The Genomics of Isolated Populations of Gampsocleis glabra (Orthoptera: Tettigoniidae) in Central and Western Europe

Habitat destruction and fragmentation are among the major current threats to global biodiversity. Fragmentation may also affect species with good dispersal abilities. We study the heath bushcricket Gampsocleis glabra, a specialist of steppe-like habitats across Europe that are highly fragmented, investigating if these isolated populations can be distinguished using population genomics and if there are any traces of admixture or dispersal among them. We try to answer these questions using genome-wide SNP data generated with ddRAD sequencing. We calculated F-statistics and visualized differentiation using STRUCTURE plots. While limited by the difficulty of sampling this threatened species, our results show that all populations except one that was represented by a singleton were clearly distinct, with pairwise FST values between 0.010 and 0.181. STRUCTURE indicated limited but visible admixture across most populations and probably also an exchange of individuals between populations of Germany and The Netherlands. We conclude that in G. glabra, a certain amount of gene flow has persisted, at least in the past, also among populations that are isolated today. We also detect a possibly more recent dispersal event between a population in The Netherlands and one in Germany, which may be human aided. We suggest that the conservation of larger populations should be maintained, that efforts should be taken to restore abandoned habitat, that the preservation even of small habitat fragments may be beneficial for the conservation of this species, and that these habitats should be regularly monitored for possible (re-)colonization.

Time Trends in Trajectories of Forearm Mineral Content and Bone Size during Childhood-Results from Cross-Sectional Measurements with the Same Apparatus Four Decades Apart

Evidence suggests that single photon absorptiometry (SPA)-measured forearm bone mineral density (BMD) is lower in contemporary children in Malmö than it was four decades ago, but the fracture incidence in the at-risk population (all Malmö children) has been stable during the same period. The aim of this study was to evaluate if improvements in skeletal structure over time may explain this observation. In 2017-2018 we measured distal forearm bone mineral content (BMC; mg/cm) and periosteal diameter (mm) in 238 boys and 204 girls aged 7-15 using SPA. Based on the SPA measurements, we calculated forearm BMD (mg/cm²), bone mineral apparent density (BMAD, mg/cm³), section modulus, and strength index (BMAD × section modulus). The results were compared with those derived from measurements of 55 boys and 61 girls of the same ages using the same scanner in 1979-1981. We used log-linear regression with age, sex, and cohort as predictors to investigate differences in trait trajectories (trait versus age slopes [mean percent difference in beta values (95% confidence interval)]). SPA-measured forearm BMC was lower at each age in 2017-2018 compared to 1979-1981 (a mean age and sex adjusted relative difference of 9.1%), the forearm BMC trajectory was similar in 2017-2018 to that in 1979-1981 (reference) [0.0%/year (-1.0%, 1.0%)], while the 2017-2018 forearm periosteal diameter trajectory was steeper [1.1%/year (0.3%, 2.0%)]. Since bone size influences both BMD (BMC divided by scanned area) and mechanical characteristics, the forearm BMD trajectory was flatter in 2017-2018 [-1.1%/year (-2.0%, -0.2%)] and the forearm section modulus trajectory steeper [3.9%/year (1.4%, 6.4%)]. Forearm strength index trajectory was similar [1.8%/year (-0.5%, 4.1%)]. The lower SPA-measured forearm BMD trajectory in contemporary children compared to four decades ago may be offset by changes in forearm bone structure, resulting in similar overall bone strength. © 2023 The Authors. JBMR Plus published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research.

Associations Among Hip Structure, Bone Mineral Density, and Strength Vary With External Bone Size in White Women

