1
|
Ortiz D, Pekár S, Dianat M. A consequential one-night stand: Episodic historical hybridization leads to mitochondrial takeover in sympatric desert ant-eating spiders. Mol Phylogenet Evol 2024; 199:108167. [PMID: 39103025 DOI: 10.1016/j.ympev.2024.108167] [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: 04/29/2024] [Revised: 07/03/2024] [Accepted: 08/01/2024] [Indexed: 08/07/2024]
Abstract
Disentangling the genomic intricacies underlying speciation and the causes of discordance between sources of evidence can offer remarkable insights into evolutionary dynamics. The ant-eating spider Zodarion nitidum, found across the Middle East and Egypt, displays yellowish and blackish morphs that co-occur sympatrically. These morphs additionally differ in behavioral and physiological features and show complete pre-mating reproductive isolation. In contrast, they possess similar sexual features and lack distinct differences in their mitochondrial DNA. We analyzed both Z. nitidum morphs and outgroups using genome-wide and additional mitochondrial DNA data. The genomic evidence indicated that Yellow and Black are reciprocally independent lineages without signs of recent admixture. Interestingly, the sister group of Yellow is not Black but Z. luctuosum, a morphologically distinct species. Genomic gene flow analyses pinpointed an asymmetric nuclear introgression event, with Yellow contributing nearly 5 % of its genome to Black roughly 320,000 years ago, intriguingly aligning with the independently estimated origin of the mitochondrial DNA of Black. We conclude that the blackish and yellowish morphs of Z. nitidum are long-diverged distinct species, and that the ancient and modest genomic introgression event registered resulted in a complete mitochondrial takeover of Black by Yellow. This investigation underscores the profound long-term effects that even modest hybridization events can have on the genome of organisms. It also exemplifies the utility of phylogenetic networks for estimating historical events and how integrating independent lines of evidence can increase the reliability of such estimations.
Collapse
Affiliation(s)
- David Ortiz
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czechia.
| | - Stano Pekár
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Malahat Dianat
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czechia; Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czechia
| |
Collapse
|
2
|
Hofmann S, Podsiadlowski L, Andermann T, Matschiner M, Baniya CB, Litvinchuk SN, Martin S, Masroor R, Yang J, Zheng Y, Jablonski D, Schmidt J. The last of their kind: Is the genus Scutiger (Anura: Megophryidae) a relict element of the paleo-transhimalaya biota? Mol Phylogenet Evol 2024:108166. [PMID: 39127262 DOI: 10.1016/j.ympev.2024.108166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 07/08/2024] [Accepted: 07/31/2024] [Indexed: 08/12/2024]
Abstract
The orographic evolution of the Himalaya-Tibet Mountain system continues to be a subject of controversy, leading to considerable uncertainty regarding the environment and surface elevation of the Tibetan Plateau during the Cenozoic era. As many geoscientific (but not paleontological) studies suggest, elevations close to modern heights exist in vast areas of Tibet since at least the late Paleogene, implicating the presence of large-scale alpine environments for more than 30 million years. To explore a recently proposed alternative model that assumes a warm temperate environment across paleo-Tibet, we carried out a phylogeographic survey using genomic analyses of samples covering the range of endemic lazy toads (Scutiger) across the Himalaya-Tibet orogen. We identified two main clades, with several, geographically distinct subclades. The long temporal gap between the stem and crown age of Scutiger may suggest high extinction rates. Diversification within the crown group, depending on the calibration, occurred either from the Mid-Miocene or Late-Miocene and continued until the Holocene. The present-day Himalayan Scutiger fauna could have evolved from lineages that existed on the southern edges of the paleo-Tibetan area (the Transhimalaya = Gangdese Shan), while extant species living on the eastern edge of the Plateau originated probably from the eastern edges of northern parts of the ancestral Tibetan area (Hoh Xil, Tanggula Shan). Based on the Mid-Miocene divergence time estimation and ancestral area reconstruction, we propose that uplift-associated aridification of a warm temperate Miocene-Tibet, coupled with high extirpation rates of ancestral populations, and species range shifts along drainage systems and epigenetic transverse valleys of the rising mountains, is a plausible scenario explaining the phylogenetic structure of Scutiger. This hypothesis aligns with the fossil record but conflicts with geoscientific concepts of high elevated Tibetan Plateau since the late Paleogene. Considering a Late-Miocene/Pliocene divergence time, an alternative scenario of dispersal from SE Asia into the East, Central, and West Himalaya cannot be excluded, although essential evolutionary and biogeographic aspects remain unresolved within this model.
Collapse
Affiliation(s)
- Sylvia Hofmann
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, D-53113 Bonn, Germany.
| | - Lars Podsiadlowski
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, D-53113 Bonn, Germany.
| | - Tobias Andermann
- Evolutionary Biology Centre, Uppsala University, 75236 Uppsala, Sweden.
| | | | - Chitra B Baniya
- Central Department of Botany, Tribhuvan University, Kirtipur 44618, Kathmandu, Nepal
| | - Spartak N Litvinchuk
- Institute of Cytology of the Russian Academy of Sciences, St. Peterburg 194064, Russia
| | - Sebastian Martin
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, D-53113 Bonn, Germany.
| | - Rafaqat Masroor
- Pakistan Museum of Natural History, Islamabad 44000, Pakistan
| | - Jianhuan Yang
- Kadoorie Conservation China, Kadoorie Farm and Botanic Garden, Hongkong, China.
| | - Yuchi Zheng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; Kadoorie Conservation China, Kadoorie Farm and Botanic Garden, Hongkong, China.
| | - Daniel Jablonski
- Department of Zoology, Comenius University in Bratislava, 842 15 Bratislava, Slovakia.
| | - Joachim Schmidt
- General and Systematic Zoology, Institute of Biosciences, University of Rostock, 18055 Rostock, Germany
| |
Collapse
|
3
|
Davis HR, Sanford HT, Das I, Nashriq I, Leaché AD. Establishing species boundaries in Bornean geckos. Biol Lett 2024; 20:20240157. [PMID: 39140204 PMCID: PMC11322891 DOI: 10.1098/rsbl.2024.0157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 05/29/2024] [Accepted: 07/10/2024] [Indexed: 08/15/2024] Open
Abstract
Species delimitation using mitochondrial DNA (mtDNA) remains an important and accessible approach for discovering and delimiting species. However, delimiting species with a single locus (e.g. DNA barcoding) is biased towards overestimating species diversity. The highly diverse gecko genus Cyrtodactylus is one such group where delimitation using mtDNA remains the paradigm. In this study, we use genomic data to test putative species boundaries established using mtDNA within three recognized species of Cyrtodactylus on the island of Borneo. We predict that multi-locus genomic data will estimate fewer species than mtDNA, which could have important ramifications for the species diversity within the genus. We aim to (i) investigate the correspondence between species delimitations using mtDNA and genomic data, (ii) infer species trees for each target species, and (iii) quantify gene flow and identify migration patterns to assess population connectivity. We find that species diversity is overestimated and that species boundaries differ between mtDNA and nuclear data. This underscores the value of using genomic data to reassess mtDNA-based species delimitations for taxa lacking clear species boundaries. We expect the number of recognized species within Cyrtodactylus to continue increasing, but, when possible, genomic data should be included to inform more accurate species boundaries.
Collapse
Affiliation(s)
- Hayden R. Davis
- Department of Biology, Burke Museum of Natural History and Culture, University of Washington, Seattle, WA98195, USA
| | - Henry T. Sanford
- Department of Biology, Burke Museum of Natural History and Culture, University of Washington, Seattle, WA98195, USA
| | - Indraneil Das
- Institute of Biodiversity and Environmental Conservation, Universiti of Malaysia, Sarawak, Kota Samarahan, Malaysia
| | - Izneil Nashriq
- Institute of Biodiversity and Environmental Conservation, Universiti of Malaysia, Sarawak, Kota Samarahan, Malaysia
| | - Adam D. Leaché
- Department of Biology, Burke Museum of Natural History and Culture, University of Washington, Seattle, WA98195, USA
| |
Collapse
|
4
|
Singh Yadav S, Tariq R, Kumar Padhy P, Saxena A, Rai P, Srivastava V, Kumar N, Kumar Sharma S, Priya S. A multiplex DNA probe-based method for simultaneous identification of adulteration in meat samples. FOOD CHEMISTRY. MOLECULAR SCIENCES 2024; 8:100200. [PMID: 38525270 PMCID: PMC10960131 DOI: 10.1016/j.fochms.2024.100200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 02/26/2024] [Accepted: 03/13/2024] [Indexed: 03/26/2024]
Abstract
Meat adulteration and admixing are prevalent malpractices observed in processed and raw meat samples, where the consumption of adulterated meat has been associated with food allergies, financial losses, and consumer distrust. Meat authentication is pivotal to address these concerns. The meat authenticity can be determined through genetic, protein, and immunological markers and advanced detection methods. However, these methods often target a single species and lack the specificity to distinguish closely related species. Here, in the present study, we have developed a multiplex detection method based on the species-specific primers and probes, that can target four meat species in one reaction. The developed method amplifies the mitochondrial genomic regions of chicken, pork, sheep and goat using TaqMan multiplex probe-based RT-qPCR assay. Unique pairs of species-specific primers and probes that target specific mitochondrial DNA (mtDNA) regions of each species were designed and screened for specificity and sensitivity. The detection limit for species identification using the designed primers in real-time qPCR assays was 0.1 picogram per microliter (pg/μL) DNA detected in singleplex reaction and facilitates the simultaneous detection of closely related species, such as goat and sheep. Further, DNA-based probes were utilized in a multiplex real-time qPCR assay to identify chicken, pork, sheep and goat DNA in a single tube reaction. The multiplex assay was validated for raw and processed meat products, demonstrating its applications in ensuring the quality of meat products and safeguarding consumer interests.
Collapse
Affiliation(s)
- Smriti Singh Yadav
- Systems Toxicology Group, CSIR - Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Ramsha Tariq
- Systems Toxicology Group, CSIR - Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India
| | - Prabeen Kumar Padhy
- Systems Toxicology Group, CSIR - Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India
| | - Apoorva Saxena
- Food Toxicology Group, CSIR - Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India
| | - Pawankumar Rai
- Food Toxicology Group, CSIR - Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India
| | - Vikas Srivastava
- Systems Toxicology Group, CSIR - Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India
| | - Navjot Kumar
- CSIR - Central Electronics Engineering Research Institute, CFC-1, Malviya Industrial Area, Jaipur 302017, Rajasthan, India
| | - Sandeep Kumar Sharma
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Food Toxicology Group, CSIR - Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India
| | - Smriti Priya
- Systems Toxicology Group, CSIR - Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| |
Collapse
|
5
|
Zhang D, She H, Wang S, Wang H, Li S, Cheng Y, Song G, Jia C, Qu Y, Rheindt FE, Olsson U, Alström P, Lei F. Phylogenetic Conflict Between Species Tree and Maternally Inherited Gene Trees in a Clade of Emberiza Buntings (Aves: Emberizidae). Syst Biol 2024; 73:279-289. [PMID: 38157277 DOI: 10.1093/sysbio/syad078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 12/06/2023] [Accepted: 12/27/2023] [Indexed: 01/03/2024] Open
Abstract
Different genomic regions may reflect conflicting phylogenetic topologies primarily due to incomplete lineage sorting and/or gene flow. Genomic data are necessary to reconstruct the true species tree and explore potential causes of phylogenetic conflict. Here, we investigate the phylogenetic relationships of 4 Emberiza species (Aves: Emberizidae) and discuss the potential causes of the observed mitochondrial non-monophyly of Emberiza godlewskii (Godlewski's bunting) using phylogenomic analyses based on whole genome resequencing data from 41 birds. Analyses based on both the whole mitochondrial genome and ~39 kilobases from the non-recombining W chromosome reveal sister relationships between each the northern and southern populations of E. godlewskii with E. cioides and E. cia, respectively. In contrast, the monophyly of E. godlewskii is reflected by the phylogenetic signal of autosomal and Z chromosomal sequence data as well as demographic inference analyses, which-in combination-support the following tree topology: ([{E. godlewskii, E. cia}, E. cioides], E. jankowskii). Using D-statistics, we detected multiple gene flow events among different lineages, indicating pervasive introgressive hybridization within this clade. Introgression from an unsampled lineage that is sister to E. cioides or introgression from an unsampled mitochondrial + W chromosomal lineage of E. cioides into northern E. godlewskii may explain the phylogenetic conflict between the species tree estimated from genome-wide data versus mtDNA/W tree topologies. These results underscore the importance of using genomic data for phylogenetic reconstruction and species delimitation.
Collapse
Affiliation(s)
- Dezhi Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Huishang She
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Shangyu Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Haitao Wang
- School of Life Sciences, Jilin Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130024, China
| | - Shi Li
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Yalin Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Chenxi Jia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Republic of Singapore
| | - Urban Olsson
- Department of Biology and Environmental Science, University of Gothenburg, Box 463, SE-405 30 Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Gothenburg, Sweden
| | - Per Alström
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18 D, SE-752 36 Uppsala, Sweden
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, 100049 Beijing, China
| |
Collapse
|
6
|
Nie X, Zhang Y, Chu S, Yu W, Liu Y, Yan B, Zhao S, Gao W, Li C, Shi X, Zheng R, Fang K, Qin L, Xing Y. New insights into the evolution and local adaptation of the genus Castanea in east Asia. HORTICULTURE RESEARCH 2024; 11:uhae147. [PMID: 38988617 PMCID: PMC11233864 DOI: 10.1093/hr/uhae147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 05/20/2024] [Indexed: 07/12/2024]
Abstract
Chestnut plants (Castanea) are important nut fruit trees worldwide. However, little is known regarding the genetic relationship and evolutionary history of different species within the genus. How modern chestnut plants have developed local adaptation to various climates remains a mystery. The genomic data showed that Castanea henryi first diverged in the Oligocene ~31.56 million years ago, followed by Castanea mollissima, and the divergence between Castanea seguinii and Castanea crenata occurred in the mid-Miocene. Over the last 5 million years, the population of chestnut plants has continued to decline. A combination of selective sweep and environmental association studies was applied to investigate the genomic basis of chestnut adaptation to different climates. Twenty-two candidate genes were associated with temperature and precipitation. We also revealed the molecular mechanism by which CmTOE1 interacts with CmZFP8 and CmGIS3 to promote the formation of non-glandular trichomes for adaptation to low temperature and high altitudes. We found a significant expansion of CER1 genes in Chinese chestnut (C. mollissima) and verified the CmERF48 regulation of CmCER1.6 adaptation to drought environments. These results shed light on the East Asian chestnut plants as a monophyletic group that had completed interspecific differentiation in the Miocene, and provided candidate genes for future studies on adaptation to climate change in nut trees.
