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Uvizl M, Puechmaille SJ, Power S, Pippel M, Carthy S, Haerty W, Myers EW, Teeling EC, Huang Z. Comparative Genome Microsynteny Illuminates the Fast Evolution of Nuclear Mitochondrial Segments (NUMTs) in Mammals. Mol Biol Evol 2024; 41:msad278. [PMID: 38124445 PMCID: PMC10764098 DOI: 10.1093/molbev/msad278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 11/16/2023] [Accepted: 12/12/2023] [Indexed: 12/23/2023] Open
Abstract
The escape of DNA from mitochondria into the nuclear genome (nuclear mitochondrial DNA, NUMT) is an ongoing process. Although pervasively observed in eukaryotic genomes, their evolutionary trajectories in a mammal-wide context are poorly understood. The main challenge lies in the orthology assignment of NUMTs across species due to their fast evolution and chromosomal rearrangements over the past 200 million years. To address this issue, we systematically investigated the characteristics of NUMT insertions in 45 mammalian genomes and established a novel, synteny-based method to accurately predict orthologous NUMTs and ascertain their evolution across mammals. With a series of comparative analyses across taxa, we revealed that NUMTs may originate from nonrandom regions in mtDNA, are likely found in transposon-rich and intergenic regions, and unlikely code for functional proteins. Using our synteny-based approach, we leveraged 630 pairwise comparisons of genome-wide microsynteny and predicted the NUMT orthology relationships across 36 mammals. With the phylogenetic patterns of NUMT presence-and-absence across taxa, we constructed the ancestral state of NUMTs given the mammal tree using a coalescent method. We found support on the ancestral node of Fereuungulata within Laurasiatheria, whose subordinal relationships are still controversial. This study broadens our knowledge on NUMT insertion and evolution in mammalian genomes and highlights the merit of NUMTs as alternative genetic markers in phylogenetic inference.
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Affiliation(s)
- Marek Uvizl
- Department of Zoology, National Museum, 19300 Prague, Czech Republic
- Department of Zoology, Faculty of Science, Charles University, 12844 Prague, Czech Republic
| | - Sebastien J Puechmaille
- Institut des Sciences de l’Evolution de Montpellier (ISEM), University of Montpellier, 34095 Montpellier, France
- Institut Universitaire de France, Paris, France
| | - Sarahjane Power
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Martin Pippel
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- National Bioinformatics Infrastructure Sweden, Uppsala, Sweden
| | - Samuel Carthy
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Wilfried Haerty
- Earlham Institute, Norwich Research Park, Colney Ln, NR4 7UZ Norwich, UK
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Eugene W Myers
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Emma C Teeling
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Zixia Huang
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
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2
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Srinivasulu B, Srinivasulu A. A new species of the Miniopterus australis species complex (Chiroptera: Miniopteridae) from the Western Ghats, India. Zootaxa 2023; 5296:233-249. [PMID: 37518447 DOI: 10.11646/zootaxa.5296.2.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Indexed: 08/01/2023]
Abstract
The genus Miniopterus is highly diverse in cryptic species. Based on integrated approaches of morphometrics, echolocation call analysis, and molecular phylogenetics, we present evidence of a hitherto undescribed species, Srini's Bent-winged bat Miniopterus srinii sp. nov.. The new species, found in the Western Ghats of southern Karnataka, India, closely resembles the Small Bent-winged bat Miniopterus pusillus, found elsewhere in Karnataka, Kerala, and Tamil Nadu, India. Although it shows external similarity with Miniopterus pusillus sensu stricto from the Nicobar Islands, the new species is relatively larger and distinct in craniodental measurements and echolocation call parameters, despite slight overlaps. Importantly, Miniopterus srinii exhibits morphological convergence with Miniopterus pusillus as despite similarities in morphologies, there is a significant genetic distance of 10.84 ± 0.22%. The new cryptic species shares distribution with Miniopterus phillipsi and Miniopterus pusillus in the Western Ghats, further highlighting the need to study both the genus' cryptic diversity, and the region's conservation importance.
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Affiliation(s)
- Bhargavi Srinivasulu
- Department of Zoology; University College of Science; Osmania University; Hyderabad - 500007; Telangana State; India Centre for Biodiversity and Conservation Studies; #F5; CFRD Building; Osmania University; Hyderabad - 500007; Telangana State; India.
| | - Aditya Srinivasulu
- Ecology and Conservation Lab; School of Biological Sciences; University of Reading; Whiteknights; Reading; United Kingdom.
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3
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Kundu S, Kamalakannan M, Mukherjee T, Banerjee D, Kim HW. Genetic Characterization and Insular Habitat Enveloping of Endangered Leaf-Nosed Bat, Hipposideros nicobarulae (Mammalia: Chiroptera) in India: Phylogenetic Inference and Conservation Implication. Genes (Basel) 2023; 14:genes14030765. [PMID: 36981035 PMCID: PMC10048616 DOI: 10.3390/genes14030765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/16/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
The Nicobar leaf-nosed Bat (Hipposideros nicobarulae) was described in the early 20th century; however, its systematic classification has been debated for over 100 years. This endangered and endemic species has achieved species status through morphological data in the last 10 years. However, the genetic information and phylogenetic relationships of H. nicobarulae remain neglected. The generated mitochondrial cytochrome b gene (mtCytb) sequences (438 bp) of H. nicobarulae contains 53.42-53.65% AT composition and 1.82% variable sites. The studied species, H. nicobarulae maintains an 8.1% to 22.6% genetic distance from other Hipposideros species. The genetic divergence estimated in this study is congruent with the concept of gene speciation in bats. The Bayesian and Maximum-Likelihood phylogenies clearly discriminated all Hipposideros species and showed a sister relationship between H. nicobarulae and H. cf. antricola. Current mtCytb-based investigations of H. nicobarulae have confirmed the species status at the molecular level. Further, the MaxEnt-based species distribution modelling illustrates the most suitable habitat of H. nicobarulae (294 km2), of which the majority (171 km2) is located on Great Nicobar Island. The present study suggests rigorous sampling across the range, taxonomic coverage, the generation of multiple molecular markers (mitochondrial and nuclear), as well as more ecological information, which will help in understanding population genetic structure, habitat suitability, and the implementation of appropriate conservation action plans for H. nicobarulae and other Hipposideros species.
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Affiliation(s)
- Shantanu Kundu
- Department of Marine Biology, Pukyong National University, Busan 48513, Republic of Korea
| | | | - Tanoy Mukherjee
- Agricultural and Ecological Research Unit, Indian Statistical Institute, Kolkata 700108, India
| | - Dhriti Banerjee
- Western Ghat Regional Centre, Zoological Survey of India, Kozhikode 673006, India
- Zoological Survey of India, M Block, New Alipore, Kolkata 700053, India
| | - Hyun-Woo Kim
- Department of Marine Biology, Pukyong National University, Busan 48513, Republic of Korea
- Marine Integrated Biomedical Technology Center, National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea
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Enriquez MS, Swanson N, Putland RL, Tait T, Gluesenkamp AG, McGaugh SE, Mensinger AF. Evidence for rapid divergence of sensory systems between Texas populations of the Mexican tetra (Astyanax mexicanus). Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.1085975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023] Open
Abstract
Population divergence is often quantified using phenotypic variation. However, because sensory abilities are more difficult to discern, we have little information on the plasticity and rate of sensory change between different environments. The Mexican tetra (Astyanax mexicanus) is a fish distributed throughout Southern Texas and Northern Mexico and has evolved troglomorphic phenotypes, such as vestigial eyes and reduced pigmentation, when surface ancestors invaded caves in the past several hundred thousand years. In the early 1900s, surface A. mexicanus were introduced to the karstic Edwards-Trinity Aquifer in Texas. Subsequent cave colonization of subterranean environments resulted in fish with phenotypic and behavioral divergence from their surface counterparts, allowing examination of how new environments lead to sensory changes. We hypothesized that recently introduced cave populations would be more sensitive to light and sound when compared to their surface counterparts. We quantified divergence using auditory evoked potentials (AEPs) and particle acceleration levels (PALs) to measure differences in sound sensitivity, and electroretinography (ERGs) to measure light sensitivity. We also compared these results to measurements taken from native populations and lab-born individuals of the introduced populations. Honey Creek Cave fish were significantly more sensitive than proximate Honey Creek surface fish to sound pressure levels between 0.6 and 0.8 kHz and particle acceleration levels between 0.4 and 0.8 kHz. Pairwise differences were found between San Antonio Zoo surface and the facultative subterranean San Pedro Springs and Blue Hole populations, which exhibited more sensitivity to particle acceleration levels between 0.5 and 0.7 kHz. Electroretinography results indicate no significant differences between populations, although Honey Creek Cave fish may be trending toward reduced visual sensitivity. Auditory thresholds between wild-caught and lab-raised populations of recently invaded fish show significant differences in sensitivity, suggesting that these traits are plastic. Collectively, while these results may point to the rapid divergence of A. mexicanus in cave habitats, it also highlights the responsive plasticity of A. mexicanus auditory system to disparate environments.
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Benda P, Uvizl M, Vallo P, Reiter A, Uhrin M. A Revision of the Rhinolophus hipposideros group (Chiroptera: Rhinolophidae) with Definition of an Additional Species from the Middle East. ACTA CHIROPTEROLOGICA 2023. [DOI: 10.3161/15081109acc2022.24.2.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Petr Benda
- Department of Zoology, Department of Zoology, National Museum (Natural History), Václavské nám. 68, CZ-115 79 Praha 1, Czech Republic
| | - Marek Uvizl
- Department of Zoology, Department of Zoology, National Museum (Natural History), Václavské nám. 68, CZ-115 79 Praha 1, Czech Republic
| | - Peter Vallo
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Květná 8, CZ-603 65 Brno, Czech Republic
| | - Antonín Reiter
- South Moravian Museum in Znojmo, Přemyslovců 129/8, CZ-669 02 Znojmo, Czech Republic
| | - Marcel Uhrin
- Department of Zoology, Institute of Biology and Ecology, Faculty of Science, P. J. Šafárik University, Šrobárova 2, SK-041 80 Košice, Slovakia
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Gumbs R, Gray CL, Böhm M, Burfield IJ, Couchman OR, Faith DP, Forest F, Hoffmann M, Isaac NJB, Jetz W, Mace GM, Mooers AO, Safi K, Scott O, Steel M, Tucker CM, Pearse WD, Owen NR, Rosindell J. The EDGE2 protocol: Advancing the prioritisation of Evolutionarily Distinct and Globally Endangered species for practical conservation action. PLoS Biol 2023; 21:e3001991. [PMID: 36854036 PMCID: PMC9974121 DOI: 10.1371/journal.pbio.3001991] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023] Open
Abstract
The conservation of evolutionary history has been linked to increased benefits for humanity and can be captured by phylogenetic diversity (PD). The Evolutionarily Distinct and Globally Endangered (EDGE) metric has, since 2007, been used to prioritise threatened species for practical conservation that embody large amounts of evolutionary history. While there have been important research advances since 2007, they have not been adopted in practice because of a lack of consensus in the conservation community. Here, building from an interdisciplinary workshop to update the existing EDGE approach, we present an "EDGE2" protocol that draws on a decade of research and innovation to develop an improved, consistent methodology for prioritising species conservation efforts. Key advances include methods for dealing with uncertainty and accounting for the extinction risk of closely related species. We describe EDGE2 in terms of distinct components to facilitate future revisions to its constituent parts without needing to reconsider the whole. We illustrate EDGE2 by applying it to the world's mammals. As we approach a crossroads for global biodiversity policy, this Consensus View shows how collaboration between academic and applied conservation biologists can guide effective and practical priority-setting to conserve biodiversity.