Bone mineral density (BMD) is heavily relied upon to reflect structural changes affecting hip strength and fracture risk. Strong correlations between BMD and strength are needed to provide confidence that structural changes are reflected in BMD and, in turn, strength. This study investigated how variation in bone structure gives rise to variation in BMD and strength and tested whether these associations differ with external bone size. Cadaveric proximal femurs (n = 30, White women, 36-89+ years) were imaged using nanocomputed tomography (nano-CT) and loaded in a sideways fall configuration to assess bone strength and brittleness. Bone voxels within the nano-CT images were projected onto a plane to create pseudo dual-energy X-ray absorptiometry (pseudo-DXA) images consistent with a clinical DXA scan. A validation study using 19 samples confirmed pseudo-DXA measures correlated significantly with those measured from a commercially available DXA system, including bone mineral content (BMC) (R ²  = 0.95), area (R ²  = 0.58), and BMD (R ²  = 0.92). BMD-strength associations were conducted using multivariate linear regression analyses with the samples divided into narrow and wide groups by pseudo-DXA area. Nearly 80% of the variation in strength was explained by age, body weight, and pseudo-DXA BMD for the narrow subgroup. Including additional structural or density distribution information in regression models only modestly improved the correlations. In contrast, age, body weight, and pseudo-DXA BMD explained only half of the variation in strength for the wide subgroup. Including bone density distribution or structural details did not improve the correlations, but including post-yield deflection (PYD), a measure of bone material brittleness, did increase the coefficient of determination to more than 70% for the wide subgroup. This outcome suggested material level effects play an important role in the strength of wide femoral necks. Thus, the associations among structure, BMD, and strength differed with external bone size, providing evidence that structure-function relationships may be improved by judiciously sorting study cohorts into subgroups. © 2022 The Authors. JBMR Plus published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research.

Phytochemicals and Their Correlation with Molecular Data in Micromeria and Clinopodium (Lamiaceae) Taxa

A study of the phytochemical and molecular characteristics of ten Micromeria and six Clinopodium taxa (family Lamiaceae) distributed in the Balkan Peninsula was carried out. The phytochemicals detected in essential oils by gas chromatography, mass spectrometry, and molecular data amplified fragment length polymorphism were used to study the taxonomic relationships among the taxa and the correlations between phytochemical and molecular data. STRUCTURE analysis revealed three genetic groups, while Bayesian Analysis of Population Structure grouped the studied taxa into 11 clusters nested in the groups obtained by STRUCTURE. Principal components analysis performed with the 21 most represented compounds in the essential oils yielded results that were partly consistent with those obtained by STRUCTURE and neighbour-joining analyses. However, their geographic distributions did not support the genetic grouping of the studied taxa and populations. The Mantel test showed a significant correlation between the phytochemical and genetic data (r = 0.421, p < 0.001). Genetic distance explained 17.8% of the phytochemical distance between populations. The current taxonomic position of several of the studied taxa is yet to be satisfactorily resolved, and further studies are needed. Such future research should include nuclear and plastid DNA sequences from a larger sample of populations and individuals.

Analysis of genetic diversity among Onobrychis accessions with high agronomic performance by simple sequence repeat (SSR) markers

BACKGROUND

Onobrychis viciifolia Scop. is a short-lived perennial cool-season legume used for forage production. It is a common native species in Asia Minor, especially in Turkey, the districts of the Caucasus, and the Caspian fringes. It can grow well in a broad range of climatic and soil types found in Asia, Europe, and North America. It is a non-bloating crop, making it suitable for use in both hay and pasture.

METHODS AND RESULTS

The aim was to assess the diversity of the 83 sainfoin genotypes selected based on their high agronomic performance from a germplasm collection evaluated in the experimental field of Tekirdag Namik Kemal University, Turkey. Ten nuclear simple sequence repeat (nSSR) primers (OVK036, OVK046, OVK094, OVK101, OVK125, OVK161, OVK174, OVM033, OVM061, and OVM125) were used in the study. All nSSR loci were found to be polymorphic and totally 92 alleles were detected. The mean observed number of alleles per locus was calculated as 9.2. Among the genetic diversity parameters, Shannon Index (I = 0.375), unbiased genetic diversity value (uh = 0.243), and mean polymorphic information content (PIC = 0.240) were calculated. The genetic distance value varied between 0.43 and 0.95. Based on the dendrogram built by the UPGMA clustering method using genetic distance values, it was observed that the studied sainfoin genotypes were divided into two main clusters, whereas the STRUCTURE analysis results had high support for three clusters.

CONCLUSIONS

The results obtained from this study provide important information on the genetic structures of the studied sainfoin genotypes and their genetic relationship. Therefore acquired genetic data will be useful in designing more efficient polycross nurseries, allowing open pollination of best performing and genetically diverse genotypes in the isolated conditions, which will increase genetic gain in sainfoin breeding programs.

