GENETIC STRUCTURE AND MALE-MEDIATED GENE FLOW IN THE GHOST BAT (MACRODERMA GIGAS)

The Australian ghost bat is a large, opportunistic carnivorous species that has undergone a marked range contraction toward more mesic, tropical sites over the past century. Comparison of mitochondrial DNA (mtDNA) control region sequences and six nuclear microsatellite loci in 217 ghost bats from nine populations across subtropical and tropical Australia revealed strong population subdivision (mtDNA φ_ST = 0.80; microsatellites UR_ST = 0.337). Low-latitude (tropical) populations had higher heterozygosity and less marked phylogeographic structure and lower subdivision among sites within regions (within Northern Territory [NT] and within North Queensland [NQ]) than did populations at higher latitudes (subtropical sites; central Queensland [CQ]), although sampling of geographically proximal breeding sites is unavoidably restricted for the latter. Gene flow among populations within each of the northern regions appears to be male biased in that the difference in population subdivision for mtDNA and microsatellites (NT φ_ST = 0.39, UR_ST = 0.02; NQ φ_ST = 0.60, UR_ST = ?0.03) is greater than expected from differences in the effective population size of haploid versus diploid loci. The high level of population subdivision across the range of the ghost bat contrasts with evidence for high gene flow in other chiropteran species and may be due to narrow physiological tolerances and consequent limited availability of roosts for ghost bats, particularly across the subtropical and relatively arid regions. This observation is consistent with the hypothesis that the contraction of the species' range is associated with late Holocene climate change. The extreme isolation among higher-latitude populations may predispose them to additional local extinctions if the processes responsible for the range contraction continue to operate.     

Population subdivision and gene flow in Danish house mice

Genetic subdivision in local populations of the European house mice, Mus musculus domesticus and M. m. musculus, was analysed to study patterns of gene flow. The data consisted of frequencies of microsatellite alleles in 16 samples (250 individuals) from a total of 11 sites in Jutland, which included successive samples from three sites. Sequences of the control region of mitochondrial DNA in three successive samples from one site were also analysed. Microsatellite genotype frequencies within samples were close to Hardy-Weinberg expectations. Levels of microsatellite differentiation among samples (θ= 0.05–0.21) corresponded to limited gene flow at migration-drift equilibrium (N_m= 1–5). Weak isolation by distance for microsatellites in M. m. musculus suggested that gene flow tends to occur among neighbouring sites. Estimates of effective population size over a few generations were much lower than those corresponding to the long periods needed for arrival at mutation-drift equilibrium. This suggested that subpopulations had been influenced by gene flow since formation, or had originated recently from genetically diverse founders.     

Island Populations, Human Introductions and the Limitations of Genetic Analyses: the Case of the Sardinian Red Deer (Cervus elaphus corsicanus)

The Corsican red deer (Cervus elaphus corsicanus) is endemic to the Tyrrhenian islands of Corsica and Sardinia. It has been regarded as an introduced species and has allegedly been present on the islands since the beginning of the Neolithic culture some 8,000 years ago. In this review, we present the results of relevant genetic analyses and discuss their implications for the origin of C. e. corsicanus. Different genetic studies hypothesize that the most probable ancestral populations for Sardianian red deer were alternatively, the Near East, North Africa, or mainland Italy. These respective scenarios are evaluated and it is concluded that geneticists have not yet been unable to definitively solve the problem. However, a natural colonization of the Tyrrhenian islands from mainland Italy via the Tuscan archipelago is not only in accordance with palaeontological findings but also with at least some of the genetic data.     

Behavioural vs. molecular sources of conflict between nuclear and mitochondrial DNA: the role of male-biased dispersal in a Holarctic sea duck

Genetic studies of waterfowl (Anatidae) have observed the full spectrum of mitochondrial (mt) DNA population divergence, from apparent panmixia to deep, reciprocally monophyletic lineages. Yet, these studies often found weak or no nuclear (nu) DNA structure, which was often attributed to male‐biased gene flow, a common behaviour within this family. An alternative explanation for this ‘conflict’ is that the smaller effective population size and faster sorting rate of mtDNA relative to nuDNA lead to different signals of population structure. We tested these alternatives by sequencing 12 nuDNA introns for a Holarctic pair of waterfowl subspecies, the European goosander (Mergus merganser merganser) and the North American common merganser (M. m. americanus), which exhibit strong population structure in mtDNA. We inferred effective population sizes, gene flow and divergence times from published mtDNA sequences and simulated expected differentiation for nuDNA based on those histories. Between Europe and North America, nuDNA Ф_ST was 3.4‐fold lower than mtDNA Ф_ST, a result consistent with differences in sorting rates. However, despite geographically structured and monophyletic mtDNA lineages within continents, nuDNA Ф_ST values were generally zero and significantly lower than predicted. This between‐ and within‐continent contrast held when comparing mtDNA and nuDNA among published studies of ducks. Thus, male‐mediated gene flow is a better explanation than slower sorting rates for limited nuDNA differentiation within continents, which is also supported by nonmolecular data. This study illustrates the value of quantitatively testing discrepancies between mtDNA and nuDNA to reject the null hypothesis that conflict simply reflects different sorting rates.     

