The impact of mating systems and dispersal on fine-scale genetic structure at maternally, paternally and biparentally inherited markers

For decades, studies have focused on how dispersal and mating systems influence genetic structure across populations or social groups. However, we still lack a thorough understanding of how these processes and their interaction shape spatial genetic patterns over a finer scale (tens-hundreds of metres). Using uniparentally inherited markers may help answer these questions, yet their potential has not been fully explored. Here, we use individual-level simulations to investigate the effects of dispersal and mating system on fine-scale genetic structure at autosomal, mitochondrial and Y chromosome markers. Using genetic spatial autocorrelation analysis, we found that dispersal was the major driver of fine-scale genetic structure across maternally, paternally and biparentally inherited markers. However, when dispersal was restricted (mean distance = 100 m), variation in mating behaviour created strong differences in the comparative level of structure detected at maternally and paternally inherited markers. Promiscuity reduced spatial genetic structure at Y chromosome loci (relative to monogamy), whereas structure increased under polygyny. In contrast, mitochondrial and autosomal markers were robust to differences in the specific mating system, although genetic structure increased across all markers when reproductive success was skewed towards fewer individuals. Comparing males and females at Y chromosome vs. mitochondrial markers, respectively, revealed that some mating systems can generate similar patterns to those expected under sex-biased dispersal. This demonstrates the need for caution when inferring ecological and behavioural processes from genetic results. Comparing patterns between the sexes, across a range of marker types, may help us tease apart the processes shaping fine-scale genetic structure.

Genetic spatial autocorrelation can readily detect sex-biased dispersal

Sex-biased dispersal is expected to generate differences in the fine-scale genetic structure of males and females. Therefore, spatial analyses of multilocus genotypes may offer a powerful approach for detecting sex-biased dispersal in natural populations. However, the effects of sex-biased dispersal on fine-scale genetic structure have not been explored. We used simulations and multilocus spatial autocorrelation analysis to investigate how sex-biased dispersal influences fine-scale genetic structure. We evaluated three statistical tests for detecting sex-biased dispersal: bootstrap confidence intervals about autocorrelation r values and recently developed heterogeneity tests at the distance class and whole correlogram levels. Even modest sex bias in dispersal resulted in significantly different fine-scale spatial autocorrelation patterns between the sexes. This was particularly evident when dispersal was strongly restricted in the less-dispersing sex (mean distance <200 m), when differences between the sexes were readily detected over short distances. All tests had high power to detect sex-biased dispersal with large sample sizes (n ≥ 250). However, there was variation in type I error rates among the tests, for which we offer specific recommendations. We found congruence between simulation predictions and empirical data from the agile antechinus, a species that exhibits male-biased dispersal, confirming the power of individual-based genetic analysis to provide insights into asymmetries in male and female dispersal. Our key recommendations for using multilocus spatial autocorrelation analyses to test for sex-biased dispersal are: (i) maximize sample size, not locus number; (ii) concentrate sampling within the scale of positive structure; (iii) evaluate several distance class sizes; (iv) use appropriate methods when combining data from multiple populations; (v) compare the appropriate groups of individuals.

Natal dispersal and social organization of the swamp antechinus (Antechinus minimus) in a high-density island population

Radiotelemetry, mark–recapture trapping, and microsatellite analysis of genetic variation among three subpopulations were used to investigate the natal dispersal patterns, genetic structure, and social organization within a high-density island population of an insectivorous marsupial, the swamp antechinus ( Antechinus minimus (É. Geoffroy Saint-Hilaire, 1803)). Both demographic and genetic data indicated a high degree of philopatry for both sexes. Associated with high philopatry is low gene flow, often leading to high population genetic structuring. However, there was only weak evidence to support this; allele frequencies and genotype composition of one population tended to be different from the other two. Interestingly, timing of breeding of this subpopulation was delayed compared with the other two subpopulations. The philopatry of both sexes and the apparent lack of kin avoidance behaviour could lead to inbreeding. However, no apparent inbreeding effects were observed and offspring survival was high compared with mainland populations. The fact that male home-range size increased during the breeding season, overlapping with several females, and single females were found nesting with different males at the time of mating (and vice versa) indicates a promiscuous mating system. Potentially, this may reduce inbreeding to some extent. Alternatively, inbreeding may not be purposefully avoided, potentially leading to purging of detrimental alleles, thereby reducing their damaging effects on inbreeding.