Inference of recent admixture using genotype data

The inference of biogeographic ancestry (BGA) has become a focus of forensic genetics. Misinference of BGA can have profound unwanted consequences for investigations and society. We show that recent admixture can lead to misclassification and erroneous inference of ancestry proportions, using state of the art analysis tools with (i) simulations, (ii) 1000 genomes project data, and (iii) two individuals analyzed using the ForenSeq DNA Signature Prep Kit. Subsequently, we extend existing tools for estimation of individual ancestry (IA) by allowing for different IA in both parents, leading to estimates of parental individual ancestry (PIA), and a statistical test for recent admixture. Estimation of PIA outperforms IA in most scenarios of recent admixture. Furthermore, additional information about parental ancestry can be acquired with PIA that may guide casework.

The impact of estimator choice: Disagreement in clustering solutions across K estimators for Bayesian analysis of population genetic structure across a wide range of empirical data sets

The software program STRUCTURE is one of the most cited tools for determining population structure. To infer the optimal number of clusters from STRUCTURE output, the ΔK method is often applied. However, a recent study relying on simulated microsatellite data suggested that this method has a downward bias in its estimation of K and is sensitive to uneven sampling. If this finding holds for empirical data sets, conclusions about the scale of gene flow may have to be revised for a large number of studies. To determine the impact of method choice, we applied recently described estimators of K to re-estimate genetic structure in 41 empirical microsatellite data sets; 15 from a broad range of taxa and 26 from one phylogenetic group, coral. We compared alternative estimates of K (Puechmaille statistics) with traditional (ΔK and posterior probability) estimates and found widespread disagreement of estimators across data sets. Thus, one estimator alone is insufficient for determining the optimal number of clusters; this was regardless of study organism or evenness of sampling scheme. Subsequent analysis of molecular variance (AMOVA) did not necessarily clarify which clustering solution was best. To better infer population structure, we suggest a combination of visual inspection of STRUCTURE plots and calculation of the alternative estimators at various thresholds in addition to ΔK. Disagreement between traditional and recent estimators may have important biological implications, such as previously unrecognized population structure, as was the case for many studies reanalysed here.

Machine-learning-based detection of adaptive divergence of the stream mayfly Ephemera strigata populations

Adaptive divergence is a key mechanism shaping the genetic variation of natural populations. A central question linking ecology with evolutionary biology is how spatial environmental heterogeneity can lead to adaptive divergence among local populations within a species. In this study, using a genome scan approach to detect candidate loci under selection, we examined adaptive divergence of the stream mayfly Ephemera strigata in the Natori River Basin in northeastern Japan. We applied a new machine-learning method (i.e., random forest) besides traditional distance-based redundancy analysis (dbRDA) to examine relationships between environmental factors and adaptive divergence at non-neutral loci. Spatial autocorrelation analysis based on neutral loci was employed to examine the dispersal ability of this species. We conclude the following: (a) E. strigata show altitudinal adaptive divergence among the populations in the Natori River Basin; (b) random forest showed higher resolution for detecting adaptive divergence than traditional statistical analysis; and (c) separating all markers into neutral and non-neutral loci could provide full insight into parameters such as genetic diversity, local adaptation, and dispersal ability.

Differentiation of Asian population samples using the Illumina ForenSeq kit

The Kidd set of ancestry informative SNPs are included in Illumina's ForenSeq DNA Signature Kit. We had previously reported on the capability of these SNPs together with some phenotypic SNPs with ancestry informative properties in differentiating individuals from the Chinese, Malay and Indian populations in Singapore. The Singapore population is primarily made up of Chinese, Malays and Indians, with individuals from other Asian countries making up the rest. In this study, we evaluated the ancestry prediction capabilities of the ForenSeq kit in 484 unrelated individuals of self-declared Bangladeshi, Burmese, Filipino, Indonesian and Vietnamese origin. 750 Chinese, Malay and Indian individuals previously reported were included in this study. 48 ancestry SNPs and 12 phenotypic SNPs with ancestry informative properties were selected for analyses. Ancestry modelling in STRUCTURE showed that the eight tested populations could be better classified as five. Principal component analysis also showed that the eight populations clustered in five groups based on general geographic location within Asia; with Chinese clustering with Vietnamese, Malays clustering with Indonesians, Indians clustering with Bangladeshi, and the Burmese and Filipino populations clustering in-between and overlapping with the Chinese and Malay populations. The 60 SNPs analysed could account for only 23 % of the variation between the populations. The lack of distinction between the populations resulted in poor (43 % correct self-classification) cross-validation using Snipper. While this was improved by merging the co-clustering populations into five groups (East, South-East, South Asian, Burmese & Filipino), successful self-classification was still relatively low (69 %). While the 60 tested ancestry informative markers were able to differentiate between individuals of East, South-East and South Asian origin, they are not sufficiently informative to effectively discriminate between Chinese, Malays and Indians, and Bangladeshi, Burmese, Filipino, Indonesian and Filipino populations in the country.

