1
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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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2
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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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3
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Jiang N, Xue DY, Han HX, Cheng R. Estimating hybridization as a consequence of climatic fluctuations: A case study of two geometridae species. Mol Phylogenet Evol 2021; 161:107168. [PMID: 33798671 DOI: 10.1016/j.ympev.2021.107168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 02/05/2021] [Accepted: 03/26/2021] [Indexed: 10/21/2022]
Abstract
In some cases, the phylogenetic analysis based on the mitochondrial DNA (mtDNA) and the nuclear DNA (ncDNA) are discordant. There are three major causes of the discordance within insects, including hybridization, incomplete lineage sorting (ILS) and infection by Wolbachia. In this study, we used a combination of multilocus and coalescent analyses to explore these processes occurred during the evolutionary history of Limbatochlamys rosthorni Rothschild, 1894 and Limbatochlamys pararosthorni Han and Xue, 2005. The ncDNA phylogenetic tree supported two reciprocally monophyletic species, whereas the mtDNA results failed to reveal such a structure and revealed an extensive level of admixture between two species. Because of very low Wolbachia infection rates (<20%), we firstly excluded this reason for the discordance. The fixed nucleotide differences and large genetic distances (1.5-2.5%) at the ncDNA genes suggested that the lineage sorting process between these two species is nearly complete and two species have experienced a prolonged period of independent evolution. Thus, we secondly excluded ILS. Sharing haplotypes, mtDNA gene flow occurring and the transitional samples with morphological features supported hybridization. The distribution contraction during glaciations and postglacial distribution expansion might have facilitated hybridization. Taken together, our study indicates that the current genetic structure of L. rosthorni and L. pararosthorni is the results of contraction and fragmentation into separated refugia during glaciations, followed by postglacial expansion and admixture.
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Affiliation(s)
- Nan Jiang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Da-Yong Xue
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Hong-Xiang Han
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
| | - Rui Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
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4
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Meng X, Liu T, Zhang L, Jin L, Sun K, Feng J. Effects of Colonization, Geography and Environment on Genetic Divergence in the Intermediate Leaf-Nosed Bat, Hipposideros larvatus. Animals (Basel) 2021; 11:733. [PMID: 33800251 PMCID: PMC7998825 DOI: 10.3390/ani11030733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 02/27/2021] [Accepted: 03/03/2021] [Indexed: 11/16/2022] Open
Abstract
Determining the evolutionary history and population drivers, such as past large-scale climatic oscillations, stochastic processes and ecological adaptations, represents one of the aims of evolutionary biology. Hipposideros larvatus is a common bat species in Southern China, including Hainan Island. We examined genetic variation in H. larvatus using mitochondrial DNA and nuclear microsatellites. We found a population structure on both markers with a geographic pattern that corresponds well with the structure on mainland China and Hainan Island. To understand the contributions of geography, the environment and colonization history to the observed population structure, we tested isolation by distance (IBD), isolation by adaptation (IBA) and isolation by colonization (IBC) using serial Mantel tests and RDA analysis. The results showed significant impacts of IBD, IBA and IBC on neutral genetic variation, suggesting that genetic variation in H. larvatus is greatly affected by neutral processes, environmental adaptation and colonization history. This study enriches our understanding of the complex evolutionary forces that shape the distribution of genetic variation in bats.
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Affiliation(s)
- Xiangfeng Meng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China; (X.M.); (T.L.); (L.Z.); (J.F.)
| | - Tong Liu
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China; (X.M.); (T.L.); (L.Z.); (J.F.)
| | - Lin Zhang
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China; (X.M.); (T.L.); (L.Z.); (J.F.)
| | - Longru Jin
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China; (X.M.); (T.L.); (L.Z.); (J.F.)
| | - Keping Sun
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China; (X.M.); (T.L.); (L.Z.); (J.F.)
- 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; (X.M.); (T.L.); (L.Z.); (J.F.)
