Is the Gibraltar strait a barrier to gene flow for the bat Myotis myotis (Chiroptera: Vespertilionidae)?

Cryptic Diversity and Demographic Expansion of Plasmodium knowlesi Malaria Vectors in Malaysia

Although Malaysia is considered free of human malaria, there has been a growing number of Plasmodium knowlesi cases. This alarming trend highlighted the need for our understanding of this parasite and its associated vectors, especially considering the role of genetic diversity in the adaptation and evolution among vectors in endemic areas, which is currently a significant knowledge gap in their fundamental biology. Thus, this study aimed to investigate the genetic diversity of Anopheles balabacensis, Anopheles cracens, Anopheles introlatus, and Anopheles latens-the vectors for P. knowlesi malaria in Malaysia. Based on cytochrome c oxidase 1 (CO1) and internal transcribed spacer 2 (ITS2) markers, the genealogic networks of An. latens showed a separation of the haplotypes between Peninsular Malaysia and Malaysia Borneo, forming two distinct clusters. Additionally, the genetic distances between these clusters were high (2.3-5.2% for CO1) and (2.3-4.7% for ITS2), indicating the likely presence of two distinct species or cryptic species within An. latens. In contrast, no distinct clusters were observed in An. cracens, An. balabacensis, or An. introlatus, implying a lack of pronounced genetic differentiation among their populations. It is worth noting that there were varying levels of polymorphism observed across the different subpopulations, highlighting some levels of genetic variation within these mosquito species. Nevertheless, further analyses revealed that all four species have undergone demographic expansion, suggesting population growth and potential range expansion for these vectors in this region.

Reply to the comment by Morales et al. on “Population genetics reveal Myotis keenii (Keen’s myotis) and Myotis evotis (long-eared myotis) to be a single species”

A.E. Morales et al. (2021. Can. J. Zool. 99(5): 415–422) provided no new evidence to alter the conclusions of C.L. Lausen et al. (2019. Can. J. Zool. 97(3): 267–279). We present background information, relevant comparisons, and clarification of analyses to further strengthen our conclusions. The genesis of the original “evotis–keenii” study in British Columbia (Canada) was to differentiate Myotis keenii (Merriam, 1895) (Keen’s myotis), with one of the smallest North American bat distributions, from sympatric Myotis evotis (H. Allen, 1864) (long-eared myotis), using something other than the suggested post-mortem skull size comparison, but no differentiating trait could be found, leading to the molecular genetics examination of C.L. Lausen et al. (2019). We present cumulative data that rejects the 1979 hypothesis of M. keenii as a distinct species. A.E. Morales et al. (2021) inaccurately portray C.L. Lausen et al.’s (2019) question and results; present inaccurate morphological and outdated distribution data; overstate the impact of homoplasy without supporting evidence; and misinterpret evidence of population structure.

The taxonomic status of Myotis nesopolus larensis (Chiroptera, Vespertilionidae) and new insights on the diversity of Caribbean Myotis

Myotis nesopolus currently comprises two subspecies. The nominate subspecies (M. n. nesopolus) occurs on the Caribbean islands of Curaçao and Bonaire, Netherlands Antilles, whereas M. n. larensis is known from mainland South America in northeastern Colombia and northwestern Venezuela. Our Maximum Likelihood phylogenetic analyses of cytochrome-b gene sequences recovered M. nesopolus as a paraphyletic group, with M. n. nesopolus and M. n. larensis as non-sister lineages. The haplotype network indicates that these two subspecies do not share any haplotypes and are in different evolutionary trajectories. Additionally, these two subspecies can be distinguished on the basis of qualitative and quantitative morphological traits. This pattern supports the recognition of M. nesopolus and M. larensis as full species. Our results also reveal that the assemblage of Caribbean Myotis do not form a monophyletic group. Caribbean species are phylogenetically close to mainland species from northern South America and Central America, suggesting that colonization of Caribbean islands happened multiple times.

Bats Out of Africa: Disentangling the Systematic Position and Biogeography of Bats in Cabo Verde

Cabo Verde Archipelago presents one of the largest knowledge gaps in the distribution and taxonomy of bats in the world. Old works indicated that there are five species classified as European taxa. We have conducted an integrative taxonomy to revise the systematic position and distribution of Cabo Verdean bats with molecular, morphological, and ecological data, to test their native or exotic origin, and infer possible colonization patterns based on fieldwork and museum samples. Results showed that Cabo Verde Hypsugo is closely related to those from the Canary Islands, in which the taxonomic status is under debate, presenting unique mitochondrial and nuclear haplotypes. We also expanded the distribution of Taphozous nudiventris for Fogo Island through pellets and acoustic identification, showed unique haplotypes for this species, and that Miniopterus schreibersii shared a haplotype with European, North African, and Western Asian specimens. The morphological and acoustic identification of Cabo Verdean specimens was challenging because of the lack of modern morphological descriptions and similarity of echolocation calls within the same genus. More studies are definitely needed to access the systematic of bat species in the archipelago, but this work is the first step for the establishment of conservation actions of the probable only native Cabo Verdean mammals.

