scholarly journals Two species of Southeast Asian cats in the genus Catopuma with diverging histories: an island endemic forest specialist and a widespread habitat generalist

2016 ◽  
Vol 3 (10) ◽  
pp. 160350 ◽  
Author(s):  
Riddhi P. Patel ◽  
Daniel W. Förster ◽  
Andrew C. Kitchener ◽  
Mark D. Rayan ◽  
Shariff W. Mohamed ◽  
...  
Keyword(s):  
Late Pleistocene ◽  
Species Distribution ◽  
Nucleotide Diversity ◽  
Demographic History ◽  
Population Expansion ◽  
Molecular Data ◽  
Peninsular Malaysia ◽  
Sister Species ◽  
Morphological Data ◽  
Island Endemic

Background. The bay cat Catopuma badia is endemic to Borneo, whereas its sister species the Asian golden cat Catopuma temminckii is distributed from the Himalayas and southern China through Indochina, Peninsular Malaysia and Sumatra. Based on morphological data, up to five subspecies of the Asian golden cat have been recognized, but a taxonomic assessment, including molecular data and morphological characters, is still lacking. Results. We combined molecular data (whole mitochondrial genomes), morphological data (pelage) and species distribution projections (up to the Late Pleistocene) to infer how environmental changes may have influenced the distribution of these sister species over the past 120 000 years. The molecular analysis was based on sequenced mitogenomes of 3 bay cats and 40 Asian golden cats derived mainly from archival samples. Our molecular data suggested a time of split between the two species approximately 3.16 Ma and revealed very low nucleotide diversity within the Asian golden cat population, which supports recent expansion of the population. Discussion. The low nucleotide diversity suggested a population bottleneck in the Asian golden cat, possibly caused by the eruption of the Toba volcano in Northern Sumatra (approx. 74 kya), followed by a continuous population expansion in the Late Pleistocene/Early Holocene. Species distribution projections, the reconstruction of the demographic history, a genetic isolation-by-distance pattern and a gradual variation of pelage pattern support the hypothesis of a post-Toba population expansion of the Asian golden cat from south China/Indochina to Peninsular Malaysia and Sumatra. Our findings reject the current classification of five subspecies for the Asian golden cat, but instead support either a monotypic species or one comprising two subspecies: (i) the Sunda golden cat, distributed south of the Isthmus of Kra: C. t. temminckii and (ii) Indochinese, Indian, Himalayan and Chinese golden cats, occurring north of the Isthmus: C. t. moormensis .

Genome-wide Assessment Elucidates Connectivity and the Evolutionary History of the Highly Dispersive Marine Invertebrate Littoraria Flava (Littorinidae:Gastropoda)

2020 ◽  
Author(s):  
Thainá Cortez ◽  
Rafael Viana Amaral ◽  
Thadeu Sobral-Souza ◽  
Sonia Andrade
Keyword(s):  
Population Dynamics ◽  
Species Distribution ◽  
Marine Invertebrate ◽  
Demographic History ◽  
Population Expansion ◽  
Marine Ecosystems ◽  
Assignment Test ◽  
Niche Modelling ◽  
Marine Gastropod ◽  
Haplotype Networks

Abstract Background: An important goal of population genetics studies in marine ecosystems is understanding how connectivity patterns, both spatial and temporal, are influenced by historical and evolutionary factors. When it comes to dispersion and connectivity in marine ecosystems, the role of historical and evolutionary factors over population dynamics andstructure still remains enigmatic. We evaluated the demographic history and population structure of Littoraria flava, a highly dispersive and widely distributed marine gastropod on the Brazilian intertidal zone, to predict the effects of such factors on intrapopulation divergence. To test the hypotheses that (1) the species has historically high levels of geneflow on a macrogeographic spatial scale and (2) the species distribution in rocky shores consists of subpopulations due to high degrees of environmental heterogeneity, we collected specimens along the Brazilian coastline and combined different sets of genetic markers (mitochondrial DNA, nuclear internal transcribed spacer 2, and single nucleotide polymorphisms) with niche-based modeling to predict species paleodistribution.Results: Low genetic structure was observed along the coastline, and all clustering and migration analyses supported the high gene flow over long distances hypothesis (> 3,000 km). Three genetic clusters were identified by the assignment test, each mostly composed of individuals from the three sampled regions. No fine-scale variation was observed for any location. The neutrality tests and the haplotype networks suggest that L. flava had experienced population bottleneck followed by population expansion. Both paleodistribution and coalescent simulations highlight that expansion events occurred in the Southeastern coastline during the Pleistocene interglacial cycles (21 kya).Conclusions: This is the first study on the South American coast that highlights the demographic history on a marine gastropod based on genomic markers associated with niche modelling. We found that climatic changes since the interglacial periods are potentially relevant drivers for the species distribution in the past. Our findings could enhance the understanding of the population dynamics under an evolutionary view for widely distributed non-model marine organisms.