Collapse
Affiliation(s)
- Xinghua Nie
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
| | - Yu Zhang
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
| | - Shihui Chu
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
| | - Wenjie Yu
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
| | - Yang Liu
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
| | - Boqian Yan
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
| | - Shuqing Zhao
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
| | - Wenli Gao
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
| | - Chaoxin Li
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
| | - Xueteng Shi
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China
| | - Ruijie Zheng
- Liaoning Economic Forest Research Institute, Liaoning Academy of Agricultural Sciences, Dalian, 116000, China
| | - Kefeng Fang
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China
| | - Ling Qin
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
| | - Yu Xing
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
| |
Collapse
|
7
|
Yang S, Huang J, Qu Y, Zhang D, Tan Y, Wen S, Song Y. Phylogenetic incongruence in an Asiatic species complex of the genus Caryodaphnopsis (Lauraceae). BMC PLANT BIOLOGY 2024; 24:616. [PMID: 38937691 PMCID: PMC11212351 DOI: 10.1186/s12870-024-05050-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 04/19/2024] [Indexed: 06/29/2024]
Abstract
BACKGROUND Caryodaphnopsis, a group of tropical trees (ca. 20 spp.) in the family Lauraceae, has an amphi-Pacific disjunct distribution: ten species are distributed in Southeast Asia, while eight species are restricted to tropical rainforests in South America. Previously, phylogenetic analyses using two nuclear markers resolved the relationships among the five species from Latin America. However, the phylogenetic relationships between the species in Asia remain poorly known. RESULTS Here, we first determined the complete mitochondrial genome (mitogenome), plastome, and the nuclear ribosomal cistron (nrDNA) sequences of C. henryi with lengths of 1,168,029 bp, 154,938 bp, and 6495 bp, respectively. We found 2233 repeats and 368 potential SSRs in the mitogenome of C. henryi and 50 homologous DNA fragments between its mitogenome and plastome. Gene synteny analysis revealed a mass of rearrangements in the mitogenomes of Magnolia biondii, Hernandia nymphaeifolia, and C. henryi and only six conserved clustered genes among them. In order to reconstruct relationships for the ten Caryodaphnopsis species in Asia, we created three datasets: one for the mitogenome (coding genes and ten intergenic regions), another for the plastome (whole genome), and the other for the nuclear ribosomal cistron. All of the 22 Caryodaphnopsis individuals were divided into four, five, and six different clades in the phylogenies based on mitogenome, plastome, and nrDNA datasets, respectively. CONCLUSIONS The study showed phylogenetic conflicts within and between nuclear and organellar genome data of Caryodaphnopsis species. The sympatric Caryodaphnopsis species in Hekou and Malipo SW China may be related to the incomplete lineage sorting, chloroplast capture, and/or hybridization, which mixed the species as a complex in their evolutionary history.
Collapse
Affiliation(s)
- Shiting Yang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Ministry of Education) and Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, Guangxi Normal University, Guilin, 541004, Guangxi, China
| | - Jiepeng Huang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Ministry of Education) and Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, Guangxi Normal University, Guilin, 541004, Guangxi, China
| | - Yaya Qu
- Southwest Forestry University, Kunming, 650224, Yunnan, China
| | - Di Zhang
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences & Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, 666303, China
| | - Yunhong Tan
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences & Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, 666303, China
| | - Shujun Wen
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guangxi Institute of Botany, Guilin, 541006, China.
| | - Yu Song
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Ministry of Education) and Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, Guangxi Normal University, Guilin, 541004, Guangxi, China.
| |
Collapse
|
8
|
Lichman V, Ozerov M, López ME, Noreikiene K, Kahar S, Pukk L, Burimski O, Gross R, Vasemägi A. Whole-genome analysis reveals phylogenetic and demographic history of Eurasian perch. JOURNAL OF FISH BIOLOGY 2024. [PMID: 38897597 DOI: 10.1111/jfb.15821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 04/19/2024] [Accepted: 05/14/2024] [Indexed: 06/21/2024]
Abstract
The contemporary diversity and distribution of species are shaped by their evolutionary and ecological history. This can be deciphered with the help of phylogenetic and demographic analysis methods, ideally combining and supplementing information from mitochondrial and nuclear genomes. In this study, we investigated the demographic history of Eurasian perch (Perca fluviatilis), a highly adaptable teleost with a distribution range across Eurasia. We combined whole-genome resequencing data with available genomic resources to analyse the phylogeny, phylogeography, and demographic history of P. fluviatilis populations from Europe and Siberia. We identified five highly diverged evolutionary mtDNA lineages, three of which show a strong signal of admixture in the Baltic Sea region. The estimated mean divergence time between these lineages ranged from 0.24 to 1.42 million years. Based on nuclear genomes, two distinct demographic trajectories were observed in European and Siberian samples reflecting contrasting demographic histories ca. 30,000-100,000 years before the present. A comparison of mtDNA and nuclear DNA evolutionary trees and AMOVA revealed concordances, as well as incongruences, between the two types of data, most likely reflecting recent postglacial colonization and hybridization events. Overall, our findings demonstrate the power and usefulness of genome-wide information for delineating historical processes that have shaped the genome of P. fluviatilis. We also highlight the added value of data-mining existing transcriptomic resources to complement novel sequence data, helping to shed light on putative glacial refugia and postglacial recolonization routes.
Collapse
Affiliation(s)
- Vitalii Lichman
- Institute of Veterinary Medicine and Animal Sciences, Chair of Aquaculture, Estonian University of Life Sciences, Tartu, Estonia
| | - Mikhail Ozerov
- Biodiversity Unit, University of Turku, Turku, Finland
- Department of Aquatic Resources, Institute of Freshwater Research, Swedish University of Agricultural Sciences, Drottningholm, Sweden
- Department of Biology, University of Turku, Turku, Finland
| | - María-Eugenia López
- Department of Aquatic Resources, Institute of Freshwater Research, Swedish University of Agricultural Sciences, Drottningholm, Sweden
| | - Kristina Noreikiene
- Institute of Veterinary Medicine and Animal Sciences, Chair of Aquaculture, Estonian University of Life Sciences, Tartu, Estonia
- Department of Botany and Genetics, Vilnius University, Vilnius, Lithuania
| | - Siim Kahar
- Institute of Veterinary Medicine and Animal Sciences, Chair of Aquaculture, Estonian University of Life Sciences, Tartu, Estonia
| | - Lilian Pukk
- Institute of Veterinary Medicine and Animal Sciences, Chair of Aquaculture, Estonian University of Life Sciences, Tartu, Estonia
| | - Oksana Burimski
- Institute of Veterinary Medicine and Animal Sciences, Chair of Aquaculture, Estonian University of Life Sciences, Tartu, Estonia
| | - Riho Gross
- Institute of Veterinary Medicine and Animal Sciences, Chair of Aquaculture, Estonian University of Life Sciences, Tartu, Estonia
| | - Anti Vasemägi
- Institute of Veterinary Medicine and Animal Sciences, Chair of Aquaculture, Estonian University of Life Sciences, Tartu, Estonia
- Department of Aquatic Resources, Institute of Freshwater Research, Swedish University of Agricultural Sciences, Drottningholm, Sweden
| |
Collapse
|
9
|
Wang N, Shan C, Chen D, Hu Y, Sun Y, Wang Y, Liang B, Liang W. "Isolation by Gentes with Asymmetric Migration" shapes the genetic structure of the common cuckoo in China. Integr Zool 2024. [PMID: 38872343 DOI: 10.1111/1749-4877.12853] [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: 06/15/2024]
Abstract
Amid coevolutionary arms races between brood parasitic birds and their diverse host species, the formation of host-specific races, or gentes, has drawn significant research focus. Nevertheless, numerous questions about gentes evolutionary patterns persist. Here, we investigated the potential for gentes evolution across multiple common cuckoo (Cuculus canorus) populations parasitizing diverse host species in China. Using maternal (mitochondrial and W-linked DNA) and biparental (autosomal and Z-linked DNA) markers, we found consistent clustering of cuckoo gentes (rather than geographical populations) into distinct clades in matrilineal gene trees, indicating robust differentiation. In contrast, biparental markers indicated intermixing of all gentes, suggesting asymmetric gene flow regardless of geography. Unlike the mitonuclear discordance commonly resulting from incomplete lineage sorting, adaptive introgression, or demographic disparities, the observed pattern in brood parasitic cuckoos might reflect biased host preferences between sexes. We hereby present the "Isolation by Gentes with Asymmetric Migration" model. According to this model, the maternal line differentiation of the common cuckoo in China is potentially driven by host preferences in females, whereas males maintained the integrity of the cuckoo species through random mating. To achieve this, cuckoo males could perform flexible migration among gentes or engage in early copulation with females before reaching the breeding sites, allowing female cuckoos to store sperm from various gentes. Future studies collecting additional samples from diverse cuckoo gentes with overlapping distribution and investigating the migratory and copulation patterns of each sex would enhance our understanding of sex-biased differentiation among cuckoo populations in China.
Collapse
Affiliation(s)
- Ning Wang
- School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Chengbin Shan
- School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Dan Chen
- School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Yunbiao Hu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yuehua Sun
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Ying Wang
- School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Bin Liang
- School of Life Sciences, Inner Mongolia University, Hohhot, China
- Inner Mongolia Engineering Technology Research Center of Germplasm Resources Conservation and Utilization, Hohhot, China
| | - Wei Liang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China
| |
Collapse
|
10
|
Marcionetti A, Bertrand JAM, Cortesi F, Donati GFA, Heim S, Huyghe F, Kochzius M, Pellissier L, Salamin N. Recurrent gene flow events occurred during the diversification of clownfishes of the skunk complex. Mol Ecol 2024; 33:e17347. [PMID: 38624248 DOI: 10.1111/mec.17347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 03/15/2024] [Accepted: 03/26/2024] [Indexed: 04/17/2024]
Abstract
Clownfish (subfamily Amphiprioninae) are an iconic group of coral reef fish that evolved a mutualistic interaction with sea anemones, which triggered the adaptive radiation of the clade. Within clownfishes, the "skunk complex" is particularly interesting. Besides ecological speciation, interspecific gene flow and hybrid speciation are thought to have shaped the evolution of the group. We investigated the mechanisms characterizing the diversification of this complex. By taking advantage of their disjunct geographical distribution, we obtained whole-genome data of sympatric and allopatric populations of the three main species of the complex (Amphiprion akallopisos, A. perideraion and A. sandaracinos). We examined population structure, genomic divergence and introgression signals and performed demographic modelling to identify the most realistic diversification scenario. We excluded scenarios of strict isolation or hybrid origin of A. sandaracinos. We discovered moderate gene flow from A. perideraion to the ancestor of A. akallopisos + A. sandaracinos and weak gene flow between the species in the Indo-Australian Archipelago throughout the diversification of the group. We identified introgressed regions in A. sandaracinos and detected in A. perideraion two large regions of high divergence from the two other species. While we found that gene flow has occurred throughout the species' diversification, we also observed that recent admixture was less pervasive than initially thought, suggesting a role of host repartition or behavioural barriers in maintaining the genetic identity of the species in sympatry.
Collapse
Affiliation(s)
- Anna Marcionetti
- Department of Computational Biology, Génopode, University of Lausanne, Lausanne, Switzerland
| | - Joris A M Bertrand
- Department of Computational Biology, Génopode, University of Lausanne, Lausanne, Switzerland
- Laboratoire Génome et Développement Des Plantes (UMR 5096 UPVD/CNRS), University of Perpignan via Domitia, Perpignan, France
| | - Fabio Cortesi
- School of the Environment and Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Giulia F A Donati
- EAWAG Swiss Federal Institute of Aquatic Science & Technology, Dübendorf, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Sara Heim
- Department of Computational Biology, Génopode, University of Lausanne, Lausanne, Switzerland
| | - Filip Huyghe
- Marine Biology - Ecology, Evolution and Genetics, Vrije Universiteit Brussel (VUB), Pleinlaan 2, Brussels, Belgium
| | - Marc Kochzius
- Marine Biology - Ecology, Evolution and Genetics, Vrije Universiteit Brussel (VUB), Pleinlaan 2, Brussels, Belgium
| | - Loïc Pellissier
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
- Ecosystems and Landscape Evolution, Department of Environmental System Science, Institute of Terrestrial Ecosystems, ETH Zürich, Zurich, Switzerland
| | - Nicolas Salamin
- Department of Computational Biology, Génopode, University of Lausanne, Lausanne, Switzerland
| |
Collapse
|
11
|
Drozdova PB, Madyarova EV, Gurkov AN, Saranchina AE, Romanova EV, Petunina JV, Peretolchina TE, Sherbakov DY, Timofeyev MA. Lake Baikal amphipods and their genomes, great and small. Vavilovskii Zhurnal Genet Selektsii 2024; 28:317-325. [PMID: 38952708 PMCID: PMC11214899 DOI: 10.18699/vjgb-24-36] [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: 01/31/2024] [Revised: 02/28/2024] [Accepted: 02/28/2024] [Indexed: 07/03/2024] Open
Abstract
Endemic amphipods (Crustacea: Amphipoda) of Lake Baikal represent an outstanding example of large species flocks occupying a wide range of ecological niches and originating from a handful of ancestor species. Their development took place at a restricted territory and is thus open for comprehensive research. Such examples provide unique opportunities for studying behavioral, anatomic, or physiological adaptations in multiple combinations of environmental conditions and thus attract considerable attention. The existing taxonomies of this group list over 350 species and subspecies, which, according to the molecular phylogenetic studies of marker genes, full transcriptomes and mitochondrial genomes, originated from at least two introductions into the lake. The studies of allozymes and marker genes have revealed a significant cryptic diversity in Baikal amphipods, as well as a large variance in genetic diversity within some morphological species. Crossing experiments conducted so far for two morphological species suggest that the differences in the mitochondrial marker (cytochrome c oxidase subunit I gene) can potentially be applied for making predictions about reproductive isolation. For about one-tenth of the Baikal amphipod species, nuclear genome sizes and chromosome numbers are known. While genome sizes vary within one order of magnitude, the karyotypes are relatively stable (2n = 52 for most species studied). Moreover, analysis of the diversity of repeated sequences in nuclear genomes showed significant between-species differences. Studies of mitochondrial genomes revealed some unusual features, such as variation in length and gene order, as well as duplications of tRNA genes, some of which also underwent remolding (change in anticodon specificity due to point mutations). The next important steps should be (i) the assembly of whole genomes for different species of Baikal amphipods, which is at the moment hampered by complicated genome structures with high repeat content, and (ii) updating species taxonomy taking into account all the data.
Collapse
Affiliation(s)
- P B Drozdova
- Irkutsk State University, Irkutsk, Russia Baikal Research Centre, Irkutsk, Russia
| | | | - A N Gurkov
- Irkutsk State University, Irkutsk, Russia Baikal Research Centre, Irkutsk, Russia
| | | | - E V Romanova
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - J V Petunina
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - T E Peretolchina
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - D Y Sherbakov
- Irkutsk State University, Irkutsk, Russia Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia Novosibirsk State University, Novosibirsk, Russia
| | | |
Collapse
|
12
|
Thureborn O, Wikström N, Razafimandimbison SG, Rydin C. Plastid phylogenomics and cytonuclear discordance in Rubioideae, Rubiaceae. PLoS One 2024; 19:e0302365. [PMID: 38768140 PMCID: PMC11104678 DOI: 10.1371/journal.pone.0302365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 04/03/2024] [Indexed: 05/22/2024] Open
Abstract
In this study of evolutionary relationships in the subfamily Rubioideae (Rubiaceae), we take advantage of the off-target proportion of reads generated via previous target capture sequencing projects based on nuclear genomic data to build a plastome phylogeny and investigate cytonuclear discordance. The assembly of off-target reads resulted in a comprehensive plastome dataset and robust inference of phylogenetic relationships, where most intratribal and intertribal relationships are resolved with strong support. While the phylogenetic results were mostly in agreement with previous studies based on plastome data, novel relationships in the plastid perspective were also detected. For example, our analyses of plastome data provide strong support for the SCOUT clade and its sister relationship to the remaining members of the subfamily, which differs from previous results based on plastid data but agrees with recent results based on nuclear genomic data. However, several instances of highly supported cytonuclear discordance were identified across the Rubioideae phylogeny. Coalescent simulation analysis indicates that while ILS could, by itself, explain the majority of the discordant relationships, plastome introgression may be the better explanation in some cases. Our study further indicates that plastomes across the Rubioideae are, with few exceptions, highly conserved and mainly conform to the structure, gene content, and gene order present in the majority of the flowering plants.
