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Kotsakiozi P, Antoniou A, Psonis N, Sagonas Κ, Karameta E, Ilgaz Ç, Kumlutaş Y, Avcı A, Jablonski D, Darriba D, Stamatakis A, Lymberakis P, Poulakakis N. Cryptic diversity and phylogeographic patterns of Mediodactylus species in the Eastern Mediterranean region. Mol Phylogenet Evol 2024; 197:108091. [PMID: 38719080 DOI: 10.1016/j.ympev.2024.108091] [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: 09/08/2023] [Revised: 04/18/2024] [Accepted: 05/04/2024] [Indexed: 05/20/2024]
Abstract
Cryptic diversity poses a great obstacle in our attempts to assess the current biodiversity crisis and may hamper conservation efforts. The gekkonid genus Mediodactylus, a well-known case of hidden species and genetic diversity, has been taxonomically reclassified several times during the last decade. Focusing on the Mediterranean populations, a recent study within the M. kotschyi species complex using classic mtDNA/nuDNA markers suggested the existence of five distinct species, some being endemic and some possibly threatened, yet their relationships have not been fully resolved. Here, we generated genome-wide SNPs (using ddRADseq) and applied molecular species delimitation approaches and population genomic analyses to further disentangle these relationships. Τhe most extensive nuclear dataset, so far, encompassing 2,360 loci and ∼ 699,000 bp from across the genome of Mediodactylus gecko, enabled us to resolve previously obscure phylogenetic relationships among the five, recently elevated, Mediodactylus species and to support the hypothesis that the taxon includes several new, undescribed species. Population genomic analyses within each of the proposed species showed strong genetic structure and high levels of genetic differentiation among populations.
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Affiliation(s)
- Panayiota Kotsakiozi
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knossos Avenue, Heraklion 71409, Greece; Department of Biology, School of Sciences and Engineering, University of Crete, Vassilika Vouton, Heraklion 70013, Greece.
| | - Aglaia Antoniou
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Heraklion 71003, P.O. Box 2214, Crete, Greece
| | - Nikolaos Psonis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knossos Avenue, Heraklion 71409, Greece; Department of Biology, School of Sciences and Engineering, University of Crete, Vassilika Vouton, Heraklion 70013, Greece
| | - Κostas Sagonas
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knossos Avenue, Heraklion 71409, Greece; Department of Biology, School of Sciences and Engineering, University of Crete, Vassilika Vouton, Heraklion 70013, Greece
| | - Emmanouela Karameta
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knossos Avenue, Heraklion 71409, Greece; Department of Biology, School of Sciences and Engineering, University of Crete, Vassilika Vouton, Heraklion 70013, Greece
| | - Çetin Ilgaz
- Department of Biology, Faculty of Science, Dokuz Eylül University, Buca/İzmir 35160, Türkiye
| | - Yusuf Kumlutaş
- Department of Biology, Faculty of Science, Dokuz Eylül University, Buca/İzmir 35160, Türkiye
| | - Aziz Avcı
- Department of Biology, Faculty of Science, Aydın Adnan Menderes University, Aydın 09010, Türkiye
| | - Daniel Jablonski
- Department of Zoology, Comenius University in Bratislava, Mlynská dolina, Ilkovičova 6, 84215 Bratislava, Slovakia
| | - Diego Darriba
- Computer Architecture Group, Centro de investigación CITIC, University of A Coruña, A Coruña, Spain
| | - Alexandros Stamatakis
- Institute of Computer Science, Foundation for Research and Technology-Hellas, Greece; Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany; Department of Informatics, Institute of Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe 76128, Germany
| | - Petros Lymberakis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knossos Avenue, Heraklion 71409, Greece
| | - Nikos Poulakakis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knossos Avenue, Heraklion 71409, Greece; Department of Biology, School of Sciences and Engineering, University of Crete, Vassilika Vouton, Heraklion 70013, Greece
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2
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Garg KM, Gwee CY, Chattopadhyay B, Ng NS, Prawiradilaga DM, David G, Fuchs J, Hung Le Manh, Martinez J, Olsson U, Vuong Tan Tu, Chhin S, Alström P, Lei F, Rheindt FE. When colors mislead: Genomics and bioacoustics prompt re-classification of Asian flycatcher radiation (Aves: Niltavinae). Mol Phylogenet Evol 2024; 193:107999. [PMID: 38160993 DOI: 10.1016/j.ympev.2023.107999] [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: 09/11/2023] [Revised: 11/10/2023] [Accepted: 12/25/2023] [Indexed: 01/03/2024]
Abstract
Traditional classification of many animals, including birds, has been highly dependent on external morphological characters like plumage coloration. However, both bioacoustics and genetic or genomic data have revolutionized our understanding of the relationships of certain lineages and led to sweeping taxonomic re-organizations. In this study, we present a case of erroneous delimitation of genus boundaries in the species-rich flycatcher subfamily Niltavinae. Genera within this subfamily have historically been delineated based on blue versus brown male body plumage until recent studies based on a few mitochondrial and nuclear loci unearthed several cases of generic misclassification. Here we use extensive bioacoustic data from 43 species and genomic data from 28 species for a fundamental reclassification of species in the Niltavinae. Our study reveals that song is an important trait to classify these birds even at the genus level, whereas plumage traits exhibit ample convergence and have led to numerous historic misattributions. Our taxonomic re-organization leads to new biogeographic limits of major genera, such that the genus Cyornis now only extends as far east as the islands of Sulawesi, Sula, and Banggai, whereas Eumyias is redefined to extend far beyond Wallace's Line to the islands of Seram and Timor. Our conclusions advise against an over-reliance on morphological traits and underscore the importance of integrative datasets.
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Affiliation(s)
- Kritika M Garg
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore; Centre for Interdisciplinary Archaeological Research, Ashoka University, Sonipat, India; Department of Biology, Ashoka University, Sonipat, India
| | - Chyi Yin Gwee
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore; Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Munich, Germany
| | - Balaji Chattopadhyay
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore; Department of Biology, Ashoka University, Sonipat, India; Trivedi School of Biosciences, Ashoka University, Sonipat, India
| | - Nathaniel S Ng
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Dewi M Prawiradilaga
- Research Center for Biosystematics and Evolution, National Research and Innovation Agency (BRIN), Bogor-Cibinong, West Java, Indonesia
| | - Gabriel David
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore; Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden; Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing, China
| | - Jérôme Fuchs
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, 22 S U, EPHE, UA CP51, Paris, France
| | - Hung Le Manh
- Institute of Ecology and Biological Resources, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | | | - Urban Olsson
- Systematics and Biodiversity, Department of Biology and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden; Gothenburg Global Biodiversity Center, Göteborg, Sweden
| | - Vuong Tan Tu
- Institute of Ecology and Biological Resources, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Sophea Chhin
- Department of Biodiversity, General Directorate of Policy and Strategy, Ministry of Environment, Phnom Penh, Cambodia
| | - Per Alström
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden; Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore.
