Social network analysis of mating patterns in American black bears (Ursus americanus)

Community structure of the solitary giant pandas is maintained by indirect social connections

BACKGROUND

Indirect interactions between individual solitary mammals, such as the giant panda, are often overlooked because of their nature, yet are important for maintaining the necessary sociality in solitary species.

METHODS AND RESULTS

Here, we determined the genetic identity of all giant panda individuals in a local population and matched these identities with their associations to determine social network of this solitary animal. Total thirty-five giant panda individuals were found in our field survey, and we constructed genetic and social networks for thirty-three individuals who successfully obtained genetic, age and sex information. The results showed that sex had great impact on both social network and genetic network, and age may have the potential to influence the social network of the giant pandas. Adult males, mostly in the central of the social network, which appeared significantly larger network connections than adult females. Due to the female-biased dispersal pattern of wild giant pandas, male-male pairs showed higher relatedness than female-female ones and multi-generational patrilinear assemblages are expected in the study area.

CONCLUSIONS

The relatedness of individuals has an influence on the formation of community social structure of giant pandas, and indirect interactions among solitary giant pandas potentially function to reduce competition for resources and inbreeding.

Harvest is associated with the disruption of social and fine-scale genetic structure among matrilines of a solitary large carnivore

Harvest can disrupt wildlife populations by removing adults with naturally high survival. This can reshape sociospatial structure, genetic composition, fitness, and potentially affect evolution. Genetic tools can detect changes in local, fine-scale genetic structure (FGS) and assess the interplay between harvest-caused social and FGS in populations. We used data on 1614 brown bears, Ursus arctos, genotyped with 16 microsatellites, to investigate whether harvest intensity (mean low: 0.13 from 1990 to 2005, mean high: 0.28 from 2006 to 2011) caused changes in FGS among matrilines (8 matrilines; 109 females ≥4 years of age), sex-specific survival and putative dispersal distances, female spatial genetic autocorrelation, matriline persistence, and male mating patterns. Increased harvest decreased FGS of matrilines. Female dispersal distances decreased, and male reproductive success was redistributed more evenly. Adult males had lower survival during high harvest, suggesting that higher male turnover caused this redistribution and helped explain decreased structure among matrilines, despite shorter female dispersal distances. Adult female survival and survival probability of both mother and daughter were lower during high harvest, indicating that matriline persistence was also lower. Our findings indicate a crucial role of regulated harvest in shaping populations, decreasing differences among "groups," even for solitary-living species, and potentially altering the evolutionary trajectory of wild populations.

Dynamic shifts in social network structure and composition within a breeding hybrid population

Mating behaviour and the timing of reproduction can inhibit genetic exchange between closely related species; however, these reproductive barriers are challenging to measure within natural populations. Social network analysis provides promising tools for studying the social context of hybridization, and the exchange of genetic variation, more generally. We test how social networks within a hybrid population of California Callipepla californica and Gambel's quail Callipepla gambelii change over discrete periods of a breeding season. We assess patterns of phenotypic and genotypic assortment, and ask whether altered associations between individuals (association rewiring), or changes to the composition of the population (individual turnover) drive network dynamics. We use genetic data to test whether social associations and relatedness between individuals correlate with patterns of parentage within the hybrid population. To achieve these aims, we combine RFID association data, phenotypic data and genomic measures with social network analyses. We adopt methods from the ecological network literature to quantify shifts in network structure and to partition changes into those due to individual turnover and association rewiring. We integrate genomic data into networks as node-level attributes (ancestry) and edges (relatedness, parentage) to test links between social and parentage networks. We show that rewiring of associations between individuals that persist across network periods, rather than individual turnover, drives the majority of the changes in network structure throughout the breeding season, and that the traits involved in phenotypic/genotypic assortment were highly dynamic over time. Social networks were randomly assorted based on genetic ancestry, suggesting weak behavioural reproductive isolation within this hybrid population. Finally, we show that the strength of associations within the social network, but not levels of genetic relatedness, predicts patterns of parentage. Social networks play an important role in population processes such as the transmission of disease and information, yet there has been less focus on how networks influence the exchange of genetic variation. By integrating analyses of social structure, phenotypic assortment and reproductive outcomes within a hybrid zone, we demonstrate the utility of social networks for analysing links between social context and gene flow within wild populations.

