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Parsimony haplotype networks for Cynopterus sphinx and Rousettus leschenaulti. Parsimony haplotype networks for a) Cynopterus sphinx and b) Rousettus leschenaulti. Haplotypes are colour coded based on sampling locality, as follows: Guangdong = dark green, Yunnan = light green, Hainan = blue, Guangxi = yellow, Vietnam = red, India = pink. Circles are sized in proportion to the number of individuals with that haplotype. doi:10.1371/journal.pone.0013903.g003
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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 organizatio...
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Northeast India with two biodiversity hotspots is recognized as a biodiversity-rich region. However, several extant animals including chiropterans are currently at jeopardy due to habitat loss, electrocution mortality, and other anthropogenic threats. This study examines the efficacy of mitochondrial Cytochrome b (mtCytb) sequences for species-leve...
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... El nivel de diversidad y flujo genético también se relaciona directamente con la capacidad de dispersión. Las especies con limitada capacidad de dispersión tienden a mostrar una mayor estructura poblacional en comparación con especies con una gran capacidad de dispersión (Storz et al., 2001, Chen et al., 2010. ...
La variabilidad genética es un factor importante para la supervivencia de los individuos ya que permite a los individuos adaptarse a los cambios ambientales. A pesar de que al Nasua narica se le considera el único carnívoro verdaderamente sociable que habita en los bosques neotropicales, se sospecha que las poblaciones que habitan en Norteamérica se han aislado genéticamente de forma gradual, debido principalmente a la fragmentación y pérdida de hábitat.
Se analizaron la variabilidad y estructura genética del N. narica en cinco poblaciones de México (Parque Museo de La Venta, Parque Nacional El Tepozteco, Puerto Morelos, Punta Raza y Reserva de la Biosfera de Chamela-Cuixmala) mediante el uso de marcadores moleculares, 12 microsatélites específicos y un fragmento del gen de citocromo b. Los resultados mostraron niveles de moderados a altos en los indicadores de variabilidad genética para ambos marcadores genéticos. La heterocigosidad esperada (HE) fue de 0.664, mientras que la heterocigosidad observada (HO) fue de 0.774. La mayoría de los microsatélites se encontraron en equilibrio de Hardy-Weinberg. Todos los loci fueron polimórficos en las cinco poblaciones y el promedio de alelos por locus fue de 5.033 ± 1.794 (DE). La diversidad haplotípica (h) para las poblaciones en conjunto fue 0.968 ± 0.008 (DE) y la diversidad nucleotídica (π) de 0.007 ± 0.001 (DE).
Se registraron 22 haplotipos distintos, la mayoría fueron específicos de una de las áreas muestreadas, sólo tres se compartieron entre las distintas poblaciones. Se encontraron diferencias significativas entre las poblaciones de la Costa del Pacífico (Punta Raza y Reserva de la Biosfera Chamela-Cuixmala), las del centro (Parque Nacional El Tepozteco) y sureste del país (Parque Museo La Venta y Puerto Morelos), corroborando que el aislamiento genético tiene un efecto significativo en ésta especie resultando en una estructura genética compuesta por cinco diferentes subpoblaciones.
... The high level of genetic diversity observed in R. leschenaulti can be described using four factors: (i) extra-colony copulations without permanent dispersal from the parent colony, (ii) absence of substructure, (iii) greater vagility of the species (an adaptation associated with cave roosting) and (iv) seasonal migration. These factors are the consequences of higher levels of gene flow among colonies 26 . In spite of coming from geographically different locations in Tamil Nadu, populations from Tirupparankundram and Vengadachalapuram as well as Palayamkottai and Aralvaimozhi, appeared genetically closely connected to each other. ...
... Therefore, depending on whether mating occurs prior to or during migration, it may offer additional chances to encourage gene flow among colonies. Additionally, one of the adaptations displayed by this species is greater vagility which is associated with cave roosting 26 . ...
... If the population distribution is continuous, gene flow may also be larger than the ability of an individual species to disperse. These results suggest that R. leschenaulti mating before or during migration may offer additional possibilities to encourage gene flow 26 . Due to the adaptability of R. leschenaulti to cave roosting and extra-colony copulations without permanent dispersal from the natal colony, the majority of genetic variation distributed within populations is not surprising and may be due to significant levels of gene flow. ...