Gene transfer across species boundaries in bryophytes: evidence from major life cycle stages in Homalothecium lutescens and H. sericeum

BACKGROUND AND AIMS

The mosses Homalothecium lutescens and H. sericeum are genetically, morphologically and ecologically differentiated; mixed populations sometimes occur. In sympatric populations, intermediate character states among gametophytes and sporophytes have been observed, suggesting hybridization and introgression in such populations.

METHODS

We determined genotypes using bi-allelic co-dominant single nucleotide polymorphism (SNP) markers, specific to either H. lutescens or H. sericeum, to estimate the degree of genetic mixing in 449 moss samples collected from seven sympatric and five allopatric populations on the island of Öland, south Sweden. The samples represented three generations: haploid maternal gametophytes; diploid sporophytes; and haploid sporelings.

KEY RESULTS

Admixture analyses of SNP genotypes identified a majority as pure H. lutescens or H. sericeum, but 76 samples were identified as mildly admixed (17 %) and 17 samples (3.8 %) as strongly admixed. Admixed samples were represented in all three generations in several populations. Hybridization and introgression were bidirectional.

CONCLUSIONS

Our results demonstrate that admixed genomes are transferred between the generations, so that the populations behave as true hybrid zones. Earlier studies of sympatric bryophyte populations with admixed individuals have not been able to show that admixed alleles are transferred beyond the first generation. The presence of true hybrid zones has strong evolutionary implications because genetic material transferred across species boundaries can be directly exposed to selection in the long-lived haploid generation of the bryophyte life cycle, and contribute to local adaptation, long-term survival and speciation.

Tall Pinus luzmariae trees with genes from P. herrerae

CONTEXT

Pinus herrerae and P. luzmariae are endemic to western Mexico, where they cover an area of more than 1 million hectares. Pinus herrerae is also cultivated in field trials in South Africa and South America, because of its considerable economic importance as a source of timber and resin. Seed quality, afforestation success and desirable traits may all be influenced by the presence of hybrid trees in seed stands.

AIMS

We aimed to determine the degree of hybridization between P. herrerae and P. luzmariae in seed stands of each species located in the Sierra Madre Occidental, Durango, Mexico.

METHODS

AFLP molecular markers from samples of 171 trees across five populations were analyzed with STRUCTURE and NewHybrids software to determine the degree of introgressive hybridization. The accuracy of STRUCTURE and NewHybrids in detecting hybrids was quantified using the software Hybridlab 1.0. Morphological analysis of 131 samples from two populations of P. herrerae and two populations of P. luzmariae was also conducted by Random Forest classification. The data were compared by Principal Coordinate Analysis (PCoA) in GenAlex 6.501.

RESULTS

Hybridization between Pinus herrerae and P. luzmariae was observed in all seed stands under study and resulted in enhancement of desirable silvicultural traits in the latter species. In P. luzmariae, only about 16% molecularly detected hybrids correspond to those identified on a morphological basis. However, the morphology of P. herrerae is not consistent with the molecularly identified hybrids from one population and is only consistent with 3.3 of those from the other population.

CONCLUSIONS

This is the first report of hybrid vigour (heterosis) in Mexican pines. Information about hybridization and introgression is essential for developing effective future breeding programs, successful establishment of plantations and management of natural forest stands. Understanding how natural hybridization may influence the evolution and adaptation of pines to climate change is a cornerstone to sustainable forest management including adaptive silviculture.

An ancestry informative marker panel design for individual ancestry estimation of Hispanic population using whole exome sequencing data

Background

Europeans and American Indians were major genetic ancestry of Hispanics in the U.S. These ancestral groups have markedly different incidence rates and outcomes in many types of cancers. Therefore, the genetic admixture may cause biased genetic association study with cancer susceptibility variants specifically in Hispanics. For example, the incidence rate of liver cancer has been shown with substantial disparity between Hispanic, Asian and non-Hispanic white populations. Currently, ancestry informative marker (AIM) panels have been widely utilized with up to a few hundred ancestry-informative single nucleotide polymorphisms (SNPs) to infer ancestry admixture. Notably, current available AIMs are predominantly located in intron and intergenic regions, while the whole exome sequencing (WES) protocols commonly used in translational research and clinical practice do not cover these markers. Thus, it remains challenging to accurately determine a patient’s admixture proportion without additional DNA testing.

