Autosomal Microsatellite Loci Research Articles

Microsatellites confirm the distinctness of Bedouins among ethnic Qatari subpopulations

Background: Microsatellite markers are highly versatile tools used in a wide array of applications including paternity testing, forensic analysis, and disease markers. However, the allele frequencies of these markers can vary greatly depending on ethnic subpopulations. Thus, the discovery of three distinct Qatari ethnic subpopulations (Bedouin, Persian, and African) has prompted the need to determine the allele frequencies that are more representative of the subpopulations. Objectives: This study aims to analyze 15 autosomal microsatellite loci from individuals belonging to each subpopulation and to generate the corresponding allele frequency tables. Additionally, the microsatellite markers were further investigated to examine the mating behaviors within each subpopulation as well as looking into a possible relationship between the markers and the type 2 diabetes mellitus (T2DM). Methods: DNA samples isolated from 266 individuals of interest (Bedouin, Persian, or African) were amplified using PCR and subjected to electrophoresis. The results were analyzed using various population genetics software such as FSTAT, GenAlEx, and GENEPOP to calculate several population parameters including inbreeding coefficients, allele frequencies, and expected and observed heterozygosity. Results: The results showed that the Bedouin subpopulation was distinct from the other two subpopulations. Furthermore, the Bedouin and African subpopulations were found to have a small positive inbreeding coefficient, while the Persian subpopulation displayed a slight outbreeding pattern. Lastly, two microsatellite loci showed tantalizing differences between diabetic and non-diabetic participants. Conclusions: The distinctness of the Bedouin population could be attributable to the heterogeneity of the Persian and African subpopulations, while the positive inbreeding coefficients could be explained by the relatively high rates of consanguineous marriages. The allele frequency tables generated for each subpopulation through this study can be used to strengthen microsatellite-based genetic testing; however, more studies are needed to further examine the potential relationship between T2DM and microsatellites.

Genetic Structure of the Vulnerable Tricolored Bat (Perimyotis subflavus)

The tricolored bat (Perimyotis subflavus) has experienced extensive declines in regional abundance — near 30% as of 2013 — due to disease, habitat loss, and anthropogenic conflict. There is urgency to determine whether the species should be protected in the United States; however, critical species-specific information required to make this decision is lacking. Here, we address those critical knowledge gaps by (i) estimating genetic diversity, and (ii) assessing population structure. We utilized sequence data from a 562 base pair region of the mitochondrial genome and eight autosomal microsatellite loci from 14 sampling locations across the core of P. subflavus' range and found substantial diversity in both data types. Further, we found contrasting patterns of population structure between the data types. Weak evidence for population structure was detected using the mitochondrial data, with the most probable population break dividing eastern and western sampling sites, and evidence for isolation-by-distance across the sampled region. Conversely, we detected no evidence for structure or isolation-by-distance using microsatellite data, revealing a panmictic population. The findings reported here represent a baseline understanding of genetic diversity and structure for P. subflavus; additional analyses using samples collected post white-nose syndrome emergence are required to understand losses in genetic diversity due to recent population declines.

The origin and population genetics of wolves in the north Hungarian mountains

The grey wolf (Canis lupus) is one of the most challenging species to conserve in our modern and crowded world. Due to various factors, most European wolf populations are currently growing. In Hungary, numbers have increased since the 2000s. Although spontaneous recolonisation from Slovakia is considered to be the most likely mechanism by the majority of experts, some stakeholders claim that hand-reared individuals have been released. To determine the origin of wolves in northern Hungary, we analysed samples of free-ranging wolves collected in Slovakia and Hungary as well as samples from wolves in private enclosures in the region. We also included reference samples from domestic dogs. All samples were genotyped at 14 canine autosomal tetranucleotide microsatellite loci (STR) and analysed using multivariate, Bayesian methods. Hungarian wolf samples were also analysed using kinship methods. In the free-ranging wolf samples, all loci were polymorphic with 3–12 alleles. The overall observed (Ho) and unbiased expected (uHE) heterozygosities were 0.60–0.66 and 0.69–0.71, respectively. Parental and sibling relationships were also found among Hungarian individuals: three generations of a pack in the Bükk Mountains were identified. Samples from free-ranging wolves clustered separately from those of captive wolves and dogs. However, genetic similarities were found between Slovakian and Hungarian wolf samples. Our analyses indicate a Slovakian origin of the sampled Hungarian wolves, and we found no evidence that individuals originating in captivity have played any role in the recolonisation process. Kinship relationships and moderate genetic diversity suggest that there is ongoing gene flow across the Slovakian–Hungarian border.