Population Connectivity Predicts Vulnerability to White-Nose Syndrome in the Chilean Myotis (Myotis chiloensis) - A Genomics Approach

Despite its peculiar distribution, the biology of the southernmost bat species in the world, the Chilean myotis (Myotis chiloensis), has garnered little attention so far. The species has a north-south distribution of c. 2800 km, mostly on the eastern side of the Andes mountain range. Use of extended torpor occurs in the southernmost portion of the range, putting the species at risk of bat white-nose syndrome, a fungal disease responsible for massive population declines in North American bats. Here, we examined how geographic distance and topology would be reflected in the population structure of M. chiloensis along the majority of its range using a double digestion RAD-seq method. We sampled 66 individuals across the species range and discovered pronounced isolation-by-distance. Furthermore, and surprisingly, we found higher degrees of heterozygosity in the southernmost populations compared to the north. A coalescence analysis revealed that our populations may still not have reached secondary contact after the Last Glacial Maximum. As for the potential spread of pathogens, such as the fungus causing WNS, connectivity among populations was noticeably low, especially between the southern hibernatory populations in the Magallanes and Tierra del Fuego, and more northerly populations. This suggests the probability of geographic spread of the disease from the north through bat-to-bat contact to susceptible populations is low. The study presents a rare case of defined population structure in a bat species and warrants further research on the underlying factors contributing to this. See the graphical abstract here. https://doi.org/10.25387/g3.12173385

Integrating population genetics to define conservation units from the core to the edge of Rhinolophus ferrumequinum western range

The greater horseshoe bat (Rhinolophus ferrumequinum) is among the most widespread bat species in Europe but it has experienced severe declines, especially in Northern Europe. This species is listed Near Threatened in the European IUCN Red List of Threatened Animals, and it is considered to be highly sensitive to human activities and particularly to habitat fragmentation. Therefore, understanding the population boundaries and demographic history of populations of this species is of primary importance to assess relevant conservation strategies. In this study, we used 17 microsatellite markers to assess the genetic diversity, the genetic structure, and the demographic history of R. ferrumequinum colonies in the western part of its distribution. We identified one large population showing high levels of genetic diversity and large population size. Lower estimates were found in England and northern France. Analyses of clustering and isolation by distance suggested that the Channel and the Mediterranean seas could impede R. ferrumequinum gene flow. These results provide important information to improve the delineation of R. ferrumequinum management units. We suggest that a large management unit corresponding to the population ranging from Spanish Basque Country to northern France must be considered. Particular attention should be given to mating territories as they seem to play a key role in maintaining high levels of genetic mixing between colonies. Smaller management units corresponding to English and northern France colonies must also be implemented. These insular or peripheral colonies could be at higher risk of extinction in the near future.

The Gambian epauletted fruit bat shows increased genetic divergence in the Ethiopian highlands and in an area of rapid urbanization

The Gambian epauletted fruit bat (Epomophorus gambianus) is an abundant species that roosts in both urban and rural settings. The possible role of E. gambianus as a reservoir host of zoonotic diseases underlines the need to better understand the species movement patterns. So far, neither observational nor phylogenetic studies have identified the dispersal range or behavior of this species. Comparative analyses of mitochondrial and nuclear markers from 20 localities across the known distribution of E. gambianus showed population panmixia, except for the populations in Ethiopia and southern Ghana (Accra and Ve-Golokwati). The Ethiopian population may be ancestral and is highly divergent to the species across the rest of its range, possibly reflecting isolation of an ancient colonization along an east-west axis. Mitochondrial haplotypes in the Accra population display a strong signature of a past bottleneck event; evidence of either an ancient or recent bottleneck using microsatellite data, however, was not detected. Demographic analyses identified population expansion in most of the colonies, except in the female line of descent in the Accra population. The molecular analyses of the colonies from Ethiopia and southern Ghana show gender dispersal bias, with the mitochondrial DNA fixation values over ten times those of the nuclear markers. These findings indicate free mixing of the species across great distances, which should inform future epidemiological studies.

