Population Divergence History Research Articles

Genetic diversities in wild and cultivated populations of the two closely-related medical plants species, Tripterygium Wilfordii and T. Hypoglaucum (Celastraceae)

BackgroundThe sustainable supply of medicinal plants is important, and cultivating and domesticating them has been suggested as an optimal strategy. However, this can lead to a loss of genetic diversity. Tripterygium wilfordii Hook. f. is a medicinal plant commonly used in traditional Chinese medicine, but its wild populations are dwindling due to excessive harvesting. To protect the species and meet the increasing demand, it is urgent to cultivate it on a large scale. However, distinguishing between T. wilfordii and T. hypoglaucum, two similar species with different medicinal properties, is challenging. Therefore, it is crucial to understand the genetic diversity and population structure of these species for their sustainable utilization.ResultsIn this study, we investigated the genetic diversity and population structure of the two traditional medicinal semiwoody vines plant species, Tripterygium wilfordii and T. hypoglaucum, including wild and cultivated populations using chloroplast DNA (cpDNA) sequences and microsatellite loci. Our results indicated that the two species maintain a high level of genetic divergence, indicating possible genetic bases for the different contents of bioactive compounds of the two species. T. wilfordii showed lower genetic diversity and less subdivided population structures of both markers than T. hypoglaucum. The potential factors in shaping these interesting differences might be differentiated pollen-to-seed migration rates, interbreeding, and history of population divergence. Analyses of cpDNA and microsatellite loci supported that the two species are genetically distinct entities. In addition, a significant reduction of genetic diversity was observed for cultivated populations of the two species, which mainly resulted from the small initial population size and propagated vegetative practice during their cultivation.ConclusionOur findings indicate significant genetic divergence between T. wilfordii and T. hypoglaucum. The genetic diversity and population structure analyses provide important insights into the sustainable cultivation and utilization of these medicinal plants. Accurate identification and conservation efforts are necessary for both species to ensure the safety and effectiveness of crude drug use. Our study also highlighted the importance of combined analyses of different DNA markers in addressing population genetics of medicinal plants because of the contrasts of inheritance and rates of gene flow. Large-scale cultivation programs should consider preserving genetic diversity to enhance the long-term sustainability of T. wilfordii and T. hypoglaucum. Our study proposed that some populations showed higher genetic diversity and distinctness, which can be considered with priority for conservation and as the sources for future breeding and genetic improvement.

Geogenomic Predictors of Genetree Heterogeneity Explain Phylogeographic and Introgression History: A Case Study in an Amazonian Bird (Thamnophilus aethiops).

Can knowledge about genome architecture inform biogeographic and phylogenetic inference? Selection, drift, recombination, and gene flow interact to produce a genomic landscape of divergence wherein patterns of differentiation and genealogy vary nonrandomly across the genomes of diverging populations. For instance, genealogical patterns that arise due to gene flow should be more likely to occur on smaller chromosomes, which experience high recombination, whereas those tracking histories of geographic isolation (reduced gene flow caused by a barrier) and divergence should be more likely to occur on larger and sex chromosomes. In Amazonia, populations of many bird species diverge and introgress across rivers, resulting in reticulated genomic signals. Herein, we used reduced representation genomic data to disentangle the evolutionary history of 4 populations of an Amazonian antbird, Thamnophilus aethiops, whose biogeographic history was associated with the dynamic evolution of the Madeira River Basin. Specifically, we evaluate whether a large river capture event ca. 200 Ka, gave rise to reticulated genealogies in the genome by making spatially explicit predictions about isolation and gene flow based on knowledge about genomic processes. We first estimated chromosome-level phylogenies and recovered 2 primary topologies across the genome. The first topology (T1) was most consistent with predictions about population divergence and was recovered for the Z-chromosome. The second (T2), was consistent with predictions about gene flow upon secondary contact. To evaluate support for these topologies, we trained a convolutional neural network to classify our data into alternative diversification models and estimate demographic parameters. The best-fit model was concordant with T1 and included gene flow between non-sister taxa. Finally, we modeled levels of divergence and introgression as functions of chromosome length and found that smaller chromosomes experienced higher gene flow. Given that (1) genetrees supporting T2 were more likely to occur on smaller chromosomes and (2) we found lower levels of introgression on larger chromosomes (and especially the Z-chromosome), we argue that T1 represents the history of population divergence across rivers and T2 the history of secondary contact due to barrier loss. Our results suggest that a significant portion of genomic heterogeneity arises due to extrinsic biogeographic processes such as river capture interacting with intrinsic processes associated with genome architecture. Future phylogeographic studies would benefit from accounting for genomic processes, as different parts of the genome reveal contrasting, albeit complementary histories, all of which are relevant for disentangling the intricate geogenomic mechanisms of biotic diversification. [Amazonia; biogeography; demographic modeling; gene flow; gene tree; genome architecture; geogenomics; introgression; linked selection; neural network; phylogenomic; phylogeography; reproductive isolation; speciation; species tree.].