Use of genetic methods to establish male-biased dispersal in a cryptic mammal, the swamp wallaby (Wallabia bicolor)

Mammalian dispersal tends to be male-biased although female-biased dispersal has also been reported in a range of taxa. Most of our knowledge on mammalian sex-biased dispersal is based on studies of eutherians and less work has been done on the direction and causes of sex-biased dispersal in marsupials. This study investigated dispersal of swamp wallabies between two habitat patches in South Gippsland, Victoria, using genetic methods. A Bayesian clustering test showed a high level of genetic exchange between the two habitat patches despite their separation by 10–17 km of cleared land, a creek and a highway. Females in the overall sample were more closely related to each other than males were to each other and females within habitat patches were more closely related than females between habitat patches whereas the converse was true for males. Bayesian inference showed that more males were migrating from the east to the west habitat patch whereas the converse was true for females and the male migration rate was higher than the female migration rate. The differential migration rate did not cause a significant difference in relatedness between patches in females but it did in males. These relatedness and migration patterns indicate that dispersal in the swamp wallaby is male-biased.

The long-term effects of logging for woodchips on small mammal populations

Context. Long-term studies are internationally recognised as an essential component of achieving ecologically sustainable forest management with respect to fauna. Aims. This study aimed to assess longer-term responses of small mammals to logging by returning in 1998 to our 1980–83 study sites in south-eastern New South Wales, Australia. Methods. Three age-classes of forest were surveyed: unlogged; 18–19-year-old regrowth; and 26–34-year-old regrowth. Key results. Rattus fuscipes remained affected by logging, and there were significantly fewer R. fuscipes males in logged, north-west-facing sites than at other sites, although the effect was less pronounced in 1998 than in 1980–83. Antechinus agilis females were significantly less numerous in south-east-facing, unlogged forest. This was not expected from the 1980–83 results. Antechinus swainsonii, which had disappeared following a fire in 1980, had returned to the forest by 1998. A. swainsonii females showed a significant preference for south-east-facing slopes and this relationship was consistent between logged and unlogged forest. No members of Mus musculus or Sminthopsis leucopus, which were present in 1980–83, were caught in 1998. Conclusions. As in the 1980s study, the responses of small mammal species to logging history were varied and species specific. Implications. In our study area, we predict that sustained logging for woodchips will continue to deplete its populations of small mammals. This adds to the case for a more robust and sustained approach to researching and managing our forest fauna.

Dispersal and the influence of rainfall on a population of the carnivorous marsupial swamp antechinus (Antechinus minimus maritimus)

Although there is evidence that recent climatic changes have had significant impacts on a wide range of species in the Northern Hemisphere, the influence of climate change, particularly drought, on Australian native small mammal species is poorly understood. In this study we investigated dispersal patterns and the influence of rainfall on the swamp antechinus (Antechinus minimus maritimus). Peak abundance occurred after the highest total annual rainfall for two decades, in 2001. A year later the population had declined to 10% of the peak. Birth dates appeared to occur three weeks earlier following a year of high rainfall. The dispersal of nine litters of pouch young (n = 62) was assessed following two breeding seasons. Young males remained on the natal site until December–January and dispersed before the breeding season. New males entered the population between January and June. More than 50% of females were residents and remained on the site to breed; the remaining females were trapped only once. After the male die-off the movements of pregnant females increased and they appeared to expand their home ranges. A. minimus exhibits philopatry of females and dispersal of males, as observed in other Antechinus species but dispersal occurs 2–3 months after weaning. This contrasts with juveniles of other Antechinus species that disperse abruptly after weaning. This study provides evidence that precipitation does have a major effect on the abundance of dasyurid species, making them vulnerable to drought and local or regional extinctions, particularly in areas of fragmented habitat and drying climates.