scholarly journals Parapatric speciation with recurrent gene flow of two sexual dichromatic pheasants

2021 ◽  
Author(s):  
Zheng Li ◽  
Jie Zhou ◽  
Minzhi Gao ◽  
Wei Liang ◽  
Lu Dong
Keyword(s):  
Sexual Selection ◽  
Gene Flow ◽  
Late Pleistocene ◽  
Approximate Bayesian Computation ◽  
De Novo ◽  
Demographic History ◽  
Population Expansion ◽  
Secondary Contact ◽  
Bayesian Computation ◽  
Approximate Bayesian

Background: Understanding speciation has long been a fundamental goal of evolutionary biology. It is widely accepted that speciation requires an interruption of gene flow to generate strong reproductive isolation between species, in which sexual selection may play an important role by generating and maintaining sexual dimorphism. The mechanism of how sexual selection operated in speciation with gene flow remains an open question and the subject of many research. Two species in genus Chrysolophus, Golden pheasant (C. pictus) and Lady Amherst's pheasant (C. amherstiae), which both exhibit significant plumage dichromatism, are currently parapatric in the southwest China with several hybrid recordings in field. Methods: In this research, we estimated the pattern of gene flow during the speciation of two pheasants using the Approximate Bayesian Computation (ABC) method based on the multiple genes data. With a new assembled de novo genome of Lady Amherst's pheasant and resequencing of widely distributed individuals, we reconstructed the demographic history of the two pheasants by pairwise sequentially Markovian coalescent (PSMC). Results: The results provide clear evidence that the gene flow between the two pheasants were consistent with the prediction of isolation with migration model for allopatric populations, indicating that there was long-term gene flow after the initially divergence (ca. 2.2 million years ago), and further support the secondary contact when included the parapatric populations since around 30 ka ongoing gene flow to now, which might be induced by the population expansion of the Golden pheasant in late Pleistocene. Conclusions: The results of the study support the scenario of speciation between Golden pheasant (C. pictus) and Lady Amherst's pheasant (C. amherstiae) with cycles of mixing-isolation-mixing due to the dynamics of natural selection and sexual selection in late Pleistocene that provide a good research system as evolutionary model to test reinforcement selection in speciation. Keywords: Golden pheasant (Chrysolophus pictus), Lady Amherst's pheasant (Chrysolophus amherstiae), speciation, gene flow, Approximate Bayesian Computation (ABC), Pairwise Sequentially Markovian coalescent (PSMC).

Morphological data, molecular data, and total evidence in phylogenetic analysis

1995 ◽  
Vol 73 (S1) ◽  
pp. 667-676 ◽  
Author(s):  
Anders Tehler
Keyword(s):  
Molecular Phylogeny ◽  
Sequence Data ◽  
Molecular Data ◽  
Sister Species ◽  
Total Evidence ◽  
Morphological Data ◽  
Data Sets ◽  
Data Set ◽  
Morphological And Molecular Data ◽  
Congruence Test

