Corrigendum.

BackgroundNear the junction of three major continents, the Caucasus region has been an important thoroughfare for human migration. While the Caucasus Mountains have diverted human traffic to the few lowland regions that provide a gateway from north to south between the Caspian and Black Seas, highland populations have been isolated by their remote geographic location and their practice of patrilocal endogamy. We investigate how these cultural and historical differences between highland and lowland populations have affected patterns of genetic diversity. We test 1) whether the highland practice of patrilocal endogamy has generated sex-specific population relationships, and 2) whether the history of migration and military conquest associated with the lowland populations has left Central Asian genes in the Caucasus, by comparing genetic diversity and pairwise population relationships between Daghestani populations and reference populations throughout Europe and Asia for autosomal, mitochondrial, and Y-chromosomal markers.ResultsWe found that the highland Daghestani populations had contrasting histories for the mitochondrial DNA and Y-chromosome data sets. Y-chromosomal haplogroup diversity was reduced among highland Daghestani populations when compared to other populations and to highland Daghestani mitochondrial DNA haplogroup diversity. Lowland Daghestani populations showed Turkish and Central Asian affinities for both mitochondrial and Y-chromosomal data sets. Autosomal population histories are strongly correlated to the pattern observed for the mitochondrial DNA data set, while the correlation between the mitochondrial DNA and Y-chromosome distance matrices was weak and not significant.ConclusionThe reduced Y-chromosomal diversity exhibited by highland Daghestani populations is consistent with genetic drift caused by patrilocal endogamy. Mitochondrial and Y-chromosomal phylogeographic comparisons indicate a common Near Eastern origin of highland populations. Lowland Daghestani populations show varying influence from Near Eastern and Central Asian populations.

Orobanche cumana Wallr. known as sunflower broomrape is a holoparasitic plant that causes huge yield losses in sunflower (Helianthus annuus L.) fields. Genetic characterization, genetic diversity, and race determination studies in O. cumana are very significant for preventing threats in sunflower fields. In this study, the broomrape populations sampled from Edirne, Kırklareli, Tekirdağ, and Adana provinces were used for genetic characterization. The sensitive Özdemirbey sunflower variety was used for growing O. cumana individuals. Eight simple sequence repeat (SSR) loci (Ocum52, Ocum70, Ocum81, Ocum87, Ocum108, Ocum141, Ocum160, and Ocum196) were used for the evaluation of genetic characterization and diversity of broomrape populations. All studied SSR loci were found to be polymorphic and yielded a total of 22 alleles in 143 samples analyzed. Na = 2.089 (mean number of alleles per locus), Ne = 1.390 (mean effective alleles), I = 0.392 (mean Shannon’s information index), Ho = 0.156 (mean observed heterozygosity), He = 0.239 (mean expected heterozygosity), and PIC = 0.228 (mean polymorphic information content) were calculated to assess genetic diversity of O. cumana populations.. As a result of molecular variance analysis, it was concluded that found that the genetic diversity of the populations was 38% among the population. The remaining 23% and 39% were due to among individuals and within individuals, respectively. The UPGMA method and STRUCTURE analysis divided the studied populations into 2 groups. Cluster I included LK2013, HT2016, T2018, and LE2013 populations, while group 2 included AE2003, AD2018, and MT2013 populations. The results we obtained have enabled us to reach important genetic diversity information about O. cumana, and the information obtained will provide important contributions for planned studies in the future.

Hypoxia is one of the most important factors affecting survival at high altitude, and the major hemoglobin protein is a likely target of selection. We compared population genetic structure in the alphaA and betaA hemoglobin subunits (HBA2 and HBB) of five paired lowland and highland populations of Andean dabbling ducks to unlinked reference loci. In the hemoglobin genes, parallel amino acid replacements were overrepresented in highland lineages, and one to five derived substitutions occurred at external solvent-accessible positions on the alpha and beta subunits, at alpha(1)beta(1) intersubunit contacts, or in close proximity to inositolpentaphosphate (IPP) binding sites. Coalescent analyses incorporating the stochasticity of drift and mutation indicated that hemoglobin alleles were less likely to be transferred between highland and lowland populations than unlinked alleles at five other loci. Amino acid replacements that were overrepresented in the highlands were rarely found within lowland populations, suggesting that alleles segregating at high frequency in the highlands may be maladaptive in the lowlands and vice versa. Most highland populations are probably nonmigratory and locally adapted to the Altiplano, but gene flow for several species may be sufficiently high to retard divergence at unlinked loci. Heterozygosity was elevated in the alphaA or betaA subunits of highland populations exhibiting high gene flow between the southern lowlands and the highlands and in highland species that disperse seasonally downslope to midelevation environments from the central Andean plateau. However, elevated heterozygosity occurred more frequently in the alphaA subunit but not simultaneously in both subunits, suggesting that selection may be more constrained by epistasis in the betaA subunit. Concordant patterns among multiple species with different evolutionary histories and depths of historical divergence and gene flow suggest that the major hemoglobin genes of these five dabbling duck species have evolved adaptively in response to high-altitude hypoxia in the Andes.