Genetic Evidence Documents Extra-Pair Paternity in Breeding Colonies of the Wood Stork Mycteria americana (Ciconiidae) in Cuba

The Wood Stork Mycteria americana is a rare resident bird species in the Caribbean, where it has small population sizes and reduced genetic variability. In the present study, we inferred the mating systems of the only two breeding colonies of Wood Stork known in the Caribbean, which are located in two of its most important wetlands: the Zapata Swamp Wetland and the Sabana-Camagüey Archipelago, both in Cuba. We sampled growing feathers of 27 chicks from 11 nests and analyzed genetic data from the most variable autosomal microsatellite loci described for the species. We estimated the relatedness between chicks by using the Queller-Goodnight coefficient and two maximum likelihood methods of kinship reconstruction. Evidence of monogamy was found in 27% of the nests analyzed, nest parasitism in the 36%, and extra-pair paternity in the 18%, while for the rest, inconsistencies among the methods were detected. Our results constitute the first evidence of extra-pair paternity for the Wood Stork and corroborate the usefulness of a non-invasive approach to perform kinship analysis in a poorly studied species.

Edible dormouse (Glis glis) population study in south‐western Poland provides evidence of multiple paternity and communal nesting

AbstractThe mating system of small populations, isolated as a result of habitat fragmentation, is a key factor in their survival. As such populations are at risk of losing their genetic variation, reduction of their evolutionary potential is a distinct possibility. A flexible mating system may therefore provide a means of maintaining genetic variation. The mating system of the edible dormouse (Glis glis), a small arboreal rodent endangered by the fragmentation of its habitats, is not well understood. To date, only one study has provided evidence of multiple paternity in dormice. We present the results of a four‐year study of eight isolated dormouse populations. Using 138 individuals and 10 polymorphic autosomal microsatellite loci, we examined the prevalence of multiple paternity in these populations. In addition, we investigated the frequency of communal nesting and the genetic relationships between the females and juveniles occupying a single nest box. We found a high prevalence of multiple paternity (70% of the litters were multiple‐sired), a weak genetic relationship between the juveniles and the accompanying females (in 81% of cases the female residing with juveniles in a nest box was not their biological mother) and a 10.5% frequency of communal nesting in all nests. Given the low genetic variability of dormice, the multiple paternity and promiscuity observed in this species can help to maintain its genetic diversity.

Genetic diversity, population structure and ancestral origin of KwaZulu-Natal native chicken ecotypes using microsatellite and mitochondrial DNA markers

South African native chicken breeds are no exception to the declining of local domestic breeds that has long been recognised and found associated with the commercialisation of breeding in domestic animals. The aims of the study were: (i) to provide a comprehensive view of genetic variation in four KwaZulu-Natal indigenous chicken populations (Jozini, Newcastle, Pietermaritzburg, and Port Shepstone), and (ii) to estimate the extent of differentiation of the village populations from three conserved South African indigenous pure breeds (Potchefstroom koekoek, Ovambo, and Venda) by genotyping individuals at 19 autosomal microsatellite loci. Finally, (iii) new information to the history of KwaZulu-Natal indigenous chicken populations was made available by exploring their phylogenetic relationship and their possible maternal origin through the mitochondrial DNA. The results suggested noticeable genetic diversity within and between ecotypes with clear sub-structuring between them. The indigenous populations had high genetic diversity (observed heterozygosity ranging from 0.61 in Pietermaritzburg to 0.70 in Jozini) while conserved populations showed considerable within population inbreeding coefficient (from 0.01 in Potchefstroom koekoek to 0.18 in Ovambo). Median-joining network analyses indicated the dominance of haplogroup E suggesting a likely Southeast Asia and/or Indian subcontinent origin. The presence of haplogroup B and C not only emphasises multiple maternal origin but also highlights genetic introgression of local chickens with commercial genotypes. These results highlighted the importance of local breeds as a genetic reservoir; moreover, the conservation of local breeds may play an important role in the local economy as a source of high-quality products for consumers. Highlights The genetic variation and differentiation of KwaZulu-Natal indigenous chicken populations and pure South African chicken breeds is investigated. The village populations showed a noticeable genetic variability with clear sub-structuring between them. The results can be used to improve a sustainable breeding and conservation programs to control possible genetic dilution with commercial genotypes.