Whole-genome resequencing reveals recent divergence of geographic populations of the dung beetle Phelotrupes auratus with color variation.

Knowledge of population divergence history is key to understanding organism diversification mechanisms. The geotrupid dung beetle Phelotrupes auratus, which inhabits montane forests and exhibits three color forms (red, green, and indigo), diverged into five local populations (west/red, south/green, south/indigo, south/red, and east/red) in the Kinki District of Honshu, Japan, based on the combined interpretation of genetic cluster and color-form data. Here, we estimated the demographic histories of these local populations using the newly assembled draft genome sequence of P. auratus and whole-genome resequencing data obtained from each local population. Using coalescent simulation analysis, we estimated P. auratus population divergences at ca. 3800, 2100, 600, and 200 years ago, with no substantial gene flow between diverged populations, implying the existence of persistent barriers to gene flow. Notably, the last two divergence events led to three local populations with different color forms. The initial divergence may have been affected by climatic cooling around that time, and the last three divergence events may have been associated with the increasing impact of human activities. Both climatic cooling and increasing human activity may have caused habitat fragmentation and a reduction in the numbers of large mammals supplying food (dung) for P. auratus, thereby promoting the decline, segregation, and divergence of local populations. Our research demonstrates that geographic population divergence in an insect with conspicuous differences in traits such as body color may have occurred rapidly under the influence of human activity.

Population genetic patterns of a mangrove‐associated frog reveal its colonization history and habitat connectivity

AbstractAimTo understand the impact of historical and contemporary habitat distributions and connectivity on the spatial patterns of a species' genetic variation and divergence, we examined the phylogenetic relationship, population genetic structure and demographic history of a mangrove‐specialist, the crab‐eating frog (Fejervarya cancrivora) from 10 geographic populations in China and northern Vietnam.LocationSoutheast Asian coasts, especially the southern China and northern Vietnam coasts.MethodsWe used the sequences of three mitochondrial DNA (mtDNA) regions to infer phylogenetic relationships and divergence times between our samples and those from other Southeast Asian countries. Thirteen nuclear microsatellite loci were used to analyse population genetic structure. Ancient and more recent demographic history was assessed using mtDNA and microsatellite data, respectively, and population divergence history scenarios were evaluated using approximate Bayesian computation.ResultsThe mtDNA haplotypes from China joined the F. cancrivora clades from the Philippines, Thailand and Bangladesh, which diverged from the clades from Malaysia and Indonesia. Microsatellite analyses revealed three genetically differentiated clusters and a strong pattern of isolation by distance at the individual level. Ancient population sizes were relatively stable, but genetic signatures of recent population declines were detected. Population divergence history analyses supported that Hainan populations were ancestral to those of the Guangdong, Guangxi and northern Vietnam populations.Main conclusionsOur results suggest that F. cancrivora's contemporary genetic patterns have been shaped by past and present habitat conformations. This species may have dispersed along the coast from Southeast Asia to China during Pleistocene glaciations when sea levels were low, colonizing the Hainan area first. It subsequently spread to mainland China coasts when sea levels rose and shorelines withdrew. Additionally, current declines and fragmentation of mangrove forests have likely exacerbated population reductions and genetic divergences among now disjunct populations. This study provides a framework for understanding the population history of mangrove‐associated biota and thus aids conservation management of this critical ecosystem.

Evidence for ephemeral ring species formation during the diversification history of western fence lizards (Sceloporus occidentalis).

