A class of highly polymorphic tetranucleotide repeats for canine genetic mapping

Phylogeographic analyses of an endemic Neotropical fox (Lycalopex vetulus) reveal evidence of hybridization with a different canid species (L. gymnocercus)

The hoary fox (Lycalopex vetulus) is the only species of the Canidae (Mammalia: Carnivora) endemic to Brazil, and so far has been the target of few genetic studies. Using microsatellites and mtDNA markers, we investigated its present genetic diversity and population structure. We also tested the hypothesis that this species currently hybridizes with the pampas fox (L. gymnocercus), as suggested by previous mtDNA data from two individuals. We collected tissue and blood samples from animals representing most of the two species' distributions in Brazil (n = 87), including their recently discovered geographic contact zone in São Paulo state. We observed that the hoary fox exhibits high levels of genetic diversity and low levels of population structure. We identified six individuals from São Paulo state with clear evidence of hybridization based on introgressed pampas fox mitochondrial DNA and/or admixed microsatellite genotypes (three individuals bore both types of evidence). These results demonstrate the existence of admixed individuals between hoary and pampas foxes in southeastern Brazil, representing the first identified case of interspecies admixture between native South American canids. We discuss our findings in the context of the evolutionary history of these foxes and address potential conservation implications of this interspecies hybridization process.

Small but Mighty: Genetic Diversity of the Thai Ridgeback Dog Population

Originating in Thailand, the Thai Ridgeback dog is known for its unique fur ridge that grows in the opposite direction along its back. Selective breeding and a limited populations in Thailand have led to significant close inbreeding among related individuals. The current Thai Ridgeback population is assumed to have experienced a loss of genetic diversity and bottleneck events. Furthermore, studies on the genetic diversity and structure of Thai Ridgeback dogs are limited. Therefore, the aim of this study was to assess the genetic diversity in Thai Ridgeback dogs. Microsatellite genotyping and mitochondrial DNA D-loop sequences were used to assess genetic diversity in 105 Thai Ridgeback dogs from various farms throughout Thailand. Significant genetic diversity and minimal inbreeding were observed in the current Thai Ridgeback population. Signs of bottlenecks were not observed because the exchange of genetic material among Thai Ridgeback owners effectively preserved the genetic diversity. Moreover, the genetic parameters in this study supported owner-to-owner exchanges animals for mating programs. To sustain the genetic diversity of Thai Ridgeback dogs, the use of genetic parameters to manage genetic closeness while preserving breed characteristics is essential. These data are crucial for ensuring demographic stability, which is pivotal for long-term conservation and effective population management.

Optimizing Bangkaew dog breed identification using DNA technology

BACKGROUND

The Bangkaew dog is an indigenous dog breed in the Phitsanulok province of Thailand. This breed is recognized by the Fédération Cynologique Internationale (FCI), a global canine organization. The unique traits of the Bangkaew breed lead to purebred selection for breeding, while only their traits and pedigree from parental history are recorded. Determination of the risk of inbreeding depression and the origin of unknown DNA profiles is essential due to the challenges in predicting puppy characteristics, which are crucial for breed management and conservation.

OBJECTIVE

This study aimed to emphasize that current allelic frequency data for the Bangkaew dog breed must be considered for precise individual identification.

METHODS

Approximately 82 Bangkaew dogs from various Thai localities were studied using 15 microsatellite markers for genotypic monitoring and individual identification. Maternal genetic inheritance was assessed via mtDNA D-loop analysis.

RESULTS

The results revealed high genetic diversity in the Bangkaew breed, indicating low potential for inbreeding. We also found that using a 15 loci microsatellite panel was effective for the identification of Bangkaew dogs. The optimized 10 loci microsatellite genotyping panel developed in this study presents improved identification testing efficiency, promoting both time- and cost-effectiveness.

CONCLUSION

Analysis of microsatellite DNA markers in Bangkaew dogs using an optimized panel of 10 loci selected from 15 loci effectively facilitated individual identification. This approach not only enhances time and cost efficiency, but also provides accurate allelic frequency estimates, which are crucial for the realistic evaluation of DNA evidence.

Patterns of Wolf Dispersal Respond to Harvest Density across an Island Complex

Wolves are highly mobile predators and can disperse across a variety of habitats and over long distances. However, less is known about dispersal capabilities across water and among islands. The biogeography of island systems fosters spatially structured local populations, and their degree of connectivity may influence the dynamics and long-term viability of the regional population. We sought to quantify wolf dispersal rate, distance, and dispersal sex bias throughout Prince of Wales Island, a 6670 km2 island in southeast Alaska, and the surrounding islands that constitute the wildlife management unit (9025 km2). We also investigated patterns of dispersal in relation to hunting and trapping intensity and wolf population density. We used DNA data collected during 2012-2021 long-term monitoring efforts and genotyped 811 wolves, 144 of which (18%) were dispersers. Annual dispersal rates were 9-23% and had a weakly positive relationship with wolf density. Wolves dispersed 41.9 km on average (SD = 23.7 km), and males and females did not disperse at different rates. Of the dispersing wolves, 107 died, and the majority (n = 81) died before they were able to settle. The leading manner of death was trapping (97% of mortalities), and wolves tended to disperse from areas with low harvest density to areas where harvest density was relatively higher. Dispersal occurred both to and from small islands and the larger Prince of Wales Island, indicating bidirectional as opposed to asymmetrical movement, and the genetic overlap of wolf groups demonstrates connectivity throughout this naturally patchy system. Island ecosystems have different predator-prey dynamics and recolonization processes than large, intact systems due to their isolation and restricted sizes; thus, a better understanding of the degree of population connectivity including dispersal patterns among islands in the Prince of Wales archipelago could help inform the management and research strategies of these wolves.