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3
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Cheng R, Luo A, Orr M, Ge D, Hou Z, Qu Y, Guo B, Zhang F, Sha Z, Zhao Z, Wang M, Shi X, Han H, Zhou Q, Li Y, Liu X, Shao C, Zhang A, Zhou X, Zhu C. Cryptic diversity begets challenges and opportunities in biodiversity research. Integr Zool 2024. [PMID: 38263700 DOI: 10.1111/1749-4877.12809] [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] [Indexed: 01/25/2024]
Abstract
How many species of life are there on Earth? This is a question that we want to know but cannot yet answer. Some scholars speculate that the number of species may reach 2.2 billion when considering cryptic diversity and that each morphology-based insect species may contain an average of 3.1 cryptic species. With nearly two million described species, such high estimates of cryptic diversity would suggest that cryptic species are widespread. The development of molecular species delimitation has led to the discovery of a large number of cryptic species, and cryptic biodiversity has gradually entered our field of vision and attracted more attention. This paper introduces the concept of cryptic species, how they evolve, and methods by which they may be discovered and confirmed, and provides theoretical and methodological guidance for the study of hidden species. A workflow of how to confirm cryptic species is provided. In addition, the importance and reliability of multi-evidence-based integrated taxonomy are reaffirmed as a way to better standardize decision-making processes. Special focus on cryptic diversity and increased funding for taxonomy is needed to ensure that cryptic species in hyperdiverse groups are discoverable and described. An increased focus on cryptic species in the future will naturally arise as more difficult groups are studied, and thereby, we may finally better understand the rules governing the evolution and maintenance of cryptic biodiversity.
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Affiliation(s)
- Rui Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Arong Luo
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Michael Orr
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Entomologie, Staatliches Museum für Naturkunde Stuttgart, Stuttgart, Germany
| | - Deyan Ge
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Zhong'e Hou
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Baocheng Guo
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Feng Zhang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Zhongli Sha
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Zhe Zhao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Mingqiang Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Xiaoyu Shi
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Hongxiang Han
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Qingsong Zhou
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yuanning Li
- Institute of Oceanography, Shandong University, Qingdao, China
| | - Xingyue Liu
- Department of Entomology, China Agricultural University, Beijing, China
| | - Chen Shao
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Aibing Zhang
- College of Life Science, Capital Normal University, Beijing, China
| | - Xin Zhou
- Department of Entomology, China Agricultural University, Beijing, China
| | - Chaodong Zhu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Integrated Pest Management, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences/International College, University of Chinese Academy of Sciences, Beijing, China
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4
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Garg KM, Lamba V, Sanyal A, Dovih P, Chattopadhyay B. Next Generation Sequencing Revolutionizes Organismal Biology Research in Bats. J Mol Evol 2023:10.1007/s00239-023-10107-2. [PMID: 37154841 PMCID: PMC10166039 DOI: 10.1007/s00239-023-10107-2] [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: 08/25/2022] [Accepted: 03/29/2023] [Indexed: 05/10/2023]
Abstract
The advent of next generation sequencing technologies (NGS) has greatly accelerated our understanding of critical aspects of organismal biology from non-model organisms. Bats form a particularly interesting group in this regard, as genomic data have helped unearth a vast spectrum of idiosyncrasies in bat genomes associated with bat biology, physiology, and evolution. Bats are important bioindicators and are keystone species to many eco-systems. They often live in proximity to humans and are frequently associated with emerging infectious diseases, including the COVID-19 pandemic. Nearly four dozen bat genomes have been published to date, ranging from drafts to chromosomal level assemblies. Genomic investigations in bats have also become critical towards our understanding of disease biology and host-pathogen coevolution. In addition to whole genome sequencing, low coverage genomic data like reduced representation libraries, resequencing data, etc. have contributed significantly towards our understanding of the evolution of natural populations, and their responses to climatic and anthropogenic perturbations. In this review, we discuss how genomic data have enhanced our understanding of physiological adaptations in bats (particularly related to ageing, immunity, diet, etc.), pathogen discovery, and host pathogen co-evolution. In comparison, the application of NGS towards population genomics, conservation, biodiversity assessment, and functional genomics has been appreciably slower. We reviewed the current areas of focus, identifying emerging topical research directions and providing a roadmap for future genomic studies in bats.
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Affiliation(s)
- Kritika M Garg
- Centre for Interdisciplinay Archaeological Research, Ashoka University, Sonipat, Haryana, 131029, India
- Department of Biology, Ashoka University, Sonipat, Haryana, 131029, India
- Centre for Climate Change and Sustainability (3CS), Ashoka University, Sonipat, Haryana, 131029, India
| | - Vinita Lamba
- Trivedi School of Biosciences, Ashoka University, Sonipat, Haryana, 131029, India
- J. William Fulbright College of Arts and Sciences, Department of Biological Sciences, University of Arkansas, Fayetteville, AR72701, USA
| | - Avirup Sanyal
- Trivedi School of Biosciences, Ashoka University, Sonipat, Haryana, 131029, India
- Ecology and Evolution, National Centre for Biological Sciences, Bangalore, 560065, India
| | - Pilot Dovih
- Centre for Climate Change and Sustainability (3CS), Ashoka University, Sonipat, Haryana, 131029, India
- Ecology and Evolution, National Centre for Biological Sciences, Bangalore, 560065, India
- School of Chemistry and Biotechnology, Sastra University, Thanjavur, Tamil Nadu, 613401, India
| | - Balaji Chattopadhyay
- Centre for Climate Change and Sustainability (3CS), Ashoka University, Sonipat, Haryana, 131029, India.
- Trivedi School of Biosciences, Ashoka University, Sonipat, Haryana, 131029, India.