Speciation with Gene Flow in North American Myotis Bats

Growing evidence supports the idea that species can diverge in the presence of gene flow. However, most methods of phylogeny estimation do not consider this process, despite the fact that ignoring gene flow is known to bias phylogenetic inference. Furthermore, studies that do consider divergence-with-gene-flow typically do so by estimating rates of gene flow using a isolation-with-migration model (IM), rather than evaluating scenarios of gene flow (such as divergence-with-gene flow or secondary contact) that represent very different types of diversification. In this investigation, we aim to infer the recent phylogenetic history of a clade of western long-eared bats while evaluating a number of different models that parameterize gene flow in a variety of ways. We utilize PHRAPL, a new tool for phylogeographic model selection, to compare the fit of a broad set of demographic models that include divergence, migration, or both among Myotis evotis, $M$. thysanodes and M. keenii. A genomic data set consisting of 808 loci of ultraconserved elements was used to explore such models in three steps using an incremental design where each successive set was informed by, and thus more focused than, the previous set of models. Specifically, the three steps were to (i) assess whether gene flow should be modeled and identify the best topologies, (ii) infer directionality of migration using the best topologies, and (iii) estimate the timing of gene flow. The best model (AIC model weight ${\sim}0.98$) included two divergence events (($M$. evotis, $M$. thysanodes), M. keenii) accompanied by gene flow at the initial stages of divergence. These results provide a striking example of speciation-with-gene-flow in an evolutionary lineage. [Myotis bats; PHRAPL; P2C2M; phylogeographic model selection; speciation with gene flow.].

Genetic diversity and structure related to expansion history and habitat isolation: stone marten populating rural-urban habitats

Background

Population genetic diversity and structure are determined by past and current evolutionary processes, among which spatially limited dispersal, genetic drift, and shifts in species distribution boundaries have major effects. In most wildlife species, environmental modifications by humans often lead to contraction of species’ ranges and/or limit their dispersal by acting as environmental barriers. However, in species well adapted to anthropogenic habitat or open landscapes, human induced environmental changes may facilitate dispersal and range expansions. In this study, we analysed whether isolation by distance and deforestation, among other environmental features, promotes or restricts dispersal and expansion in stone marten (Martes foina) populations.

Results

We genotyped 298 martens from eight sites at twenty-two microsatellite loci to characterize the genetic variability, population structure and demographic history of stone martens in Poland. At the landscape scale, limited genetic differentiation between sites in a mosaic of urban, rural and forest habitats was mostly influenced by isolation by distance. Statistical clustering and multivariate analyses showed weak genetic structuring with two to four clusters and a high rate of gene flow between them. Stronger genetic differentiation was detected for one stone marten population (NE1) located inside a large forest complex. Genetic differentiation between this site and all others was 20% higher than between other sites separated by similar distances. The genetic uniqueness index of NE1 was also twofold higher than in other sites. Past demographic history analyses showed recent expansion of this species in north-eastern Poland. A decrease in genetic diversity from south to north, and MIGRAINE analyses indicated the direction of expansion of stone marten.

Conclusions

Our results showed that two processes, changes in species distribution boundaries and limited dispersal associated with landscape barriers, affect genetic diversity and structure in stone marten. Analysis of local barriers that reduced dispersal and large scale analyses of genetic structure and demographic history highlight the importance of isolation by distance and forest cover for the past colonization of central Europe by stone marten. This confirmed the hypothesis that human-landscape changes (deforestation) accelerated stone marten expansion, to which climate warming probably has also been contributing over the last few decades.

Electronic supplementary material

The online version of this article (10.1186/s12898-017-0156-6) contains supplementary material, which is available to authorized users.

Contacts in the last 90,000 years over the Strait of Gibraltar evidenced by genetic analysis of wild boar (Sus scrofa)

Contacts across the Strait of Gibraltar in the Pleistocene have been studied in different research papers, which have demonstrated that this apparent barrier has been permeable to human and fauna movements in both directions. Our study, based on the genetic analysis of wild boar (Sus scrofa), suggests that there has been contact between Africa and Europe through the Strait of Gibraltar in the Late Pleistocene (at least in the last 90,000 years), as shown by the partial analysis of mitochondrial DNA. Cytochrome b and the control region from North African wild boar indicate a close relationship with European wild boar, and even some specimens belong to a common haplotype in Europe. The analyses suggest the transformation of the wild boar phylogeography in North Africa by the emergence of a natural communication route in times when sea levels fell due to climatic changes, and possibly through human action, since contacts coincide with both the Last Glacial period and the increasing human dispersion via the strait.

Contrasting evolutionary patterns between two haplogroups of Haematobia exigua (Diptera: Muscidae) from the mainland and islands of Southeast Asia

Uncovering the hidden diversity and evolutionary history of arthropods of medico-veterinary importance could have significant implications for vector-borne disease control and epidemiological intervention. The buffalo fly Haematobia exigua is an obligate bloodsucking ectoparasite of livestock. As an initial step towards understanding its population structures and biogeographic patterns, we characterized partial cytochrome c oxidase subunit I (COI) and cytochrome b (Cytb) sequences of H. exigua from three distinct geographic regions in Southeast Asia. We detected two distinct mitochondrial haplogroups of H. exigua in our surveyed geographic regions. Haplogroup I is widespread in the Southeast Asian mainland whereas haplogroup II is generally restricted to the type population Java Island. Both haplogroups were detected co-occurring on Borneo Island. Additionally, both haplogroups have undergone contrasting evolutionary histories, with haplogroup I exhibited a high level of mitochondrial diversity indicating a population expansion during the Pleistocene era dating back to 98,000 years ago. However, haplogroup II presented a low level of mitochondrial diversity which argues against the hypothesis of recent demographic expansion.