Divergence is often ephemeral, and populations that diverge in response to regional topographic and climatic factors may not remain reproductively isolated when they come into secondary contact. We investigated the geographical structure and evolutionary history of population divergence within Sceloporus occidentalis (western fence lizard), a habitat generalist with a broad distribution that spans the major biogeographical regions of Western North America. We used double digest RAD sequencing to infer population structure, phylogeny and demography. Population genetic structure is hierarchical and geographically structured with evidence for gene flow between biogeographical regions. Consistent with the isolation-expansion model of divergence during Quaternary glacial-interglacial cycles, gene flow and secondary contact are supported as important processes explaining the demographic histories of populations. Although populations may have diverged as they spread northward in a ring-like manner around the Sierra Nevada and southern Cascade Ranges, there is strong evidence for gene flow among populations at the northern terminus of the ring. We propose the concept of an "ephemeral ring species" and contrast S.occidentalis with the classic North American ring species, Ensatina eschscholtzii. Contrary to expectations of lower genetic diversity at northern latitudes following post-Quaternary-glaciation expansion, the ephemeral nature of divergence in S.occidentalis has produced centres of high genetic diversity for different reasons in the south (long-term stability) vs. the north (secondary contact).

Genomic landscape of the global oak phylogeny.

The tree of life is highly reticulate, with the history of population divergence emerging from populations of gene phylogenies that reflect histories of introgression, lineage sorting and divergence. In this study, we investigate global patterns of oak diversity and test the hypothesis that there are regions of the oak genome that are broadly informative about phylogeny. We utilize fossil data and restriction-site associated DNA sequencing (RAD-seq) for 632 individuals representing nearly 250 Quercus species to infer a time-calibrated phylogeny of the world's oaks. We use a reversible-jump Markov chain Monte Carlo method to reconstruct shifts in lineage diversification rates, accounting for among-clade sampling biases. We then map the >20000 RAD-seq loci back to an annotated oak genome and investigate genomic distribution of introgression and phylogenetic support across the phylogeny. Oak lineages have diversified among geographic regions, followed by ecological divergence within regions, in the Americas and Eurasia. Roughly 60% of oak diversity traces back to four clades that experienced increases in net diversification, probably in response to climatic transitions or ecological opportunity. The strong support for the phylogeny contrasts with high genomic heterogeneity in phylogenetic signal and introgression. Oaks are phylogenomic mosaics, and their diversity may in fact depend on the gene flow that shapes the oak genome.

Asynchronous diversification of snakes in the North American warm deserts

AbstractAimWe quantify the degree to which co‐distributed snakes across the Cochise Filter Barrier (CFB) have a shared history of population divergence and estimate the timing of divergence for each taxon pair.LocationNorth America.MethodsA single locus dataset was collected (n = 747 individuals) for 12 snake taxon pairs. Phylogeographical structure was estimated for each taxon. Redundancy analyses were used to assess the importance of geographical distance, climate and putative barriers to gene flow in structuring genetic diversity. Hierarchical approximate Bayesian computation was used to estimate the magnitude of synchronicity in divergence times across a well‐documented phylogeographical barrier. Lastly, gene divergence and population divergence times were estimated using multiple methods.ResultsThere is substantial phylogeographical structure in many of the snake taxa, particularly at the CFB. A model containing distance, climate and barriers explained the greatest amount of genetic variation in nearly all taxa. When each variable was examined separately, climate explained the most variation. The hABC model testing indicates that there is overwhelming support for asynchronous phylogeographical histories within these co‐distributed taxa. Estimated divergence times range throughout the Quaternary and Neogene.Main ConclusionsWe demonstrate that the 12 snake taxon pairs studied here have diversified within the desert Southwest forming distinct Sonoran and Chihuahuan populations, illustrating the importance of this region in driving diversification in North American taxa. Although these groups exhibit the same pattern of lineage formation, there is strong support for asynchronous diversification and little concordance in divergence time estimates.

An algorithm for computing the gene tree probability under the multispecies coalescent and its application in the inference of population tree.