Genetic variation in field voles (Microtus agrestis) from the British Isles: selective sweeps or population bottlenecks?

The Eurasian field vole (Microtus agrestis) comprises three evolutionarily significant units (ESUs). The northern ESU is found at higher latitudes across the western Palaearctic region and includes six, largely allopatric, mitochondrial DNA lineages that were derived from population bottlenecks. One of these lineages is found in southern Britain and nearby areas of continental Europe. A prominent sub-lineage is nested within, and therefore derived from, the part of this lineage occupying southern Britain. The sub-lineage consists of an abundant central haplotype together with a series of closely related haplotypes, a distribution that would result from either a recent population bottleneck or a selective sweep. To distinguish between these, we sequenced a Y-chromosome marker in 167 field voles from Britain and Europe, and analysed a panel of 13 autosomal microsatellite loci in 144 field voles from eight populations in Britain. The Y-chromosome marker showed a continental-scale pattern of variation that was not aligned with that of the mitochondrial marker, while microsatellite variation did not show any evidence for a bottleneck, tentatively favouring selection instead. This implies a role for both stochastic and selective processes in generating phylogeographical patterns at different scales in the field vole.

Bonobos' saliva remaining on the pith of terrestrial herbaceous vegetation can serve as non-invasive wild genetic resources.

Evaluating the genetic diversity of natural populations of endangered species is important for conservation. Although the genetic analysis of wildlife usually requires collecting DNA non-invasively, the variety of non-invasive DNA sampling methods is limited for each species. We present a method to obtain DNA of an endangered species, the bonobo (Pan paniscus), in which the pith of the terrestrial herbaceous vegetation (THV) that they consumed was newly utilized. We investigated the (1) frequency of encountering remnant saliva on three types of THV pith; (2) concentrations of DNA in the saliva samples by the real-time quantitative PCR; and (3) rates of positive PCR, accurate genotyping, and allelic drop out by analyzing two autosomal microsatellite loci (D7s817 and D9s910). The number of remnant saliva samples was recorded by following the bonobo groups on a daily basis. The frequency of encountering DNA samples was higher in saliva samples than in fecal samples. More than half of the saliva samples remaining on two types of THV pith provided sufficient concentrations of bonobo DNA (> 200pg/μl). Rates of positive PCR and accurate genotyping were high, and allelic drop out rate was low when the amount of template DNA was above 200pg per reaction. Our results suggest that the remnants of bonobo saliva on the pith of THV are a potential resource for obtaining DNA, and better than other kinds of samples from the perspective of the abundant sampling opportunities.

Development of a 12-plex of new microsatellite markers using a novel universal primer method to evaluate the genetic diversity of jaguars (Panthera onca) from North American zoological institutions

Maintenance of genetic diversity in both zoo-managed and wild animals is critical to population health. Jaguars are considered Near Threatened throughout their geographic range, and are Endangered in the United States. Genetic diversity of zoo-managed jaguar populations in North America using microsatellite markers has not been reported. To evaluate genetic diversity in jaguars housed in North American zoological institutions compared to wild and other zoo jaguar populations, we created a 12-plex of ten tetranucleotide (n = 10) and two pentanucleotide (n = 2) autosomal microsatellite loci that have not previously been described for use in jaguars, using a universal primer approach which minimizes cost and DNA quantity requirements. A subset of jaguars from North American zoological institutions (n = 35, approximately 28% of population) were genotyped using DNA extracted from whole blood. Microsatellite loci were polymorphic with a range of 3–10 alleles (average 6.42 alleles per locus), and expected heterozygosity (He) between 0.47 and 0.85. Overall population He was 0.73. Probability of identity of individuals (PI) and siblings (PIsibs) were 6.7 × 10− 13 and 2.1 × 10− 5, respectively, confirming that this panel can be used reliably to identify individuals. Using this novel multiplex microsatellite panel, we concluded that jaguars from the North American zoo population have high genetic diversity, comparable to reported wild and other zoo jaguar populations.

