Population Genetic Tools Research Articles

Development of 26 SNP markers in Dabry’s sturgeon (Acipenser dabryanus) based on high-throughput sequencing

Dabry’s sturgeon (Acipenser dabryanus) is an endemic freshwater species in China mainly distributed in the mainstream of the upper Yangtze River and its tributaries. Due to river fragmentation, sand/gravel extraction, over-fishing, and water pollution, the wild population of Dabry’s sturgeon suffered a dramatic decline. In the present study, 26 novel single nucleotide polymorphism (SNP) markers were developed based on high-throughput sequencing. Genetic diversity analysis revealed that the values of observed heterozygosity (Ho) and expected heterozygosity (He) varied from 0.1000 to 0.9000 and from 0.0974 to 0.5115, respectively, and the minor allele frequency ranged from 0.0500 to 0.4750. Only three loci showed significant deviation from Hardy–Weinberg equilibrium after Bonferroni correction. The SNP markers will serve as a valuable tool for further population genetics, genetic breeding, and resource conservation in this species.

An Evolutionary Genetic Perspective on Cancer Biology

Cancer biology can be better understood by drawing upon methods and concepts from evolutionary genetics. Cancer progression proceeds through somatic evolution, being driven by selection on clonal lineages via the differential survival and proliferation of cell lines. This within-patient evolution can be modeled and analyzed using population genetic and phylogenetic tools to identify mutations and genotypes that are under directional selection during tumor growth, spatial differentiation, and metastasis. Evolutionary genetics can also explain the persistence of cancer within populations. A minority of cancers are associated with inherited risk alleles, which are maintained in populations through genetic drift or antagonistic pleiotropy. Finally, cancer biology can be understood from a macroevolutionary perspective as a case study of evolutionary cooperation and conflict between different levels of biological organization.

Bee conservation in the age of genomics

Many wild and managed bee pollinators have experienced population declines over the past several decades, and molecular and population genetic tools have been valuable in understanding conservation threats across the bee tree of life. Emerging genomic tools have the potential to improve classical applications of conservation genetics, such as assessing species status, and quantifying genetic diversity, gene flow and effective population sizes. Genomic tools can also revolutionize novel research in bee conservation and management, including the identification of loci underlying adaptive and economically desirable traits, such as those involved in disease susceptibility, responses to multiple environmental stressors, and even discovering and understanding the hidden diversity of beneficial microorganisms associated with bees. In this perspective, we provide a survey of some of the ways genomic tools can be applied to bee conservation to bridge the gap between basic and applied genomics research.

PReFerSim: fast simulation of demography and selection under the Poisson Random Field model

PReFerSim is freely available at: https://github.com/LohmuellerLab/PReFerSim CONTACT: klohmueller@ucla.eduSupplementary information: Supplementary data are available at Bioinformatics online.

The haplomatch program for comparing Y-chromosome STR-haplotypes and its application to the analysis of the origin of Don Cossacks

STR haplotypes of the Y chromosome are widely used as effective genetic markers in studies of human populations and in forensic DNA analysis. The task often arises to compare the spectrum of haplotypes in individuals or entire populations. Performing this task manually is too laborious and thus unrealistic. We propose an algorithm for counting similarity between STR haplotypes. This algorithm is suitable for massive analyses of samples. It is implemented in the computer program Haplomatch, which makes it possible to find haplotypes that differ from the target haplotype by 0, 1, 2, 3, or more mutational steps. The program may operate in two modes: comparison of individuals and comparison of populations. Flexibility of the program (the possibility of using any external database), its usability (MS Excel spreadsheets are used), and the capability of being applied to other chromosomes and other species could make this software a new useful tool in population genetics and forensic and genealogical studies. The Haplomatch software is freely available on our website www.genofond.ru. The program is applied to studying the gene pool of Cossacks. Experimental analysis of Y-chromosomal diversity in a representative set (N = 131) of Upper Don Cossacks is performed. Analysis of the STR haplotypes detects genetic proximity of Cossacks to East Slavic populations (in particular, to Southern and Central Russians, as well as to Ukrainians), which confirms the hypothesis of the origin of the Cossacks mainly due to immigration from Russia and Ukraine. Also, a small genetic influence of Turkicspeaking Nogais is found, probably caused by their occurrence in the Don Voisko as part of the Tatar layer. No similarities between haplotype spectra of Cossacks and Caucasus populations are found. This case study demonstrates the effectiveness of the Haplomatch software in analyzing large sets of STR haplotypes.

