Recent Population History Research Articles

Improved inference of population histories by integrating genomic and epigenomic data.

With the availability of high-quality full genome polymorphism (SNPs) data, it becomes feasible to study the past demographic and selective history of populations in exquisite detail. However, such inferences still suffer from a lack of statistical resolution for recent, for example bottlenecks, events, and/or for populations with small nucleotide diversity. Additional heritable (epi)genetic markers, such as indels, transposable elements, microsatellites, or cytosine methylation, may provide further, yet untapped, information on the recent past population history. We extend the Sequential Markovian Coalescent (SMC) framework to jointly use SNPs and other hyper-mutable markers. We are able to (1) improve the accuracy of demographic inference in recent times, (2) uncover past demographic events hidden to SNP-based inference methods, and (3) infer the hyper-mutable marker mutation rates under a finite site model. As a proof of principle, we focus on demographic inference in Arabidopsis thaliana using DNA methylation diversity data from 10 European natural accessions. We demonstrate that segregating single methylated polymorphisms (SMPs) satisfy the modeling assumptions of the SMC framework, while differentially methylated regions (DMRs) are not suitable as their length exceeds that of the genomic distance between two recombination events. Combining SNPs and SMPs while accounting for site- and region-level epimutation processes, we provide new estimates of the glacial age bottleneck and post-glacial population expansion of the European A. thaliana population. Our SMC framework readily accounts for a wide range of heritable genomic markers, thus paving the way for next-generation inference of evolutionary history by combining information from several genetic and epigenetic markers.

Five Centuries of Settlement Dynamics and Mobility in the Northern Raja Ampat Islands of West Papua

ABSTRACT We explore changes to settlement and mobility in the northern Raja Ampat Islands (Waigeo, Gam, and Batanta) over the past five centuries, a time when speakers of several Austronesian languages were moving throughout the archipelago. The evidence shows: (1) some settlement relocations were rapid, occurring within a generation, while other settlements remained fixed for hundreds of years; and (2) there were numerous clan and family scale movements that led to high levels of intermarriage between language groups and settlements. The results demonstrate that far from being a place of stasis caught between the worlds of Maluku and New Guinea, Raja Ampat settlement and mobility were highly dynamic. This dynamism prompts us to rethink the relationship between today’s settlement locations, their language affiliations, and the meta-narratives about their recent population histories. We propose that the deeper past of Raja Ampat may have also been characterized by dynamic movement and social flux.

Unravelling the determinants of human health in French Polynesia: the MATAEA project.

French Polynesia is a French overseas collectivity in the Southeast Pacific, comprising 75 inhabited islands across five archipelagoes. The human settlement of the region corresponds to the last massive migration of humans to empty territories, but its timeline is still debated. Despite their recent population history and geographical isolation, inhabitants of French Polynesia experience health issues similar to those of continental countries. Modern lifestyles and increased longevity have led to a rise in non-communicable diseases (NCDs) such as obesity, diabetes, hypertension, and cardiovascular diseases. Likewise, international trade and people mobility have caused the emergence of communicable diseases (CDs) including mosquito-borne and respiratory diseases. Additionally, chronic pathologies including acute rheumatic fever, liver diseases, and ciguatera, are highly prevalent in French Polynesia. However, data on such diseases are scarce and not representative of the geographic fragmentation of the population. The present project aims to estimate the prevalence of several NCDs and CDs in the population of the five archipelagoes, and identify associated risk factors. Moreover, genetic analyses will contribute to determine the sequence and timings of the peopling history of French Polynesia, and identify causal links between past genetic adaptation to island environments, and present-day susceptibility to certain diseases. This cross-sectional survey is based on the random selection of 2,100 adults aged 18-69 years and residing on 18 islands from the five archipelagoes. Each participant answered a questionnaire on a wide range of topics (including demographic characteristics, lifestyle habits and medical history), underwent physical measurements (height, weight, waist circumference, arterial pressure, and skin pigmentation), and provided biological samples (blood, saliva, and stool) for biological, genetic and microbiological analyses. For the first time in French Polynesia, the present project allows to collect a wide range of data to explore the existence of indicators and/or risk factors for multiple pathologies of public health concern. The results will help health authorities to adapt actions and preventive measures aimed at reducing the incidence of NCDs and CDs. Moreover, the new genomic data generated in this study, combined with anthropological data, will increase our understanding of the peopling history of French Polynesia. https://clinicaltrials.gov/, identifier: NCT06133400.