Did Late Pleistocene climate change result in parallel genetic structure and demographic bottlenecks in sympatric Central African crocodiles,Mecistops and Osteolaemus?

The mid‐Holocene has had profound demographic impacts on wildlife on the African continent, although there is little known about the impacts on species from Central Africa. Understanding the impacts of climate change on codistributed species can enhance our understanding of ecosystem dynamics and for formulating restoration objectives. We took a multigenome comparative approach to examine the phylogeographic structure of two poorly known Central African crocodile species—Mecistops sp. aff. cataphractus and Osteolaemus tetraspis. In addition, we conducted coalescent‐based demographic reconstructions to test the hypothesis that population decline was driven by climate change since the Last Glacial Maximum, vs. more recent anthropogenic pressures. Using a hierarchical Bayesian model to reconstruct demographic history, we show that both species had dramatic declines (>97%) in effective population size in the 'period following the Last Glacial Maximum 1,500–18,000 YBP. Identification of genetic structuring showed both species have similar regional structure corresponding to major geological features (i.e., hydrologic basin) and that small observed differences between them are best explained by the differences in their ecology and the likely impact that climate change had on their habitat needs. Our results support our hypothesis that climatic effects, presumably on forest and wetland habitat, had a congruent negative impact on both species.     

Population structure and gene flow reversals in Atlantic salmon (Salmo salar) over contemporary and long-term temporal scales: effects of population size and life history

Metapopulation dynamics are increasingly invoked in management and conservation of endangered species. In this context, asymmetrical gene flow patterns can be density dependent, with migration occurring mainly from larger into smaller populations, which may depend on it for their persistence. Using genetic markers, such patterns have recently been documented for various organisms including salmonids, suggesting this may be a more general pattern. However, metapopulation theory does not restrict gene flow asymmetry to 'source-sink' structures, nor need these patterns be constant over longer evolutionary timescales. In anadromous salmonids, gene flow can be expected to be shaped by various selective pressures underlying homing and dispersal ('straying') behaviours. The relative importance of these selective forces will vary spatially and for populations of different census size. Furthermore, the consequences of life-history variation among populations for dispersal and hence gene flow remain poorly quantified. We examine population structure and connectivity in Atlantic salmon (Salmo salar L.) from Newfoundland and Labrador, a region where populations of this species are relatively pristine. Using genetic variation at 13 microsatellite loci from samples (N=1346) collected from a total of 20 rivers, we examine connectivity at several regional and temporal scales and test the hypothesis that the predominant direction of gene flow is from large into small populations. We reject this hypothesis and find that the directionality of migration is affected by the temporal scale over which gene flow is assessed. Whereas large populations tend to function as sources of dispersal over contemporary timescales, such patterns are often changed and even reversed over evolutionary, coalescent-derived timescales. These patterns of population structure furthermore vary between different regions and are compatible with demographic and life-history attributes. We find no evidence for sex-biased dispersal underlying gene flow asymmetry. Our findings caution against generalizations concerning the directionality of gene flow in Atlantic salmon and emphasize the need for detailed regional study, if such information is to be meaningfully applied in conservation and management of salmonids.     

Phylogeographic patterns in Drosophila montana

The Drosophila virilis species group offers valuable opportunities for studying the roles of chromosomal re-arrangements and mating signals in speciation. The 13 species are divided into two subgroups, the montana and virilis 'phylads'. There is greater differentiation among species within the montana phylad in both karyotype and acoustic signals than exists among members of the virilis phylad. Drosophila montana is a divergent species which is included in the montana phylad. Here, we analyse the phylogeography of D. montana to provide a framework for understanding divergence of acoustic signals among populations. We analysed mitochondrial sequences corresponding to the cytochrome oxidase I and cytochrome oxidase II genes, as well as 16 microsatellite loci, from 108 lines of D. montana covering most of the species' range. The species shows a clear genetic differentiation between North American and Scandinavian populations. Microsatellite allele frequencies and mitochondrial DNA haplotypes gave significant FST values between populations from Canada, USA and Finland. A Bayesian analysis of population structure based on the microsatellite frequencies showed four genetically distinct groups, corresponding to these three populations plus a small sample from Japan. A network based on mitochondrial haplotypes showed two Finnish clades of very different shape and variability, and another clade with all sequences from North America and Japan. All D. montana populations showed evidence of demographic expansion but the patterns inferred by coalescent analysis differed between populations. The divergence times between Scandinavian and North American clades were estimated to range from 450,000 to 900,000 years with populations in Canada and the USA possibly representing descendants of different refugial populations. Long-term separation of D. montana populations could have provided the opportunity for differentiation observed in male signal traits, especially carrier frequency of the song, but relaxation of sexual selection during population expansion may have been necessary.