Contrasting Genetic Structure in Two Co-Distributed Species of Old World Fruit Bat

The fulvous fruit bat (Rousettus leschenaulti) and the greater short-nosed fruit bat (Cynopterus sphinx) are two abundant and widely co-distributed Old World fruit bats in Southeast and East Asia. The former species forms large colonies in caves while the latter roots in small groups in trees. To test whether these differences in social organization and roosting ecology are associated with contrasting patterns of gene flow, we used mtDNA and nuclear loci to characterize population genetic subdivision and phylogeographic histories in both species sampled from China, Vietnam and India. Our analyses from R. leschenaulti using both types of marker revealed little evidence of genetic structure across the study region. On the other hand, C. sphinx showed significant genetic mtDNA differentiation between the samples from India compared with China and Vietnam, as well as greater structuring of microsatellite genotypes within China. Demographic analyses indicated signatures of past rapid population expansion in both taxa, with more recent demographic growth in C. sphinx. Therefore, the relative genetic homogeneity in R. leschenaulti is unlikely to reflect past events. Instead we suggest that the absence of substructure in R. leschenaulti is a consequence of higher levels of gene flow among colonies, and that greater vagility in this species is an adaptation associated with cave roosting

Data from: Hierarchical polygyny in multiparous lesser flat-headed bats

How males gain access to mates and the potential for female choice will determine whether polygyny can operate at several levels, from within litters and groups to the wider population. Female lesser flat-headed bats (Tylonycteris pachypus) form maternity groups in bamboo stems. Unusually for bats, they are multiparous, providing the opportunity to test whether multi-level polygyny differs among males depending on whether they roost with females, with males, or are solitary. We genotyped 662 individuals from 54 internodes and undertook parentage of 165 litters. Our results revealed 170 sets of paternal twins/triplets, of which 96 were full-sibs and 74 were half-sibs. We found that males captured roosting with females typically sired more offspring overall than did other males, and also showed a greater tendency to monopolise paternity within both litters and roosting groups. In comparison, males that sired fewer full sibs were assigned more maternal half sibs. These latter individuals, which included solitary males and those from all-male groups might gain copulations either via roaming with furtive mating or during visits by females. Indeed, female lesser flat-headed bats store sperm, so could benefit from multiple mating to reduce genetic incompatibilities. At the same time, however, we found no evidence our outbreeding. Finally, relatedness and mtDNA analyses revealed that polygyny also operated within matrilineal kin, suggesting a system that might promote social cohesiveness. Future studies of individual movements will help to determine the extent to which mixed paternities in litters, matrilines and groups are driven by male or female behaviour

Data from: Historical introgression and the persistence of ghost alleles in the intermediate horseshoe bat (Rhinolophus affinis)

Phylogenetic conflicts between genetic markers can help to disentangle complex histories of phylogeography and introgression among taxa. We previously proposed that the Chinese mainland subspecies of the intermediate horseshoe bat Rhinolophus affinis himalayanus colonized Hainan Island to form the subspecies R. a. hainanus. Subsequent recolonization of the mainland formed a third taxon, R. a macrurus, and a secondary contact zone with the ancestral himalayanus. To test for historical and recurrent genetic exchange between these mainland subspecies, we sampled populations of each from two parapatric zones and undertook analyses using one mtDNA marker, three nuclear genes and 14 microsatellites. Nuclear DNA, echolocation call frequencies and morphological data all recovered two taxa; however, a mtDNA phylogeny revealed two himalayanus clades, of which one clustered with macrurus, as well as some shared or related mtDNA haplotypes in eastern populations. Isolation-with-migration (IM) models suggested some mtDNA gene flow from macrurus to himalayanus. However, strong population structure in himalayanus raises the possibility that macrurus captured mtDNA from a coastal population of himalayanus that has since become rare or extinct. To reconcile these two sets of results, we suggest that the IM estimates might reflect historical mtDNA gene flow among populations of himalayanus, before mtDNA was subsequently captured by macrurus. Finally, microsatellite-based ABC analyses supported the island origin of macrurus; however, mtDNA-based ABC analyses suggest this taxon might have evolved on the mainland. Our findings highlight the importance of understanding population history and structure for interpreting hybridization and introgression events