The effect of elevated UV-B (280–320 nm) radiation levels on Silene vulgaris: A comparison between a highland and a lowland population

BackgroundSample size is one of the critical factors affecting the accuracy of the estimation of population genetic diversity parameters. Small sample sizes often lead to significant errors in determining the allelic richness, which is one of the most important and commonly used estimators of genetic diversity in populations. Correct estimation of allelic richness in natural populations is challenging since they often do not conform to model assumptions. Here, we introduce a simple and robust approach to estimate the genetic diversity in large natural populations based on the empirical data for finite sample sizes.ResultsWe developed a non-linear regression model to infer genetic diversity estimates in large natural populations from finite sample sizes. The allelic richness values predicted by our model were in good agreement with those observed in the simulated data sets and the true allelic richness observed in the source populations. The model has been validated using simulated population genetic data sets with different evolutionary scenarios implied in the simulated populations, as well as large microsatellite and allozyme experimental data sets for four conifer species with contrasting patterns of inherent genetic diversity and mating systems. Our model was a better predictor for allelic richness in natural populations than the widely-used Ewens sampling formula, coalescent approach, and rarefaction algorithm.ConclusionsOur regression model was capable of accurately estimating allelic richness in natural populations regardless of the species and marker system. This regression modeling approach is free from assumptions and can be widely used for population genetic and conservation applications.

BackgroundThe Tasmanian devil (Sarcophilus harrisii) has undergone a recent, drastic population decline due to the highly contagious devil facial tumor disease. The tumor is one of only two naturally occurring transmissible cancers and is almost inevitably fatal. In 2006 a disease-free insurance population was established to ensure that the Tasmanian devil is protected from extinction. The insurance program is dependent upon preserving as much wild genetic diversity as possible to maximize the success of subsequent reintroductions to the wild. Accurate genotypic data is vital to the success of the program to ensure that loss of genetic diversity does not occur in captivity. Until recently, microsatellite markers have been used to study devil population genetics, however as genetic diversity is low in the devil and potentially decreasing in the captive population, a more sensitive genotyping assay is required.MethodsUtilising the devil reference genome and whole genome re-sequencing data, we have identified polymorphic regions for use in a custom genotyping assay. These regions were amplified using PCR and sequenced on the Illumina MiSeq platform to refine a set a markers to genotype the Tasmanian devil insurance population.ResultsWe have developed a set of single nucleotide polymorphic (SNP) markers, assayed by amplicon sequencing, that provide a high-throughput method for monitoring genetic diversity and assessing familial relationships among devils. To date we have used a total of 267 unique SNPs within both putatively neutral and functional loci to genotype 305 individuals in the Tasmanian devil insurance population. We have used these data to assess genetic diversity in the population as well as resolve the parentage of 21 offspring.ConclusionsOur molecular data has been incorporated with studbook management practices to provide more accurate pedigree information and to inform breeding recommendations. The assay will continue to be used to monitor the genetic diversity of the insurance population of Tasmanian devils with the aim of reducing inbreeding and maximizing success of reintroductions to the wild.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2020-4) contains supplementary material, which is available to authorized users.

Central China has a rich terrain with a temperate monsoon climate and varied natural environments for the Chinese honeybee (Apis cerana cerana). However, little comprehensive research on population genetic diversity has been done in this area. A population survey of the structure and genetic diversity of Apis cerana cerana in this area is deeply needed for understanding adaptation to variable environments and providing more references for the protection of honeybee biodiversity. In this study, we present a dataset of 72 populations of Chinese honeybees collected from nine sites by whole genome sequencing in Central China. We obtained 2,790,214,878 clean reads with an average covering a depth of 22×. A total of 27,361,052 single nucleotide polymorphisms (SNPs) were obtained by mapping to the reference genome with an average mapping rate of 93.03%. Genetic evolution analysis was presented via the population structure and genetic diversity based on the datasets of SNPs. It showed that Apis cerana cerana in plains exhibited higher genetic diversity than in mountain areas. The mantel test between Apis cerana cerana groups revealed that some physical obstacles, especially the overurbanization of the plains, contributed to the differentiation. This study is conducive to elucidating the evolution of Apis cerana in different environments and provides a theoretical basis for investigating and protecting the Chinese honeybee.