Results

In this study we designed an unique AIM panel that infers 3-way genetic admixture from three distinct and selective continental populations (African (AFR), European (EUR), and East Asian (EAS)) within evolutionarily conserved exonic regions. Initially, about 1 million exonic SNPs from selective three populations in the 1000 Genomes Project were trimmed by their linkage disequilibrium (LD), restricted to biallelic variants, and finally we optimized to an AIM panel with 250 SNP markers, or the UT-AIM250 panel, using their ancestral informativeness statistics. Comparing to published AIM panels, UT-AIM250 performed better accuracy when we tested with three ancestral populations (accuracy: 0.995 ± 0.012 for AFR, 0.997 ± 0.007 for EUR, and 0.994 ± 0.012 for EAS). We further demonstrated the performance of the UT-AIM250 panel to admixed American (AMR) samples of the 1000 Genomes Project and obtained similar results (AFR, 0.085 ± 0.098; EUR, 0.665 ± 0.182; and EAS, 0.250 ± 0.205) to previously published AIM panels (Phillips-AIM34: AFR, 0.096 ± 0.127, EUR, 0.575 ± 0.290, and EAS, 0.330 ± 0.315; Wei-AIM278: AFR, 0.070 ± 0.096, EUR, 0.537 ± 0.267, and EAS, 0.393 ± 0.300). Subsequently, we applied the UT-AIM250 panel to a clinical dataset of 26 self-reported Hispanic patients in South Texas with hepatocellular carcinoma (HCC). We estimated the admixture proportions using WES data of adjacent non-cancer liver tissues (AFR, 0.065 ± 0.043; EUR, 0.594 ± 0.150; and EAS, 0.341 ± 0.160). Similar admixture proportions were identified from corresponding tumor tissues. In addition, we estimated admixture proportions of The Cancer Genome Atlas (TCGA) collection of hepatocellular carcinoma (TCGA-LIHC) samples (376 patients) using the UT-AIM250 panel. The panel obtained consistent admixture proportions from tumor and matched normal tissues, identified 3 possible incorrectly reported race/ethnicity, and/or provided race/ethnicity determination if necessary.

Conclusions

Here we demonstrated the feasibility of using evolutionarily conserved exonic regions to infer admixture proportions and provided a robust and reliable control for sample collection or patient stratification for genetic analysis. R implementation of UT-AIM250 is available at https://github.com/chenlabgccri/UT-AIM250.

Genetic Diversity and Structure Analysis Assessed by SSR Markers in a Large Collection of Vitis Cultivars from the Island of Crete, Greece

The grape (Vitis vinifera L.) cultivars in the island of Crete, Greece represent one of the oldest populations of the species; nevertheless, very scarce information is available about its genetic structure. In this study, Vitis cultivars collected from the island of Crete were characterized using microsatellite markers. A broad germplasm collection representing 44 inferred Vitis cultivars, a total of 163 accessions, from the area of Crete including 37 wine and 7 table cultivars were fingerprinted employing thirteen (13) standardized simple sequence repeat (SSR, microsatellite) loci. SSR allelic analysis and a similarity dendrogram construction (cluster analysis) was followed by a hierarchical STRUCTURE analysis. The mean observed (Ho) and expected heterozygosity (He) were 0.7372 and 0.7686, respectively. The cumulative probability of identity was very low with a value of 3.18 × 10e^-15. According to the cluster analysis, twenty-nine of the 44 Vitis cultivars were presented in single clusters and five cultivars were presented as distinct single accessions. In addition, ten (10) cases of synonyms and ten (10) groups of homonyms were also identified. STRUCTURE analysis provided evidence for three genetic groups (putative ancestry groups). Hierarchical STRUCTURE analysis revealed further stratification within each of the three ancestry groups. This work provides the molecular fingerprinting of 44 Vitis cultivars and an initial proposal in their ancestry. In the future, molecular genetic information along with morphological (ampelographic) data will provide an intergraded characterization of existing diversity and will allow for its use in breeding efforts and in commercial viticulture.