Cyprus as an ancient hub for house mice and humans

AbstractAimThe distribution of the western house mouse (Mus musculus domesticus) around the world has been strongly influenced by the movement of humans. The close association between the house mouse and human phylogeography has been primarily studied in the peripheral distribution of the species. Here, we inferred the complex colonization history of Cyprus, situated close to the centre of the house mouse distribution and one of the first European islands to be colonized by the species. We investigated the resulting complexity of house mouse population genetics as well as considering the value of the house mouse as a bioproxy for studying modern human movement.LocationThe study was carried out on Cyprus.MethodsThe analysis was performed using 221 new mitochondrial D‐loop sequences and assessed the fine‐scale population genetic structure using 18 autosomal microsatellite loci from 191 modern house mice specimens.ResultsWe found a high genetic variability in the island that is illustrated by the presence of individuals from 9 of the 11 previously identified house mouse haplogroups for the D‐loop, reflecting the hub‐like nature of the island to mice. Two main waves of mouse introductions were tentatively identified based on coalescent and mismatch analysis. The first is apparently related to the Bronze Age expansion and the second one to more recent human movements. Cyprus represents an island with high complexity due to different introductions related to human transport and activity.Main conclusionsThe dispersal of mice along with humans has left a complex footprint on the island with two main waves of introductions suggested. The phylogeography of the house mouse on Cyprus is in concordance with the complex human colonization history of the island and validates the use of the house mouse as a proxy to study human migration.

Infanticide in brown bear: a case-study in the Italian Alps – Genetic identification of perpetrator and implications in small populations

Sexually Selected Infanticide (SSI) is thought of as a male reproductive strategy in social mammalian species, because females who lose cubs may quickly re-enter oestrus. SSI has rarely been documented in non-social mammals and, in brown bears, SSI has been studied mainly in an eco-ethological perspective. The authors examined the first genetically documented infanticide case which occurred in May 2015 in brown bears in Italy (Trentino, Central-Eastern Alps). The infanticide killed two cubs and their mother. Hair samples were collected from the corpses as well as saliva, through swabs on mother’s wounds, with the aim of identifying the genotype of the perpetrator. The samples were genotyped by PCR amplification of 15 autosomal microsatellite loci, following the protocol routinely used for individual bear identifications within the Interregional Action Plan for Brown Bear Conservation in the Central-Eastern Alps (PACOBACE). Reliable genotypes were obtained from the mother, cubs and putative perpetrator. The genotypes were matched with those populating the PACOBACE database and genealogies were reconstructed. Both mother and perpetrator genotypes were already present in the database. Kinship analyses confirmed mother-cubs relationships and identified the father of the cubs. In this study, for the first time, the authors used the open-source LRmix STUDIO software, designed to analyse human forensic genetic profiles, to solve a case in wildlife. Through LRmix STUDIO, those alleles that do not belong to the victims were isolated and, finally, the perpetrator was identified. This study presents a method that allows, through the application of different models, the genetic identification of the conspecific perpetrator with the highest probability. The identification of the infanticidal male is relevant for the better management and conservation of wild populations with small effective population size (Ne) and low population growth rate, especially in the case of recently established populations in human-dominated landscapes. This procedure will have predictably wide applications, supplying important data in the monitoring of small and isolated populations.

Extraction of DNA from captive-sourced feces and molted feathers provides a novel method for conservation management of New Zealand kiwi (Apteryx spp.).