- School of Life Science, Jilin Agricultural University, Changchun 130118, China
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5
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Li X, Liu T, Li A, Zhang L, Dai W, Jin L, Sun K, Feng J. Genetic polymorphisms and the independent evolution of major histocompatibility complex class II‐
DRB
in sibling bat species
Rhinolophus episcopus
and
Rhinolophus siamensis. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12462] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Xiaolin Li
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization Northeast Normal University Changchun China
| | - Tong Liu
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization Northeast Normal University Changchun China
| | - Aoqiang Li
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization Northeast Normal University Changchun China
| | - Lin 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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6
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Abstract
The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has emerged as a major threat to global health. Although varied SARS-CoV-2-related coronaviruses have been isolated from bats and SARS-CoV-2 may infect bat, the structural basis for SARS-CoV-2 to utilize the human receptor counterpart bat angiotensin-converting enzyme 2 (bACE2) for virus infection remains less understood. Here, we report that the SARS-CoV-2 spike protein receptor binding domain (RBD) could bind to bACE2 from Rhinolophus macrotis (bACE2-Rm) with substantially lower affinity compared with that to the human ACE2 (hACE2), and its infectivity to host cells expressing bACE2-Rm was confirmed with pseudotyped SARS-CoV-2 virus and SARS-CoV-2 wild virus. The structure of the SARS-CoV-2 RBD with the bACE2-Rm complex was determined, revealing a binding mode similar to that of hACE2. The analysis of binding details between SARS-CoV-2 RBD and bACE2-Rm revealed that the interacting network involving Y41 and E42 of bACE2-Rm showed substantial differences with that to hACE2. Bats have extensive species diversity and the residues for RBD binding in bACE2 receptor varied substantially among different bat species. Notably, the Y41H mutant, which exists in many bats, attenuates the binding capacity of bACE2-Rm, indicating the central roles of Y41 in the interaction network. These findings would benefit our understanding of the potential infection of SARS-CoV-2 in varied species of bats.
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7
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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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8
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Mao X, Tsagkogeorga G, Thong VD, Rossiter SJ. Resolving evolutionary relationships among six closely related taxa of the horseshoe bats (Rhinolophus) with targeted resequencing data. Mol Phylogenet Evol 2019; 139:106551. [DOI: 10.1016/j.ympev.2019.106551] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 06/11/2019] [Accepted: 07/01/2019] [Indexed: 01/04/2023]
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9
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Chattopadhyay B, Garg KM, Ray R, Rheindt FE. Fluctuating fortunes: genomes and habitat reconstructions reveal global climate-mediated changes in bats' genetic diversity. Proc Biol Sci 2019; 286:20190304. [PMID: 31530139 PMCID: PMC6784725 DOI: 10.1098/rspb.2019.0304] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 08/23/2019] [Indexed: 12/21/2022] Open
Abstract
Over the last approximately 2.6 Myr, Earth's climate has been dominated by cyclical ice ages that have profoundly affected species' population sizes, but the impact of impending anthropogenic climate change on species' extinction potential remains a worrying problem. We investigated 11 bat species from different taxonomic, ecological and geographical backgrounds using combined information from palaeoclimatic habitat reconstructions and genomes to analyse biotic impacts of historic climate change. We discover tightly correlated fluctuations between species' historic distribution and effective population size, identify frugivores as particularly susceptible to global warming, pinpoint large insectivores as having overall low effective population size and flag the onset of the Holocene (approx. 10-12 000 years ago) as the period with the generally lowest effective population sizes across the last approximately 1 Myr. Our study shows that combining genomic and palaeoclimatological approaches reveals effects of climatic shifts on genetic diversity and may help predict impacts of future climate change.