Genetic Monitoring of Grey Wolves in Latvia Shows Adverse Reproductive and Social Consequences of Hunting

Nowadays, genetic research methods play an important role in animal population studies. Since 2009, genetic material from Latvian wolf specimens obtained through hunting has been systematically gathered. This study, spanning until 2021, scrutinizes the consequences of regulated wolf hunting on population genetic metrics, kinship dynamics, and social organization. We employed 16 autosomal microsatellites to investigate relationships between full siblings and parent-offspring pairs. Our analysis encompassed expected and observed heterozygosity, inbreeding coefficients, allelic diversity, genetic distance and differentiation, mean pairwise relatedness, and the number of migrants per generation. The Latvian wolf population demonstrated robust genetic diversity with minimal inbreeding, maintaining stable allelic diversity and high heterozygosity over time and it is not fragmented. Our findings reveal the persistence of conventional wolf pack structures and enduring kinship groups. However, the study also underscores the adverse effects of intensified hunting pressure, leading to breeder loss, pack disruption, territorial displacement, and the premature dispersal of juvenile wolves.

An Illusion of Barriers to Gene Flow in Suburban Coyotes (Canis latrans): Spatial and Temporal Population Structure across a Fragmented Landscape in Southern California

Carnivores with large home ranges are especially vulnerable to habitat fragmentation. As coyotes (Canis latrans) are often found living in highly modified landscapes, it is unclear how urban and suburban development impact gene flow between their populations. This study evaluated gene flow among coyotes inhabiting California sage scrub fragments within the highly developed Pomona Valley, California. We genotyped microsatellites from scat samples collected from four study sites to examine population structure between coyotes separated by a major freeway, coyotes separated by suburban development, and finally, coyotes in contiguous, natural habitat sites over 15 months. Though coyotes from all four sites were genetically distinct, near-complete turnover of individuals in sites and examination of temporal genetic structure and relatedness within one site indicated the movement of family groups through natural fragments over time. Thus, we argue that solely examining spatial genetic structure may create the illusion of genetic barriers among coyote populations where they may not exist, and that incorporating temporal components of genetic variation is critical to understanding gene flow across space and time in highly mobile animals. Understanding how to better study and manage coyotes, an apex predator, is key to the conservation of the endangered California sage scrub ecosystem.

Variation in adult and pup wolf diets at natal den sites is influenced by forest composition and configuration

Although wolves are wide-ranging generalist carnivores throughout their life cycle, during the pup-rearing season wolf activity is focused on natal den sites where pup survival depends upon pack members provisioning food. Because prey availability is influenced by habitat quality within the home range, we investigated the relative importance of prey species for adults and pups and further examined the relationship between habitat characteristics, wolf diet, and litter size on Prince of Wales Island (POW) in Southeast Alaska. During 2012-2020, we detected 13 active den sites within the home ranges of nine wolf packs. We estimated minimum pup counts using motion-detecting cameras and individual genotypes from noninvasive samples (hair: n = 322; scat: n = 227) and quantified wolf diet composition using fecal DNA metabarcoding (n = 538). We assessed habitat composition, configuration, and connectivity within denning and annual home ranges estimated using wolf GPS-collar data. Contrary to expectations, wolves had a more constricted diet during denning season (April 15-July 31), and within this season pups had a narrower dietary niche (species richness [S] = 4) focused more on deer (relative frequency of occurrence [O/I] = 0.924) than adults (S = 15; deer O/I = 0.591). Litter size had a positive relationship with the relative frequency of deer in a wolf pack's diet. Wolf consumption of deer was positively associated with the proportion of young-growth forest (≤25 years old) within denning and annual home ranges. High levels of vegetation patch interspersion, and the density of closed logging roads were also important predictors, suggesting these habitat qualities were influential for increasing the availability of deer to wolves. Our results contrast with previous research indicating wolf pup diets included more alternate prey (i.e., beaver) than adults and emphasize the importance of deer to wolf viability on POW, especially during denning season.

Allogeneic peripheral blood haematopoietic stem cell transplantation for the treatment of dogs with high-grade B-cell lymphoma

Autologous peripheral blood haematopoietic stem cell transplantation (HCT) cures 33%-40% of dogs with high-grade B-cell lymphoma. We hypothesized, based on human allogeneic bone marrow transplantation literature, that transplanting dogs using canine donor leukocyte-matched CD34+ cells would lead to fewer relapses and increased cure rates. We retrospectively reviewed medical records of dogs diagnosed with high-grade B-cell lymphoma who received an identical allogeneic HCT. A total of 15 dogs transplanted at four facilities were identified. Five of fifteen dogs relapsed before transplant. The mean number of donor CD34+ cells/kg harvested and infused into recipient dogs was 8.0 × 10⁶ /kg (range: 2.08 × 10⁶ /kg-2.9 × 10⁷ /kg). The median disease-free interval and overall survival of all dogs was 1095 days (range: 9-2920 days) and 1115 days (range: 9-2920 days), respectively. Two of five dogs, not in remission at transplant, died in the hospital. The median disease-free interval and overall survival of the remaining three dogs was 25 days (range: 15-250 days) and 1100 days (range: 66-1902 days), respectively. The median disease-free interval and overall survival of the 10 dogs who had not relapsed was 1235 days (range: 19-2920 days) and 1235 days (range: 19-2920 days), respectively. One dog died soon after discharge of presumed gastric-dilatation-volvulus. Eight of nine remaining dogs lived >4 yrs post-alloHCT, leading to a cure rate of 89%. Acute graft versus host disease was seen in three dogs. These results suggest that allogeneic HCT can cure ~50% more dogs than those treated with autologous HCT.