Reduced reproductive fitness of an endemic insular juniper population: An eco-genetic mediation hypothesis

The mutual reinforcement of multiple drivers of global change erodes ecosystem services and accelerates plant population decline worldwide. This is particularly the case for island ecosystems where anthropogenic activity has imperilled insular floras for centuries. Different hypotheses have put forward the combined effects of environmental shifts and genetic factors in driving fecundity decline in threatened populations. In this study, we combined population genetic tools and structural equation models to test the eco-genetic mediation hypothesis, that the environmental conditions influence genetic variation, which in turn affects plant fitness. Our study species is Juniperus cedrus, an endangered juniper species endemic to the Canary Islands. Juniper woodlands have been depleted since the arrival of human inhabitants confined extant populations to marginal lands. More recently, long-distance dispersers have been extirpated from the study area, potentially eliminating connectivity among fragmented populations. We expected strong intrapopulation subdivision and high levels of inbreeding and kinship that should negatively affect individual fitness. We found evidence of population subdivision into several mating neighbourhoods (K=13), some of them highly inbred. However, contrary to our expectations, neither inbreeding nor mean kinship mediated a population response to environmental factors. Our results suggest three remedial actions to reverse the declining demographic trends: (i) re-establish native vegetation to ameliorate local environmental conditions; (ii) restore dispersal services to increase connectivity; and (iii) monitor fitness decline to identify lagged effects associated with deforestation. Overall, this study shows that structural equation models combined with population genetic techniques are suitable tools to identify high-order effects among multiple drivers of global change that underlie forest decline.

Development of microsatellite markers for Manilkara maxima T.D. Penn. (Sapotaceae) and their use in conservation genetics.

Manilkara maxima is an endemic tree species of the Atlantic Forest in southern Bahia, Brazil. It is considered important for forest conservation due to its mutualistic interactions with endemic and endangered animals. Our aim was to develop microsatellite markers to estimate genetic diversity in order to provide information for effectiveness of future conservation programs. We used next generation sequencing technology to develop the first specific microsatellite markers for M. maxima. Seventeen new microsatellite loci were applied in 72 individuals sampled in three natural populations. On average, the number of alleles per loci was 8.8. The expected heterozygosity varied between 0.72 and 0.77, indicating that the developed set of molecular markers is useful for genetic diversity studies. Additionally, the estimated value for the combined probability of exclusion (Q) was greater than 0.999, which indicates the powerful of these molecular tools for paternity and kinship analysis. Our results demonstrate that the set of microsatellites developed in this work is a powerful tool for population genetics, molecular ecology and conservation biology purposes.

Tracking the elusive history of diversification in plant-herbivorous insect-parasitoid food webs: insights from figs and fig wasps.

The food webs consisting of plants, herbivorous insects and their insect parasitoids are a major component of terrestrial biodiversity. They play a central role in the functioning of all terrestrial ecosystems, and the number of species involved is mind-blowing (Nyman et al. 2015). Nevertheless, our understanding of the evolutionary and ecological determinants of their diversity is still in its infancy. In this issue of Molecular Ecology, Sutton et al. (2016) open a window into the comparative analysis of spatial genetic structuring in a set of comparable multitrophic models, involving highly species-specific interactions: figs and fig wasps. This is the first study to compare genetic structure using population genetics tools in a fig-pollinating wasp (Pleistodontes imperialis sp1) and its main parasitoid (Sycoscapter sp.A). The fig-pollinating wasp has a discontinuous spatial distribution that correlates with genetic differentiation, while the parasitoid bridges the discontinuity by parasitizing other pollinator species on the same host fig tree and presents basically no spatial genetic structure. The full implications of these results for our general understanding of plant-herbivorous insect-insect parasitoids diversification become apparent when envisioned within the framework of recent advances in fig and fig wasp biology.

DNA Sequencing in Cultural Heritage.

During the last three decades, DNA analysis on degraded samples revealed itself as an important research tool in anthropology, archaeozoology, molecular evolution, and population genetics. Application on topics such as determination of species origin of prehistoric and historic objects, individual identification of famous personalities, characterization of particular samples important for historical, archeological, or evolutionary reconstructions, confers to the paleogenetics an important role also for the enhancement of cultural heritage. A really fast improvement in methodologies in recent years led to a revolution that permitted recovering even complete genomes from highly degraded samples with the possibility to go back in time 400,000years for samples from temperate regions and 700,000years for permafrozen remains and to analyze even more recent material that has been subjected to hard biochemical treatments. Here we propose a review on the different methodological approaches used so far for the molecular analysis of degraded samples and their application on some case studies.