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Affiliation(s)
| | - Kritika M. Garg
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Rajasri Ray
- Center for Ecological Sciences, Indian Institute of Science, Bangalore, 560012 Karnataka, India
- Centre for Studies in Ethnobiology, Biodiversity and Sustainability (CEiBa), BG Road, Mokdumpur, Malda-732103 West Bengal, India
| | - Frank E. Rheindt
- Department of Biological Sciences, National University of Singapore, Singapore
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10
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Feijó A, Wang Y, Sun J, Li F, Wen Z, Ge D, Xia L, Yang Q. Research trends on bats in China: A twenty-first century review. Mamm Biol 2019; 98:163-172. [PMID: 32218717 PMCID: PMC7091750 DOI: 10.1016/j.mambio.2019.09.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 09/07/2019] [Indexed: 12/25/2022]
Abstract
In this century, China has sustained unparalleled economic development, leading to exponentially growing investments in scientific research. Yet, the demand for research-funding is large and tracing the current knowledge is a key step to define priority research topics. In this same span, studies on bats in China have uncovered an overlooked diversity and revealed novelties in bats’ evolutionary history and life-history aspects. All this 21st-century knowledge, however, is scattered and a large part is concealed from most of the international scientific community in Mandarin-language articles. Here, we summarize the post-millennium (2000–2017) research on bats in China and point out trends and future directions based on neglected topics, groups, and regions. In addition, we provide an up-to-date list of bat species in China. We retrieved 594 publications related to bats in China, nearly half were written in Mandarin. At least 147 bat species are present in China, which places it among the most bat-rich countries in the world. There was a significant positive trend on the number of publications, from 12.5 annual average in 2000–2005 to 46.5 in recent years, reflecting the Chinese economic-scientific development in this century. We found marked taxonomic and spatial biases. Half of the studies in this century focused on Rhinolophus, Myotis, and Hipposideros, and the southern and eastern provinces were the most studied. Systematic/taxonomy and Ecology were the predominant topics post-millennium, whereas only 10 articles have clear conservation-driven goals. Our review shows that the majority of studies were focused on the least concern, cave-dweller species, and on bat-rich provinces. Future projects should address the effects of human-modified landscapes on bat community to define proper conservation actions. We discuss some priority actions and projects that will help to enhance bat protection in China.
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Affiliation(s)
- Anderson Feijó
- 119Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road, Chaoyang District, Beijing, 100101 China
| | - Yanqun Wang
- 119Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road, Chaoyang District, Beijing, 100101 China.,Key Laboratory of Animal Disease Detection and Prevention in Panxi District, Xichang College, 415000 Xichang, Sichuan Province, China
| | - Jian Sun
- 119Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road, Chaoyang District, Beijing, 100101 China
| | - Feihong Li
- 119Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road, Chaoyang District, Beijing, 100101 China
| | - Zhixin Wen
- 119Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road, Chaoyang District, Beijing, 100101 China
| | - Deyan Ge
- 119Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road, Chaoyang District, Beijing, 100101 China
| | - Lin Xia
- 119Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road, Chaoyang District, Beijing, 100101 China
| | - Qisen Yang
- 119Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road, Chaoyang District, Beijing, 100101 China
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11
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Demos TC, Webala PW, Goodman SM, Kerbis Peterhans JC, Bartonjo M, Patterson BD. Molecular phylogenetics of the African horseshoe bats (Chiroptera: Rhinolophidae): expanded geographic and taxonomic sampling of the Afrotropics. BMC Evol Biol 2019; 19:166. [PMID: 31434566 PMCID: PMC6704657 DOI: 10.1186/s12862-019-1485-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 07/19/2019] [Indexed: 11/24/2022] Open
Abstract
Background The Old World insectivorous bat genus Rhinolophus is highly speciose. Over the last 15 years, the number of its recognized species has grown from 77 to 106, but knowledge of their interrelationships has not kept pace. Species limits and phylogenetic relationships of this morphologically conservative group remain problematic due both to poor sampling across the Afrotropics and to repeated instances of mitochondrial-nuclear discordance. Recent intensive surveys in East Africa and neighboring regions, coupled with parallel studies by others in West Africa and in Southern Africa, offer a new basis for understanding its evolutionary history. Results We investigated phylogenetic relationships and intraspecific genetic variation in the Afro-Palearctic clade of Rhinolophidae using broad sampling. We sequenced mitochondrial cytochrome-b (1140 bp) and four independent and informative nuclear introns (2611 bp) for 213 individuals and incorporated sequence data from 210 additional individuals on GenBank that together represent 24 of the 33 currently recognized Afrotropical Rhinolophus species. We addressed the widespread occurrence of mito-nuclear discordance in Rhinolophus by inferring concatenated and species tree phylogenies using only the nuclear data. Well resolved mitochondrial, concatenated nuclear, and species trees revealed phylogenetic relationships and population structure of the Afrotropical species and species groups. Conclusions Multiple well-supported and deeply divergent lineages were resolved in each of the six African Rhinolophus species groups analyzed, suggesting as many as 12 undescribed cryptic species; these include several instances of sympatry among close relatives. Coalescent lineage delimitation offered support for new undescribed lineages in four of the six African groups in this study. On the other hand, two to five currently recognized species may be invalid based on combined mitochondrial and/or nuclear phylogenetic analyses. Validation of these cryptic lineages as species and formal relegation of current names to synonymy will require integrative taxonomic assessments involving morphology, ecology, acoustics, distribution, and behavior. The resulting phylogenetic framework offers a powerful basis for addressing questions regarding their ecology and evolution. Electronic supplementary material The online version of this article (10.1186/s12862-019-1485-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Terrence C Demos
- Integrative Research Center, Field Museum of Natural History, Chicago, IL, 60605, USA.