Wolf Dispersal Patterns in the Italian Alps and Implications for Wildlife Diseases Spreading

Simple Summary

Wildlife dispersal directly influences population expansion patterns, and may have indirect effects on the spread of wildlife diseases. For many species, little is known about dispersal, despite its importance to conservation. We documented the natural dispersal processes of an expanding wolf (Canis lupus) population in the Italian Alps to understand the dynamics of the recolonization pattern and identify diseases that might be connected with the process through the use of non-invasive genetic sampling over a 20-year period. By documenting 55 dispersal events, with an average minimum straight dispersal distance of 65.8 km (±67.7 km), from 7.7 km to 517.2 km, we discussed the potential implications for maintaining genetic diversity of the population and for wildlife diseases spreading.

Abstract

Wildlife dispersal directly influences population expansion patterns, and may have indirect effects on the spread of wildlife diseases. Despite its importance to conservation, little is known about dispersal for several species. Dispersal processes in expanding wolf (Canis lupus) populations in Europe is not well documented. Documenting the natural dispersal pattern of the expanding wolf population in the Alps might help understanding the overall population dynamics and identifying diseases that might be connected with the process. We documented 55 natural dispersal events of the expanding Italian wolf alpine population over a 20-year period through the use of non-invasive genetic sampling. We examined a 16-locus microsatellite DNA dataset of 2857 wolf samples mainly collected in the Western Alps. From this, we identified 915 individuals, recaptured 387 (42.3%) of individuals, documenting 55 dispersal events. On average, the minimum straight dispersal distance was 65.8 km (±67.7 km), from 7.7 km to 517.2 km. We discussed the potential implications for maintaining genetic diversity of the population and for wildlife diseases spreading.

Settlement of a stable wolf pack in a highly anthropic area of Pisan hills: Relationship with animal husbandry and hunting in a human-wolf coexistence perspective

Anthropic areas play a pivot role for main wolf conservation challenges. Wolf presence in the higher Pisan hills has been well documented while wolf settlement in the lower Pisan hills is still uncertain. In this study, long-term information on wolf presence in a highly anthropic area of the lower Pisan hills was collected by using non-invasive monitoring techniques. Furthermore, both the relationship of this predator with human activity and the impact of hunting on wolf presence have been investigated. The results obtained indicate the presence of a stable and reproductive wolf pack composed by both Italian wolf and hybrids individuals in the municipalities of Crespina Lorenzana and Casciana Terme Lari. A high impact of wolf on livestock was recorded in this area since no prevention systems were adopted by farmers. Wolf appears not to have a negative impact on wild boar population. Similarly, wild boar drive hunting does not appear to affect the wolf pack presence in the area. Thereby wolf may play a key role as controller of wild population. Prevention strategies improvement becomes instrumental to promote wolf-human coexistence. Further investigation to monitor pack hybridization level and turnover and to assess the impact of packs on wild population and livestock in anthropic areas is desirable.

Genetic signature of immigrants and their effect on genetic diversity in the recently established Scandinavian wolf population

Transboundary connectivity is a key component when conserving and managing animal species that require large areas to maintain viable population sizes. Wolves Canis lupus recolonized the Scandinavian Peninsula in the early 1980s. The population is geographically isolated and relies on immigration to not lose genetic diversity and to maintain long term viability. In this study we address (1) to what extent the genetic diversity among Scandinavian wolves has recovered during 30 years since its foundation in relation to the source populations in Finland and Russia, (2) if immigration has occurred from both Finland and Russia, two countries with very different wolf management and legislative obligations to ensure long term viability of wolves, and (3) if immigrants can be assumed to be unrelated. Using 26 microsatellite loci we found that although the genetic diversity increased among Scandinavian wolves (n = 143), it has not reached the same levels found in Finland (n = 25) or in Russia (n = 19). Low genetic differentiation between Finnish and Russian wolves, complicated our ability to determine the origin of immigrant wolves (n = 20) with respect to nationality. Nevertheless, based on differences in allelic richness and private allelic richness between the two countries, results supported the occurrence of immigration from both countries. A priori assumptions that immigrants are unrelated is non-advisable, since 5.8% of the pair-wise analyzed immigrants were closely related. To maintain long term viability of wolves in Northern Europe, this study highlights the potential and need for management actions that facilitate transboundary dispersal.

Identification of Wolf-Dog Hybrids in Europe – An Overview of Genetic Studies

Significant development of genetic tools during the last decades provided opportunities for more detailed analyses and deeper understanding of species hybridization. New genetic markers allowed for reliable identification of admixed individuals deriving from recent hybridization events (a few generations) and those originating from crossings up to 19 generations back. Implementation of microsatellites (STRs) together with Bayesian clustering provided abundant knowledge regarding presence of admixed individuals in numerous populations and helped understand the problematic nature of studying hybridization (i.a., defining a reliable thresholds for recognizing individuals as admixed or obtaining well-grounded results representing actual proportion of hybrids in a population). Nevertheless, their utilization is limited to recent crossbreeding events. Single Nucleotide Polymorphisms (SNPs) proved to be more sensible tools for admixture analyses furnishing more reliable knowledge, especially for older generation backcrosses. Small sets of Ancestry Informative Markers (AIMs) of both types of markers were effective enough to implement in monitoring programs, however, SNPs seem to be more appropriate because of their ability to identify admixed individuals up to 3rd generations. The main aim of this review is to summarize abundant knowledge regarding identification of wolf-dog hybrids in Europe and discuss the most relevant problems relating to the issue, together with advantages and disadvantages of implemented markers and approaches.