Beta-PSMC: uncovering more detailed population history using beta distribution

BackgroundInferring the demographic history of a population is essential in population genetic studies. Though the inference methods based on the sequentially Markov coalescent can present the population history in detail, these methods assume that the population size remains unchanged in each time interval during discretizing the hidden state in the hidden Markov model. Therefore, these methods fail to uncover the detailed population history in each time interval.ResultsWe present a new method called Beta-PSMC, which introduces the probability density function of a beta distribution with a broad variety of shapes into the Pairwise Sequentially Markovian Coalescent (PSMC) model to refine the population history in each discretized time interval in place of the assumption that the population size is unchanged. Using simulation, we demonstrate that Beta-PSMC can uncover more detailed population history, and improve the accuracy and resolution of the recent population history inference. We also apply Beta-PSMC to infer the population history of Adélie penguin and find that the fluctuation in population size is contrary to the temperature change 15–27 thousand years ago.ConclusionsBeta-PSMC extends PSMC by allowing more detailed fluctuation of population size in each discretized time interval with the probability density function of beta distribution and will serve as a useful tool for population genetics.

Human impact on the recent population history of the elusive European wildcat inferred from whole genome data

BackgroundThe extent and impact of evolutionary change occurring in natural populations in response to rapid anthropogenic impact is still poorly understood on the genome-wide level. Here, we explore the genetic structure, demographic history, population differentiation, and domestic introgression based on whole genome data of the endangered European wildcat in Germany, to assess potential genomic consequences of the species’ recent spread across human-dominated cultural landscapes.ResultsReconstruction of demographic history and introgression rates based on 47 wildcat and 37 domestic cat genomes suggested late introgression between wild and domestic cat, coinciding with the introduction of domestic cat during the Roman period, but overall relatively low rates of hybridization and introgression from domestic cats. Main population divergence found between an eastern and central German wildcat clade was found to be of rather recent origin (200 y), and thus the likely consequence of anthropogenic persecution and resulting isolation in population refugia. We found similar effective population sizes and no substantial inbreeding across populations. Interestingly, highly differentiated genes between wild cat populations involved in the tryptophan-kynurenine-serotonin pathway were revealed, which plays a role in behavioral processes such as stress susceptibility and tolerance, suggesting that differential selection acted in the populations.ConclusionsWe found strong evidence for substantial recent anthropogenic impact on the genetic structure of European wildcats, including recent persecution-driven population divergence, as well as potential adaptation to human-dominate environments. In contrast, the relatively low levels of domestic introgression and inbreeding found in this study indicate a substantial level of “resistance” of this elusive species towards major anthropogenic impacts, such as the omnipresence of domestic cats as well as substantial habitat fragmentation. While those findings have strong implications for ongoing conservation strategies, we demand closer inspection of selective pressures acting on this and other wildlife species in anthropogenic environments.

Population structure and population history of the black fly Simulium chumpornense (Diptera: Simuliidae) from Thailand

Understanding genetic structure and diversity of insect vectors is crucial for disease epidemiology. In this study, mitochondrial cytochrome c oxidase I sequences were used to infer genetic diversity, genetic structure and population history of the black fly, Simulium chumpornense Takaoka and Kuvangkadilok, a suspected vector of blood protozoa of the genus Leucocytozoon and Trypanosoma. High intraspecific genetic divergence (max. 3.76%) was found among 142 specimens obtained from 19 locations across Thailand. A median joining network revealed two genetic lineages (A and B) that were geographically associated. Lineage A is representative of central and northeastern regions. Lineage B represents specimens from diverse locations in northern, western, and southern Thailand, including the type locality. Mismatch distribution and the neutrality tests provided signals of past population expansions in both lineages. The expansion time dating back to the end of last glaciations at 12,000 - 15,000 years ago is possibly related to increasing of precipitation at the end of last glacial period. Despite recent population history, population pairwise FST analysis revealed that almost all population comparisons were genetically significantly different. The high level of genetic structuring is possibly a result of historical isolation of the population that survived in different refugia sites during the dry conditions during glaciations.

