Fine-scale genetic structure in Ethiopian wolves imposed by sociality, migration, and population bottlenecks

Long-term Small Population Size, Deleterious Variation, and Altitude Adaptation in the Ethiopian Wolf, a Severely Endangered Canid

Ethiopian wolves, a canid species endemic to the Ethiopian Highlands, have been steadily declining in numbers for decades. Currently, out of 35 extant species, it is now one of the world's most endangered canids. Most conservation efforts have focused on preventing disease, monitoring movements and behavior, and assessing the geographic ranges of sub-populations. Here, we add an essential layer by determining the Ethiopian wolf's demographic and evolutionary history using high-coverage (∼40×) whole-genome sequencing from 10 Ethiopian wolves from the Bale Mountains. We observe exceptionally low diversity and enrichment of weakly deleterious variants in the Ethiopian wolves in comparison with two North American gray wolf populations and four dog breeds. These patterns are consequences of long-term small population size, rather than recent inbreeding. We infer the demographic history of the Ethiopian wolf and find it to be concordant with historic records and previous genetic analyses, suggesting Ethiopian wolves experienced a series of both ancient and recent bottlenecks, resulting in a census population size of fewer than 500 individuals and an estimated effective population size of approximately 100 individuals. Additionally, long-term small population size may have limited the accumulation of strongly deleterious recessive mutations. Finally, as the Ethiopian wolves have inhabited high-altitude areas for thousands of years, we searched for evidence of high-altitude adaptation, finding evidence of positive selection at a transcription factor in a hypoxia-response pathway [CREB-binding protein (CREBBP)]. Our findings are pertinent to continuing conservation efforts and understanding how demography influences the persistence of deleterious variation in small populations.

Population genetic structures at multiple spatial scales: importance of social groups in European badgers

Population viability and metapopulation dynamics are strongly affected by gene flow. Identifying ecological correlates of genetic structure and gene flow in wild populations is therefore a major issue both in evolutionary ecology and species management. Studying the genetic structure of populations also enables identification of the spatial scale at which most gene flow occurs, hence the scale of the functional connectivity, which is of paramount importance for species ecology. In this study, we examined the genetic structure of a social, continuously distributed mammal, the European badger (Meles meles), both at large spatial scales (among populations) and fine (within populations) spatial scales. The study was carried out in 11 sites across France utilizing a noninvasive hair trapping protocol at 206 monitored setts. We identified 264 badgers genotyped at 24 microsatellite DNA loci. At the large scale, we observed high and significant genetic differentiation among populations (global Fst = 0.139; range of pairwise Fst [0.046–0.231]) that was not related to the geographic distance among sites, suggesting few large-scale dispersal events. Within populations, we detected a threshold value below which badgers were genetically close (< 400 m), highlighting that sociality is the major structuring process within badger populations at the fine scale.

Conservation implications for dingoes from the maternal and paternal genome: Multiple populations, dog introgression, and demography

It is increasingly common for apex predators to face a multitude of complex conservation issues. In Australia, dingoes are the mainland apex predator and play an important role in ecological functioning. Currently, however, they are threatened by hybridization with modern domestic dogs in the wild. As a consequence, we explore how increasing our understanding of the evolutionary history of dingoes can inform management and conservation decisions. Previous research on whole mitochondrial genome and nuclear data from five geographical populations showed evidence of two distinct lineages of dingo. Here, we present data from a broader survey of dingoes around Australia using both mitochondrial and Y chromosome markers and investigate the timing of demographic expansions. Biogeographic data corroborate the presence of at least two geographically subdivided genetic populations, southeastern and northwestern. Demographic modeling suggests that dingoes have undergone population expansion in the last 5,000 years. It is not clear whether this stems from expansion into vacant niches after the extinction of thylacines on the mainland or indicates the arrival date of dingoes. Male dispersal is much more common than female, evidenced by more diffuse Y haplogroup distributions. There is also evidence of likely historical male biased introgression from domestic dogs into dingoes, predominately within southeastern Australia. These findings have critical practical implications for the management and conservation of dingoes in Australia; particularly a focus must be placed upon the threatened southeastern dingo population.

The effect of relatedness and pack size on territory overlap in African wild dogs

BACKGROUND

Spacing patterns mediate competitive interactions between conspecifics, ultimately increasing fitness. The degree of territorial overlap between neighbouring African wild dog (Lycaon pictus) packs varies greatly, yet the role of factors potentially affecting the degree of overlap, such as relatedness and pack size, remain unclear. We used movement data from 21 wild dog packs to calculate the extent of territory overlap (20 dyads).