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Affiliation(s)
- Rikki Gumbs
- Conservation and Policy, Zoological Society of London, Regent’s Park, London, United Kingdom
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, Berkshire, United Kingdom
- IUCN SSC Phylogenetic Diversity Task Force, London, United Kingdom
- Science and Solutions for a Changing Planet DTP, Grantham Institute, Imperial College London, South Kensington, London, United Kingdom
| | - Claudia L. Gray
- Conservation and Policy, Zoological Society of London, Regent’s Park, London, United Kingdom
| | - Monika Böhm
- Institute of Zoology, Zoological Society of London, Regent’s Park, London, United Kingdom
- Global Center for Species Survival, Indianapolis Zoological Society, Indianapolis, Indiana, United States of America
| | - Ian J. Burfield
- BirdLife International, David Attenborough Building, Cambridge, United Kingdom
| | - Olivia R. Couchman
- Conservation and Policy, Zoological Society of London, Regent’s Park, London, United Kingdom
| | - Daniel P. Faith
- School of Philosophical and Historical Inquiry, The University of Sydney, Sydney, Australia
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey, United Kingdom
| | - Michael Hoffmann
- Conservation and Policy, Zoological Society of London, Regent’s Park, London, United Kingdom
| | - Nick J. B. Isaac
- UK Centre for Ecology & Hydrology, Crowmarsh Gifford, Wallingford, United Kingdom
| | - Walter Jetz
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
- Center for Biodiversity and Global Change, Yale University, New Haven, Connecticut, United States of America
| | - Georgina M. Mace
- Department of Genetics, Evolution & Environment, University College London, London, United Kingdom
| | - Arne O. Mooers
- Biological Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Kamran Safi
- Max-Planck Institute of Animal Behavior, Department of Migration, Radolfzell, Germany
- University of Konstanz, Department of Biology, Konstanz, Germany
| | - Oenone Scott
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | - Mike Steel
- Biomathematics Research Centre, University of Canterbury, Christchurch, New Zealand
| | - Caroline M. Tucker
- Environment, Ecology and Energy Program, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - William D. Pearse
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, Berkshire, United Kingdom
- Department of Biology and Ecology Center, Utah State University, Logan, Utah, United States of America
| | - Nisha R. Owen
- Conservation and Policy, Zoological Society of London, Regent’s Park, London, United Kingdom
- IUCN SSC Phylogenetic Diversity Task Force, London, United Kingdom
- On the EDGE Conservation, London, United Kingdom
| | - James Rosindell
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, Berkshire, United Kingdom
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7
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Li J, Sun K, Dai W, Leng H, Feng J. Divergence in interspecific and intersubspecific gene expression between two closely related horseshoe bats ( Rhinolophus). J Mammal 2022. [DOI: 10.1093/jmammal/gyac103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Abstract
Closely related species have been used as representative systems to investigate the genetic mechanisms involved in the early stages of species differentiation. Previous studies have indicated that variation in gene expression might be a sensitive indicator of initial species divergence, although the role of expression divergence, and especially that associated with phenotypic variation remained relatively undefined. For three organs (cochlea, brain, and liver) from two closely related bat species (Rhinolophus siamensis and R. episcopus), the interspecific and intersubspecific gene expression profiles were compared using transcriptomics in this study. Striking organ specificity of expression was observed, and expression profiles exhibited similarities between cochlea and brain tissues. Numerous differentially expressed genes (DEGs) were identified for each organ in the interspecific comparison (cochlea/brain/liver: 1,069/647/692) and intersubspecific comparison (608/528/368). Functional enrichment analysis indicated vital variation in expression related to the immune system, ion activities, neuronal function, and multisensory system regulation in both comparisons. DEGs relevant to the variation in echolocation calls (RF) were found, and some of them were involved in the pivotal patterns of expression variation. The regulation of immune, ion channel, neural activity, and sophisticated sensory functions at the expression level might be key mechanisms in the early species divergence of bats, and the expression variation related to acoustical signal could have played a crucial part. This study expands our knowledge of gene expression and patterns of variation for three key organs to echolocation at both the interspecific and intersubspecific levels. Further, the framework described here provides insight into the genetic basis of phenotypic variation during the incipient stage of species differentiation.
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Affiliation(s)
- Jun Li
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University , Changchun 130117 , China
- Key Laboratory of Vegetation Ecology, Ministry of Education , Changchun 130024 , China
| | - Keping Sun
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University , Changchun 130117 , China
- Key Laboratory of Vegetation Ecology, Ministry of Education , Changchun 130024 , China
| | - Wentao Dai
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University , Changchun 130117 , China
- Key Laboratory of Vegetation Ecology, Ministry of Education , Changchun 130024 , China
| | - Haixia Leng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University , Changchun 130117 , China
- Key Laboratory of Vegetation Ecology, Ministry of Education , Changchun 130024 , China
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University , Changchun 130117 , China
- College of Life Science, Jilin Agricultural University , Changchun 130118 , China
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Li J, Sun K, Dai W, Leng H, Li A, Feng J. Extensive Adaptive Variation in Gene Expression within and between Closely Related Horseshoe Bats (Chiroptera, Rhinolophus) Revealed by Three Organs. Animals (Basel) 2022; 12:ani12233432. [PMID: 36496954 PMCID: PMC9741297 DOI: 10.3390/ani12233432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
In the process of species differentiation and adaption, the relative influence of natural selection on gene expression variation often remains unclear (especially its impact on phenotypic divergence). In this study, we used differentially expressed genes from brain, cochlea, and liver samples collected from two species of bats to determine the gene expression variation forced by natural selection when comparing at the interspecific (Rhinolophus siamensis and R. episcopus episcopus) and the intraspecific (R. e. episcopus and R. episcopus spp.) levels. In both cases, gene expression variation was extensively adaptive (>66.0%) and mainly governed by directional selection, followed by stabilizing selection, and finally balancing selection. The expression variation related to acoustic signals (resting frequency, RF) and body size (forearm length, FA) was also widely governed by natural selection (>69.1%). Different functional patterns of RF- or FA-related adaptive expression variation were found between the two comparisons, which manifested as abundant immune-related regulations between subspecies (indicating a relationship between immune response and phenotypic adaption). Our study verifies the extensive adaptive expression variation between both species and subspecies and provides insight into the effects of natural selection on species differentiation and adaptation as well as phenotypic divergence at the expression level.
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Affiliation(s)
- Jun Li
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China
- Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun 130024, China
| | - Keping Sun
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China
- Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun 130024, China
- Correspondence: (K.S.); (J.F.)
| | - Wentao Dai
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China
- Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun 130024, China
| | - Haixia Leng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China
- Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun 130024, China
| | - Aoqiang Li
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China
- Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun 130024, China
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China
- College of Life Science, Jilin Agricultural University, Changchun 130118, China
- Correspondence: (K.S.); (J.F.)
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9
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Lin A, Feng J, Kanwal JS. Geographic Variation in Social Vocalizations of the Great Himalayan Leaf-Nosed Bat, Hipposideros armiger: Acoustic Overflow Across Population Boundaries. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.948324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Bat populations employ rich vocal repertoires for social communication in addition to emitting sound pulses for echolocation. Acoustic parameters of echolocation pulses can vary with the context in which they are emitted, and also with the individual and across populations as a whole. The acoustic parameters of social vocalizations, or “calls”, also vary with the individual and context, but not much is known about their variation across populations at different geographic locations. Here, we leveraged the detailed acoustic classification of social vocalizations available for the Great Himalayan leaf-nosed bat, Hipposideros armiger, to examine geographic variation in five commonly emitted simple syllable types. We hypothesized that individuals within geographically dispersed populations communicate using spectrographically similar constructs or “syllable types”. We also examined whether call syllables vary discordantly with the correlation pattern observed for echolocation pulses across those same geographic regions. Furthermore, we postulated that the acoustic boundaries of a syllable type are not uniquely constrained to its variation within a particular population of the same subspecies. To test our hypotheses, we obtained recordings of social calls of H. a. armiger from nine locations within the oriental region. These locations were consolidated into five geographic regions based on previously established region-specific differences in the peak frequency of echolocation pulses. A multivariate cluster analysis established that unlike echolocation pulses, syllable types exhibit a relatively large variance. Analysis of this variance showed significant differences in Least Squares Means estimates, establishing significant population-level differences in the multiparametric means of individual syllable types across geographic regions. Multivariate discriminant analysis confirmed the presence of region-specific centroids for different syllable constructs, but also showed a large overlap of their multiparametric boundaries across geographic regions. We propose that despite differences in the population-specific core construct of a syllable type, bats maximize acoustic variation across individuals within a population irrespective of its overflow and overlap with other populations.
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Walters AD, Trujillo DA, Berg DJ. Micro-endemic species of snails and amphipods show population genetic structure across very small geographic ranges. Heredity (Edinb) 2022; 128:325-337. [PMID: 35318433 PMCID: PMC9076663 DOI: 10.1038/s41437-022-00521-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 02/22/2022] [Accepted: 02/22/2022] [Indexed: 11/08/2022] Open
Abstract
Understanding variation in population genetic structure, even across small distances and for species with extremely limited ranges, is critical for conservation planning and the development of effective management strategies for imperiled species. Organisms that occupy the same geographic extent can maintain different population structures, ranging from highly diverged to panmictic. Such differences can result from differences in biological characteristics such as dispersal ability or demographic history. We used microsatellite loci to evaluate population genetic structure and variation of four desert spring invertebrates having high to low dispersal ability: the lung snail Physa acuta, two species of gilled snails (Juturnia kosteri and Pyrgulopsis roswellensis; family Hydrobiidae) and the amphipod Gammarus desperatus. The study location represents entire species ranges for the micro-endemic hydrobiids and G. desperatus, while P. acuta is ubiquitous throughout much of North America. We found little evidence of significant population genetic structure for P. acuta and J. kosteri, but much more for P. roswellensis and G. desperatus. Our results demonstrate differences in habitat preference and/or dispersal ability between the species. This information provides insight into how gene flow shapes varying population genetic structure between species across small spatial scales (<100 km2). Most importantly, our results suggest that conservation agencies should not consider these micro-endemic species to be composed of single populations, but rather, that management plans for such species should account for population genetic variation across the species' ranges.
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Affiliation(s)
| | | | - David J Berg
- Department of Biology, Miami University, Hamilton, OH, USA
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11
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Uvizl M, Benda P. Intraspecific Variation of Myotis emarginatus (Chiroptera: Vespertilionidae) Inferred from Mitochondrial and Nuclear Genetic Markers. ACTA CHIROPTEROLOGICA 2022. [DOI: 10.3161/15081109acc2021.23.2.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Marek Uvizl
- Department of Zoology, Faculty of Science, Charles University in Prague, Viničná 7, 128 44 Praha 2, Czech Republic
| | - Petr Benda
- Department of Zoology, Faculty of Science, Charles University in Prague, Viničná 7, 128 44 Praha 2, Czech Republic
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12
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Abduriyim S, Kasimu T, Lan JK, Pu ZL, Bai JL, Wang YC. Morphological and molecular confirmation of the common pipistrelle bat, Pipistrellus pipistrellus Schreber, 1774 (Vespertilionidae: Chiroptera), in Xinjiang, China. MAMMALIA 2021. [DOI: 10.1515/mammalia-2021-0045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
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.