Is population genetic structure of vascular plants shaped more by ecological or geographic factors? A study case on the Mediterranean endemic Centaurea filiformis (Asteraceae)

All known populations of the Sardinian endemic Centaurea filiformis Viv. (Asteraceae) were studied in order to understand the impact of both geographic and ecological factors on the genetic structuring of this species. Fourteen populations and 234 individuals were sampled. The demographic structure of the populations and the reproductive ecology were estimated in 28 plots. Population genetic analyses were based on SSR markers. Genetic structure was investigated by spatial Bayesian methods. Average densities of 0.51 individuals m^-2 were detected, with a prevalence of adults. Ten species of pollinators were identified; C. filiformis ability to self-pollinate and myrmecochory were demonstrated experimentally. The populations displayed an average heterozygosity value of H_e  = 0.576 and high genetic differentiation (overall F_ST  = 0.218). Bayesian analysis suggests that five is the most probable number of gene pools of origin. A strong correlation between geographic distances and genetic distances among populations was highlighted. The demographic population structure of C. filiformis is dominated by adults, suggesting that it is a stable-regressive or senile species, investing more in local persistence than colonisation ability. Despite the scattered distribution, the populations studied do not present evidence of genetic erosion. The analysis of genetic differentiation reveals very high differentiation levels among populations, thus indicating that effective barriers exist against gene flow. A general conclusion is that population distribution results in a clear genetic structure for the populations studied, and that geography and not ecology is shaping the present distribution of this species.

japonica, focusing on within population flower color polymorphism

How phenotypic or genetic diversity is maintained in a natural habitat is a fundamental question in evolutionary biology. Flower color polymorphism in plants is a common polymorphism. Hepatica nobilis var. japonica on the Sea of Japan (SJ) side of the Japanese mainland exhibits within population flower color polymorphism (e.g., white, pink, and purple), while only white flowers are observed on the Pacific Ocean (PO) side. To determine the relationships between flower color polymorphism, within and among populations, and the genetic structure of H. nobilis var. japonica, we estimated the genetic variation using simple sequence repeat (SSR) markers. First, we examined whether cryptic lineages corresponding to distinct flower colors contribute to the flower color polymorphisms in H. nobilis var. japonica. In our field observations, no bias in color frequency was observed among populations on Sado Island, a region with high variation in flower color. Simple sequence repeat (SSR) analyses revealed that 18% of the genetic variance was explained by differences among populations, whereas no genetic variation was explained by flower color hue or intensity (0% for both components). These results indicate that the flower color polymorphism is likely not explained by cryptic lineages that have different flower colors. In contrast, populations in the SJ and PO regions were genetically distinguishable. As with the other plant species in these regions, refugial isolation and subsequent migration history may have caused the genetic structure as well as the spatially heterogeneous patterns of flower color polymorphisms in H. nobilis var. japonica.

Quantitative evaluation of hybridization and the impact on biodiversity conservation

Anthropogenic hybridization is an increasing conservation threat worldwide. In South Africa, recent hybridization is threatening numerous ungulate taxa. For example, the genetic integrity of the near‐threatened bontebok (Damaliscus pygargus pygargus) is threatened by hybridization with the more common blesbok (D. p. phillipsi). Identifying nonadmixed parental and admixed individuals is challenging based on the morphological traits alone; however, molecular analyses may allow for accurate detection. Once hybrids are identified, population simulation software may assist in determining the optimal conservation management strategy, although quantitative evaluation of hybrid management is rarely performed. In this study, our objectives were to describe species‐wide and localized rates of hybridization in nearly 3,000 individuals based on 12 microsatellite loci, quantify the accuracy of hybrid assignment software (STRUCTURE and NEWHYBRIDS), and determine an optimal threshold of bontebok ancestry for management purposes. According to multiple methods, we identified 2,051 bontebok, 657 hybrids, and 29 blesbok. More than two‐thirds of locations contained at least some hybrid individuals, with populations varying in the degree of introgression. HYBRIDLAB was used to simulate four generations of coexistence between bontebok and blesbok, and to optimize a threshold of ancestry, where most hybrids will be detected and removed, and the fewest nonadmixed bontebok individuals misclassified as hybrids. Overall, a threshold Q‐value (admixture coefficient) of 0.90 would remove 94% of hybrid animals, while a threshold of 0.95 would remove 98% of hybrid animals but also 8% of nonadmixed bontebok. To this end, a threshold of 0.90 was identified as optimal and has since been implemented in formal policy by a provincial nature conservation agency. Due to widespread hybridization, effective conservation plans should be established and enforced to conserve native populations that are genetically unique.

