scholarly journals Phylogenetic relationships and genetic diversity of the Polypedates leucomystax complex in Thailand

2017 ◽  
Author(s):  
Kittisak Buddhachat ◽  
Chatmongkon Suwannapoom
Keyword(s):  
Isolation By Distance ◽  
Population Expansion ◽  
Climatic Conditions ◽  
Bayesian Posterior Probability ◽  
Tree Frog ◽  
Biogeographical Distribution ◽  
Haplotype Networks ◽  
Clade C ◽  
Polypedates Leucomystax ◽  
Isthmus Of Kra

Controversy in the taxonomic evaluation of the Asian tree frog Polypedates leucomystax complex presents the challenging task of gaining insight into its biogeographical distribution and diversification. Here, we describe the dispersion and genetic relationship of these species in Thailand where we connect the population of the P. leucomystax complex of the Sunda Islands to the mainland population based on the mitochondrial cytochrome c oxidase subunit I (COI) gene, derived from 266 samples. Our maternal genealogy implies that there are four well-supported lineages in Thailand, consisting of Northern A (clade A: Polypedates sp.), Nan (clade B: P. cf. impresus), Southern (clade C: P. cf. leucomystax) and Northern B (clade D: P. cf. megacephalus), with Bayesian posterior probability >0.9. Phylogeny and haplotype networks indicate that clades A, B and D are sympatric. In contrast, clade C (P. cf. leucomystax) and clade D (P. cf. megacephalus) are genetically divergent due to the geographical barrier of the Isthmus of Kra, resulting in allopatric distribution. Climatic conditions, in particular rainfall, that differ on each side of the Isthmus of Kra may play an important role in limiting the immigration of both clades. For the within-populations of either clades C or D, there was no significant correlation between geographic and genetic distance by the isolation-by-distance test, indicating intraspecific gene flow of each clade. Population expansion occurred in clade C, whereas clade D showed a constant population. Taken together, the P. leucomystax complex in Southeast Asia may be diversified by climatic oscillation, leading to allopatric and/or sympatric speciation.

scholarly journals Phylogenetic relationships and genetic diversity of the Polypedates leucomystax complex in Thailand

2017 ◽  
Author(s):  
Kittisak Buddhachat ◽  
Chatmongkon Suwannapoom
Keyword(s):  
Isolation By Distance ◽  
Population Expansion ◽  
Climatic Conditions ◽  
Bayesian Posterior Probability ◽  
Tree Frog ◽  
Biogeographical Distribution ◽  
Haplotype Networks ◽  
Clade C ◽  
Polypedates Leucomystax ◽  
Isthmus Of Kra

Controversy in the taxonomic evaluation of the Asian tree frog Polypedates leucomystax complex presents the challenging task of gaining insight into its biogeographical distribution and diversification. Here, we describe the dispersion and genetic relationship of these species in Thailand where we connect the population of the P. leucomystax complex of the Sunda Islands to the mainland population based on the mitochondrial cytochrome c oxidase subunit I (COI) gene, derived from 266 samples. Our maternal genealogy implies that there are four well-supported lineages in Thailand, consisting of Northern A (clade A: Polypedates sp.), Nan (clade B: P. cf. impresus), Southern (clade C: P. cf. leucomystax) and Northern B (clade D: P. cf. megacephalus), with Bayesian posterior probability >0.9. Phylogeny and haplotype networks indicate that clades A, B and D are sympatric. In contrast, clade C (P. cf. leucomystax) and clade D (P. cf. megacephalus) are genetically divergent due to the geographical barrier of the Isthmus of Kra, resulting in allopatric distribution. Climatic conditions, in particular rainfall, that differ on each side of the Isthmus of Kra may play an important role in limiting the immigration of both clades. For the within-populations of either clades C or D, there was no significant correlation between geographic and genetic distance by the isolation-by-distance test, indicating intraspecific gene flow of each clade. Population expansion occurred in clade C, whereas clade D showed a constant population. Taken together, the P. leucomystax complex in Southeast Asia may be diversified by climatic oscillation, leading to allopatric and/or sympatric speciation.

scholarly journals Phylogenetic relationships and genetic diversity of thePolypedates leucomystaxcomplex in Thailand

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4263 ◽  
Author(s):  
Kittisak Buddhachat ◽  
Chatmongkon Suwannapoom
Keyword(s):  
Isolation By Distance ◽  
Genetic Relationships ◽  
Population Expansion ◽  
Population Based ◽  
Climatic Conditions ◽  
Bayesian Posterior Probability ◽  
Tree Frog ◽  
Haplotype Networks ◽  
Clade C ◽  
Isthmus Of Kra