Collapse
Affiliation(s)
- Olle Thureborn
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Niklas Wikström
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
- The Bergius Foundation, The Royal Academy of Sciences, Stockholm, Sweden
| | | | - Catarina Rydin
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
- The Bergius Foundation, The Royal Academy of Sciences, Stockholm, Sweden
| |
Collapse
|
13
|
Main DC, Taft JM, Geneva AJ, Jansenvan Vuuren B, Tolley KA. The efficacy of single mitochondrial genes at reconciling the complete mitogenome phylogeny-a case study on dwarf chameleons. PeerJ 2024; 12:e17076. [PMID: 38708350 PMCID: PMC11067893 DOI: 10.7717/peerj.17076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 02/19/2024] [Indexed: 05/07/2024] Open
Abstract
Although genome-scale data generation is becoming more tractable for phylogenetics, there are large quantities of single gene fragment data in public repositories and such data are still being generated. We therefore investigated whether single mitochondrial genes are suitable proxies for phylogenetic reconstruction as compared to the application of full mitogenomes. With near complete taxon sampling for the southern African dwarf chameleons (Bradypodion), we estimated and compared phylogenies for the complete mitogenome with topologies generated from individual mitochondrial genes and various combinations of these genes. Our results show that the topologies produced by single genes (ND2, ND4, ND5, COI, and COIII) were analogous to the complete mitogenome, suggesting that these genes may be reliable markers for generating mitochondrial phylogenies in lieu of generating entire mitogenomes. In contrast, the short fragment of 16S commonly used in herpetological systematics, produced a topology quite dissimilar to the complete mitogenome and its concatenation with ND2 weakened the resolution of ND2. We therefore recommend the avoidance of this 16S fragment in future phylogenetic work.
Collapse
Affiliation(s)
- Devon C. Main
- Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Johannesburg, Gauteng, South Africa
| | - Jody M. Taft
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, South Africa
- South African National Biodiversity Institute, Kirstenbosch Research Centre, Claremont, South Africa
| | - Anthony J. Geneva
- Department of Biology, Center for Computational and Integrative Biology, Rutgers, The State University of New Jersey, Camden, NJ, United States of America
| | - Bettine Jansenvan Vuuren
- Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Johannesburg, Gauteng, South Africa
| | - Krystal A. Tolley
- Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Johannesburg, Gauteng, South Africa
- South African National Biodiversity Institute, Kirstenbosch Research Centre, Claremont, South Africa
| |
Collapse
|
14
|
Haberski A, Caterino MS. A review of Nearctic Lathrobium (Coleoptera, Staphylinidae), with revision and descriptions of new flightless species from the mountains of the southeastern U.S. Zookeys 2024; 1198:193-277. [PMID: 38708381 PMCID: PMC11066506 DOI: 10.3897/zookeys.1198.118355] [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: 01/07/2024] [Accepted: 03/15/2024] [Indexed: 05/07/2024] Open
Abstract
Species of the genus Lathrobium Gravenhorst (Coleoptera: Staphylinidae: Paederinae) from North America north of Mexico are reviewed and 41 species are recognized. Morphology and mitochondrial COI sequence data were used to guide species designations in three flightless lineages endemic to the southern Appalachian Mountains, a biologically diverse region known for cryptic diversity. Using a combination of phylogeny, algorithm-based species delimitation analyses, and genitalic morphology, five new cryptic species are described and possible biogeographic scenarios for their speciation hypothesized: L.balsamense Haberski & Caterino, sp. nov., L.camplyacra Haberski & Caterino, sp. nov., L.islae Haberski & Caterino, sp. nov., L.lividum Haberski & Caterino, sp. nov., L.smokiense Haberski & Caterino, sp. nov. Five additional species are described: L.absconditum Haberski & Caterino, sp. nov., L.hardeni Haberski & Caterino, sp. nov., L.lapidum Haberski & Caterino, sp. nov., L.solum Haberski & Caterino, sp. nov., and L.thompsonorum Haberski & Caterino, sp. nov. Two species are transferred from Lathrobium to Pseudolathra Casey: Pseudolathraparcum (LeConte, 1880), comb. nov. and Pseudolathratexana (Casey, 1905), comb. nov. Twenty-six names are reduced to synonymy. Lectotypes are designated for 47 species. Larvae are described where known, and characters of possible diagnostic value are summarized. Species diagnoses, distributions, illustrations of male and female genitalia, and a key to Lathrobium species known from the Nearctic region (including several introduced species) are provided.
Collapse
Affiliation(s)
- Adam Haberski
- Department of Plant & Environmental Sciences, Clemson University, Clemson, SC 29634-0310, USAClemson UniversityClemsonUnited States of America
| | - Michael S. Caterino
- Department of Plant & Environmental Sciences, Clemson University, Clemson, SC 29634-0310, USAClemson UniversityClemsonUnited States of America
| |
Collapse
|
15
|
D’Ercole J, Dapporto L, Opler P, Schmidt CB, Ho C, Menchetti M, Zakharov EV, Burns JM, Hebert PDN. A genetic atlas for the butterflies of continental Canada and United States. PLoS One 2024; 19:e0300811. [PMID: 38568891 PMCID: PMC10990199 DOI: 10.1371/journal.pone.0300811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 03/05/2024] [Indexed: 04/05/2024] Open
Abstract
Multi-locus genetic data for phylogeographic studies is generally limited in geographic and taxonomic scope as most studies only examine a few related species. The strong adoption of DNA barcoding has generated large datasets of mtDNA COI sequences. This work examines the butterfly fauna of Canada and United States based on 13,236 COI barcode records derived from 619 species. It compiles i) geographic maps depicting the spatial distribution of haplotypes, ii) haplotype networks (minimum spanning trees), and iii) standard indices of genetic diversity such as nucleotide diversity (π), haplotype richness (H), and a measure of spatial genetic structure (GST). High intraspecific genetic diversity and marked spatial structure were observed in the northwestern and southern North America, as well as in proximity to mountain chains. While species generally displayed concordance between genetic diversity and spatial structure, some revealed incongruence between these two metrics. Interestingly, most species falling in this category shared their barcode sequences with one at least other species. Aside from revealing large-scale phylogeographic patterns and shedding light on the processes underlying these patterns, this work also exposed cases of potential synonymy and hybridization.
Collapse
Affiliation(s)
- Jacopo D’Ercole
- Centre for Biodiversity Genomics, Guelph, Ontario, Canada
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Leonardo Dapporto
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Paul Opler
- Colorado State University, Fort Collins, Colorado, United States of America
| | - Christian B. Schmidt
- Canadian National Collection of Insects, Arachnids and Nematodes, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Chris Ho
- Centre for Biodiversity Genomics, Guelph, Ontario, Canada
| | | | | | - John M. Burns
- Department of Entomology, Smithsonian Institution, Washington, DC, United States of America
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics, Guelph, Ontario, Canada
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| |
Collapse
|
16
|
Martins ARP, Warren NB, McMillan WO, Barrett RDH. Spatiotemporal dynamics in butterfly hybrid zones. INSECT SCIENCE 2024; 31:328-353. [PMID: 37596954 DOI: 10.1111/1744-7917.13262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/13/2023] [Accepted: 07/21/2023] [Indexed: 08/21/2023]
Abstract
Evaluating whether hybrid zones are stable or mobile can provide novel insights for evolution and conservation biology. Butterflies exhibit high sensitivity to environmental changes and represent an important model system for the study of hybrid zone origins and maintenance. Here, we review the literature exploring butterfly hybrid zones, with a special focus on their spatiotemporal dynamics and the potential mechanisms that could lead to their movement or stability. We then compare different lines of evidence used to investigate hybrid zone dynamics and discuss the strengths and weaknesses of each approach. Our goal with this review is to reveal general conditions associated with the stability or mobility of butterfly hybrid zones by synthesizing evidence obtained using different types of data sampled across multiple regions and spatial scales. Finally, we discuss spatiotemporal dynamics in the context of a speciation/divergence continuum, the relevance of hybrid zones for conservation biology, and recommend key topics for future investigation.
Collapse
Affiliation(s)
- Ananda R Pereira Martins
- Redpath Museum, McGill University, 859 Sherbrooke Street West, Montreal, Quebec, Canada
- Smithsonian Tropical Research Institute, Gamboa, Panama City, Panama
| | - Natalie B Warren
- Redpath Museum, McGill University, 859 Sherbrooke Street West, Montreal, Quebec, Canada
| | - W Owen McMillan
- Smithsonian Tropical Research Institute, Gamboa, Panama City, Panama
| | - Rowan D H Barrett
- Redpath Museum, McGill University, 859 Sherbrooke Street West, Montreal, Quebec, Canada
| |
Collapse
|
17
|
Sánchez KI, Recknagel H, Elmer KR, Avila LJ, Morando M. Tracing evolutionary trajectories in the presence of gene flow in South American temperate lizards (Squamata: Liolaemus kingii group). Evolution 2024; 78:716-733. [PMID: 38262697 DOI: 10.1093/evolut/qpae009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 12/20/2023] [Accepted: 01/17/2024] [Indexed: 01/25/2024]
Abstract
Evolutionary processes behind lineage divergence often involve multidimensional differentiation. However, in the context of recent divergences, the signals exhibited by each dimension may not converge. In such scenarios, incomplete lineage sorting, gene flow, and scarce phenotypic differentiation are pervasive. Here, we integrated genomic (RAD loci of 90 individuals), phenotypic (linear and geometric traits of 823 and 411 individuals, respectively), spatial, and climatic data to reconstruct the evolutionary history of a speciation continuum of liolaemid lizards (Liolaemus kingii group). Specifically, we (a) inferred the population structure of the group and contrasted it with the phenotypic variability; (b) assessed the role of postdivergence gene flow in shaping phylogeographic and phenotypic patterns; and (c) explored ecogeographic drivers of diversification across time and space. We inferred eight genomic clusters exhibiting leaky genetic borders coincident with geographic transitions. We also found evidence of postdivergence gene flow resulting in transgressive phenotypic evolution in one species. Predicted ancestral niches unveiled suitable areas in southern and eastern Patagonia during glacial and interglacial periods. Our study underscores integrating different data and model-based approaches to determine the underlying causes of diversification, a challenge faced in the study of recently diverged groups. We also highlight Liolaemus as a model system for phylogeographic and broader evolutionary studies.
Collapse
Affiliation(s)
- Kevin I Sánchez
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales, Consejo Nacional de Investigaciones Científicas y Técnicas (IPEEC-CONICET), Puerto Madryn, Chubut, Argentina
| | - Hans Recknagel
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Kathryn R Elmer
- School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Luciano J Avila
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales, Consejo Nacional de Investigaciones Científicas y Técnicas (IPEEC-CONICET), Puerto Madryn, Chubut, Argentina
| | - Mariana Morando
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales, Consejo Nacional de Investigaciones Científicas y Técnicas (IPEEC-CONICET), Puerto Madryn, Chubut, Argentina
- Departamento de Biología y Ambiente, Universidad Nacional de la Patagonia San Juan Bosco, Sede Puerto Madryn, Puerto Madryn, Chubut, Argentina
| |
Collapse
|
18
|
Duran DP, Laroche RA, Roman SJ, Godwin W, Herrmann DP, Bull E, Egan SP. Species delimitation, discovery and conservation in a tiger beetle species complex despite discordant genetic data. Sci Rep 2024; 14:6617. [PMID: 38503840 PMCID: PMC10951344 DOI: 10.1038/s41598-024-56875-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 03/12/2024] [Indexed: 03/21/2024] Open
Abstract
In an age of species declines, delineating and discovering biodiversity is critical for both taxonomic accuracy and conservation. In recent years, there has been a movement away from using exclusively morphological characters to delineate and describe taxa and an increase in the use of molecular markers to describe diversity or through integrative taxonomy, which employs traditional morphological characters, as well as genetic or other data. Tiger beetles are charismatic, of conservation concern, and much work has been done on the morphological delineation of species and subspecies, but few of these taxa have been tested with genetic analyses. In this study, we tested morphologically based taxonomic hypotheses of polymorphic tiger beetles in the Eunota circumpicta (LaFerté-Sénectère, 1841) species complex using multilocus genomic and mtDNA analyses. We find multiple cryptic species within the previous taxonomic concept of Eunota circumpicta, some of which were historically recognized as subspecies. We found that the mtDNA and genomic datasets did not identify the same taxonomic units and that the mtDNA was most at odds with all other genetic and morphological patterns. Overall, we describe new cryptic diversity, which raises important conservation concerns, and provide a working example for testing species and subspecies validity despite discordant data.
Collapse
Affiliation(s)
- Daniel P Duran
- Department of Environmental Science, Rowan University, Glassboro, NJ, 08028, USA.
| | - Robert A Laroche
- Department of BioSciences, Rice University, Houston, TX, 77005, USA
| | - Stephen J Roman
- Florida State Collection of Arthropods, Gainesville, FL, 32608, USA
| | - William Godwin
- Sam Houston State Natural History Collection, Huntsville, TX, 77340, USA
| | | | - Ethan Bull
- Department of BioSciences, Rice University, Houston, TX, 77005, USA
| | - Scott P Egan
- Department of BioSciences, Rice University, Houston, TX, 77005, USA
| |
Collapse
|
19
|
Wacker KS, Winger BM. An Elevational Phylogeographic Diversity Gradient in Neotropical Birds Is Decoupled from Speciation Rates. Am Nat 2024; 203:362-381. [PMID: 38358813 DOI: 10.1086/728598] [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] [Indexed: 02/17/2024]
Abstract
AbstractA key question about macroevolutionary speciation rates is whether they are controlled by microevolutionary processes operating at the population level. For example, does spatial variation in population genetic differentiation underlie geographical gradients in speciation rates? Previous work suggests that speciation rates increase with elevation in Neotropical birds, but underlying population-level gradients remain unexplored. Here, we characterize elevational phylogeographic diversity between montane and lowland birds in the megadiverse Andes-Amazonian system and assess its relationship to speciation rates to evaluate the link between population-level differentiation and species-level diversification. We aggregated and georeferenced nearly 7,000 mitochondrial DNA sequences across 103 species or species complexes in the Andes and Amazonia and used these sequences to describe phylogeographic differentiation across both regions. Our results show increased levels of both discrete and continuous metrics of population structure in the Andean mountains compared with the Amazonian lowlands. However, higher levels of population differentiation do not predict higher rates of speciation in our dataset. Multiple potential factors may lead to our observed decoupling of initial population divergence and speciation rates, including the ephemerality of incipient species and the multifaceted nature of the speciation process, as well as methodological challenges associated with estimating rates of population differentiation and speciation.
