False cleavers (Galium spurium L.) is an aggressive weed from the Rubiaceae. Here we assemble a chromosome scale draft of its genome, laying the foundations for determining the genetic basis of auxinic herbicide resistance and for systematic research into its polyphyletic genus. We use the genome to examine the population genetics in material from the Canadian Prairies and, in concert with a common greenhouse experiment, to examine whether the phenotypic variation observed in the field results primarily from genetic or environmental factors. The genome assembly covers approximately 85% of G. spurium’s expected 360Mbp genome size with 94% of BUSCO genes complete and most single copy (89%). Approximately 37% of the genome is repetitive elements and 35,540 genes were annotated using RNA-Seq data, including 100 homologs for genes involved or, potentially involved in, herbicide resistance. The genome shows strong synteny with other members of the Rubiaceae including smooth bedstraw (Cruciata laevipes Opiz) and robusta coffee [Coffea canephora (Pierre ex Froehner]. Double digested RADseq data for the 19 populations from the Canadian Prairies indicated that G. spurium has high levels of population structure (FST = 0.54) and inbreeding (FIS =0.86) with low levels of hetrozygosity (HO = 0.02) and nucleotide diversity (π = 0.0003). Variation in flowering time and seed weight largely overlapped among populations grown in the greenhouse. A redundancy analysis investigating genotype-phenotype associations showed few associations between SNP variation and these characteristics. In contrast, the majority of SNPs under selection were associated with mericarp hook density. This suggests that for most traits, environmental variation rather than genetic variation likely underlies phenotypic differences observed in the field. Several genes of interest including several homologs involved in the assembly of the Skp1-Culliun-F-Box IR1/AFB E3 ubiquitin ligase complex (e.g. CAND1, ECR1) are located in areas of the genome with evidence of selection and are targets for further investigation.

Bivalve molluscs are a diverse group of animals with particular economic and ecological importance. Their morphological characteristics frequently confuse their identification leading to mislabelling of edible species. Genetic diversity is critical to the resilience of marine bivalve populations in the face of environmental stressors such as ocean acidification and warming. In this study, we characterized the phylogeny and defined the first DNA barcodes of six marine bivalves [Ostrea edulis (Linnaeus, 1758) Arca noae (Linnaeus, 1758), Pinctada radiata (Leach, 1814), Venus verrucosa (Linnaeus, 1758), Calllista chione (Linnaeus, 1758) and Ruditapes decussatus (Linnaeus, 1758)] sampled from different coastal areas of Aegean and Ionian Seas using the molecular markers cytochrome c oxidase subunit I (COI) and 18S ribosomal RNA (18S rRNA). Further, COI gene was employed to investigate the population genetic diversity since 18S rRNA exhibited no conspecific differences. The sequence of 18S rRNA successfully discriminated the bivalves at family or superfamily level but occasionally proved insufficient for species identification. Contrariwise, COI was highly informative and could reliably distinguish all species. Population haplotype diversity was moderate to high and was always accompanied by generally low nucleotide diversity, indicating genetically closely related haplotypes. The invasive Pinctada radiata was found to be panmictic even among distant sampling areas, while Ostrea edulis was the only species that exhibited moderate levels of population subdivision. Finally, here we report for the first time the presence of Ostrea stentina in Thermaikos Gulf sampled among Ostrea edulis specimens, demonstrating a new invasive bivalve species in Eastern Mediterranean.

Three species of the Old World genus Dipsacus L. are considered invasive in the Americas, yet they may differ in how they spread and reproduce and in their genetic diversity. Differences in invasion method may suggest that different management techniques are needed for each species. We performed genetic analyses on 572 plants in 69 populations from the United States, Argentina, and Eurasia with the goals of analyzing taxonomy, diversity, mode of reproduction, population structure, and founder effect of each of these species’ invasions, as well as looking for evidence of recent or ongoing hybridization. We found Indian teasel [Dipsacus sativus (L.) Honck.] to be lowest in diversity and possibly reliant on self-pollination more than the other species, Fuller’s teasel (Dipsacus fullonum L.) and cutleaf teasel (Dipsacus laciniatus L.). We found no evidence of hybridization within the invasions and no support for D. sativus as a subspecies of D. fullonum. The closest genetic matches of D. fullonum from the United States to the native range were with Hungary and Spain, while the closest match for D. fullonum between Argentina and the native range was with Spain. Dipsacus laciniatus from the United States most closely matched with samples from Russia. Population structure information regarding these three weedy Dipsacus species can help us understand their invasive processes as well as give insight into their management and the development of a biological control program.