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5
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Ng EYX, Li S, Zhang D, Garg KM, Song G, Martinez J, Hung LM, Tu VT, Fuchs J, Dong L, Olsson U, Huang Y, Alström P, Rheindt FE, Lei F. Genome‐wide
SNPs
confirm plumage polymorphism and hybridisation within a
Cyornis
flycatcher species complex. ZOOL SCR 2022. [DOI: 10.1111/zsc.12568] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Elize Y. X. Ng
- Department of Biological Sciences National University of Singapore Singapore Singapore
- Discipline of Biological Science, School of Natural Sciences University of Tasmania Hobart Tasmania Australia
| | - Siqi Li
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology Chinese Academy of Sciences Beijing China
- College of Life Sciences Shaanxi Normal University Xi'an China
| | - Dezhi Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Kritika M. Garg
- Department of Biological Sciences National University of Singapore Singapore Singapore
- Centre for Interdisciplinary Archaeological Research Ashoka University Sonipat India
- Department of Biology Ashoka University Sonipat India
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology Chinese Academy of Sciences Beijing China
| | | | - Le Manh Hung
- Institute of Ecology and Biological Resources, Graduate University of Science and Technology Vietnam Academy of Science and Technology Hanoi Vietnam
| | - Vuong Tan Tu
- Institute of Ecology and Biological Resources, Graduate University of Science and Technology Vietnam Academy of Science and Technology Hanoi Vietnam
| | - Jérôme Fuchs
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle CNRS, 22 S U, EPHE, UA CP51 Paris France
| | - Lu Dong
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences Beijing Normal University Beijing China
| | - Urban Olsson
- Systematics and Biodiversity, Department of Biology and Environmental Sciences University of Gothenburg Gothenburg Sweden
- Gothenburg Global Biodiversity Center Göteborg Sweden
| | - Yuan Huang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Per Alström
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology Chinese Academy of Sciences Beijing China
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre Uppsala University Uppsala Sweden
| | - Frank E. Rheindt
- Department of Biological Sciences National University of Singapore Singapore Singapore
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
- Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Kunming China
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6
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Chattopadhyay B, Garg KM, Ray R, Mendenhall IH, Rheindt FE. Novel de Novo Genome of Cynopterus brachyotis Reveals Evolutionarily Abrupt Shifts in Gene Family Composition across Fruit Bats. Genome Biol Evol 2021; 12:259-272. [PMID: 32068833 PMCID: PMC7151552 DOI: 10.1093/gbe/evaa030] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/12/2020] [Indexed: 12/01/2022] Open
Abstract
Major novel physiological or phenotypic adaptations often require accompanying modifications at the genic level. Conversely, the detection of considerable contractions and/or expansions of gene families can be an indicator of fundamental but unrecognized physiological change. We sequenced a novel fruit bat genome (Cynopterus brachyotis) and adopted a comparative approach to reconstruct the evolution of fruit bats, mapping contractions and expansions of gene families along their evolutionary history. Despite a radical change in life history as compared with other bats (e.g., loss of echolocation, large size, and frugivory), fruit bats have undergone surprisingly limited change in their genic composition, perhaps apart from a potentially novel gene family expansion relating to telomere protection and longevity. In sharp contrast, within fruit bats, the new Cynopterus genome bears the signal of unusual gene loss and gene family contraction, despite its similar morphology and lifestyle to two other major fruit bat lineages. Most missing genes are regulatory, immune-related, and olfactory in nature, illustrating the diversity of genomic strategies employed by bats to contend with responses to viral infection and olfactory requirements. Our results underscore that significant fluctuations in gene family composition are not always associated with obvious examples of novel physiological and phenotypic adaptations but may often relate to less-obvious shifts in immune strategies.
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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, Karnataka, India.,Centre for Studies in Ethnobiology, Biodiversity and Sustainability (CEiBa), Mokdumpur, Malda, West Bengal, India
| | - Ian H Mendenhall
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, Singapore
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7
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Sangavi D, Murugan CM, Mahandran V, Marimuthu G, Thiruchenthil Nathan P. Adaptive foraging tactics of greater short-nosed fruit bats on a spiny shrub and its effect on seed dispersal. J ETHOL 2021. [DOI: 10.1007/s10164-021-00711-4] [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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8
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García NC, Robinson WD. Current and Forthcoming Approaches for Benchmarking Genetic and Genomic Diversity. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.622603] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The current attrition of biodiversity extends beyond loss of species and unique populations to steady loss of a vast genomic diversity that remains largely undescribed. Yet the accelerating development of new techniques allows us to survey entire genomes ever faster and cheaper, to obtain robust samples from a diversity of sources including degraded DNA and residual DNA in the environment, and to address conservation efforts in new and innovative ways. Here we review recent studies that highlight the importance of carefully considering where to prioritize collection of genetic samples (e.g., organisms in rapidly changing landscapes or along edges of geographic ranges) and what samples to collect and archive (e.g., from individuals of little-known subspecies or populations, even of species not currently considered endangered). Those decisions will provide the sample infrastructure to detect the disappearance of certain genotypes or gene complexes, increases in inbreeding levels, and loss of genomic diversity as environmental conditions change. Obtaining samples from currently endangered, protected, and rare species can be particularly difficult, thus we also focus on studies that use new, non-invasive ways of obtaining genomic samples and analyzing them in these cases where other sampling options are highly constrained. Finally, biological collections archiving such samples face an inherent contradiction: their main goal is to preserve biological material in good shape so it can be used for scientific research for centuries to come, yet the technologies that can make use of such materials are advancing faster than collections can change their standardized practices. Thus, we also discuss current and potential new practices in biological collections that might bolster their usefulness for future biodiversity conservation research.
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9
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Psonis N, Antoniou A, Karameta E, Darriba D, Stamatakis A, Lymberakis P, Poulakakis N. The wall lizards of the Balkan peninsula: Tackling questions at the interface of phylogenomics and population genomics. Mol Phylogenet Evol 2021; 159:107121. [PMID: 33609707 DOI: 10.1016/j.ympev.2021.107121] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 01/12/2021] [Accepted: 02/09/2021] [Indexed: 11/24/2022]
Abstract
Wall lizards of the genus Podarcis (Sauria, Lacertidae) are the predominant reptile group in southern Europe, including 24 recognized species. Mitochondrial DNA data have shown that, with the exception of P. muralis, the Podarcis species distributed in the Balkan peninsula form a species group that is further sub-divided into two subgroups: the one of "P. tauricus" consisting of P. tauricus, P. milensis, P. gaigeae, and P. melisellensis, and the other of "P. erhardii" comprising P. erhardii, P. levendis, P. cretensis, and P. peloponnesiacus. In an attempt to explore the Balkan Podarcis phylogenomic relationships, assess the levels of genetic structure and to re-evaluate the number of extant species, we employed phylogenomic and admixture approaches on ddRADseq (double digested Restriction site Associated DNA sequencing) genomic data. With this efficient Next Generation Sequencing approach, we were able to obtain a large number of genomic loci randomly distributed throughout the genome and use them to resolve the previously obscure phylogenetic relationships among the different Podarcis species distributed in the Balkans. The obtained phylogenomic relationships support the monophyly of both aforementioned subgroups and revealed several divergent lineages within each subgroup, stressing the need for taxonomic re-evaluation of Podarcis' species in Balkans. The phylogenomic trees and the species delimitation analyses confirmed all recently recognized species (P. levendis, P. cretensis, and P. ionicus) and showed the presence of at least two more species, one in P. erhardii and the other in P. peloponnesiacus.