RESULTS

On average, unrelated neighbouring packs had low levels of overlap restricted to the peripheral regions of their 95% utilisation kernels. Related neighbours had significantly greater levels of peripheral overlap. Only one unrelated dyad included overlap between 75%-75% kernels, but no 50%-50% kernels overlapped. However, eight of 12 related dyads overlapped between their respective 75% kernels and six between the frequented 50% kernels. Overlap between these more frequented kernels confers a heightened likelihood of encounter, as the mean utilisation intensity per unit area within the 50% kernels was 4.93 times greater than in the 95% kernels, and 2.34 times greater than in the 75% kernels. Related packs spent significantly more time in their 95% kernel overlap zones than did unrelated packs. Pack size appeared to have little effect on overlap between related dyads, yet among unrelated neighbours larger packs tended to overlap more onto smaller packs' territories. However, the true effect is unclear given that the model's confidence intervals overlapped zero.

CONCLUSIONS

Evidence suggests that costly intraspecific aggression is greatly reduced between related packs. Consequently, the tendency for dispersing individuals to establish territories alongside relatives, where intensively utilised portions of ranges regularly overlap, may extend kin selection and inclusive fitness benefits from the intra-pack to inter-pack level. This natural spacing system can affect survival parameters and the carrying capacity of protected areas, having important management implications for intensively managed populations of this endangered species.

New insights on the history of canids in Oceania based on mitochondrial and nuclear data

How and when dingoes arrived in Oceania poses a fascinating question for scientists with interest in the historical movements of humans and dogs. The dingo holds a unique position as top terrestrial predator of Australia and exists in a wild state. In the first geographical survey of genetic diversity in the dingo using whole mitochondrial genomes, we analysed 16,428 bp in 25 individuals from five separate populations. We also investigated 13 nuclear loci to compare with the mitochondrial population history patterns. Phylogenetic analyses based upon mitochondrial DNA and nuclear DNA support the hypothesis that there are at least two distinct populations of dingo, one of which occurs in the northwest and the other in the southeast of the continent. Conservative molecular dating based upon mitochondrial DNA suggest that the lineages split approximately 8300 years before present, likely outside Australia but within Oceania. The close relationship between dingoes and New Guinea Singing Dogs suggests that plausibly dingoes spread into Australia via the land bridge between Papua New Guinea and Australia although seafaring introductions cannot be rejected. The geographical distribution of these divergent lineages suggests there were multiple independent dingo immigrations. Importantly, the observation of multiple dingo populations suggests the need for revision of existing conservation and management programs that treat dingoes as a single homogeneous population.

Novel Y-chromosome short tandem repeats in Sus scrofa and their variation in European wild boar and domestic pig populations

Y-chromosome markers are important tools for studying male-specific gene flow within and between populations, hybridization patterns and kinship. However, their use in non-human mammals is often hampered by the lack of Y-specific polymorphic markers. We identified new male-specific short tandem repeats (STRs) in Sus scrofa using the available genome sequence. We selected four polymorphic loci (5-10 alleles per locus), falling in one duplicated and two single-copy regions. A total of 32 haplotypes were found by screening 211 individuals from eight wild boar populations across Europe and five domestic pig populations. European wild boar were characterized by significantly higher levels of haplotype diversity compared to European domestic pigs (H_D  = 0.904 ± 0.011 and H_D  = 0.491 ± 0.077 respectively). Relationships among STR haplotypes were investigated by combining them with single nucleotide polymorphisms at two linked genes (AMELY and UTY) in a network analysis. A differentiation between wild and domestic populations was observed (F_ST  = 0.229), with commercial breeds sharing no Y haplotype with the sampled wild boar. Similarly, a certain degree of geographic differentiation was observed across Europe, with a number of local private haplotypes and high diversity in northern populations. The described Y-chromosome markers can be useful to track male inheritance and gene flow in wild and domestic populations, promising to provide insights into evolutionary and population genetics in Sus scrofa.

Canine distemper in endangered Ethiopian wolves

Investigation into mortalities within endangered species can direct conservation efforts.

The Ethiopian wolf (Canis simensis) is the world’s rarest canid; ≈500 wolves remain. The largest population is found within the Bale Mountains National Park (BMNP) in southeastern Ethiopia, where conservation efforts have demonstrated the negative effect of rabies virus on wolf populations. We describe previously unreported infections with canine distemper virus (CDV) among these wolves during 2005–2006 and 2010. Death rates ranged from 43% to 68% in affected subpopulations and were higher for subadult than adult wolves (83%–87% vs. 34%–39%). The 2010 CDV outbreak started 20 months after a rabies outbreak, before the population had fully recovered, and led to the eradication of several focal packs in BMNP’s Web Valley. The combined effect of rabies and CDV increases the chance of pack extinction, exacerbating the typically slow recovery of wolf populations, and represents a key extinction threat to populations of this highly endangered carnivore.

