Deriving dispersal distances from genetic data

Timing and distance of natal dispersal in Asian black bears

Dispersal has important implications for population ecology and genetics of a species through redistribution of individuals. In most mammals, males leave their natal area before they reach sexual maturity, whereas females are commonly philopatric. Here, we investigate the patterns of natal dispersal in the Asian black bear (Ursus thibetanus) based on data from 550 bears (378 males, 172 females) captured or removed in Gunma and Tochigi prefectures on central Honshu Island, Japan in 2003–2018. We used genetic data and parentage analysis to investigate sex-biased differences in the distance of natal dispersal. We further investigated the age of dispersal using spatial autocorrelation analysis, that is, the change in the correlation between genetic and geographic distances in each sex and age group. Our results revealed that male dispersal distances (mean ± SE = 17.4 ± 3.5 km) were significantly farther than female distances (4.8 ± 1.7 km), and the results were not affected by years of mast failures, a prominent forage source for this population. Based on an average adult female home range radius of 1.8 km, 96% of the males and 50% of the females dispersed. In the spatial autocorrelation analysis, the changes in the relationship between genetic and geographic distances were more pronounced in males compared to females. Males seem to mostly disperse at age 3 regardless of mast productivity, and they gradually disperse far from their home range, but young and inexperienced males may return to their natal home range in years with poor food conditions. The results suggest that factors driving the dispersal process seem to be population structure-based instead of forage availability-based. In females, a significant genetic relationship was observed among all individuals in the group with a minimum age of 6 years within a distance of 2 km, which resulted in the formation of matrilineal assemblages.

Whole genome sequencing and the application of a SNP panel reveal primary evolutionary lineages and genomic variation in the lion (Panthera leo)

Background

Previous phylogeographic studies of the lion (Panthera leo) have improved our insight into the distribution of genetic variation, as well as a revised taxonomy which now recognizes a northern (Panthera leo leo) and a southern (Panthera leo melanochaita) subspecies. However, existing whole range phylogeographic studies on lions either consist of very limited numbers of samples, or are focused on mitochondrial DNA and/or a limited set of microsatellites. The geographic extent of genetic lineages and their phylogenetic relationships remain uncertain, clouded by massive sampling gaps, sex-biased dispersal and incomplete lineage sorting.

Results

In this study we present results of low depth whole genome sequencing and subsequent variant calling in ten lions sampled throughout the geographic range, resulting in the discovery of >150,000 Single Nucleotide Polymorphisms (SNPs). Phylogenetic analyses revealed the same basal split between northern and southern populations, as well as four population clusters on a more local scale. Further, we designed a SNP panel, including 125 autosomal and 14 mitochondrial SNPs, which was tested on >200 lions from across their range. Results allow us to assign individuals to one of these four major clades (West & Central Africa, India, East Africa, or Southern Africa) and delineate these clades in more detail.

Conclusions

The results presented here, particularly the validated SNP panel, have important applications, not only for studying populations on a local geographic scale, but also for tracing samples of unknown origin for forensic purposes, and for guiding conservation management of ex situ populations. Thus, these genomic resources not only contribute to our understanding of the evolutionary history of the lion, but may also play a crucial role in conservation efforts aimed at protecting the species in its full diversity.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08510-y.

Spatiotemporal Genetic Diversity of Lions Reveals the Influence of Habitat Fragmentation across Africa

Direct comparisons between historical and contemporary populations allow for detecting changes in genetic diversity through time and assessment of the impact of habitat fragmentation. Here, we determined the genetic architecture of both historical and modern lions to document changes in genetic diversity over the last century. We surveyed microsatellite and mitochondrial genome variation from 143 high-quality museum specimens of known provenance, allowing us to directly compare this information with data from several recently published nuclear and mitochondrial studies. Our results provide evidence for male-mediated gene flow and recent isolation of local subpopulations, likely due to habitat fragmentation. Nuclear markers showed a significant decrease in genetic diversity from the historical (HE = 0.833) to the modern (HE = 0.796) populations, whereas mitochondrial genetic diversity was maintained (Hd = 0.98 for both). Although the historical population appears to have been panmictic based on nDNA data, hierarchical structure analysis identified four tiers of genetic structure in modern populations and was able to detect most sampling locations. Mitogenome analyses identified four clusters: Southern, Mixed, Eastern, and Western and were consistent between modern and historically sampled haplotypes. Within the last century, habitat fragmentation caused lion subpopulations to become more geographically isolated as human expansion changed the African landscape. This resulted in an increase in fine-scale nuclear genetic structure and loss of genetic diversity as lion subpopulations became more differentiated, whereas mitochondrial structure and diversity were maintained over time.