| | - Paul W Webala
- Department of Forestry and Wildlife Management, Maasai Mara University, Narok, Kenya
| | - Steven M Goodman
- Integrative Research Center, Field Museum of Natural History, Chicago, IL, 60605, USA.,Association Vahatra, BP 3972, 101, Antananarivo, Madagascar
| | - Julian C Kerbis Peterhans
- Integrative Research Center, Field Museum of Natural History, Chicago, IL, 60605, USA.,College of Professional Studies, Roosevelt University, Chicago, IL, 60605, USA
| | | | - Bruce D Patterson
- Integrative Research Center, Field Museum of Natural History, Chicago, IL, 60605, USA
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12
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Liu T, Sun K, Csorba G, Zhang K, Zhang L, Zhao H, Jin L, Thong VD, Xiao Y, Feng J. Species delimitation and evolutionary reconstruction within an integrative taxonomic framework: A case study on Rhinolophus macrotis complex (Chiroptera: Rhinolophidae). Mol Phylogenet Evol 2019; 139:106544. [PMID: 31252069 DOI: 10.1016/j.ympev.2019.106544] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 06/21/2019] [Accepted: 06/24/2019] [Indexed: 10/26/2022]
Abstract
Species delimitation and evolutionary reconstruction remain challenging for non-model species that have experienced reticulate evolution and exhibit conflicting patterns of differentiation among multiple lines of evidence, such as mitochondrial and nuclear data and phenotypes. Here, we applied an integrative taxonomic approach to a case study of Rhinolophus macrotis complex, whose taxonomic status remains controversial, to provide insight into the systematics and evolutionary history of these species. By integrating traditional genetic markers with different modes of inheritance, genome-wide SNPs as well as phenotypic characteristics, we clarified the presence of three closely related species, R. episcopus, R. siamensis, and R. osgoodi, within this complex, and proposed a new taxonomic treatment for R. osgoodi. Our results suggested that hybridization and introgression are the main causes of low mtDNA divergence in these species. Combined with the demographic inference, we deduced that glacial-interglacial cycles drove geographic isolation and secondary contacts of these species, then promoted hybridization and lineage fusion among them, finally resulting in a reticulate evolutionary pattern. Overall, our study highlights the importance of combining multiple types of data to delimit species, especially those with conserved morphology, and to reveal the sophisticated processes of speciation.
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Affiliation(s)
- Tong Liu
- 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.
| | - Gábor Csorba
- Department of Zoology, Hungarian Natural History Museum, Budapest, Hungary
| | - Kangkang Zhang
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Lin Zhang
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Hanbo Zhao
- 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
| | - Vu Dinh Thong
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Viet Nam; Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, Hanoi, Viet Nam
| | - Yanhong Xiao
- 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; College of Life Science, Jilin Agricultural University, Changchun, China.
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13
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Zhang L, Sun K, Liu T, Zhao H, Csorba G, Jin L, Thong VD, Feng J. Multilocus phylogeny and species delimitation within the philippinensis
group (Chiroptera: Rhinolophidae). ZOOL SCR 2018. [DOI: 10.1111/zsc.12308] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Lin Zhang
- 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
| | - Tong Liu
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization; Northeast Normal University; Changchun China
| | - Hanbo Zhao
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization; Northeast Normal University; Changchun China
| | - Gábor Csorba
- Department of Zoology; Hungarian Natural History Museum; Budapest Hungary
| | - Longru Jin
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization; Northeast Normal University; Changchun China
| | - Vu Dinh Thong
- Graduate University of Science and Technology; Vietnam Academy of Science and Technology; Hanoi Vietnam
- Institute of Ecology and Biological Resources; Vietnam Academy of Science and Technology; Hanoi Vietnam
| | - 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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