Fine-scale population structure and demographic history of British Pakistanis

Previous genetic and public health research in the Pakistani population has focused on the role of consanguinity in increasing recessive disease risk, but little is known about its recent population history or the effects of endogamy. Here, we investigate fine-scale population structure, history and consanguinity patterns using genotype chip data from 2,200 British Pakistanis. We reveal strong recent population structure driven by the biraderi social stratification system. We find that all subgroups have had low recent effective population sizes (Ne), with some showing a decrease 15‒20 generations ago that has resulted in extensive identity-by-descent sharing and homozygosity, increasing the risk of recessive disorders. Our results from two orthogonal methods (one using machine learning and the other coalescent-based) suggest that the detailed reporting of parental relatedness for mothers in the cohort under-represents the true levels of consanguinity. These results demonstrate the impact of cultural practices on population structure and genomic diversity in Pakistanis, and have important implications for medical genetic studies.

Genomic Variation and Recent Population Histories of Spotted (Strix occidentalis) and Barred (Strix varia) Owls.

Spotted owls (SOs, Strix occidentalis) are a flagship species inhabiting old-growth forests in western North America. In recent decades, their populations have declined due to ongoing reductions in suitable habitat caused by logging, wildfires, and competition with the congeneric barred owl (BO, Strix varia). The northern spotted owl (S. o. caurina) has been listed as “threatened” under the Endangered Species Act since 1990. Here, we use an updated SO genome assembly along with 51 high-coverage whole-genome sequences to examine population structure, hybridization, and recent changes in population size in SO and BO. We found that potential hybrids identified from intermediate plumage morphology were a mixture of pure BO, F1 hybrids, and F1 × BO backcrosses. Also, although SO underwent a population bottleneck around the time of the Pleistocene–Holocene transition, their population sizes rebounded and show no evidence of any historical (i.e., 100–10,000 years ago) population decline. This suggests that the current decrease in SO abundance is due to events in the past century. Finally, we estimate that western and eastern BOs have been genetically separated for thousands of years, instead of the previously assumed recent (i.e., <150 years) divergence. Although this result is surprising, it is unclear where the ancestors of western BO lived after the separation. In particular, although BO may have colonized western North America much earlier than the first recorded observations, it is also possible that the estimated divergence time reflects unsampled BO population structure within central or eastern North America.

Recent genetic connectivity and clinal variation in chimpanzees

Much like humans, chimpanzees occupy diverse habitats and exhibit extensive behavioural variability. However, chimpanzees are recognized as a discontinuous species, with four subspecies separated by historical geographic barriers. Nevertheless, their range-wide degree of genetic connectivity remains poorly resolved, mainly due to sampling limitations. By analyzing a geographically comprehensive sample set amplified at microsatellite markers that inform recent population history, we found that isolation by distance explains most of the range-wide genetic structure of chimpanzees. Furthermore, we did not identify spatial discontinuities corresponding with the recognized subspecies, suggesting that some of the subspecies-delineating geographic barriers were recently permeable to gene flow. Substantial range-wide genetic connectivity is consistent with the hypothesis that behavioural flexibility is a salient driver of chimpanzee responses to changing environmental conditions. Finally, our observation of strong local differentiation associated with recent anthropogenic pressures portends future loss of critical genetic diversity if habitat fragmentation and population isolation continue unabated.

Genetic structure, phylogeography and potential distribution modeling suggest a population expansion in the mesquite Prosopis laevigata since the last interglacial

Patterns of genetic and phylogeographic structure and recent population history of plant species in the Mexican arid zones have been scarcely investigated. Prosopis laevigata is the most widely spread species of mesquite in Mexico, with extensive populations in the arid and semiarid zones of the central and northern plateaus and scattered presence in southern Mexico. We evaluated the genetic and phylogeographic structure of this species to infer its recent demographic history. We genotyped six nuclear microsatellite loci and sequenced the psbA3´-trnH chloroplast DNA (cpDNA) region in individuals from 21 populations covering the whole distribution of the species. Nuclear genetic diversity was moderately high (HE = 0.527), and genetic differentiation was moderate (FST = 0.16). A positive correlation between genetic diversity and latitude was observed. The cpDNA analyses indicated a lack of phylogeographic structure in P. laevigata (GST = 0.090, NST = 0.101; P = 0.497). Historical demography statistics indicated a population expansion supported by a skyline plot analysis, the star-like shape of the haplotype network, and the unimodal shape of the mismatch distribution. Ecological niche modeling suggested a contracted distribution into west-central Mexico during the Last Interglacial (~ 140 Ka), followed by an expansion in both northwards and southwards directions in the Last Glacial Maximum (~ 22 Ka), which continued in the mid-Holocene (~ 6 Ka) and the present. Results are congruent with a recent population growth and colonization of newly opened arid zones by P. laevigata populations. This pattern is consistent with the high capacity of colonization of nutrient-poor areas, high germination rates and resistance to drought reported for Prosopis species.