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Affiliation(s)
- Nikolaos Psonis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knosos Avenue, Irakleio 71409, Greece; Department of Biology, School of Sciences and Engineering, University of Crete, Vassilika Vouton, Irakleio 70013, Greece.
| | - Aglaia Antoniou
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Gournes Pediados, Irakleio, P.O. Box 2214, 71003 Crete, Greece
| | - Emmanouela Karameta
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knosos Avenue, Irakleio 71409, Greece; Department of Biology, School of Sciences and Engineering, University of Crete, Vassilika Vouton, Irakleio 70013, Greece
| | - Diego Darriba
- Universidade da Coruña, CITIC, Computer Architecture Group, Campus de Elviña, 15071 A Coruña, Spain
| | - Alexandros Stamatakis
- The Exelixis Lab, Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany; Karlsruhe Institute of Technology, Institute for Theoretical Informatics, Postfach 6980, 76128 Karlsruhe, Germany
| | - Petros Lymberakis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knosos Avenue, Irakleio 71409, Greece
| | - Nikos Poulakakis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knosos Avenue, Irakleio 71409, Greece; Department of Biology, School of Sciences and Engineering, University of Crete, Vassilika Vouton, Irakleio 70013, Greece
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10
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Garg KM, Chattopadhyay B. Gene Flow in Volant Vertebrates: Species Biology, Ecology and Climate Change. J Indian Inst Sci 2021; 101:165-176. [PMID: 34155425 PMCID: PMC8207815 DOI: 10.1007/s41745-021-00239-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 05/05/2021] [Indexed: 02/06/2023]
Abstract
Gene flow, the exchange of genetic material between populations is an important biological process, which shapes and maintains biodiversity. The successful movement of individuals between populations depends on multiple factors determined by species biology and the environment. One of the most important factors regulating gene flow is the ability to move, and flight allows individuals to easily move across geographical barriers. Volant vertebrates are found on some of the remotest islands and contribute significantly to the biodiversity and ecosystem. The availability of next-generation sequencing data for non-model animals has substantially improved our understanding of gene flow and its consequences, allowing us to look at fine-scale patterns. However, most of our understanding regarding gene flow comes from the temperate regions and the Neotropics. The lack of studies from species-rich Asia is striking. In this review, we outline the importance of gene flow and the factors affecting gene flow, especially for volant vertebrates. We especially discuss research studies from tropical biomes of South and Southeast Asia, highlight the lacuna in literature and provide an outline for future studies in this species-rich region.
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Affiliation(s)
- Kritika M. Garg
- grid.418831.70000 0004 0500 991XInstitute of Bioinformatics and Applied Biotechnology, Bengaluru, Karnataka India ,grid.449178.70000 0004 5894 7096Department of Biology, Ashoka University, Sonipat, Haryana India
| | - Balaji Chattopadhyay
- grid.449178.70000 0004 5894 7096Trivedi School of Biosciences, Ashoka University, Sonipat, Haryana India
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11
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Monadjem A, Shapiro JT, Richards LR, Karabulut H, Crawley W, Nielsen IB, Hansen A, Bohmann K, Mourier T. Systematics of West African Miniopterus with the Description of a New Species. ACTA CHIROPTEROLOGICA 2020. [DOI: 10.3161/15081109acc2019.21.2.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Ara Monadjem
- Department of Biological Sciences, University of Eswatini, Private Bag 4, Kwaluseni, Eswatini
| | - Julie T. Shapiro
- School of Natural Resources and Environment, University of Florida, 103 Black Hall, Gainesville FL, 32611, USA
| | - Leigh R. Richards
- Durban Natural Science Museum, PO Box 4085, Durban, 4000, Republic of South Africa
| | - Hatice Karabulut
- Department of Molecular Biology and Genetics, Middle East Technical University, Ankara 06800, Turkey
| | - Wing Crawley
- 53 Rosebank Crescent, Exeter, Devon EX4 6EH, United Kingdom
| | - Ida Broman Nielsen
- Centre for GeoGenetics, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, Denmark
| | - Anders Hansen
- Centre for GeoGenetics, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, Denmark
| | - Kristine Bohmann
- Section for EvoGenomics, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, Denmark
| | - Tobias Mourier
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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12
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Tan HZ, Ng EYX, Tang Q, Allport GA, Jansen JJFJ, Tomkovich PS, Rheindt FE. Population genomics of two congeneric Palaearctic shorebirds reveals differential impacts of Quaternary climate oscillations across habitats types. Sci Rep 2019; 9:18172. [PMID: 31796810 PMCID: PMC6890745 DOI: 10.1038/s41598-019-54715-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 11/08/2019] [Indexed: 02/07/2023] Open
Abstract
Intracontinental biotic divisions across the vast Palaearctic region are not well-characterized. Past research has revealed patterns ranging from a lack of population structure to deep divergences along varied lines of separation. Here we compared biogeographic patterns of two Palaearctic shorebirds with different habitat preferences, Whimbrel (Numenius phaeopus) and Eurasian curlew (N. arquata). Using genome-wide markers from populations across the Palaearctic, we applied a multitude of population genomic and phylogenomic approaches to elucidate population structure. Most importantly, we tested for isolation by distance and visualized barriers and corridors to gene flow. We found shallow Palaearctic population structure in subpolar bog and tundra-breeding whimbrels, consistent with other species breeding at a similarly high latitude, indicating connectivity across the tundra belt, both presently and during southward shifts in periods of global cooling. In contrast, the temperate grassland-breeding Eurasian curlew emerged in three distinct clades corresponding to glacial refugia. Barriers to gene flow coincided with areas of topographic relief in the central Palaearctic for whimbrels and further east for Eurasian curlews. Our findings highlight the interplay of historic and ecological factors in influencing present-day population structure of Palaearctic biota.
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Affiliation(s)
- Hui Zhen Tan
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558, Singapore
| | - Elize Ying Xin Ng
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558, Singapore
| | - Qian Tang
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558, Singapore
| | - Gary A Allport
- BirdLife International, The David Attenborough Building, Pembroke Street, Cambridge, CB2 3QZ, UK
| | - Justin J F J Jansen
- Naturalis Biodiversity Center, Leiden, P.O. Box 9517, 2300 RA, Leiden, The Netherlands
| | - Pavel S Tomkovich
- Zoological Museum, Lomonosov Moscow State University, Bolshaya Nikitskaya Str. 2, Moscow, 125009, Russia
| | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558, Singapore.