Taxonomic uncertainty of the Asian tree frogPolypedates leucomystaxcomplex presents the challenging task of inferring its biogeographical history. Here, we describe its dispersion and the genetic relationships among different populations in Thailand, where we connect the population of theP. leucomystaxcomplex of the Sunda Islands to the Indochina (mainland) population based on analyses of 266 sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene. Our maternal genealogy implies that there are four well-supported lineages in Thailand, consisting of Northern A (clade A:Polypedatessp.), Nan (clade B:P.cf.impresus), Southern (clade C:P. cf.leucomystax) and Northern D (clade D:P.cf.megacephalus), with Bayesian posterior probability >0.9. Phylogeny and haplotype networks indicate that clades A, B and D are sympatric. In contrast, clade C (P. cf.leucomystax) and clade D (P.cf.megacephalus) are genetically divergent due to the geographical barrier of the Isthmus of Kra, resulting in an allopatric distribution. Climatic conditions, in particular differences in rainfall on each side of the Isthmus of Kra, may play an important role in limiting the immigration of both clades. For the within-populations of either clades C or D, there was no significant correlation between geographic and genetic distance by the isolation-by-distance test, indicating intraspecific-dispersal of each clade. Population expansion occurred in clade C, whereas clade D showed a constant population. Taken together, theP. leucomystaxcomplex in South East Asia may have diversified under climatic pressure, leading to allopatric and/or sympatric speciation.

scholarly journals Phylogeography and population genetics of Macronycteris commersonii s.s. (Chiroptera: Hipposideridae), an endemic Malagasy bat

2018 ◽  
Author(s):  
Andrinajoro R Rakotoarivelo ◽  
Steven M Goodman ◽  
M Corrie Schoeman ◽  
Sandi Willows-Munro
Keyword(s):  
Sequence Data ◽  
Isolation By Distance ◽  
Population Expansion ◽  
Recent Common Ancestor ◽  
Climate Conditions ◽  
Most Recent Common Ancestor ◽  
Pleistocene Climate ◽  
Clade C ◽  
Distance Model ◽  
Forested Areas

Macronycteris commersonii (Hipposideridae), a bat species endemic to Madagascar, is widespread across the island, utilising open woodland, degraded habitats, and forested areas from sea level to 1325 m. We investigated the fine-scale phylogeographic history and relationships of populations occurring in the western half of the island using sequence data from two mitochondrial DNA regions and extensive geographical sampling. Our results indicated a highly supported monophyletic group of M. commersonii, in which the Northern Madagascar Clade C formed a single monophyletic clade. The most recent common ancestor of M. commersonii was dated to 0.82 million years ago (mid-Pleistocene). Population expansion events were inferred for Clade B from approximately 130,000 to 70,000 years BP. Bayesian clustering and AMOVA analyses inferred week population genetic structure and sequence data indicated that genetic subdivisions do not support an isolation-by-distance model. Lineage dispersal, genetic divergence, and expansion events of M. commersonii were likely to be associated with Pleistocene climate fluctuations. Our data suggested that the northern and the central western regions of Madagascar may have acted as refugia for this species during periods of cooler and drier climate conditions associated with the Pleistocene.

scholarly journals Phylogeography and population genetics of Macronycteris commersonii s.s. (Chiroptera: Hipposideridae), an endemic Malagasy bat

2018 ◽  
Author(s):  
Andrinajoro R Rakotoarivelo ◽  
Steven M Goodman ◽  
M Corrie Schoeman ◽  
Sandi Willows-Munro
Keyword(s):  
Sequence Data ◽  
Isolation By Distance ◽  
Population Expansion ◽  
Recent Common Ancestor ◽  
Climate Conditions ◽  
Most Recent Common Ancestor ◽  
Pleistocene Climate ◽  
Clade C ◽  
Distance Model ◽  
Forested Areas

Macronycteris commersonii (Hipposideridae), a bat species endemic to Madagascar, is widespread across the island, utilising open woodland, degraded habitats, and forested areas from sea level to 1325 m. We investigated the fine-scale phylogeographic history and relationships of populations occurring in the western half of the island using sequence data from two mitochondrial DNA regions and extensive geographical sampling. Our results indicated a highly supported monophyletic group of M. commersonii, in which the Northern Madagascar Clade C formed a single monophyletic clade. The most recent common ancestor of M. commersonii was dated to 0.82 million years ago (mid-Pleistocene). Population expansion events were inferred for Clade B from approximately 130,000 to 70,000 years BP. Bayesian clustering and AMOVA analyses inferred week population genetic structure and sequence data indicated that genetic subdivisions do not support an isolation-by-distance model. Lineage dispersal, genetic divergence, and expansion events of M. commersonii were likely to be associated with Pleistocene climate fluctuations. Our data suggested that the northern and the central western regions of Madagascar may have acted as refugia for this species during periods of cooler and drier climate conditions associated with the Pleistocene.