Major developments in the field of genetics in the past few decades have revolutionised notions of what it means to be human. Although currently only a few populations around the world practise a hunting and gathering lifestyle, this mode of subsistence has characterised members of our species since its very origins and allowed us to migrate across the planet. Therefore, the geographical distribution of hunter–gatherer populations, dependence on local ecosystems and connections to past populations and neighbouring groups have provided unique insights into our evolutionary origins. However, given the vulnerable status of hunter–gatherers worldwide, the development of the field of anthropological genetics requires that we reevaluate how we conduct research with these communities. Here, we review how the inclusion of hunter–gatherer populations in genetics studies has advanced our understanding of human origins, ancient population migrations and interactions as well as phenotypic adaptations and adaptability to different environments, and the important scientific and medical applications of these advancements. At the same time, we highlight the necessity to address yet unresolved questions and identify areas in which the field may benefit from improvements.

The hangul Cervus hanglu hanglu, a Critically Endangered mountain ungulate of Jammu and Kashmir, India, faces the imminent threat of population loss and extinction. Effective management of its largest viable population in Dachigam National Park in the Kashmir Himalaya requires reliable demographic information. Using 14 microsatellite markers we identified 293 individuals (208 females and 85 males) through faecal analysis, and generated data on the genetic status and population size of the hangul in its winter habitat. The mean expected and observed heterozygosities of 0.62 and 0.59 are comparable to those of several red deer Cervus elaphus populations elsewhere. The effective population sizes were 46.3 and 93.7 when the frequencies of rare alleles were considered to be 0.050 and 0.010, respectively. The average mean kinship of the population was 0.34, and there was no evidence of a recent bottleneck event. In genetic mark–recapture analysis the best model included an effect of sex on both detection and recapture probabilities. Detection of males was highest in November, coinciding with the hangul breeding season, whereas detection of females was highest in December. Our estimate of the hangul population using genetic mark–recapture with bootstrapping was 394 individuals. To our knowledge, this is the first study to use genetic data to estimate the population of the hangul. It will guide future studies of this subspecies and also serve as an impetus for identifying founder animals for captive breeding, and for connecting the population in Dachigam National Park with the other small, isolated populations to ensure the long-term survival of this subspecies.

Ilex paraguariensis A. St.-Hil. (yerba mate) (Aquifoliaceae Bercht. & J. Presl) is a plant species with great economic and cultural importance because its leaves are processed and ground to make infusions like mate or tereré. The species is distributed in a continuous area that includes Southern Brazil and part of Paraguay and Argentina. Uruguay represents the Southern distribution limit of the species, where small populations can be found as part of ravine forests. Although there are previous reports of molecular markers for this and other species in the genus, the available markers were not informative enough to represent the intra- and interpopulation genetic diversity in marginal Uruguayan populations. In this study, we developed highly informative polymorphic microsatellite markers to be used in genetic studies in I. paraguariensis. Markers were identified in contigs from the genome sequence of two individuals and then tested for amplification and polymorphism content in a diverse panel. Markers which passed these filters were tested on populations from Uruguay. They detected higher diversity within populations (in terms of number of alleles and heterozygosity) than previously reported, and levels of heterozygosity similar to those reported for two Brazilian populations. This subset of seven markers were successfully multiplexed, substantially reducing the costs of the analysis. Combined with previously reported nuclear and plastid markers, they can be used to evaluate the genetic diversity of rear-edge populations, identify genotypes for paternity studies and provide relevant information for the conservation and management of germplasm.

Multiple parasites can infect a single host, creating a dynamic environment where each parasite must compete over host resources. Such interactions can cause greater harm to the host than single infections and can also have negative consequences for the parasites themselves. In their first intermediate hosts, trematodes multiply asexually and can eventually reach up to 20% of the host's biomass. In most species, it is unclear whether this biomass results from a single infection or co-infection by 2 or more infective stages (miracidia), the latter being more likely a priori in areas where prevalence of infection is high. Using as model system the trematode Bucephalus minimus and its first intermediate host cockles, we examined the genetic diversity of the cytochrome c oxidase subunit I region in B. minimus from 3 distinct geographical areas and performed a phylogeographic study of B. minimus populations along the Northeast Atlantic coast. Within localities, the high genetic variability found across trematodes infecting different individual cockles, compared to the absence of variability within the same host, suggests that infections could be generally originating from a single miracidium. On a large spatial scale, we uncovered significant population structure of B. minimus, specifically between the north and south of Bay of Biscay. Although other explanations are possible, we suggest this pattern may be driven by the population structure of the final host.