Automated genotyping of microsatellite loci from feces with high throughput sequences

Ecological and conservation genetic studies often use noninvasive sampling, especially with elusive or endangered species. Because microsatellites are generally short in length, they can be amplified from low quality samples such as feces. Microsatellites are highly polymorphic so few markers are enough for reliable individual identification, kinship determination, or population characterization. However, the genotyping process from feces is expensive and time consuming. Given next-generation sequencing (NGS) and recent software developments, automated microsatellite genotyping from NGS data may now be possible. These software packages infer the genotypes directly from sequence reads, increasing throughput. Here we evaluate the performance of four software packages to genotype microsatellite loci from Iberian wolf (Canis lupus) feces using NGS. We initially combined 46 markers in a single multiplex reaction for the first time, of which 19 were included in the final analyses. Megasat was the software that provided genotypes with fewer errors. Coverage over 100X provided little additional information, but a relatively high number of PCR replicates were necessary to obtain a high quality genotype from highly unoptimized, multiplexed reactions (10 replicates for 18 of the 19 loci analyzed here). This could be reduced through optimization. The use of new bioinformatic tools and next-generation sequencing data to genotype these highly informative markers may increase throughput at a reasonable cost and with a smaller amount of laboratory work. Thus, high throughput sequencing approaches could facilitate the use of microsatellites with fecal DNA to address ecological and conservation questions.

Genetic Diversity and Relatedness among Captive African Painted Dogs in North America

African painted dogs (Lycaon pictus, APD) are highly endangered, with fewer than 7000 remaining in nature. Captive breeding programs can preserve a genetically diverse population and provide a source of individuals for reintroductions. However, most programs are initiated from few founders and suffer from low genetic diversity and inbreeding. The aims of this study were to use molecular markers to assess genetic variation, inbreeding, and relatedness among APDs in the North American captive population, to use these data to realign studbook records, and to compare these data to wild populations and to the European captive population to facilitate the development of a global management plan. We sequenced mitochondrial and major histocompatibility (MHC) class II loci and genotyped 14 microsatellite loci from 109 APDs from 34 institutions in North America. We identified three likely studbook errors and resolved ten cases of uncertain paternity. Overall, microsatellite heterozygosity was higher than reported in Europe, but effective population size estimates were lower. Mitochondrial sequence variation was extremely limited, and there were fewer MHC haplotypes than in Europe or the wild. Although the population did not show evidence of significant inbreeding overall, several individuals shared high relatedness values, which should be incorporated into future breeding programs.

Evolution of haematopoietic cell transplantation for canine blood disorders and a platform for solid organ transplantation

Pre-clinical haematopoietic cell transplantation (HCT) studies in canines have proven to be invaluable for establishing HCT as a highly successful clinical option for the treatment of malignant and non-malignant haematological diseases in humans. Additionally, studies in canines have shown that immune tolerance, established following HCT, enabled transplantation of solid organs without the need of lifelong immunosuppression. This progress has been possible due to multiple biological similarities between dog and mankind. In this review, the hurdles that were overcome and the methods that were developed in the dog HCT model which made HCT clinically possible are examined. The results of these studies justify the question whether HCT can be used in the veterinary clinical practice for more wide-spread successful treatment of canine haematologic and non-haematologic disorders and whether it is prudent to do so.

How the west was won: genetic reconstruction of rapid wolf recolonization into Germany's anthropogenic landscapes

Following massive persecution and eradication, strict legal protection facilitated a successful reestablishment of wolf packs in Germany, which has been ongoing since 2000. Here, we describe this recolonization process by mitochondrial DNA control-region sequencing, microsatellite genotyping and sex identification based on 1341 mostly non-invasively collected samples. We reconstructed the genealogy of German wolf packs between 2005 and 2015 to provide information on trends in genetic diversity, dispersal patterns and pack dynamics during the early expansion process. Our results indicate signs of a founder effect at the start of the recolonization. Genetic diversity in German wolves is moderate compared to other European wolf populations. Although dispersal among packs is male-biased in the sense that females are more philopatric, dispersal distances are similar between males and females once only dispersers are accounted for. Breeding with close relatives is regular and none of the six male wolves originating from the Italian/Alpine population reproduced. However, moderate genetic diversity and inbreeding levels of the recolonizing population are preserved by high sociality, dispersal among packs and several immigration events. Our results demonstrate an ongoing, rapid and natural wolf population expansion in an intensively used cultural landscape in Central Europe.

First wolves in Luxembourg since 1893, originating from the Alpine and Central European populations

Considering the spread of the grey wolf (Canis lupus) in Europe over the past 30 years, Luxembourg took some measures to prepare for the return of this apex predator, including the establishment of a management plan that notably addresses the issue of wolf depredation on livestock. Here we present the results of genetic analyses of putative wolf saliva, hair and scat samples collected from or near prey carcasses between 2015 and 2020. In two cases, the wolf was confirmed via DNA analysis: in July 2017 near Garnich and in April 2020 near Niederanven, both assigned to category C1 (hard evidence). A third case was classified as C2 (confirmed observation) based on prey carcass characteristics, while genetic analysis yielded no result. These are the first confirmed records of wolves in Luxemburg since 1893. Moreover, the two C1-cases originated from the Alpine (Garnich) and Central European (Niederanven) populations. Given similar developments in the neighboring countries and regions, we conclude that the area including the Benelux countries as well as Rhineland-Palatinate, Saarland and Northern France may well become a melting pot for wolves of the two aforementioned populations in the coming years and decades.