... During recent years, numerous studies have shown that different bat species exhibit dissimilar levels of vulnerability to habitat fragmentation (e.g., Asher, 2009;Meyer et al., 2009;Lino et al., 2019;Rodríguez et al., 2020). The response of a particular species to local or widespread environmental change likely depends on species-specific ecological traits, including their degree of specialization to a particular habitat and the capability to move over fragmented forests (Meyer et al., 2008b;Chen et al., 2010;Anderson et al., 2018;Budinski et al., 2019). Other factors, such as life history traits, ecological plasticity, and characteristics of the habitat matrix in which they occur, could also substantially influence the response to habitat loss of a particular species (Schulze et al., 2000). ...
Vagility, ecological requirements, and forest patches can all influence gene flow among populations. These aspects are critical forthe maintenance of genetic diversity in populations. Ectophylla alba is a fruit bat belonging to the family Phyllostomidae withspecialized feeding and habitat requirements. Studies examining population genetics in this specialist bat are lacking. In this study,ten microsatellite loci were used to evaluate the current genetic structure of this bat species. Six localities in Costa Rica w ereevaluated. These localities are included in a landscape with remnants of lowland forests surrounded by cattle pastures, plantat ions,urban areas, and roads. Our results suggest a genetic population with moderate genetic diversity that was observed at most stud iedloci, with a statistically non-significant difference between the observed and expected heterozygosity. Most of the genetic variationwas observed within rather than among sampled populations. The Mantel test showed a non-significant correlation between geneticdiversity and geographic distance. These results suggest that E. alba populations have not shown an effect of habitat fragmentationin the studied area. We argue that the increase of forest patches is too recent to alter genetic diversity among sampled locali ties.Current migration among populations appears to be high enough to balance allele frequencies among localities.
... During recent years, numerous studies have shown that different bat species exhibit dissimilar levels of vulnerability to habitat fragmentation (e.g., Asher, 2009;Meyer et al., 2009;Lino et al., 2019;Rodríguez et al., 2019). The response of a particular species to local or widespread environmental change likely depends on species-specific ecological traits, including their degree of specialization to a particular habitat and the capability to move over fragmented forests (Meyer et al., 2008b;Chen et al., 2010;Anderson et al., 2018;Budinski et al., 2019). Other factors, such as life history traits, ecological plasticity, and characteristics of the habitat matrix in which they occur, could also substantially influence the response to habitat loss of a particular species (Schulze et al., 2000). ...
... Members of the genus Rousettus are capable of long-distance movements of 10 to 25 km from their day roost site per night for foraging (Bastian et al., 2001;Lučan et al., 2016); and gene exchange between populations from different areas can result in low genetic interpopulation structure. In R. leschenaultii, analysis of mitochondrial and nuclear markers has shown no evidence of genetic structure between the populations of India and China (Chen et al., 2010), indicating a broad geographical dispersal. However, certain populations of R. aegyptiacus in sub-Saharan Africa show notable genetic structure (Stribna et al., 2019;Hassanin et al., 2020). ...
... The ability of Rousettus to echolocate (Waters and Vollrath, 2003), which is rare among pteropodid bats, their use of caves for day roosting sites and lack of dependence on trees for roosting (Chen et al., 2010), favoured the colonization of a range of habitats. This ecological breadth permitted members of the genus to expand their distribution in Asia, Middle East, Africa and Indian Ocean islands. ...
The Old World tropical and subtropical frugivorous bat genus Rousettus (Pteropodidae) contains species with broad distributions, as well as those occurring in restricted geographical areas, particularly islands. Herein we review the role of Rousettus as a keystone species from a global “One Health” approach and related to ecosystem functioning, zoonotic disease and public health. Rousettus are efficient at dispersing seeds and pollinating flowers; their role in forest regeneration is related to their ability to fly considerable distances during nightly foraging bouts and their relatively small body size, which allows them to access fruits in forested areas with closed vegetation. Rousettus are also reservoirs for various groups of pathogens (viruses, bacteria, fungi, protozoa), which, by definition, are infectious agents causing disease. The study of day roosts of different species of Rousettus and the successful establishment of captive breeding colonies have provided important details related to the infection dynamics of their associated pathogens. Large-scale conversion of forested areas into agricultural landscapes has increased contact between humans and Rousettus, therefore augmenting the chances of infectious agent spillover. Many crucial scientific details are still lacking related to members of this genus, which have direct bearing on the prevention of emerging disease outbreaks, as well as the conservation of these bats. The public should be better informed on the capacity of fruit bats as keystone species for large scale forest regeneration and in spreading pathogens. Precise details on the transmission of zoonotic diseases of public health importance associated with Rousettus should be given high priority.