Next generation sequencing technologies have facilitated a shift from a few targeted loci in population genetic studies to whole genome approaches. Here, we review the types of questions and inferences regarding the population biology and evolution of parasitic helminths being addressed within the field of population genomics. Topics include parabiome, hybridization, population structure, loci under selection and linkage mapping. We highlight various advances, and note the current trends in the field, particularly a focus on human-related parasites despite the inherent biodiversity of helminth species. We conclude by advocating for a broader application of population genomics to reflect the taxonomic and life history breadth displayed by helminth parasites. As such, our basic knowledge about helminth population biology and evolution would be enhanced while the diversity of helminths in itself would facilitate population genomic comparative studies to address broader ecological and evolutionary concepts.

Microsatellite markers can provide valuable information about gene flow and population history. We developed and tested new microsatellites for the nitrophilic lichenized fungus Xanthoria parietina and studied its genetic diversity and structure within the urban area of Munich, Bavaria. We compared its local genetic pattern with that of its photobiont partner Trebouxia decolorans, for which existing microsatellites were applied. For comparison, a reference site with clean air was included in the sampling. We found support for three genetic clusters in the fungus X. parietina, which occurred intermingled in collecting sites. There was a high degree of admixture within fungal populations and individuals, and analysis of molecular variance revealed a lack of population structure in the mycobiont. The Trebouxia photobiont, in contrast, exhibited structured populations which grouped into two to five genetic clusters, and individuals showed less admixture than in the mycobiont. This indicates that the two lichen partners differ in their ability to move around in the landscape. The microsatellite markers we report are polymorphic and are suitable for population genetic studies.

Cruzia tentaculata is a helminth parasite of marsupials and has a wide geographic distribution from Mexico to Argentina. The aim of this study was to analyse the genetic population structure of this nematode along the Atlantic Forest biome. Cruzia tentaculata specimens were recovered from Didelphis aurita, Didelphis albiventris and Philander quica in 9 localities. Morphological and morphometric data were investigated for phenotypic diversity among localities and hosts using multivariate discriminant analysis of principal components. Phylogenetic relationships of C. tentaculata were determined using maximum likelihood and Bayesian inference. The population structure was analysed by fixation indices, molecular variance analysis, Tajima's D and Fu's Fs neutrality tests, Mantel tests and Bayesian clustering analysis. A higher significant morphometric difference for males was observed between localities. In the haplogroup networks, 2 groups were recovered, separating locations from the north and from the south/southeast. The morphometric variation in C. tentaculata between different localities was compatible with this north and southeast/south pattern, suggesting adaptation to different ecological conditions. Population genetic analyses suggested a pattern of evolutionary processes driven by Pleistocene glacial refugia in the northeast and southeast of the Atlantic Forest based on the distribution of genetic diversity.

Parasites might represent a helpful tool in understanding the historical dispersion and phylogeography of their hosts. In order to reveal whether the migration routes and diversification of hosts can be traceable in the genetic structures of their parasites, we investigated the diversity of paramphistomoid trematodes of Pelophylax frogs in 2 geographically distant European regions. Water frogs belonging to the genus Pelophylax represent a striking example of a species with a high variety of ecological adaptations and a rich evolutionary history. The parasites were collected from 2 Balkan endemic species, P. epeiroticus and P. kurtmuelleri, and 2 species in Slovakia, P. esculentus and P. ridibundus. While in Slovakia, Pelophylax frogs harboured 2 species, the diplodiscid Diplodiscus subclavatus and the cladorchiid Opisthodiscus diplodiscoides, only the former was recorded in the south-western Balkans. Remarkably high genetic diversity (16 unique mitochondrial cox1 haplotypes, recognized among 60 novel sequences) was observed in D. subclavatus, and subsequent phylogenetic analyses revealed a strong population-genetic structure associated with geographical distribution. We also evidenced the existence of 2 divergent D. subclavatus cox1 haplogroups in the south-western Balkans, which might be associated with the historical diversification of endemic water frogs in the regional glacial microrefugia.