Molecular investigation of three leopards death: A case of suspicious revenge killing

We report a case study wherein we established the putative cause of the death of three leopards by identifying the species and number of individual prey species from the gut contents using molecular tools. In a National Park within Northern part of India, the suspicious death of three leopards (Panthera pardus) was reported from different localities on the same day. The gut contents from the three leopard carcasses were collected during postmortem and sent to us to confirm the prey species. We used mitochondrial DNA cytochrome b (Cyt b) and control region (CR), and nuclear microsatellites for molecular identification of species and individual identification, respectively, from the gut contents. Mitochondrial sequences confirmed that the undigested remnants collected from the gut contents were of the domestic dog (Canis lupus familiaris). Furthermore, the microsatellite analysis of the gut contents highlighted the consumption of the same dog by all the three deceased leopards. Since the National Park was one of the major human-wildlife interaction zones, consuming the same dog by the leopards implies suspicious poisoning for revenge. The use of dog carcass for the possible poisoning for the mass-scale killing of the protected species is a severe wildlife offense.

Jackal in hide: detection dogs show first success in the quest for golden jackal (Canis aureus) scats

Golden jackal (Canis aureus) monitoring in central Europe generates more interest and becomes increasingly important with the species’ appearance in areas where it was previously unestablished. For genetic monitoring of golden jackals via scat collection, the distinction of jackal scats from those of related species such as the red fox (Vulpes vulpes) is crucial: if done incorrectly, it can falsify diet studies or inflate costs of DNA analyses. In this study, we tested the potential benefits of using domestic dogs to specifically find jackal scats. We used trained scat detection dogs to locate and identify golden jackal scats in an area of dense shrubland, with the species’ presence previously confirmed via bioacoustic monitoring. On a total of 133 km of transects covering at least two golden jackal groups, two human-dog teams found 34 putative golden jackal scats. A total of 26 of these were successfully genetically analysed, of which 19 were attributed to 13 individual golden jackals, an accuracy rate of 73%. Our results show that detection dogs can successfully differentiate golden jackal scats from other species. This tool can be applied to detect golden jackal presence and establish more reliable estimates of group number and size than previously determined through bioacoustic stimulation. By combining both methods, questions about family structures and kinship, seasonal differences in habitat use and territory sizes can be answered. The regular use of detection dogs can present an efficient method to monitor golden jackals on a long-term basis and to learn more about their behaviour and population dynamics.

Towards high–throughput analyses of fecal samples from wildlife

High–throughput sequencing offers new possibilities in molecular ecology and conservation studies. However, its potential has not yet become fully exploited for noninvasive studies of free–ranging animals, such as those based on feces. High–throughput sequencing allows sequencing of short DNA fragments and could allow simultaneous genotyping of a very large number of samples and markers at a low cost. The application of high throughput genotyping to fecal samples from wildlife has been hindered by several labor–intensive steps. We evaluate alternative protocols which could allow higher throughput for two of these steps: sample collection and DNA extraction. Two different field sampling and seven different DNA extraction methods are tested here on grey wolf (Canis lupus) feces. There was high variation in genotyping success rates. The field sampling method based on surface swabbing performed much worse than the extraction from a fecal fragment. In addition, there is a lot of room for improvement in the DNA extraction step. Optimization of protocols can lead to very much more efficient, cheaper and higher throughput noninvasive monitoring. Selection of appropriate markers is still of paramount importance to increase genotyping success.

Does harvest affect genetic diversity in grey wolves?

Harvest can affect vital rates such as reproduction and survival, but also genetic measures of individual and population health. Grey wolves (Canis lupus) live and breed in groups, and effective population size is a small fraction of total abundance. As a result, genetic diversity of wolves may be particularly sensitive to harvest. We evaluated how harvest affected genetic diversity and relatedness in wolves. We hypothesized that harvest would (a) reduce relatedness of individuals within groups in a subpopulation but increase relatedness of individuals between groups due to increased local immigration, (b) increase individual heterozygosity and average allelic richness across groups in subpopulations and (c) add new alleles to a subpopulation and decrease the number of private alleles in subpopulations due to an increase in breeding opportunities for unrelated individuals. We found harvest had no effect on observed heterozygosity of individuals or allelic richness at loci within subpopulations but was associated with a small, biologically insignificant effect on within-group relatedness values in grey wolves. Harvest was, however, positively associated with increased relatedness of individuals between groups and a net gain (+16) of alleles into groups in subpopulations monitored since harvest began, although the number of private alleles in subpopulations overall declined. Harvest likely created opportunities for wolves to immigrate into nearby groups and breed, thereby making groups in subpopulations more related over time. Harvest appears to affect genetic diversity in wolves at the group and population levels, but its effects are less apparent at the individual level given the population sizes we studied.

Scent marking in wolves Canis lupus inhabiting managed lowland forests in Poland

In wolves Canis lupus, scent marking plays an important role in territory defence. In Europe, studies on patterns of scent marking in wolves have mostly been conducted in mountains or primeval forests, but since these areas are characterised by low human activity, the impact of people on this behaviour has been neglected. We conducted a study that combined genetic methods with an analysis of the spatial distribution of wolf territory markings in lowland managed forests with high human activity. We found that scent markings are deposited by all members of wolf family groups. Wolves most intensively marked crossroads and their vicinity, especially on roads only accessible for four-wheel drive cars. Our study provides further evidence that crossroads of forest roads play a crucial role in wolf scent marking. The results of our study may be useful during inventories of wolf populations based on collecting indirect signs of their presence or non-invasive genetic sampling.