Dispersal, Mating Events and Fine-Scale Genetic Structure in the Lesser Flat-Headed Bats

<div><p>Population genetic structure has important consequences in evolutionary processes and conservation genetics in animals. Fine-scale population genetic structure depends on the pattern of landscape, the permanent movement of individuals, and the dispersal of their genes during temporary mating events. The lesser flat-headed bat (<em>Tylonycteris pachypus</em>) is a nonmigratory Asian bat species that roosts in small groups within the internodes of bamboo stems and the habitats are fragmented. Our previous parentage analyses revealed considerable extra-group mating in this species. To assess the spatial limits and sex-biased nature of gene flow in the same population, we used 20 microsatellite loci and mtDNA sequencing of the ND2 gene to quantify genetic structure among 54 groups of adult flat-headed bats, at nine localities in South China. AMOVA and <em>F</em>_ST estimates revealed significant genetic differentiation among localities. Alternatively, the pairwise <em>F</em>_ST values among roosting groups appeared to be related to the incidence of associated extra-group breeding, suggesting the impact of mating events on fine-scale genetic structure. Global spatial autocorrelation analyses showed positive genetic correlation for up to 3 km, indicating the role of fragmented habitat and the specialized social organization as a barrier in the movement of individuals among bamboo forests. The male-biased dispersal pattern resulted in weaker spatial genetic structure between localities among males than among females, and fine-scale analyses supported that relatedness levels within internodes were higher among females than among males. Finally, only females were more related to their same sex roost mates than to individuals from neighbouring roosts, suggestive of natal philopatry in females.</p> </div

Distribution of pairwise <i>F</i>_ST among roosting groups within localities (from microsatellite data).

<p>Distribution of pairwise <i>F</i>_ST among roosting groups within localities (from microsatellite data).</p

Correlogram plots of the genetic autocorrelation coefficient (<i>r</i>) as a function of distance.

<p>Upper (U) and lower (L) confidence limits (two red lines) bind the 95% confidence interval about the null hypothesis of no spatial structure for the combined data set as determined by 1000 permutations. (A) all individuals (n = 296), (B) females (n = 227), (C) males (n = 69).</p

Distributions of pairwise relatedness values within internodes in each locality from microsatellite data.

<p>(A) females within internodes (locality numbers = 8), (B) males within internodes (locality numbers = 3), (C) females between internodes (locality numbers = 8), (D) males between internodes (locality numbers = 6). NA, missing plot because of less than five comparisons within localities. Values within each plot stand for mean±SD.</p

Pairwise <i>F</i>_ST estimates for genetic differentiation among localities.

<p>Below the diagonal for microsatellite data and above the diagonal for mtDNA data. KC locality was deleted because of less than five samples within it.</p><p>Significance level:</p>*<p><i>P</i><0.05,</p>**<p><i>P</i><0.01.</p

Global spatial autocorrelation analysis of all 296 individuals.

<p>N: number of pairwise comparisons; <i>r</i>: correlation coefficient; U and L: upper and lower bounds for the 95% confidence interval about the null hypothesis of no spatial structure, U<i>r</i> and L<i>r</i>: 95% error bounds about r as determined by bootstrap resampling. The probability <i>P</i> of a one-tailed test for positive autocorrelation, permutated <i>r</i> and bootstrapped <i>r</i> are also shown.</p

Distribution of the nine sampled localities of <i>Tylonycteris pachypus</i> from Chongzuo District, Guangxi Province, China.

<p>The left part shows the sampled roosting groups as dark dots in each locality (some dots are overlapped, given some groups coming from the same bamboo clusters).</p