov., is established based on DNA sequence data from ITS, LSU, SSU, tef1-α, rpb1, rpb2, acl1, act, cmdA, and his3 gene regions, and it is characterized by morphological differences in septum numbers and single conidial mass.

Molecular phylogeny of the pond skaters (Gerrinae), discussion of the fossil record and a checklist of species assigned to the subfamily (Hemiptera: Heteroptera: Gerridae)

2014 ◽  
Vol 45 (3) ◽  
pp. 251-281 ◽  
Author(s):  
Jakob Damgaard ◽  
Felipe Ferraz Figueiredo Moreira ◽  
Tom A. Weir ◽  
Herbert Zettel
Keyword(s):  
Fossil Record ◽  
Sequence Data ◽  
Phylogenetic Reconstruction ◽  
Sister Group ◽  
Species Group ◽  
28S Rrna ◽  
Parsimony Analysis ◽  
Dna Sequence Data ◽  
Genes Encoding ◽  
Future Revision

The phylogenetic relationships among selected species and genera of Gerrinae (Heteroptera: Gerridae) were investigated in a parsimony analysis of 2268 bp of DNA sequence data from the genes encoding COI + II, 16S rRNA and 28S rRNA. The taxa represented 12 of 15 recognized genera of Gerrinae and with outgroup taxa from all other subfamilies of Gerridae, including three of five recognized genera of Eotrechinae, which is considered the sister-group of Gerrinae. The resulting phylogeny shows that Gerrinae is not monophyletic, since a clade comprising Gerris, Aquarius, Limnoporus, Tachygerris, Eurygerris and Gigantometra is more closely related to representatives of the subfamily Eotrechinae than to a clade comprising Limnogonus, Neogerris, Limnometra, Tenagogerris and Tenagogonus. The two currently recognized gerrine tribes, Tachygerrini and Gerrini, were also paraphyletic, since Eurygerris was sister-group to Gigantometra, while Tachygerris was sister-group to Limnoporus + Aquarius + Gerris. Limnogonus and Neogerris were found to be strongly supported sister-taxa, and their sister-group was a clade comprising Limnometra, Tenagogerris and Tenagogonus, none of which were monophyletic. Finally, Aquarius chilensis (Berg, 1881) was sister-group to a clade comprising Aquarius amplus (Drake & Harris, 1938), A. remigis (Say, 1832) and A. remigoides (Gallant & Fairbairn, 1993), recognized as the A. remigis species group, and the entire clade was sister-group to Gerris. Based on the phylogenetic reconstruction, we outline possible diagnostic character combinations for a future revision of the Gerrinae and discuss the fossil record. While some of the relationships reinstate earlier ideas, e.g., Limnogonus and Neogerris being sister groups, many others are poorly supported and poorly diagnosed, and therefore, we retain from drawing taxonomic conclusions until data is available from the remaining genera, which can support a future generic revision of the Gerrinae. The updated checklist of species assigned to the subfamily is therefore based on the established taxonomy.

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