BackgroundUnderstanding how behavioural dynamics, inter-individual variability and individual interactions scale-up to shape the spatial spread and dispersal of animal populations is a major challenge in ecology. For biocontrol agents, such as the microscopic Trichogramma parasitic wasps, an understanding of movement strategies is also critical to predict pest-suppression performance in the field.MethodsWe experimentally studied the spatial propagation of groups of parasitoids and their patterns of parasitism. We investigated whether population spread is density-dependent, how it is affected by the presence of hosts, and whether the spatial distribution of parasitism (dispersal kernel) can be predicted from the observed spread of individuals. Using a novel experimental device and high-throughput imaging techniques, we continuously tracked the spatial spread of groups of parasitoids over large temporal and spatial scales (8 h; and 6 m, ca. 12,000 body lengths). We could thus study how population density, the presence of hosts and their spatial distribution impacted the rate of population spread, the spatial distribution of individuals during population expansion, the overall rate of parasitism and the dispersal kernel (position of parasitism events).ResultsHigher population density accelerated population spread, but only transiently: the rate of spread reverted to low values after 4 h, in a “tortoise-hare” effect. Interestingly, the presence of hosts suppressed this transiency and permitted a sustained high rate of population spread. Importantly, we found that population spread did not obey classical diffusion, but involved dynamical switches between resident and explorer movement modes. Population distribution was therefore not Gaussian, though surprisingly the distribution of parasitism (dispersal kernel) was.ConclusionsEven homogenous asexual groups of insects develop behavioural heterogeneities over a few hours, and the latter control patterns of population spread. Behavioural switching between resident and explorer states determined population distribution, density-dependence and dispersal. A simple Gaussian dispersal kernel did not reflect classical diffusion, but rather the interplay of several non-linearities at individual level. These results highlight the need to take into account behaviour and inter-individual heterogeneity to understand population spread in animals.

Linum suffruticosum s.l. is a taxonomic complex widespread in the Western Mediterranean basin. The complex is characterized by a high phenotypic and cytogenetic diversity, and by a unique three-dimensional heterostyly system that makes it an obligate outcrosser. We studied the patterns of genetic diversity and structure of populations throughout the entire distribution of L. suffruticosum s.l. with microsatellite markers. We analysed their relationships with various biological and ecological variables, including the morph ratio and sex organ reciprocity of populations measured with a novel multi-dimensional method. Populations consistently showed an approximate 1:1 morph ratio with high sex organ reciprocity and high genetic diversity. We found high genetic differentiation of populations, showing a pattern of isolation by distance. The Rif mountains in NW Africa were the most important genetic barrier. The taxonomic treatment within the group was not related to the genetic differentiation of populations, but to their environmental differentiation. Genetic diversity was unrelated to latitude, elevation, population size, niche suitability or breeding system. However, there was a clear influence of ploidy level on the genetic diversity of populations, and a seeming centre-periphery pattern in its distribution. Our results suggest that polyploidization events, high outcrossing rates, isolation by distance and important geographical barriers to gene flow have played major roles in the microevolutionary history of this species complex.

Wetlands are one of the most threatened ecosystems in the world because more than 70% of the area worldwide has been lost since 1900. Wetland plant species rely greatly on water for seeds and propagules, which may lead to a downstream unidirectional dispersal and accumulation of genetic diversity downstream. However, several species show no support for unidirectional genetic diversity, revealing the complexity of population dynamics and gene flow in wetlands. Here, we used microsatellite loci to address how the past demographic dynamics shaped the contemporary spatial pattern in genetic diversity and population structure of Cyperus papyrus in wetlands of Southeast Africa. Using spatially explicit analysis and coalescent modelling, we found no support for unidirectional dispersal. Instead, we found higher genetic diversity in populations upstream than downstream in the river basin. We also found high admixture among populations, most likely due to connections between adjacent river basins during sporadic floods, and ongoing gene flow due to bird-mediated seed dispersal. Our results suggest stepping-stone migration due to strong isolation-by-distance, but not necessarily unidirectional. Moreover, the past demographic dynamics in the Holocene shaped the current pattern of genetic diversity and structure, leading to higher genetic diversity in populations upstream the Zambezi river basin. Our results also point to the very low genetic diversity of C. papyrus populations in Southeast Africa and the need for management and conservation strategies to guarantee the long-term persistence of the species in the region.