Urban coyotes are genetically distinct from coyotes in natural habitats

Urbanization is increasing throughout the world, transforming natural habitats. Coyotes (Canis latrans) are found in highly urban, suburban, rural and undeveloped mountainous habitats, making them an exemplary model organism to investigate the effects of urbanization on animals. We hypothesized that coyotes in natural habitats are more genetically related to distant coyotes in similar natural habitats and less related to coyotes in urban areas due to natal habitat-biased dispersal. We also hypothesized that increasing urbanization would result in decreased genetic diversity due to habitat fragmentation, dispersal barriers and genetic drift. We analyzed 10 microsatellite genetic markers from 125 individual coyotes sampled across a spectrum of highly urban to highly natural areas in southern California. Most coyotes clustered into four distinct genetic populations, whereas others appeared to have admixed ancestry. Three genetic populations were associated primarily with urban habitats in Los Angeles and Orange Counties. In contrast, the remaining population was associated with more naturally vegetated land near the surrounding mountains. Coyotes living in natural areas formed a genetically distinct cluster despite long geographic distances separating them. Genetic diversity was negatively associated with urban/suburban land cover and local road density, and positively associated with the relative amount of natural vegetation. These results indicate that genetic differentiation and loss of genetic diversity coincided with the extremely rapid expansion of Greater Los Angeles throughout the 1900s. Thus, urbanization reduces gene flow and erodes genetic diversity even in a habitat generalist thought to be minimally impacted by land development.

A unified STR profiling system across multiple species with whole genome sequencing data

Background

Short tandem repeats (STRs) serve as genetic markers in forensic scenes due to their high polymorphism in eukaryotic genomes. A variety of STRs profiling systems have been developed for species including human, dog, cat, cattle, etc. Maintaining these systems simultaneously can be costly. These mammals share many high similar regions along their genomes. With the availability of the massive amount of the whole genomics data of these species, it is possible to develop a unified STR profiling system. In this study, our objective is to propose and develop a unified set of STR loci that could be simultaneously applied to multiple species.

Result

To find a unified STR set, we collected the whole genome sequence data of the concerned species and mapped them to the human genome reference. Then we extracted the STR loci across the species. From these loci, we proposed an algorithm which selected a subset of loci by incorporating the optimized combined power of discrimination. Our results show that the unified set of loci have high combined power of discrimination, >1−10⁻⁹, for both individual species and the mixed population, as well as the random-match probability, <10⁻⁷ for all the involved species, indicating that the identified set of STR loci could be applied to multiple species.

Conclusions

We identified a set of STR loci which shared by multiple species. It implies that a unified STR profiling system is possible for these species under the forensic scenes. The system can be applied to the individual identification or paternal test of each of the ten common species which are Sus scrofa (pig), Bos taurus (cattle), Capra hircus (goat), Equus caballus (horse), Canis lupus familiaris (dog), Felis catus (cat), Ovis aries (sheep), Oryctolagus cuniculus (rabbit), and Bos grunniens (yak), and Homo sapiens (human). Our loci selection algorithm employed a greedy approach. The algorithm can generate the loci under different forensic parameters and for a specific combination of species.

Dynamic range expansion leads to establishment of a new, genetically distinct wolf population in Central Europe

Local extinction and recolonization events can shape genetic structure of subdivided animal populations. The gray wolf (Canis lupus) was extirpated from most of Europe, but recently recolonized big part of its historical range. An exceptionally dynamic expansion of wolf population is observed in the western part of the Great European Plain. Nonetheless, genetic consequences of this process have not yet been fully understood. We aimed to assess genetic diversity of this recently established wolf population in Western Poland (WPL), determine its origin and provide novel data regarding the population genetic structure of the grey wolf in Central Europe. We utilized both spatially explicit and non-explicit Bayesian clustering approaches, as well as a model-independent, multivariate method DAPC, to infer genetic structure in large dataset (881 identified individuals) of wolf microsatellite genotypes. To put the patterns observed in studied population into a broader biogeographic context we also analyzed a mtDNA control region fragment widely used in previous studies. In comparison to a source population, we found slightly reduced allelic richness and heterozygosity in the newly recolonized areas west of the Vistula river. We discovered relatively strong west-east structuring in lowland wolves, probably reflecting founder-flush and allele surfing during range expansion, resulting in clear distinction of WPL, eastern lowland and Carpathian genetic groups. Interestingly, wolves from recently recolonized mountainous areas (Sudetes Mts, SW Poland) clustered together with lowland, but not Carpathian wolf populations. We also identified an area in Central Poland that seems to be a melting pot of western, lowland eastern and Carpathian wolves. We conclude that the process of dynamic recolonization of Central European lowlands lead to the formation of a new, genetically distinct wolf population. Together with the settlement and establishment of packs in mountains by lowland wolves and vice versa, it suggests that demographic dynamics and possibly anthropogenic barriers rather than ecological factors (e.g. natal habitat-biased dispersal patterns) shape the current wolf genetic structure in Central Europe.

Genome-wide mining of microsatellites in king cobra (Ophiophagus hannah) and cross-species development of tetranucleotide SSR markers in Chinese cobra (Naja atra)