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Affiliation(s)
- Shamshidin Abduriyim
- Xinjiang Production and Construction Corps Key Laboratory of Oasis Town and Mountain-Basin System Ecology, Shihezi University , Shihezi , China
- College of Life Science, Shihezi University , Shihezi 832003 , Xinjiang , China
| | - Tuerxunpaxia Kasimu
- College of Animal Science and Technology, Shihezi University , Shihezi 832003 , Xinjiang , China
| | - Jing-Kai Lan
- Xinjiang Production and Construction Corps Key Laboratory of Oasis Town and Mountain-Basin System Ecology, Shihezi University , Shihezi , China
| | - Zi-Li Pu
- Xinjiang Production and Construction Corps Key Laboratory of Oasis Town and Mountain-Basin System Ecology, Shihezi University , Shihezi , China
| | - Jin-Long Bai
- Xinjiang Production and Construction Corps Key Laboratory of Oasis Town and Mountain-Basin System Ecology, Shihezi University , Shihezi , China
| | - You-Cai Wang
- Xinjiang Production and Construction Corps Key Laboratory of Oasis Town and Mountain-Basin System Ecology, Shihezi University , Shihezi , China
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Krásová J, Mikula O, Bryja J, Baptista NL, António T, Aghová T, Šumbera R. Biogeography of Angolan rodents: The first glimpse based on phylogenetic evidence. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13435] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
- Jarmila Krásová
- Department of Zoology Faculty of Science University of South Bohemia České Budějovice Czech Republic
- Institute of Vertebrate Biology of the Czech Academy of Sciences Brno Czech Republic
| | - Ondřej Mikula
- Institute of Vertebrate Biology of the Czech Academy of Sciences Brno Czech Republic
- Institute of Animal Physiology and Genetics of the Czech Academy of Sciences Brno Czech Republic
| | - Josef Bryja
- Institute of Vertebrate Biology of the Czech Academy of Sciences Brno Czech Republic
- Department of Botany and Zoology Faculty of Science Masaryk University Brno Czech Republic
| | - Ninda L. Baptista
- Instituto Superior de Ciências da Educação da Huíla (ISCED‐Huíla) Lubango Angola
- CIBIO‐InBIO Centro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do Porto Vairão Portugal
- Faculdade de Ciências Universidade do Porto Porto Portugal
| | - Telmo António
- Instituto Superior de Ciências da Educação da Huíla (ISCED‐Huíla) Lubango Angola
| | - Tatiana Aghová
- Centre of OncocytogenomicsInstitute of Medical Biochemistry and Laboratory DiagnosticsGeneral University Hospital and First Faculty of MedicineCharles University Prague Czech Republic
| | - Radim Šumbera
- Department of Zoology Faculty of Science University of South Bohemia České Budějovice Czech Republic
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14
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Baldwin HJ, Vallo P, Ruiz AT, Anti P, Nkrumah EE, Badu EK, Oppong SK, Kalko EKV, Tschapka M, Stow AJ. Concordant patterns of genetic, acoustic, and morphological divergence in the West African Old World leaf‐nosed bats of the
Hipposideros caffer
complex. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Heather J. Baldwin
- Institute of Evolutionary Ecology and Conservation Genomics Ulm University Ulm Germany
- Department of Biological Sciences Macquarie University Sydney NSW Australia
| | - Peter Vallo
- Institute of Evolutionary Ecology and Conservation Genomics Ulm University Ulm Germany
- Institute of Vertebrate Biology of the Czech Academy of Sciences Brno Czech Republic
| | - A. Tonatiuh Ruiz
- Institute of Neural Information Processing Ulm University Ulm Germany
| | - Priscilla Anti
- Department of Wildlife and Range Management Kwame Nkrumah University of Science and Technology Kumasi Ghana
| | - Evans E. Nkrumah
- Department of Wildlife and Range Management Kwame Nkrumah University of Science and Technology Kumasi Ghana
| | - Ebenezer K. Badu
- Department of Wildlife and Range Management Kwame Nkrumah University of Science and Technology Kumasi Ghana
| | - Samuel K. Oppong
- Department of Wildlife and Range Management Kwame Nkrumah University of Science and Technology Kumasi Ghana
| | - Elisabeth K. V. Kalko
- Institute of Evolutionary Ecology and Conservation Genomics Ulm University Ulm Germany
- Smithsonian Tropical Research Institute Balboa Panama
| | - Marco Tschapka
- Institute of Evolutionary Ecology and Conservation Genomics Ulm University Ulm Germany
- Smithsonian Tropical Research Institute Balboa Panama
| | - Adam J. Stow
- Department of Biological Sciences Macquarie University Sydney NSW Australia
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15
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Tamura N, Boonkhaw P, Prayoon U, Phan QT, Yu P, Liu X, Hayashi F. Geographical variation in squirrel mating calls and their recognition limits in the widely distributed species complex. Behav Ecol Sociobiol 2021. [DOI: 10.1007/s00265-021-03022-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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16
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Baveja P, Garg KM, Chattopadhyay B, Sadanandan KR, Prawiradilaga DM, Yuda P, Lee JGH, Rheindt FE. Using historical genome-wide DNA to unravel the confused taxonomy in a songbird lineage that is extinct in the wild. Evol Appl 2021; 14:698-709. [PMID: 33767745 PMCID: PMC7980273 DOI: 10.1111/eva.13149] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 10/13/2020] [Indexed: 11/29/2022] Open
Abstract
Urgent conservation action for terminally endangered species is sometimes hampered by taxonomic uncertainty, especially in illegally traded animals that are often cross-bred in captivity. To overcome these problems, we used a genomic approach to analyze historical DNA from museum samples across the Asian Pied Starling (Gracupica contra) complex in tropical Asia, a popular victim of the ongoing songbird crisis whose distinct Javan population ("Javan Pied Starling") is extinct in the wild and subject to admixture in captivity. Comparing genomic profiles across the entire distribution, we detected three deeply diverged lineages at the species level characterized by a lack of genomic intermediacy near areas of contact. Our study demonstrates that the use of historical DNA can be instrumental in delimiting species in situations of taxonomic uncertainty, especially when modern admixture may obfuscate species boundaries. Results of our research will enable conservationists to commence a dedicated ex situ breeding program for the Javan Pied Starling, and serve as a blueprint for similar conservation problems involving terminally endangered species subject to allelic infiltration from close congeners.
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Affiliation(s)
- Pratibha Baveja
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
| | - Kritika M. Garg
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
- Institute of Bioinformatics and Applied BiotechnologyBangaloreIndia
| | - Balaji Chattopadhyay
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
| | - Keren R. Sadanandan
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
- Max Planck Institute for OrnithologySeewiesenGermany
| | | | - Pramana Yuda
- Fakultas TeknobiologiUniversitas Atma Jaya YogyakartaYogyakartaIndonesia
| | - Jessica G. H. Lee
- Department of Conservation and ResearchWildlife Reserves SingaporeSingaporeSingapore
| | - Frank E. Rheindt
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
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17
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Liu T, Zhang K, Dai W, Jin L, Sun K, Feng J. Evolutionary insights into
Rhinolophus episcopus
(Chiroptera, Rhinolophidae) in China: Isolation by distance, environment, or sensory system? J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12394] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tong Liu
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization Northeast Normal University Changchun China
| | - Kangkang Zhang
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization Northeast Normal University Changchun China
| | - Wentao Dai
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization Northeast Normal University Changchun China
| | - Longru Jin
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization Northeast Normal University Changchun China
| | - Keping Sun
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization Northeast Normal University Changchun China
- Key Laboratory of Vegetation Ecology Ministry of Education Changchun China
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization Northeast Normal University Changchun China
- College of Life Science Jilin Agricultural University Changchun China
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18
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Ahmim M, Dalhoumi R, Măntoiu DS. First data on the acoustic characteristics of some Chiropteran species from northern Algeria. BIOACOUSTICS 2020. [DOI: 10.1080/09524622.2019.1620634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Mourad Ahmim
- Faculté des Sciences de la Nature et de la Vie – Laboratoire de Recherche en Ecologie et Environnement, Université de Bejaia, Bejaia, Algérie
| | - Ridha Dalhoumi
- Faculté des Sciences de Bizerte – Laboratoire de Biosurveillance de l’Environnement, Université de Carthage, Carthage, Tunisie
| | - Dragoş Stefan Măntoiu
- Institute of Speleology “Emil Racoviţă”, Cluj Napoca, Napoca, Romania
- Wilderness Research and Conservation, Bucharest, Romania
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19
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Extensive Genetic Diversity of Polyomaviruses in Sympatric Bat Communities: Host Switching versus Coevolution. J Virol 2020; 94:JVI.02101-19. [PMID: 32075934 DOI: 10.1128/jvi.02101-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 02/11/2020] [Indexed: 01/17/2023] Open
Abstract
Polyomaviruses (PyVs) are small DNA viruses carried by diverse vertebrates. The evolutionary relationships of viruses and hosts remain largely unclear due to very limited surveillance in sympatric communities. In order to investigate whether PyVs can transmit among different mammalian species and to identify host-switching events in the field, we conducted a systematic study of a large collection of bats (n = 1,083) from 29 sympatric communities across China which contained multiple species with frequent contact. PyVs were detected in 21 bat communities, with 192 PyVs identified in 186 bats from 15 species within 6 families representing at least 28 newly described PyVs. Surveillance results and phylogenetic analyses surprisingly revealed three interfamily PyV host-switching events in these sympatric bat communities: two distinct PyVs were identified in two bat species in restricted geographical locations, while another PyV clustered phylogenetically with PyVs carried by bats from a different host family. Virus-host relationships of all discovered PyVs were also evaluated, and no additional host-switching events were found. PyVs were identified in different horseshoe bat species in sympatric communities without observation of host-switching events, showed high genomic identities, and clustered with each other. This suggested that even for PyVs with high genomic identities in closely related host species, the potential for host switching is low. In summary, our findings revealed that PyV host switching in sympatric bat communities can occur but is limited and that host switching of bat-borne PyVs is relatively rare on the predominantly evolutionary background of codivergence with their hosts.IMPORTANCE Since the discovery of murine polyomavirus in the 1950s, polyomaviruses (PyVs) have been considered highly host restricted in mammals. Sympatric bat communities commonly contain several different bat species in an ecological niche facilitating viral transmission, and they therefore represent a model to identify host-switching events of PyVs. In this study, we screened PyVs in a large number of bats in sympatric communities from diverse habitats across China. We provide evidence that cross-species bat-borne PyV transmission exists, though is limited, and that host-switching events appear relatively rare during the evolutionary history of these viruses. PyVs with close genomic identities were also identified in different bat species without host-switching events. Based on these findings, we propose an evolutionary scheme for bat-borne PyVs in which limited host-switching events occur on the background of codivergence and lineage duplication, generating the viral genetic diversity in bats.
