scholarly journals Genetic Differentiation and Demographic History of Three Cerris Oak Species in China Based on Nuclear Microsatellite Makers

Forests ◽  
2021 ◽  
Vol 12 (9) ◽  
pp. 1164
Author(s):  
Xiao-Dan Chen ◽  
Xiao Zhang ◽  
Hao Zhang ◽  
Tao Zhou ◽  
Yue-Mei Zhao ◽  
...  
Keyword(s):  
Genetic Differentiation ◽  
Climatic Change ◽  
Ecological Niche Modeling ◽  
Demographic History ◽  
Natural Populations ◽  
Population History ◽  
Climatic Oscillations ◽  
History Analysis ◽  
Spatiotemporal Population Dynamics ◽  
Approximate Bayesian

Knowledge of interspecific divergence and population expansions/contractions of dominant forest trees in response to geological events and climatic oscillations is of major importance to understand their evolution and demography. However, the interspecific patterns of genetic differentiation and spatiotemporal population dynamics of three deciduous Cerris oak species (Q. acutissima, Q. variabilis and Q. chenii) that are widely distributed in China remain poorly understood. In this study, we genotyped 16 nuclear loci in 759 individuals sampled from 44 natural populations of these three sibling species to evaluate the plausible demographical scenarios of the closely related species. We also tested the hypothesis that macro- and microevolutionary processes of the three species had been triggered and molded by Miocene–Pliocene geological events and Quaternary climatic change. The Bayesian cluster analysis showed that Q. acutissima and Q. chenii were clustered in the same group, whereas Q. variabilis formed a different genetic cluster. An approximate Bayesian computation (ABC) analyses suggested that Q. variabilis and Q. acutissima diverged from their most common ancestor around 19.84 Ma, and subsequently Q. chenii diverged from Q. acutissima at about 9.6 Ma, which was significantly associated with the episodes of the Qinghai–Tibetan Plateau (QTP). In addition, ecological niche modeling and population history analysis showed that these three Cerris oak species repeatedly underwent considerable ‘expansion–contraction’ during the interglacial and glacial periods of the Pleistocene, although they have varying degrees of tolerance for the climatic change. Overall, these findings indicated geological and climatic changes during the Miocene–Pliocene and Pleistocene as causes of species divergence and range shifts of dominant tree species in the subtropical and warm temperature areas in China.

Genetic and morphological differentiation among populations of the Rivoli’s Hummingbird (Eugenes fulgens) species complex (Aves: Trochilidae)

The Auk ◽  
2020 ◽  
Vol 137 (4) ◽  
Author(s):  
Luz E Zamudio-Beltrán ◽  
Juan Francisco Ornelas ◽  
Andreia Malpica ◽  
Blanca E Hernández-Baños
Keyword(s):  
Genetic Variation ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
Species Complex ◽  
Ecological Niche Modeling ◽  
Demographic History ◽  
Morphological Differentiation ◽  
Last Interglacial ◽  
Haplotype Networks ◽  
Isthmus Of Tehuantepec

Abstract Genetic variation and phylogeographic studies have been crucial for understanding mechanisms of speciation. We analyzed genetic variation and phylogeography to reconstruct the demographic history of the Rivoli’s Hummingbird (Eugenes fulgens) species complex and also evaluated their morphological differentiation. This widely distributed species inhabits the highlands of Mexico and northern Central America, with 2 subspecies separated by the Isthmus of Tehuantepec (west: E. f. fulgens, east: E. f. viridiceps). We surveyed genetic variation in 2 mitochondrial DNA markers (mtDNA, with 129 individuals) and nuclear DNA (6 microsatellites, with 85 individuals). We also inferred the demographic history, estimated divergence times, and analyzed morphological variation using 470 vouchered specimens. We modeled the current potential distribution of the species using ecological niche modeling and projected it into the past to model the effects of the Pleistocene climatic cycles. Haplotype networks, pairwise FST comparisons, AMOVA, and morphological analysis revealed differences between geographically isolated populations separated by the Isthmus of Tehuantepec (IT; corresponding to the 2 recognized subspecies: fulgens and viridiceps), and by the Motagua-Polochic-Jocotán (MPJ) system fault. Demographic scenarios revealed a contraction in distribution during the last interglacial, and expansion during the Last Glacial Maximum (LGM) with little change since the LGM. Divergence between groups separated by the Isthmus of Tehuantepec ~59,600 yr ago occurred in the presence of gene flow, suggesting that the Isthmus of Tehuantepec is a semipermeable barrier to gene flow. STRUCTURE analyses of microsatellite data detected 3 genetically differentiated groups. Several results fit a model of recent lineage divergence, including a significant signal of genetic differentiation, demographic expansion, decreased gene flow from past to present, and northward expansion during the LGM and contraction during the interglacial periods. We conclude that the genetic differentiation of E. fulgens in the Madrean Pine-Oak Woodlands resulted from recent geographical isolation of populations separated by natural barriers (IT and MPJ).

