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

Morphological and molecular confirmation of the common pipistrelle bat, Pipistrellus pipistrellus Schreber, 1774 (Vespertilionidae: Chiroptera), in Xinjiang, China

Species identification is pivotal in taxonomy, systematics, evolutionary biology and conservation biology. We collected bats that died of natural causes in Shihezi city, Xinjiang, China, and carried out morphological and genetic identification. Morphologically, all individuals were adults/subadults or juveniles of Pipistrellus pipistrellus. We found one haplotype for the mitochondrial gene ND1 and five for the mitochondrial gene cytochrome b (Cytb) among six specimens. Phylogenetically, all the Cytb sequences grouped with P. pipistrellus. We confirm this species’ occurrence in Xinjiang, China.

Parapatric genetic divergence among deep evolutionary lineages in the Mediterranean green crab, Carcinus aestuarii (Brachyura, Portunoidea, Carcinidae), accounts for a sharp phylogeographic break in the Eastern Mediterranean

BACKGROUND

Recently, population genetic studies of Mediterranean marine species highlighted patterns of genetic divergence and phylogeographic breaks, due to the interplay between impacts of Pleistocene climate shifts and contemporary hydrographical barriers. These factors markedly shaped the distribution of marine organisms and their genetic makeup. The present study is part of an ongoing effort to understand the phylogeography and evolutionary history of the highly dispersive Mediterranean green crab, Carcinus aestuarii (Nardo, 1847), across the Mediterranean Sea. Recently, marked divergence between two highly separated haplogroups (genetic types I and II) of C. aestuarii was discerned across the Siculo-Tunisian Strait, suggesting an Early Pleistocene vicariant event. In order to better identify phylogeographic patterns in this species, a total of 263 individuals from 22 Mediterranean locations were analysed by comparing a 587 basepair region of the mitochondrial gene Cox1 (cytochrome oxidase subunit 1). The examined dataset is composed of both newly generated sequences (76) and previously investigated ones (187).

RESULTS

Our results unveiled the occurrence of a highly divergent haplogroup (genetic type III) in the most north-eastern part of the Mediterranean Sea. Divergence between the most distinct type III and the common ancestor of both types I and II corresponds to the Early Pleistocene and coincides with the historical episode of separation between types I and II. Our results also revealed strong genetic divergence among adjacent regions (separating the Aegean and Marmara seas from the remaining distribution zone) and confirmed a sharp phylogeographic break across the Eastern Mediterranean. The recorded parapatric genetic divergence, with the potential existence of a contact zone between both groups in the Ionian Sea and notable differences in the demographic history, suggest the likely impact of paleoclimatic events, as well as past and contemporary oceanographic processes, in shaping genetic variability of this species.

CONCLUSIONS

Our findings not only provide further evidence for the complex evolutionary history of the green crab in the Mediterranean Sea, but also stress the importance of investigating peripheral areas in the species' distribution zone in order to fully understand the distribution of genetic diversity and unravel hidden genetic units and local patterns of endemism.

Molecular ecology studies of species radiations: current research gaps, opportunities and challenges

Understanding the drivers and limits of species radiations is a crucial goal of evolutionary genetics and molecular ecology, yet research on this topic has been hampered by the notorious difficulty of connecting micro- and macroevolutionary approaches to studying the drivers of diversification. To chart the current research gaps, opportunities and challenges of molecular ecology approaches to studying radiations, we examine the literature in the journal Molecular Ecology and revisit recent high-profile examples of evolutionary genomic research on radiations. We find that available studies of radiations are highly unevenly distributed among taxa, with many ecologically important and species-rich organismal groups remaining severely understudied, including arthropods, plants and fungi. Most studies employed molecular methods suitable over either short or long evolutionary time scales, such as microsatellites or restriction site-associated DNA sequencing (RAD-seq) in the former case and conventional amplicon sequencing of organellar DNA in the latter. The potential of molecular ecology studies to address and resolve patterns and processes around the species level in radiating groups of taxa is currently limited primarily by sample size and a dearth of information on radiating nuclear genomes as opposed to organellar ones. Based on our literature survey and personal experience, we suggest possible ways forward in the coming years. We touch on the potential and current limitations of whole-genome sequencing (WGS) in studies of radiations. We suggest that WGS and targeted ('capture') resequencing emerge as the methods of choice for scaling up the sampling of populations, species and genomes, including currently understudied organismal groups and the genes or regulatory elements expected to matter most to species radiations.