Population Genomics of Nymphon australe Hodgson, 1902 (Pycnogonida, Nymphonidae) in the Western Antarctic

Within the Southern Ocean, the Antarctic Circumpolar Current is hypothesized to facilitate a circumpolar distribution for many taxa, even though some, such as pycnogonids, are assumed to have limited ability to disperse, based on brooding life histories and adult ambulatory capabilities. With a number of contradictions to circumpolarity reported in the literature for other pycnogonids, alternative hypotheses have been explored, particularly for Nymphon australe, the most common species of Pycnogonida (sea spider) in the Southern Ocean. Glacial events have been hypothesized to impact the capacity of organisms to colonize suitable areas without ice coverage as refuge and without the eurybathic capacity to colonize deeper areas. In this study, we examine populations of one presumed circumpolar species, the pycnogonid N. australe, from throughout the Western Antarctic, using a 2b-RAD approach to detect genetic variation with single-nucleotide polymorphisms. Using this approach, we found that N. australe included two distinct groups from within >5000-km sampling region. By using a discriminant analysis of principle components, sparse nonnegative matrix factorization, and admixture coefficient analysis, two distinctive populations were revealed in the Western Antarctic: one covered distances greater than 5000 km (Weddell, Western Antarctic Peninsula, and Ross Sea), and the other shared limited connectivity entrained within the Amundsen Sea. Under further scrutiny of the 3086 single-nucleotide polymorphisms in the data set, only 78 loci had alignment stacks between the two populations. We propose that the populations analyzed are divergent enough to constitute two different species from within this common Antarctic genus known for its phenotypic plasticity.

Genetic insights into dispersal distance and disperser fitness of African lions (Panthera leo) from the latitudinal extremes of the Kruger National Park, South Africa

Background

Female lions generally do not disperse far beyond their natal range, while males can disperse distances of over 200 km. However, in bush-like ecosystems dispersal distances less than 25 km are reported. Here, we investigate dispersal in lions sampled from the northern and southern extremes of Kruger National Park, a bush-like ecosystem in South Africa where bovine tuberculosis prevalence ranges from low to high across a north-south gradient.

Results

A total of 109 individuals sampled from 1998 to 2004 were typed using 11 microsatellite markers, and mitochondrial RS-3 gene sequences were generated for 28 of these individuals. Considerable north-south genetic differentiation was observed in both datasets. Dispersal was male-biased and generally further than 25 km, with long-distance male gene flow (75–200 km, detected for two individuals) confirming that male lions can travel large distances, even in bush-like ecosystems. In contrast, females generally did not disperse further than 20 km, with two distinctive RS-3 gene clusters for northern and southern females indicating no or rare long-distance female dispersal. However, dispersal rate for the predominantly non-territorial females from southern Kruger (fraction dispersers ≥0.68) was higher than previously reported. Of relevance was the below-average body condition of dispersers and their low presence in prides, suggesting low fitness.

Conclusions

Large genetic differences between the two sampling localities, and low relatedness among males and high dispersal rates among females in the south, suggestive of unstable territory structure and high pride turnover, have potential implications for spread of diseases and the management of the Kruger lion population.

Electronic supplementary material

The online version of this article (10.1186/s12863-018-0607-x) contains supplementary material, which is available to authorized users.