Patterns of genetic differentiation and population history of endemic isopods (Asellidae) from ancient Lake Ohrid: combining allozyme and mtDNA data

2013 ◽  
Vol 8 (9) ◽  
pp. 854-875 ◽  
Author(s):  
Adrianna Kilikowska ◽  
Anna Wysocka ◽  
Artur Burzyński ◽  
Goce Kostoski ◽  
Joanna Rychlińska ◽  
...  
Keyword(s):  
Genetic Differentiation ◽  
Demographic History ◽  
Horizontal Distribution ◽  
Population History ◽  
Main Role ◽  
Ancient Lake ◽  
Lake Ohrid ◽  
History Of ◽  
Allozyme Loci ◽  
Parapatric Speciation

AbstractAncient lakes as places of extensive speciation processes have been characterized by a high degree of endemicity and biodiversity. The most outstanding European ancient lake is the oligotrophic and karstic Balkan Lake Ohrid. The lake is inhabited by a number of endemic species, but their evolutionary history is largely unresolved. in the present study, the genetic structure, gene genealogy and demographic history of the representatives of the Ohridian endemic Proasellus species were studied using both biparentally (allozyme loci) and maternally (partial mitochondrial cytochrome oxidase subunit I gene) inherited markers. Both data sets gave similar results and supported discrepancies among genetic differentiation, the current morphology-based taxonomy and bathymetric segregation. Horizontal distribution of endemic Proasellus species (Lake Ohrid vs adjacent feeder springs) within the lake presumably promote parapatric speciation whereas the main role of vertical barriers into diversification processes was not fully supported. The analyses of demographic history suggested the decline of endemic isopod populations. The radiation of endemic Proasellus populations within the lake could have started from the sublittoral/profundal zone towards the littoral or in the opposite direction — from the littoral to the profundal. Our analyses did not exclude both possibilities.

scholarly journals Robust estimation of recent effective population size from number of independent origins in soft sweeps

2018 ◽  
Author(s):  
Bhavin S. Khatri ◽  
Austin Burt
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Demographic History ◽  
Population Sample ◽  
Natural Populations ◽  
Population History ◽  
Effective Population ◽  
Current Frequency ◽  
Population Size Estimate ◽  
Recurrent Mutations

Estimating recent effective population size is of great importance in characterising and predicting the evolution of natural populations. Methods based on nucleotide diversity may underestimate current day effective population sizes due to historical bottlenecks, whilst methods that reconstruct demographic history typically only detect long-term variations. However, soft selective sweeps, which leave a fingerprint of mutational history by recurrent mutations on independent haplotype backgrounds, holds promise of an estimate more representative of recent population history. Here we present a simple and robust method of estimation based only on knowledge of the number of independent recurrent origins and the current frequency of the beneficial allele in a population sample, independent of the strength of selection and age of the mutation. Using a forward time theoretical framework, we show the mean number of origins is a function of θ = 2Nμ and current allele frequency, through a simple equation, and the distribution is approximately Poisson. This estimate is robust to whether mutants pre-existed before selection arose, and is equally accurate for diploid populations with incomplete dominance. For fast (e.g., seasonal) demographic changes compared to time scale for fixation of the mutant allele, and for moderate peak-to-trough ratios, we show our constant population size estimate can be used to bound the maximum and minimum population size. Applied to the Vgsc gene of Anopheles gambiae, we estimate an effective population size of roughly 6 × 107, and including seasonal demographic oscillations, a minimum effective population size greater than 6 × 106 and a maximum less than 3 × 109.