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.

Effect of oceanic straits on gene flow in the recently endangered little brown bat (Myotis lucifugus) in maritime Canada: implications for the spread of white-nose syndrome

White-nose syndrome is rapidly spreading in eastern North America, causing mass mortality of hibernating bats. We characterized levels of genetic diversity and population structure of the little brown bat (Myotis lucifugus (Le Conte, 1831)) in eastern Canada to infer the extent to which oceanic straits may be barriers to movement. To quantify metrics of gene flow and infer movement dynamics, we genotyped 679 M. lucifugus at nine nuclear microsatellites (nDNA) and sequenced a portion of the mitochondrial DNA (mtDNA). We found high levels of genetic diversity and little population structure, with ≈13-fold higher differentiation of mtDNA than nDNA markers, suggesting that structuring patterns largely result from female philopatry. Discriminant analysis of principle components suggested that the subtle underlying structure was not concordant with sampling site. Regional differentiation (FST, Dest, Mantel test residuals) is mostly consistent with genetic isolation by distance. However, samples from Newfoundland showed genetic differentiation over and above the effects of distance, lower levels of genetic diversity, and less genetic connectivity with other sampled regions. Despite this, oceanic straits in the Gulf of Saint Lawrence do not appear to create an impenetrable barrier to movement, therefore it may be possible for white-nose syndrome to spread to Newfoundland.

Parasite diversity of European Myotis species with special emphasis on Myotis myotis (Microchiroptera, Vespertilionidae) from a typical nursery roost

Background

Bats belong to one of the most species-rich orders within the Mammalia. They show a worldwide distribution, a high degree of ecological diversification as well as a high diversity of associated parasites and pathogens. Despite their prominent and unique role, the knowledge of their parasite-host-relationships as well as the mechanisms of co-evolutionary processes are, partly due to strict conservation regulations, scarce.

Methods

Juvenile specimens of the greater mouse-eared bat (Myotis myotis) from a roosting colony in Gladenbach (Hesse, Germany) were examined for their metazoan endo-and ectoparasite infections and pathogens. Morphometric data were recorded and the individuals were checked for Lyssavirus-specific antigen using a direct immunofluorescence test. For unambiguous species identification, the bats were analysed by cyt-b sequence comparison.

Results

Myotis myotis were parasitized by the six insect and arachnid ectoparasite species, i.e. Ixodes ricinus, Ischnopsyllus octactenus, Ichoronyssus scutatus, Steatonyssus periblepharus, Spinturnix myoti and Cimex dissimilis. Additionally, the nematode Molinostrongylus alatus and the cestode Vampirolepis balsaci were recorded. Each bat was parasitized by at least four species. The parasites showed partially extreme rates of infection, never recorded before, with more than 1,440 parasites per single host. Ichoronyssus scutatus, Steatonyssus periblepharus, Vampirolepis balsaci and Molinostrongylus alatus are recorded for the first time in Germany. A checklist for Europe is presented containing records of 98 parasite species of 14 Myotis species.

Conclusions

The Myotis myotis from Gladenbach (Hesse, Germany) were parasitized by a diverse parasite fauna with high infestation rates. We assume that in juvenile Myotis the number of parasites is generally higher than in adults due to only later acquired immune competence and behavioural adaptations. Our results revealed new insights into parasite fauna of M. myotis and European bats in general. The finding of endoparasitic cyclophyllidean cestodes that have a two-host lifecycle is, considering the stationary behaviour of the juvenile bats, rather unusual and suggests a non-predatory transmission mechanism (e.g. via autoinfection).

A new insight gained from the collated literature was that the European wide composition of the Myotis parasite fauna is dominated by a few specific taxonomic groups in Europe.