Reduced Genetic Diversity and Increased Dispersal in Guigna (Leopardus guigna) in Chilean Fragmented Landscapes

Landscape fragmentation is often a major cause of species extinction as it can affect a wide variety of ecological processes. The impact of fragmentation varies among species depending on many factors, including their life-history traits and dispersal abilities. Felids are one of the groups most threatened by fragmented landscapes because of their large home ranges, territorial behavior, and low population densities. Here, we model the impacts of habitat fragmentation on patterns of genetic diversity in the guigna (Leopardus guigna), a small felid that is closely associated with the heavily human-impacted temperate rainforests of southern South America. We assessed genetic variation in 1798 base pairs of mitochondrial DNA sequences, 15 microsatellite loci, and 2 sex chromosome genes and estimated genetic diversity, kinship, inbreeding, and dispersal in 38 individuals from landscapes with differing degrees of fragmentation on Chiloé Island in southern Chile. Increased fragmentation was associated with reduced genetic diversity, but not with increased kinship or inbreeding. However, in fragmented landscapes, there was a weaker negative correlation between pairwise kinship and geographic distance, suggesting increased dispersal distances. These results highlight the importance of biological corridors to maximize connectivity in fragmented landscapes and contribute to our understanding of the broader genetic consequences of habitat fragmentation, especially for forest-specialist carnivores.

Single nucleotide polymorphism-based dispersal estimates using noninvasive sampling

Quantifying dispersal within wild populations is an important but challenging task. Here we present a method to estimate contemporary, individual-based dispersal distance from noninvasively collected samples using a specialized panel of 96 SNPs (single nucleotide polymorphisms). One main issue in conducting dispersal studies is the requirement for a high sampling resolution at a geographic scale appropriate for capturing the majority of dispersal events. In this study, fecal samples of brown bear (Ursus arctos) were collected by volunteer citizens, resulting in a high sampling resolution spanning over 45,000 km² in Gävleborg and Dalarna counties in Sweden. SNP genotypes were obtained for unique individuals sampled (n = 433) and subsequently used to reconstruct pedigrees. A Mantel test for isolation by distance suggests that the sampling scale was appropriate for females but not for males, which are known to disperse long distances. Euclidean distance was estimated between mother and offspring pairs identified through the reconstructed pedigrees. The mean dispersal distance was 12.9 km (SE 3.2) and 33.8 km (SE 6.8) for females and males, respectively. These results were significantly different (Wilcoxon’s rank-sum test: P-value = 0.02) and are in agreement with the previously identified pattern of male-biased dispersal. Our results illustrate the potential of using a combination of noninvasively collected samples at high resolution and specialized SNPs for pedigree-based dispersal models.

Evaluation of microsatellite markers for populations studies and forensic identification of African lions (Panthera leo)

The South African lion (Panthera leo) population is highly fragmented. One-third of its wild lions occur in small (<1000 km(2)) reserves. These lions were reintroduced from other areas of the species' historical range. Management practices on these reserves have not prioritized genetic provenance or heterozygosity. These trends potentially constrain the conservation value of these lions. To ensure the best management and long-term survival of these subpopulations as a viable collective population, the provenance and current genetic diversity must be described. Concurrently, poaching of lions to supply a growing market for lion bones in Asia may become a serious conservation challenge in the future. Having a standardized, validated method for matching confiscated lion parts with carcasses will be a key tool in investigating these crimes. We evaluated 28 microsatellites in the African lion using samples from 18 small reserves and 1 captive facility in South Africa, two conservancies in Zimbabwe, and Kruger National and Kgalagadi Transfrontier Parks to determine the loci most suited for population management and forensic genetic applications. Twelve microsatellite loci with a match probability of 1.1×10(-5) between siblings were identified for forensics. A further 10 could be added for population genetics studies.