Two data sets, one morphological and one molecular, for ascolocular fungi have been analysed separately for taxonomic congruence and in combination for total evidence. Data were analysed with cladistic parsimony, the total support test, and the congruence test. The morphological data set comprised 15 characters and four species, Arthonia radiata, Dendrographa leucophaea, Lecanactis abietina, and Schismatomma pericleum (Arthoniales). The molecular data include the same species and comprised sequence data with 21 informative sites from approximately half of the 18S ribosomal RNA gene. The morphological phylogeny is corroborated by the molecular phylogeny with regard to relationships of Arthonia radiata, Schismatomma pericleum, and Dendrographa leucophaea. But in the molecular phylogeny Lecanactis abietina is placed as a sister species to the former three species. In the phylogeny inferred from morphological data Lecanactis abietina and Dendrographa leucophaea constitute a sister pair with Schismatomma pericleum followed by Arthonia radiata as subsequent sister taxa. The consensus obtained from the taxonomic congruence method was fully collapsed and uninformative. The combined morphological and molecular data in total evidence produced one most parsimonious cladogram. In total evidence Lecanactis abietina is placed as sister species to Schismatomma pericleum and Dendrographa leucophaea all with Arthonia radiata as sister species. The most resolved and phylogenetically informative hypothesis was obtained from cladistic parsimony analysis using total evidence. A review of congruence between morphological and molecular data in determining gross relationships within the Eumycota and Ascomycetes is also given. Key words: Ascomycetes, Arthoniales, phylogeny, cladistics, taxonomic congruence, total evidence, 18SrDNA.

scholarly journals Demographic history and interspecific hybridization of four Shorea species (Dipterocarpaceae) from Peninsular Malaysia inferred from nucleotide polymorphism in nuclear gene regions

2008 ◽  
Vol 38 (5) ◽  
pp. 996-1007 ◽  
Author(s):  
Hiroko Ishiyama ◽  
Nobuyuki Inomata ◽  
Tsuneyuki Yamazaki ◽  
Nor Aini Ab Shukor ◽  
Alfred E. Szmidt
Keyword(s):  
Interspecific Hybridization ◽  
Sequence Data ◽  
Demographic History ◽  
Nuclear Gene ◽  
Population Expansion ◽  
Peninsular Malaysia ◽  
Gene Region ◽  
Putative Hybrid ◽  
Nucleotide Polymorphism ◽  
D Values

Shorea acuminata Dyer, Shorea curtisii Dyer ex King, Shorea leprosula Miq., and Shorea parvifolia Dyer are dominant tree species in the tropical rainforest of Peninsular Malaysia, which experienced several climatic changes during Pleistocene. To investigate the current population structure and demographic history of these species, we analyzed levels and patterns of nucleotide polymorphism of the nuclear gene region PgiC. We also used sequence data of the GapC gene region obtained in our previous study. Negative Tajima’s D values observed in both investigated gene regions for S. curtisii, S. leprosula, and S. parvifolia implied that all three species have experienced population expansion events. Little to moderate levels of population differentiation in S. acuminata and S. curtisii suggested recent divergence of the investigated populations after postglacial colonization of the Peninsular Malaysia. In addition, some haplotypes were similar or identical to haplotypes of the other species. The existence of such haplotypes could be partially explained by interspecific hybridization. Indeed, we found some putative hybrid individuals. Interspecific hybridization among closely related species might have contributed to the polymorphism of the investigated species.

scholarly journals Two new Bacidina species (Lecanorales, Ascomycota) from Pakistan

2020 ◽  
Vol 58 ◽  
pp. 25-34
Author(s):  
Maham Fatima ◽  
Kamran Habib ◽  
Paweł Czarnota ◽  
Abdul Nasir Khalid
Keyword(s):  
Molecular Data ◽  
Sister Species ◽  
Morphological Data ◽  
Green Colour ◽  
Its Nrdna

Bacidina margallensis and B. iqbalii from Pakistan are described and illustrated. Phylogeny of ITS nrDNA region confirms their position within the genus Bacidina, and morphological data make them distinct from other known species of the genus. Based on molecular data, corticolous Bacidina margallensis appears to be a sister species to B. chloroticula, but morphologically, when dry, is the most similar to known from Europe B. mendax because of the granular and warted greenish grey thallus, whitish-cream to dark brown and often piebald apothecia. It differs from that species by shorter, wider and less septate ascospores; 1–3-septate in B. margallensis vs 3–5(6)-septate in B. mendax, and by unusual parrot-green colour of wet thallus. Saxicolous Bacidina iqbalii is closely related to B. neosquamulosa but differs in having crustaceous thallus, transculent when wet entirely pale apothecia, larger asci and less septate large ascospores.

