Population substructuring in Schreibers' long-fingered bat (Miniopterus schreibersii) in South Africa

Schreibers' long-fingered bat, Miniopterus schreibersi migrates seasonally between winter (hibernacula) and summer (maternity) colonies in South Africa. Previous behavioural studies suggested that roost fidelity is well developed in this species, and that juvenile dispersal may be limited, possibly in both sexes. If males and/or females are strongly philopatric, this may lead to restricted gene flow among colonies, resulting in genetically distinct breeding subpopulations. The population structure of M. schreibersii in South Africa was investigated using microsatellites and mitochondrial DNA (mtDNA), with the aim of determining the degree of genetic differentiation among colonies, and the extent and direction of bat movement among the colonies. A genomic library was constructed for M. schreibersii, and was screened for (CA)0 and (GA)0 microsatellite repeats. Five novel, highly polymorphic loci were identified. These five loci, and an existing mammalian microsatellite locus, were amplified in. 301 individuals, sampled from ten colonies throughout South Africa. Significant genetic heterogeneity exists within the M. schreibersii population, such that the population can be subdivided into three partially discrete breeding subpopulations. Little genetic differentiation exists between colonies withi

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

Phylogeographic analyses reveal cryptic subdivisions and unexpected connections among Myotis lucifugus populations

Until recently, the little brown bat (Myotis lucifugus) was a common bat species in North America. However, this species faces a significant threat from white-nose syndrome (WNS), which will likely result in the listing of M. lucifugus as a priority species in eastern parts of its range. The aim of this study is to examine the genetic structure of M. lucifugus, and thereby infer the impact that WNS is likely to have on M. lucifugus populations. Samples were collected from over 500 individuals from eastern hibernacula and from maternity colonies throughout the United States and Canada. Both mitochondrial (cytochrome oxidase I) and nuclear (14 microsatellites) loci were examined. Our data reveal restricted gene flow among females, but not males, from winter colonies. This mitochondrial genetic structure mirrors topographical variation across the region. Broader sampling of summer maternity colonies reveals a role for the Rocky Mountains as a historically significant, although not complete, barrier to gene flow among both males and females. Microsatellite data indicate that colonies in the Rockies provide opportunities for admixture between characteristically eastern and western lineages, suggesting that these mountains are unlikely to act as barriers to the westward spread of WNS across the continent. Our results will help us to place current patterns of mortality and disease spread in eastern North America in the broader context of population-level processes across the range of this species

Field identification of two morphologically similar bats, Miniopterus schreibersii natalensis and Miniopterus fraterculus (Chiroptera: Vespertilionidae)

Miniopterus schreibersii natalensis and Miniopterus fraterculus are two morphologically similar, but genetically distinct, species of insectivorous bat that, more often than not, share roosts. Identifying these two species in the field is difficult because of an overlap in the ranges of both forearm and mass. We thus attempted to find morphological features that could be used to distinguish between these two species in the field. We compared cranial and external morphological measurements from museum specimens of the two species, using principal component analysis and discriminant function analysis, to determine which variables could be used to discriminate between them. Length of the hind foot and total body length were identified as the variables responsible for most of the variation between these two species. Miniopterus s. natalensis has a longer total body length (113.6 ± 3.5 mm) than M. fraterculus (102.2 ± 4.8mm) but a relatively shorter hind foot (9.1 ± 0.6 mm, 9.8 ± 0.8 mm, respectively). A function generated from standardized canonical variables, (HF × 0.279417) – (TL × 0.989306) + 100, and based on length of hind foot (HF) and total body length (TL) generated function scores <0 for M. s. natalensis and >0 for M. fraterculus. On the basis that positive values (above zero) indicated M. fraterculus, and negative values (below zero) indicated M. s. natalensis, we were able to correctly assign 20 individuals to their respective species using the above function. These individuals were previously identified as M. fraterculus or M. s. natalensis from their mtDNA sequences. The function thus provides a useful tool for discriminating between the two species in the field.Keywords: cryptic species, field identification, morpholog

Cumberland Island Genotypes

Microsatellite genotypes of all bobcat scats collected on Cumberland Island (1st spreadsheet tab), and summary of genotypes of 9 bobcats that could be individually identified (2nd spreadsheet tab). Amplification conditions are described in primary manuscript (Diefenbach et al.) and in associated supplementary information

Data from: Population and genetic outcomes 20 years after reintroducing bobcats (Lynx rufus) to Cumberland Island, Georgia USA

In 1988–1989, 32 bobcats Lynx rufus were reintroduced to Cumberland Island (CUIS), Georgia, USA, from which they had previously been extirpated. They were monitored intensively for 3 years immediately post-reintroduction, but no estimation of the size or genetic diversity of the population had been conducted in over 20 years since reintroduction. We returned to CUIS in 2012 to estimate abundance and effective population size of the present-day population, as well as to quantify genetic diversity and inbreeding. We amplified 12 nuclear microsatellite loci from DNA isolated from scats to establish genetic profiles to identify individuals. We used spatially explicit capture–recapture population estimation to estimate abundance. From nine unique genetic profiles, we estimate a population size of 14.4 (SE = 3.052) bobcats, with an effective population size (Ne) of 5–8 breeding individuals. This is consistent with predictions of a population viability analysis conducted at the time of reintroduction, which estimated the population would average 12–13 bobcats after 10 years. We identified several pairs of related bobcats (parent-offspring and full siblings), but ~75% of the pairwise comparisons were typical of unrelated individuals, and only one individual appeared inbred. Despite the small population size and other indications that it has likely experienced a genetic bottleneck, levels of genetic diversity in the CUIS bobcat population remain high compared to other mammalian carnivores. The reintroduction of bobcats to CUIS provides an opportunity to study changes in genetic diversity in an insular population without risk to this common species. Opportunities for natural immigration to the island are limited; therefore, continued monitoring and supplemental bobcat reintroductions could be used to evaluate the effect of different management strategies to maintain genetic diversity and population viability. The successful reintroduction and maintenance of a bobcat population on CUIS illustrates the suitability of translocation as a management tool for re-establishing felid populations