Applying Population Genetic Approaches within Languages

The adoption of evolutionary approaches to study language change as a type of non-biological evolution has gained increasing interest and introduced a variety of quantitative tools to linguistics. The focus has thus far mainly been on language families, or ‘linguistic macroevolution,’ and taken the shape of linguistic phylogenetics. Here we explore whether evolutionary methods could be applicable for studying intra-lingual variation (‘linguistic microevolution’) by testing a population genetic clustering method for analyzing the ‘population structure’ of Finnish dialects. We compare the results with traditional dialect divisions established in the literature and with K-medoids clustering, which is free from biological assumptions. The results are encouragingly similar to each other and agree with traditional views, suggesting that population genetic tools could be a useful addition to the dialectological toolkit. We also show how the results of the model-based clustering could serve as a basis for further study.

P-B23 Prevalence of Ebola viral entry resistance in a diverse population

Whole-genome sequencing (WGS) is fast evolving into a population genetics tool to estimate effect of sequence variants on human health and fitness. However, predicting the role of variants that confer protection remains challenging. Given this, we hypothesized that use of large population datasets and integrative-omics data could be used to delineate the role of protective variants in specific genes involved in Ebola viral pathogenesis. As a pilot study we performed trio-based WGS on 3060 ethnically diverse individuals derived from a study in which infants (and both parents) undergo WGS, as well as other omic analyses, at birth, and are then followed prospectively. Variants in genes (eg, NPC1, CTSB, VPS11, VPS33A, etc.) known to play key roles in Ebola viral entry into human cells were evaluated for overall variant burden and loss-of-function via protein truncation. An additional gene (NPC2) with overlapping biochemical role but no clear role in Ebola viral entry pathway was used as control. Additionally, RNASeq was performed on a subset of individuals. We screened WGS data for variants with predicted large functional effects in the gene set. We identified 69 novel variants (not in dbSNP v.144), of which 7 were missense and 4 protein truncating in NPC1 in heterozygous state, compared to 3 rare missense variants in control gene NPC2. Furthermore, we identified heterozygous protein truncating mutations in genes within the Ebola viral entry pathway (eg, CTSB = 7; VPS11 = 3; VPS41 = 3) compared to only 1 heterozygous variant in NPC1. Based on NPC1 variation spectrum in our cohort, and corresponding to results from previous biological models, we predicted that 0.11%–0.37% of our diverse population would have resistance to Ebola virus. RNASeq analysis of heterozygous NPC1 truncation variants showed skew in the allelic- distribution. We conclude that whole genome and transcriptome data can serve as a tool for predictive analysis of viral susceptibility and resistance.

Computationally Efficient Composite Likelihood Statistics for Demographic Inference.

Many population genetics tools employ composite likelihoods, because fully modeling genomic linkage is challenging. But traditional approaches to estimating parameter uncertainties and performing model selection require full likelihoods, so these tools have relied on computationally expensive maximum-likelihood estimation (MLE) on bootstrapped data. Here, we demonstrate that statistical theory can be applied to adjust composite likelihoods and perform robust computationally efficient statistical inference in two demographic inference tools: ∂a∂i and TRACTS. On both simulated and real data, the adjustments perform comparably to MLE bootstrapping while using orders of magnitude less computational time.

Development and preliminary evaluation of a genomewide single nucleotide polymorphisms resource generated by RAD-seq for the small yellow croaker (Larimichthys polyactis).

Recent advances in high-throughput sequencing technologies have offered the possibility to generate genomewide sequence data to delineate previously unidentified genetic structure, obtain more accurate estimates of demographic parameters and to evaluate potential adaptive divergence. Here, we identified 27556 single nucleotide polymorphisms for the small yellow croaker (Larimichthys polyactis) using restriction-site-associated DNA (RAD) sequencing of 24 individuals from two populations. Significant sources of genetic variation were identified, with an average nucleotide diversity (π) of 0.00105±0.000425 across individuals, and long-term effective population size was thus estimated to range between 26172 and 261716. According to the results, no differentiation between the two populations was detected based on the SNP data set of top quality score per contig or neutral loci. However, the two analysed populations were highly differentiated based on SNP data set of both top FST value per contig and the outlier SNPs. Moreover, local adaptation was highlighted by an FST -based outlier tests implemented in LOSITAN and a total of 538 potentially locally selected SNPs were identified. blast2go annotation of contigs containing the outlier SNPs yielded hits for 37 (66%) of 56 significant blastx matches. Candidate genes for local adaptation constituted a wide array of biological functions, including cellular response to oxidative stress, actin filament binding, ion transmembrane transport and synapse assembly. The generated SNP resources in this study provided a valuable tool for future population genetics and genomics studies of L.polyactis.