Glacial allopatry vs. postglacial parapatry and peripatry: the case of hedgehogs

Although hedgehogs are well-known examples of postglacial recolonisation, the specific processes that shape their population structures have not been examined by detailed sampling and fast-evolving genetic markers in combination with model based clustering methods. This study aims to analyse the impacts of isolation within glacial refugia and of postglacial expansion on the population structure of the Northern White-breasted hedgehog (Erinaceus roumanicus). It also discusses the role of the processes at edges of species distribution in its evolutionary history. The maternally inherited mitochondrial control region and the bi-parentally inherited nuclear microsatellites were used to examine samples within the Central Europe, Balkan Peninsula and adjacent islands. Bayesian coalescent inference and neutrality tests proposed a recent increase in the population size. The most pronounced pattern of population structure involved differentiation of the insular populations in the Mediterranean Sea and the population within the contact zone with E. europaeus in Central Europe. An interspecies hybrid was detected for the first time in Central Europe. A low genetic diversity was observed in Crete, while the highest genetic distances among individuals were found in Romania. The recent population in the post-refugial area related to the Balkan Peninsula shows a complex pattern with pronounced subpopulations located mainly in the Pannonian Basin and at the Adriatic and Pontic coasts. Detailed analyses indicate that parapatry and peripatry may not be the only factors that limit range expansion, but also strong microevolutionary forces that may change the genetic structure of the species. Here we present evidence showing that population differentiation may occur not only during the glacial restriction of the range into the refugia, but also during the interglacial range expansion. Population differentiation at the Balkan Peninsula and adjacent regions could be ascribed to diversification in steppe/forest biomes and complicated geomorphology, including pronounced geographic barriers as Carpathians.

Speciation processes in putative island endemic sister bat species: false impressions from mitochondrial DNA and microsatellite data

Cases of geographically restricted co-occurring sister taxa are rare and may point to potential divergence with gene flow. The two bat species Murina gracilis and Murina recondita are both endemic to Taiwan and are putative sister species. To test for nonallopatric divergence and gene flow in these taxa, we generated sequences using Sanger and next-generation sequencing, and combined these with microsatellite data for coalescent-based analyses. MtDNA phylogenies supported the reciprocally monophyletic sister relationship between M. gracilis and M. recondita; however, clustering of microsatellite genotypes revealed several cases of species admixture suggesting possible introgression. Sequencing of microsatellite flanking regions revealed that admixture signatures stemmed from microsatellite allele homoplasy rather than recent introgressive hybridization, and also uncovered an unexpected sister relationship between M. recondita and the continental species Murina eleryi, to the exclusion of M. gracilis. To dissect the basis of these conflicts between ncDNA and mtDNA, we analysed sequences from 10 anonymous ncDNA loci with *beast and isolation-with-migration and found two distinct clades of M. eleryi, one of which was sister to M. recondita. We conclude that Taiwan was colonized by the ancestor of M. gracilis first, followed by the ancestor of M. recondita after a period of allopatric divergence. After colonization, the mitochondrial genome of M. recondita was replaced by that of the resident M. gracilis. This study illustrates how apparent signatures of sympatric divergence can arise from complex histories of allopatric divergence, colonization and hybridization, thus highlighting the need for rigorous analyses to distinguish between such scenarios.

Hidden diversity in Senegalese bats and associated findings in the systematics of the family Vespertilionidae

INTRODUCTION

The Vespertilionidae is the largest family of bats, characterized by high occurrence of morphologically convergent groups, which impedes the study of their evolutionary history. The situation is even more complicated in the tropics, where certain regions remain under-sampled.