Dual phylogenetic origins of Nigerian lions (Panthera leo)

Lion fecal DNA extracts from four individuals each from Yankari Game Reserve and Kainji-Lake National Park (central northeast and west Nigeria, respectively) were Sanger-sequenced for the mitochondrial cytochrome b gene. The sequences were aligned against 61 lion reference sequences from other parts of Africa and India. The sequence data were analyzed further for the construction of phylogenetic trees using the maximum-likelihood approach to depict phylogenetic patterns of distribution among sequences. Our results show that Nigerian lions grouped together with lions from West and Central Africa. At the smaller geographical scale, lions from Kainji-Lake National Park in western Nigeria grouped with lions from Benin (located west of Nigeria), whereas lions from Yankari Game Reserve in central northeastern Nigeria grouped with the lion populations in Cameroon (located east of Nigeria). The finding that the two remaining lion populations in Nigeria have different phylogenetic origins is an important aspect to consider in future decisions regarding management and conservation of rapidly shrinking lion populations in West Africa.

Individual identification and genetic variation of lions (Panthera leo) from two protected areas in Nigeria

This survey was conducted in two protected areas in Nigeria to genetically identify individual lions and to determine the genetic variation within and between the populations. We used faecal sample DNA, a non-invasive alternative to the risky and laborious task of taking samples directly from the animals, often preceded by catching and immobilization. Data collection in Yankari Game Reserve (YGR) spanned through a period of five years (2008 -2012), whereas data in Kainji Lake National Park (KLNP) was gathered for a period of three years (2009, 2010 and 2012). We identified a minimum of eight individuals (2 males, 3 females, 3 unknown) from YGR and a minimum of ten individuals (7 males, 3 females) from KLNP. The two populations were found to be genetically distinct as shown by the relatively high fixation index (FST  = 0.17) with each population exhibiting signs of inbreeding (YGR FIS  = 0.49, KLNP FIS  = 0.38). The genetic differentiation between the Yankari and Kainji lions is assumed to result from large spatial geographic distance and physical barriers reducing gene flow between these two remaining wild lion populations in Nigeria. To mitigate the probable inbreeding depression in the lion populations within Nigeria it might be important to transfer lions between parks or reserves or to reintroduce lions from the zoos back to the wild.

Genetic structure, spatial organization, and dispersal in two populations of bat-eared foxes

We incorporated radio-telemetry data with genetic analysis of bat-eared foxes (Otocyon megalotis) from individuals in 32 different groups to examine relatedness and spatial organization in two populations in South Africa that differed in density, home-range sizes, and group sizes. Kin clustering occurred only for female dyads in the high-density population. Relatedness was negatively correlated with distance only for female dyads in the high-density population, and for male and mixed-sex dyads in the low-density population. Home-range overlap of neighboring female dyads was significantly greater in the high compared to low-density population, whereas overlap within other dyads was similar between populations. Amount of home-range overlap between neighbors was positively correlated with genetic relatedness for all dyad-site combinations, except for female and male dyads in the low-density population. Foxes from all age and sex classes dispersed, although females (mostly adults) dispersed farther than males. Yearlings dispersed later in the high-density population, and overall exhibited a male-biased dispersal pattern. Our results indicated that genetic structure within populations of bat-eared foxes was sex-biased, and was interrelated to density and group sizes, as well as sex-biases in philopatry and dispersal distances. We conclude that a combination of male-biased dispersal rates, adult dispersals, and sex-biased dispersal distances likely helped to facilitate inbreeding avoidance in this evolutionarily unique species of Canidae.

Using population genetic tools to develop a control strategy for feral cats (Felis catus) in Hawai'i

Population genetics can provide information about the demographics and dynamics of invasive species that is beneficial for developing effective control strategies. We studied the population genetics of feral cats on Hawai‘i Island by microsatellite analysis to evaluate genetic diversity and population structure, assess gene flow and connectivity among three populations, identify potential source populations, characterise population dynamics, and evaluate sex-biased dispersal. High genetic diversity, low structure, and high number of migrants per generation supported high gene flow that was not limited spatially. Migration rates revealed that most migration occurred out of West Mauna Kea. Effective population size estimates indicated increasing cat populations despite control efforts. Despite high gene flow, relatedness estimates declined significantly with increased geographic distance and Bayesian assignment tests revealed the presence of three population clusters. Genetic structure and relatedness estimates indicated male-biased dispersal, primarily from Mauna Kea, suggesting that this population should be targeted for control. However, recolonisation seems likely, given the great dispersal ability that may not be inhibited by barriers such as lava flows. Genetic monitoring will be necessary to assess the effectiveness of future control efforts. Management of other invasive species may benefit by employing these population genetic tools.