Although some taxa are increasing in number due to active management and predator control, the overall number of kiwi (Apteryx spp.) is declining. Kiwi are cryptic and rare, meaning current monitoring tools, such as call counts, radio telemetry, and surveys using detection dogs are labor‐intensive, yield small datasets, and require substantial resources or provide inaccurate estimates of population sizes. A noninvasive genetic approach could help the conservation effort. We optimized a panel of 23 genetic markers (22 autosomal microsatellite loci and an allosomal marker) to discriminate between all species of kiwi and major lineages within species, while simultaneously determining sex. Markers successfully amplified from both fecal and shed feather DNA samples collected in captivity. We found that DNA extraction was more efficient from shed feathers, but DNA quality was greater with feces, although this was sampling dependent. Our microsatellite panel was able to distinguish between contemporary kiwi populations and lineages and provided PI values in the range of 4.3 × 10−5 to 2.0 × 10−19, which in some cases were sufficient for individualization and mark–recapture studies. As such, we have tested a wide‐reaching, noninvasive molecular approach that will improve conservation management by providing better parameter estimates associated with population ecology and demographics such as abundance, growth rates, and genetic diversity.

Population-level assessment of genetic diversity and habitat fragmentation in critically endangered Grauer's gorillas.

The critically endangered Grauer's gorilla (Gorilla beringei graueri) has experienced an estimated 77% population decline within a single generation. Although crucial for informed conservation decisions, there is no clear understanding about population structure and distribution of genetic diversity across the species' highly fragmented range. We fill this gap by studying several core and peripheral Grauer's gorilla populations throughout their distribution range. We generated genetic profiles for a sampling of an unstudied population of Grauer's gorillas from within the species' core range at 13 autosomal microsatellite loci and combined them with previously published and newly generated data from four other Grauer's gorilla populations, two mountain gorilla populations, and one western lowland gorilla population. In agreement with previous studies, the genetic diversity of Grauer's gorillas is intermediate, falling between western lowland and mountain gorillas. Among Grauer's gorilla populations, we observe lower genetic diversity and high differentiation in peripheral compared with central populations, indicating a strong effect of genetic drift and limited gene flow among small, isolated forest fragments. Although genetically less diverse, peripheral populations are frequently essential for the long-term persistence of a species and migration between peripheral and core populations may significantly enrich the overall species genetic diversity. Thus, in addition to central Grauer's gorilla populations from the core of the distribution range that clearly deserve conservation attention, we argue that conservation strategies aiming to ensure long-term species viability should include preserving peripheral populations and enhancing habitat connectivity.

Triploidy in a sexually dimorphic passerine provides new evidence for the effect of the W chromosome on secondary sexual traits in birds

In birds, there are two main models for the determination of sex: the ‘Z Dosage’ model in which the number, or dose, of Z chromosomes determines sex, and the ‘Dominant W’ model which argues that a specific gene in the W chromosome may influence Z gene expression and determine sex. The best evidence for W determination of sex comes from birds with 2 copies of the Z chromosome paired with a single W (e.g. ZZW) which are nonetheless females. Here, we expand the species where such a mechanism may operate by reporting a case of a triploid Neotropical passerine bird with sexually dimorphic plumage, the São Paulo marsh antwren Formicivora paludicola. Evidence from 17 autosomal unlinked microsatellite loci, and CHD1 sex‐linked locus, indicate that this individual is a 3n ZZW triploid with intermediate plumage pattern. This example expands our knowledge of sex determination mechanisms in birds by demonstrating that both the W and the two Z chromosomes affect the expression of morphological secondary sexual traits in a non‐galliform bird.

Extensive genetic differentiation detected within a model marsupial, the tammar wallaby (Notamacropus eugenii)