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13
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Chattopadhyay B, Garg KM, Soo YJ, Low GW, Frechette JL, Rheindt FE. Conservation genomics in the fight to help the recovery of the critically endangered Siamese crocodile Crocodylus siamensis. Mol Ecol 2019; 28:936-950. [PMID: 30659682 DOI: 10.1111/mec.15023] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 12/03/2018] [Indexed: 12/13/2022]
Abstract
Endangered species are often characterized by low genetic diversity and it is imperative for conservation efforts to incorporate the knowledge obtained from genetic studies for effective management. However, despite the promise of technological advances in sequencing, application of genome-wide data to endangered populations remains uncommon. In the present study we pursued a holistic conservation-genomic approach to inform a field-based management programme of a Critically Endangered species, the Siamese crocodile Crocodylus siamensis. Using thousands of single nucleotide polymorphisms from throughout the genome, we revealed signals of introgression from two other crocodile species within our sample of both wild and captive-bred Siamese crocodiles from Cambodia. Our genetic screening of the Siamese crocodiles resulted in the subsequent re-introduction of 12 individuals into the wild as well as the selection of four individuals for captive breeding programmes. Comparison of intraspecific genetic diversity revealed an alarmingly low contemporary effective population size in the wild (<50) with evidence of a recent bottleneck around Tonle Sap Lake. We also projected a probable future extinction in the wild (within fewer than five generations) in this population in the absence of re-introduction efforts. However, an increase in the number of potential breeders through re-introductions, including the one resulting from this project, could counter this trend. Our results have been implemented in ongoing re-introduction and captive breeding programmes, with major implications for the conservation management of Siamese crocodiles, and provide a blueprint for the rescue effort of other "terminally ill" populations of critically endangered species.
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Affiliation(s)
- Balaji Chattopadhyay
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Kritika M Garg
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Yun Jing Soo
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Gabriel W Low
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | | | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
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14
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Olival KJ, Latinne A, Islam A, Epstein JH, Hersch R, Engstrand RC, Gurley ES, Amato G, Luby SP, Daszak P. Population genetics of fruit bat reservoir informs the dynamics, distribution and diversity of Nipah virus. Mol Ecol 2019; 29:970-985. [PMID: 31652377 DOI: 10.1111/mec.15288] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 10/21/2019] [Accepted: 10/21/2019] [Indexed: 12/26/2022]
Abstract
The structure and connectivity of wildlife host populations may influence zoonotic disease dynamics, evolution and therefore spillover risk to people. Fruit bats in the genus Pteropus, or flying foxes, are the primary natural reservoir for henipaviruses-a group of emerging paramyxoviruses that threaten livestock and public health. In Bangladesh, Pteropus medius is the reservoir for Nipah virus-and viral spillover has led to human fatalities nearly every year since 2001. Here, we use mitochondrial DNA and nuclear microsatellite markers to measure the population structure, demographic history and phylogeography of P. medius in Bangladesh. We combine this with a phylogeographic analysis of all known Nipah virus sequences and strains currently available to better inform the dynamics, distribution and evolutionary history of Nipah virus. We show that P. medius is primarily panmictic, but combined analysis of microsatellite and morphological data shows evidence for differentiation of two populations in eastern Bangladesh, corresponding to a divergent strain of Nipah virus also found in bats from eastern Bangladesh. Our demographic analyses indicate that a large, expanding population of flying foxes has existed in Bangladesh since the Late Pleistocene, coinciding with human population expansion in South Asia, suggesting repeated historical spillover of Nipah virus likely occurred. We present the first evidence of mitochondrial introgression, or hybridization, between P. medius and flying fox species found in South-East Asia (P. vampyrus and P. hypomelanus), which may help to explain the distribution of Nipah virus strains across the region.
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Affiliation(s)
| | | | | | | | - Rebecca Hersch
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA
| | - Rachel C Engstrand
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA
| | | | - George Amato
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA
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15
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Çilingir FG, Seah A, Horne BD, Som S, Bickford DP, Rheindt FE. Last exit before the brink: Conservation genomics of the Cambodian population of the critically endangered southern river terrapin. Ecol Evol 2019; 9:9500-9510. [PMID: 31534671 PMCID: PMC6745661 DOI: 10.1002/ece3.5434] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 05/04/2019] [Accepted: 06/11/2019] [Indexed: 11/14/2022] Open
Abstract
The southern river terrapin, Batagur affinis is one of the world's 25 most endangered freshwater turtle species. The major portion of the global population is currently found in peninsular Malaysia, with the only remnant Indochinese population in southern Cambodia. For more than a decade, wild nests in this remnant Cambodian population have been fenced and hatchlings reared in captivity. Here we amplified 10 microsatellite markers from all 136 captive individuals, obtained 2,658 presumably unlinked and neutral single nucleotide polymorphisms from 72 samples with ddRAD-seq, and amplified 784 bp of mtDNA from 50 samples. Our results reveal that the last Indochinese population comprised only four kinship groups as of 2012, with all offspring sired from <10 individuals in the wild. We demonstrate an obvious decrease in genetic contributions of breeders in the wild from 2006-2012 and identify high-value breeders instrumental for ex-situ management of the contemporary genetic stock of the species.
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Affiliation(s)
- F. Gözde Çilingir
- Department of Biological SciencesNational University of SingaporeSingapore CitySingapore
| | - Adeline Seah
- Department of Biological SciencesNational University of SingaporeSingapore CitySingapore
- Wildlife Conservation Society, Bronx ZooBronxNew YorkUSA
| | - Brian D. Horne
- Wildlife Conservation Society, Bronx ZooBronxNew YorkUSA
| | - Sitha Som
- Wildlife Conservation SocietyPhnom PenhCambodia
| | - David P. Bickford
- Department of Biological SciencesNational University of SingaporeSingapore CitySingapore
- Present address:
Department of BiologyUniversity of La VerneLa VerneCaliforniaUSA
| | - Frank E. Rheindt
- Department of Biological SciencesNational University of SingaporeSingapore CitySingapore
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16
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Kundu S, Kumar V, Tyagi K, Rath S, Pakrashi A, Saren PC, Laishram K, Chandra K. Mitochondrial DNA identified bat species in northeast India: electrocution mortality and biodiversity loss. MITOCHONDRIAL DNA PART B-RESOURCES 2019; 4:2454-2458. [PMID: 33365582 PMCID: PMC7687647 DOI: 10.1080/23802359.2019.1638320] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Northeast India with two biodiversity hotspots is recognized as a biodiversity-rich region. However, several extant animals including chiropterans are currently at jeopardy due to habitat loss, electrocution mortality, and other anthropogenic threats. This study examines the efficacy of mitochondrial Cytochrome b (mtCytb) sequences for species-level identification of five electrocuted bat specimens from Manipur state. The similarity search results in the global database, Kimura 2 parameter (K2P) genetic distances, and neighbor-joining (NJ) tree identified all bat specimens into two species, Cynopterus sphinx and Megaerops niphanae. The detection of M. niphanae is the first record of this mammal from the state. In comparison with other Pteropodidae species, the genetic distances clearly discriminate both C. sphinx (7.9–30.2%) and M. niphanae (12.2–25.7%). In addition, the combined tree analysis of present and earlier genetic information of C. sphinx suggested the presence of cryptic lineages and sympatric population in India. This similar approach with more sampling from a wide distribution area could assist the future genetics research on chiropterans and their precise conservation.