The complete genome sequence provides the opportunity for genome-wide and coding region analysis of SSRs in the king cobra and for cross-species identification of microsatellite markers in the Chinese cobra. In the Ophiophagus hannah genome, tetranucleotide repeats (38.03%) were the most abundant category, followed by dinucleotides (23.03%), pentanucleotides (13.07%), mononucleotides (11.78%), trinucleotides (11.49%) and hexanucleotides (2.6%). Twenty predominant motifs in the O. hannah genome were (A)n (C)n, (AC)n, (AG)n, (AT)n, (AGG)n, (AAT)n, (AAG)n, (AAC)n, (ATG)n, (ATAG)n, (AAGG)n, (ATCT)n, (CCTT)n, (ATTT)n, (AAAT)n, (AATAG)n, (ATTCT)n, (ATATGT)n, (AGATAT)n. In total, 4344 SSRs were found in coding sequences (CDSs). Tetranucleotides (52.79%) were the most abundant microsatellite type in CDS, followed by trinucleotides (28.50%), dinucleotides (11.02%), pentanucleotides (4.42%), mononucleotides (1.77%), and hexanucleotides (1.50%). A total of 984 CDSs containing microsatellites were assigned 11152 Gene Ontology (GO) functional terms. Gene Ontology (GO) analysis demonstrated that cellular process, cell and binding were the most frequent GO terms in biological process, cellular component and molecular function, respectively. Thirty-two novel highly polymorphic (PIC > 0.5) SSR markers for Naja atra were developed from cross-species amplification based on the tetranucleotide microsatellite sequences in the king cobra genome. The number of alleles (N_A) per locus had between 3 and 11 alleles with an average of 6.5, the polymorphism information content (PIC) value ranged from 0.521 to 0.858 (average = 0.707), the observed heterozygosity (Ho) of 32 microsatellite loci ranged from 0.292 to 0.875 (mean = 0.678), the expected heterozygosity (H_E) ranged from 0.561 to 0.889 (average = 0.761), and 3 microsatellite loci exhibited statistically significant departure from Hardy-Weinberg equilibrium (HWE) after Bonferroni correction (p < 0.003).

Standardization and validation of a panel of cross-species microsatellites to individually identify the Asiatic wild dog (Cuon alpinus)

BACKGROUND

The Asiatic wild dog or dhole (Cuon alpinus) is a highly elusive, monophyletic, forest dwelling, social canid distributed across south and Southeast Asia. Severe pressures from habitat loss, prey depletion, disease, human persecution and interspecific competition resulted in global population decline in dholes. Despite a declining population trend, detailed information on population size, ecology, demography and genetics is lacking. Generating reliable information at landscape level for dholes is challenging due to their secretive behaviour and monomorphic physical features. Recent advances in non-invasive DNA-based tools can be used to monitor populations and individuals across large landscapes. In this paper, we describe standardization and validation of faecal DNA-based methods for individual identification of dholes. We tested this method on 249 field-collected dhole faeces from five protected areas of the central Indian landscape in the state of Maharashtra, India.

RESULTS

We tested a total of 18 cross-species markers and developed a panel of 12 markers for unambiguous individual identification of dholes. This marker panel identified 101 unique individuals from faecal samples collected across our pilot field study area. These loci showed varied level of amplification success (57-88%), polymorphism (3-9 alleles), heterozygosity (0.23-0.63) and produced a cumulative misidentification rate or PID(unbiased) and PID(sibs) value of 4.7 × 10-10 and 1.5 × 10-4, respectively, indicating a high statistical power in individual discrimination from poor quality samples.

CONCLUSION

Our results demonstrated that the selected panel of 12 microsatellite loci can conclusively identify dholes from poor quality, non-invasive biological samples and help in exploring various population parameters. This genetic approach would be useful in dhole population estimation across its range and will help in assessing population trends and other genetic parameters for this elusive, social carnivore.

Consideration of sample source for establishing reliable genetic microsatellite data from mammalian carnivore specimens held in natural history collections

Specimens from natural history collections (NHCs) are increasingly being used for genetic studies and can provide information on extinct populations, facilitate comparisons of historical and contemporary populations, produce baseline data before environmental changes, and elucidate patterns of change. Destructive sampling for DNA may be in disagreement with NHC goals of long-term care and maintenance. Differentiating quality among sample sources can direct destructive sampling to the source predicted to yield the highest quality DNA and most reliable data, potentially reducing damage to specimens, laboratory costs, and genotyping errors. We used the kit fox (Vulpes macrotis) as a model species and evaluated the quality and reliability of genetic data obtained from carnivoran specimens via three different sample sources: cranial bones, nasal bones, and toepads. We quantified variation in microsatellite amplification success and genotyping error rates and assessed the reliability of source-specific genic data. Toepads had the highest amplification success rates and lowest genotyping error rates. Shorter loci had higher amplification success and lower allelic dropout rates than longer loci. There were substantial differences in the reliability of resulting multilocus genotypes. Toepads produced the most reliable data, required the fewest replicates, and therefore, had the lowest costs to achieve reliable data. Our results demonstrate that the quality of DNA obtained from specimens varies by sample source and can inform NHCs when evaluating requests for destructive sampling. Our results suggest that prior to large-scale specimen sampling, researchers should conduct pilot studies to differentiate among source-specific data reliability, identify high performing loci, reduce costs of analyses, and minimize destructive sampling.

Geographic patterns in morphometric and genetic variation for coyote populations with emphasis on southeastern coyotes

Prior to 1900, coyotes (Canis latrans) were restricted to the western and central regions of North America, but by the early 2000s, coyotes became ubiquitous throughout the eastern United States. Information regarding morphological and genetic structure of coyote populations in the southeastern United States is limited, and where data exist, they are rarely compared to those from other regions of North America. We assessed geographic patterns in morphology and genetics of coyotes with special consideration of coyotes in the southeastern United States. Mean body mass of coyote populations increased along a west-to-east gradient, with southeastern coyotes being intermediate to western and northeastern coyotes. Similarly, principal component analysis of body mass and linear body measurements suggested that southeastern coyotes were intermediate to western and northeastern coyotes in body size but exhibited shorter tails and ears from other populations. Genetic analyses indicated that southeastern coyotes represented a distinct genetic cluster that differentiated strongly from western and northeastern coyotes. We postulate that southeastern coyotes experienced lower immigration from western populations than did northeastern coyotes, and over time, genetically diverged from both western and northeastern populations. Coyotes colonizing eastern North America experienced different selective pressures than did stable populations in the core range, and we offer that the larger body size of eastern coyotes reflects an adaptation that improved dispersal capabilities of individuals in the expanding range.