... Considering that R. leschenaultii migrates annually back and forth between Iran and India and also this species is a potential reservoir of several viruses, such as ebolavirus, coronaviruses, and flaviviruses, we assessed morphological and population genetic differences between this species and the morphologically similar R. aegyptiacus to provide diagnostic tools for future medical research. Furthermore, the hypothesis of the range expansion of these two species of fruit bats mentioned by Chen et al. 26 and Stribna et al. 27 was also examined to predict the long-term dynamic of bat-borne pathogens in response to climate change based on epidemiological triad. We also refer to genetic and morphological differences between these two species of megabats from Iran as they are a potential reservoir of the coronavirus. ...
Background: Bats are potential reservoir hosts for vector-borne diseases that can transmit many bacterial and viral agents to humans. Fruit bats are considered reservoirs of many viruses and they are of major importance in the medical sciences for controlling and preventing vector-borne diseases. This study aimed to compare the morphological and genetic differences of two fruit bat species, Rousettus aegyptiacus and R. leschenaultii in Iran, implying anessential need for taxonomic expertise in applied medical sciences. Methods: In this experimental study, we collected and identified 26 specimens of bats belonging to two fruit bat species from the southeast of Iran. The morphological and genetic differences were characterized between recently recorded migratory fruit bat R. leschenaultii and the morphologically similar and resident R. aegyptiacus. The haplotype network was generated using the program POPART. The nucleotide variation and population differentiation were calculated in DNAsp. Furthermore, we considered additional records of 15 specimens from three widespread bat species in the north of Iran. Results: Morphological characterization of two fruit bat species showed R. aegyptiacus is larger than R. leschenaultii in morphometric variables except tail length (TL) for both sexes. The demographic analyses revealed that all haplotypes of R. leschenaulti formed a single haplogroup in the species' distributional range. In contrast, haplotypes of R. aegyptiacus were divided into five haplogroups respecting taxa/localities. The results represent a strong signature of population expansion for these two species of bats. Conclusion: Population of the fruit bats throughout their ranges in the Middle East may indicate an increased risk of the spread of viral agents over time. Therefore, precise identification of hosts and vectors in applied medical sciences is essential to conduct standard procedures.
... Among mammals, bats (order Chiroptera) represent the only truly volant group and may provide an opportunity to test hypotheses about the role of dispersal in maintaining panmixia. Several species of bats have been reported to show patterns of panmixia including Tadarida brasiliensis in North America (Russell et al., 2005;Speer et al., 2017) as well as Pteropus sp., Nyctalus noctula, Rousettus lesche naultii, Cynopterus sphinx, Eptesicus serotinus, and Epomophorus gambianus in the Old World (Webb and Tidemann, 1996;Petit and Mayer, 1999;Chen et al., 2010;Peel et al., 2013;Moussy et al., 2015;Riesle-Sbarbaro et al., 2018). Despite these examples, panmixia is thought to be relatively rare in bats, with most species exhibiting patterning of genetic structure across their range (Juste et al., 2009;Clare et al., 2013;Stoffberg et al., 2012). ...
