Sex‐linked genetic diversity and differentiation in a globally distributed avian species complex

Tetrastigma loheri (Vitaceae) is a vine species native to Borneo and the Philippines. Because it is a commonly encountered forest species in the Philippines, T. loheri is potentially suitable for studying patterns of genetic diversity and connectivity among fragmented forestecosystems in various parts of this country. However, previous research suggests that T. loheri is part of a species complex in the Philippines (i.e. the T. loheri s. l. complex) that potentially also contains Philippine plants identified as T. diepenhorstii, T. philippinense, T. stenophyllum, andT. trifoliolatum. This uncertainty about its taxonomic delimitation can make it challenging to draw conclusions that are relevant to conservation from genetic studies using this species. Here, we tested the hypothesis that T. loheri s. l. is composed of more than one species in the Philippines.For this, we used generalized mixed Yule coalescent (GMYC) and Poisson tree process (PTP) species delimitation models to identify clades within DNA sequence phylogenies of T. loheri s. l. that might constitute species within this complex. Although these methods identified several putative species, these are statistically poorly supported and subsequent random forest analyses using a geometric morphometric leafshape dataset and several other vegetative characters did not result in the identification of characters that can be used to discriminate these putative species morphologically. Furthermore, the results of principal component and principal coordinates analyses of these data suggest the absence of morphological discontinuities within the species complex. Under a unified species concept that uses phylogenetic and morphological distinction as operational criteria for species recognition, we therefore conclude that the currently available data do not support recognizing multiple species in the T. loheri s. l. complex. This implies that T. loheri is best considered as a single, morphologically variable specieswhen used for studying patterns of genetic diversity and connectivity in the Philippines.

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Genetic Diversity in the Paramecium aurelia Species Complex

Molecular Biology and Evolution ◽

10.1093/molbev/msn266 ◽

2008 ◽

Vol 26 (2) ◽

pp. 421-431 ◽

Cited By ~ 56

Author(s):

F. Catania ◽

F. Wurmser ◽

A. A. Potekhin ◽

E. Przybos ◽

M. Lynch

Keyword(s):

Genetic Diversity ◽

Species Complex

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Toward a resolution of the cosmopolitan Botryllus schlosseri species complex (Ascidiacea, Styelidae): mitogenomics and morphology of clade E (Botryllus gaiae)

Zoological Journal of the Linnean Society ◽

10.1093/zoolinnean/zlaa023 ◽

2020 ◽

Cited By ~ 1

Author(s):

Riccardo Brunetti ◽

Francesca Griggio ◽

Francesco Mastrototaro ◽

Fabio Gasparini ◽

Carmela Gissi

Keyword(s):

Species Complex ◽

Taxonomic Status ◽

Intestinal Loop ◽

Botryllus Schlosseri ◽

Colonial Ascidian ◽

Coding Regions ◽

Nucleotide Divergence ◽

Globally Distributed ◽

Entire Mitochondrial Genome ◽

Identical Gene

Abstract Botryllus schlosseri is a model colonial ascidian and a marine invader. It is currently recognized as a species complex comprising five genetically divergent clades, with clade A globally distributed and clade E found only in Europe. This taxon has also been recently redescribed by designation of a clade A specimen as the neotype. To clarify the taxonomic status of clade E and its relationship to clade A, we examine the entire mitochondrial genome and study the morphology of clade E. The mitogenome of clade E has an identical gene order to clade A, but substantially differs in the size of several non-coding regions. Remarkably, the nucleotide divergence of clade A-clade E is incompatible with the intraspecies ascidian divergence, but similar to the congeneric one and almost identical to the divergence between species once considered morphologically indistinguishable (e.g. the pair Ciona intestinalis (Linnaeus, 1767)-Ciona robusta Hoshino & Tokioka, 1967, and the pair Botrylloides niger Herdman, 1886-Botrylloides leachii (Savigny, 1816)). Clade E differs morphologically from the Botryllusschlosseri neotype mainly in the number and appearance of the stomach folds, and the shape of the anal opening, the first intestinal loop and the typhlosole. Our integrative taxonomical approach clearly distinguishes clade E as a species separate from Botryllusschlosseri, with unique morphological and molecular characters. Therefore, we here describe clade E as the new species Botryllus gaiae sp. nov.

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Multiple markers, niche modelling, and bioregions analyses to evaluate the genetic diversity of a plant species complex

BMC Evolutionary Biology ◽

10.1186/s12862-017-1084-y ◽

2017 ◽

Vol 17 (1) ◽

Cited By ~ 10

Author(s):

Ana Lúcia A. Segatto ◽

Maikel Reck-Kortmann ◽

Caroline Turchetto ◽

Loreta B. Freitas

Keyword(s):

Genetic Diversity ◽

Plant Species ◽

Species Complex ◽

Niche Modelling ◽

Multiple Markers

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Genetic Diversity of the Ralstonia solanacearum Species Complex in the Southwest Indian Ocean Islands

Frontiers in Plant Science ◽

10.3389/fpls.2017.02139 ◽

2017 ◽

Vol 8 ◽

Cited By ~ 7

Author(s):

Noura Yahiaoui ◽

Jean-Jacques Chéron ◽

Santatra Ravelomanantsoa ◽

Azali A. Hamza ◽

Bobb Petrousse ◽

...