Motivation: Gene tree represents the evolutionary history of gene lineages that originate from multiple related populations. Under the multispecies coalescent model, lineages may coalesce outside the species (population) boundary. Given a species tree (with branch lengths), the gene tree probability is the probability of observing a specific gene tree topology under the multispecies coalescent model. There are two existing algorithms for computing the exact gene tree probability. The first algorithm is due to Degnan and Salter, where they enumerate all the so-called coalescent histories for the given species tree and the gene tree topology. Their algorithm runs in exponential time in the number of gene lineages in general. The second algorithm is the STELLS algorithm (2012), which is usually faster but also runs in exponential time in almost all the cases.Results: In this article, we present a new algorithm, called CompactCH, for computing the exact gene tree probability. This new algorithm is based on the notion of compact coalescent histories: multiple coalescent histories are represented by a single compact coalescent history. The key advantage of our new algorithm is that it runs in polynomial time in the number of gene lineages if the number of populations is fixed to be a constant. The new algorithm is more efficient than the STELLS algorithm both in theory and in practice when the number of populations is small and there are multiple gene lineages from each population. As an application, we show that CompactCH can be applied in the inference of population tree (i.e. the population divergence history) from population haplotypes. Simulation results show that the CompactCH algorithm enables efficient and accurate inference of population trees with much more haplotypes than a previous approach.Availability: The CompactCH algorithm is implemented in the STELLS software package, which is available for download at http://www.engr.uconn.edu/ywu/STELLS.html.Contact: ywu@engr.uconn.eduSupplementary information: Supplementary data are available at Bioinformatics online.

A coalescent-based method for population tree inference with haplotypes.

Population trees represent past population divergence histories. The inference of population trees can be useful for the study of population evolution. With the size of data increases in large-scale population genetic projects, such as the 1000 Genomes Project, there are new computational challenges for ancestral population inference, including population tree inference. Existing methods for population tree inference are mainly designed for unlinked genetic variants (e.g. single nucleotide polymorphisms or SNPs). There is a potential loss of information by not considering the haplotypes. In this article, we propose a new population tree inference method (called STELLSH) based on coalescent likelihood. The likelihood is for haplotypes over multiple SNPs within a non-recombining region, not unlinked variants. Unlike many existing ancestral inference methods, STELLSH does not use Monte Carlo approaches when computing the likelihood. For efficient computation, the likelihood model is approximated but still retains much information about population divergence history. STELLSH can find the maximum likelihood population tree based on the approximate likelihood. We show through simulation data and the 1000 Genomes Project data that STELLSH gives reasonably accurate inference results. STELLSH is reasonably efficient for data of current interest and can scale to handle whole-genome data. The population tree inference method STELLSH has been implemented as part of the STELLS program: http://www.engr.uconn.edu/∼ywu/STELLS.html.

Genetic structure and hierarchical population divergence history of Acer mono var. mono in South and Northeast China.

Knowledge of the genetic structure and evolutionary history of tree species across their ranges is essential for the development of effective conservation and forest management strategies. Acer mono var. mono, an economically and ecologically important maple species, is extensively distributed in Northeast China (NE), whereas it has a scattered and patchy distribution in South China (SC). In this study, the genetic structure and demographic history of 56 natural populations of A. mono var. mono were evaluated using seven nuclear microsatellite markers. Neighbor-joining tree and STRUCTURE analysis clearly separated populations into NE and SC groups with two admixed-like populations. Allelic richness significantly decreased with increasing latitude within the NE group while both allelic richness and expected heterozygosity showed significant positive correlation with latitude within the SC group. Especially in the NE region, previous studies in Quercus mongolica and Fraxinus mandshurica have also detected reductions in genetic diversity with increases in latitude, suggesting this pattern may be common for tree species in this region, probably due to expansion from single refugium following the last glacial maximum (LGM). Approximate Bayesian Computation-based analysis revealed two major features of hierarchical population divergence in the species’ evolutionary history. Recent divergence between the NE group and the admixed-like group corresponded to the LGM period and ancient divergence of SC groups took place during mid-late Pleistocene period. The level of genetic differentiation was moderate (FST = 0.073; G′ST = 0.278) among all populations, but significantly higher in the SC group than the NE group, mirroring the species’ more scattered distribution in SC. Conservation measures for this species are proposed, taking into account the genetic structure and past demographic history identified in this study.

Phylogeography of the Trans-Volcanic bunchgrass lizard (Sceloporus bicanthalis) across the highlands of south-eastern Mexico

We quantify the population divergence processes that shaped population genetic structure in the Trans-Volcanic bunchgrass lizard (Sceloporus bicanthalis) across the highlands of south-eastern Mexico. Multilocus genetic data from nine nuclear loci and mitochondrial (mt)DNA were used to estimate the population divergence history for 47 samples of S. bicanthalis. Bayesian clustering methods partitioned S. bicanthalis into three populations: (1) a southern population in Oaxaca and southern Puebla; (2) a population in western Puebla; and (3) a northern population with a broad distribution across Hidalgo, Puebla, and Veracruz. The multilocus nuclear data and mtDNA both supported a Late Pleistocene increase in effective population size, and the nuclear data revealed low levels of unidirectional gene flow from the widespread northern population into the southern and western populations. Populations of S. bicanthalis experienced different demographic histories during the Pleistocene, and phylogeographical patterns were similar to those observed in many co-distributed highland taxa. Although we recommend continuing to recognize S. bicanthalis as a single species, future research on the evolution of viviparity could gain novel insights by contrasting physiological and genomic patterns among the different populations located across the highlands of south-eastern Mexico.