Incidence of Multiple Paternity and Inbreeding in High-Density Brown Bear Populations on the Shiretoko Peninsula, Hokkaido, Japan

Understanding the breeding ecology of a species is essential for the appropriate conservation and management of wildlife. In brown bears, females occasionally copulate with multiple males in one breeding season, which may lead to multiple paternity in a single litter. In contrast, inbreeding, a potential factor in the reduction of genetic diversity, may occur, particularly in threatened populations. However, few studies have reported the frequency of these phenomena in brown bear populations. Here, we investigated the incidence of multiple paternity and inbreeding in a high-density brown bear population on the Shiretoko Peninsula in Hokkaido, Japan. A total of 837 individuals collected from 1998 to 2017 were genotyped at 21 microsatellite loci, and parentage analysis was performed. Out of 70-82 litters with ≥2 offspring, 14.6-17.1% of litters were sired by multiple males. This was comparable to the rate reported in a Scandinavian population, although population density and litter size, factors that potentially affect the incidence of multiple paternity, differed between the 2 populations. Out of 222 mother-father mating pairs, 6 litters (2.7%) resulted from matings between fathers and daughters. Additionally, 1 (0.5%) and 4 (1.8%) cases of mating between maternal half-siblings and between paternal half-siblings, respectively, were observed; however, no cases of mating between mothers and sons or between full siblings were observed. Our results suggest that male-biased natal dispersal effectively limits mating between closely related individuals (aside from fathers and daughters) in brown bears.

Accounting for Age Structure and Spatial Structure in Eco-Evolutionary Analyses of a Large, Mobile Vertebrate

The idealized concept of a population is integral to ecology, evolutionary biology, and natural resource management. To make analyses tractable, most models adopt simplifying assumptions, which almost inevitably are violated by real species in nature. Here, we focus on both demographic and genetic estimates of effective population size per generation (Ne), the effective number of breeders per year (Nb), and Wright's neighborhood size (NS) for black bears (Ursus americanus) that are continuously distributed in the northern lower peninsula of Michigan, United States. We illustrate practical application of recently developed methods to account for violations of 2 common, simplifying assumptions about populations: 1) reproduction occurs in discrete generations and 2) mating occurs randomly among all individuals. We use a 9-year harvest dataset of >3300 individuals, together with genetic determination of 221 parent-offspring pairs, to estimate male and female vital rates, including age-specific survival, age-specific fecundity, and age-specific variance in fecundity (for which empirical data are rare). We find strong evidence for overdispersed variance in reproductive success of same-age individuals in both sexes, and we show that constraints on litter size have a strong influence on results. We also estimate that another life-history trait that is often ignored (skip breeding by females) has a relatively modest influence, reducing Nb by 9% and increasing Ne by 3%. We conclude that isolation by distance depresses genetic estimates of Nb, which implicitly assume a randomly mating population. Estimated demographic NS (100, based on parent-offspring dispersal) was similar to genetic NS (85, based on regression of genetic distance and geographic distance), indicating that the >36000 km2 study area includes about 4-5 black-bear neighborhoods. Results from this expansive data set provide important insight into effects of violating assumptions when estimating evolutionary parameters for long-lived, free-ranging species. In conjunction with recently developed analytical methodology, the ready availability of nonlethal DNA sampling methods and the ability to rapidly and cheaply survey many thousands of molecular markers should facilitate eco-evolutionary studies like this for many more species in nature.

Using Networks to Connect Individual-Level Reproductive Behavior to Population Patterns

We propose an application of network analysis to determine which traits and behaviors predict fertilizations within and between populations. This approach quantifies how reproductive behavior between individuals shapes patterns of selection and gene flow, filling an important gap in our understanding of the connection between evolutionary processes and emergent patterns.

Assessing Behavioral Associations in a Hybrid Zone through Social Network Analysis: Complex Assortative Behaviors Structure Associations in a Hybrid Quail Population

Behavior can strongly influence rates and patterns of hybridization between animal populations and species. Yet few studies have examined reproductive behaviors in natural hybrid zones within the fine-scale social context in which they naturally occur. We use radio-frequency identification tags with social network analyses to test whether phenotypic similarity in plumage and mass correlate with social behavior throughout a breeding season in a California and Gambel's quail hybrid zone. We use a novel approach to partition phenotypic variation in a way that does not confound differences between sexes and species, and we illustrate the complex ways that phenotype and behavior structure the social environment, mating opportunities, and male-male associations. Associations within the admixed population were random with respect to species-specific plumage but showed strong patterns of assortment based on sexually dimorphic plumage, monomorphic plumage, and mass. Weak behavioral reproductive isolation in this admixed population may be the result of complex patterns of phenotypic assortment based on multiple traits rather than a lack of phenotypic discrimination. More generally, our results support the utility of social network analyses for analyzing behavioral factors affecting genetic exchange between populations and species.