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Affiliation(s)
- Shantanu Kundu
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Vikas Kumar
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Kaomud Tyagi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Shibananda Rath
- Freshwater Fish Section, Zoological Survey of India, Kolkata, India
| | - Avas Pakrashi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | | | - Kosygin Laishram
- Freshwater Fish Section, Zoological Survey of India, Kolkata, India
| | - Kailash Chandra
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India.,Freshwater Fish Section, Zoological Survey of India, Kolkata, India.,Wildlife Section, Zoological Survey of India, Kolkata, India
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17
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Gwee CY, Eaton JA, Garg KM, Alström P, Van Balen S(B, Hutchinson RO, Prawiradilaga DM, Le MH, Rheindt FE. Cryptic diversity in Cyornis (Aves: Muscicapidae) jungle-flycatchers flagged by simple bioacoustic approaches. Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Chyi Yin Gwee
- Department of Biological Sciences, National University of Singapore, Singapore
| | - James A Eaton
- Birdtour Asia Ltd, Littleover, Derby, United Kingdom
| | - Kritika M Garg
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Per Alström
- Department of Ecology and Genetics, Animal Ecology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
- Swedish Species Information Centre, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | | | | | - Dewi M Prawiradilaga
- Research Centre for Biology, Indonesian Institute of Sciences (LIPI), Cibinong Science Centre, Jalan Raya Jakarta Bogor, Indonesia
| | - Manh Hung Le
- Graduated University of Science and Technology, Vietnam Academy of Science and Technology (VAST), Caugiay, Hanoi, Vietnam
| | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, Singapore
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18
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Wu W, Ng WL, Yang JX, Li WM, Ge XJ. High cryptic species diversity is revealed by genome-wide polymorphisms in a wild relative of banana, Musa itinerans, and implications for its conservation in subtropical China. BMC PLANT BIOLOGY 2018; 18:194. [PMID: 30217175 PMCID: PMC6137913 DOI: 10.1186/s12870-018-1410-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 08/31/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Species delimitation is a challenging but essential task in conservation biology. Morphologically similar species are sometimes difficult to recognize even after examination by experienced taxonomists. With the advent of molecular approaches in species delimitation, this hidden diversity has received much recent attention. In addition to DNA barcoding approaches, analytical tools based on the multi-species coalescence model (MSC) have been developed for species delimitation. Musa itinerans is widely distributed in subtropical Asia, and at least six varieties have been documented. However, the number of evolutionarily distinct lineages remains unknown. RESULTS Using genome resequencing data of five populations (making up four varieties), we examined genome-wide variation and found four varieties that were evolutionary significant units. A Bayesian Phylogenetics and Phylogeography (BP&P) analysis using 123 single copy nuclear genes support three speciation events of M. itinerans varieties with robust posterior speciation probabilities; However, a Bayes factor delimitation of species with genomic data (BFD*) analysis using 1201 unlinked single nucleotide polymorphisms gave decisive support for a five-lineage model. When reconciling divergence time estimates with a speciation time scale, a modified three-lineage model was consistent with that of BP&P, in which the speciation time of two varieties (M. itinerans var. itinerans and M. itinerans var. lechangensis) were dated to 26.2 kya and 10.7 kya, respectively. In contrast, other two varieties (M. itinerans var. chinensis and M. itinerans var. guangdongensis) diverged only 3.8 kya in the Anthropocene; this may be a consequence of genetic drift rather than a speciation event. CONCLUSION Our results showed that the M. itinerans species complex harbours high cryptic species diversity. We recommend that M. itinerans var. itinerans and M. itinerans var. lechangensis be elevated to subspecies status, and the extremely rare latter subspecies be given priority for conservation. We also recommend that the very recently diverged M. itinerans var. chinensis and M. itinerans var. guangdongensis should be merged under the subspecies M. itinerans var. chinensis. Finally, we speculate that species delimitation of recently diverged lineages may be more effective using genome-wide bi-allelic SNP markers with BFD* than by using unlinked loci and BP&P.
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Affiliation(s)
- Wei Wu
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510275 China
| | - Wei-Lun Ng
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510275 China
| | - Jun-Xin Yang
- Center for Environmental Remediation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101 China
| | - Wei-Ming Li
- Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, 524091 China
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, the Chinese Academy of Sciences, Guangzhou, 510650 China
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19
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Chakravarty R, Chattopadhyay B, Ramakrishnan U, Sivasundar A. Comparative Population Structure in Species of Bats Differing in Ecology and Morphology in the Andaman Islands, India. ACTA CHIROPTEROLOGICA 2018. [DOI: 10.3161/15081109acc2018.20.1.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Rohit Chakravarty
- Post-Graduate Program in Wildlife Biology and Conservation, Wildlife Conservation Society-India, Bangalore 560097, India and National Centre for Biological Sciences, Bangalore 560065, India
| | - Balaji Chattopadhyay
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558
| | - Uma Ramakrishnan
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bellary Road, Bangalore 560065, India
| | - Arjun Sivasundar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bellary Road, Bangalore 560065, India
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20
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Bourgeois S, Senn H, Kaden J, Taggart JB, Ogden R, Jeffery KJ, Bunnefeld N, Abernethy K, McEwing R. Single-nucleotide polymorphism discovery and panel characterization in the African forest elephant. Ecol Evol 2018; 8:2207-2217. [PMID: 29468037 PMCID: PMC5817121 DOI: 10.1002/ece3.3854] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Revised: 12/17/2017] [Accepted: 12/29/2017] [Indexed: 12/14/2022] Open
Abstract
The continuing decline in forest elephant (Loxodonta cyclotis) numbers due to poaching and habitat reduction is driving the search for new tools to inform management and conservation. For dense rainforest species, basic ecological data on populations and threats can be challenging and expensive to collect, impeding conservation action in the field. As such, genetic monitoring is being increasingly implemented to complement or replace more burdensome field techniques. Single-nucleotide polymorphisms (SNPs) are particularly cost-effective and informative markers that can be used for a range of practical applications, including population census, assessment of human impact on social and genetic structure, and investigation of the illegal wildlife trade. SNP resources for elephants are scarce, but next-generation sequencing provides the opportunity for rapid, inexpensive generation of SNP markers in nonmodel species. Here, we sourced forest elephant DNA from 23 samples collected from 10 locations within Gabon, Central Africa, and applied double-digest restriction-site-associated DNA (ddRAD) sequencing to discover 31,851 tags containing SNPs that were reduced to a set of 1,365 high-quality candidate SNP markers. A subset of 115 candidate SNPs was then selected for assay design and validation using 56 additional samples. Genotyping resulted in a high conversion rate (93%) and a low per allele error rate (0.07%). This study provides the first panel of 107 validated SNP markers for forest elephants. This resource presents great potential for new genetic tools to produce reliable data and underpin a step-change in conservation policies for this elusive species.