Polymorphism analyses of 19 STRs in Labrador Retriever population from China and its heterozygosity comparisons with other retriever breeds

Pure breed dogs of Western origin are increasingly more popular in China as is a need to differentiate breeds and individual dogs for personal and forensic reasons. Research on genetic diversities of the canine population in China is rarely conducted. In this study, genetic distributions and forensic efficiencies of 19 canine STR loci in Labrador Retriever population from China were evaluated by using one available commercial canine kit in China. This panel was used to genetically define 214 Labrador Retrievers in China, as an example of one of the most important Western breeds and to compare them with Labrador Retrievers from America based on three overlapping STR loci. Moreover, genetic relationship analyses between Labrador Retriever population and two reference populations in America were performed. All 19 STR loci were polymorphic and conformed to Hardy-Weinberg equilibrium in the studied population. The STR panel was able to discern individual dogs with a high degree of accuracy. Breed-wide genetic heterozygosity comparisons based on present and published allele frequencies revealed that the studied population had the lower genetic heterozygosity than canine populations in America. Principal component analysis among Labrador Retriever population and other reference populations showed that the studied Labrador Retrievers were genetically close to the retriever breeds in America. Population genetic structure analyses among these canine breeds further revealed genetic differentiations between the studied Labrador Retriever population and other compared breeds. In conclusion, these STR loci had relatively high forensic values in Labrador Retriever population in China, which could be employed for individual identification and kinship testing.

Two decades of non-invasive genetic monitoring of the grey wolves recolonizing the Alps support very limited dog introgression

Potential hybridization between wolves and dogs has fueled the sensitive conservation and political debate underlying the recovery of the grey wolf throughout Europe. Here we provide the first genetic analysis of wolf-dog admixture in an area entirely recolonized, the northwestern Alps. As part of a long-term monitoring program, we performed genetic screening of thousands of non-invasive samples collected in Switzerland and adjacent territories since the return of the wolf in the mid-1990s. We identified a total of 115 individuals, only 2 of them showing significant signs of admixture stemming from past interbreeding with dogs, followed by backcrossing. This low rate of introgression (<2% accounting for all wolves ever detected over 1998–2017) parallels those from other European populations, especially in Western Europe (<7%). Despite potential hybridization with stray dogs, few founders and strong anthropogenic pressures, the genetic integrity of the Alpine population has remained intact throughout the entire recolonization process. In a context of widespread misinformation, this finding should reduce conflicts among the different actors involved and facilitate wolf conservation. Real-time genetic monitoring will be necessary to identify potential hybrids and support an effective management of this emblematic population.

Evaluating effective population size and genetic diversity of a declining kit fox population using contemporary and historical specimens

Loss of genetic diversity has serious conservation consequences (e.g., loss of adaptive potential, reduced population viability), but is difficult to evaluate without developing long-term, multigenerational datasets. Alternatively, historical samples can provide insights into changes in genetic diversity and effective population size (N e). Kit foxes (Vulpes macrotis) are a species of conservation concern across much of their range. In western Utah, kit fox abundance has declined precipitously from historical levels, causing concern about population persistence. We analyzed genetic samples from museum specimens and contemporary scats to evaluate temporal changes in (a) genetic diversity and (b) N e for kit foxes in western Utah, and (c) discuss our findings with respect to population risk and conservation. The N e of kit foxes in western Utah has decreased substantially. When compared to established conservation thresholds for N e (e.g., the 50/500 rule), observed levels suggest the population may be at risk of inbreeding depression and local extinction. In contrast, we found no significant decrease in genetic diversity associated with declining N e. We detected evidence of low levels of immigration into the population and suspect genetic diversity may have been maintained by this previously undescribed gene flow from adjacent populations. Low or intermittent immigration may serve to temper the potential short-term negative consequences of low N e. We recommend that kit fox conservation efforts focus on evaluating and maintaining landscape connectivity. We demonstrate how historical specimens can provide a baseline of comparison for contemporary populations, highlighting the importance of natural history collections to conservation during a period of declining funding and support.

Estimating densities for sympatric kit foxes (Vulpes macrotis) and coyotes (Canis latrans) using noninvasive genetic sampling

Kit fox (Vulpes macrotis Merriam, 1888) populations in the Great Basin Desert have declined and are of increasing concern for managers. Increasing coyote (Canis latrans Say, 1823) abundance and subsequent intraguild interactions may be one cause for this decline. Concurrent monitoring of carnivores is challenging and therefore rarely conducted. One possible solution for monitoring elusive carnivores is using noninvasive genetic sampling. We used noninvasive genetic sampling to collect fecal DNA from kit foxes and coyotes and estimate their densities from 2013–2014 in Utah, USA. We identified individuals based on microsatellite genotypes and estimated density with multisession spatially explicit capture–recapture models. Mean kit fox density was 0.02 foxes·km−2, while coyote densities were up to four times greater (0.07–0.08 coyotes·km−2). Kit fox densities were significantly lower than densities in the 1950s but were comparable with estimates from the late 1990s, suggesting that populations may be stabilizing after a precipitous decline. Our kit fox density estimates were among the lowest documented for the species. Our coyote density estimate was the first reported in our region and revealed that despite seemingly high abundance, densities are low compared with other regions. Our results suggested that kit foxes may be able to coexist with coyotes.