The tropical coniferous genus Dacrydium is widespread in Kalimantan, Indonesia. Four species can still be found in Borneo. Locally known as Alau, this genus thrives in a range of habitats from heath to deep-peat forests especially in Central Kalimantan. This genus is currently threatened by logging, fires and forest conversion forto other uses. The objectives of this study wereas to unravel the genetic diversity of Dacrydium in the study area which is a large unified diverse landscape. Our research was conducted in heath forests located within PT Taiyoung Engreen logging company area in the Gunung Mas District, and PT Dasa Intiga in the Kapuas District and in deep-peat swamp forest located in Sebangau National Park in the Palangkaraya District. The four species that are suspected to exist in Kalimantan, namely Dacrydium beccarii Parl., Dacrydium pectinatum de Laub., Dacrydium elatum (Roxb.)Wall. ex Hook. and Dacrydium xanthandrum Pilg. were met in various abundances. Genetic data were tested by isoenzyme analysis with 20 samples of each species of D. beccarii and D. pectinatum from each site. The results showed that D. beccarii and D. pectinatum have a large number of missing alleles, rare alleles, and individual alleles, which are found in different species in the three research sites, all show their own genetic peculiarities. That makes it necessary to develop a strategy to protect the genus Alau quite locally, especially D. pectinatum is of high concern as it is quite threatened. Genetic diversity values of D. beccarii and D. pectinatum have genetic diversity in population 0.478 and 0,447, interpopulation diversity 0.208 and 0,253, roportion of genetic diversity between populations to total genetic diversity 0.289 and 0,350 with fixation index values (-0.021) and 0,187 (≈0) it has a tendency to random mating. Itis necessary to implement a strategy for saving Dacrydium. This can be implemented from our research site. Actions will include the translocating of individual seedlings between research sites where each has a private allele with different advantages to be planted in all original habitat to increase genetic variation, and establish demonstration plots to safeguard genetic variation and diversity, and additionally carry out genetic enrichment planting, especially for D pectinatum.

Hippophae rhamnoides ssp. sinensis is an ecologically and economically important species that has been widely used as a pioneer plant in China. In this study, we employed both nuclear ISSR and maternal cpSSR markers to survey the genetic diversity and structure of populations of ssp. sinensis representing three different landscapes, the northwestern desert and grassland region, the alpine vegetation region of the Qinghai-Tibetan Plateau, and the northeastern humid forest region. In all, 12 natural populations with a scattered distribution in the area were studied. The genetic diversities of populations were found to be uneven, and the total genetic diversity was low on the basis of both types of marker. Mantel tests based on both individual Euclidean distance matrices and population genetic distance (measured by Φpt) matrices showed that the two marker systems detected similar trends with respect to genetic distances between populations. The analysis of molecular variance (AMOVA) revealed significant differentiation among populations and among regions for both types of marker. Although the detected pattern of isolation-by-distance among all sampled populations confirmed the earlier colonization pathway, the low level of gene flow and the lack of isolation by distance within each region suggested the presence of an additional dispersal barrier. UPGMA dendrograms and PCA plots also revealed clear clustering and significant regional differentiation. Our results indicate that the genetic structure of ssp. sinensis has been affected by habitat fragmentation and restricted population sizes. We propose that the biology of reproduction and ecology have played determinant roles in the development of the regional structure of populations. The genetic information obtained will help to establish conservation strategies and programs for sustainable management of H. rhamnoides ssp. sinensis.