Elucidating the spatio‐temporal dynamics of an emerging wildlife pathogen using approximate Bayesian computation

Emerging pathogens constitute a severe threat for human health and biodiversity. Determining the status (native or non-native) of emerging pathogens, and tracing back their spatio-temporal dynamics, is crucial to understand the eco-evolutionary factors promoting their emergence, to control their spread and mitigate their impacts. However, tracing back the spatio-temporal dynamics of emerging wildlife pathogens is challenging because (i) they are often neglected until they become sufficiently abundant and pose socio-economical concerns and (ii) their geographical range is often little known. Here, we combined classical population genetics tools and approximate Bayesian computation (i.e. ABC) to retrace the dynamics of Tracheliastes polycolpus, a poorly documented pathogenic ectoparasite emerging in Western Europe that threatens several freshwater fish species. Our results strongly suggest that populations of T.polycolpus in France emerged from individuals originating from a unique genetic pool that were most likely introduced in the 1920s in central France. From this initial population, three waves of colonization occurred into peripheral watersheds within the next two decades. We further demonstrated that populations remained at low densities, and hence undetectable, during 10years before a major demographic expansion occurred, and before its official detection in France. These findings corroborate and expand the few historical records available for this emerging pathogen. More generally, our study demonstrates how ABC can be used to determine the status, reconstruct the colonization history and infer key evolutionary parameters of emerging wildlife pathogens with low data availability, and for which samples from the putative native area are inaccessible.

Phylogenetic analysis of She population from Fujian Province in China based on 26 Y-STR Loci*

The She people, with a population of about 710,000, are the largest minority in Fujian province. They live primarily in the mountainous areas of Fujian Province and also present in Zhejiang, Jiangxi, Guangdong, Anhui, Hunan and Taiwan. Currently, Y-STR analysis has well characterized and become an essential tool in forensic and population genetics. In the present study, we investigated genetic and phylogenetic relationship between the She population, which included 53 unrelated She males living in the Fujian Province and typed for 26 Y-STR loci, and 13 reference populations. We found that the She population has the closest relationship with the Miao population, followed by the populations from south China.

Population Genetics and Reproductive Strategies of African Trypanosomes: Revisiting Available Published Data.

Trypanosomatidae are a dangerous family of Euglenobionta parasites that threaten the health and economy of millions of people around the world. More precisely describing the population biology and reproductive mode of such pests is not only a matter of pure science, but can also be useful for understanding parasite adaptation, as well as how parasitism, specialization (parasite specificity), and complex life cycles evolve over time. Studying this parasite’s reproductive strategies and population structure can also contribute key information to the understanding of the epidemiology of associated diseases; it can also provide clues for elaborating control programs and predicting the probability of success for control campaigns (such as vaccines and drug therapies), along with emergence or re-emergence risks. Population genetics tools, if appropriately used, can provide precise and useful information in these investigations. In this paper, we revisit recent data collected during population genetics surveys of different Trypanosoma species in sub-Saharan Africa. Reproductive modes and population structure depend not only on the taxon but also on the geographical location and data quality (absence or presence of DNA amplification failures). We conclude on issues regarding future directions of research, in particular vis-à-vis genotyping and sampling strategies, which are still relevant yet, too often, neglected issues.

Mapping genetic determinants of viral traits with FST and quantitative trait locus (QTL) approaches

The genetic determinism of viral traits can generally be dissected using either forward or reverse genetics because the clonal reproduction of viruses does not require the use of approaches based on laboratory crosses. Nevertheless, we hypothesized that recombinant viruses could be analyzed as sexually reproducing organisms, using either a quantitative trait loci (QTL) approach or a locus-by-locus fixation index (FST). Locus-by-locus FST analysis, and four different regressions and interval mapping algorithms of QTL analysis were applied to a phenotypic and genotypic dataset previously obtained from 47 artificial recombinant genomes generated between two begomovirus species. Both approaches assigned the determinant of within-host accumulation—previously identified using standard virology approaches—to a region including the 5׳ end of the replication-associated protein (Rep) gene and the upstream intergenic region. This study provides a proof of principle that QTL and population genetics tools can be extended to characterize the genetic determinants of viral traits.