Taxonomic evaluation of the bent-winged bat (Miniopterus) populations occurring in Iran inferred from mitochondrial cytochrome-b sequences

We studied the genetic differentiation and taxonomy of the bent-wing bat (

What story does geographic separation of insular bats tell? A case study on Sardinian rhinolophids

Competition may lead to changes in a species’ environmental niche in areas of sympatry and shifts in the niche of weaker competitors to occupy areas where stronger ones are rarer. Although mainland Mediterranean (Rhinolophus euryale) and Mehely’s (R. mehelyi) horseshoe bats mitigate competition by habitat partitioning, this may not be true on resource-limited systems such as islands. We hypothesize that Sardinian R. euryale (SAR) have a distinct ecological niche suited to persist in the south of Sardinia where R. mehelyi is rarer. Assuming that SAR originated from other Italian populations (PES) – mostly allopatric with R. mehelyi – once on Sardinia the former may have undergone niche displacement driven by R. mehelyi. Alternatively, its niche could have been inherited from a Maghrebian source population. We: a) generated Maxent Species Distribution Models (SDM) for Sardinian populations; b) calibrated a model with PES occurrences and projected it to Sardinia to see whether PES niche would increase R. euryale’s sympatry with R. mehelyi; and c) tested for niche similarity between R. mehelyi and PES, PES and SAR, and R. mehelyi and SAR. Finally we predicted R. euryale’s range in Northern Africa both in the present and during the Last Glacial Maximum (LGM) by calibrating SDMs respectively with SAR and PES occurrences and projecting them to the Maghreb. R. mehelyi and PES showed niche similarity potentially leading to competition. According to PES’ niche, R. euryale would show a larger sympatry with R. mehelyi on Sardinia than according to SAR niche. Such niches have null similarity. The current and LGM Maghrebian ranges of R. euryale were predicted to be wide according to SAR’s niche, negligible according to PES’ niche. SAR’s niche allows R. euryale to persist where R. mehelyi is rarer and competition probably mild. Possible explanations may be competition-driven niche displacement or Maghrebian origin.

Physiological vagility and its relationship to dispersal and neutral genetic heterogeneity in vertebrates

Vagility is the inherent power of movement by individuals. Vagility and the available duration of movement determine the dispersal distance individuals can move to interbreed, which affects the fine-scale genetic structure of vertebrate populations. Vagility and variation in population genetic structure are normally explained by geographic variation and not by the inherent power of movement by individuals. We present a new, quantitative definition for physiological vagility that incorporates aerobic capacity, body size, body temperature and the metabolic cost of transport, variables that are independent of the physical environment. Physiological vagility is the speed at which an animal can move sustainably based on these parameters. This meta-analysis tests whether this definition of physiological vagility correlates with empirical data for maximal dispersal distances and measured microsatellite genetic differentiation with distance {[F(ST)/[1-F(ST))]/ln distance} for amphibians, reptiles, birds and mammals utilizing three locomotor modes (running, flying, swimming). Maximal dispersal distance and physiological vagility increased with body mass for amphibians, reptiles and mammals utilizing terrestrial movement. The relative slopes of these relationships indicate that larger individuals require longer movement durations to achieve maximal dispersal distances. Both physiological vagility and maximal dispersal distance were independent of body mass for flying vertebrates. Genetic differentiation with distance was greatest for terrestrial locomotion, with amphibians showing the greatest mean and variance in differentiation. Flying birds, flying mammals and swimming marine mammals showed the least differentiation. Mean physiological vagility of different groups (class and locomotor mode) accounted for 98% of the mean variation in genetic differentiation with distance in each group. Genetic differentiation with distance was not related to body mass. The physiological capacity for movement (physiological vagility) quantitatively predicts genetic isolation by distance in the vertebrates examined.

Phylogeography and postglacial recolonization of Europe by Rhinolophus hipposideros: evidence from multiple genetic markers

The demographic history of Rhinolophus hipposideros (lesser horseshoe bat) was reconstructed across its European, North African and Middle-Eastern distribution prior to, during and following the most recent glaciations by generating and analysing a multimarker data set. This data set consisted of an X-linked nuclear intron (Bgn; 543 bp), mitochondrial DNA (cytb-tRNA-control region; 1630 bp) and eight variable microsatellite loci for up to 373 individuals from 86 localities. Using this data set of diverse markers, it was possible to determine the species' demography at three temporal stages. Nuclear intron data revealed early colonization into Europe from the east, which pre-dates the Quaternary glaciations. The mtDNA data supported multiple glacial refugia across the Mediterranean, the largest of which were found in the Ibero-Maghreb region and an eastern location (Anatolia/Middle East)-that were used by R. hipposideros during the most recent glacial cycles. Finally, microsatellites provided the most recent information on these species' movements since the Last Glacial Maximum and suggested that lineages that had diverged into glacial refugia, such as in the Ibero-Maghreb region, have remained isolated. These findings should be used to inform future conservation management strategies for R. hipposideros and show the power of using a multimarker data set for phylogeographic studies.

The effect of host social system on parasite population genetic structure: comparative population genetics of two ectoparasitic mites and their bat hosts

Background

The population genetic structure of a parasite, and consequently its ability to adapt to a given host, is strongly linked to its own life history as well as the life history of its host. While the effects of parasite life history on their population genetic structure have received some attention, the effect of host social system has remained largely unstudied. In this study, we investigated the population genetic structure of two closely related parasitic mite species (Spinturnix myoti and Spinturnix bechsteini) with very similar life histories. Their respective hosts, the greater mouse-eared bat (Myotis myotis) and the Bechstein’s bat (Myotis bechsteinii) have social systems that differ in several substantial features, such as group size, mating system and dispersal patterns.