Modern phylogeographic methods have confirmed that species with broad ranges often exhibit fine-scale patterns of genetic variation that are not reflected in their morphology. Recent genetic analyses of the straw-colored fruit bat (Eidolon helvum) deviate from this trend in identifying this species as broadly panmictic across its range in Sub-Saharan Africa. However, the limitations of sampling, along with potential for modern anthropogenic impacts to distort observed patterns, suggest that additional work is needed to assess true historical patterns of geographic variation in this species. We used Next Generation Sequencing (NGS) methods to assess patterns of variation found in historical samples of E. helvum and its sister species, E. dupreanum (a Malagasy endemic). Patterns of genomic variation observed among specimens collected between 1909 and 1983 were compared with those from more recently collected tissue samples from across much of the range of the genus. Our genetic analyses confirm that E. helvum and E. dupreanum are distinct species as traditionally recognized. Congruent with results from prior analyses of modern samples, no patterns of spatial genomic structuring were identified in E. helvum across continental Africa in either recent times or earlier in the 20th century. These results suggest that the currently observed pattern of panmixia in E. helvum is not a recent phenomenon; significant gene flow is apparently ongoing in this species across an exceptionally large area. This suggests that potentially zoonotic pathogens previously associated with populations of E. helvum may be similarly distributed or episodically transmitted across broad areas by this species. Our study additionally demonstrates that analyses utilizing ‘archival’ DNA from older specimens in museum collections have the potential to illuminate patterns of both past and contemporary biodiversity, and to help assess the impacts of habitat loss and climate change on species at the genomic level.
... Non-lethal tissue collection methods for subsequent DNA extraction (wing membrane, tail membrane, or tail tips) [17,18], can enhance species identification in bat capture-release studies and allow for additional research such as phylogeographic analysis [19]. The main pro of this sampling strategy is to affect natural populations as less as possible, acquiring particular relevance in the study of threatened species. ...
Bats are among the most diverse, widespread, and abundant mammals. In Argentina, 67 species of bats have been recorded, belonging to 5 families and 29 genera. These high levels of biodiversity are likely to complicate identification at fieldwork, especially between closely related species, where external morphology-based approaches are the only immediate means for a priori species assignment. The use of molecular markers can enhance species identification, and acquires particular relevance in capture-release studies. In this study, we discuss the extent of the use of the mitochondrial cytochrome b gene for species identification, comparing external morphology identification with a molecular phylogenetic classification based on this marker, under the light of current bat systematics. We analyzed 33 samples collected in an eco-epidemiological survey in the province of Santa Fe (Argentina). We further sequenced 27 museum vouchers to test the accuracy of cytochrome b -based phylogenies in taxonomic identification of bats occurring in the Pampean/Chacoan regions of Argentina. The cytochrome b gene was successfully amplified in all Molossid and Vespertilionid species except for Eptesicus , for which we designed a new reverse primer. The resulting Bayesian phylogeny was congruent with current systematics. Cytochrome b proved useful for species-level delimitation in non-conflicting genera ( Eumops , Dasypterus , Molossops ) and has infrageneric resolution in more complex lineages ( Eptesicus , Myotis , Molossus ). We discuss four sources of incongruence that may act separately or in combination: 1) molecular processes, 2) biology, 3) limitations in identification, and 4) errors in the current taxonomy. The present study confirms the general applicability of cytochrome b -based phylogenies in eco-epidemiological studies, but its resolution and reliability depend mainly, but not solely, on the level of genetic differentiation within each bat genus.
... Furthermore, to test whether their habitat associations informed past demographic histories in response to changes in forest extent that occurred during the Last Glacial Maximum (LGM). Species with similar habitat associations are expected to depict similar demographic histories due to shared biogeographic histories (Chen et al., 2010). I hypothesize concordance in population genetic trends for species utilising similar habitats (Campbell et al., 2006) iv. ...
... We aimed to test if habitat associations have played an important role in determining bat species' responses to changes in forest that occurred during the LGM. Species with similar habitat associations are expected to depict similar demographic histories due to shared biogeographical histories (Chen et al., 2010). We hypothesized concordance in population genetic trends for species utilising similar habitats (Campbell et al., 2006): forest associated species should show high levels of population structure as their distribution is dependent on fragmented forests, while habitat generalists should demonstrate low geographical structuring as suitable habitats are more widely available. ...
Bats are a highly diverse mammalian order and are some of the most economically important non-domesticated vertebrates, providing many ecosystem services that contribute to the global economy. Yet, they remain a largely understudied taxon, particularly in the Eastern Cape province of South Africa, in which basic surveys of bat assemblages utilising indigenous forests are lacking. Indigenous forests constitute South Africa’s smallest and most fragmented biome yet support disproportionally high biodiversity. They have been fragmented throughout most of their evolutionary history due to global palaeoclimatic shifts; the responses of bats to forest fragmentation and historical climatic shifts in this habitat have been poorly studied.