Population genetics of autopolyploids under a mixed mating model and the estimation of selfing rate.

Nowadays, the population genetics analysis of autopolyploid species faces many difficulties due to (i) limited development of population genetics tools under polysomic inheritance, (ii) difficulties to assess allelic dosage when genotyping individuals and (iii) a form of inbreeding resulting from the mechanism of 'double reduction'. Consequently, few data analysis computer programs are applicable to autopolyploids. To contribute bridging this gap, this article first derives theoretical expectations for the inbreeding and identity disequilibrium coefficients under polysomic inheritance in a mixed mating model. Moment estimators of these coefficients are proposed when exact genotypes or just markers phenotypes (i.e. allelic dosage unknown) are available. This led to the development of estimators of the selfing rate based on adult genotypes or phenotypes and applicable to any even-ploidy level. Their statistical performances and robustness were assessed by numerical simulations. Contrary to inbreeding-based estimators, the identity disequilibrium-based estimator using phenotypes is robust (absolute bias generally < 0.05), even in the presence of double reduction, null alleles or biparental inbreeding due to isolation by distance. A fairly good precision of the selfing rate estimates (root mean squared error < 0.1) is already achievable using a sample of 30-50 individuals phenotyped at 10 loci bearing 5-10 alleles each, conditions reachable using microsatellite markers. Diallelic markers (e.g. SNP) can also perform satisfactorily in diploids and tetraploids but more polymorphic markers are necessary for higher ploidy levels. The method is implemented in the software SPAGeDi and should contribute to reduce the lack of population genetics tools applicable to autopolyploids.

A new method for studying population genetics of cyst nematodes based on Pool-Seq and genomewide allele frequency analysis.

Cyst nematodes are important agricultural pests responsible for billions of dollars of losses each year. Plant resistance is the most effective management tool, but it requires a close monitoring of population genetics. Current technologies for pathotyping and genotyping cyst nematodes are time-consuming, expensive and imprecise. In this study, we capitalized on the reproduction mode of cyst nematodes to develop a simple population genetic analysis pipeline based on genotyping-by-sequencing and Pool-Seq. This method yielded thousands of SNPs and allowed us to study the relationships between populations of different origins or pathotypes. Validation of the method on well-characterized populations also demonstrated that it was a powerful and accurate tool for population genetics. The genomewide allele frequencies of 23 populations of golden nematode, from nine countries and representing the five known pathotypes, were compared. A clear separation of the pathotypes and fine genetic relationships between and among global populations were obtained using this method. In addition to being powerful, this tool has proven to be very time- and cost-efficient and could be applied to other cyst nematode species.

DEVELOPING DROUGHT AND SALT RESISTANT GRAPE ROOTSTOCKS

Grape breeders are beginning to consider the consequences of a changing climate and expanding human population. One inescapable conclusion is that there will be less water available for viticulture given the need to produce staple food crops. Summer arid areas like California are ideal for fruit culture, but these soils tend to be more alkaline and prone to problems with salinity, which is controlled by leaching with good quality water. Thus, it seems prudent to expedite the development of grape rootstocks with strong resistance to drought and salinity. Such a breeding program is underway at UC Davis. Modified assays for salt resistance have been developed allowing seedlings to be tested quickly and accurately. We have made extensive collections of Vitis species from across the desert regions of the southwestern United States. Very strong examples of chloride exclusion have been found in accessions of V. acerifolia, V. arizonica, V. berlandieri, V. doaniana and V. girdiana. We are also evaluating the root systems of this region?s Vitis species by characterizing root angles, the development of persistent structural roots, and the ability of fibrous roots to regrow after periods of drought. Mapping populations are being generated and phenotyped for the above traits to develop genetic markers for rootstock breeding efforts. Such mapping can also lead to a better understanding of the genes and mechanisms controlling drought and salt resistance. However, these breeding efforts are complicated by a poor understanding of the grape germplasm in the southwestern US, which leads to confusion regarding species characteristics, taxonomy and sources of resistance. Populations of these species exist in or near springs and are widely separated by deserts and mountains. They experience frequent migration events due to the movement of birds carrying seeds up watercourses or between disjunct populations. Consequently, it can be very difficult to define individuals as a given species; more often they appear to be hybrids that intergrade with species on the fringes of their distribution. Our efforts to use landscape and population genetics tools to define these important species and their hybrids will also be discussed.