scholarly journals Robust Estimation of Recent Effective Population Size from Number of Independent Origins in Soft Sweeps

2019 ◽  
Vol 36 (9) ◽  
pp. 2040-2052 ◽  
Author(s):  
Bhavin S Khatri ◽  
Austin Burt
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Demographic History ◽  
Population Sample ◽  
Natural Populations ◽  
Population History ◽  
Effective Population ◽  
Current Frequency ◽  
Population Size Estimate ◽  
Recurrent Mutations

Abstract Estimating recent effective population size is of great importance in characterizing and predicting the evolution of natural populations. Methods based on nucleotide diversity may underestimate current day effective population sizes due to historical bottlenecks, whereas methods that reconstruct demographic history typically only detect long-term variations. However, soft selective sweeps, which leave a fingerprint of mutational history by recurrent mutations on independent haplotype backgrounds, holds promise of an estimate more representative of recent population history. Here, we present a simple and robust method of estimation based only on knowledge of the number of independent recurrent origins and the current frequency of the beneficial allele in a population sample, independent of the strength of selection and age of the mutation. Using a forward-time theoretical framework, we show the mean number of origins is a function of θ=2Nμ and current allele frequency, through a simple equation, and the distribution is approximately Poisson. This estimate is robust to whether mutants preexisted before selection arose and is equally accurate for diploid populations with incomplete dominance. For fast (e.g., seasonal) demographic changes compared with time scale for fixation of the mutant allele, and for moderate peak-to-trough ratios, we show our constant population size estimate can be used to bound the maximum and minimum population size. Applied to the Vgsc gene of Anopheles gambiae, we estimate an effective population size of roughly 6×107, and including seasonal demographic oscillations, a minimum effective population size >3×107, and a maximum <6×109, suggesting a mean ∼109.

Connection, isolation and reconnection: Quaternary climatic oscillations and the Andes shaped the phylogeographical patterns of the Patagonian bee Centris cineraria (Apidae)

2020 ◽  
Vol 131 (2) ◽  
pp. 396-416 ◽  
Author(s):  
María Sosa-Pivatto ◽  
Gonzalo A Camps ◽  
Matías C Baranzelli ◽  
Anahí Espíndola ◽  
Alicia N Sérsic ◽  
...  
Keyword(s):  
Demographic History ◽  
Joint Effect ◽  
Secondary Contact ◽  
Glacial Refugium ◽  
Distribution Models ◽  
Climatic Oscillations ◽  
The Andes ◽  
History Of ◽  
Spatio Temporal ◽  
Approximate Bayesian

Abstract The joint effect of the Andes as a geographical barrier and the Quaternary glaciations as promoters of genetic divergence remains virtually unexplored in southern South America. To help fill this knowledge gap, in this study we investigated the demographic history of Centris cineraria, a solitary bee mainly distributed in Patagonia. We used mitochondrial and nuclear markers and performed phylogeographical and dating analyses, adjusted spatio-temporal diffusion and species distribution models, and used Approximate Bayesian Computation to identify likely historical demographic scenarios. Our results revealed that during glacial periods the Andes represented a barrier due to the extent of the ice-sheets and the occurrence of unsuitable habitats, while interglacials allowed for gene flow across the Andes. Secondary contact between previously isolated lineages was evident across at least two low-altitude Andean areas, the northern one being a putative glacial refugium. Our findings also suggest that C. cineraria has persisted in situ in four periglacial refugia located along a north–south transect, congruent with the maximum extent of the ice sheet during the Greatest Patagonian Glaciation. As the first phylogeographical study of Patagonian insects, our work reveals that the interaction between Quaternary climatic oscillations and the Andes as a barrier was the main driver of the spatial and demographic history of C. cineraria.

scholarly journals Patterns of genetic differentiation and the footprints of historical migrations in the Iberian Peninsula