Spatial genetic patterns indicate mechanism and consequences of large carnivore cohabitation within development

Patterns of human development are shifting from concentrated housing toward sprawled housing intermixed with natural land cover, and wildlife species increasingly persist in close proximity to housing, roads, and other anthropogenic features. These associations can alter population dynamics and evolutionary trajectories. Large carnivores increasingly occupy urban peripheries, yet the ecological consequences for populations established entirely within urban and exurban landscapes are largely unknown. We applied a spatial and landscape genetics approach, using noninvasively collected genetic data, to identify differences in black bear spatial genetic patterns across a rural‐to‐urban gradient and quantify how development affects spatial genetic processes. We quantified differences in black bear dispersal, spatial genetic structure, and migration between differing levels of development within a population primarily occupying areas with >6 houses/km² in western Connecticut. Increased development disrupted spatial genetic structure, and we found an association between increased housing densities and longer dispersal. We also found evidence that roads limited gene flow among bears in more rural areas, yet had no effect among bears in more developed ones. These results suggest dispersal behavior is condition‐dependent and indicate the potential for landscapes intermixing development and natural land cover to facilitate shifts toward increased dispersal. These changes can affect patterns of range expansion and the phenotypic and genetic composition of surrounding populations. We found evidence that subpopulations occupying more developed landscapes may be sustained by male‐biased immigration, creating potentially detrimental demographic shifts.

Spatial genetic structure in American black bears (Ursus americanus): female philopatry is variable and related to population history

Previously, American black bears (Ursus americanus) were thought to follow the pattern of female philopatry and male-biased dispersal. However, recent studies have identified deviations from this pattern. Such flexibility in dispersal patterns can allow individuals greater ability to acclimate to changing environments. We explored dispersal and spatial genetic relatedness patterns across ten black bear populations-including long established (historic), with known reproduction >50 years ago, and newly established (recent) populations, with reproduction recorded <50 years ago-in the Interior Highlands and Southern Appalachian Mountains, United States. We used spatially explicit, individual-based genetic simulations to model gene flow under scenarios with varying levels of population density, genetic diversity, and female philopatry. Using measures of genetic distance and spatial autocorrelation, we compared metrics between sexes, between population types (historic and recent), and among simulated scenarios which varied in density, genetic diversity, and sex-biased philopatry. In empirical populations, females in recent populations exhibited stronger patterns of isolation-by-distance (IBD) than females and males in historic populations. In simulated populations, low-density populations had a stronger indication of IBD than medium- to high-density populations; however, this effect varied in empirical populations. Condition-dependent dispersal strategies may permit species to cope with novel conditions and rapidly expand populations. Pattern-process modeling can provide qualitative and quantitative means to explore variable dispersal patterns, and could be employed in other species, particularly to anticipate range shifts in response to changing climate and habitat conditions.

Detecting black bear source-sink dynamics using individual-based genetic graphs

Source-sink dynamics affects population connectivity, spatial genetic structure and population viability for many species. We introduce a novel approach that uses individual-based genetic graphs to identify source-sink areas within a continuously distributed population of black bears (Ursus americanus) in the northern lower peninsula (NLP) of Michigan, USA. Black bear harvest samples (n = 569, from 2002, 2006 and 2010) were genotyped at 12 microsatellite loci and locations were compared across years to identify areas of consistent occupancy over time. We compared graph metrics estimated for a genetic model with metrics from 10 ecological models to identify ecological factors that were associated with sources and sinks. We identified 62 source nodes, 16 of which represent important source areas (net flux > 0.7) and 79 sink nodes. Source strength was significantly correlated with bear local harvest density (a proxy for bear density) and habitat suitability. Additionally, resampling simulations showed our approach is robust to potential sampling bias from uneven sample dispersion. Findings demonstrate black bears in the NLP exhibit asymmetric gene flow, and individual-based genetic graphs can characterize source-sink dynamics in continuously distributed species in the absence of discrete habitat patches. Our findings warrant consideration of undetected source-sink dynamics and their implications on harvest management of game species.

Demographic mechanisms underpinning genetic assimilation of remnant groups of a large carnivore

Current range expansions of large terrestrial carnivores are occurring following human-induced range contraction. Contractions are often incomplete, leaving small remnant groups in refugia throughout the former range. Little is known about the underlying ecological and evolutionary processes that influence how remnant groups are affected during range expansion. We used data from a spatially explicit, long-term genetic sampling effort of grizzly bears (Ursus arctos) in the Northern Continental Divide Ecosystem (NCDE), USA, to identify the demographic processes underlying spatial and temporal patterns of genetic diversity. We conducted parentage analysis to evaluate how reproductive success and dispersal contribute to spatio-temporal patterns of genetic diversity in remnant groups of grizzly bears existing in the southwestern (SW), southeastern (SE) and east-central (EC) regions of the NCDE. A few reproductively dominant individuals and local inbreeding caused low genetic diversity in peripheral regions that may have persisted for multiple generations before eroding rapidly (approx. one generation) during population expansion. Our results highlight that individual-level genetic and reproductive dynamics play critical roles during genetic assimilation, and show that spatial patterns of genetic diversity on the leading edge of an expansion may result from historical demographic patterns that are highly ephemeral.