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Affiliation(s)
- Stéphanie Bourgeois
- Agence Nationale des Parcs NationauxLibrevilleGabon
- WildGenes LaboratoryThe Royal Zoological Society of ScotlandEdinburgh ZooEdinburghUK
- Biological and Environmental SciencesFaculty of Natural SciencesUniversity of StirlingStirlingUK
| | - Helen Senn
- WildGenes LaboratoryThe Royal Zoological Society of ScotlandEdinburgh ZooEdinburghUK
| | - Jenny Kaden
- WildGenes LaboratoryThe Royal Zoological Society of ScotlandEdinburgh ZooEdinburghUK
| | - John B. Taggart
- Aquaculture Pathfoot BuildingUniversity of StirlingStirlingUK
| | - Rob Ogden
- TRACE Wildlife Forensics NetworkEdinburghUK
- Royal (Dick) School of Veterinary Studies & The Roslin InstituteUniversity of EdinburghEdinburghUK
| | - Kathryn J. Jeffery
- Agence Nationale des Parcs NationauxLibrevilleGabon
- Biological and Environmental SciencesFaculty of Natural SciencesUniversity of StirlingStirlingUK
- Institut de Recherche en Écologie TropicaleLibrevilleGabon
| | - Nils Bunnefeld
- Biological and Environmental SciencesFaculty of Natural SciencesUniversity of StirlingStirlingUK
| | - Katharine Abernethy
- Biological and Environmental SciencesFaculty of Natural SciencesUniversity of StirlingStirlingUK
- Institut de Recherche en Écologie TropicaleLibrevilleGabon
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21
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Harrisson KA, Amish SJ, Pavlova A, Narum SR, Telonis‐Scott M, Rourke ML, Lyon J, Tonkin Z, Gilligan DM, Ingram BA, Lintermans M, Gan HM, Austin CM, Luikart G, Sunnucks P. Signatures of polygenic adaptation associated with climate across the range of a threatened fish species with high genetic connectivity. Mol Ecol 2017; 26:6253-6269. [DOI: 10.1111/mec.14368] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 09/22/2017] [Accepted: 09/25/2017] [Indexed: 12/25/2022]
Affiliation(s)
- Katherine A. Harrisson
- School of Biological Sciences Monash University Clayton Vic. Australia
- Department of Ecology Environment and Evolution School of Life Sciences La Trobe University Bundoora Vic. Australia
- Arthur Rylah Institute for Environmental Research Heidelberg Vic. Australia
| | - Stephen J. Amish
- Conservation Genomics Group Division of Biological Sciences University of Montana Missoula MT USA
- Flathead Lake Biological Station University of Montana Polson MT USA
| | - Alexandra Pavlova
- School of Biological Sciences Monash University Clayton Vic. Australia
| | - Shawn R. Narum
- Columbia River Inter‐Tribal Fish Commission Hagerman Fish Culture Experiment Station Hagerman IDUSA
| | | | - Meaghan L. Rourke
- Department of Primary Industries DPI Fisheries Narrandera NSW Australia
| | - Jarod Lyon
- Arthur Rylah Institute for Environmental Research Heidelberg Vic. Australia
| | - Zeb Tonkin
- Arthur Rylah Institute for Environmental Research Heidelberg Vic. Australia
| | - Dean M. Gilligan
- Department of Primary Industries DPI Fisheries, Batemans Bay Fisheries Office Batemans Bay NSW Australia
| | | | - Mark Lintermans
- Institute for Applied Ecology University of Canberra Canberra ACT Australia
| | - Han Ming Gan
- Centre for Integrative Ecology School of Life and Environmental Sciences Deakin University Geelong Vic. Australia
- School of Science Monash University Malaysia Petaling Jaya Selangor Malaysia
- Genomics Facility, Tropical Medicine and Biology Platform Monash University Malaysia Petaling Jaya Selangor Malaysia
| | - Christopher M. Austin
- Centre for Integrative Ecology School of Life and Environmental Sciences Deakin University Geelong Vic. Australia
- School of Science Monash University Malaysia Petaling Jaya Selangor Malaysia
- Genomics Facility, Tropical Medicine and Biology Platform Monash University Malaysia Petaling Jaya Selangor Malaysia
| | - Gordon Luikart
- Conservation Genomics Group Division of Biological Sciences University of Montana Missoula MT USA
- Flathead Lake Biological Station University of Montana Polson MT USA
| | - Paul Sunnucks
- School of Biological Sciences Monash University Clayton Vic. Australia
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22
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Natesh M, Atla G, Nigam P, Jhala YV, Zachariah A, Borthakur U, Ramakrishnan U. Conservation priorities for endangered Indian tigers through a genomic lens. Sci Rep 2017; 7:9614. [PMID: 28851952 PMCID: PMC5575265 DOI: 10.1038/s41598-017-09748-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 07/31/2017] [Indexed: 11/21/2022] Open
Abstract
Tigers have lost 93% of their historical range worldwide. India plays a vital role in the conservation of tigers since nearly 60% of all wild tigers are currently found here. However, as protected areas are small (<300 km2 on average), with only a few individuals in each, many of them may not be independently viable. It is thus important to identify and conserve genetically connected populations, as well as to maintain connectivity within them. We collected samples from wild tigers (Panthera tigris tigris) across India and used genome-wide SNPs to infer genetic connectivity. We genotyped 10,184 SNPs from 38 individuals across 17 protected areas and identified three genetically distinct clusters (corresponding to northwest, southern and central India). The northwest cluster was isolated with low variation and high relatedness. The geographically large central cluster included tigers from central, northeastern and northern India, and had the highest variation. Most genetic diversity (62%) was shared among clusters, while unique variation was highest in the central cluster (8.5%) and lowest in the northwestern one (2%). We did not detect signatures of differential selection or local adaptation. We highlight that the northwest population requires conservation attention to ensure persistence of these tigers.