RESULTS

Two hundred and thirteen vespertilionid bats from Senegal (West Africa) were studied with the use of non-differentially stained karyotypes and multi-locus sequence data analysed with maximum likelihood and Bayesian methods. These bats were identified as 10 different taxa, five of which were distinctive from their nominate species (Pipistrellus hesperidus, Nycticeinops schlieffenii, Scotoecus hirundo, Neoromicia nana and N. somalica), based on both karyotypes and molecular data. These five cryptic taxa are unrelated, suggesting that these West African populations have long been isolated from other African regions. Additionally, we phylogenetically analysed 166 vespertilionid taxa from localities worldwide using GenBank data (some 80% of the genera of the family) and 14 representatives of closely related groups, together with our Senegalese specimens. The systematic position of several taxa differed from previous studies and the tribes Pipistrellini and Vespertilionini were redefined. The African Pipistrellus rueppellii was basal to the Pipistrellus/Nyctalus clade and the Oriental species Glischropus tylopus was basal to the East Asian pipistrelles within the tribe Pipistrellini. The African genus Neoromicia was confirmed to be diphyletic. Based on GenBank data, Eptesicus was polyphyletic, with the Asian E. nasutus and E. dimissus both supported as phylogenetically distinct from the Eptesicus clade. The subfamily Scotophilinae was confirmed as one of the basal branches of Vespertilionidae.

CONCLUSIONS

New taxa and new systematic arrangements show that there is still much to resolve in the vespertilionids and that West Africa is a biogeographic hotspot with more diversity to be discovered.

Phylogenetic and demographic insights into Kuhl's pipistrelle, Pipistrellus kuhlii, in the Middle East

Kuhl's pipistrelle is found from Europe and North Africa all of the way to Asia, yet studies have thus far concentrated on the western limit of its distribution. Here we form a multi-marker picture of the diversity of Kuhl's pipistrelle at a mid point in the Arabian peninsula in an attempt to redress the western sampling bias and to represent a region from which no genetic data has thus far been presented for this species. The three Arabian Cytochrome b haplotypes showed a clear divergence of 19 substitutions from those found in either Europe or North Africa. Molecular dating suggests the Arabian population split from the remaining Kuhl's somewhere between 0.7 and 1.7 million years before present around the time of a series of aridification events across northern Africa. Well supported lineages within Arabia are typical of that which may be seen after an expansion from multiple Pleistocene refugia, but may also reflect the loss of intermediate haplotypes during historical population fluctuations. A long-term population contraction coincides with climatic changes towards those conditions more typical of contemporary Arabia.

Hybridization hotspots at bat swarming sites

During late summer and early autumn in temperate zones of the Northern Hemisphere, thousands of bats gather at caves, mainly for the purpose of mating. We demonstrated that this swarming behavior most probably leads not only to breeding among bats of the same species but also interbreeding between different species. Using 14 nuclear microsatellites and three different methods (the Bayesian assignment approaches of STRUCTURE and NEWHYBRIDS and a principal coordinate analysis of pairwise genetic distances), we analyzed 375 individuals belonging to three species of whiskered bats (genus Myotis) at swarming sites across their sympatric range in southern Poland. The overall hybridization rate varied from 3.2 to 7.2%. At the species level, depending on the method used, these values ranged from 2.1-4.6% in M. mystacinus and 3.0-3.7% in M. brandtii to 6.5-30.4% in M. alcathoe. Hybrids occurred in about half of the caves we studied. In all three species, the sex ratio of hybrids was biased towards males but the observed differences did not differ statistically from those noted at the population level. In our opinion, factors leading to the formation of these admixed individuals and their relatively high frequency are: i) swarming behaviour at swarming sites, where high numbers of bats belonging to several species meet; ii) male-biased sex ratio during the swarming period; iii) the fact that all these bats are generally polygynous. The highly different population sizes of different species at swarming sites may also play some role. Swarming sites may represent unique hybrid hotspots, which, as there are at least 2,000 caves in the Polish Carpathians alone, may occur on a massive scale not previously observed for any group of mammal species in the wild. Evidently, these sites should be treated as focal points for the conservation of biodiversity and evolutionary processes.