The tammar wallaby (Notamacropus eugenii) is one of the most intensively studied of all macropodids and was the first Australasian marsupial to have its genome sequenced. However, comparatively little is known about genetic diversity and differentiation amongst the morphologically distinct allopatric populations of tammar wallabies found in Western (WA) and South Australia (SA). Here we compare autosomal and Y-linked microsatellite genotypes, as well as sequence data (~600 bp) from the mitochondrial DNA (mtDNA) control region (CR) in tammar wallabies from across its distribution. Levels of diversity at autosomal microsatellite loci were typically high in the WA mainland and Kangaroo Island (SA) populations (A = 8.9–10.6; He = 0.77–0.78) but significantly reduced in other endemic island populations (A = 3.8–4.1; He = 0.41–0.48). Autosomal and Y-linked microsatellite loci revealed a pattern of significant differentiation amongst populations, especially between SA and WA. The Kangaroo Island and introduced New Zealand population showed limited differentiation. Multiple divergent mtDNA CR haplotypes were identified within both SA and WA populations. The CR haplotypes of tammar wallabies from SA and WA show reciprocal monophyly and are highly divergent (14.5%), with levels of sequence divergence more typical of different species. Within WA tammar wallabies, island populations each have unique clusters of highly related CR haplotypes and each is most closely related to different WA mainland haplotypes. Y-linked microsatellite haplotypes show a similar pattern of divergence although levels of diversity are lower. In light of these differences, we suggest that two subspecies of tammar wallaby be recognized; Notamacropus eugenii eugenii in SA and N. eugenii derbianus in WA. The extensive neutral genetic diversity and inter-population differentiation identified within tammar wallabies should further increase the species value and usefulness as a model organism.

Fine-scale genetic structure analyses reveal dispersal patterns in a critically endangered primate, Trachypithecus leucocephalus.

Dispersal is a critically important life history trait of social organisms that has a major impact on the population genetic structure and social relationships within groups. Primates exhibit highly diversified dispersal and philopatry patterns, but knowledge of these patterns is difficult to obtain and usually limited to observations of a small number of focal social groups or individuals. Here, we investigated the dispersal pattern of a critically endangered colobine monkey, the white-headed langur (Trachypithecus leucocephalus), using molecular approaches, and sex-specific population genetic structure analyses at fine geographical scales. We non-invasively collected 403 fecal samples from 41 social groups across 90% of the langur's range in Fusui (FS) and Chongzuo (CZ) in southwestern Guangxi Province, China. We identified 214 unique individuals from the samples by genotyping 15 polymorphic autosomal microsatellite loci, a sex-specific marker, and sequencing the mitochondrial DNA (mtDNA) hypervariable region I (HVRI). We found higher intragroup than intergroup genetic relatedness in males and females in both populations. A significant positive correlation between genetic distance and geographical distance, that is a pattern of isolation-by-distance, was detected in females from the FS population, but not in males. Spatial autocorrelation analyses revealed high within-group relatedness in both sexes and populations, as well as an additional positive correlation at the 0.5-km distance class in females from the FS population. Furthermore, we inferred first-generation migrants using genetic assignment tests. Our results suggest that male T. leucocephalus disperse at random distances within habitat areas, whereas dispersal of females may mainly occur among adjacent groups near their home site. Our study provides the first genetic evidence for sex-biased dispersal in T. leucocephalus, which has important management and conservation implications for the species.

Genetic identification of a non-native species introgression into wild population of the field cricket Gryllus campestris (Orthoptera: Gryllidae) in Central Europe

Two species of the genus Gryllus occur in Europe: G. campestris and G. bimaculatus. The first is widely distributed in the north-western Palaearctic, while the second, G. bimaculatus, occurs predominantly in the Mediterranean area. There is a visible pattern in the distribution of G. campestris, the insect being rare and threatened in the western part of its range, whereas it is still abundant in the east. Despite the fact that this species is commonly used in laboratory experiments, its natural populations are poorly characterised. In the present study, we analysed cricket populations from the lower Oder and Vistula River valleys in Poland. Based on the phylogeny of the mtDNA cytochrome b fragment, we found that 17% of the individuals studied had a G. bimaculatus-like mtDNA haplotype. Analyses of 11 autosomal microsatellite loci failed to reveal any clear genetic differentiation between individuals assigned to these two clades. This suggests, along with the spatial distribution of G. bimaculatus-like haplotypes, successful interbreeding of G. bimaculatus with native populations of G. campestris. However, both the nuclear data and additional analyses of two X-chromosome-linked microsatellite loci revealed incomplete introgression. Human-mediated introgression seems to be the most plausible explanation of the observed genotypic pattern such that caution needs to be taken in conservation efforts carried out in the western part of the species' range.