The liver fluke Opisthorchis viverrini is a foodborne trematode that, in chronic infection, is a leading cause of bile-duct cancer – cholangiocarcinoma. Cats and dogs are acknowledged as reservoir hosts of this parasite. However, this assumption is based on morphological similarity of flukes recovered from these hosts, without any molecular genetic evidence. The aim of this study was to obtain molecular data from O. viverrini eggs present in feces of humans and cats in the same locality in Thanya sub-district, Kalasin, Thailand. The mitochondrial cytochrome c oxidase subunit 1 (cox1) gene was used as the marker for a population-genetic study. A DNA fragment of the cox1 gene was amplified from stool samples and subjected to nucleotide sequencing. Phylogenetic and haplotype network analyses were performed. The cox1 sequences of O. viverrini eggs from humans and cats largely formed separate clades on the phylogenetic trees, with an Fst value of 0.64 (P < 0.05), indicating largely distinct populations in the 2 species. However, 5 samples from cats were placed in the human cluster and 1 sample from a human was placed in the cat cluster. This suggests that host specificity of ‘human’ and ‘cat’ clades is not absolute. These results indicate that there are 2 populations of O. viverrini, one circulates primarily in humans and the other in cats. However, cross-transmission can occur between these 2 hosts. Taken altogether, the population-genetic evidence from this study partially supports the assumption that the cat can act as a reservoir host of O. viverrini.

In this paper an exact rejection algorithm for simulating paths of the coupled Wright–Fisher diffusion is introduced. The coupled Wright–Fisher diffusion is a family of multivariate Wright–Fisher diffusions that have drifts depending on each other through a coupling term and that find applications in the study of networks of interacting genes. The proposed rejection algorithm uses independent neutral Wright–Fisher diffusions as candidate proposals, which are only needed at a finite number of points. Once a candidate is accepted, the remainder of the path can be recovered by sampling from neutral multivariate Wright–Fisher bridges, for which an exact sampling strategy is also provided. Finally, the algorithm’s complexity is derived and its performance demonstrated in a simulation study.

Swayne's hartebeest Alcelaphus buselaphus swaynei was once widely distributed in the Horn of Africa. By the early 20th century, however, it was extirpated across most of its range and is now limited to two relict populations in the Ethiopian Rift Valley and categorized as Endangered on the IUCN Red List. In this study, we estimated the size and genetic diversity of these two remaining populations, with a particular focus on competition with livestock. We used a total block count method for both Swayne's hartebeest and livestock population counts, and faecal samples for a population genetic analysis. We estimated the total population of Swayne's hartebeest to be 1,528, with 518 individuals in Senkele Swayne's Hartebeest Sanctuary and 1,010 individuals in Maze National Park. Livestock densities were 212 and 153 times those of Swayne's hartebeest in Senkele Swayne's Hartebeest Sanctuary and Maze National Park, respectively. Among 73 mitochondrial D-loop sequences (34 from Senkele Swayne's Hartebeest Sanctuary and 39 from Maze National Park), we found 22 haplotypes (Senkele 12, Maze 16, shared 6). Population genetic parameters suggest only weak sub-structuring between the two populations (FST = 0.164). Despite the positive population trends in both protected areas, the spatial overlap with livestock may lead to future population decline as a result of resource competition and disease transmission. We therefore recommend further translocation to other protected areas within the species’ former range.

In this paper, we introduce a family of processes with values on the nonnegative integers that describes the dynamics of populations where individuals are allowed to have different types of interactions. The types of interactions that we consider include pairwise interactions, such as competition, annihilation, and cooperation; and interactions among several individuals that can be viewed as catastrophes. We call such families of processes branching processes with interactions. Our aim is to study their long-term behaviour under a specific regime of the pairwise interaction parameters that we introduce as the subcritical cooperative regime. Under such a regime, we prove that a process in this class comes down from infinity and has a moment dual which turns out to be a jump-diffusion that can be thought as the evolution of the frequency of a trait or phenotype, and whose parameters have a classical interpretation in terms of population genetics. The moment dual is an important tool for characterizing the stationary distribution of branching processes with interactions whenever such a distribution exists; it is also an interesting object in its own right.