Tracing the origins of recent Queensland fruit fly incursions into South Australia, Tasmania and New Zealand

Incursions of the Queensland fruit fly Bactrocera tryoni (Qfly) into areas without permanent Qfly populations present serious threats to the Australian and New Zealand horticultural industries. Identifying the origins of recent incursions will help reduce future threats by enabling the targeting of problematic incursion routes for more stringent quarantine protocols. Here we present an analytical framework based on supervised and unsupervised machine learning to identify the origins and recent population history of incursion individuals. Our framework is based on a recently developed reference dataset of genome-wide markers for 35 Qfly populations from across the ranges of Qfly and the related taxon Bactrocera aquilonis (NTfly). We apply our framework to recent incursions into New Zealand, Tasmania and South Australia. Two distinct Qfly sources were identified for incursions into New Zealand (total 18 individuals), one from the east coast of Australia and one from New Caledonia. All eight recent incursion collections analysed (total 85 individuals) from South Australia and Tasmania most likely originated from just one of six clusters of populations in our reference database, Qfly from the east coast of Australia. None were found to originate from clusters containing NTfly or Qfly/NTfly hybrids in the Northern Territory or north Western Australia. Several, but not all, of the collections showed signals of small founding population size and two Tasmanian collections each included individuals apparently derived from three different sources within the east coast of Australia. In total, several more incursion events were detected than previously known, although some were founded by relatively few individuals.

Differences in local population history at the finest level: the case of the Estonian population

Several recent studies detected fine-scale genetic structure in human populations. Hence, groups conventionally treated as single populations harbour significant variation in terms of allele frequencies and patterns of haplotype sharing. It has been shown that these findings should be considered when performing studies of genetic associations and natural selection, especially when dealing with polygenic phenotypes. However, there is little understanding of the practical effects of such genetic structure on demography reconstructions and selection scans when focusing on recent population history. Here we tested the impact of population structure on such inferences using high-coverage (~30×) genome sequences of 2305 Estonians. We show that different regions of Estonia differ in both effective population size dynamics and signatures of natural selection. By analyzing identity-by-descent segments we also reveal that some Estonian regions exhibit evidence of a bottleneck 10–15 generations ago reflecting sequential episodes of wars, plague and famine, although this signal is virtually undetected when treating Estonia as a single population. Besides that, we provide a framework for relating effective population size estimated from genetic data to actual census size and validate it on the Estonian population. This approach may be widely used both to cross-check estimates based on historical sources as well as to get insight into times and/or regions with no other information available. Our results suggest that the history of human populations within the last few millennia can be highly region specific and cannot be properly studied without taking local genetic structure into account.

Recent effective population size in Eastern European plain Russians correlates with the key historical events

Effective population size reflects the history of population growth, contraction, and structuring. When the effect of structuring is negligible, the inferred trajectory of the effective population size can be informative about the key events in the history of a population. We used the IBDNe and DoRIS approaches, which exploit the data on IBD sharing between genomes, to reconstruct the recent effective population size in two population datasets of Russians from Eastern European plain: (1) ethnic Russians sampled from the westernmost part of Russia; (2) ethnic Russians, Bashkirs, and Tatars sampled from the Volga-Ural region. In this way, we examined changes in effective population size among ethnic Russians that reside in their historical area at the West of the plain, and that expanded eastward to come into contact with the indigenous peoples at the East of the plain. We compared the inferred demographic trajectories of each ethnic group to written historical data related to demographic events such as migration, war, colonization, famine, establishment, and collapse of empires. According to IBDNe estimations, 200 generations (~6000 years) ago, the effective size of the ancestral populations of Russians, Bashkirs, and Tatars hovered around 3,000, 30,000, and 8,000 respectively. Then, the ethnic Russians exponentially grew with increasing rates for the last 115 generations and become the largest ethnic group of the plain. Russians do not show any drop in effective population size after the key historical conflicts, including the Mongol invasion. The only exception is a moderate drop in the 17th century, which is well known in Russian history as The Smuta. Our analyses suggest a more eventful recent population history for the two small ethnic groups that came into contact with ethnic Russians in the Volga-Ural region. We found that the effective population size of Bashkirs and Tatars started to decrease during the time of the Mongol invasion. Interestingly, there is an even stronger drop in the effective population size that coincides with the expansion of Russians to the East. Thus, 15–20 generations ago, i.e. in the 16–18th centuries in the trajectories of Bashkirs and Tatars, we observe the bottlenecks of four and twenty thousand, respectively. Our results on the recent effective population size correlate with the key events in the history of populations of the Eastern European plain and have importance for designing biomedical studies in the region.