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20
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Foley NM, Petit EJ, Brazier T, Finarelli JA, Hughes GM, Touzalin F, Puechmaille SJ, Teeling EC. Drivers of longitudinal telomere dynamics in a long‐lived bat species,
Myotis myotis. Mol Ecol 2020; 29:2963-2977. [PMID: 32105386 DOI: 10.1111/mec.15395] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 01/20/2020] [Accepted: 02/18/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Nicole M. Foley
- School of Biology and Environmental Science Science Centre West University College Dublin Belfield, Dublin Ireland
| | - Eric J. Petit
- ESE, Ecology and Ecosystem Health Agrocampus Ouest INRAE Rennes France
| | - Thomas Brazier
- ESE, Ecology and Ecosystem Health Agrocampus Ouest INRAE Rennes France
| | - John A. Finarelli
- School of Biology and Environmental Science Science Centre West University College Dublin Belfield, Dublin Ireland
| | - Graham M. Hughes
- School of Biology and Environmental Science Science Centre West University College Dublin Belfield, Dublin Ireland
| | - Frédéric Touzalin
- School of Biology and Environmental Science Science Centre West University College Dublin Belfield, Dublin Ireland
| | - Sébastien J. Puechmaille
- School of Biology and Environmental Science Science Centre West University College Dublin Belfield, Dublin Ireland
- Zoological Institute and Museum University of Greifswald Greifswald Germany
- ISEM Univ Montpellier, CNRS, EPHE, IRD Montpellier France
| | - Emma C. Teeling
- School of Biology and Environmental Science Science Centre West University College Dublin Belfield, Dublin Ireland
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21
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Tournayre O, Pons J, Leuchtmann M, Leblois R, Piry S, Filippi‐Codaccioni O, Loiseau A, Duhayer J, Garin I, Mathews F, Puechmaille S, Charbonnel N, Pontier D. Integrating population genetics to define conservation units from the core to the edge of Rhinolophus ferrumequinum western range. Ecol Evol 2019; 9:12272-12290. [PMID: 31832159 PMCID: PMC6854333 DOI: 10.1002/ece3.5714] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/11/2019] [Accepted: 09/11/2019] [Indexed: 11/06/2022] Open
Abstract
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.
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Affiliation(s)
- Orianne Tournayre
- CBGPINRACIRADIRDMontpellier SupAgroUniversité de MontpellierMontferrier‐sur‐Lez CedexFrance
| | - Jean‐Baptiste Pons
- LabEx ECOFECT «Ecoevolutionary Dynamics of Infectious Diseases»Université de LyonLyonFrance
| | | | - Raphael Leblois
- CBGPINRACIRADIRDMontpellier SupAgroUniversité de MontpellierMontferrier‐sur‐Lez CedexFrance
| | - Sylvain Piry
- CBGPINRACIRADIRDMontpellier SupAgroUniversité de MontpellierMontferrier‐sur‐Lez CedexFrance
| | | | - Anne Loiseau
- CBGPINRACIRADIRDMontpellier SupAgroUniversité de MontpellierMontferrier‐sur‐Lez CedexFrance
| | - Jeanne Duhayer
- LabEx ECOFECT «Ecoevolutionary Dynamics of Infectious Diseases»Université de LyonLyonFrance
| | - Inazio Garin
- Department of Zoology and Animal Cell BiologyUniversity of the Basque CountryLeioaThe Basque Country
| | - Fiona Mathews
- College of Life SciencesUniversity of SussexFalmerUK
| | - Sébastien Puechmaille
- ISEMUniv MontpellierCNRSEPHEIRDMontpellierFrance
- Groupe Chiroptères de Midi‐Pyrénées (CREN‐GCMP)ToulouseFrance
| | - Nathalie Charbonnel
- CBGPINRACIRADIRDMontpellier SupAgroUniversité de MontpellierMontferrier‐sur‐Lez CedexFrance
| | - Dominique Pontier
- LabEx ECOFECT «Ecoevolutionary Dynamics of Infectious Diseases»Université de LyonLyonFrance
- CNRSLaboratoire de Biométrie et Biologie ÉvolutiveUMR5558Université Lyon 1Université de LyonVilleurbanneFrance
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22
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Gürün K, Furman A, Juste J, Ramos Pereira MJ, Palmeirim JM, Puechmaille SJ, Hulva P, Presetnik P, Hamidovic D, Ibáñez C, Karataş A, Allegrini B, Georgiakakis P, Scaravelli D, Uhrin M, Nicolaou H, Abi-Said MR, Nagy ZL, Gazaryan S, Bilgin R. A continent-scale study of the social structure and phylogeography of the bent-wing bat, Miniopterus schreibersii (Mammalia: Chiroptera), using new microsatellite data. J Mammal 2019. [DOI: 10.1093/jmammal/gyz153] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
AbstractMiniopterus schreibersii is a cave-dwelling bat species with a wide distribution in the western Palearctic spanning southern and central Europe, North Africa, Anatolia, the Middle East, and the Caucasus. We investigated the social structure and its effects on the genetic makeup of this species, using 10 nuclear microsatellite markers and a partial fragment of the mitochondrial cytochrome b gene. Samples were examined from the species' entire circum-Mediterranean range. Local structuring that was previously detected among populations of M. schreibersii using mitochondrial markers was not observed for microsatellite markers, indicating male-biased dispersal for the species. Some support was found for postglacial expansions in Europe, with Anatolia potentially acting as the primary refugium during the Last Glacial Maximum (LGM). However, support for this hypothesis is not as strong as that previously detected using mitochondrial DNA markers. This is likely due to the diminishing effect of male-mediated dispersal, replenishing the nuclear diversity faster than the mitochondrial diversity in regions that are relatively far from the glacial refugia.
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Affiliation(s)
- Kanat Gürün
- Institute of Environmental Sciences, Boğaziçi University, Bebek, Istanbul 34342, Turkey
| | - Andrzej Furman
- Institute of Environmental Sciences, Boğaziçi University, Bebek, Istanbul 34342, Turkey
| | - Javier Juste
- Estación Biológica de Doñana (CSIC), Avda. Américo Vespucio s/n, Seville 41092, Spain
| | - Maria J Ramos Pereira
- CIBER of Epidemiology and Public Health (CIBERESP), Madrid 28029, Spain
- Department of Zoology, Institute of Biosciences, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, Porto Alegre, RS 91540-000, Brazil
- Centre for Environmental and Marine Studies, Wildlife Research Unit, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Jorge M Palmeirim
- Center for Ecology, Evolution and Environmental Change, Dept. Biologia Animal, Faculdade de Ciencias, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Sebastien J Puechmaille
- University College Dublin, School of Biological and Environmental Sciences, Belfield, Dublin 4, Ireland
- Zoology Institute, University of Greifswald, 17489 Greifswald, Germany
- Chauves-souris Aveyron (CSA), 12310, Vimenet, France
| | - Pavel Hulva
- Department of Zoology, Faculty of Science, Charles University in Prague, Viničná 7, CZ-128 44 Praha 2, Czech Republic
- Department of Biology and Ecology, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic
| | - Primoz Presetnik
- Centre for Cartography of Fauna and Flora, Ljubljana Office, Klunova 3, SI-1000, Ljubljana, Slovenia
| | - Daniela Hamidovic
- Croatian Biospeleological Society, Zagreb, Demetrova 1, 10000 Zagreb, Croatia
| | - Carlos Ibáñez
- Estación Biológica de Doñana (CSIC), Avda. Américo Vespucio s/n, Seville 41092, Spain
| | - Ahmet Karataş
- Department of Biology, Niğde University, Niğde 51100, Turkey
| | | | - Panagiotis Georgiakakis
- Natural History Museum of Crete, University of Crete, Knossos Ave., P.O. Box: 2208, GR71 409 Irakleion, Crete, Greece
| | - Dino Scaravelli
- Department Veterinary Medical Sciences, University of Bologna, via Tolara di Sopra 50, 40064 Ozzano dell'Emilia (BO), Italy
| | - Marcel Uhrin
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Moyzesova 11, SK-040 01 Košice, Slovakia
- Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Kamycká 1176, 165 21 Praha 6, Czech Republic
| | - Haris Nicolaou
- Parks and Environment Sector, Forestry Department, Ministry of Agriculture, Natural Resources and Environment, 1414 Nicosia, Cyprus
| | - Mounir R Abi-Said
- Animal Encounter, Aley, Lebanon
- Faculty of Sciences II, Lebanese University, Al Fanar, 90656 Jdeidet, Lebanon
| | | | - Suren Gazaryan
- Institute of Ecology of Mountain Territories RAS, Armand 37A360000, Nalchik, Russia
| | - Raşit Bilgin
- Institute of Environmental Sciences, Boğaziçi University, Bebek, Istanbul 34342, Turkey
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23
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Uvizl M, Šmíd J, Aghová T, Varadínová ZK, Benda P. Molecular Phylogeny and Systematics of the Sheath-Tailed Bats from the Middle East (Emballonuridae: Taphozous and Coleura). ACTA CHIROPTEROLOGICA 2019. [DOI: 10.3161/15081109acc2019.21.1.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Marek Uvizl
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44 Praha, Czech Republic
| | - Jiří Šmíd
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44 Praha, Czech Republic
| | - Tatiana Aghová
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44 Praha, Czech Republic
| | | | - Petr Benda
- Department of Zoology, National Museum (Natural History), Václavské náměstí 68, 115 79 Praha, Czech Republic
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24
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Mammola S, Cardoso P, Culver DC, Deharveng L, Ferreira RL, Fišer C, Galassi DMP, Griebler C, Halse S, Humphreys WF, Isaia M, Malard F, Martinez A, Moldovan OT, Niemiller ML, Pavlek M, Reboleira ASPS, Souza-Silva M, Teeling EC, Wynne JJ, Zagmajster M. Scientists' Warning on the Conservation of Subterranean Ecosystems. Bioscience 2019. [DOI: 10.1093/biosci/biz064] [Citation(s) in RCA: 113] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Abstract
In light of recent alarming trends in human population growth, climate change, and other environmental modifications, a “Warning to humanity” manifesto was published in BioScience in 2017. This call reiterated most of the ideas originally expressed by the Union of Concerned Scientists in 1992, including the fear that we are “pushing Earth's ecosystems beyond their capacities to support the web of life.” As subterranean biologists, we take this opportunity to emphasize the global importance and the conservation challenges associated with subterranean ecosystems. They likely represent the most widespread nonmarine environments on Earth, but specialized subterranean organisms remain among the least documented and studied. Largely overlooked in conservation policies, subterranean habitats play a critical role in the function of the web of life and provide important ecosystem services. We highlight the main threats to subterranean ecosystems and propose a set of effective actions to protect this globally important natural heritage.
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25
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Dávalos LM, Lancaster WC, Núñez-Novas MS, León YM, Lei B, Flanders J, Russell AL. A coalescent-based estimator of genetic drift, and acoustic divergence in the Pteronotus parnellii species complex. Heredity (Edinb) 2019; 122:417-427. [PMID: 30120366 PMCID: PMC6460761 DOI: 10.1038/s41437-018-0129-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 07/04/2018] [Accepted: 07/06/2018] [Indexed: 01/12/2023] Open
Abstract
Determining the processes responsible for phenotypic variation is one of the central tasks of evolutionary biology. While the importance of acoustic traits for foraging and communication in echolocating mammals suggests adaptation, the seldom-tested null hypothesis to explain trait divergence is genetic drift. Here we derive FST values from multi-locus coalescent isolation-with-migration models, and couple them with estimates of quantitative trait divergence, or PST, to test drift as the evolutionary process responsible for phenotypic divergence in island populations of the Pteronotus parnellii species complex. Compared to traditional comparisons of PST to FST, the migration-based estimates of FST are unidirectional instead of bidirectional, simultaneously integrate variation among loci and individuals, and posterior densities of PST and FST can be compared directly. We found the evolution of higher call frequencies is inconsistent with genetic drift for the Hispaniolan population, despite many generations of isolation from its Puerto Rican counterpart. While the Hispaniolan population displays dimorphism in call frequencies, the higher frequency of the females is incompatible with sexual selection. Instead, cultural drift toward higher frequencies among Hispaniolan females might explain the divergence. By integrating Bayesian coalescent and trait analyses, this study demonstrates a powerful approach to testing genetic drift as the default evolutionary mechanism of trait differentiation between populations.