Inference of Ancestry in Forensic Analysis II: Analysis of Genetic Data

Three approaches applicable to the analysis of forensic ancestry-informative marker data-STRUCTURE, principal component analysis, and the Snipper Bayesian classification system-are reviewed. Detailed step-by-step guidance is provided for adjusting parameter settings in STRUCTURE with particular regard to their effect when differentiating populations. Several enhancements to the Snipper online forensic classification portal are described, highlighting the added functionality they bring to particular aspects of ancestry-informative SNP analysis in a forensic context.

SNP diversity within and among Brassica rapa accessions reveals no geographic differentiation

Genetic diversity was studied in a collection of 61 accessions of Brassica rapa, which were mostly oil-type turnip rapes but also included two oil-type subsp. dichotoma and five subsp. trilocularis accessions, as well as three leaf-type subspecies (subsp. japonica, pekinensis, and chinensis) and five turnip cultivars (subsp. rapa). Two-hundred and nine SNP markers, which had been discovered by amplicon resequencing, were used to genotype 893 plants from the B. rapa collection using Illumina BeadXpress. There was great variation in the diversity indices between accessions. With STRUCTURE analysis, the plant collection could be divided into three groups that seemed to correspond to morphotype and flowering habit but not to geography. According to AMOVA analysis, 65% of the variation was due to variation within accessions, 25% among accessions, and 10% among groups. A smaller subset of the plant collection, 12 accessions, was also studied with 5727 GBS-SNPs. Diversity indices obtained with GBS-SNPs correlated well with those obtained with Illumina BeadXpress SNPs. The developed SNP markers have already been used and will be used in future plant breeding programs as well as in mapping and diversity studies.

Does genetic distance between parental species influence outcomes of hybridization among coral reef butterflyfishes?

Christmas Island is located at the overlap of the Indian and Pacific Ocean marine provinces and is a hot spot for marine hybridization. Here, we evaluate the ecological framework and genetic consequences of hybridization between butterflyfishes Chaetodon guttatissimus and Chaetodon punctatofasciatus. Further, we compare our current findings to those from a previous study of hybridization between Chaetodon trifasciatus and Chaetodon lunulatus. For both species groups, habitat and dietary overlap between parental species facilitate frequent heterospecific encounters. Low abundance of potential mates promotes heterospecific pair formation and the breakdown of assortative mating. Despite similarities in ecological frameworks, the population genetic signatures of hybridization differ between the species groups. Mitochondrial and nuclear data from C. guttatissimus × C. punctatofasciatus (1% divergence at cyt b) show bidirectional maternal contributions and relatively high levels of introgression, both inside and outside the Christmas Island hybrid zone. In contrast, C. trifasciatus × C. lunulatus (5% cyt b divergence) exhibit unidirectional mitochondrial inheritance and almost no introgression. Back-crossing of hybrid C. guttatissimus × C. punctatofasciatus and parental genotypes may eventually confound species-specific signals within the hybrid zone. In contrast, hybrids of C. trifasciatus and C. lunulatus may coexist with and remain genetically distinct from the parents. Our results, and comparisons with hybridization studies in other reef fish families, indicate that genetic distance between hybridizing species may be a factor influencing outcomes of hybridization in reef fish, which is consistent with predictions from terrestrially derived hybridization theory.

Sequence analysis of single-copy genes in two wild olive subspecies: nucleotide diversity and potential use for testing admixture

The wild olive distribution extends from the Mediterranean region to south Asia and Austral Africa. The species is also invasive, particularly in Australia. Here, we investigated the sequence variation at five nuclear single-copy genes in 41 native and invasive accessions of the Mediterranean and African olive subspecies. The nucleotide diversity was assessed and the phylogenetic relationships between alleles were depicted with haplotype networks. A Bayesian clustering method (STRUCTURE) was applied to identify the main gene pools. We found an average of 18.4 alleles per locus. Native Mediterranean and African olives only share one allele, which testifies for ancient admixture on the Red Sea hills. The presence of divergent alleles in the Mediterranean olive, as well as the identification of two main genetic clusters, suggests a complex origin with two highly differentiated gene pools from the eastern and western Mediterranean that recently admixed. In the invasive range, relatively high nucleotide diversity is observed as a consequence of the introduction of alleles from two subspecies. Our data confirm that four invasive individuals are early-generation hybrids. Finally, the utility of single-copy gene sequences in olive population genomic and phylogenetic studies is briefly discussed.

