The Experts below are selected from a list of 222 Experts worldwide ranked by ideXlab platform
Chaolun Allen Chen - One of the best experts on this subject based on the ideXlab platform.
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genetic connectivity and Historical Demography of the blue barred parrotfish scarus ghobban in the western indian ocean
Marine Biology, 2010Co-Authors: Shakil Visram, Mingche Yang, Ruby Moothien Pillay, Sadri Said, Oskar Henriksson, Mats Grahn, Chaolun Allen ChenAbstract:Studies on genetic connectivity are essential for the design of management strategies for coral reef fisheries. In this study we used a mitochondrial DNA marker to investigate population structure of the reef-associated parrotfish, Scarus ghobban, from four countries, Kenya, Mauritius, Seychelles and Tanzania, in the western Indian Ocean. We obtained nucleotide sequences of the mitochondrial control region for 117 individuals. Measures of haplotype diversity were relatively high. Pairwise population differentiation (FST) was low, but not always non-significant. Analysis of molecular variance (AMOVA) showed genetic differentiation between groups, when the data was partitioned into two groups consisting of samples from Mauritius and Tanzania in one group, and samples from Kenya and Seychelles in another group. Direction of gene flow was estimated using a Bayesian approach. Migration was sometimes asymmetric or directional, coinciding with the flow of major oceanic and coastal currents in the region. Mismatch distributions, based on the observed number of differences among haplotype pairs, produced a unimodal distribution, indicative of recent demographic expansion. Phylogenetic analyses revealed three clades without any geographic structure, suggesting recent migration between Historically isolated lineages. We reconstructed the Historical Demography of S. ghobban and examined it in the context of Pleistocene climate stages and changes in relative sea level. Overall, these results showed that populations of S. ghobban are genetically diverse and have relatively high gene flow, with some genetic structuring in the western Indian Ocean.
Stephane Boissinot - One of the best experts on this subject based on the ideXlab platform.
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multi locus phylogeographic and population genetic analysis of anolis carolinensis Historical Demography of a genomic model species
PLOS ONE, 2012Co-Authors: Marc Tollis, Gavriel Ausubel, Dhruba Ghimire, Stephane BoissinotAbstract:The green anole (Anolis carolinensis) has been widely used as an animal model in physiology and neurobiology but has recently emerged as an important genomic model. The recent sequencing of its genome has shed new light on the evolution of vertebrate genomes and on the process that govern species diversification. Surprisingly, the patterns of genetic diversity within natural populations of this widespread and abundant North American lizard remain relatively unknown. In the present study, we use 10 novel nuclear DNA sequence loci (N = 62 to 152) and one mitochondrial locus (N = 226) to delimit green anole populations and infer their Historical Demography. We uncovered four evolutionarily distinct and geographically restricted lineages of green anoles using phylogenetics, Bayesian clustering, and genetic distance methods. Molecular dating indicates that these lineages last shared a common ancestor ∼2 million years ago. Summary statistics and analysis of the frequency distributions of DNA polymorphisms strongly suggest range-wide expansions in population size. Using Bayesian Skyline Plots, we inferred the timing of population size expansions, which differ across lineages, and found evidence for a relatively recent and rapid westward expansion of green anoles across the Gulf Coastal Plain during the mid-Pleistocene. One surprising result is that the distribution of genetic diversity is not consistent with a latitudinal shift caused by climatic oscillations as is observed for many co-distributed taxa. This suggests that the most recent Pleistocene glacial cycles had a limited impact on the geographic distribution of the green anole at the northern limits of its range.
G J Kenagy - One of the best experts on this subject based on the ideXlab platform.
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Historical Demography and genetic structure of sister species deermice peromyscus in the north american temperate rain forest
Molecular Ecology, 2003Co-Authors: Xiaoguang Zheng, Brian S Arbogast, G J KenagyAbstract:To investigate the evolutionary and biogeographical history of Peromyscus keeni and P. maniculatus within the coastal forest ecosystem of the Pacific Northwest of North America, we sampled 128 individuals from 43 localities from southeastern Alaska through Oregon. We analysed mitochondrial DNA variation using DNA sequence data from the mitochondrial cytochrome-b (cyt-b) gene and control region, and we found two distinct clades consistent with the morphological designation of the two species. The sequence divergence between the two clades was 0.0484 substitutions per site for cyt-b and 0.0396 for the control region, suggesting that divergence of the two clades occurred during the middle to late Pleistocene. We also examined the Historical Demography of the two clades using stepwise and exponential expansion models, both of which indicated recent rapid population growth. Furthermore, using the program migrate we found evidence of migration from populations north of the Fraser River (British Columbia) to the south in both clades. This study demonstrates the utility of these model-based demographic methods in illuminating the evolutionary and biogegographic history of natural systems.
Andrew J Dewoody - One of the best experts on this subject based on the ideXlab platform.