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Affiliation(s)
- Liliana M Dávalos
- Department of Ecology and Evolution and Consortium for Inter-Disciplinary Environmental Research, Stony Brook University, Stony Brook, NY, 11794, USA.
| | - Winston C Lancaster
- Department of Biological Sciences, California State University, Sacramento, CA, 95819, USA
- Department of Biology, University of Alabama, Birmingham, AL, 35294, USA
| | - Miguel S Núñez-Novas
- Museo Nacional de Historia Natural Profesor Eugenio De Jesús Marcano. César Nicolás Penson Street esq. Máximo Gómez, Plaza de la Cultura, Santo Domingo, Dominican Republic
| | - Yolanda M León
- Instituto Tecnológico de Santo Domingo y Grupo Jaragua, Santo Domingo, Dominican Republic
| | - Bonnie Lei
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
- Microsoft, One Microsoft Way, Redmond, WA, 98052, USA
| | - Jon Flanders
- School of Biological Sciences, Life Sciences Building, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
- Bat Conservation International, 500 North Capital of Texas Highway, Austin, TX, 78746, USA
| | - Amy L Russell
- Department of Biology, Grand Valley State University, Allendale, MI, 49401, USA.
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26
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Wu X, Pang Y, Luo B, Wang M, Feng J. Function of Distress Calls in Least Horseshoe Bats: A Field Study Using Playback Experiments. ACTA CHIROPTEROLOGICA 2019. [DOI: 10.3161/15081109acc2018.20.2.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Xiu Wu
- Key Laboratory of Southwest China Wildlife Resources Conservation of Ministry of Education, China West Normal University, Nanchong 637009, China
| | - Yulan Pang
- Key Laboratory of Southwest China Wildlife Resources Conservation of Ministry of Education, China West Normal University, Nanchong 637009, China
| | - Bo Luo
- Key Laboratory of Southwest China Wildlife Resources Conservation of Ministry of Education, China West Normal University, Nanchong 637009, China
| | - Man Wang
- Key Laboratory of Southwest China Wildlife Resources Conservation of Ministry of Education, China West Normal University, Nanchong 637009, China
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, 255 Jingyue Street, Changchun 130117, China
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27
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Filippi-Codaccioni O, Beugin MP, de Vienne DM, Portanier E, Fouchet D, Kaerle C, Muselet L, Queney G, Petit EJ, Regis C, Pons JB, Pontier D. Coexistence of two sympatric cryptic bat species in French Guiana: insights from genetic, acoustic and ecological data. BMC Evol Biol 2018; 18:175. [PMID: 30458712 PMCID: PMC6247516 DOI: 10.1186/s12862-018-1289-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 11/02/2018] [Indexed: 01/29/2023] Open
Abstract
Background The distinction between lineages of neotropical bats from the Pteronotus parnellii species complex has been previously made according to mitochondrial DNA, and especially morphology and acoustics, in order to separate them into two species. In these studies, either sample sizes were too low when genetic and acoustic or morphological data were gathered on the same individuals, or genetic and other data were collected on different individuals. In this study, we intensively sampled bats in 4 caves and combined all approaches in order to analyse genetic, morphologic, and acoustic divergence between these lineages that live in the same caves in French Guiana. Results A multiplex of 20 polymorphic microsatellite markers was developed using the 454-pyrosequencing technique to investigate for the first time the extent of reproductive isolation between the two lineages and the population genetic structure within lineages. We genotyped 748 individuals sampled between 2010 and 2015 at the 20 nuclear microsatellite loci and sequenced a portion of the cytochrome c oxydase I gene in a subset of these. Two distinct, non-overlapping haplogroups corresponding to cryptic species P. alitonus and P. rubiginosus were revealed, in accordance with previous findings. No spatial genetic structure between caves was detected for both species. Hybridization appeared to be quite limited (0.1–4%) using microsatellite markers whereas introgression was more common (7.5%) and asymmetric for mitochondrial DNA (mtDNA). Conclusions The extremely low rate of hybridization could be explained by differences in life cycle phenology between species as well as morphological and acoustical distinction between sexes in one or the other species. Taken together, these results add to our growing understanding of the nature of species boundaries in Pteronotus parnelli, but deserve more in-depth studies to understand the evolutionary processes underlying asymmetric mtDNA introgression in this group of cryptic species. Electronic supplementary material The online version of this article (10.1186/s12862-018-1289-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ondine Filippi-Codaccioni
- University Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558, F-69622, Villeurbanne, France.,Université de Lyon, LabEx Ecofect, Nadine Cizaire, 92 rue Pasteur, CS 30122 69361, Lyon Cedex 07, France.,SEISE 26 bis Barrouil, 33720, Illats, France
| | - Marie-Pauline Beugin
- University Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558, F-69622, Villeurbanne, France.,Université de Lyon, LabEx Ecofect, Nadine Cizaire, 92 rue Pasteur, CS 30122 69361, Lyon Cedex 07, France.,ANTAGENE, Animal Genomics Laboratory, 6 allée du Levant, 69890, La Tour de Salvagny (Lyon), France
| | - Damien M de Vienne
- University Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558, F-69622, Villeurbanne, France.,Université de Lyon, LabEx Ecofect, Nadine Cizaire, 92 rue Pasteur, CS 30122 69361, Lyon Cedex 07, France
| | - Elodie Portanier
- University Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558, F-69622, Villeurbanne, France.,Université de Lyon, VetAgro Sup - Campus Vétérinaire de Lyon, 1 Avenue Bourgelat, BP 83, F-69280, Marcy l'Etoile, France.,Office National de la Chasse et de la Faune Sauvage - Unité Faune de Montagne, 147 Route de Lodève, Les Portes du Soleil, F-34990, Juvignac, France
| | - David Fouchet
- University Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558, F-69622, Villeurbanne, France.,Université de Lyon, LabEx Ecofect, Nadine Cizaire, 92 rue Pasteur, CS 30122 69361, Lyon Cedex 07, France
| | - Cecile Kaerle
- ANTAGENE, Animal Genomics Laboratory, 6 allée du Levant, 69890, La Tour de Salvagny (Lyon), France
| | - Lina Muselet
- ANTAGENE, Animal Genomics Laboratory, 6 allée du Levant, 69890, La Tour de Salvagny (Lyon), France
| | - Guillaume Queney
- ANTAGENE, Animal Genomics Laboratory, 6 allée du Levant, 69890, La Tour de Salvagny (Lyon), France
| | - Eric J Petit
- UMR ESE, Ecology and Ecosystem Health, INRA, Agrocampus Ouest, 65 rue de Saint-Brieuc, 35042, Rennes Cedex, France
| | - Corinne Regis
- University Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558, F-69622, Villeurbanne, France.,Université de Lyon, LabEx Ecofect, Nadine Cizaire, 92 rue Pasteur, CS 30122 69361, Lyon Cedex 07, France
| | - Jean-Baptiste Pons
- University Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558, F-69622, Villeurbanne, France.,Université de Lyon, LabEx Ecofect, Nadine Cizaire, 92 rue Pasteur, CS 30122 69361, Lyon Cedex 07, France
| | - Dominique Pontier
- University Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558, F-69622, Villeurbanne, France. .,Université de Lyon, LabEx Ecofect, Nadine Cizaire, 92 rue Pasteur, CS 30122 69361, Lyon Cedex 07, France.
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28
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High Duty Cycle Echolocation May Constrain the Evolution of Diversity within Horseshoe Bats (Family: Rhinolophidae). DIVERSITY-BASEL 2018. [DOI: 10.3390/d10030085] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The phenotype of organisms is the net result of various evolutionary forces acting upon their lineages over time. When an innovative trait arises that confers a substantial advantage in terms of survival and reproduction, the evolution of adaptive complexes between such an innovation and other traits may constrain diversification of that lineage. The specialized echolocation system of the Rhinolophidae may represent such an innovation which affects other parts of the phenotype. We investigated a potential constraint on the diversity of phenotypes of several species of horseshoe bats within a phylogenetic framework. If phenotypic convergence stems from stasis as a result of the specialized echolocation system, phenotypes should converge not only among members of the same species and between sexes but also among species. We analyzed the phenotypic diversity of >800 individuals of 13–16 species. The phenotypes in the horseshoe bats did indeed converge. There was no sexual size dimorphism in mass, forearm length and wingspan within species and there was marked interspecific similarity in both wing and echolocation variables but marked variability in body mass. Furthermore, correlations of wing and echolocation variables with mass suggest that variability within horseshoe bats was largely the result of selection on body size with allometric responses in wing and echolocation parameters, a potential consequence of constraints imposed by their specialized echolocation.
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29
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Lehnen L, Schorcht W, Karst I, Biedermann M, Kerth G, Puechmaille SJ. Using Approximate Bayesian Computation to infer sex ratios from acoustic data. PLoS One 2018; 13:e0199428. [PMID: 29928036 PMCID: PMC6013104 DOI: 10.1371/journal.pone.0199428] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 06/07/2018] [Indexed: 11/28/2022] Open
Abstract
Population sex ratios are of high ecological relevance, but are challenging to determine in species lacking conspicuous external cues indicating their sex. Acoustic sexing is an option if vocalizations differ between sexes, but is precluded by overlapping distributions of the values of male and female vocalizations in many species. A method allowing the inference of sex ratios despite such an overlap will therefore greatly increase the information extractable from acoustic data. To meet this demand, we developed a novel approach using Approximate Bayesian Computation (ABC) to infer the sex ratio of populations from acoustic data. Additionally, parameters characterizing the male and female distribution of acoustic values (mean and standard deviation) are inferred. This information is then used to probabilistically assign a sex to a single acoustic signal. We furthermore develop a simpler means of sex ratio estimation based on the exclusion of calls from the overlap zone. Applying our methods to simulated data demonstrates that sex ratio and acoustic parameter characteristics of males and females are reliably inferred by the ABC approach. Applying both the ABC and the exclusion method to empirical datasets (echolocation calls recorded in colonies of lesser horseshoe bats, Rhinolophus hipposideros) provides similar sex ratios as molecular sexing. Our methods aim to facilitate evidence-based conservation, and to benefit scientists investigating ecological or conservation questions related to sex- or group specific behaviour across a wide range of organisms emitting acoustic signals. The developed methodology is non-invasive, low-cost and time-efficient, thus allowing the study of many sites and individuals. We provide an R-script for the easy application of the method and discuss potential future extensions and fields of applications. The script can be easily adapted to account for numerous biological systems by adjusting the type and number of groups to be distinguished (e.g. age, social rank, cryptic species) and the acoustic parameters investigated.