This study addresses these gaps with the broad aims of compiling a species inventory from 17 forests across the Eastern Cape and KwaZulu-Natal provinces; assessing the effects of fragmentation and biogeography on taxonomic and functional diversity of bat assemblages; and determining how genetic diversity and population genetic structure are informed by forest habitat associations and fragmentation. A multi-faceted approach of sampling methods, including capture and acoustic recording, and species identification techniques (morphology, acoustics, and DNA barcoding) were used to assemble an inventory of 25 species, with range extensions noted for six species. The first reference call library of hand released bats for forests in this region is presented, which may be used for species identification in further acoustic surveys. A minimum acoustic monitoring period of 6 to 7 nights per forest is recommended for future surveys.
Forest biogeography was an important determinant of the functional diversity of insectivorous bat assemblages. Forest edge effects were found to demonstrate a positive relationship with functional evenness, thus motivating for maintenance and conservation of forest edges, particularly in temperate regions. Larger forearm length and low wing loading were identified as morphological traits exhibiting greater sensitivity to fragmentation, flagging species exhibiting these traits as potentially vulnerable to habitat fragmentation.
The effect of historical climate-induced fluctuations of forest extent on population genetic structuring and demographic histories for six species was investigated using two mitochondrial markers, cytochrome b and D-loop. Population genetic trends were not informed by forest habitat associations, but rather by species-specific traits of dispersal ability, philopatry, and roost utilisation. Low genetic diversity and high population structure identify two species, Rhinolophus swinnyi and Laephotis botswanae, for conservation priority. Demographic responses to the Last Glacial Maximum (LGM) were not detected, with all six species displaying population expansions over this time. It appears that volant insectivores in eastern South Africa were less affected by the harsh conditions of the LGM than elsewhere.
The dusky pipistrelle (Pipistrellus hesperidus) was used as a model organism to investigate the gene flow, genetic diversity, and migration of a forest-utilising species across the region with the use of eight microsatellite markers. The effects of urbanisation and agricultural development on gene flow were also examined. Findings of low population structure, low migration rates, and two genetic discontinuities were presented. This species does not depict dependence on forested habitats to maintain genetic connectivity on the landscape. The data also suggest that agricultural development and urbanisation have not yet had an impact on gene flow, thus providing a baseline with which to monitor the effects of future anthropic development on this species.
Overall, this study has provided novel insights into the taxonomic, functional, and genetic diversity of forest-utilising bats in relation to biogeographical history and fragmentation within eastern South Africa.
... These two regions are hotspots of CoV phylogenetic diversity, harboring evolutionarily old and phylogenetically diverse lineages of αand β-CoVs. South western China acted as a refugium during Quaternary glaciation for numerous plant and animal species, including several bat species, such as R. affinis 65 , Rhinolophus sinicus 66 , Myotis davidii 67 , and Cynopterus sphinx 68 . The stable and long-term persistence of bats and other mammals throughout the Quaternary may explain the deep macroevolutionary diversity of bat-CoVs in these regions 69 . ...
Bats are presumed reservoirs of diverse coronaviruses (CoVs) including progenitors of Severe Acute Respiratory Syndrome (SARS)-CoV and SARS-CoV-2, the causative agent of COVID-19. However, the evolution and diversification of these coronaviruses remains poorly understood. Here we use a Bayesian statistical framework and a large sequence data set from bat-CoVs (including 630 novel CoV sequences) in China to study their macroevolution, cross-species transmission and dispersal. We find that host-switching occurs more frequently and across more distantly related host taxa in alpha- than beta-CoVs, and is more highly constrained by phylogenetic distance for beta-CoVs. We show that inter-family and -genus switching is most common in Rhinolophidae and the genus Rhinolophus. Our analyses identify the host taxa and geographic regions that define hotspots of CoV evolutionary diversity in China that could help target bat-CoV discovery for proactive zoonotic disease surveillance. Finally, we present a phylogenetic analysis suggesting a likely origin for SARS-CoV-2 in Rhinolophus spp. bats.