Compatible genetic and ecological estimates of dispersal rates in insect (Coenagrion mercuriale: Odonata: Zygoptera) populations: analysis of ‘neighbourhood size’ using a more precise estimator

Genetic and demographic estimates of dispersal are often thought to be inconsistent. In this study, we use the damselfly Coenagrion mercuriale (Odonata: Zygoptera) as a model to evaluate directly the relationship between estimates of dispersal rate measured during capture-mark-recapture fieldwork with those made from the spatial pattern of genetic markers in linear and two-dimensional habitats. We estimate the 'neighbourhood size' (Nb) - the product of the mean axial dispersal rate between parent and offspring and the population density - by a previously described technique, here called the regression method. Because C. mercuriale is less philopatric than species investigated previously by the regression method we evaluate a refined estimator that may be more applicable for relatively mobile species. Results from simulations and empirical data sets reveal that the new estimator performs better under most situations, except when dispersal is very localized relative to population density. Analysis of the C. mercuriale data extends previous results which demonstrated that demographic and genetic estimates of Nb by the regression method are equivalent to within a factor of two at local scales where genetic estimates are less affected by habitat heterogeneity, stochastic processes and/or differential selective regimes. The corollary is that with a little insight into a species' ecology the pattern of spatial genetic structure provides quantitative information on dispersal rates and/or population densities that has real value for conservation management.

Genetics of recent habitat contraction and reduction in population size: does isolation by distance matter?

Fragmentation and loss of natural habitats are recognized as major threats to contemporary flora and fauna. Detecting past or current reductions in population size is therefore a major aim in conservation genetics. Statistical methods developed to this purpose have tended to ignore the effects of spatial population structure. However in many species, individual dispersal is restricted in space and fine-scale spatial structure such as isolation by distance (IBD) is commonly observed in continuous populations. Using a simulation-based approach, we investigated how comparative and single-point methods, traditionally used in a Wright-Fisher (WF) population context for detecting population size reduction, behave for IBD populations. We found that a complex 'quartet' of factors was acting that includes restricted dispersal, population size (i.e. habitat size), demographic history, and sampling scale. After habitat reduction, IBD populations were characterized by a stronger inertia in the loss of genetic diversity than WF populations. This inertia increases with the strength of IBD, and decreases when the sampling scale increases. Depending on the method used to detect a population size reduction, a local sampling can be more informative than a sample scaled to habitat size or vice versa. However, IBD structure led in numerous cases to incorrect inferences on population demographic history. The reanalysis of a real microsatellite data set of skink populations from fragmented and intact rainforest habitats confirmed most of our simulation results.

Natal dispersal and parental escorting predict relatedness between mates in a passerine bird

Although relatedness between mates is of considerable evolutionary and ecological significance, the way in which the level of relatedness is determined by different behavioural processes remains largely unknown. We investigated the role of behaviour in predicting mate relatedness in great tits using genotypic markers and detailed observations. We studied how mate relatedness is influenced by natal dispersal, inbreeding/outbreeding avoidance after natal dispersal and a behaviour not previously considered that influences membership to social aggregations, namely family escorting behaviour by parents. Among locally born individuals, the level of mate relatedness decreased with natal dispersal distance for females, but not for males. In contrast, mate relatedness was negatively related to the extent of family movements for males, but not for females. However, family movements did not predict dispersal distance for either sex. Local recruits were more related to their mates than immigrants, but this was only significant for females. No evidence was found for inbreeding/outbreeding avoidance after dispersal. Our results suggest that, in highly mobile species, mating options are spatially and/or socially limited, and that parents influence mating options of their offspring before dispersal.