Genetic reconstruction of the population dynamics of a carnivorous marsupial (Antechinus flavipes) in response to floods

Human activities such as regulating river flows, logging and removing fallen timber adversely affect floodplain ecosystems around the world. Studies of the dynamics of floodplain-dwelling populations will help to understand the effects of altered flood regimes and to manage and restore floodplains. The yellow-footed antechinus (Antechinus flavipes) is the only small, native, carnivorous mammal (Marsupialia) on many degraded floodplains in south-eastern Australia, where its abundance appears to increase with proximity to floods, which is partly due to enhanced survival (as inferred from increased abundance of second-year females). We analysed population genetic patterns and maternity among samples collected following the period of postnatal dispersal, in the years preceding and following planned floods, at different distances from flood locations along the Murray River. Our genic and genotypic analyses of mitochondrial DNA (mtDNA) control region haplotypes and 11 microsatellite loci demonstrated high immigration rates into sites in close proximity to floods. All sampled males emigrated from their natal sites to points of capture, while some females were philopatric. There were high rates of dispersal of males among all sites within a partially flooded forest, while females dispersed more to locations closest to inundations rather than to distant places. These results suggest that environmental flows are beneficial to antechinus both by enhancing adult survival and promoting dispersal of females.

Phylogeography and environmental correlates of a cap on reproduction: teat number in a small marsupial, Antechinus agilis

Natural selection should optimize litter size in response to the distribution and abundance of resources during breeding. In semelparous, litter-bearing antechinuses, teat number limits litter size. Consequently adaptation has been inferred in explaining intraspecific, geographic variability in teat number for several Antechinus spp. The phylogeography of teat number variation and associated genetic divergence were assessed in A. agilis using nine microsatellites and mitochondrial cytochrome b sequence data. Six-teat Otway Range animals were divergent in microsatellite allele identity and frequencies: samples from three Otway six-teat sites demonstrated significantly greater similarity genetically to those from six-teat animals approximately 250 km to the west, than to nearby Otway 10-teat samples, or to the six-teat animals at Wilsons Promontory. Gene flow between Otway phenotypes appears to have been limited for sufficient time to enable different microsatellite alleles to evolve. Nonetheless, nuclear genetic evidence suggested only incomplete reproductive isolation, and mitochondrial DNA (mtDNA) haplotypes showed no association with teat number. Other populations across the range were no more genetically differentiated from one another than expected from geographic separation. Principal components and distance-based redundancy analyses found an association between environmental variables and geographic distribution of A. agilis teat number - six-teat animals inhabit more temperate forests, whilst those with more teats experience greater seasonality. The apparent restricted breeding between phenotypically distinct animals, together with phylogenetically separate groups of six-teat animals in different locations with similar environments, are consistent with the hypothesis that adaptation to different habitats drives teat number variation in A. agilis.

Genetic structure in a solitary rodent (Ctenomys talarum): implications for kinship and dispersal

The genetic structure of a population provides critical insights into patterns of kinship and dispersal. Although genetic evidence of kin structure has been obtained for multiple species of social vertebrates, this aspect of population biology has received considerably less attention among solitary taxa in which spatial and social relationships are unlikely to be influenced by kin selection. Nevertheless, significant kin structure may occur in solitary species, particularly if ecological or life history traits limit individual vagility. To explore relationships between genetic structure, kinship, and dispersal in a solitary vertebrate, we compared patterns of genetic variation in two demographically distinct populations of the talar tuco-tuco (Ctenomys talarum), a solitary species of subterranean rodent from Buenos Aires Province, Argentina. Based on previous field studies of C. talarum at Mar de Cobo (MC) and Necochea (NC), we predicted that natal dispersal in these populations is male biased, with dispersal distances for males and females being greater at NC. Analyses of 12 microsatellite loci revealed that in both populations, kin structure was more apparent among females than among males. Between populations, kinship and genetic substructure were more pronounced at MC. Thus, our findings were consistent with predicted patterns of dispersal for these animals. Collectively, these results indicate that populations of this solitary species are characterized by significant kin structure, suggesting that, even in the absence of sociality and kin selection, the spatial distributions and movements of individuals may significantly impact patterns of genetic diversity among conspecifics.