EVOLUTION OF COADAPTATION IN A TWO-LOCUS EPISTATIC SYSTEM

Although recent advances in genome biology have dramatically increased our understanding of the contribution of gene interactions to the development of complex phenotypes, we still lack general agreement on the process and mechanisms responsible for the evolution of epistatic systems. Even if genes in a species are indeed integrated into coadapted complexes of interacting components, simple additive evolution may eventually result in epistatic differentiation of populations. Consequently, the prevalence of epistatic gene action does not tell us anything about the role of epistatic selection in the history of population divergence. To elucidate the contribution of epistatic selection in the evolution of coadaptation, we investigate the fixation process of two mutations that interact synergistically to enhance fitness. We show by diffusion analysis and simulations that epistatic selection on cosegregating variants does not by itself promote the evolution of epistatic systems; rather, accumulation of neutral mutations may play a crucial role, creating an appropriate genetic milieu for adaptive evolution in the future generations.

Phylogeography of the calanoid copepods Calanus helgolandicus and C. euxinus suggests Pleistocene divergences between Atlantic, Mediterranean, and Black Sea populations

Molecular systematic analyses of marine taxa are crucial for recording ocean biodiversity, so too are elucidation of the history of population divergence and the dynamics of speciation. In this paper we present the joined phylogeography of the calanoid copepod Calanus helgolandicus (Claus 1863) from the North East (NE) Atlantic and the Adriatic Sea and the closely related C. euxinus (Hulsemann 1991) from the Black Sea based on sequences of a mitochondrial Cytochrome Oxidase subunit I (COI) fragment. Coalescent-based Bayesian methods and minimum spanning networks are used to reconstruct the history of population divergence. Our results reveal that copepod populations from all three basins share a great number of haplotypes and demonstrate a close genetic affinity of C. euxinus with C. helgolandicus. The data do not support significant genetic structuring among samples within seas. Coalescent analyses suggest divergences between NE Atlantic, Mediterranean, and Black Sea populations dating back to the middle Pleistocene, with the NE Atlantic–Mediterranean divergence being the earliest and the Mediterranean–Black Sea divergence the most recent. These middle Pleistocene dates are much older than the estimated dates of colonisation of the Mediterranean and Black Seas based on paleoclimatic scenarios. Our results do not rule out that the assumed colonisations took place but they indicate that the populations colonising the Mediterranean and the Black Sea were already, and have since remained, diverged. The chaetognath Sagitta setosa, which has a comparable distribution pattern and feeds upon the copepods, provides a unique opportunity to compare phylogeographic patterns and distinguish among alternative hypotheses. The dates produced in this paper are in agreement with those estimated elsewhere for S. setosa. We propose that a great deal of the genetic make-up of marine planktonic populations comprises divergences that date back to long before the last glacial maximum. We consider questions on the taxonomic status of C. euxinus to remain open. However, its high genetic affinity to the C. helgolandicus calls for further investigation.

EVOLUTION OF COADAPTATION IN A TWO-LOCUS EPISTATIC SYSTEM

Although recent advances in genome biology have dramatically increased our understanding of the contribution of gene interactions to the development of complex phenotypes, we still lack general agreement on the process and mechanisms responsible for the evolution of epistatic systems. Even if genes in a species are indeed integrated into coadapted complexes of interacting components, simple additive evolution may eventually result in epistatic differentiation of populations. Consequently, the prevalence of epistatic gene action does not tell us anything about the role of epistatic selection in the history of population divergence. To elucidate the contribution of epistatic selection in the evolution of coadaptation, we investigate the fixation process of two mutations that interact synergistically to enhance fitness. We show by diffusion analysis and simulations that epistatic selection on cosegregating variants does not by itself promote the evolution of epistatic systems; rather, accumulation of neutral mutations may play a crucial role, creating an appropriate genetic milieu for adaptive evolution in the future generations.