Range-wide genetic analysis of little brown bat (myotis lucifugus) populations: estimating the risk of spread of white-nose syndrome

The little brown bat (Myotis lucifugus) is one of the most widespread bat species in North America and is experiencing severe population declines because of an emerging fungal disease, white-nose syndrome (WNS). To manage and conserve this species effectively it is important to understand patterns of gene flow and population connectivity to identify possible barriers to disease transmission. However, little is known about the population genetic structure of little brown bats, and to date, no studies have investigated population structure across their entire range. We examined mitochondrial DNA and nuclear microsatellites in 637 little brown bats (including all currently recognized subspecific lineages) from 29 locations across North America, to assess levels of genetic variation and population differentiation across the range of the species, including areas affected by WNS and those currently unaffected. We identified considerable spatial variation in patterns of female dispersal and significant genetic variation between populations in eastern versus western portions of the range. Overall levels of nuclear genetic differentiation were low, and there is no evidence for any major barriers to gene flow across their range. However, patterns of mtDNA differentiation are highly variable, with high ΦST values between most sample pairs (including between all western samples, between western and eastern samples, and between some eastern samples), while low mitochondrial differentiation was observed within two groups of samples found in central and eastern regions of North America. Furthermore, the Alaskan population was highly differentiated from all others, and western populations were characterized by isolation by distance while eastern populations were not. These data raise the possibility that the current patterns of spread of WNS observed in eastern North America may not apply to the entire range and that there may be broad-scale spatial variation in the risk of WNS transmission and occurrence if the disease continues to spread west

A Family Matter: Conclusive Resolution of the Taxonomic Position of the Long-Fingered Bats, Miniopterus

The long-fingered bats (Miniopterus sp.) are among the most widely distributed mammals in the world. However, despite recent focus on the systematics of these bats, their taxonomic position has not been resolved. Traditionally, they are considered to be sole members of Miniopterinae, 1 of 5 subfamilies within the largest family of bats, the Vespertilionidae. However, this classification has increasingly been called into question. Miniopterines differ extensively from other vespertilionids in numerous aspects of morphology, embryology, immunology, and, most recently, genetics. Recent molecular studies have proposed that the miniopterines are sufficiently distinct from vespertilionids that Miniopterinae should be elevated to full familial status. However, controversy remains regarding the relationship of the putative family, Miniopteridae to existing Vespertilionidae and to the closely related free-tailed bats, the Molossidae. We report here the first conclusive analysis of the taxonomic position of Miniopterus relative to all other bat families. We generated one of the largest chiropteran data sets to date, incorporating ∼11 kb of sequence data from 16 nuclear genes, from representatives of all bat families and 2 Miniopterus species. Our data confirm the distinctiveness of Miniopterus, and we support previous recommendations to elevate these bats to full familial status. We estimate that they diverged from all other bat species approximately 49–38 MYA, which is comparable to most other bat families. Furthermore, we find very strong support from all phylogenetic methods for a sister group relationship between Miniopteridae and Vespertilionidae. The Molossidae diverged from these lineages approximately 54–43 MYA and form a sister group to the Miniopteridae–Vespertilionidae clade

Genetic Structure of Little Brown Bats (Myotis lucifugus) Corresponds with Spread of White-Nose Syndrome among Hibernacula

Until recently, the little brown bat (Myotis lucifugus) was one of the most common bat species in North America. However, this species currently faces a significant threat from the emerging fungal disease white-nose syndrome (WNS). The aims of this study were to examine the population genetic structure of M. lucifugus hibernating colonies in Pennsylvania (PA) and West Virginia (WV), and to determine whether that population structure may have influenced the pattern of spread of WNS. Samples were obtained from 198 individuals from both uninfected and recently infected colonies located at the crest of the disease front. Both mitochondrial (636bp of cytochrome oxidase I) and nuclear (8 microsatellites) loci were examined. Although no substructure was evident from nuclear DNA, female-mediated gene flow was restricted between hibernacula in western PA and the remaining colonies in eastern and central PA and WV. This mitochondrial genetic structure mirrors topographic variation across the region: 3 hibernating colonies located on the western Appalachian plateau were significantly differentiated from colonies located in the central mountainous and eastern lowland regions, suggesting reduced gene flow between these clusters of colonies. Consistent with the hypothesis that WNS is transmitted primarily through bat-to-bat contact, these same 3 hibernating colonies in westernmost PA remained WNS-free for 1–2 years after the disease had swept through the rest of the state, suggesting that female migration patterns may influence the spread of WNS across the landscape

Data and R code to estimate abundance

This zip folder contains: (1) file containing the locations of ID'd individuals on Cumberland Island; (2) the locations of transects (x-y of center of each 200-m segment); (3) shapefiles of island boundary (multiple files); (4) R code for spatially explicit capture-recapture population estimation (SECR) for abundanc