The socio-genetics of a complex society: female gelada relatedness patterns mirror association patterns in a multilevel society

Multilevel societies with fission-fusion dynamics--arguably the most complex animal societies--are defined by two or more nested levels of organization. The core of these societies are modular social units that regularly fission and fuse with one another. Despite convergent evolution in disparate taxa, we know strikingly little about how such societies form and how fitness benefits operate. Understanding the kinship structure of complex societies could inform us about the origins of the social structure as well as about the potential for individuals in these societies to accrue indirect fitness benefits. Here, we combined genetic and behavioural data on geladas (Theropithecus gelada), an Old World Monkey, to complete the most comprehensive socio-genetic analysis of a multilevel society to date. In geladas, individuals in the core social 'units', associate at different frequencies to form 'teams', 'bands' and, the largest aggregations, 'communities'. Units were composed of closely related females, and females remained with their close kin during permanent fissions of units. Interestingly, female-female relatedness also significantly predicted between-unit, between-team and between-band association patterns, while male-male relatedness did not. Thus, it is likely that the socio-genetic structure of gelada society results from females maintaining associations with their female relatives during successive unit fissions--possibly in an attempt to balance the direct and indirect fitness benefits of group living. Overall, the persistence of associations among related females across generations appears to drive the formation of higher levels of gelada society, suggesting that females seek kin for inclusive fitness benefits at multiple levels of gelada society.

Fine-scale spatial genetic structure of Dalbergia nigra (Fabaceae), a threatened and endemic tree of the Brazilian Atlantic Forest

The Atlantic Forest is one of the most diverse ecosystems in the world and considered a hotspot of biodiversity conservation. Dalbergia nigra (Fabaceae) is a tree endemic to the Brazilian Atlantic Forest, and has become threatened due to overexploitation of its valuable timber. In the present study, we analyzed the genetic diversity and fine-scale spatial genetic structure of D. nigra in an area of primary forest of a large reserve. All adult individuals (N = 112) were sampled in a 9.3 ha plot, and genotyped for microsatellite loci. Our results indicated high diversity with a mean of 8.6 alleles per locus, and expected heterozygosity equal to 0.74. The co-ancestry coefficients were significant for distances among trees up to 80 m. The Sp value was equal to 0.017 and indirect estimates of gene dispersal distances ranged from 89 to 144 m. No strong evidence of bottleneck or effects of human-disturbance was found. This study highlights that long-term efforts to protect a large area of Atlantic Forest have been effective towards maintaining the genetic diversity of D. nigra. The results of this study are important towards providing a guide for seed collection for ex-situ conservation and reforestation programmes of this threatened species.

Spatial and temporal patterns of neutral and adaptive genetic variation in the endangered African wild dog (Lycaon pictus)

Deciphering patterns of genetic variation within a species is essential for understanding population structure, local adaptation and differences in diversity between populations. Whilst neutrally evolving genetic markers can be used to elucidate demographic processes and genetic structure, they are not subject to selection and therefore are not informative about patterns of adaptive variation. As such, assessments of pertinent adaptive loci, such as the immunity genes of the major histocompatibility complex (MHC), are increasingly being incorporated into genetic studies. In this study, we combined neutral (microsatellite, mtDNA) and adaptive (MHC class II DLA-DRB1 locus) markers to elucidate the factors influencing patterns of genetic variation in the African wild dog (Lycaon pictus); an endangered canid that has suffered extensive declines in distribution and abundance. Our genetic analyses found all extant wild dog populations to be relatively small (N(e)  < 30). Furthermore, through coalescent modelling, we detected a genetic signature of a recent and substantial demographic decline, which correlates with human expansion, but contrasts with findings in some other African mammals. We found strong structuring of wild dog populations, indicating the negative influence of extensive habitat fragmentation and loss of gene flow between habitat patches. Across populations, we found that the spatial and temporal structure of microsatellite diversity and MHC diversity were correlated and strongly influenced by demographic stability and population size, indicating the effects of genetic drift in these small populations. Despite this correlation, we detected signatures of selection at the MHC, implying that selection has not been completely overwhelmed by genetic drift.

Major histocompatibility complex diversity in the endangered Ethiopian wolf (Canis simensis)

The major histocompatibility complex (MHC) influences immune response to infection and vaccination. In most species, MHC genes are highly polymorphic, but few wild canid populations have been investigated. In Ethiopian wolves, we identified four DLA (dog leucocyte antigen)-DRB1, two DLA-DQA1 and five DQB1 alleles. Ethiopian wolves, the world's rarest canids with fewer than 500 animals worldwide, are further endangered and threatened by rabies. Major rabies outbreaks in the Bale Mountains of southern Ethiopia (where over half of the Ethiopian wolf population is located) have killed over 75% of wolves in the affected sub-populations. In 2004, following a rabies outbreak, 77 wolves were vaccinated, and 19 were subsequently recaptured to monitor the effectiveness of the intervention. Pre- and post-vaccination rabies antibody titres were available for 18 animals, and all of the animals sero-converted after vaccination. We compared the haplotype frequencies of this group of 18 with the post-vaccination antibody titre, and showed that one haplotype was associated with a lower response (uncorrected P < 0.03). In general, Ethiopian wolves probably have an adequate amount of MHC variation to ensure the survival of the species. However, we sampled only the largest Ethiopian wolf population in Bale, and did not take the smaller populations further north into consideration.