Analysis of the differences between Syntormon pallipes and S. pseudospicatus (Diptera: Dolichopodidae): morphological and molecular data

2019 ◽  
Vol 28 (2) ◽  
pp. 305-316
Author(s):  
M.A. Chursina ◽  
I.Ya. Grichanov
Keyword(s):  
Dna Analysis ◽  
Distinct Species ◽  
Molecular Data ◽  
Wing Shape ◽  
Morphological Data ◽  
12S Rrna ◽  
Separate Species ◽  
Geometric Morphometric ◽  
Geometric Morphometric Analysis ◽  
Morphological And Molecular Data

The recent catalogues of the family Dolichopodidae considered Syntormon pallipes (Fabricius, 1794) and S. pseudospicatus Strobl, 1899 as separate species. In this study, we used three approaches to estimate the significance of differences between the two species: molecular analysis (COI and 12S rRNA sequences), analysis of leg colour characters and geometric morphometric analysis of wing shape. The morphological data confirmed the absence of significant differences between S. pallipes and S. pseudospicatus found in the DNA analysis. Significant differences in the wing shape of two species have not been revealed. Hence, according to our data, there is no reason to consider S. pseudospicatus as a distinct species.

scholarly journals Low Nucleotide Diversity in Chimpanzees and Bonobos

Genetics ◽  
2003 ◽  
Vol 164 (4) ◽  
pp. 1511-1518 ◽  
Author(s):  
Ning Yu ◽  
Michael I Jensen-Seaman ◽  
Leona Chemnick ◽  
Judith R Kidd ◽  
Amos S Deinard ◽  
...  
Keyword(s):  
Nucleotide Diversity ◽  
Nuclear Dna ◽  
Demographic History ◽  
Nuclear Genome ◽  
Limited Data ◽  
Effective Population ◽  
East Central ◽  
Dna Diversity ◽  
History Of ◽  
Mtdna Diversity

Abstract Comparison of the levels of nucleotide diversity in humans and apes may provide much insight into the mechanisms of maintenance of DNA polymorphism and the demographic history of these organisms. In the past, abundant mitochondrial DNA (mtDNA) polymorphism data indicated that nucleotide diversity (π) is more than threefold higher in chimpanzees than in humans. Furthermore, it has recently been claimed, on the basis of limited data, that this is also true for nuclear DNA. In this study we sequenced 50 noncoding, nonrepetitive DNA segments randomly chosen from the nuclear genome in 9 bonobos and 17 chimpanzees. Surprisingly, the π value for bonobos is only 0.078%, even somewhat lower than that (0.088%) for humans for the same 50 segments. The π values are 0.092, 0.130, and 0.082% for East, Central, and West African chimpanzees, respectively, and 0.132% for all chimpanzees. These values are similar to or at most only 1.5 times higher than that for humans. The much larger difference in mtDNA diversity than in nuclear DNA diversity between humans and chimpanzees is puzzling. We speculate that it is due mainly to a reduction in effective population size (Ne) in the human lineage after the human-chimpanzee divergence, because a reduction in Ne has a stronger effect on mtDNA diversity than on nuclear DNA diversity.

scholarly journals Disentangling relationships among eastern Mediterranean Cymbalaria including description of a novel species from the southern Peloponnese (Greece)

2021 ◽  
Vol 307 (2) ◽  
Author(s):  
Pau Carnicero ◽  
Núria Garcia-Jacas ◽  
Llorenç Sáez ◽  
Theophanis Constantinidis ◽  
Mercè Galbany-Casals
Keyword(s):  
Eastern Mediterranean ◽  
Phylogenetic Analyses ◽  
Taxonomic Revision ◽  
Distribution Patterns ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Long Distance ◽  
Aegean Islands ◽  
Molecular Phylogenetic

AbstractThe eastern Mediterranean basin hosts a remarkably high plant diversity. Historical connections between currently isolated areas across the Aegean region and long-distance dispersal events have been invoked to explain current distribution patterns of species. According to most recent treatments, at least two Cymbalaria species occur in this area, Cymbalaria microcalyx and C. longipes. The former comprises several intraspecific taxa, treated at different ranks by different authors based on morphological data, evidencing the need of a taxonomic revision. Additionally, some populations of C. microcalyx show exclusive morphological characters that do not match any described taxon. Here, we aim to shed light on the systematics of eastern Mediterranean Cymbalaria and to propose a classification informed by various sources of evidence. We performed molecular phylogenetic analyses using ITS, 3’ETS, ndhF and rpl32-trnL sequences and estimated the ploidy level of some taxa performing relative genome size measures. Molecular data combined with morphology support the division of traditionally delimited C. microcalyx into C. acutiloba, C. microcalyx and C. minor, corresponding to well-delimited nrDNA lineages. Furthermore, we propose to combine C. microcalyx subsp. paradoxa at the species level. A group of specimens previously thought to belong to Cymbalaria microcalyx constitute a well-defined phylogenetic and morphological entity and are described here as a new species, Cymbalaria spetae. Cymbalaria longipes is non-monophyletic, but characterized by being glabrous and diploid, unlike other eastern species. The nrDNA data suggest at least two dispersals from the mainland to the Aegean Islands, potentially facilitated by marine regressions.