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Affiliation(s)
- Meghana Natesh
- National Center for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, 560065, India. .,Shanmugha Arts, Science, Technology and Research Academy (SASTRA) University, Tirumalaisamudram, Thanjavur, 613401, Tamil Nadu, India.
| | - Goutham Atla
- National Center for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, 560065, India
| | - Parag Nigam
- Wildlife Institute of India, Chandrabani, Dehradun, 248001, India
| | | | - Arun Zachariah
- Kerala Veterinary and Animal Sciences University, Lakkidi Post, Pookode, Kerala, 673576, India
| | - Udayan Borthakur
- Aaranyak, 12 Kanaklata Path in Lachit Path, Ajanta Path, Survey, Beltola, Guwahati, 781028, Assam, India
| | - Uma Ramakrishnan
- National Center for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, 560065, India.
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Melville J, Haines ML, Boysen K, Hodkinson L, Kilian A, Smith Date KL, Potvin DA, Parris KM. Identifying hybridization and admixture using SNPs: application of the DArTseq platform in phylogeographic research on vertebrates. ROYAL SOCIETY OPEN SCIENCE 2017; 4:161061. [PMID: 28791133 PMCID: PMC5541528 DOI: 10.1098/rsos.161061] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 06/14/2017] [Indexed: 05/04/2023]
Abstract
Next-generation sequencing (NGS) approaches are increasingly being used to generate multi-locus data for phylogeographic and evolutionary genetics research. We detail the applicability of a restriction enzyme-mediated genome complexity reduction approach with subsequent NGS (DArTseq) in vertebrate study systems at different evolutionary and geographical scales. We present two case studies using SNP data from the DArTseq molecular marker platform. First, we used DArTseq in a large phylogeographic study of the agamid lizard Ctenophorus caudicinctus, including 91 individuals and spanning the geographical range of this species across arid Australia. A low-density DArTseq assay resulted in 28 960 SNPs, with low density referring to a comparably reduced set of identified and sequenced markers as a cost-effective approach. Second, we applied this approach to an evolutionary genetics study of a classic frog hybrid zone (Litoria ewingii-Litoria paraewingi) across 93 individuals, which resulted in 48 117 and 67 060 SNPs for a low- and high-density assay, respectively. We provide a docker-based workflow to facilitate data preparation and analysis, then analyse SNP data using multiple methods including Bayesian model-based clustering and conditional likelihood approaches. Based on comparison of results from the DArTseq platform and traditional molecular approaches, we conclude that DArTseq can be used successfully in vertebrates and will be of particular interest to researchers working at the interface between population genetics and phylogenetics, exploring species boundaries, gene exchange and hybridization.
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Affiliation(s)
- Jane Melville
- Department of Sciences, Museum Victoria, Carlton, Victoria 3052, Australia
- Author for correspondence: Jane Melville e-mail:
| | - Margaret L. Haines
- Department of Sciences, Museum Victoria, Carlton, Victoria 3052, Australia
| | - Katja Boysen
- Department of Sciences, Museum Victoria, Carlton, Victoria 3052, Australia
| | - Luke Hodkinson
- Department of Sciences, Museum Victoria, Carlton, Victoria 3052, Australia
| | - Andrzej Kilian
- Diversity Arrays Technology, University of Canberra, Bruce, Australian Capital Territory 2617, Australia
| | | | | | - Kirsten M. Parris
- School of Ecosystem and Forest Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
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24
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Ng NSR, Wilton PR, Prawiradilaga DM, Tay YC, Indrawan M, Garg KM, Rheindt FE. The effects of Pleistocene climate change on biotic differentiation in a montane songbird clade from Wallacea. Mol Phylogenet Evol 2017; 114:353-366. [PMID: 28501612 DOI: 10.1016/j.ympev.2017.05.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 04/03/2017] [Accepted: 05/08/2017] [Indexed: 11/16/2022]
Abstract
The role of Pleistocene Ice Age in tropical diversification is poorly understood, especially in archipelagos, in which glaciation-induced sea level fluctuations may lead to complicated changes in land distribution. To assess how Pleistocene land bridges may have facilitated gene flow in tropical archipelagos, we investigated patterns of diversification in the rarely-collected rusty-bellied fantail Rhipidura teysmanni (Passeriformes: Rhipiduridae) complex from Wallacea using a combination of bioacoustic traits and whole-genome sequencing methods (dd-RADSeq). We report a biogeographic leapfrog pattern in the vocalizations of these birds, and uncover deep genomic divergence among island populations despite the presence of intermittent land connections between some. We demonstrate how rare instances of genetic introgression have affected the evolution of this species complex, and document the presence of double introgressive mitochondrial sweeps, highlighting the dangers of using only mitochondrial DNA in evolutionary research. By applying different tree inference approaches, we demonstrate how concatenation methods can give inaccurate results when investigating divergence in closely-related taxa. Our study highlights high levels of cryptic avian diversity in poorly-explored Wallacea, elucidates complex patterns of Pleistocene climate-mediated diversification in an elusive montane songbird, and suggests that Pleistocene land bridges may have accounted for limited connectivity among montane Wallacean biota.
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Affiliation(s)
- Nathaniel S R Ng
- National University of Singapore, Department of Biological Sciences, 14 Science Drive 4, Singapore 117543, Singapore
| | - Peter R Wilton
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, United States
| | - Dewi Malia Prawiradilaga
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jalan Raya Jakarta Bogor KM 46, Cibinong Science Center, Cibinong 16911, Indonesia
| | - Ywee Chieh Tay
- National University of Singapore, Department of Biological Sciences, 14 Science Drive 4, Singapore 117543, Singapore
| | - Mochamad Indrawan
- Center for Biodiversity Strategies, Lab Biologi Laut, Gedung E, FMIPA, Universitas Indonesia, 16424, Indonesia
| | - Kritika M Garg
- National University of Singapore, Department of Biological Sciences, 14 Science Drive 4, Singapore 117543, Singapore.
| | - Frank E Rheindt
- National University of Singapore, Department of Biological Sciences, 14 Science Drive 4, Singapore 117543, Singapore.
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25
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Mao X, Tsagkogeorga G, Bailey SE, Rossiter SJ. Genomics of introgression in the Chinese horseshoe bat (Rhinolophus sinicus) revealed by transcriptome sequencing. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Xiuguang Mao
- Institute of Estuarine and Coastal Research, East China Normal University, Shanghai 200062, China
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Georgia Tsagkogeorga
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Sebastian E. Bailey
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Stephen J. Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
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