Toxoplasma gondii: prevalence in species and genotypes of British bats (Pipistrellus pipistrellus and P. pygmaeus)

Few studies have investigated Toxoplasma gondii infections in bat populations and none have reported its presence in protected British bat species. Using a collection of dead/euthanased bats collected from Lancashire, UK, two species of bats (Pipistrellus pipistrellus and Pipistrellus pygmaeus) were tested using a highly sensitive SAG1-PCR method specific for detection of T. gondii DNA (n=77; 71 P. pipistrellus and 6 P. pygmaeus). Whilst some potential bias may exist in the sampling strategy, an overall prevalence of 10.39% (±6.06%; 95%CI) was detected. All P. pipistrellus, were also genotyped using eleven polymorphic microsatellite loci to determine their local population structure. The programme STRUCTURE revealed that the majority of individuals (83%) were derived from one interbreeding population, and the remaining individuals (17%) had mixed genetic origins. There was no significant difference in the frequency of T. gondii infection or geographical distribution between subclusters. As all British bats are insectivorous, the routes of infection with T. gondii remain elusive. However, the locally large and panmictic gene pool suggests that intraspecies transmission could be applicable.

How many marker loci are necessary? Analysis of dominant marker data sets using two popular population genetic algorithms

The number of marker loci required to answer a given research question satisfactorily is especially important for dominant markers since they have a lower information content than co-dominant marker systems. In this study, we used simulated dominant marker data sets to determine the number of dominant marker loci needed to obtain satisfactory results from two popular population genetic analyses: STRUCTURE and AMOVA (analysis of molecular variance). Factors such as migration, level of population differentiation, and unequal sampling were varied in the data sets to mirror a range of realistic research scenarios. AMOVA performed well under all scenarios with a modest quantity of markers while STRUCTURE required a greater number, especially when populations were closely related. The popular ΔK method of determining the number of genetically distinct groups worked well when sampling was balanced, but underestimated the true number of groups with unbalanced sampling. These results provide a window through which to interpret previous work with dominant markers and we provide a protocol for determining the number of markers needed for future dominant marker studies.

An overview of STRUCTURE: applications, parameter settings, and supporting software

Objectives: We present an up-to-date review of STRUCTURE software: one of the most widely used population analysis tools that allows researchers to assess patterns of genetic structure in a set of samples. STRUCTURE can identify subsets of the whole sample by detecting allele frequency differences within the data and can assign individuals to those sub-populations based on analysis of likelihoods. The review covers STRUCTURE's most commonly used ancestry and frequency models, plus an overview of the main applications of the software in human genetics including case-control association studies (CCAS), population genetics, and forensic analysis. The review is accompanied by supplementary material providing a step-by-step guide to running STRUCTURE.

Methods: With reference to a worked example, we explore the effects of changing the principal analysis parameters on STRUCTURE results when analyzing a uniform set of human genetic data. Use of the supporting software: CLUMPP and distruct is detailed and we provide an overview and worked example of STRAT software, applicable to CCAS.

Conclusion: The guide offers a simplified view of how STRUCTURE, CLUMPP, distruct, and STRAT can be applied to provide researchers with an informed choice of parameter settings and supporting software when analyzing their own genetic data.

Hybridization and invasion: one of North America's most devastating invasive plants shows evidence for a history of interspecific hybridization

Hybridization has been hypothesized to influence invasion through the generation of novel phenotypes and/or increased levels of genetic variance. Based on morphology, hybrids between diffuse knapweed and spotted knapweed, two invasive plants in North America, are present in the invaded range. Some individuals within most diffuse knapweed sites in North America exhibit intermediate diffuse × spotted floral morphology. We examined hybridization at the molecular level, using amplified fragment length polymorphisms. Approximately a quarter of the assayed North American diffuse knapweed individuals exhibited evidence of introgression from spotted knapweed. However, plants with intermediate morphology did not show evidence of mixed ancestry more often than the plants with typical diffuse knapweed morphology. The high proportion of hybrid individuals in North American diffuse knapweed sites found here, combined with evidence from recent studies, suggests that diffuse knapweed was likely introduced with admixed individuals, and the hybrids are not newly created postintroduction. A century of backcrossing with diffuse knapweed has likely decoupled the relationship between morphology and admixture at the molecular level. In contrast to the scenario encountered in North America, in the native range where diploid diffuse and spotted knapweed overlap, hybrid swarms are common. In such sites, the floral phenotype aligns more closely with the genotype.