2018 ◽  
Author(s):  
Clare Bycroft ◽  
Ceres Fernandez-Rozadilla ◽  
Clara Ruiz-Ponte ◽  
Inés Quintela-García ◽  
Ángel Carracedo ◽  
...  
Keyword(s):  
Population Structure ◽  
Genetic Differentiation ◽  
Iberian Peninsula ◽  
Association Studies ◽  
Demographic History ◽  
African Ancestry ◽  
Population History ◽  
Human Populations ◽  
Fine Scale ◽  
The North

Genetic differences within or between human populations (population structure) has been studied using a variety of approaches over many years. Recently there has been an increasing focus on studying genetic differentiation at fine geographic scales, such as within countries. Identifying such structure allows the study of recent population history, and identifies the potential for confounding in association studies, particularly when testing rare, often recently arisen variants. The Iberian Peninsula is linguistically diverse, has a complex demographic history, and is unique among European regions in having a centuries-long period of Muslim rule. Previous genetic studies of Spain have examined either a small fraction of the genome or only a few Spanish regions. Thus, the overall pattern of fine-scale population structure within Spain remains uncharacterised. Here we analyse genome-wide genotyping array data for 1,413 Spanish individuals sampled from all regions of Spain. We identify extensive fine-scale structure, down to unprecedented scales, smaller than 10 Km in some places. We observe a major axis of genetic differentiation that runs from east to west of the peninsula. In contrast, we observe remarkable genetic similarity in the north-south direction, and evidence of historical north-south population movement. Finally, without making particular prior assumptions about source populations, we show that modern Spanish people have regionally varying fractions of ancestry from a group most similar to modern north Moroccans. The north African ancestry results from an admixture event, which we date to 860 - 1120 CE, corresponding to the early half of Muslim rule. Our results indicate that it is possible to discern clear genetic impacts of the Muslim conquest and population movements associated with the subsequent Reconquista.

scholarly journals Demographic history and genetic differentiation of an endemic and endangered Ulmus lamellosa (Ulmus)

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Huimin Hou ◽  
Hang Ye ◽  
Zhi Wang ◽  
Jiahui Wu ◽  
Yue Gao ◽  
...  
Keyword(s):  
Genetic Differentiation ◽  
Demographic History ◽  
Critical Role ◽  
Divergence Time ◽  
Evolutionary Process ◽  
Northern China ◽  
Endangered Plant ◽  
Important Data ◽  
Climatic Oscillations ◽  
Group A

Abstract Background Ulmus lamellosa (one of the ancient species of Ulmus) is an endemic and endangered plant that has undergone climatic oscillations and geographical changes. The elucidation of its demographic history and genetic differentiation is critical for understanding the evolutionary process and ecological adaption to forests in Northern China. Results Polymorphic haplotypes were detected in most populations of U. lamellosa via DNA sequencing. All haplotypes were divided into three phylogeographic clades fundamentally corresponding to their geographical distribution, namely THM (Taihang Mountains), YM (Yinshan Mountains), and YSM (Yanshan Mountains) groups. The YSM group, which is regarded as ancestral, possessed higher genetic diversity and significant genetic variability in contrast to the YSM and YM groups. Meanwhile, the divergence time of intraspecies haplotypes occurred during the Miocene-Pliocene, which was associated with major Tertiary geological and/or climatic events. Different degrees of gene exchanges were identified between the three groups. During glaciation, the YSM and THM regions might have served as refugia for U. lamellosa. Based on ITS data, range expansion was not expected through evolutionary processes, except for the THM group. A series of mountain uplifts (e.g., Yanshan Mountains and Taihang Mountains) following the Miocene-Pliocene, and subsequently quaternary climatic oscillations in Northern China, further promoted divergence between U. lamellosa populations. Conclusions Geographical topology and climate change in Northern China played a critical role in establishing the current phylogeographic structural patterns of U. lamellosa. These results provide important data and clues that facilitate the demographic study of tree species in Northern China.

scholarly journals Going down the rabbit hole: a review on methods characterizing selection and demography in natural populations