scholarly journals Population genetics of Aedes albopictus (Diptera: Culicidae) in its native range in Lao People’s Democratic Republic

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Maysa Tiemi Motoki ◽  
Dina Madera Fonseca ◽  
Elliott Frederic Miot ◽  
Bruna Demari-Silva ◽  
Phoutmany Thammavong ◽  
...  
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Aedes Albopictus ◽  
Isolation By Distance ◽  
Genetic Locus ◽  
Lao Pdr ◽  
Phylogenetic Network ◽  
Population Expansion ◽  
Recent Population Expansion ◽  
The Usa

Abstract Background The Asian tiger mosquito, Aedes (Stegomyia) albopictus (Skuse) is an important worldwide invasive species and can be a locally important vector of chikungunya, dengue and, potentially, Zika. This species is native to Southeast Asia where populations thrive in both temperate and tropical climates. A better understanding of the population structure of Ae. albopictus in Lao PDR is very important in order to support the implementation of strategies for diseases prevention and vector control. In the present study, we investigated the genetic variability of Ae. albopictus across a north-south transect in Lao PDR. Methods We used variability in a 1337-bp fragment of the mitochondrial cytochrome c oxidase subunit 1 gene (cox1), to assess the population structure of Ae. albopictus in Lao PDR. For context, we also examined variability at the same genetic locus in samples of Ae. albopictus from Thailand, China, Taiwan, Japan, Singapore, Italy and the USA. Results We observed very high levels of genetic polymorphism with 46 novel haplotypes in Ae. albopictus from 9 localities in Lao PDR and Thailand populations. Significant differences were observed between the Luangnamtha population and other locations in Lao PDR. However, we found no evidence of isolation by distance. There was overall little genetic structure indicating ongoing and frequent gene flow among populations or a recent population expansion. Indeed, the neutrality test supported population expansion in Laotian Ae. albopictus and mismatch distribution analyses showed a lack of low frequency alleles, a pattern often seen in bottlenecked populations. When samples from Lao PDR were analyzed together with samples from Thailand, China, Taiwan, Japan, Singapore, Italy and the USA, phylogenetic network and Bayesian cluster analysis showed that most populations from tropical/subtropical regions are more genetically related to each other, than populations from temperate regions. Similarly, most populations from temperate regions are more genetically related to each other, than those from tropical/subtropical regions. Conclusions Aedes albopictus in Lao PDR are genetically related to populations from tropical/subtropical regions (i.e. Thailand, Singapore, and California and Texas in the USA). The extensive gene flow among locations in Lao PDR indicates that local control is undermined by repeated introductions from untreated sites.

scholarly journals Expansion of Genetic Diversity in Randomly Mating Founder Populations of Alternaria brassicicola Infecting Cakile maritima in Australia

2010 ◽  
Vol 76 (6) ◽  
pp. 1946-1954 ◽  
Author(s):  
C. C. Linde ◽  
J. A. Liles ◽  
P. H. Thrall
Keyword(s):  
Genetic Diversity ◽  
Plant Pathogens ◽  
Isolation By Distance ◽  
Population Expansion ◽  
Alternaria Brassicicola ◽  
Evolutionary Potential ◽  
Recent Population Expansion ◽  
Fungal Plant Pathogens ◽  
Cakile Maritima ◽  
Founder Populations

ABSTRACT Founder populations of fungal plant pathogens are expected to have low levels of genetic diversity coupled with further genetic drift due to, e.g., limited host availability, which should result in additional population bottlenecks. This study used microsatellite markers in the interaction between Cakile maritima and the fungal pathogen Alternaria brassicicola to explore genetic expectations associated with such situations. The host, C. maritima, was introduced into Australia approximately 100 years ago, but it is unknown whether the pathogen was already present in Australia, as it has a wide occurrence, or whether it was introduced to Australia on brassicaceous hosts. Eleven A. brassicicola populations were studied, and all showed moderate levels of gene and genotypic diversity. Chi-square tests of the frequencies of mating type alleles, a large number of genotypes, and linkage equilibrium among microsatellite loci all suggest A. brassicicola reproduces sexually. Significant genetic differentiation was found among populations, but there was no evidence for isolation by distance effects. Bayesian analyses identified eight clusters where the inferred clusters did not represent geographical populations but instead consisted of individuals admixed from all populations. Further analysis indicated that fungal populations were more likely to have experienced a recent population expansion than a population bottleneck. It is suggested that A. brassicicola has been introduced into Australia multiple times, potentially increasing the diversity and size of any A. brassicola populations already present there. Combined with its ability to reproduce sexually, such processes appear to have increased the evolutionary potential of the pathogen through recent population expansions.