Collapse
|
20
|
Reuber VM, Westbury MV, Rey-Iglesia A, Asefa A, Farwig N, Miehe G, Opgenoorth L, Šumbera R, Wraase L, Wube T, Lorenzen ED, Schabo DG. Topographic barriers drive the pronounced genetic subdivision of a range-limited fossorial rodent. Mol Ecol 2024; 33:e17271. [PMID: 38279205 DOI: 10.1111/mec.17271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 12/20/2023] [Accepted: 01/08/2024] [Indexed: 01/28/2024]
Abstract
Due to their limited dispersal ability, fossorial species with predominantly belowground activity usually show increased levels of population subdivision across relatively small spatial scales. This may be exacerbated in harsh mountain ecosystems, where landscape geomorphology limits species' dispersal ability and leads to small effective population sizes, making species relatively vulnerable to environmental change. To better understand the environmental drivers of species' population subdivision in remote mountain ecosystems, particularly in understudied high-elevation systems in Africa, we studied the giant root-rat (Tachyoryctes macrocephalus), a fossorial rodent confined to the afro-alpine ecosystem of the Bale Mountains in Ethiopia. Using mitochondrial and low-coverage nuclear genomes, we investigated 77 giant root-rat individuals sampled from nine localities across its entire ~1000 km2 range. Our data revealed a distinct division into a northern and southern group, with no signs of gene flow, and higher nuclear genetic diversity in the south. Landscape genetic analyses of the mitochondrial and nuclear genomes indicated that population subdivision was driven by slope and elevation differences of up to 500 m across escarpments separating the north and south, potentially reinforced by glaciation of the south during the Late Pleistocene (~42,000-16,000 years ago). Despite this landscape-scale subdivision between the north and south, weak geographic structuring of sampling localities within regions indicated gene flow across distances of at least 16 km at the local scale, suggesting high, aboveground mobility for relatively long distances. Our study highlights that despite the potential for local-scale gene flow in fossorial species, topographic barriers can result in pronounced genetic subdivision. These factors can reduce genetic variability, which should be considered when developing conservation strategies.
Collapse
Affiliation(s)
- Victoria M Reuber
- Department of Biology, Conservation Ecology, University of Marburg, Marburg, Germany
| | | | | | - Addisu Asefa
- Department of Biology, Conservation Ecology, University of Marburg, Marburg, Germany
- Ethiopian Wildlife Conservation Authority, Addis Ababa, Ethiopia
| | - Nina Farwig
- Department of Biology, Conservation Ecology, University of Marburg, Marburg, Germany
| | - Georg Miehe
- Department of Geography, Vegetation Geography, University of Marburg, Marburg, Germany
| | - Lars Opgenoorth
- Department of Biology, Plant Ecology & Geobotany, University of Marburg, Marburg, Germany
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Radim Šumbera
- Department of Zoology, University of South Bohemia, České Budějovice, Czech Republic
| | - Luise Wraase
- Department of Geography, Environmental Informatics, University of Marburg, Marburg, Germany
| | - Tilaye Wube
- Department of Zoological Sciences, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - Dana G Schabo
- Department of Biology, Conservation Ecology, University of Marburg, Marburg, Germany
| |
Collapse
|
21
|
Jiao X, Wu L, Zhang D, Wang H, Dong F, Yang L, Wang S, Amano HE, Zhang W, Jia C, Rheindt FE, Lei F, Song G. Landscape Heterogeneity Explains the Genetic Differentiation of a Forest Bird across the Sino-Himalayan Mountains. Mol Biol Evol 2024; 41:msae027. [PMID: 38318973 PMCID: PMC10919924 DOI: 10.1093/molbev/msae027] [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: 06/05/2023] [Revised: 01/26/2024] [Accepted: 01/31/2024] [Indexed: 02/07/2024] Open
Abstract
Mountains are the world's most important centers of biodiversity. The Sino-Himalayan Mountains are global biodiversity hotspot due to their extremely high species richness and endemicity. Ample research investigated the impact of the Qinghai-Tibet Plateau uplift and Quaternary glaciations in driving species diversification in plants and animals across the Sino-Himalayan Mountains. However, little is known about the role of landscape heterogeneity and other environmental features in driving diversification in this region. We utilized whole genomes and phenotypic data in combination with landscape genetic approaches to investigate population structure, demography, and genetic diversity in a forest songbird species native to the Sino-Himalayan Mountains, the red-billed leiothrix (Leiothrix lutea). We identified 5 phylogeographic clades, including 1 in the East of China, 1 in Yunnan, and 3 in Tibet, roughly consistent with differences in song and plumage coloration but incongruent with traditional subspecies boundaries. Isolation-by-resistance model best explained population differentiation within L. lutea, with extensive secondary contact after allopatric isolation leading to admixture among clades. Ecological niche modeling indicated relative stability in the extent of suitable distribution areas of the species across Quaternary glacial cycles. Our results underscore the importance of mountains in the diversification of this species, given that most of the distinct genetic clades are concentrated in a relatively small area in the Sino-Himalayan Mountain region, while a single shallow clade populates vast lower-lying areas to the east. This study highlights the crucial role of landscape heterogeneity in promoting differentiation and provides a deep genomic perspective on the mechanisms through which diversity hotspots form.
Collapse
Affiliation(s)
- Xiaolu Jiao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Lei Wu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Dezhi Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Huan Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Feng Dong
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Le Yang
- Tibet Plateau Institute of Biology, Lhasa 850000, China
| | - Shangyu Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | | | - Weiwei Zhang
- Center for Wildlife Resources Conservation Research, Jiangxi Agricultural University, Nanchang, China
| | - Chenxi Jia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - 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
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
22
|
Lizano AMD, Kim KM, Juinio-Meñez MA, Ravago-Gotanco R. Pseudocryptic diversity and species boundaries in the sea cucumber Stichopus cf. horrens (Echinodermata: Stichopodidae) revealed by mitochondrial and microsatellite markers. Sci Rep 2024; 14:4886. [PMID: 38418859 PMCID: PMC10901784 DOI: 10.1038/s41598-024-54987-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 02/19/2024] [Indexed: 03/02/2024] Open
Abstract
Morphologically cryptic and pseudo-cryptic species pose a challenge to taxonomic identification and assessments of species diversity and distributions. Such is the case for the sea cucumber Stichopus horrens, commonly confused with Stichopus monotuberculatus. Here, we used mitochondrial cytochrome oxidase subunit I (COI) and microsatellite markers to examine genetic diversity in Stichopus cf. horrens throughout the Philippine archipelago, to aid species identification and clarify species boundaries. Phylogenetic analysis reveals two recently diverged COI lineages (Clade A and Clade B; c. 1.35-2.54 Mya) corresponding to sequence records for specimens identified as S. monotuberculatus and S. horrens, respectively. Microsatellite markers reveal two significantly differentiated genotype clusters broadly concordant with COI lineages (Cluster 1, Cluster 2). A small proportion of individuals were identified as later-generation hybrids indicating limited contemporary gene flow between genotype clusters, thus confirming species boundaries. Morphological differences in papillae distribution and form are observed for the two species, however tack-like spicules from the dorsal papillae are not a reliable diagnostic character. An additional putative cryptic species was detected within Clade B-Cluster 2 specimens warranting further examination. We propose that these lineages revealed by COI and genotype data be referred to as Stichopus cf. horrens species complex.
Collapse
Affiliation(s)
- Apollo Marco D Lizano
- Faculty of Biosciences & Aquaculture, Nord University, Bodø, Norway.
- Marine Science Institute, University of the Philippines, 1101, Diliman Quezon City, Philippines.
| | - Kenneth M Kim
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Marine Science Institute, University of the Philippines, 1101, Diliman Quezon City, Philippines
| | | | - Rachel Ravago-Gotanco
- Marine Science Institute, University of the Philippines, 1101, Diliman Quezon City, Philippines
| |
Collapse
|
23
|
Kaenkaew C, Chan AHE, Saralamba N, Ruangsittichai J, Chaisiri K, Charoennitiwat V, Thaenkham U. Molecular insights versus morphological traits: rethinking identification of the closely related Angiostrongylus cantonensis and Angiostrongylus malaysiensis. Parasit Vectors 2024; 17:56. [PMID: 38326886 PMCID: PMC10851580 DOI: 10.1186/s13071-024-06140-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 01/17/2024] [Indexed: 02/09/2024] Open
Abstract
BACKGROUND The closely related Angiostrongylus cantonensis and Angiostrongylus malaysiensis have been reported to coexist in Thailand and share similar hosts and life cycles. Recently, in an angiostrongyliasis outbreak in Thailand, both A. cantonensis and A. malaysiensis were found in the cerebrospinal fluid of affected patients. Morphological similarities, overlapping distribution, shared hosts and habitats, and the close genetics of the two Angiostrongylus species can complicate accurate species identification. Addressing these challenges, this study aims to evaluate whether a correlation between the morphological and genetic identities of A. cantonensis and A. malaysiensis can improve species identification accuracy. METHODS Angiostrongylus spp. specimens from five zoogeographical regions in Thailand were subjected to morphological and molecular identification using the mitochondrial cytochrome b gene and the nuclear internal transcribed spacer 2 region (ITS2). The morphological characters for males and females were then validated using the species identity obtained from the nuclear ITS2 region. RESULTS The results revealed that morphological misidentifications between these two closely related species are common due to overlapping morphological characters. Although certain male traits such as body length and width aided species differentiation, female traits were found to be less reliable. Furthermore, hybrid forms (8.2%) were revealed through the ITS2 results, which can further complicate morphological identification. Mito-nuclear discordance was also present in 1.9% of the Angiostrongylus specimens from Thailand, suggesting a complex historical interbreeding between the species. CONCLUSIONS Based on our findings, we suggest that nuclear ITS2 is a reliable marker for species identification of A. cantonensis and A. malaysiensis, especially in regions where both species coexist. Additionally, the scope and consequences of hybridization between the two closely related Angiostrongylus species should be further investigated in Thailand.
Collapse
Affiliation(s)
- Chanisara Kaenkaew
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Abigail Hui En Chan
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Naowarat Saralamba
- Department of Molecular Tropical Medicine and Molecular Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Jiraporn Ruangsittichai
- Department of Medical Entomology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Kittipong Chaisiri
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | | | - Urusa Thaenkham
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
| |
Collapse
|
24
|
Kostova R, Borissov S, Bobeva A, Bekchiev R. At a crossroads: Genetic lineages and dispersal routes of Morimusasper (Sulzer, 1776) s.l. (Coleoptera, Cerambycidae) in Bulgaria. Biodivers Data J 2024; 12:e116619. [PMID: 38352120 PMCID: PMC10862347 DOI: 10.3897/bdj.12.e116619] [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: 11/30/2023] [Accepted: 02/02/2024] [Indexed: 02/16/2024] Open
Abstract
The present study fills a knowledge gap in the distribution and genetic variation of Morimus populations in the Balkans, by studiyng the representatives of the genus in Bulgaria - M.asperfunereus Mulsant, 1862, M.verecundusbulgaricus Danilevsky, 2016 and M.orientalis Reitter, 1894. Additional information is provided for Albania and northern Greece. The mitochondrial cytochrome C oxidase subunit I (COI) marker and the nuclear internal transcribed spacer 2 (ITS2) were used for the genetic analyses. Three of the previously-defined mitochondrial lineages (Lb/HgA, L2 and L3) were detected in Bulgaria, as well as a new lineage (Str) from the Strandzha Mountains (south-eastern Bulgaria). A total of 24 distinct haplotypes, 20 of them in Bulgaria, were found. Bulgarian populations of Morimus demonstrated relatively high nucleotide diversity. The L3 COI lineage was confirmed as the most diverse and frequent in the Balkans. The L3 lineage is dominant in most of Bulgaria, but was not identified in the easternmost parts near the Black Sea coast, where the L2 and Str lineages were found. New data highlighted two dispersal routes of the L2 mitochondrial lineage on the Balkan Peninsula: 1) northwards along the Black Sea coast and 2) westwards, across the Balkans where only disjunct populations remain. North-western Bulgaria seems to be the eastern limit of the basal lineage Lb/HgA distribution. Our results show high levels of genetic exchange between most of the mitochondrially defined lineages, yet some of the easternmost populations probably remained isolated for comparatively longer periods.
Collapse
Affiliation(s)
- Rumyana Kostova
- Sofia University, Faculty of Biology, Sofia, BulgariaSofia University, Faculty of BiologySofiaBulgaria
| | - Simeon Borissov
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Sofia, BulgariaInstitute of Biodiversity and Ecosystem Research, Bulgarian Academy of SciencesSofiaBulgaria
| | - Aneliya Bobeva
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Sofia, BulgariaInstitute of Biodiversity and Ecosystem Research, Bulgarian Academy of SciencesSofiaBulgaria
| | - Rostislav Bekchiev
- National Museum of Natural History, Bulgarian Academy of Sciences, Sofia, BulgariaNational Museum of Natural History, Bulgarian Academy of SciencesSofiaBulgaria
| |
Collapse
|
25
|
Mochales-Riaño G, Burriel-Carranza B, Barros MI, Velo-Antón G, Talavera A, Spilani L, Tejero-Cicuéndez H, Crochet PA, Piris A, García-Cardenete L, Busais S, Els J, Shobrak M, Brito JC, Šmíd J, Carranza S, Martínez-Freiría F. Hidden in the sand: Phylogenomics unravel an unexpected evolutionary history for the desert-adapted vipers of the genus Cerastes. Mol Phylogenet Evol 2024; 191:107979. [PMID: 38040070 DOI: 10.1016/j.ympev.2023.107979] [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: 10/05/2023] [Revised: 11/24/2023] [Accepted: 11/26/2023] [Indexed: 12/03/2023]
Abstract
The desert vipers of the genus Cerastes are a small clade of medically important venomous snakes within the family Viperidae. According to published morphological and molecular studies, the group is comprised by four species: two morphologically similar and phylogenetically sister taxa, the African horned viper (Cerastes cerastes) and the Arabian horned viper (Cerastes gasperettii); a more distantly related species, the Saharan sand viper (Cerastes vipera), and the enigmatic Böhme's sand viper (Cerastes boehmei), only known from a single specimen in captivity allegedly captured in Central Tunisia. In this study, we sequenced one mitochondrial marker (COI) as well as genome-wide data (ddRAD sequencing) from 28 and 41 samples, respectively, covering the entire distribution range of the genus to explore the population genomics, phylogenomic relationships and introgression patterns within the genus Cerastes. Additionally, and to provide insights into the mode of diversification of the group, we carried out niche overlap analyses considering climatic and habitat variables. Both nuclear phylogenomic reconstructions and population structure analyses have unveiled an unexpected evolutionary history for the genus Cerastes, which sharply contradicts the morphological similarities and previously published mitochondrial approaches. Cerastes cerastes and C. vipera are recovered as sister taxa whilst C. gasperettii is a sister taxon to the clade formed by these two species. We found a relatively high niche overlap (OI > 0.7) in both climatic and habitat variables between C. cerastes and C. vipera, contradicting a potential scenario of sympatric speciation. These results are in line with the introgression found between the northwestern African populations of C. cerastes and C. vipera. Finally, our genomic data confirms the existence of a lineage of C. cerastes in Arabia. All these results highlight the importance of genome-wide data over few genetic markers to study the evolutionary history of species.