2016 ◽  
Author(s):  
Yann Bourgeois ◽  
Khaled Michel Hazzouri ◽  
Ben Warren
Keyword(s):  
Evolutionary Biology ◽  
Population Genomics ◽  
Demographic History ◽  
Natural Populations ◽  
Population History ◽  
Functional Ecology ◽  
Next Generation Sequencing Ngs ◽  
Genome Scale ◽  
Analytical Tools ◽  
Constant Improvement

1. Characterizing species history and identifying loci underlying local adaptation is crucial in functional ecology, evolutionary biology, conservation and agronomy. The ongoing and constant improvement of next-generation sequencing (NGS) techniques has facilitated the production of an ever-increasing number of genetic markers across genomes of non-model species. 2. The study of variation in these markers across natural populations has deepened the understanding of how population history and selection act on genomes. Population genomics now provides tools to better integrate selection into a historical framework, and take into account selection when reconstructing demographic history. However, this improvement has come with a burst of analytical tools that can confuse users. 3. Such confusion can limit the amount of information effectively retrieved from complex genomic datasets. In addition, the lack of a unified analytical pipeline impairs the diffusion of the most recent analytical tools into fields like conservation biology. 4. To address this need, we describe possible analytical protocols and link these with more than 70 methods dealing with genome-scale datasets. We summarise the strategies they use to infer demographic history and selection, and discuss some of their limitations. A website listing these methods is available at www.methodspopgen.com.

scholarly journals An Integrated Framework for the Inference of Viral Population History From Reconstructed Genealogies

Genetics ◽  
2000 ◽  
Vol 155 (3) ◽  
pp. 1429-1437
Author(s):  
Oliver G Pybus ◽  
Andrew Rambaut ◽  
Paul H Harvey
Keyword(s):  
Maximum Likelihood ◽  
Sequence Data ◽  
Demographic History ◽  
Population History ◽  
Maximum Likelihood Estimates ◽  
Viral Population ◽  
True Parameter ◽  
Subtype B ◽  
Exponential Growth Model ◽  
Parameter Values

Abstract We describe a unified set of methods for the inference of demographic history using genealogies reconstructed from gene sequence data. We introduce the skyline plot, a graphical, nonparametric estimate of demographic history. We discuss both maximum-likelihood parameter estimation and demographic hypothesis testing. Simulations are carried out to investigate the statistical properties of maximum-likelihood estimates of demographic parameters. The simulations reveal that (i) the performance of exponential growth model estimates is determined by a simple function of the true parameter values and (ii) under some conditions, estimates from reconstructed trees perform as well as estimates from perfect trees. We apply our methods to HIV-1 sequence data and find strong evidence that subtypes A and B have different demographic histories. We also provide the first (albeit tentative) genetic evidence for a recent decrease in the growth rate of subtype B.

scholarly journals GENETIC DIFFERENTIATION BETWEEN GEOGRAPHICALLY DISTANT POPULATIONS OF DROSOPHILA MELANOGASTER

Genetics ◽  
1982 ◽  
Vol 101 (2) ◽  
pp. 235-256
Author(s):  
Rama S Singh ◽  
Donal A Hickey ◽  
Jean David
Keyword(s):  
Drosophila Melanogaster ◽  
Genetic Differentiation ◽  
Gene Frequency ◽  
Natural Populations ◽  
Allozyme Variation ◽  
Clinal Variation ◽  
Significant Genetic Differentiation ◽  
African Populations ◽  
Latitudinal Clines ◽  
North And South

ABSTRACT We have studied allozyme variation at 26 gene loci in nine populations of Drosophila melanogaster originating on five different continents. The distant populations show significant genetic differentiation. However, only half of the loci studied have contributed to this differentiation; the other half show identical patterns in all populations. The genetic differentiation in North American, European and African populations is correlated with the major climatic differences between north and south. These differences arise mainly from seven loci that show gene-frequency patterns suggestive of latitudinal clines in allele frequencies. The clinal variation is such that subtropical populations are more heterozygous than temperate populations. These results are discussed in relation to the selectionist and neutralist hypotheses of genetic variation in natural populations.

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