The effects of habitat fragmentation via forestry plantation establishment on spatial genotypic structure in the small marsupial carnivore, Antechinus agilis

Dispersal is an important influence on species' distributions, patch colonization and population persistence in fragmented habitat. We studied the impacts of habitat fragmentation resulting from establishment of an exotic pine plantation on dispersal of the marsupial carnivore, Antechinus agilis. We applied spatial analyses of individual multilocus microsatellite genotypes and mitochondrial haplotypes to study patterns of gene flow in fragmented habitat and natural habitat 'control' areas, and how this is affected by the spatial dispersion of habitat patches, the presence of corridors and a 'mainland' source of migrants. Spatial analysis of molecular variance and partial Mantel tests confirmed the absence of cryptic barriers to gene flow in continuous habitat, which if present would confound the comparison of genetic structures in fragmented vs. unfragmented habitats. Spatial genotypic structure suggested that although dispersal was male-biased in both habitat types, fragmentation restricted dispersal of males more than that of females and the degree of restriction of male dispersal was dependent on the geographical isolation of the patch. The scale of positive genotypic structure in fragmented habitat was restricted to the two closest patches for females and the three closest patches for males. Our results provide evidence for significantly increased gene flow through habitat corridors relative to that across the matrix and for significantly lower gene flow between 'mainland' unfragmented habitat and habitat patches relative to that within either habitat type, suggesting a behavioural barrier to crossing habitat interfaces.

Population density and presence of the mother are related to natal dispersal in male and female Antechinus stuartii

In common with most mammals, the frequency of natal dispersal in antechinuses is strongly male-biased. Inbreeding avoidance has been put forward as the most likely explanation, with juvenile dispersal being driven by the mother. Dispersal distances and factors affecting emigration and immigration of each sex have not previously been studied in antechinuses, because of the difficulty of following the fates of individual dispersers. I studied a dense population of brown antechinuses (Antechinus stuartii) of known parentage in linear habitat that could be comprehensively trapped, and determined the fate of 27 females and 14 males that survived to dispersal age. Juvenile males dispersed not only more frequently than females (71% v. 11%), but also much further (maximum known distance: 1230 m v. 270 m). Males dispersed further if they had been raised in an area of low population density, and were more likely to immigrate into an area with a higher density of females than the natal site. Death of the mother disrupted normal home-range establishment, resulting in frequent philopatry of sons and dispersal of some daughters. Some females emigrated after young were weaned, and this also prompted dispersal of daughters. There was no evidence that daughters with surviving, philopatric mothers were more likely to survive to breed. I conclude that male-biased dispersal appears to result not only from costs of inbreeding, but also partly by the benefits of finding a site with more mating opportunities.

Genetic diversity and population structure of Tasmanian devils, the largest marsupial carnivore

Genetic diversity and population structure were investigated across the core range of Tasmanian devils (Sarcophilus laniarius; Dasyuridae), a wide-ranging marsupial carnivore restricted to the island of Tasmania. Heterozygosity (0.386-0.467) and allelic diversity (2.7-3.3) were low in all subpopulations and allelic size ranges were small and almost continuous, consistent with a founder effect. Island effects and repeated periods of low population density may also have contributed to the low variation. Within continuous habitat, gene flow appears extensive up to 50 km (high assignment rates to source or close neighbour populations; nonsignificant values of pairwise FST), in agreement with movement data. At larger scales (150-250 km), gene flow is reduced (significant pairwise FST) but there is no evidence for isolation by distance. The most substantial genetic structuring was observed for comparisons spanning unsuitable habitat, implying limited dispersal of devils between the well-connected, eastern populations and a smaller northwestern population. The genetic distinctiveness of the northwestern population was reflected in all analyses: unique alleles; multivariate analyses of gene frequency (multidimensional scaling, minimum spanning tree, nearest neighbour); high self-assignment (95%); two distinct populations for Tasmania were detected in isolation by distance and in Bayesian model-based clustering analyses. Marsupial carnivores appear to have stronger population subdivisions than their placental counterparts.