Keyword(s):

Genetic Diversity ◽

Indian Ocean ◽

Ralstonia Solanacearum ◽

Species Complex ◽

Southwest Indian Ocean ◽

Ocean Islands

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The Case for Adopting the “Species Complex” Nomenclature for the Etiologic Agents of Cryptococcosis

mSphere ◽

10.1128/msphere.00357-16 ◽

2017 ◽

Vol 2 (1) ◽

Cited By ~ 139

Author(s):

Kyung J. Kwon-Chung ◽

John E. Bennett ◽

Brian L. Wickes ◽

Wieland Meyer ◽

Christina A. Cuomo ◽

...

Keyword(s):

Genetic Diversity ◽

Phylogenetic Analysis ◽

Cryptococcus Neoformans ◽

Species Complex ◽

Intermediate Step ◽

Separate Species ◽

Content Type ◽

Etiologic Agents ◽

Genotypic Characteristics ◽

Biological Differences

ABSTRACT Cryptococcosis is a potentially lethal disease of humans/animals caused by Cryptococcus neoformans and Cryptococcus gattii. Distinction between the two species is based on phenotypic and genotypic characteristics. Recently, it was proposed that C. neoformans be divided into two species and C. gattii into five species based on a phylogenetic analysis of 115 isolates. While this proposal adds to the knowledge about the genetic diversity and population structure of cryptococcosis agents, the published genotypes of 2,606 strains have already revealed more genetic diversity than is encompassed by seven species. Naming every clade as a separate species at this juncture will lead to continuing nomenclatural instability. In the absence of biological differences between clades and no consensus about how DNA sequence alone can delineate a species, we recommend using “Cryptococcus neoformans species complex” and “C. gattii species complex” as a practical intermediate step, rather than creating more species. This strategy recognizes genetic diversity without creating confusion.

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Genetic Diversity and Epizootiology ofChlamydophila psittaciPrevalent among the Captive and Feral Avian Species Based on VD2 Region ofompAGene

Microbiology and Immunology ◽

10.1111/j.1348-0421.2006.tb03839.x ◽

2006 ◽

Vol 50 (9) ◽

pp. 663-678 ◽

Cited By ~ 30

Author(s):

Rajesh Chahota ◽

Hirohito Ogawa ◽

Yoko Mitsuhashi ◽

Kenji Ohya ◽

Tsuyoshi Yamaguchi ◽

...

Keyword(s):

Genetic Diversity ◽

Avian Species

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Genetic diversity of a Botrytis cinerea cryptic species complex in Hungary

Microbiological Research ◽

10.1016/j.micres.2011.10.006 ◽

2012 ◽

Vol 167 (5) ◽

pp. 283-291 ◽

Cited By ~ 29

Author(s):

Éva Fekete ◽

Erzsébet Fekete ◽

László Irinyi ◽

Levente Karaffa ◽

Mariann Árnyasi ◽

...

Keyword(s):

Genetic Diversity ◽

Cryptic Species ◽

Botrytis Cinerea ◽

Species Complex ◽

Cryptic Species Complex

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Analysis of the Genetic Diversity Associated With the Drug Resistance and Pathogenicity of Influenza A Virus Isolated in Bangladesh From 2002 to 2019

Frontiers in Microbiology ◽

10.3389/fmicb.2021.735305 ◽

2021 ◽

Vol 12 ◽

Author(s):

Md. Golzar Hossain ◽

Sharmin Akter ◽

Priya Dhole ◽

Sukumar Saha ◽

Taheruzzaman Kazi ◽

...

Keyword(s):

Genetic Diversity ◽

Drug Resistance ◽

Influenza A Virus ◽

Influenza A ◽

Neuraminidase Inhibitor ◽

Avian Species ◽

Lower Prevalence ◽

Bioinformatic Tools ◽

Wide Range ◽

And Control

The subtype prevalence, drug resistance- and pathogenicity-associated mutations, and the distribution of the influenza A virus (IAV) isolates identified in Bangladesh from 2002 to 2019 were analyzed using bioinformatic tools. A total of 30 IAV subtypes have been identified in humans (4), avian species (29), and environment (5) in Bangladesh. The predominant subtypes in human and avian species are H1N1/H3N2 and H5N1/H9N2, respectively. However, the subtypes H5N1/H9N2 infecting humans and H3N2/H1N1 infecting avian species have also been identified. Among the avian species, the maximum number of subtypes (27) have been identified in ducks. A 3.56% of the isolates showed neuraminidase inhibitor (NAI) resistance with a prevalence of 8.50, 1.33, and 2.67% in avian species, humans, and the environment, respectively, the following mutations were detected: V116A, I117V, D198N, I223R, S247N, H275Y, and N295S. Prevalence of adamantane-resistant IAVs was 100, 50, and 30.54% in humans, the environment, and avian species, respectively, the subtypes H3N2, H1N1, H9N2, and H5N2 were highly prevalent, with the subtype H5N1 showing a comparatively lower prevalence. Important PB2 mutations such D9N, K526R, A588V, A588I, G590S, Q591R, E627K, K702R, and S714R were identified. A wide range of IAV subtypes have been identified in Bangladesh with a diversified genetic variation in the NA, M2, and PB2 proteins providing drug resistance and enhanced pathogenicity. This study provides a detailed analysis of the subtypes, and the host range of the IAV isolates and the genetic variations related to their proteins, which may aid in the prevention, treatment, and control of IAV infections in Bangladesh, and would serve as a basis for future investigations.

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