Results

We found that the two mite species have strongly differing population genetic structures. In S. myoti we found high levels of genetic diversity and very little pairwise differentiation, whereas in S. bechsteini we observed much less diversity, strongly differentiated populations and strong temporal turnover. These differences are likely to be the result of the differences in genetic drift and dispersal opportunities afforded to the two parasites by the different social systems of their hosts.

Conclusions

Our results suggest that host social system can strongly influence parasite population structure. As a result, the evolutionary potential of these two parasites with very similar life histories also differs, thereby affecting the risk and evolutionary pressure exerted by each parasite on its host.

Nonstationary patterns of isolation-by-distance: inferring measures of local genetic differentiation with Bayesian kriging

Patterns of isolation-by-distance (IBD) arise when population differentiation increases with increasing geographic distances. Patterns of IBD are usually caused by local spatial dispersal, which explains why differences of allele frequencies between populations accumulate with distance. However, spatial variations of demographic parameters such as migration rate or population density can generate nonstationary patterns of IBD where the rate at which genetic differentiation accumulates varies across space. To characterize nonstationary patterns of IBD, we infer local genetic differentiation based on Bayesian kriging. Local genetic differentiation for a sampled population is defined as the average genetic differentiation between the sampled population and fictive neighboring populations. To avoid defining populations in advance, the method can also be applied at the scale of individuals making it relevant for landscape genetics. Inference of local genetic differentiation relies on a matrix of pairwise similarity or dissimilarity between populations or individuals such as matrices of F_ST between pairs of populations. Simulation studies show that maps of local genetic differentiation can reveal barriers to gene flow but also other patterns such as continuous variations of gene flow across habitat. The potential of the method is illustrated with two datasets: single nucleotide polymorphisms from human Swedish populations and dominant markers for alpine plant species.

Molecular phylogenetic reconstructions identify East Asia as the cradle for the evolution of the cosmopolitan genus Myotis (Mammalia, Chiroptera)

Sequences of the mitochondrial cytochrome b (1140 bp) and nuclear Rag 2 (1148 bp) genes were used to assess the evolutionary history of the cosmopolitan bat genus Myotis, based on a worldwide sampling of over 88 named species plus 7 species with uncertain nomenclature. Phylogenetic reconstructions of this comprehensive taxon sampling show that most radiation of species occurred independently within each biogeographic region. Our molecular study supports an early divergence of species from the New World, where all Nearctic and Neotropical species plus a lineage from the Palaearctic constitute a monophyletic clade, sister to the remaining Old World taxa. The major Old World clade includes all remaining Eurasian taxa, most Oriental species, one Oceanian, and all Ethiopian species. Another lineage, including M. latirostris from Taiwan, appears at the base of these two major biogeographic clades and, because it bears nyctalodont molars, could be considered as a distinct genus. However, this molar configuration is also found in crown-group species, indicating that these dental characters are variable in the genus Myotis and may confound interpretation of the fossil record. Molecular datings suggest an origin of all recent Myotis in the early Miocene (about 21MYA with 95% highest posterior density interval 23-20MYA). This period was characterized by a global climatic cooling that reduced the availability of tropical habitats and favoured the development of more temperate vegetation. This sharp climatic change might have triggered the evolution of Myotis in the Northern continents, because Myotis ancestors seem to have been well adapted and successful in such temperate habitats. Ancestral area reconstructions based on the molecular phylogeny suggest that the eastern portion of the Asian continent was an important center of origin for the early diversification of all Myotis lineages, and involved relatively few subsequent transcontinental range expansions.

Fragmentation of Atlantic forest has not affected gene flow of a widespread seed-dispersing bat

Habitat loss and resultant fragmentation are major threats to biodiversity, particularly in tropical and subtropical ecosystems. It is increasingly urgent to understand fragmentation effects, which are often complex and vary across taxa, time and space. We determined whether recent fragmentation of Atlantic forest is causing population subdivision in a widespread and important Neotropical seed disperser: Artibeus lituratus (Chiroptera: Phyllostomidae). Genetic structure within highly fragmented forest in Paraguay was compared to that in mostly contiguous forest in neighbouring Misiones, Argentina. Further, observed genetic structure across the fragmented landscape was compared with expected levels of structure for similar time spans in realistic simulated landscapes under different degrees of reduction in gene flow. If fragmentation significantly reduced successful dispersal, greater population differentiation and stronger isolation by distance would be expected in the fragmented than in the continuous landscape, and genetic structure in the fragmented landscape should be similar to structure for simulated landscapes where dispersal had been substantially reduced. Instead, little genetic differentiation was observed, and no significant correlation was found between genetic and geographic distance in fragmented or continuous landscapes. Furthermore, comparison of empirical and simulated landscapes indicated empirical results were consistent with regular long-distance dispersal and high migration rates. Our results suggest maintenance of high gene flow for this relatively mobile and generalist species, which could be preventing or significantly delaying reduction in population connectivity in fragmented habitat. Our conclusions apply to A. lituratus in Interior Atlantic Forest, and do not contradict broad evidence that habitat fragmentation is contributing to extinction of populations and species, and poses a threat to biodiversity worldwide.