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Historical Demography of bird populations from hispaniola assessed by nuclear and mitochondrial gene sequences
Folia Zoologica, 2015Co-Authors: Anna L Fahey, Robert E Ricklefs, Andrew J DewoodyAbstract:Molecular markers can be used to infer the demographic history of a given species, but many historic processes simultaneously impact multiple species. Thus, comparative Historical Demography has the potential to provide insight into drivers of evolution. In this study, we used nuclear DNA (nDNA) sequences to corroborate (or refute) demographic inferences based on earlier mitochondrial DNA (mtDNA) data from 16 species of Hispaniola birds. Our previously published analysis suggested population expansion in five of six migratory species (following glacial retreat in North America), with less evidence of expansion in non-migratory species. Additional molecular markers should reduce locus-specific bias, and so we generated sequence data for several nuclear loci. Test statistics associated with the nDNA provided only equivocal evidence for population expansion in 10 of the 16 species. Discordance between mtDNA and nDNA is not uncommon because the two genomes are exposed to different selective pressures and have different effective population sizes and modes of inheritance. The nDNA analyses reported here cast some doubt on our earlier mtDNA inferences. They also suggest that the signal to noise ratio of demographic statistics is typically low because of the inherent variability in selective regimes and coalescence across loci.
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dna based approaches for evaluating Historical Demography in terrestrial vertebrates
Biological Journal of The Linnean Society, 2014Co-Authors: Anna L Fahey, Robert E Ricklefs, Andrew J DewoodyAbstract:Contemporary DNA sequences can provide information about the Historical Demography of a species. However, different molecular markers are informative under different circumstances. In particular, mitochondrial (mt)DNA is uniparentally inherited and haploid in most vertebrates and thus has a smaller effective population size than diploid, biparentally inherited nuclear (n)DNA. Here, we review the characteristics of mtDNA and nDNA in the context of Historical Demography. In particular, we address how their contrasting rates of evolution and sex-biased dispersal can lead to different demographic inferences. We do so in the context of an extensive review of the vertebrate literature that describes the use of mtDNA and nDNA sequence data in demographic reconstruction. We discuss the effects of coalescence, effective population size, substitution rates, and sex-biased dispersal on informative timeframes and expected patterns of genetic differentiation. We argue that mtDNA variationin species with male-biased dispersal can imply deviations from neutrality that do not reflect actual population expansion or selection. By contrast, mtDNA can be more informative when coalescence has occurred within the recent past, which appears to be the case with many vertebrates. We also compare the application and interpretation of demographic and neutrality test statistics in Historical Demography studies. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 112, 367–386.
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comparative Historical Demography of migratory and nonmigratory birds from the caribbean island of hispaniola
Evolutionary Biology-new York, 2012Co-Authors: Anna L Fahey, Robert E Ricklefs, Steven C Latta, Andrew J DewoodyAbstract:Islands offer unique opportunities for studies of evolution and Historical Demography. We hypothesized that wintering North American migrant bird species would show genetic evidence of population expansion over recent millennia due to the expansion of their breeding distributions following the retreat of the Laurentide ice sheet. In contrast, we presumed that non-migratory species would exhibit more stable Historical demographies. We used mtDNA sequences from 649 individuals of 16 avian species on the Caribbean island of Hispaniola to test this prediction. Mismatch distributions did not differ significantly between migrants and non-migrants. However, neutrality indices indicated population expansion in the migrant species, as well as two non-migratory resident species with extensive distributions. Evidence of population expansion was less consistent in other non-migratory residents. We infer that climate prior to the Last Glacial Maximum significantly reduced effective population sizes of most migratory North American bird populations and some resident Hispaniolan bird populations. Our data further revealed that mismatch statistics were poorly correlated with and less informative than the neutrality test statistics, a consideration for future demographic studies.
Marc Tollis - One of the best experts on this subject based on the ideXlab platform.
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multi locus phylogeographic and population genetic analysis of anolis carolinensis Historical Demography of a genomic model species
PLOS ONE, 2012Co-Authors: Marc Tollis, Gavriel Ausubel, Dhruba Ghimire, Stephane BoissinotAbstract:The green anole (Anolis carolinensis) has been widely used as an animal model in physiology and neurobiology but has recently emerged as an important genomic model. The recent sequencing of its genome has shed new light on the evolution of vertebrate genomes and on the process that govern species diversification. Surprisingly, the patterns of genetic diversity within natural populations of this widespread and abundant North American lizard remain relatively unknown. In the present study, we use 10 novel nuclear DNA sequence loci (N = 62 to 152) and one mitochondrial locus (N = 226) to delimit green anole populations and infer their Historical Demography. We uncovered four evolutionarily distinct and geographically restricted lineages of green anoles using phylogenetics, Bayesian clustering, and genetic distance methods. Molecular dating indicates that these lineages last shared a common ancestor ∼2 million years ago. Summary statistics and analysis of the frequency distributions of DNA polymorphisms strongly suggest range-wide expansions in population size. Using Bayesian Skyline Plots, we inferred the timing of population size expansions, which differ across lineages, and found evidence for a relatively recent and rapid westward expansion of green anoles across the Gulf Coastal Plain during the mid-Pleistocene. One surprising result is that the distribution of genetic diversity is not consistent with a latitudinal shift caused by climatic oscillations as is observed for many co-distributed taxa. This suggests that the most recent Pleistocene glacial cycles had a limited impact on the geographic distribution of the green anole at the northern limits of its range.