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Affiliation(s)
- Lisa Lehnen
- University of Greifswald, Zoological Institute and Museum, Applied Zoology and Nature Conservation, Greifswald, Germany
| | | | - Inken Karst
- NACHTaktiv – Biologists for Bat research GbR, Erfurt, Germany
| | | | - Gerald Kerth
- University of Greifswald, Zoological Institute and Museum, Applied Zoology and Nature Conservation, Greifswald, Germany
| | - Sebastien J. Puechmaille
- University of Greifswald, Zoological Institute and Museum, Applied Zoology and Nature Conservation, Greifswald, Germany
- * E-mail:
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30
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Cummings ME, Endler JA. 25 Years of sensory drive: the evidence and its watery bias. Curr Zool 2018; 64:471-484. [PMID: 30108628 PMCID: PMC6084598 DOI: 10.1093/cz/zoy043] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 05/18/2018] [Indexed: 12/27/2022] Open
Abstract
It has been 25 years since the formalization of the Sensory Drive hypothesis was published in the American Naturalist (1992). Since then, there has been an explosion of research identifying its utility in contributing to our understanding of inter- and intra-specific variation in sensory systems and signaling properties. The main tenet of Sensory Drive is that environmental characteristics will influence the evolutionary trajectory of both sensory (detecting capabilities) and signaling (detectable features and behaviors) traits in predictable directions. We review the accumulating evidence in 154 studies addressing these questions and categorized their approach in terms of testing for environmental influence on sensory tuning, signal characteristics, or both. For the subset of studies that examined sensory tuning, there was greater support for Sensory Drive processes shaping visual than auditory tuning, and it was more prevalent in aquatic than terrestrial habitats. Terrestrial habitats and visual traits were the prevalent habitat and sensory modality in the 104 studies showing support for environmental influence on signaling properties. An additional 19 studies that found no supporting evidence for environmental influence on signaling traits were all based in terrestrial ecosystems and almost exclusively involved auditory signals. Only 29 studies examined the complete coevolutionary process between sensory and signaling traits and were dominated by fish visual communication. We discuss biophysical factors that may contribute to the visual and aquatic bias for Sensory Drive evidence, as well as biotic factors that may contribute to the lack of Sensory Drive processes in terrestrial acoustic signaling systems.
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Affiliation(s)
- Molly E Cummings
- Department of Integrative Biology, University of Texas, Austin, TX, USA
| | - John A Endler
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds, VIC, Australia
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31
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Halczok TK, Brändel SD, Flores V, Puechmaille SJ, Tschapka M, Page RA, Kerth G. Male-biased dispersal and the potential impact of human-induced habitat modifications on the Neotropical bat Trachops cirrhosus. Ecol Evol 2018; 8:6065-6080. [PMID: 29988406 PMCID: PMC6024115 DOI: 10.1002/ece3.4161] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 03/26/2018] [Accepted: 04/16/2018] [Indexed: 12/25/2022] Open
Abstract
Gene flow, maintained through natal dispersal and subsequent mating events, is one of the most important processes in both ecology and population genetics. Among mammalian populations, gene flow is strongly affected by a variety of factors, including the species' ability to disperse, and the composition of the environment which can limit dispersal. Information on dispersal patterns is thus crucial both for conservation management and for understanding the social system of a species. We used 16 polymorphic nuclear microsatellite loci in addition to mitochondrial DNA sequences (1.61 kbp) to analyse the population structure and the sex-specific pattern of natal dispersal in the frog-eating fringe-lipped bat, Trachops cirrhosus, in Central Panama. Our study revealed that-unlike most of the few other investigated Neotropical bats-gene flow in this species is mostly male-mediated. Nevertheless, distinct genetic clusters occur in both sexes. In particular, the presence of genetic differentiation in the dataset only consisting of the dispersing sex (males) indicates that gene flow is impeded within our study area. Our data are in line with the Panama Canal in connection with the widening of the Río Chagres during the canal construction acting as a recent barrier to gene flow. The sensitivity of T. cirrhosus to human-induced habitat modifications is further indicated by an extremely low capture success in highly fragmented areas. Taken together, our genetic and capture data provide evidence for this species to be classified as less mobile and thus vulnerable to habitat change, information that is important for conservation management.
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Affiliation(s)
- Tanja K. Halczok
- Zoological Institute and MuseumGreifswald UniversityGreifswaldGermany
- Smithsonian Tropical Research InstituteBalboa, AncónRepublic of Panamá
| | - Stefan D. Brändel
- Smithsonian Tropical Research InstituteBalboa, AncónRepublic of Panamá
- Institute of Evolutionary Ecology and Conservation GenomicsUniversity of UlmUlmGermany
| | - Victoria Flores
- Smithsonian Tropical Research InstituteBalboa, AncónRepublic of Panamá
- Committee on Evolutionary BiologyUniversity of ChicagoChicagoIllinois
| | | | - Marco Tschapka
- Smithsonian Tropical Research InstituteBalboa, AncónRepublic of Panamá
- Institute of Evolutionary Ecology and Conservation GenomicsUniversity of UlmUlmGermany
| | - Rachel A. Page
- Smithsonian Tropical Research InstituteBalboa, AncónRepublic of Panamá
| | - Gerald Kerth
- Zoological Institute and MuseumGreifswald UniversityGreifswaldGermany
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32
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Zhang C, Jiang T, Lu G, Lin A, Sun K, Liu S, Feng J. Geographical variation in the echolocation calls of bent-winged bats, Miniopterus fuliginosus. ZOOLOGY 2018; 131:36-44. [PMID: 29803625 DOI: 10.1016/j.zool.2018.05.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 05/10/2018] [Accepted: 05/11/2018] [Indexed: 11/16/2022]
Abstract
Evolutionary biologists had a long-standing interest in the evolutionary forces underlying geographical variation in the acoustic signals of animals. However, the evolutionary forces driving acoustic variation are still unclear. In this study, we quantified the geographical variation in the peak frequencies of echolocation calls in eight Miniopterus fuliginosus bat colonies, and assessed the forces that drive acoustic divergence. Our results demonstrated that seven of the colonies had very similar peak frequencies, while only one colony was significantly higher than the others. This similarity in echolocation call frequency among the seven colonies was likely due to frequent dispersal and migration, leading to male-mediated infiltration of nuclear genes. This infiltration enhances gene flow and weakens ecological selection, and also increases interactions in the presence of conspecifics. Significant correlations were not observed between acoustic distances and morphological distances, climatic differences, geographic distances or mtDNA genetic distances. However, variation in acoustic distances was significantly positive correlated with nDNA genetic distance, even after controlling for geographic distance. Interestingly, the relationship between call divergence and genetic distance was no longer significant after excluding the colony with the highest call frequency, which may be due to the minimal genetic distance among the other seven colonies. The highest frequencies of echolocation calls observed in the one colony may be shaped by selection pressure due to loud background noise in the area. Taken together, these results suggest that geographic divergence of echolocation calls may not be subject to genetic drift, but rather, that the strong selective pressure induced by background noise may lead to acoustic and genetic differentiation between JXT and the other colonies.
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Affiliation(s)
- Chunmian Zhang
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, Jilin, PR China
| | - Tinglei Jiang
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, Jilin, PR China.
| | - Guanjun Lu
- College of Urban and Environment Science, Changchun Normal University, Changchun, 130032, PR China
| | - Aiqing Lin
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, Jilin, PR China
| | - Keping Sun
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, Jilin, PR China
| | - Sen Liu
- Institute of Resources & Environment, Henan Polytechnic University, Jiaozuo, 454000, PR China
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, Jilin, PR China; Key Laboratory of Vegetation Ecology of Education Ministry, Institute of Grassland Science, Northeast Normal University, Changchun, Jilin, PR China.
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33
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Foley NM, Hughes GM, Huang Z, Clarke M, Jebb D, Whelan CV, Petit EJ, Touzalin F, Farcy O, Jones G, Ransome RD, Kacprzyk J, O’Connell MJ, Kerth G, Rebelo H, Rodrigues L, Puechmaille SJ, Teeling EC. Growing old, yet staying young: The role of telomeres in bats' exceptional longevity. SCIENCE ADVANCES 2018; 4:eaao0926. [PMID: 29441358 PMCID: PMC5810611 DOI: 10.1126/sciadv.aao0926] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 01/10/2018] [Indexed: 05/02/2023]
Abstract
Understanding aging is a grand challenge in biology. Exceptionally long-lived animals have mechanisms that underpin extreme longevity. Telomeres are protective nucleotide repeats on chromosome tips that shorten with cell division, potentially limiting life span. Bats are the longest-lived mammals for their size, but it is unknown whether their telomeres shorten. Using >60 years of cumulative mark-recapture field data, we show that telomeres shorten with age in Rhinolophus ferrumequinum and Miniopterus schreibersii, but not in the bat genus with greatest longevity, Myotis. As in humans, telomerase is not expressed in Myotis myotis blood or fibroblasts. Selection tests on telomere maintenance genes show that ATM and SETX, which repair and prevent DNA damage, potentially mediate telomere dynamics in Myotis bats. Twenty-one telomere maintenance genes are differentially expressed in Myotis, of which 14 are enriched for DNA repair, and 5 for alternative telomere-lengthening mechanisms. We demonstrate how telomeres, telomerase, and DNA repair genes have contributed to the evolution of exceptional longevity in Myotis bats, advancing our understanding of healthy aging.
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Affiliation(s)
- Nicole M. Foley
- School of Biology and Environmental Science, Science Centre West, University College Dublin, Belfield, Dublin 4, Ireland
| | - Graham M. Hughes
- School of Biology and Environmental Science, Science Centre West, University College Dublin, Belfield, Dublin 4, Ireland
| | - Zixia Huang
- School of Biology and Environmental Science, Science Centre West, University College Dublin, Belfield, Dublin 4, Ireland
| | - Michael Clarke
- School of Biology and Environmental Science, Science Centre West, University College Dublin, Belfield, Dublin 4, Ireland
| | - David Jebb
- School of Biology and Environmental Science, Science Centre West, University College Dublin, Belfield, Dublin 4, Ireland
| | - Conor V. Whelan
- School of Biology and Environmental Science, Science Centre West, University College Dublin, Belfield, Dublin 4, Ireland
| | - Eric J. Petit
- Ecologie et Santé des Ecosystèmes (ESE), Ecology and Ecosystem Health, Agrocampus Ouest, INRA, 35042 Rennes, France
| | - Frédéric Touzalin
- Laboratoire Évolution et Diversité Biologique, UMR 5174: Université Toulouse III, CNRS, ENFA, 118 Route de Narbonne, 31062 Toulouse cedex 9, France
| | - Olivier Farcy
- Le Groupe Chiroptères de Bretagne Vivante/SEPNB, 19 rue Gouesnou BP 62132, 29221 Brest cedex 2, France
| | - Gareth Jones
- School of Biological Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TH, UK
| | - Roger D. Ransome
- School of Biological Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TH, UK
| | - Joanna Kacprzyk
- School of Biology and Environmental Science, Science Centre West, University College Dublin, Belfield, Dublin 4, Ireland
| | - Mary J. O’Connell
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Gerald Kerth
- University of Greifswald, Loitzer Strasse 26, 17489 Greifswald, Germany
| | - Hugo Rebelo
- School of Biological Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TH, UK
- CIBIO-InBIO, Universidade do Porto, Campus de Agrário Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal
- CEABN-InBIO, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-015 Lisboa, Portugal
| | - Luísa Rodrigues
- Instituto da Conservação da Natureza e das Florestas, Avenida da República 16-16B, 1050-191 Lisboa, Portugal
| | - Sébastien J. Puechmaille
- School of Biology and Environmental Science, Science Centre West, University College Dublin, Belfield, Dublin 4, Ireland
- University of Greifswald, Loitzer Strasse 26, 17489 Greifswald, Germany
| | - Emma C. Teeling
- School of Biology and Environmental Science, Science Centre West, University College Dublin, Belfield, Dublin 4, Ireland
- Corresponding author.