scholarly journals Population genetic structure and variability in Lindera glauca (Lauraceae) indicates low levels of genetic diversity and skewed sex ratios in natural populations in mainland China

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8304 ◽  
Author(s):  
Biao Xiong ◽  
Limei Zhang ◽  
Shubin Dong ◽  
Zhixiang Zhang
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Isolation By Distance ◽  
Sex Ratios ◽  
Mainland China ◽  
Small Sample ◽  
Chloroplast Microsatellites ◽  
Wild Populations ◽  
Haplotype Networks ◽  
Low Levels

Lindera glauca (Lauraceae) is a tree of economic and ecological significance that reproduces sexually and asexually via apomictic seeds. It is widely distributed in the low-altitude montane forests of East Asia. Despite the potential implications of a mixed reproductive system in terms of genetic diversity, few studies have focused on this aspect. In this study, the genetic structure of wild populations of L. glauca was investigated via genetic analyses. Overall, 13 nuclear microsatellites (nSSRs) and five chloroplast microsatellites (cpSSRs) were used to genotype 300 individual plants, taken from 20 wild populations (a small sample size in some wild populations is due to the limitation of its specific reproduction, leading to certain limitations in the results of this study) and two cultivated populations ranging across nearly the entire natural distribution of mainland China. The populations exhibited low levels of genetic diversity (nSSR: AR = 1.75, Ho = 0.32, He = 0.36; cpSSR: Nb = 2.01, Hrs = 0.40), and no significant effect of isolation by distance between populations existed, regardless of marker type (nSSR: R2 = 0.0401, P = 0.068; cpSSR: R2 = 0.033, P = 0.091). Haplotype networks showed complex relationships among populations, and the H12 haplotype was predominant in most populations. Analyses of molecular variance obtained with nuclear markers (Fsc = 0.293, FST = 0.362) and chloroplast markers (Fsc = 0.299, FST = 0.312) were similar. The migration ratio of pollen flow versus seed flow in this study was negative (r = −1.149). Results suggest that weak barriers of dispersal between populations and/or the similarity of founders shared between neighbors and distant populations are indicative of the gene flow between populations more likely involving seeds. Wild L. glauca in mainland China was inferred to have highly skewed sex ratios with predominant females. In addition, some populations experienced a recent bottleneck effect, especially in Gujianshan, Chongqing, and southwest China (population GJS). It is suggested that few wild male individuals should be conserved in order to maintain overall genetic diversity in the wild populations of this species. These findings provide important information for the sustainable utilization and preservation of the overall genetic diversity of L. glauca.

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.

Genetic homogeneity of weathervane scallops (Patinopecten caurinus) in the northeastern Pacific

2010 ◽  
Vol 67 (11) ◽  
pp. 1827-1839 ◽  
Author(s):  
Patrick M. Gaffney ◽  
Carita M. Pascal ◽  
Jeffery Barnhart ◽  
W. Stewart Grant ◽  
James E. Seeb
Keyword(s):  
Genetic Differentiation ◽  
Gene Diversity ◽  
Isolation By Distance ◽  
Population Expansion ◽  
Gulf Of Alaska ◽  
Nucleotide Sequencing ◽  
Mt Dna ◽  
Northeastern Pacific ◽  
Nuclear Loci ◽  
Allozyme Loci

We assessed genetic differentiation among populations of weathervane scallop ( Patinopecten caurinus ) in the northeastern Pacific, extending over 2500 km in the Gulf of Alaska and southeastern Bering Sea. Variability was surveyed at nuclear loci with allozyme, microsatellite, and single nucleotide polymorphism (SNP) methods, and at mitochondrial (mt)DNA loci with SNPs and nucleotide sequencing. High levels of gene diversity were detected for allozymes (H = 0.080), microsatellites (H = 0.734), and mtDNA (h = 0.781). Genotypes at nuclear loci generally fit Hardy–Weinberg proportions, except for some microsatellite loci, for which null-allele frequencies of 0.02 to 0.34 were estimated. No allele-frequency differences were detected among samples, except for the allozyme loci Gpi and Pep-4. Overall levels of differentiation ranged from FST = 0.0004 for allozymes, FST = 0.0008 for mtDNA to FST = 0.0004 for microsatellites. No isolation by distance was found for any of the markers. A unimodal mtDNA mismatch distribution and significant excesses of low-frequency variants for allozymes, microsatellites, and mtDNA may reflect a post-glacial population expansion. The lack of genetic differentiation measured by neutral markers does not preclude the existence of locally adapted, self-sustaining populations that are important in the harvest management of this species.

Sign in / Sign up

Export Citation Format

Share Document