Environmental margin and island evolution in Middle Eastern populations of the Egyptian fruit bat

Here, we present a study of the population genetic architecture and microevolution of the Egyptian fruit bat (Rousettus aegyptiacus) at the environmental margins in the Middle East using mitochondrial sequences and nuclear microsatellites. In contrast to the rather homogenous population structure typical of cave-dwelling bats in climax tropical ecosystems, a relatively pronounced isolation by distance and population diversification was observed. The evolution of this pattern could be ascribed to the complicated demographic history at higher latitudes related to the range margin fragmentation and complex geomorphology of the studied area. Lineages from East Africa and Arabia show divergent positions. Within the northwestern unit, the most marked pattern of the microsatellite data set is connected with insularity, as demonstrated by the separate status of populations from Saharan oases and Cyprus. These demes also exhibit a reduction in genetic variability, which is presumably connected with founder effects, drift and other potential factors related to island evolution as site-specific selection. Genetic clustering indicates a semipermeability of the desert barriers in the Sahara and Arabian Peninsula and a corridor role of the Nile Valley. The results emphasize the role of the island environment in restricting the gene flow in megabats, which is also corroborated by biogeographic patterns within the family, and suggests the possibility of nascent island speciation on Cyprus. Demographic analyses suggest that the colonization of the region was connected to the spread of agricultural plants; therefore, the peripatric processes described above might be because of or strengthened by anthropogenic changes in the environment.

Post-Pleistocene range expansion of the recently imperiled eastern little brown bat (Myotis lucifugus lucifugus) from a single southern refugium

Myotis lucifugus, once among the most widespread and common bats in North America, has been forecast to be extirpated east of the Rockies in as few as 16 years by the spread of white-nose syndrome. Recent genetic research has demonstrated that this species is paraphyletic and part of a broader species complex; however, only one lineage (Myotis lucifugus lucifugus [M. l. lucifugus]) is present in eastern North America. I used molecular tools and niche modeling to validate this and investigate the role that historical biogeography has played in the phylogenetic and population genetic structure of this species to determine if the eastern subspecies represents an evolutionarily distinct population.

To establish the genetic structure within M. l. lucifugus, I densely sampled maternity colonies in Minnesota and sequenced 182 individuals for a portion of cytochrome b. Phylogenetic reconstruction and a haplotype network were used to infer the relationships among mitochondrial haplotypes. Population growth statistics were calculated to determine if there was evidence of significant expansion, and an environmental niche model (ENM) was constructed based on conditions during the last glacial maximum (LGM) to illustrate potential glacial refugia. All individuals derived from a single mitochondrial lineage. Genetic evidence points to population growth starting approximately 18 kya. ENM results show that there was likely a single large southern refugium extending across the southeastern United States and possibly several isolated refugia in western North America. Myotis lucifugus lucifugus likely maintained both a large range and a large population during the peaks of the glacial cycles, and its population appears to have expanded following the retreat of the Laurentide ice sheet. This imperiled lineage likely diverged in isolation from other members of the M. lucifugus/western long-eared Myotis during the Pleistocene.

Integrated operational taxonomic units (IOTUs) in echolocating bats: a bridge between molecular and traditional taxonomy

Background

Nowadays, molecular techniques are widespread tools for the identification of biological entities. However, until very few years ago, their application to taxonomy provoked intense debates between traditional and molecular taxonomists. To prevent every kind of disagreement, it is essential to standardize taxonomic definitions. Along these lines, we introduced the concept of Integrated Operational Taxonomic Unit (IOTU). IOTUs come from the concept of Operational Taxonomic Unit (OTU) and paralleled the Molecular Operational Taxonomic Unit (MOTU). The latter is largely used as a standard in many molecular-based works (even if not always explicitly formalized). However, while MOTUs are assigned solely on molecular variation criteria, IOTUs are identified from patterns of molecular variation that are supported by at least one more taxonomic characteristic.

Methodology/Principal Findings

We tested the use of IOTUs on the widest DNA barcoding dataset of Italian echolocating bats species ever assembled (i.e. 31 species, 209 samples). We identified 31 molecular entities, 26 of which corresponded to the morphologically assigned species, two MOTUs and three IOTUs. Interestingly, we found three IOTUs in Myotis nattereri, one of which is a newly described lineage found only in central and southern Italy. In addition, we found a level of molecular variability within four vespertilionid species deserving further analyses. According to our scheme two of them (i.e. M.bechsteinii and Plecotus auritus) should be ranked as unconfirmed candidate species (UCS).