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34
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Teeling EC, Vernes SC, Dávalos LM, Ray DA, Gilbert MTP, Myers E. Bat Biology, Genomes, and the Bat1K Project: To Generate Chromosome-Level Genomes for All Living Bat Species. Annu Rev Anim Biosci 2017; 6:23-46. [PMID: 29166127 DOI: 10.1146/annurev-animal-022516-022811] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Bats are unique among mammals, possessing some of the rarest mammalian adaptations, including true self-powered flight, laryngeal echolocation, exceptional longevity, unique immunity, contracted genomes, and vocal learning. They provide key ecosystem services, pollinating tropical plants, dispersing seeds, and controlling insect pest populations, thus driving healthy ecosystems. They account for more than 20% of all living mammalian diversity, and their crown-group evolutionary history dates back to the Eocene. Despite their great numbers and diversity, many species are threatened and endangered. Here we announce Bat1K, an initiative to sequence the genomes of all living bat species (n∼1,300) to chromosome-level assembly. The Bat1K genome consortium unites bat biologists (>148 members as of writing), computational scientists, conservation organizations, genome technologists, and any interested individuals committed to a better understanding of the genetic and evolutionary mechanisms that underlie the unique adaptations of bats. Our aim is to catalog the unique genetic diversity present in all living bats to better understand the molecular basis of their unique adaptations; uncover their evolutionary history; link genotype with phenotype; and ultimately better understand, promote, and conserve bats. Here we review the unique adaptations of bats and highlight how chromosome-level genome assemblies can uncover the molecular basis of these traits. We present a novel sequencing and assembly strategy and review the striking societal and scientific benefits that will result from the Bat1K initiative.
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Affiliation(s)
- Emma C Teeling
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland;
| | - Sonja C Vernes
- Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, 6500 AH, The Netherlands.,Donders Centre for Cognitive Neuroimaging, Nijmegen, 6525 EN, The Netherlands
| | - Liliana M Dávalos
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794-5245, USA
| | - David A Ray
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas 79409, USA
| | - M Thomas P Gilbert
- Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark.,University Museum, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Eugene Myers
- Max Planck Institute for Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | -
- *Full list of Bat1K Consortium members in Supplemental Appendix
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35
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Schöner MG, Schöner CR, Ermisch R, Puechmaille SJ, Grafe TU, Tan MC, Kerth G. Stabilization of a bat-pitcher plant mutualism. Sci Rep 2017; 7:13170. [PMID: 29030597 PMCID: PMC5640698 DOI: 10.1038/s41598-017-13535-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 09/25/2017] [Indexed: 11/23/2022] Open
Abstract
Despite the long persistence of many mutualisms, it is largely unknown which mechanisms stabilize these interactions. This is especially true if only one mutualism partner can choose alternative partners while the other cannot, resulting in a power asymmetry. According to biological market theory the choosing partner should prefer the more dependent partner if the latter offers commodities of higher quality than its competitors. We tested this prediction using Bornean carnivorous pitcher plants (Nepenthes hemsleyana) that strongly rely on faecal nitrogen of bats (Kerivoula hardwickii) which roost inside the pitchers. The bats also roost in furled leaves of various plants. Surprisingly, during field observations the bats did not always choose N. hemsleyana pitchers despite their superior quality but were generally faithful either to pitchers or to furled leaves. In behavioural experiments 21% of the leaf-roosting bats switched to pitchers, while the majority of these bats and all pitcher-roosting individuals were faithful to the roost type in which we had found them. Genetic differentiation cannot explain this faithfulness, which likely results from different roosting traditions. Such traditions could have stabilizing or destabilizing effects on various mutualisms and should be investigated in more detail.
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Affiliation(s)
- Michael G Schöner
- Zoological Institute and Museum, University of Greifswald, Loitzer Straße 26, 17489, Greifswald, Germany.
| | - Caroline R Schöner
- Zoological Institute and Museum, University of Greifswald, Loitzer Straße 26, 17489, Greifswald, Germany
| | - Rebecca Ermisch
- Zoological Institute and Museum, University of Greifswald, Loitzer Straße 26, 17489, Greifswald, Germany
| | - Sébastien J Puechmaille
- Zoological Institute and Museum, University of Greifswald, Loitzer Straße 26, 17489, Greifswald, Germany
| | - T Ulmar Grafe
- Faculty of Science, Biology, University Brunei Darussalam, Tungku Link, Gadong, 1410, Brunei Darussalam
| | - Moi Chan Tan
- Faculty of Science, Biology, University Brunei Darussalam, Tungku Link, Gadong, 1410, Brunei Darussalam
| | - Gerald Kerth
- Zoological Institute and Museum, University of Greifswald, Loitzer Straße 26, 17489, Greifswald, Germany
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36
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López-Baucells A, Torrent L, Rocha R, Pavan AC, Bobrowiec PED, Meyer CFJ. Geographical variation in the high-duty cycle echolocation of the cryptic common mustached bat Pteronotus cf. rubiginosus (Mormoopidae). BIOACOUSTICS 2017. [DOI: 10.1080/09524622.2017.1357145] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Adrià López-Baucells
- Centre for Ecology, Evolution and Environmental Changes (cE3c) Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
- Granollers Museum of Natural Sciences c/ Palaudàries, 102 - Jardins Antoni Jonch Cuspinera, Granollers, Spain
- Biological Dynamics of Forest Fragments Project (BDFFP), National Institute for Amazonian Research and Smithsonian Tropical Research Institute, Manaus, Brazil
| | - Laura Torrent
- Granollers Museum of Natural Sciences c/ Palaudàries, 102 - Jardins Antoni Jonch Cuspinera, Granollers, Spain
| | - Ricardo Rocha
- Centre for Ecology, Evolution and Environmental Changes (cE3c) Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
- Biological Dynamics of Forest Fragments Project (BDFFP), National Institute for Amazonian Research and Smithsonian Tropical Research Institute, Manaus, Brazil
- Metapopulation Research Centre, University of Helsinki, Helsinki, Finland
| | - Ana Carolina Pavan
- Departamento de Ciências Biológicas Escola Superior de Agricultura "Luiz de Queiroz" - ESALQ, University of Sao Paulo, Piracicaba, Brazil
| | - Paulo Estefano D. Bobrowiec
- Biological Dynamics of Forest Fragments Project (BDFFP), National Institute for Amazonian Research and Smithsonian Tropical Research Institute, Manaus, Brazil
- Instituto Nacional de Pesquisas da Amazônia (INPA) Coordenação de Biodiversidade, Manaus, Brazil
| | - Christoph F. J. Meyer
- Centre for Ecology, Evolution and Environmental Changes (cE3c) Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
- Biological Dynamics of Forest Fragments Project (BDFFP), National Institute for Amazonian Research and Smithsonian Tropical Research Institute, Manaus, Brazil
- Ecosystems and Environment Research Centre (EERC), School of Environment and Life Sciences, University of Salford, Salford, UK
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37
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Xie L, Sun K, Jiang T, Liu S, Lu G, Jin L, Feng J. The effects of cultural drift on geographic variation in echolocation calls of the Chinese rufous horseshoe bat (Rhinolophus sinicus
). Ethology 2017. [DOI: 10.1111/eth.12627] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Lifen Xie
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization; Northeast Normal University; Changchun China
| | - Keping Sun
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization; Northeast Normal University; Changchun China
| | - Tinglei Jiang
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization; Northeast Normal University; Changchun China
| | - Sen Liu
- Institute of Resources and Environment; Henan Polytechnic University; Henan China
| | - Guanjun Lu
- College of Urban and Environment Sciences; Changchun Normal University; Changchun China
| | - Longru Jin
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization; Northeast Normal University; Changchun China
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization; Northeast Normal University; Changchun China
- Jilin Agricultural University; Changchun China
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38
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Foley NM, Goodman SM, Whelan CV, Puechmaille SJ, Teeling E. Towards Navigating the Minotaur's Labyrinth: Cryptic Diversity and Taxonomic Revision within the Speciose Genus Hipposideros (Hipposideridae). ACTA CHIROPTEROLOGICA 2017. [DOI: 10.3161/15081109acc2017.19.1.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Nicole M. Foley
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Steven M. Goodman
- Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL, USA
- Association Vahatra, BP 3972, Antananarivo 101, Madagascar
| | - Conor V. Whelan
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Sebastien J. Puechmaille
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
- Applied Zoology and Nature Conservation, Greifswald University, Greifswald, Germany
| | - Emma Teeling
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
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39
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Dool SE, Puechmaille SJ, Kelleher C, McAney K, Teeling EC. The Effects of Human-Mediated Habitat Fragmentation on a Sedentary Woodland-Associated Species (Rhinolophus hipposideros) at Its Range Margin. ACTA CHIROPTEROLOGICA 2016. [DOI: 10.3161/15081109acc2016.18.2.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Serena E. Dool
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Sébastien J. Puechmaille
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Conor Kelleher
- Spring Lane, Carrigagulla, Ballinagree, Macroom, County Cork, Ireland
| | - Kate McAney
- The Vincent Wildlife Trust, Donaghpatrick, Headford, County Galway, Ireland
| | - Emma C. Teeling
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
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40
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Behavioural response of the greater horseshoe bat to geographical variation in echolocation calls. Behav Ecol Sociobiol 2016. [DOI: 10.1007/s00265-016-2182-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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41
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Kacprzyk J, Teeling EC, Kelleher C, Volleth M. Wing Membrane Biopsies for Bat Cytogenetics: Finding of 2n = 54 in Irish Rhinolophushipposideros (Rhinolophidae, Chiroptera, Mammalia) Supports Two Geographically Separated Chromosomal Variants in Europe. Cytogenet Genome Res 2016; 148:279-83. [PMID: 27333200 DOI: 10.1159/000447111] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/16/2016] [Indexed: 11/19/2022] Open
Abstract
In Europe, 2 different diploid chromosome numbers, 2n = 54 and 2n = 56, have been described in the lesser horseshoe bat (Rhinolophushipposideros). The eastern form with 2n = 56 extends from the Czech Republic to Greece. To date, specimens with 54 chromosomes have been reported only from Spain and Germany. This study expands the distributional area of the western variant to Ireland. Strikingly, this distribution of European chromosomal variants is in contrast to the available molecular data that indicate little genetic differentiation of R. hipposideros populations spanning Northwestern to Central Europe. Further, we have developed an optimized protocol for establishing fibroblast cell cultures, suitable for karyotype analyses, from 3-mm wing membrane biopsies. This is a useful technique for cytogenetic studies of endangered bat species, as this non-lethal sampling method imposes only minimum stress to the animal without lasting adverse effects and is routinely used to sample tissue probes for molecular genetic studies in bats.