Population Histories of the United States Revealed through Fine-Scale Migration and Haplotype Analysis

The population of the United States is shaped by centuries of migration, isolation, growth, and admixture between ancestors of global origins. Here, we assemble a comprehensive view of recent population history by studying the ancestry and population structure of more than 32,000 individuals in the US using genetic, ancestral birth origin, and geographic data from the National Geographic Genographic Project. We identify migration routes and barriers that reflect historical demographic events. We also uncover the spatial patterns of relatedness in subpopulations through the combination of haplotype clustering, ancestral birth origin analysis, and local ancestry inference. Examples of these patterns include substantial substructure and heterogeneity in Hispanics/Latinos, isolation-by-distance in African Americans, elevated levels of relatedness and homozygosity in Asian immigrants, and fine-scale structure in European descents. Taken together, our results provide detailed insights into the genetic structure and demographic history of the diverse US population.

Population genetics of the solanum fruit fly, Bactrocera latifrons (Hendel) (Diptera: Tephritidae).

The solanum fruit fly, Bactrocera latifrons (Hendel), is an important pest species of commercial plants in the family Solanaceae. In this study, the population genetic structure of B. latifrons was investigated using mitochondrial cytochrome c oxidase I sequences. A mitochondrial DNA haplotype network revealed no major genetic break, but haplotypes from recently invaded areas in Japan, Tanzania, and Kenya were genetically divergent. The overall haplotype network is approximately star-shaped, characteristic of recent demographic expansion of populations. This is also supported by large negative values of neutrality tests. Despite the overall pattern of recent population history, genetic structure analysis revealed considerable genetic structuring with 33% of pairwise comparisons being significantly different. Populations that were genetically different from the others usually possess low genetic diversity, suggesting that genetic drift is potentially a factor driving genetic differentiation. Local extinction and recolonization processes related to the availability of host plants are most likely responsible for a founder effect and subsequent genetic drift in a population.

Reconstructing recent population history while mapping rare variants using haplotypes

Haplotype-based methods are a cost-effective alternative to characterize unobserved rare variants and map disease-associated alleles. Moreover, they can be used to reconstruct recent population history, which shaped distribution of rare variants and thus can be used to guide gene mapping studies. In this study, we analysed Illumina 650 k genotyped dataset on three underrepresented populations from Eastern Europe, where ancestors of Russians came into contact with two indigenous ethnic groups, Bashkirs and Tatars. Using the IBD mapping approach, we identified two rare IBD haplotypes strongly enriched in asthma patients of distinct ethnic background. We reconstructed recent population history using haplotype-based methods to reconcile this contradictory finding. Our ChromoPainter analysis showed that these haplotypes each descend from a single ancestor coming from one of the ethnic groups studied. Next, we used DoRIS approach and showed that source populations for patients exchanged recent (<60 generations) asymmetric gene flow, which supported the ChromoPainter-based scenario that patients share haplotypes through inter-ethnic admixture. Finally, we show that these IBD haplotypes overlap with asthma-associated genomic regions ascertained in European population. This finding is consistent with the fact that the two donor populations for the rare IBD haplotypes: Russians and Tatars have European ancestry.

How rivers and historical climate oscillations impact on genetic structure in Chinese Muntjac (Muntiacus reevesi)?