Conclusions/Significance

From a systematic point of view, IOTUs are more informative than the general concept of OTUs and the more recent MOTUs. According to information content, IOTUs are closer to species, although it is important to underline that IOTUs are not species. Overall, the use of a more precise panel of taxonomic entities increases the clarity in the systematic field and has the potential to fill the gaps between modern and traditional taxonomy.

The Strait of Gibraltar as a major biogeographic barrier in Mediterranean conifers: a comparative phylogeographic survey

The Strait of Gibraltar (SG) is reputed for being both a bridge and a geographic barrier to biological exchanges between Europe and Africa. Major genetic breaks associated with this strait have been identified in various taxa, but it is unknown whether these disjunctions have been produced simultaneously or by independent biogeographic processes. Here, the genetic structure of five conifers distributed on both sides of the SG was investigated using mitochondrial (nad1 b/c, nad5-1, nad5-4 and nad7-1) and chloroplast (Pt1254, Pt15169, Pt30204, Pt36480, Pt71936 and Pt87268) DNA markers. The distribution of genetic variation was partially congruent between types of markers within the same species. Across taxa, there was a significant overlapping between the SG and the genetic breaks detected, especially for the four Tertiary species surveyed (Abies pinsapo complex, Pinus nigra, Pinus pinaster and Taxus baccata). For most of these taxa, the divergence of populations across the SG could date back to long before the Pleistocene glaciations. However, their strongly different cpDNA G(ST) and R(ST) values point out that they have had dissimilar population histories, which might include contrasting amounts of pollen-driven gene flow since their initial establishment in the region. The fifth species, Pinus halepensis, was genetically depauperated and homogenous on both sides of the SG. A further analysis of nuclear DNA sequences with coalescent-based isolation with migration models suggests a Pleistocene divergence of P. halepensis populations across the SG, which is in sharp contrast with the pre-Pleistocene divergence dates obtained for P. pinaster. Altogether, these results indicate that the genetic breaks observed across this putative biogeographical barrier have been produced by independent evolutionary processes related to the biological history of each individual species instead of a common vicariant phenomenon.

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.

Mechanisms of radiation in a bat group from the genus Pipistrellus inferred by phylogeography, demography and population genetics

Here, we present a study of the Pipistrellus pipistrellus species complex, a highly diversified bat group with a radiation centre in the Mediterranean biodiversity hotspot. The study sample comprised 583 animals from 118 localities representatively covering the bats' range in the western Palearctic. We used fast-evolving markers (the mitochondrial D-loop sequence and 11 nuclear microsatellites) to describe the phylogeography, demography and population structure of this model taxon and address details of its diversification. The overall pattern within this group includes a mosaic of phylogenetically basal, often morphologically distant, relatively small and mostly allopatric demes in the Mediterranean Basin, as well as two sympatric sibling species in the large continental part of the range. The southern populations exhibit constant size, whereas northern populations show a demographic trend of growth associated with range expansion during the Pleistocene climate oscillations. There is evidence of isolation by distance and female philopatry in P. pipistrellus sensu stricto. Although the northern populations are reproductively isolated, we detected introgression events among several Mediterranean lineages. This pattern implies incomplete establishment of reproductive isolating mechanisms in these populations as well as the existence of a past reinforcement stage in the continental siblings. The occurrence of reticulations in the radiation centre among morphologically and ecologically derived relict demes suggests that adaptive unequal gene exchange within hybridizing populations could play a role in speciation and adaptive radiation within this group.

Mites as biological tags of their hosts

Movements and spatial distribution of host populations are expected to shape the genetic structure of their parasite populations. Comparing the genetic patterns of both interacting species may improve our understanding of their evolutionary history. Moreover, genetic analyses of parasites with horizontal transmission may serve as indicators of historical events or current demographic processes that are not apparent in the genetic signature of their hosts. Here, we compared mitochondrial variation in populations of the ectoparasitic mite Spinturnix myoti with the genetic pattern of its host, the Maghrebian bat Myotis punicus in North Africa and in the islands of Corsica and Sardinia. Mite mitochondrial differentiation among populations was correlated with both host mitochondrial and nuclear differentiation, suggesting spatial co-differentiation of the lineages of the two interacting species. Therefore our results suggest that parasite dispersal is exclusively mediated by host movements, with open water between landmasses as a main barrier for host and parasite dispersal. Surprisingly the unique presence of a continental European mite lineage in Corsica was inconsistent with host phylogeographical history and strongly suggests the former presence of European mouse-eared bats on this island. Parasites may thus act as biological tags to reveal the presence of their now locally extinct host.