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.

Population genetics study of common (Pipistrellus pipistrellus) and soprano (Pipistrellus pygmaeus) pipistrelle bats from central Europe suggests interspecific hybridization

The discovery that the most widespread bat in Europe comprises cryptic species, Pipistrellus pipistrellus (Schreber, 1774) (common pipistrelle) and Pipistrellus pygmaeus (Leach, 1825) (soprano pipistrelle), provides a great opportunity to look at the mechanism of species coexistence. Based on eight nuclear microsatellite loci (n = 353), we observed similarities between the species in Poland with respect to heterozygosity, allelic richness, mean relatedness, and inbreeding coefficients. However, pronounced differences in migratory patterns (shown by assignment tests) suggest that P. pygmaeus is the more migratory species. The proportion of bats migrating between colonies differed significantly, with 17.1% and 41.8% individuals of P. pygmaeus and P. pipistrellus, respectively, confidently assigned to colonies of origin. Both species demonstrated a more migratory character in central Europe compared with the populations from the British Isles. Given the cryptic nature of the examined taxa, we also assessed whether they hybridize. Hybridization was confirmed by three methods—one based on genetic distance and two based on Bayesian approaches. The overall hybridization rate, depending on assumed threshold values, ranged from 1.7% to 13.3% for both species. We conclude that the population structuring in these pipistrelles is not homogenous across their range. Moreover, hybridization between them in continental Europe does occur and is not rare.

Microevolution of sympatry: landscape genetics of hedgehogs Erinaceus europaeus and E. roumanicus in Central Europe

We used the mitochondrial control region and nuclear microsatellites to assess the distribution patterns, population structure, demography and landscape genetics for the hedgehogs Erinaceus europaeus and Erinaceus roumanicus in a transect of the mid-European zone of sympatry. E. roumanicus was less frequent and restricted to regions with lower altitudes. Demographic analyses suggested recent population growth in this species. A comparison of patterns in the spatial variability of mitochondrial and nuclear DNA indicated less sex-biased dispersal and higher levels of gene flow in E. roumanicus. No evidence of recent hybridisation or introgression was detected. We interpreted these results by comparing with phylogeographic and palaeontological studies as well as with the occurrence of hybridisation in the Russian contact zone. We propose that Central Europe was colonised by E. roumanicus by the beginning of the Neolithic period and that there was a subsequent reinforcement stage as well as the formation of a zone of sympatry after the complete reproductive isolation of both species.

Population growth of Mexican free-tailed bats (Tadarida brasiliensis mexicana) predates human agricultural activity

Background

Human activities, such as agriculture, hunting, and habitat modification, exert a significant effect on native species. Although many species have suffered population declines, increased population fragmentation, or even extinction in connection with these human impacts, others seem to have benefitted from human modification of their habitat. Here we examine whether population growth in an insectivorous bat (Tadarida brasiliensis mexicana) can be attributed to the widespread expansion of agriculture in North America following European settlement. Colonies of T. b. mexicana are extremely large (~10⁶ individuals) and, in the modern era, major agricultural insect pests form an important component of their food resource. It is thus hypothesized that the growth of these insectivorous bat populations was coupled to the expansion of agricultural land use in North America over the last few centuries.

Results

We sequenced one haploid and one autosomal locus to determine the rate and time of onset of population growth in T. b. mexicana. Using an approximate Maximum Likelihood method, we have determined that T. b. mexicana populations began to grow ~220 kya from a relatively small ancestral effective population size before reaching the large effective population size observed today.

Conclusions

Our analyses reject the hypothesis that T. b. mexicana populations grew in connection with the expansion of human agriculture in North America, and instead suggest that this growth commenced long before the arrival of humans. As T. brasiliensis is a subtropical species, we hypothesize that the observed signals of population growth may instead reflect range expansions of ancestral bat populations from southern glacial refugia during the tail end of the Pleistocene.