For populations having dispersal described by fat-tailed kernels (kernels with tails that are not exponentially bounded), asymptotic population spread rates cannot be estimated by traditional models because these models predict continually accelerating (asymptotically infinite) invasion. The impossible predictions come from the fact that the fat-tailed kernels fitted to dispersal data have a quality (nondiscrete individuals and, thus, no moment-generating function) that never applies to data. Real organisms produce finite (and random) numbers of offspring; thus, an empirical moment-generating function can always be determined. Using an alternative method to estimate spread rates in terms of extreme dispersal events, we show that finite estimates can be derived for fat-tailed kernels, and we demonstrate how variable reproduction modifies these rates. Whereas the traditional models define spread rate as the speed of an advancing front describing the expected density of individuals, our alternative definition for spread rate is the expected velocity for the location of the furthest-forward individual in the population. The asymptotic wave speed for a constant net reproductive rate R0 is approximated as (1/T)(piuR)/2)(1/2) m yr(-1), where T is generation time, and u is a distance parameter (m2) of Clark et al.'s 2Dt model having shape parameter p = 1. From fitted dispersal kernels with fat tails and infinite variance, we derive finite rates of spread and a simple method for numerical estimation. Fitted kernels, with infinite variance, yield distributions of rates of spread that are asymptotically normal and, thus, have finite moments. Variable reproduction can profoundly affect rates of spread. By incorporating the variance in reproduction that results from variable life span, we estimate much lower rates than predicted by the standard approach, which assumes a constant net reproductive rate. Using basic life-history data for trees, we show these estimated rates to be lower than expected from previous analytical models and as interpreted from paleorecords of forest spread at the end of the Pleistocene. Our results suggest reexamination of past rates of spread and the potential for future response to climate change.

Knowledge of patterns of genetic diversity in populations of threatened species is vital for their effective conservation. Rosalia longicorn (Rosalia alpina) is an endangered and strictly protected beetle. Despite a marked decline in part of its range, the beetle has recently expanded to the lowlands of Central Europe. To facilitate a better understanding of the species' biology, recent expansion and more effective conservation measures, we investigated patterns of genetic structure among 32 populations across Central and South-east Europe. Eight microsatellite loci and a partial mitochondrial gene (cytochrome c oxidase subunit I) were used as markers. Both markers showed a significant decline in genetic diversity with latitude, suggesting a glacial refugium in north-western Greece. The cluster analysis of the nuclear marker indicated the existence of two genetically distinct lineages meeting near the border between the Western and Eastern Carpathians. By contrast, one widespread mtDNA haplotype was dominant in most populations, leading to the assumption that a rapid expansion of a single lineage occurred across the study area. The genetic differentiation among populations from the north-western part of the study area was, however, surprisingly low. They lacked any substructure and isolation-by-distance on a scale of up to 600 km. This result suggests a strong dispersal capacity of the species, as well as a lack of migration barriers throughout the study area. That the lowland populations are closely related to those from the nearby mountains indicates repeated colonization of the lowlands. Our results further suggest that R. alpina mostly lives in large, open populations. Large-scale conservation measures need to be applied to allow for its continued existence.

AimUniform spatial population distributions are predicted to result in lower among‐population genetic differentiation and higher within‐population genetic diversity than naturally patchy distributions, but there have been surprisingly few attempts to isolate this effect from confounding factors. We studied the widespread wind‐pollinated shrub Allocasuarina humilis that is common in a geologically stable landscape characterized by long‐term population persistence to test the influence of semi‐continuous versus patchy population distributions on genetic patterns. We also investigated whether A. humilis shows the high population connectedness and genetic diversity typically associated with wind pollination, a relatively uncommon and little‐studied syndrome in this landscape.LocationHeath‐shrublands (‘heath’) and forests of south‐western Australia.MethodsPopulations were sampled from heath and forest regions, which respectively exhibited semi‐continuous and patchy population distributions. Genetic structure and diversity were assessed for 27 populations using eight nuclear microsatellite markers and three chloroplast regions. Phylogeographical history was examined using Bayesian phylogeny reconstruction, parsimony analysis and tests of expansion.ResultsHigh haplotype diversity is consistent with long‐term population persistence across most of the species’ range. Nuclear markers showed low overall population differentiation and no geographical structure over c. 900 km, reflecting extensive pollen dispersal. For both marker types, patchily distributed forest populations were substantially more differentiated with significantly lower within‐population diversity than semi‐continuous heath populations. Phylogeographical analysis revealed evidence for earlier colonization of heath than forest and recent expansion into wetter forests, consistent with progressive long‐term climatic drying.Main conclusionsHigh population connectedness and genetic diversity probably resulted from wind pollination in combination with dioecy and long life span. Patchy population distributions appear to have influenced genetic structure and diversity through lower pollen and seed dispersal, lower effective population sizes and greater genetic drift. Our approach illustrates the value of minimizing confounding variables by testing the effect of a variable ecological trait within a single species.