Gender-specific dispersal distances of grizzly bears estimated by genetic analysis

Natal dispersal is difficult to quantify, and long-distance events are often undetected, leading to biased estimates. Following offspring from their natal home range to their postdispersal adult breeding home range is challenging, and gathering sufficient data for large mammals with long generation times is particularly difficult. Here we measure average sex-specific dispersal distances in grizzly bears (Ursus arctos L., 1758) using individual-based genetic analysis. We genetically sampled and generated 15-locus microsatellite genotypes for 711 grizzly bears over a range of 100 000 km2in southwestern Canada. Microsatellite markers are inherited in a Mendelian fashion, allowing us to use likelihood-based parentage analyses to estimate parent–offspring dyads. We used the distance between individually captured females of parent–offspring pairs (i.e., mother–daughter) to estimate female natal dispersal distances and found that, on average, females dispersed 14.3 km from the center of their natal home range. We used the distance between males of parent–offspring pairs (i.e., father–son) to estimate average male dispersal distances and found that males dispersed, on average, 41.9 km from their natal, or maternal, home range (mother–son dispersal distance). We used a simulation model to estimate the bias associated with measuring the father–son (male–male) distance as an estimate of the mother–son distance.

Behavioural structuring of relatedness in the spotted hyena (Crocuta crocuta) suggests direct fitness benefits of clan-level cooperation

Spotted hyenas (Crocuta crocuta) are gregarious carnivores that live in multigenerational social groups, called clans, containing one to several matrilines. Members of multiple matrilines within a clan cooperate during dangerous interactions with inter- and intraspecific competitors. The evolution of cooperation may be influenced by relatedness between individuals, which in turn is influenced by reproductive skew and mate choice, dispersal and territorial behaviours. Behavioural data exist for spotted hyenas, but corresponding data on patterns of relatedness are unavailable; this lack of data makes it difficult to assess the relative importance of selection pressures favouring cooperative behaviour within and among groups. Therefore we conducted a longitudinal analysis of relatedness within a single large clan of spotted hyenas, as well as a cross-sectional analysis of relatedness among hyenas from multiple clans. Within a clan, patterns of relatedness reflected known pedigree relationships, and relatedness was higher within than among matrilines, even across generations. Although mean within-matriline relatedness varied among matrilines, it did not decline with matriline rank. On average, clan members were not related closely, due to high levels of male-mediated gene flow among clans, and relatedness declined very slightly across clan borders. Low mean relatedness within clans suggests that spotted hyenas cooperate with unrelated clan-mates against close paternal kin in other clans. Our data also suggest that spotted hyenas must derive large net direct fitness benefits from group living and cooperation.

Parentage assignment detects frequent and large-scale dispersal in water voles

Estimating the rate and scale of dispersal is essential for predicting the dynamics of fragmented populations, yet empirical estimates are typically imprecise and often negatively biased. We maximized detection of dispersal events between small, subdivided populations of water voles (Arvicola terrestris) using a novel method that combined direct capture-mark-recapture with microsatellite genotyping to identify parents and offspring in different populations and hence infer dispersal. We validated the method using individuals known from trapping data to have dispersed between populations. Local populations were linked by high rates of juvenile dispersal but much lower levels of adult dispersal. In the spring breeding population, 19% of females and 33% of males had left their natal population of the previous year. The average interpopulation dispersal distance was 1.8 km (range 0.3-5.2 km). Overall, patterns of dispersal fitted a negative exponential function. Information from genotyping increased the estimated rate and scale of dispersal by three- and twofold, respectively, and hence represents a powerful tool to provide more realistic estimates of dispersal parameters.

Kin selection in cooperative alliances of carrion crows

In most cooperative vertebrates, delayed natal dispersal is the mechanism that leads to the formation of kin societies. Under this condition, the possibility that kin-based cooperative breeding is an unselected consequence of dispersal patterns can never be ruled out because helpers can only help their relatives. Here we show that a population of carrion crows (Corvus corone corone) fully fits the central prediction of kin selection theory that cooperative breeding should arise among relatives. On their territory, resident breeders are aided not only by nonbreeding retained offspring but also by immigrants (mainly males), with whom they share matings. Philopatry cannot account, however, for the high degree of genetic relatedness found between breeders and immigrants of the same sex that cooperate at a nest, indicating that crows actively choose to breed cooperatively with their relatives.