scholarly journals Combination of nuclear and mitochondrial markers as a useful tool to identify Ctenophthalmus species and subspecies (Siphonaptera: Ctenophthalmidae)

2021 ◽  
Author(s):  
Antonio Zurita ◽  
Cristina Cutillas
Keyword(s):  
Taxonomic Status ◽  
Molecular Study ◽  
Molecular Data ◽  
Point Of View ◽  
Morphological Data ◽  
Molecular Approach ◽  
Nuclear Marker ◽  
Mitochondrial Markers ◽  
Morphological Criteria ◽  
Mtdna Markers

AbstractCtenophthalmus is considered the largest genus within the Order Siphonaptera. From a morphological point of view, only males of this genus can be identified at species and subspecies levels using morphological keys, whereas there are no morphological criteria in order to classify females at these taxonomical levels. Furthermore, the amount of available molecular and phylogenetic data for this genus is quite scarce so far. The main objective of this work was to assess the utility of the combination of nuclear and mitochondrial markers with respect to their ability to differentiate among different subspecies within the Ctenophthalmus genus. With this purpose, we carried out a comparative morphological and molecular study of three different subspecies (Ctenophthalmus baeticus arvernus, Ctenophthalmus nobilis dobyi, and Ctenophthalmus andorrensis catalaniensis) in order to clarify and discuss its taxonomic status. In addition, our study complemented the molecular data previously provided for Ctenophthalmus baeticus boisseauorum and Ctenophthalmus apertus allani subspecies. We sequenced five different molecular markers: EF1-α, ITS1, ITS2, cox1, and cytb. Our results confirmed that morphological data by themselves are not able to discriminate among Ctenophthalmus female taxa; however, the combination of the nuclear marker EF1-α together with mtDNA markers cytb and cox1 constituted a useful taxonomical and phylogenetic tool to solve this issue. Based on these results, we consider that the use of this molecular approach should be gradually used within Ctenophthalmus genus in order to complement its classical taxonomy and clarifying the complex taxonomy of other congeneric species of fleas.

Phylogeographic structure and gene flow of Himalayan snowcock (Tetraogallus himalayensis)

2010 ◽  
Vol 60 (4) ◽  
pp. 449-465
Author(s):  
Wen Longying ◽  
Zhang Lixun ◽  
An Bei ◽  
Luo Huaxing ◽  
Liu Naifa ◽  
...  
Keyword(s):  
Demographic History ◽  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Population Expansion ◽  
Population History ◽  
Tibet Plateau ◽  
Phylogeographic Structure ◽  
Mitochondrial Cytochrome B ◽  
History Of ◽  
Qinghai Tibet Plateau

AbstractWe have used phylogeographic methods to investigate the genetic structure and population history of the endangered Himalayan snowcock (Tetraogallus himalayensis) in northwestern China. The mitochondrial cytochrome b gene was sequenced of 102 individuals sampled throughout the distribution range. In total, we found 26 different haplotypes defined by 28 polymorphic sites. Phylogenetic analyses indicated that the samples were divided into two major haplogroups corresponding to one western and one eastern clade. The divergence time between these major clades was estimated to be approximately one million years. An analysis of molecular variance showed that 40% of the total genetic variability was found within local populations, 12% among populations within regional groups and 48% among groups. An analysis of the demographic history of the populations suggested that major expansions have occurred in the Himalayan snowcock populations and these correlate mainly with the first and the second largest glaciations during the Pleistocene. In addition, the data indicate that there was a population expansion of the Tianshan population during the uplift of the Qinghai-Tibet Plateau, approximately 2 million years ago.

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