Status assessment of Eurasian lynx in Latvia linking genetics and demography—a growing population or a source–sink process?

The Eurasian lynx is managed as a game species in Latvia. A variety of demographic parameters were used to assess the current status of the Latvian lynx population and recruitment after annual harvest. Population age–gender structure and female prenatal fecundity were determined in 530 legally hunted animals over a 9-year period. Average prenatal fecundity was 3.2 ± 0.1, and evidence of reproduction was found in 87 % of the examined adult females. We found a disproportionally low number of 1- and 2-year-old lynx in the hunting bags and therefore constructed an age–gender pyramid, adjusting the survival curves to the proportions of the remaining age classes. Two hundred and eighty-eight tissue samples were analysed using 12 autosomal microsatellite loci. Groups of related individuals were identified using a group approach and supported by pairwise relationship analysis. Thirteen potential maternal–offspring relationship groups and 30 related groups of lynx individuals based on potential full-sib and half-sib relationships between the individuals within the research period were identified. Evidence from this study shows that the population is not only stable but also likely growing and that there currently appear to be no barriers preventing gene flow. We can conclude that, in general, the lynx population was sustainably maintained. The previous harvest intensity has not obstructed the conservation aim for lynx in Latvia, which is to maintain the population as stable or growing. Combining demographic and molecular analyses, this study reveals relevant reference indices that can be used in future monitoring of the lynx population in Latvia.

Local-scale genetic structure in the Japanese wild boar (Sus scrofa leucomystax): insights from autosomal microsatellites

The Japanese wild boar (Sus scrofa leucomystax) is one of the most widely distributed mammals in Japan. However, its population structure and pattern of gene flow at a regional level are poorly understood. In this study, we investigated the local-scale genetic structure of the Japanese wild boar. In total, 172 individuals sampled in Gifu Prefecture, central Japan, were genotyped for 29 autosomal microsatellite loci. Significant genetic differentiations (F ST = 0.020–0.128) were detected among some geographical areas. In addition, in the overall population (n = 172), all loci deviating from the Hardy–Weinberg equilibrium exhibited a significant deficit of heterozygotes. These results suggest the presence of genetic substructuring in the local population. Moreover, Bayesian cluster analysis revealed the presence of substructuring within the population, despite the relatively small study area (10,621 km2). Spatial Bayesian cluster analysis showed that the boundaries of subpopulations were generally consistent with landscape features (e.g. main rivers, urban areas and road and train networks). Our study implies that these landscape features play a significant role as a barrier to dispersal and gene flow in the local population of the Japanese wild boar.

Genetic investigation of Italian domestic pigeons increases knowledge about the long-bred history of Columba livia (Aves: Columbidae)

In this study, we aimed to characterise the genetic diversity of Italian pigeon breeds and describe the relationships among them and other European lineages, conjecturing which processes have led to actual breeds. We analysed the eight most diffused Italian pigeon breeds in addition to 11 foreign lineages that could have shared common ancestors or have been used in the creation of the Italian breeds. We analysed 12 autosomal microsatellite loci in 427 samples collected from 19 breeds belonging to six main groups of domestic pigeons (tumblers and highflyers, structure, owls, wattle, utility and hen). Genetic variability did not differ considerably among breeds, with an average observed heterozygosity (HO) of 0.550 ± 0.072 (max = 0.661 in breed Sottobanca; min = 0.411 in breed Frillback). The 21.34% of total genetic variation found was partitioned among breeds. Italian pigeon breeds were assigned coherently to their respective groups of origin. The analysis supports the origin of homing pigeons from English Carrier and the existence of a close relationship between Old Dutch Capuchine and Italian Owl. Despite the differences in body size, pigeons of the breeds belonging to the hen group are genetically very similar. The sub-populations recognised by breeders inside Italian Owl and Triganino are not genetically supported and their identification as new breeds ought not to be yet proposed, although they are morphologically distinguishable. Consequently, it could also be discussed how the genetic characterisation of domestic lineages could give useful information in breeding and selection processes.