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Affiliation(s)
- Joanna Kacprzyk
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
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42
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Bilgin R, Gürün K, Rebelo H, Puechmaille SJ, Maracı Ö, Presetnik P, Benda P, Hulva P, Ibáñez C, Hamidovic D, Fressel N, Horáček I, Karataş A, Karataş A, Allegrini B, Georgiakakis P, Gazaryan S, Nagy ZL, Abi-Said M, Lučan RK, Bartonička T, Nicolaou H, Scaravelli D, Karapandža B, Uhrin M, Paunović M, Juste J. Circum-Mediterranean phylogeography of a bat coupled with past environmental niche modeling: A new paradigm for the recolonization of Europe? Mol Phylogenet Evol 2016; 99:323-336. [DOI: 10.1016/j.ympev.2016.03.024] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Revised: 03/16/2016] [Accepted: 03/17/2016] [Indexed: 11/15/2022]
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43
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Dool SE, O’Donnell CFJ, Monks JM, Puechmaille SJ, Kerth G. Phylogeographic-based conservation implications for the New Zealand long-tailed bat, (Chalinolobus tuberculatus): identification of a single ESU and a candidate population for genetic rescue. CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0844-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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44
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Shi H, Dong J, Irwin DM, Zhang S, Mao X. Repetitive transpositions of mitochondrial DNA sequences to the nucleus during the radiation of horseshoe bats (Rhinolophus, Chiroptera). Gene 2016; 581:161-9. [DOI: 10.1016/j.gene.2016.01.035] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 01/20/2016] [Accepted: 01/21/2016] [Indexed: 10/22/2022]
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45
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Jiang T, Wu H, Feng J. Patterns and causes of geographic variation in bat echolocation pulses. Integr Zool 2016; 10:241-56. [PMID: 25664901 DOI: 10.1111/1749-4877.12129] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/09/2015] [Indexed: 01/26/2023]
Abstract
Evolutionary biologists have a long-standing interest in how acoustic signals in animals vary geographically, because divergent ecology and sensory perception play an important role in speciation. Geographic comparisons are valuable in determining the factors that influence divergence of acoustic signals. Bats are social mammals and they depend mainly on echolocation pulses to locate prey, to navigate and to communicate. Mounting evidence shows that geographic variation of bat echolocation pulses is common, with a mean 5-10 kHz differences in peak frequency, and a high level of individual variation may be nested in this geographical variation. However, understanding the geographic variation of echolocation pulses in bats is very difficult, because of differences in sample and statistical analysis techniques as well as the variety of factors shaping the vocal geographic evolution. Geographic differences in echolocation pulses of bats generally lack latitudinal, longitudinal and elevational patterns, and little is known about vocal dialects. Evidence is accumulating to support the fact that geographic variation in echolocation pulses of bats may be caused by genetic drift, cultural drift, ecological selection, sexual selection and social selection. Future studies could relate geographic differences in echolocation pulses to social adaptation, vocal learning strategies and patterns of dispersal. In addition, new statistical techniques and acoustic playback experiments may help to illustrate the causes and consequences of the geographic evolution of echolocation pulse in bats.
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Affiliation(s)
- Tinglei Jiang
- Jilin Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China.,Key Laboratory for Wetland Ecology and Vegetation Restoration of National Environmental Protection, Northeast Normal University, Changchun, China
| | - Hui Wu
- Jilin Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Jiang Feng
- Jilin Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China.,Key Laboratory for Wetland Ecology and Vegetation Restoration of National Environmental Protection, Northeast Normal University, Changchun, China
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46
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Puechmaille SJ. The programstructuredoes not reliably recover the correct population structure when sampling is uneven: subsampling and new estimators alleviate the problem. Mol Ecol Resour 2016; 16:608-27. [DOI: 10.1111/1755-0998.12512] [Citation(s) in RCA: 518] [Impact Index Per Article: 64.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2015] [Revised: 01/08/2016] [Accepted: 01/16/2016] [Indexed: 01/13/2023]
Affiliation(s)
- Sebastien J. Puechmaille
- Zoology Institute; University of Greifswald; Soldmannstraße 14 D-17489 Greifswald Germany
- School of Biology and Environmental Sciences; University College Dublin; Belfield Dublin 4 Ireland
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47
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Dool SE, Puechmaille SJ, Foley NM, Allegrini B, Bastian A, Mutumi GL, Maluleke TG, Odendaal LJ, Teeling EC, Jacobs DS. Nuclear introns outperform mitochondrial DNA in inter-specific phylogenetic reconstruction: Lessons from horseshoe bats (Rhinolophidae: Chiroptera). Mol Phylogenet Evol 2016; 97:196-212. [PMID: 26826601 DOI: 10.1016/j.ympev.2016.01.003] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 01/07/2016] [Accepted: 01/08/2016] [Indexed: 01/22/2023]
Abstract
Despite many studies illustrating the perils of utilising mitochondrial DNA in phylogenetic studies, it remains one of the most widely used genetic markers for this purpose. Over the last decade, nuclear introns have been proposed as alternative markers for phylogenetic reconstruction. However, the resolution capabilities of mtDNA and nuclear introns have rarely been quantified and compared. In the current study we generated a novel ∼5kb dataset comprising six nuclear introns and a mtDNA fragment. We assessed the relative resolution capabilities of the six intronic fragments with respect to each other, when used in various combinations together, and when compared to the traditionally used mtDNA. We focused on a major clade in the horseshoe bat family (Afro-Palaearctic clade; Rhinolophidae) as our case study. This old, widely distributed and speciose group contains a high level of conserved morphology. This morphological stasis renders the reconstruction of the phylogeny of this group with traditional morphological characters complex. We sampled multiple individuals per species to represent their geographic distributions as best as possible (122 individuals, 24 species, 68 localities). We reconstructed the species phylogeny using several complementary methods (partitioned Maximum Likelihood and Bayesian and Bayesian multispecies-coalescent) and made inferences based on consensus across these methods. We computed pairwise comparisons based on Robinson-Foulds tree distance metric between all Bayesian topologies generated (27,000) for every gene(s) and visualised the tree space using multidimensional scaling (MDS) plots. Using our supported species phylogeny we estimated the ancestral state of key traits of interest within this group, e.g. echolocation peak frequency which has been implicated in speciation. Our results revealed many potential cryptic species within this group, even in taxa where this was not suspected a priori and also found evidence for mtDNA introgression. We demonstrated that by using just two introns one can recover a better supported species tree than when using the mtDNA alone, despite the shorter overall length of the combined introns. Additionally, when combining any single intron with mtDNA, we showed that the result is highly similar to the mtDNA gene tree and far from the true species tree and therefore this approach should be avoided. We caution against the indiscriminate use of mtDNA in phylogenetic studies and advocate for pilot studies to select nuclear introns. The selection of marker type and number is a crucial step that is best based on critical examination of preliminary or previously published data. Based on our findings and previous publications, we recommend the following markers to recover phylogenetic relationships between recently diverged taxa (<20 My) in bats and other mammals: ACOX2, COPS7A, BGN, ROGDI and STAT5A.
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Affiliation(s)
- Serena E Dool
- Department of Biological Sciences, Animal Evolution and Systematics Group, University of Cape Town, Cape Town, South Africa; Zoological Institute and Museum, University of Greifswald, Soldmann-Straße 14, D-17487 Greifswald, Germany.
| | - Sebastien J Puechmaille
- Zoological Institute and Museum, University of Greifswald, Soldmann-Straße 14, D-17487 Greifswald, Germany; Midi-Pyrénées bat group (CREN-GCMP), Toulouse, France; School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Nicole M Foley
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland.
| | | | - Anna Bastian
- Department of Biological Sciences, Animal Evolution and Systematics Group, University of Cape Town, Cape Town, South Africa.
| | - Gregory L Mutumi
- Department of Biological Sciences, Animal Evolution and Systematics Group, University of Cape Town, Cape Town, South Africa.
| | - Tinyiko G Maluleke
- Department of Biological Sciences, Animal Evolution and Systematics Group, University of Cape Town, Cape Town, South Africa.
| | - Lizelle J Odendaal
- Department of Biological Sciences, Animal Evolution and Systematics Group, University of Cape Town, Cape Town, South Africa.
| | - Emma C Teeling
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland.
| | - David S Jacobs
- Department of Biological Sciences, Animal Evolution and Systematics Group, University of Cape Town, Cape Town, South Africa.
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48
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Teeling EC, Jones G, Rossiter SJ. Phylogeny, Genes, and Hearing: Implications for the Evolution of Echolocation in Bats. BAT BIOACOUSTICS 2016. [DOI: 10.1007/978-1-4939-3527-7_2] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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49
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Huang Z, Gallot A, Lao NT, Puechmaille SJ, Foley NM, Jebb D, Bekaert M, Teeling EC. A nonlethal sampling method to obtain, generate and assemble whole blood transcriptomes from small, wild mammals. Mol Ecol Resour 2015; 16:150-62. [PMID: 26186236 DOI: 10.1111/1755-0998.12447] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 07/08/2015] [Accepted: 07/13/2015] [Indexed: 12/01/2022]
Abstract
The acquisition of tissue samples from wild populations is a constant challenge in conservation biology, especially for endangered species and protected species where nonlethal sampling is the only option. Whole blood has been suggested as a nonlethal sample type that contains a high percentage of bodywide and genomewide transcripts and therefore can be used to assess the transcriptional status of an individual, and to infer a high percentage of the genome. However, only limited quantities of blood can be nonlethally sampled from small species and it is not known if enough genetic material is contained in only a few drops of blood, which represents the upper limit of sample collection for some small species. In this study, we developed a nonlethal sampling method, the laboratory protocols and a bioinformatic pipeline to sequence and assemble the whole blood transcriptome, using Illumina RNA-Seq, from wild greater mouse-eared bats (Myotis myotis). For optimal results, both ribosomal and globin RNAs must be removed before library construction. Treatment of DNase is recommended but not required enabling the use of smaller amounts of starting RNA. A large proportion of protein-coding genes (61%) in the genome were expressed in the blood transcriptome, comparable to brain (65%), kidney (63%) and liver (58%) transcriptomes, and up to 99% of the mitogenome (excluding D-loop) was recovered in the RNA-Seq data. In conclusion, this nonlethal blood sampling method provides an opportunity for a genomewide transcriptomic study of small, endangered or critically protected species, without sacrificing any individuals.
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Affiliation(s)
- Zixia Huang
- UCD School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Aurore Gallot
- UCD School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland.,Laboratoire de Biométrie et Biologie Évolutive, UMR 5558, Centre National de la Recherche Scientifique, Université Lyon 1, Lyon, France
| | - Nga T Lao
- UCD School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland.,Molecular Biology Laboratory, National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Sébastien J Puechmaille
- UCD School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland.,Applied Zoology and Nature Conservation, Greifswald University, J.-S.-Bach-Str. 11/12, 17489, Greifswald, Germany
| | - Nicole M Foley
- UCD School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - David Jebb
- UCD School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Michaël Bekaert
- NSilico Lifescience Limited, Melbourn Building, CIT Campus, Bishopstown, Co., Cork, Ireland
| | - Emma C Teeling
- UCD School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
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50
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O’ Donnell CFJ, Richter S, Dool S, Monks JM, Kerth G. Genetic diversity is maintained in the endangered New Zealand long-tailed bat (Chalinolobus tuberculatus) despite a closed social structure and regular population crashes. CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0763-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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