Collapse
Affiliation(s)
| | - Bernat Burriel-Carranza
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain; Museu de Ciències Naturals de Barcelona, P° Picasso s/n, Parc Ciutadella, 08003 Barcelona, Spain
| | - Margarida Isabel Barros
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
| | - Guillermo Velo-Antón
- Universidad de Vigo, Facultad de Biología, Edificio de Ciencias Experimentales, Bloque B, Planta 2, Laboratorio 39 (Grupo GEA), E-36310 Vigo, Spain
| | - Adrián Talavera
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Loukia Spilani
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Héctor Tejero-Cicuéndez
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain; Department of Biodiversity, Ecology and Evolution, Faculty of Biology, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | | | - Alberto Piris
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Luis García-Cardenete
- Agencia de Medio Ambiente y Agua de Andalucía, C/Johan G. Gutenberg, 1, 41092 Seville, Spain
| | - Salem Busais
- Department of Biology, Faculty of Education, Aden University, Yemen
| | - Johannes Els
- Breeding Centre for Endangered Arabian Wildlife, Environment and Protected Areas Authority, Sharjah, United Arab Emirates
| | - Mohammed Shobrak
- National Center for Wildlife, Prince Saud Al Faisal Wildlife Research Centre, Taif, Saudi Arabia
| | - José Carlos Brito
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Jiří Šmíd
- Department of Zoology, Faculty of Science, Charles University, Vinicná 7, Prague, Czech Republic
| | - Salvador Carranza
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Fernando Martínez-Freiría
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal.
| |
Collapse
|
26
|
Yoo N, Yoon JD, Yoo J, Kim KY, Heo JS, Kim KS. Development of molecular identification methods for Dryophytes suweonensis and D. japonicus, and their hybrids. PeerJ 2024; 12:e16728. [PMID: 38259669 PMCID: PMC10802155 DOI: 10.7717/peerj.16728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 12/06/2023] [Indexed: 01/24/2024] Open
Abstract
Background As hybridization can reduce biodiversity or cause extinction, it is important to identify both purebred parental species and their hybrids prior to conserving them. The Suwon tree frog, Dryophytes suweonensis, is an endangered wildlife species in Korea that shares its habitat and often hybridizes with the Japanese tree frog, D. japonicus. In particular, D. suweonensis, D. japonicus, and their hybrids often have abnormal ovaries and gonads, which are known causes that could threaten their existence. Methods We collected 57 individuals from six localities where D. suweonensis is known to be present. High-resolution melting curve (HRM) analysis of the mitochondrial 12S ribosomal RNA gene was performed to determine the maternal species. Thereafter, the DNA sequences of five nuclear genes (SIAH, TYR, POMC, RAG1, and C-MYC) were analyzed to determine their parental species and hybrid status. Results The HRM analysis showed that the melting temperature of D. suweonensis was in the range of 79.0-79.3 °C, and that of D. japonicus was 77.7-78.0 °C, which clearly distinguished the two tree frog species. DNA sequencing of the five nuclear genes revealed 37 single-nucleotide polymorphism (SNP) sites, and STRUCTURE analysis showed a two-group structure as the most likely grouping solution. No heterozygous position in the purebred parental sequences with Q values ≥ 0.995 were found, which clearly distinguished the two treefrog species from their hybrids; 11 individuals were found to be D. suweonensis, eight were found to be D. japonicus, and the remaining 38 individuals were found to be hybrids. Conclusion Thus, it was possible to unambiguously identify the parental species and their hybrids using HRM analysis and DNA sequencing methods. This study provided fundamental information for D. suweonensis conservation and restoration research.
Collapse
Affiliation(s)
- Nakyung Yoo
- Research Center for Endangered Species, National Institute of Ecology, Yeongyang, Republic of Korea
| | - Ju-Duk Yoon
- Research Center for Endangered Species, National Institute of Ecology, Yeongyang, Republic of Korea
| | - Jeongwoo Yoo
- Research Center for Endangered Species, National Institute of Ecology, Yeongyang, Republic of Korea
| | - Keun-Yong Kim
- Department of Genetic Analysis, AquaGenTech Co., Ltd, Busan, Republic of Korea
| | - Jung Soo Heo
- Department of Genetic Analysis, AquaGenTech Co., Ltd, Busan, Republic of Korea
| | - Keun-Sik Kim
- Research Center for Endangered Species, National Institute of Ecology, Yeongyang, Republic of Korea
| |
Collapse
|
27
|
Zhou J, Wang S, Yu S, Li Y, Qiao M, Zhao Q, Hughes E, Liu H, Bu W. Limits of mitochondrial genes in delimiting species within a Carbula species complex (Hemiptera: Pentatomidae). ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2024; 115:e22075. [PMID: 38288487 DOI: 10.1002/arch.22075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 11/27/2023] [Accepted: 12/08/2023] [Indexed: 02/01/2024]
Abstract
Molecular data has become a powerful tool for species delimitation, particularly among those that present limited morphological differences; while the mitochondrial genome, with its moderate length, low cost of sequencing and fast lineage sorting, has emerged as a practical data set. Due to the limited morphological differences among the closely related species of Carbula Stål 1865, the species boundaries between Carbula abbreviata (Motschulsky, 1866), Carbula humerigera (Uhler, 1860), and Carbula putoni (Jakovlev, 1876) have remained particularly unclear. In this study, we applied two phylogenetic reconstruction methods to two data sets (mitogenome and COI) to assess the phylogeny of Carbula distributed in Asia, and five species delimitation methods to determine the boundaries between East Asian Carbula species. Our phylogenetic analyses showed Carbula to be paraphyletic; the seven known species distributed within East Asia to form a single monophyletic group, and within this, C. abbreviata, C. humerigera, C. putoni and middle-type to comprise a C. humerigera species complex. Our results show that mitogenome data alone, while effective in the differentiation of more distantly related Carbula species, is not sufficient to accurately delimit the species within this newly described complex.
Collapse
Affiliation(s)
- Jiayue Zhou
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, PR China
| | - Shujing Wang
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, PR China
| | - Shengjie Yu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, PR China
| | - Yanfei Li
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, PR China
| | - Mu Qiao
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, PR China
| | - Qing Zhao
- College of Plant Protection, Shanxi Agricultural University, Taigu, PR China
| | | | - Huaxi Liu
- Department of Life Science, Natural History Museum, London, UK
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, PR China
| |
Collapse
|
28
|
Németh A, Mizsei E, Laczkó L, Czabán D, Hegyeli Z, Lengyel S, Csorba G, Sramkó G. Evolutionary history and systematics of European blind mole rats (Rodentia: Spalacidae: Nannospalax): Multilocus phylogeny and species delimitation in a puzzling group. Mol Phylogenet Evol 2024; 190:107958. [PMID: 37914032 DOI: 10.1016/j.ympev.2023.107958] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 11/03/2023]
Abstract
Species delimitation is a powerful approach to assist taxonomic decisions in challenging taxa where species boundaries are hard to establish. European taxa of the blind mole rats (genus Nannospalax) display small morphological differences and complex chromosomal evolution at a shallow evolutionary divergence level. Previous analyses led to the recognition of 25 'forms' in their distribution area. We provide a comprehensive framework to improve knowledge on the evolutionary history and revise the taxonomy of European blind mole rats based on samples from all but three of the 25 forms. We sequenced two nuclear-encoded genetic regions and the whole mitochondrial cytochrome b gene for phylogenetic tree reconstructions using concatenation and coalescence-based species-tree estimations. The phylogenetic analyses confirmed that Aegean N. insularis belongs to N. superspecies xanthodon, and that it represents the second known species of this superspecies in Europe. Mainland taxa reached Europe from Asia Minor in two colonisation events corresponding to two superspecies-level taxa: N. superspecies monticola (taxon established herewith) reached Europe c. 2.1 million years ago (Mya) and was followed by N. superspecies leucodon (re-defined herewith) c. 1.5 Mya. Species delimitation allowed the clarification of the taxonomic contents of the above superspecies. N. superspecies monticola contains three species geographically confined to the western periphery of the distribution of blind mole rats, whereas N. superspecies leucodon is more speciose with six species and several additional subspecies. The observed geographic pattern hints at a robust peripatric speciation process and rapid chromosomal evolution. The present treatment is thus regarded as the minimum taxonomic content of each lineage, which can be further refined based on other sources of information such as karyological traits, crossbreeding experiments, etc. The species delimitation models also allowed the recognition of a hitherto unnamed blind mole rat taxon from Albania, described here as a new subspecies.
Collapse
Affiliation(s)
- Attila Németh
- Department of Nature Conservation, Zoology and Game Management, University of Debrecen, Böszörményi u. 138, H-4032 Debrecen, Hungary; BirdLife Hungary - Hungarian Ornithological and Nature Conservation Society, Költő u. 21, H-1121 Budapest, Hungary
| | - Edvárd Mizsei
- Department of Ecology, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; DRI Conservation Ecology Research Group, Centre for Ecological Research, Hungarian Academy of Sciences, Bem tér 18/C, H-4026 Debrecen, Hungary
| | - Levente Laczkó
- Evolutionary Genomics Research Group, Department of Botany, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; HUN-REN-UD Conservation Biology Research Group, Egyetem tér 1, H-4032 Debrecen, Hungary
| | | | - Zsolt Hegyeli
- Milvus Group Bird and Nature Protection Association, Crinului St. 22, 540343 Târgu Mureş, Romania
| | - Szabolcs Lengyel
- DRI Conservation Ecology Research Group, Centre for Ecological Research, Hungarian Academy of Sciences, Bem tér 18/C, H-4026 Debrecen, Hungary
| | - Gábor Csorba
- Hungarian Natural History Museum, Baross u. 13, H-1088 Budapest, Hungary.
| | - Gábor Sramkó
- Evolutionary Genomics Research Group, Department of Botany, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; HUN-REN-UD Conservation Biology Research Group, Egyetem tér 1, H-4032 Debrecen, Hungary
| |
Collapse
|
29
|
Lavrov DV, Diaz MC, Maldonado M, Morrow CC, Perez T, Pomponi SA, Thacker RW. Phylomitogenomics bolsters the high-level classification of Demospongiae (phylum Porifera). PLoS One 2023; 18:e0287281. [PMID: 38048310 PMCID: PMC10695373 DOI: 10.1371/journal.pone.0287281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 11/15/2023] [Indexed: 12/06/2023] Open
Abstract
Class Demospongiae is the largest in the phylum Porifera (Sponges) and encompasses nearly 8,000 accepted species in three subclasses: Keratosa, Verongimorpha, and Heteroscleromorpha. Subclass Heteroscleromorpha contains ∼90% of demosponge species and is subdivided into 17 orders. The higher level classification of demosponges underwent major revision as the result of nearly three decades of molecular studies. However, because most of the previous molecular work only utilized partial data from a small number of nuclear and mitochondrial (mt) genes, this classification scheme needs to be tested by larger datasets. Here we compiled a mt dataset for 136 demosponge species-including 64 complete or nearly complete and six partial mt-genome sequences determined or assembled for this study-and used it to test phylogenetic relationships among Demospongiae in general and Heteroscleromorpha in particular. We also investigated the phylogenetic position of Myceliospongia araneosa, a highly unusual demosponge without spicules and spongin fibers, currently classified as Demospongiae incertae sedis, for which molecular data were not available. Our results support the previously inferred sister-group relationship between Heteroscleromorpha and Keratosa + Verongimorpha and suggest five main clades within Heteroscleromorpha: Clade C0 composed of order Haplosclerida; Clade C1 composed of Scopalinida, Sphaerocladina, and Spongillida; Clade C2 composed of Axinellida, Biemnida, Bubarida; Clade C3 composed of Tetractinellida; and Clade C4 composed of Agelasida, Clionaida, Desmacellida, Merliida, Suberitida, Poecilosclerida, Polymastiida, and Tethyida. The inferred relationships among these clades were (C0(C1(C2(C3+C4)))). Analysis of molecular data from M. araneosa placed it in the C3 clade as a sister taxon to the highly skeletonized tetractinellids Microscleroderma sp. and Leiodermatium sp. Molecular clock analysis dated divergences among the major clades in Heteroscleromorpha from the Cambrian to the Early Silurian, the origins of most heteroscleromorph orders in the middle Paleozoic, and the most basal splits within these orders around the Paleozoic to Mesozoic transition. Overall, the results of this study are mostly congruent with the accepted classification of Heteroscleromorpha, but add temporal perspective and new resolution to phylogenetic relationships within this subclass.
Collapse
Affiliation(s)
- Dennis V. Lavrov
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa, United States of America
| | - Maria C. Diaz
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, Florida, United States of America
- Museo Marino de Margarita, Boca de Río, Nueva Esparta, Venezuela
| | - Manuel Maldonado
- Department of Marine Ecology, Centro de Estudios Avanzados de Blanes (CEAB-CSIC), Girona, Spain
| | - Christine C. Morrow
- Zoology Department, School of Natural Sciences & Ryan Institute, NUI Galway, University Road, Galway, Ireland
- Ireland and Queen’s University Marine Laboratory, Portaferry, Northern Ireland
| | - Thierry Perez
- Institut Méditerranéen de la Biodiversité et d’Ecologie marine et continentale (IMBE), CNRS, Aix-Marseille Université, IRD, Avignon Université City, Provence, France
| | - Shirley A. Pomponi
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, Florida, United States of America
| | - Robert W. Thacker
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, United States of America
- Smithsonian Tropical Research Institute, Balboa, Panama City, Republic of Panama
| |
Collapse
|
30
|
Qin HT, Mӧller M, Milne R, Luo YH, Zhu GF, Li DZ, Liu J, Gao LM. Multiple paternally inherited chloroplast capture events associated with Taxus speciation in the Hengduan Mountains. Mol Phylogenet Evol 2023; 189:107915. [PMID: 37666379 DOI: 10.1016/j.ympev.2023.107915] [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: 10/27/2022] [Revised: 06/16/2023] [Accepted: 09/01/2023] [Indexed: 09/06/2023]
Abstract
Mountainous regions provide a multitude of habitats and opportunities for complex speciation scenarios. Hybridization leading to chloroplast capture, which can be revealed by incongruent phylogenetic trees, is one possible outcome. Four allopatric Taxus lineages (three species and an undescribed lineage) from the Hengduan Mountains, southwest China, exhibit conflicting phylogenetic relationships between nuclear and chloroplast phylogenies. Here, we use multi-omic data at the population level to investigate their historical speciation processes. Population genomic analysis based on ddRAD-seq data revealed limited contemporary inter-specific gene flow involving only populations located close to another species. In a historical context, chloroplast and nuclear data (transcriptome) consistently showed conflicting phylogenetic relationships for T. florinii and the Emei type lineage. ILS and chloroplast recombination were excluded as possible causes, and transcriptome and ddRAD-seq data revealed an absence of the mosaic nuclear genomes that characterize hybrid origin scenarios. Therefore, T. florinii appears to have originated when a lineage of T. florinii captured the T. chinensis plastid type, whereas plastid introgression in the opposite direction generated the Emei Type. All four species have distinct ecological niche based on community investigations and ecological niche analyses. We propose that the origins of both species represent very rare examples of chloroplast capture events despite the paternal cpDNA inheritance of gymnosperms. Specifically, allopatrically and/or ecologically diverged parental species experienced a rare secondary contact, subsequent hybridization and reciprocal chloroplast capture, generating two new lineages, each of which acquired a unique ecological niche. These events might have been triggered by orogenic activities of the Hengduan Mountains and an intensification of the Asian monsoon in the late Miocene, and may represent a scenario more common in these mountains than presently known.
Collapse
Affiliation(s)
- Han-Tao Qin
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China; Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Michael Mӧller
- Royal Botanic Garden Edinburgh, Edinburgh EH3 5LR, United Kingdom
| | - Richard Milne
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JH, United Kingdom
| | - Ya-Huang Luo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China; Lijiang Forest Biodiversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang 674100, Yunnan, China
| | - Guang-Fu Zhu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China; Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - De-Zhu Li
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China; Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China; University of Chinese Academy of Sciences, Beijing 100049, China; Lijiang Forest Biodiversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang 674100, Yunnan, China.
| | - Jie Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China; Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China.
| | - Lian-Ming Gao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China; Lijiang Forest Biodiversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang 674100, Yunnan, China.
| |
Collapse
|
31
|
Parkin T, Donnellan SC, Parkin B, Shea GM, Rowley JJL. Phylogeography, hybrid zones and contemporary species boundaries in the south-eastern Australian smooth frogs (Anura: Myobatrachidae: Geocrinia). Mol Phylogenet Evol 2023; 189:107934. [PMID: 37769826 DOI: 10.1016/j.ympev.2023.107934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 09/25/2023] [Indexed: 10/03/2023]
Abstract
Paleo-climatic fluctuations have driven episodic changes in species distributions, providing opportunities for populations to diverge in isolation and hybridise following secondary contact. Studies of phylogeographic diversity and patterns of gene flow across hybrid zones can provide insight into contemporary species boundaries and help to inform taxonomic and conservation inferences. Here we explore geographic diversity within the acoustically divergent yet morphologically conserved south-eastern Australian smooth frog complex and assess gene flow across a narrow hybrid zone using mitochondrial nucleotide sequences and nuclear genome-wide single nucleotide polymorphisms. Our analyses reveal the presence of an evolutionarily distinct taxon restricted to the Otway Plains and Ranges, Victoria, which forms a narrow (9-30 km wide), spatiotemporally stable (>50 years) hybrid zone with Geocrinia laevis, which we describe herein as a new species.