AbstractAimThe characterization of the genetic structure and demographic dynamics of a species can shed light on the impacts of natural landscapes, historical climate change and human activities, thus enabling us to develop appropriate protection and management strategies. In this study, we aimed to characterize how the above‐mentioned factors shaped the genetic structure and demographic history of the Chinese muntjac (Muntiacus reevesi).LocationThe reaches of the Yangtze River, China.MethodsUsing mtDNA control region sequences and 15 nuclear microsatellite loci as genetic markers, we analysed population genetic structure with a factorial correspondence analysis (FCA), AMOVA,FSTestimates and Bayesian cluster analysis. In addition, we estimated the demographic history using Bayesian skyline plot (BSP) analysis and MSVAR simulation.ResultsHigh genetic diversity was detected in Chinese muntjac populations. Population structure analysis strongly suggesting three genetic clusters (QL/BA/WLS, DB and JLS/WN/WYS). The demographic analyses showed that Chinese muntjac experienced population fluctuation during the late Pleistocene, followed by bottleneck during the Holocene.Main conclusionsThe extant Chinese muntjac populations harbour a surprisingly high genetic diversity despite of the bottleneck they went through. The populations show significant population structure separating populations in the upper, middle and lower regions of the Yangtze River, supporting the presence of three independent management units (QL/BA/WLS, DB and JLS/WN/WYS). The population demography of the Chinese muntjac presents high concordance with the rotation of glacial–interglacial in late Pleistocene. In addition, our study identified that the Chinese muntjac's recent population history may have been influenced by early human activities (8,509–1,605 years ago).

Overestimation of the adaptive substitution rate in fluctuating populations.

Estimating the proportion of adaptive substitutions (α) is of primary importance to uncover the determinants of adaptation in comparative genomic studies. Several methods have been proposed to estimate α from patterns polymorphism and divergence in coding sequences. However, estimators of α can be biased when the underlying assumptions are not met. Here we focus on a potential source of bias, i.e. variation through time in the long-term population size (N) of the considered species. We show via simulations that ancient demographic fluctuations can generate severe overestimations of α, and this is irrespective of the recent population history.

Haplotype Sharing Provides Insights into Fine-Scale Population History and Disease in Finland

Finland provides unique opportunities to investigate population and medical genomics because of its adoption of unified national electronic health records, detailed historical and birth records, and serial population bottlenecks. We assembled a comprehensive view of recent population history (≤100 generations), the timespan during which most rare-disease-causing alleles arose, by comparing pairwise haplotype sharing from 43,254 Finns to that of 16,060 Swedes, Estonians, Russians, and Hungarians from geographically andlinguistically adjacent countries with different population histories. We find much more extensive sharing in Finns, with at least one ≥ 5 cM tract on average between pairs of unrelated individuals. By coupling haplotype sharing with fine-scale birth records from more than 25,000 individuals, we find that although haplotype sharing broadly decays with geographical distance, there are pockets of excess haplotype sharing; individuals from northeast Finland typically share several-fold more of their genome in identity-by-descent segments than individuals from southwest regions. We estimate recent effective population-size changes through time across regions of Finland, and we find that there was more continuous gene flow as Finns migrated from southwest to northeast between the early- and late-settlement regions than was dichotomously described previously. Lastly, we show that haplotype sharing is locally enriched by an order of magnitude among pairs of individuals sharing rare alleles and especially among pairs sharing rare disease-causing variants. Our work provides a general framework for using haplotype sharing to reconstruct an integrative view of recent population history and gain insight into the evolutionary origins of rare variants contributing to disease.

Contrasting Patterns of Population History and Seed-mediated Gene Flow in Two Endemic Costa Rican Oak Species.

Lower Central America is an important area to study recent population history and diversification of Neotropical species due to its complex and dynamic geology and climate. Phylogeographic studies in this region are few in comparison with other regions and even less for tree species. The aim of the present study was to characterize the phylogeographic structure in 2 partially co-distributed endemic oak species (Quercus costaricensis and Q. bumelioides) of the Costa Rican mountains using chloroplast short sequence repeats (cpSSRs), and to test for the effect of geological and palaeoclimatic processes on their population history. Genetic diversity and structure, haplotype networks, patterns of seed-mediated gene flow and historical demography were estimated for both species. Results suggested contrasting patterns. Quercus costaricensis exhibited high values of genetic diversity, a marked phylogeographic structure, a north-to-south genetic diversity gradient and evidence of a demographic expansion during the Quaternary. Quercus bumelioides did not show significant genetic structure and the haplotype network and historical demography estimates suggested a recent population expansion probably during the Pleistocene-Holocene transition. The phylogeographic structure of Q. costaricensis seems to be related to Pleistocene altitudinal migration due to its higher altitudinal distribution. Meanwhile, historical seed-mediated gene flow through the lower altitudinal distribution of Q. bumelioides may have promoted the homogenization of genetic variation. Population expansion and stable availability of suitable climatic areas in both species probably indicate that palaeoclimatic changes promoted downwards altitudinal migration and formation of continuous forests allowing oak species to expand their distribution into the Panamanian mountains during glacial stages.