Collapse
Affiliation(s)
- Thomas Parkin
- Australian Museum Research Institute, Sydney NSW 2010, Australia.
| | | | - Benjamin Parkin
- Australian Museum Research Institute, Sydney NSW 2010, Australia
| | - Glenn M Shea
- Australian Museum Research Institute, Sydney NSW 2010, Australia; Sydney School of Veterinary Science B01, University of Sydney, NSW 2006, Australia
| | - Jodi J L Rowley
- Australian Museum Research Institute, Sydney NSW 2010, Australia; University of New South Wales, Sydney NSW 2052, Australia
| |
Collapse
|
32
|
Jensen A, Swift F, de Vries D, Beck RMD, Kuderna LFK, Knauf S, Chuma IS, Keyyu JD, Kitchener AC, Farh K, Rogers J, Marques-Bonet T, Detwiler KM, Roos C, Guschanski K. Complex Evolutionary History With Extensive Ancestral Gene Flow in an African Primate Radiation. Mol Biol Evol 2023; 40:msad247. [PMID: 37987553 PMCID: PMC10691879 DOI: 10.1093/molbev/msad247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 10/17/2023] [Accepted: 11/09/2023] [Indexed: 11/22/2023] Open
Abstract
Understanding the drivers of speciation is fundamental in evolutionary biology, and recent studies highlight hybridization as an important evolutionary force. Using whole-genome sequencing data from 22 species of guenons (tribe Cercopithecini), one of the world's largest primate radiations, we show that rampant gene flow characterizes their evolutionary history and identify ancient hybridization across deeply divergent lineages that differ in ecology, morphology, and karyotypes. Some hybridization events resulted in mitochondrial introgression between distant lineages, likely facilitated by cointrogression of coadapted nuclear variants. Although the genomic landscapes of introgression were largely lineage specific, we found that genes with immune functions were overrepresented in introgressing regions, in line with adaptive introgression, whereas genes involved in pigmentation and morphology may contribute to reproductive isolation. In line with reports from other systems that hybridization might facilitate diversification, we find that some of the most species-rich guenon clades are of admixed origin. This study provides important insights into the prevalence, role, and outcomes of ancestral hybridization in a large mammalian radiation.
Collapse
Affiliation(s)
- Axel Jensen
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala SE-75236, Sweden
| | - Frances Swift
- School of Biological Sciences, Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
| | - Dorien de Vries
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Robin M D Beck
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Lukas F K Kuderna
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA 94404, USA
| | - Sascha Knauf
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald – Insel Riems 17493, Germany
| | | | - Julius D Keyyu
- Tanzania Wildlife Research Institute (TAWIRI), Arusha, Tanzania
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums Scotland, Edinburgh EH1 1JF, UK
- School of Geosciences, University of Edinburgh, Edinburgh EH8 9XP, UK
| | - Kyle Farh
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA 94404, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona 08003, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08028, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) and Universitat Pompeu Fabra, Barcelona 08010, Spain
| | - Kate M Detwiler
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, FL, USA
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen 37077, Germany
| | - Katerina Guschanski
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala SE-75236, Sweden
- School of Biological Sciences, Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
| |
Collapse
|
33
|
Laroche RA, Duran DP, Lee CTA, Godwin W, Roman SJ, Herrmann DP, Egan SP. A genomic test of subspecies in the Eunota togata species group (Coleoptera: Cicindelidae): Morphology masks evolutionary relationships and taxonomy. Mol Phylogenet Evol 2023; 189:107937. [PMID: 37797795 DOI: 10.1016/j.ympev.2023.107937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 10/07/2023]
Abstract
Most of the world's biodiversity is described primarily or exclusively using morphological traits that may not always reflect the true evolutionary units. Accurate taxonomy is critical for conservation efforts and re-evaluation of traditional taxonomy may often be warranted since species and subspecies are frequently the focus of conservation and faunistic studies. Here, we test comprehensive taxonomic hypotheses of morphologically defined subspecies in the tiger beetle, Eunota togata (LaFerté-Sénectère, 1841). The four recognized subspecies were delineated based mainly on the dorsal coloration and extent of white markings termed maculations. We combine inferences from mtDNA genealogies and genome-wide multilocus data to elucidate the evolutionary relationships within the group and assess the taxonomic implications. Three of the four subspecific taxa delineated by morphology were not supported by the genomic or mtDNA data. In fact, the species-level diversity in this group was underestimated, as E. togata was found to represent three well-supported distinct species in all genetic analyses. Emerging from these analyses, we also document an intriguing example of convergent evolution in lighter colored E. togata adapting to similar white saline backgrounds. Our collective work underscores the importance of using molecular methods to reevaluate morphological based taxonomy for species and subspecies delimitation and conservation.
Collapse
Affiliation(s)
- Robert A Laroche
- Department of BioSciences, Rice University, Houston, TX 77005, USA
| | - Daniel P Duran
- Department of Environmental Science, Rowan University, Glassboro, NJ 08028, USA.
| | - Cin-Ty A Lee
- Department of Earth, Environmental & Planetary Science, Rice University, Houston, TX 77005, USA
| | - William Godwin
- Sam Houston State Natural History Collection, Huntsville, TX 77320, USA
| | | | | | - Scott P Egan
- Department of BioSciences, Rice University, Houston, TX 77005, USA
| |
Collapse
|
34
|
Lvarez R, Budaeva N. How complex is the Naineris setosa species complex? First integrative study of a presumed cosmopolitan and invasive annelid (Sedentaria: Orbiniidae). Zootaxa 2023; 5375:349-378. [PMID: 38220815 DOI: 10.11646/zootaxa.5375.3.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Indexed: 01/16/2024]
Abstract
We performed a comparative study of the specimens from the Naineris setosa complex from the Pacific and the Atlantic Oceans and re-described the syntype of N. setosa, including the selection of the lectotype. Molecular phylogenetic and species delimitation analyses based on two mitochondrial (COI and 16S) and one nuclear (28S) marker revealed the presence of three species. One clade with wide Amphi-Atlantic distribution was attributed as Naineris setosa s. str. The second Atlantic clade restricted to Southern and Southeastern Brazil was described as a new species, Naineris lanai sp. n. The third clade, reported from the Northwestern Pacific, was identified as a new species but was not formally described due to the presence of only juvenile-sized worms in the studied material. Detailed morphological descriptions of several diagnostic characters in the Naineris setosa complex are provided.
Collapse
Affiliation(s)
- Ricardo Lvarez
- Graduate program in Oceanic Coastal Systems (PGSISCO); Federal University of Paran; Pontal do Paran; Paran; Brazil.
| | - Nataliya Budaeva
- Department of Natural History; University Museum of Bergen; University of Bergen; Allgaten 41; 5007 Bergen; Norway.
| |
Collapse
|
35
|
Fukutani K, Matsui M, Nishikawa K. Population genetic structure and hybrid zone analyses for species delimitation in the Japanese toad ( Bufo japonicus). PeerJ 2023; 11:e16302. [PMID: 37901459 PMCID: PMC10607272 DOI: 10.7717/peerj.16302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 09/25/2023] [Indexed: 10/31/2023] Open
Abstract
Hybridization following secondary contact may produce different outcomes depending on the extent to which genetic diversity and reproductive barriers have accumulated during isolation. The Japanese toad, Bufo japonicus, is distributed on the main islands of Japan. In the present study, we applied multiplexed inter-simple sequence repeat genotyping by sequencing to achieve the fine-scale resolution of the genetic cluster in B. j. japonicus and B. j. formosus. We also elucidated hybridization patterns and gene flow degrees across contact zones between the clusters identified. Using SNP data, we found four genetic clusters in B. j. japonicus and B. j. formosus and three contact zones of the cluster pairs among these four clusters. The two oldest diverged lineages, B. j. japonicus and B. j. formosus, formed a narrow contact zone consistent with species distinctiveness. Therefore, we recommend that these two subspecies be elevated to the species level. In contrast, the less diverged pairs of two clusters in B. j. japonicus and B. j. formosus, respectively, admixed over a hundred kilometers, suggesting that they have not yet developed strong reproductive isolation and need to be treated as conspecifics. These results will contribute to resolving taxonomic confusion in Japanese toads.
Collapse
Affiliation(s)
- Kazumi Fukutani
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Masafumi Matsui
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Kanto Nishikawa
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
- Graduate School of Global Environmental Studies, Kyoto University, Kyoto, Japan
| |
Collapse
|
36
|
Zinevich L, Prommer M, Laczkó L, Rozhkova D, Sorokin A, Karyakin I, Bagyura J, Cserkész T, Sramkó G. Phylogenomic insights into the polyphyletic nature of Altai falcons within eastern sakers (Falco cherrug) and the origins of gyrfalcons (Falco rusticolus). Sci Rep 2023; 13:17800. [PMID: 37853004 PMCID: PMC10584951 DOI: 10.1038/s41598-023-44534-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 10/10/2023] [Indexed: 10/20/2023] Open
Abstract
The Altai falcon from Central Asia always attracted the attention of humans. Long considered a totemic bird in its native area, modern falconers still much appreciated this large-bodied and mighty bird of prey due to its rarity and unique look. The peculiar body characteristics halfway between the saker falcon (Falco cherrug) and the gyrfalcon (F. rusticolus) triggered debates about its contentious taxonomy. The weak phylogenetic signal associated with traditional genetic methods could not resolve this uncertainty. Here, we address the controversial evolutionary origin of Altai falcons by means of a genome-wide approach, Restriction-site Associated DNA sequencing, using sympatric eastern sakers falcons, allopatric western saker falcons and gyrfalcons as outgroup. This approach provided an unprecedented insight into the phylogenetic relationships of the studied populations by delivering 17,095 unlinked SNPs shedding light on the polyphyletic nature of Altai falcons within eastern sakers. Thus we concluded that the former must correspond to a low taxonomic rank, probably an ecotype or form of the latter. Also, we found that eastern sakers are paraphyletic without gyrfalcons, thus, these latter birds are best regarded as the direct sister lineage of the eastern sakers. This evolutionary relationship, corroborated also by re-analyzing the dataset with the inclusion of outgroup samples (F. biarmicus and F. peregrinus), put eastern sakers into a new light as the potential ancestral genetic source of high latitude and altitude adaptation in descendent populations. Finally, conservation genomic values hint at the stable genetic background of the studied saker populations.
Collapse
Affiliation(s)
- Liudmila Zinevich
- Koltzov Institute of Developmental Biology Russian Academy of Sciences, Moscow, Russian Federation
- All-Russian Research Institute for Environmental Protection, Moscow, Russian Federation
| | | | - Levente Laczkó
- HUN-REN-UD Conservation Biology Research Group, Egyetem tér 1, Debrecen, 4032, Hungary
- Evolutionary Genomics Research Group, Department of Botany, University of Debrecen, Egyetem tér 1, Debrecen, 4032, Hungary
| | - Daria Rozhkova
- Koltzov Institute of Developmental Biology Russian Academy of Sciences, Moscow, Russian Federation
- All-Russian Research Institute for Environmental Protection, Moscow, Russian Federation
| | - Alexander Sorokin
- All-Russian Research Institute for Environmental Protection, Moscow, Russian Federation
| | | | - János Bagyura
- MME - BirdLife Hungary, Költő utca 21, Budapest, 1121, Hungary
| | - Tamás Cserkész
- Hungarian Natural History Museum, Baross utca 13, Budapest, 1088, Hungary
| | - Gábor Sramkó
- HUN-REN-UD Conservation Biology Research Group, Egyetem tér 1, Debrecen, 4032, Hungary.
- Evolutionary Genomics Research Group, Department of Botany, University of Debrecen, Egyetem tér 1, Debrecen, 4032, Hungary.
| |
Collapse
|
37
|
Hrazdilova K, Danek O, Hrbatova A, Cervena B, Noskova E, Adamik P, Votypka J, Mihalca AD, Noureddine M, Modry D, Zurek L. Genetic analysis challenges the presence of Ixodes inopinatus in Central Europe: development of a multiplex PCR to distinguish I. inopinatus from I. ricinus. Parasit Vectors 2023; 16:354. [PMID: 37814284 PMCID: PMC10561450 DOI: 10.1186/s13071-023-05971-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 09/17/2023] [Indexed: 10/11/2023] Open
Abstract
BACKGROUND Ixodes ricinus is an important vector of several pathogens, primarily in Europe. Recently, Ixodes inopinatus was described from Spain, Portugal, and North Africa and then reported from several European countries. In this study, a multiplex polymerase chain reaction (PCR) was developed to distinguish I. ricinus from I. inopinatus and used in the surveillance of I. inopinatus in Algeria (ALG) and three regions in the Czech Republic (CZ). METHODS A multiplex PCR on TROSPA and sequencing of several mitochondrial (16S rDNA, COI) and nuclear markers (TROSPA, ITS2, calreticulin) were used to differentiate these two species and for a subsequent phylogenetic analysis. RESULTS Sequencing of TROSPA, COI, and ITS2 separated these two species into two subclades, while 16S rDNA and calreticulin could not distinguish I. ricinus from I. inopinatus. Interestingly, 23 nucleotide positions in the TROSPA gene had consistently double peaks in a subset of ticks from CZ. Cloning of these PCR products led to a clear separation of I. ricinus and I. inopinatus indicating hybridization and introgression between these two tick taxa. Based on a multiplex PCR of TROSPA and analysis of sequences of TROSPA, COI, and ITS2, the majority of ticks in CZ were I. ricinus, no I. inopinatus ticks were found, and 10 specimens showed signs of hybridization. In contrast, most ticks in ALG were I. inopinatus, four ticks were I. ricinus, and no signs of hybridization and introgression were detected. CONCLUSIONS We developed a multiplex PCR method based on the TROSPA gene to differentiate I. ricinus and I. inopinatus. We demonstrate the lack of evidence for the presence of I. inopinatus in Central Europe and propose that previous studies be re-examined. Mitochondrial markers are not suitable for distinguishing I. inopinatus from I. ricinus. Furthermore, our data indicate that I. inopinatus and I. ricinus can hybridize, and the hybrids can survive in Europe.
Collapse
Affiliation(s)
- Kristyna Hrazdilova
- Department of Chemistry and Biochemistry, Mendel University, Brno, Czech Republic
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Plzen, Czech Republic
| | - Ondrej Danek
- Institute of Parasitology, Biology Center of Czech Academy of Sciences, Budějovice, Czech Republic
- Department of Veterinary Sciences, Faculty of Agrobiology, Food and Natural Resources/CINeZ, Czech University of Life Sciences, Prague, Czech Republic
| | - Alena Hrbatova
- CEITEC, University of Veterinary Sciences, Brno, Czech Republic
| | - Barbora Cervena
- CEITEC, University of Veterinary Sciences, Brno, Czech Republic
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic
| | - Eva Noskova
- CEITEC, University of Veterinary Sciences, Brno, Czech Republic
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Peter Adamik
- Department of Zoology, Palacky University Olomouc, Olomouc, Czech Republic
| | - Jan Votypka
- Institute of Parasitology, Biology Center of Czech Academy of Sciences, Budějovice, Czech Republic
- Department of Parasitology, Charles University, Prague, Czech Republic
| | - Andrei Daniel Mihalca
- Department of Parasitology and Parasitic Diseases, University of Agricultural Sciences and Veterinary Medicine of Cluj-Napoca, Cluj-Napoca, Romania
| | - Mechouk Noureddine
- Department of Parasitology and Parasitic Diseases, University of Agricultural Sciences and Veterinary Medicine of Cluj-Napoca, Cluj-Napoca, Romania
| | - David Modry
- Institute of Parasitology, Biology Center of Czech Academy of Sciences, Budějovice, Czech Republic
- Department of Veterinary Sciences, Faculty of Agrobiology, Food and Natural Resources/CINeZ, Czech University of Life Sciences, Prague, Czech Republic
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Ludek Zurek
- Department of Chemistry and Biochemistry, Mendel University, Brno, Czech Republic.
- CEITEC, University of Veterinary Sciences, Brno, Czech Republic.
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources/CINeZ, Czech University of Life Sciences, Prague, Czech Republic.
| |
Collapse
|
38
|
Dufresnes C, Poyarkov N, Jablonski D. Acknowledging more biodiversity without more species. Proc Natl Acad Sci U S A 2023; 120:e2302424120. [PMID: 37748058 PMCID: PMC10556632 DOI: 10.1073/pnas.2302424120] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023] Open
Abstract
Delimiting and naming biodiversity is a vital step toward wildlife conservation and research. However, species delimitation must be consistent across biota so that the limited resources available for nature protection can be spent effectively and objectively. To date, newly discovered lineages typically are either left undescribed and thus remain unprotected or are being erroneously proposed as new species despite mixed evidence for completed speciation, in turn contributing to the emerging problem of taxonomic inflation. Inspired by recent conceptual and methodological progress, we propose a standardized workflow for species delimitation that combines phylogenetic and hybrid zone analyses of genomic datasets ("genomic taxonomy"), in which phylogeographic lineages that do not freely admix are ranked as species, while those that have remained fully genetically compatible are ranked as subspecies. In both cases, we encourage their formal taxonomic naming, diagnosis, and description to promote social awareness toward biodiversity. The use of loci throughout the genome overcomes the unreliability of widely used barcoding genes when phylogeographic patterns are complex, while the evaluation of divergence and reproductive isolation unifies the long-opposed concepts of lineage species and biological species. We suggest that a shift in conservation assessments from a single level (species) toward a two-level hierarchy (species and subspecies) will lead to a more balanced perception of biodiversity in which both intraspecific and interspecific diversity are valued and more adequately protected.
Collapse
Affiliation(s)
- Christophe Dufresnes
- Laboratory of Amphibian Systematics and Evolutionary Research, College of Biology and Environment, Nanjing Forestry University, Nanjing210037, People’s Republic of China
| | - Nikolay Poyarkov
- Joint Russian-Vietnamese Tropical Research and Technological Center, Hanoi122000, Vietnam
- Department of Vertebrate Zoology, Lomonosov Moscow State University, Moscow119234, Russia
| | - Daniel Jablonski
- Department of Zoology, Comenius University in Bratislava, Bratislava84215, Slovakia
| |
Collapse
|
39
|
Booker WW, Lemmon EM, Lemmon AR, Ptacek MB, Hassinger ATB, Schul J, Gerhardt HC. Biogeography and the evolution of acoustic communication in the polyploid North American grey treefrog complex. Mol Ecol 2023; 32:4863-4879. [PMID: 37401503 DOI: 10.1111/mec.17061] [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: 04/14/2023] [Revised: 06/09/2023] [Accepted: 06/15/2023] [Indexed: 07/05/2023]
Abstract
After polyploid species are formed, interactions between diploid and polyploid lineages may generate additional diversity in novel cytotypes and phenotypes. In anurans, mate choice by acoustic communication is the primary method by which individuals identify their own species and assess suitable mates. As such, the evolution of acoustic signals is an important mechanism for contributing to reproductive isolation and diversification in this group. Here, we estimate the biogeographical history of the North American grey treefrog complex, consisting of the diploid Hyla chrysoscelis and the tetraploid Hyla versicolor, focusing specifically on the geographical origin of whole genome duplication and the expansion of lineages out of glacial refugia. We then test for lineage-specific differences in mating signals by applying comparative methods to a large acoustic data set collected over 52 years that includes >1500 individual frogs. Along with describing the overall biogeographical history and call diversity, we found evidence that the geographical origin of H. versicolor and the formation of the midwestern polyploid lineage are both associated with glacial limits, and that the southwestern polyploid lineage is associated with a shift in acoustic phenotype relative to the diploid lineage with which they share a mitochondrial lineage. In H. chrysoscelis, we see that acoustic signals are largely split by Eastern and Western lineages, but that northward expansion along either side of the Appalachian Mountains is associated with further acoustic diversification. Overall, results of this study provide substantial clarity on the evolution of grey treefrogs as it relates to their biogeography and acoustic communication.
Collapse
Affiliation(s)
- William W Booker
- Department of Biological Science, Florida State University, Tallahassee, Florida, USA
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Emily Moriarty Lemmon
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, Florida, USA
| | - Margaret B Ptacek
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
| | - Alyssa T B Hassinger
- Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, Ohio, USA
| | - Johannes Schul
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, USA
| | - H Carl Gerhardt
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, USA
| |
Collapse
|
40
|
Healy TM, Burton RS. Genetic incompatibilities in reciprocal hybrids between populations of Tigriopus californicus with low to moderate mitochondrial sequence divergence. Evolution 2023; 77:2100-2108. [PMID: 37407024 DOI: 10.1093/evolut/qpad122] [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: 09/20/2022] [Revised: 06/16/2023] [Accepted: 07/05/2023] [Indexed: 07/07/2023]
Abstract
All mitochondrial-encoded proteins and RNAs function through interactions with nuclear-encoded proteins, which are critical for mitochondrial performance and eukaryotic fitness. Coevolution maintains inter-genomic (i.e., mitonuclear) compatibility within a taxon, but hybridization can disrupt coevolved interactions, resulting in hybrid breakdown. Thus, mitonuclear incompatibilities may be important mechanisms underlying reproductive isolation and, potentially, speciation. Here we utilize Pool-seq to assess the effects of mitochondrial genotype on nuclear allele frequencies in fast- and slow-developing reciprocal inter-population F2 hybrids between relatively low-divergence populations of the intertidal copepod Tigriopus californicus. We show that mitonuclear interactions lead to elevated frequencies of coevolved (i.e., maternal) nuclear alleles on two chromosomes in crosses between populations with 1.5% or 9.6% fixed differences in mitochondrial DNA nucleotide sequence. However, we also find evidence of excess mismatched (i.e., noncoevolved) alleles on three or four chromosomes per cross, respectively, and of allele frequency differences consistent with effects involving only nuclear loci (i.e., unaffected by mitochondrial genotype). Thus, our results for low-divergence crosses suggest an underlying role for mitonuclear interactions in variation in hybrid developmental rate, but despite substantial effects of mitonuclear coevolution on individual chromosomes, no clear bias favoring coevolved interactions overall.
Collapse
Affiliation(s)
- Timothy M Healy
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California-San Diego, La Jolla, CA, United States
| | - Ronald S Burton
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California-San Diego, La Jolla, CA, United States
| |
Collapse
|
41
|
Knyshov A, Gordon ERL, Masonick PK, Castillo S, Forero D, Hoey-Chamberlain R, Hwang WS, Johnson KP, Lemmon AR, Moriarty Lemmon E, Standring S, Zhang J, Weirauch C. Chromosome-Aware Phylogenomics of Assassin Bugs (Hemiptera: Reduvioidea) Elucidates Ancient Gene Conflict. Mol Biol Evol 2023; 40:msad168. [PMID: 37494292 PMCID: PMC10411492 DOI: 10.1093/molbev/msad168] [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: 03/28/2023] [Revised: 07/15/2023] [Accepted: 07/19/2023] [Indexed: 07/28/2023] Open
Abstract
Though the phylogenetic signal of loci on sex chromosomes can differ from those on autosomes, chromosomal-level genome assemblies for nonvertebrates are still relatively scarce and conservation of chromosomal gene content across deep phylogenetic scales has therefore remained largely unexplored. We here assemble a uniquely large and diverse set of samples (17 anchored hybrid enrichment, 24 RNA-seq, and 70 whole-genome sequencing samples of variable depth) for the medically important assassin bugs (Reduvioidea). We assess the performance of genes based on multiple features (e.g., nucleotide vs. amino acid, nuclear vs. mitochondrial, and autosomal vs. X chromosomal) and employ different methods (concatenation and coalescence analyses) to reconstruct the unresolved phylogeny of this diverse (∼7,000 spp.) and old (>180 Ma) group. Our results show that genes on the X chromosome are more likely to have discordant phylogenies than those on autosomes. We find that the X chromosome conflict is driven by high gene substitution rates that impact the accuracy of phylogenetic inference. However, gene tree clustering showed strong conflict even after discounting variable third codon positions. Alternative topologies were not particularly enriched for sex chromosome loci, but spread across the genome. We conclude that binning genes to autosomal or sex chromosomes may result in a more accurate picture of the complex evolutionary history of a clade.
Collapse
Affiliation(s)
- Alexander Knyshov
- Department of Entomology, University of California, Riverside, CA, USA
| | - Eric R L Gordon
- Ecology and Evolutionary Biology Department, University of Connecticut, Storrs, CT, USA
| | - Paul K Masonick
- Department of Entomology, University of California, Riverside, CA, USA
| | | | - Dimitri Forero
- Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Bogota, Colombia
| | | | - Wei Song Hwang
- Lee Kong Chian Natural History Museum, National University of Singapore, Queenstown, Singapore
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL, USA
| | | | | | - Junxia Zhang
- Key Laboratory of Zoological Systematics and Application of Hebei Province, Institute of Life Science and Green Development, College of Life Sciences, Hebei University, Baoding, Hebei, China
| | | |
Collapse
|
42
|
Martínez‐Borrego D, Arellano E, González‐Cózatl FX, Ospina‐Garcés SM, Rogers DS. Species delimitation and integrative taxonomy of the Reithrodontomys mexicanus (Rodentia: Cricetidae) cryptic complex. Ecol Evol 2023; 13:e10355. [PMID: 37529589 PMCID: PMC10387591 DOI: 10.1002/ece3.10355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 06/12/2023] [Accepted: 07/12/2023] [Indexed: 08/03/2023] Open
Abstract
Species boundaries are difficult to establish in groups with very similar morphology. As an alternative, it has been suggested to integrate multiple sources of data to clarify taxonomic problems in taxa where cryptic speciation processes have been reported. This is the case of the harvest mouse Reithrodontomys mexicanus, which has a problematic taxonomy history as it is considered a complex species. Here, we evaluate the cryptic diversity of R. mexicanus using an integrative taxonomy approach in order to detect candidate lineages at the species level. The molecular analysis used one mitochondrial (cytb) and two nuclear (Fgb-I7 and IRBP) genes. Species hypotheses were suggested based on three molecular delimitation methods (mPTP, bGMYC, and STACEY) and cytb genetic distance values. Skull and environmental space differences between the delimited species were also tested to complement the discrimination of candidate species. Based on the consensus across the delimitation methods and genetic distance values, four species were proposed, which were mostly supported by morphometric and ecological data: R. mexicanus clade I, R. mexicanus clade IIA, R. mexicanus clade IIIA, and R. mexicanus clade IIIB. In addition, the evolutionary relationships between the species that comprise the R. mexicanus group were discussed from a phylogenetic approach. Our findings present important taxonomic implications for Reithrodontomys, as the number of known species for this genus increases. Furthermore, we highlight the importance of the use of multiple sources of data in systematic studies to establish robust delimitations between species considered taxonomically complex.
Collapse
Affiliation(s)
- Daily Martínez‐Borrego
- Centro de Investigación en Biodiversidad y ConservaciónUniversidad Autónoma del Estado de MorelosCuernavacaMorelosMexico
| | - Elizabeth Arellano
- Centro de Investigación en Biodiversidad y ConservaciónUniversidad Autónoma del Estado de MorelosCuernavacaMorelosMexico
| | - Francisco X. González‐Cózatl
- Centro de Investigación en Biodiversidad y ConservaciónUniversidad Autónoma del Estado de MorelosCuernavacaMorelosMexico
| | | | - Duke S. Rogers
- Department of Biology and Monte L Bean Life Science MuseumBrigham Young UniversityProvoUtahUSA
| |
Collapse
|
43
|
Bruni G, Chiocchio A, Nascetti G, Cimmaruta R. Different patterns of introgression in a three species hybrid zone among European cave salamanders. Ecol Evol 2023; 13:e10437. [PMID: 37636870 PMCID: PMC10447881 DOI: 10.1002/ece3.10437] [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: 05/02/2023] [Revised: 08/01/2023] [Accepted: 08/07/2023] [Indexed: 08/29/2023] Open
Abstract
Hybrid zones occur where genetically distinct populations meet, mate and produce offspring with mixed ancestry. In Plethodontid salamanders, introgressive hybridization is a common phenomenon, where hybrids backcross with parental populations leading to the spread of new alleles into the parental genomes. Whereas many hybrid zones have been reported in American Plethodontid salamanders, only a single hybrid zone has been documented in European plethodontids so far, which is located at the Apuan Alps in the Italian Peninsula. Here, we describe a previously unreported hybrid zone in the Northern Apennines involving all the three Plethodontid salamander species inhabiting the Italian Peninsula. We found 21 new Speleomantes sites of occurrence, from a hitherto unexplored area located at the boundaries between three Speleomantes species ranges. Using mitochondrial (Cytb and ND2 genes) and nuclear markers (two diagnostic SNPs at the NCX1 gene), we revealed a three-way contact zone where all the three mainland species hybridize: S. strinatii, S. ambrosii and S. italicus. We observed a strong mitonuclear discordance, with mitochondrial markers showing a conspicuous geographic pattern, while diagnostic nuclear SNPs coexisted in both the same populations and individuals, providing evidence of hybridization in many possible combinations. The introgression is asymmetric, with S. italicus mitogenome usually associated with S. a. ambrosii and, to a lesser extent, to S. strinatii nuclear alleles. This finding confirms that Plethodontid are a group of choice to investigate hybridization mechanisms and suggests that behavioural, genetic and ecological components may concur in determining the direction and extent of introgression.
Collapse
Affiliation(s)
| | - Andrea Chiocchio
- Department of Ecological and Biological SciencesTuscia UniversityViterboItaly
| | - Giuseppe Nascetti
- Department of Ecological and Biological SciencesTuscia UniversityViterboItaly
| | - Roberta Cimmaruta
- Department of Ecological and Biological SciencesTuscia UniversityViterboItaly
| |
Collapse
|
44
|
Dong X, Zhang H, Zhu X, Wang K, Xue H, Ye Z, Zheng C, Bu W. Mitochondrial introgression and mito-nuclear discordance obscured the closely related species boundaries in Cletus Stål from China (Heteroptera: Coreidae). Mol Phylogenet Evol 2023; 184:107802. [PMID: 37221926 DOI: 10.1016/j.ympev.2023.107802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 04/07/2023] [Accepted: 04/18/2023] [Indexed: 05/25/2023]
Abstract
Accurate taxonomy and delimitation are of great importance for pest control strategies and management programs. Here, we focus on Cletus (Insecta: Hemiptera: Coreidae), which includes many crop pests. The species boundaries still conflict and only cytochrome c oxidase subunit I (COI) barcoding has been previously used for molecular studies. We generated new mitochondrial genome and nuclear genome-wide SNPs to explore the species boundaries of 46 Cletus samples from China using multiple species delimitation approaches. All results recovered a monophyly with high support, except for two closely related species in clade I - C. punctiger and C. graminis. Mitochondrial data demonstrated admixture in clade I, while genome-wide SNPs unambiguously identified two separate species, which were confirmed by morphological classification. Inconsistent nuclear and mitochondrial data indicated mito-nuclear discordance. Mitochondrial introgression is the most likely explanation, and more extensive sampling and more comprehensive data are needed to ascertain a pattern. Accurate species delimitation will shed light on species status; thus, an accurate taxonomy is of particular concern, as there is a pressing need to implement precise control of agricultural pests and to perform further research on diversification.
Collapse
Affiliation(s)
- Xue Dong
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Haiguang Zhang
- College of Life Science, Linyi University, Linyi 276000, China
| | - Xiuxiu Zhu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Kaibin Wang
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Huaijun Xue
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Zhen Ye
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China.
| | - Chenguang Zheng
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China.
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China.
| |
Collapse
|
45
|
Tukhbatullin A, Ermakov O, Kapustina S, Starikov V, Tambovtseva V, Titov S, Brandler O. Surrounded by Kindred: Spermophilus major Hybridization with Other Spermophilus Species in Space and Time. BIOLOGY 2023; 12:880. [PMID: 37372163 DOI: 10.3390/biology12060880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/05/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023]
Abstract
Among the numerous described cases of hybridization in mammals, the most intriguing are (a) cases of introgressive hybridization deeply affecting the evolutionary history of species, and (b) models involving not a pair of species but a multi-species complex. Therefore, the hybridization history of the russet ground squirrel Spermophilus major, whose range has repeatedly changed due to climatic fluctuations and now borders the ranges of four related species, is of great interest. The main aims of this study were to determine the direction and intensity of gene introgression, the spatial depth of the infiltration of extraneous genes into the S. major range, and to refine the hypothesis of the hybridogenic replacement of mitochondrial genomes in the studied group. Using phylogenetic analysis of the variability of mitochondrial (CR, cytb) and nuclear (SmcY, BGN, PRKCI, c-myc, i6p53) markers, we determined the contribution of neighboring species to the S. major genome. We showed that 36% of S. major individuals had extraneous alleles. All peripheral species that were in contact with S. major contributed towards its genetic variability. We also proposed a hypothesis for the sequence and localization of serial hybridization events. Our assessment of the S. major genome implications of introgression highlights the importance of implementing conservation measures to protect this species.
Collapse
Affiliation(s)
- Andrey Tukhbatullin
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Vavilova Str. 26, Moscow 119334, Russia
| | - Oleg Ermakov
- Faculty of Physics, Mathematics and Natural Sciences, Belinsky Institute of Teacher Education, Penza State University, Lermontov Str. 37, Penza 440026, Russia
| | - Svetlana Kapustina
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Vavilova Str. 26, Moscow 119334, Russia
| | - Vladimir Starikov
- Department of Biology and Biotechnology, Institute of Natural and Technical Sciences, Surgut State University, Lenin Avenue 1, Surgut 628412, Russia
| | - Valentina Tambovtseva
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Vavilova Str. 26, Moscow 119334, Russia
| | - Sergey Titov
- Faculty of Physics, Mathematics and Natural Sciences, Belinsky Institute of Teacher Education, Penza State University, Lermontov Str. 37, Penza 440026, Russia
| | - Oleg Brandler
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Vavilova Str. 26, Moscow 119334, Russia
| |
Collapse
|
46
|
Abalde S, Crocetta F, Tenorio MJ, D'Aniello S, Fassio G, Rodríguez-Flores PC, Uribe JE, M L Afonso C, Oliverio M, Zardoya R. Hidden species diversity and mito-nuclear discordance within the Mediterranean cone snail, Lautoconus ventricosus. Mol Phylogenet Evol 2023:107838. [PMID: 37286063 DOI: 10.1016/j.ympev.2023.107838] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 05/15/2023] [Accepted: 05/31/2023] [Indexed: 06/09/2023]
Abstract
The Mediterranean cone snail, Lautoconus ventricosus, is currently considered a single species inhabiting the whole Mediterranean basin and the adjacent Atlantic coasts. Yet, no population genetic study has assessed its taxonomic status. Here, we collected 245 individuals from 75 localities throughout the Mediterranean Sea and used cox1 barcodes, complete mitochondrial genomes, and genome skims to test whether L. ventricosus represents a complex of cryptic species. The maximum likelihood phylogeny based on complete mitochondrial genomes recovered six main clades (hereby named blue, brown, green, orange, red, and violet) with sufficient sequence divergence to be considered putative species. On the other hand, phylogenomic analyses based on 437 nuclear genes only recovered four out of the six clades: blue and orange clades were thoroughly mixed and the brown one was not recovered. This mito-nuclear discordance revealed instances of incomplete lineage sorting and introgression, and may have caused important differences in the dating of main cladogenetic events. Species delimitation tests proposed the existence of at least three species: green, violet, and red+blue+orange (i.e., cyan). Green plus cyan (with sympatric distributions) and violet, had West and East Mediterranean distributions, respectively, mostly separated by the Siculo-Tunisian biogeographical barrier. Morphometric analyses of the shell using species hypotheses as factor and shell length as covariate showed that the discrimination power of the studied parameters was only 70.2%, reinforcing the cryptic nature of the uncovered species, and the importance of integrative taxonomic approaches considering morphology, ecology, biogeography, and mitochondrial and nuclear population genetic variation.
Collapse
Affiliation(s)
- Samuel Abalde
- Department of Zoology, Swedish Museum of Natural History, Box 50007, 10405 Stockholm, Sweden; Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006 Madrid, Spain.
| | - Fabio Crocetta
- Department of Integrative Marine Ecology (EMI), Stazione Zoologica Anton Dohrn, Villa Comunale, I-80121 Napoli, Italy
| | - Manuel J Tenorio
- Departamento CMIM y Q. Inorgánica-INBIO, Facultad de Ciencias, Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain
| | - Salvatore D'Aniello
- Department of Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Villa Comunale, I-80121 Napoli, Italy
| | - Giulia Fassio
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Zoology-Viale dell'Università 32, 00185 Rome, Italy
| | - Paula C Rodríguez-Flores
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006 Madrid, Spain; Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge MA 02138, USA
| | - Juan E Uribe
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006 Madrid, Spain
| | - Carlos M L Afonso
- Centre of Marine Sciences (CCMAR), Universidade do Algarve, Campus de Gambelas, 8005 - 139 Faro, Portugal
| | - Marco Oliverio
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Zoology-Viale dell'Università 32, 00185 Rome, Italy
| | - Rafael Zardoya
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006 Madrid, Spain
| |
Collapse
|
47
|
Haye PA, Segovia NI. Shedding light on variation in reproductive success through studies of population genetic structure in a Southeast Pacific Coast mussel. Heredity (Edinb) 2023; 130:402-413. [PMID: 37024547 PMCID: PMC10238476 DOI: 10.1038/s41437-023-00615-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 03/23/2023] [Accepted: 03/23/2023] [Indexed: 04/08/2023] Open
Abstract
Phylogeography often focuses on the spatial dimension of genetic diversity, rarely including the temporal dynamics occurring interannually among local populations, which can provide insight into past variations in reproductive success. Currently, there is an intense aquaculture industry of Mytilus spp. on the Southeast Pacific Coast which depends entirely on the spat released by natural populations forming a relevant and sensitive social-ecological system. Temporal and spatial spat variability from natural mussel beds could be related to interannual reproductive dynamics with variable reproductive success and recruitment, which leave genetic signatures. Temporal and spatial genetic structure was evaluated in six natural beds in the Southeast Pacific (from 39°25'S to 43°07'S) on the most abundant and widespread Mytilus lineage detected, Mytilus cf. chilensis, in 4 consecutive years. Analyses included data from >180 individuals per year, with a total of 751 (mitochondrial COI) and 747 (nuclear H1) individuals, respectively. Overall, both markers showed high haplotype diversity and low spatial and temporal genetic differentiation. Likely, the high dispersal capacity of Mytilus cf. chilensis maintains population homogeneity and prevents diversity erosion. The slight differences in genetic variance of COI were better explained by differences among sites (space), and conversely, the H1 genetic variance was better explained by interannual (temporal) comparisons, which could explain temporal variability in spat availability. This study highlights the important insights achieved with the evaluation of both temporal and spatial population genetic structures in marine species with high reproductive output, which can condition the success and sustainability of the relevant social-ecological system.
Collapse
Affiliation(s)
- Pilar A Haye
- Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Coquimbo, Chile
- Instituto Milenio en Socio-Ecología Costera (SECOS), Santiago, Chile
| | - Nicolás I Segovia
- Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Coquimbo, Chile.
- Instituto Milenio en Socio-Ecología Costera (SECOS), Santiago, Chile.
| |
Collapse
|
48
|
Ho SK, Chan HK, Karraker NE. The identity of Tokays (Squamata: Gekkonidae: Gekko) from Hong Kong. Zootaxa 2023; 5297:282-290. [PMID: 37518795 DOI: 10.11646/zootaxa.5297.2.7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Indexed: 08/01/2023]
Abstract
The Tokay gecko (Gekko gecko), found throughout Southeast Asia and India, is a heavily harvested species of high commercial value. Recent studies have supported the elevation of the black morph of Tokay gecko, found only in southern China and northern Vietnam, to the species Gekko reevesii. Previous genetic studies focused on specimens of G. reevesii from southwestern populations. Hong Kong, in southeastern China, has native populations of G. reevesii. To verify the identity of G. reevesii in Hong Kong, we employed three mitochondrial genes (COI, Cytb & ND2) and constructed a matrilineal genealogy using other specimens from Guangxi (southwestern China) and northern Vietnam, as well as G. gecko from a wide range of Southeast Asian countries. Our study confirmed that G. reevesii occurs naturally in Hong Kong, but one exotic population of G. gecko, likely a translocation from international trade, was also revealed. Our study did not reject the species ranking of G. reevesii. Moreover, like previous studies, we recovered a paraphyletic G. gecko, which may reflect a species complex, hybridization or incomplete lineage sorting. More extensive sampling of the two species over a broader range of their asserted distribution together with the use of both mitochondrial and nuclear DNA are required to better investigate their biogeography.
Collapse
Affiliation(s)
- Siu-Kit Ho
- Freshwater Ecology and Conservation Laboratory; School of Biological Sciences; The University of Hong Kong; Pokfulam; Hong Kong SAR; China.
| | - Hon-Ki Chan
- Freshwater Ecology and Conservation Laboratory; School of Biological Sciences; The University of Hong Kong; Pokfulam; Hong Kong SAR; China.
| | - Nancy E Karraker
- Department of Natural Resources Science; University of Rhode Island; Kingston; Rhode Island 02881 USA.
| |
Collapse
|
49
|
Everson KM, McGinnis RC, Burdine OP, Huddleston TR, Hylick TM, Keith AL, Moore SC, O’Brien AE, Vilardo AL, Krupa JJ. Disentangling morphology and genetics in two voles ( Microtus pennsylvanicus and M. ochrogaster) in a region of sympatry. J Mammal 2023; 104:532-545. [PMID: 37287702 PMCID: PMC10243968 DOI: 10.1093/jmammal/gyac119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 11/17/2022] [Indexed: 10/09/2023] Open
Abstract
Species in recent, rapid radiations can be difficult to distinguish from one another due to incomplete sorting of traits, insufficient time for novel morphologies to evolve, and elevated rates of hybridization and gene flow. The vole genus Microtus (58 spp.) is one such system where all three factors are likely at play. In the central United States, the prairie vole, Microtus ochrogaster, and the eastern meadow vole, M. pennsylvanicus, occur in sympatry and can be distinguished on the basis of molar cusp patterns but are known to be exceptionally difficult to distinguish using external morphological characters. Using a combination of morphometrics, pelage color analyses, and phylogenetics, we explored which traits are most effective for species identification and whether these same traits can be used to identify the subspecies M. o. ohionensis. While we were able to identify six traits that differed significantly between M. ochrogaster and M. pennsylvanicus, we also found substantial measurement overlap which limits the utility of these traits for species identification. The subspecies M. o. ohionensis was particularly difficult to distinguish from M. p. pennsylvanicus, and we did not find any evidence that this subspecies forms a distinct genetic clade. Furthermore, the full species M. ochrogaster and M. pennsylvanicus did not form reciprocal clades in phylogenetic analyses. We discuss several possible reasons for these patterns, including unrecognized variation in molar cusp patterns and/or localized hybridization. Overall, our results provide useful information that will aid in the identification of these species and subspecies in the future, and provides a case study of how genetics, morphometrics, and fur color analyses can be used to disentangle signatures of evolutionary history and hybridization.
Collapse
Affiliation(s)
- Kathryn M Everson
- Department of Biology, T.H. Morgan Building, University of Kentucky, 675 Rose Street, Lexington, Kentucky 40506, USA
| | - Robert C McGinnis
- Department of Biology, T.H. Morgan Building, University of Kentucky, 675 Rose Street, Lexington, Kentucky 40506, USA
| | - Olivia P Burdine
- Department of Biology, T.H. Morgan Building, University of Kentucky, 675 Rose Street, Lexington, Kentucky 40506, USA
| | - Taniece R Huddleston
- Department of Biology, T.H. Morgan Building, University of Kentucky, 675 Rose Street, Lexington, Kentucky 40506, USA
| | - Tyler M Hylick
- Department of Biology, T.H. Morgan Building, University of Kentucky, 675 Rose Street, Lexington, Kentucky 40506, USA
| | - Audrey L Keith
- Department of Biology, T.H. Morgan Building, University of Kentucky, 675 Rose Street, Lexington, Kentucky 40506, USA
| | - Savannah C Moore
- Department of Biology, T.H. Morgan Building, University of Kentucky, 675 Rose Street, Lexington, Kentucky 40506, USA
| | - Aidan E O’Brien
- Department of Biology, T.H. Morgan Building, University of Kentucky, 675 Rose Street, Lexington, Kentucky 40506, USA
| | - Ava L Vilardo
- Department of Biology, T.H. Morgan Building, University of Kentucky, 675 Rose Street, Lexington, Kentucky 40506, USA
| | - James J Krupa
- Department of Biology, T.H. Morgan Building, University of Kentucky, 675 Rose Street, Lexington, Kentucky 40506, USA
| |
Collapse
|
50
|
Stiller J, Wilson NG, Rouse GW. Range-wide population genomics of common seadragons shows secondary contact over a former barrier and insights on illegal capture. BMC Biol 2023; 21:129. [PMID: 37248474 DOI: 10.1186/s12915-023-01628-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 05/16/2023] [Indexed: 05/31/2023] Open
Abstract
BACKGROUND Common seadragons (Phyllopteryx taeniolatus, Syngnathidae) are an emblem of the diverse endemic fauna of Australia's southern rocky reefs, the newly recognized "Great Southern Reef." A lack of assessments spanning this global biodiversity hotspot in its entirety is currently hampering an understanding of the factors that have contributed to its diversity. The common seadragon has a wide range across Australia's entire temperate south and includes a geogenetic break over a former land bridge, which has called its status as a single species into question. As a popular aquarium display that sells for high prices, common seadragons are also vulnerable to illegal capture. RESULTS Here, we provide range-wide nuclear sequences (986 variable Ultraconserved Elements) for 198 individuals and mitochondrial genomes for 140 individuals to assess species status, identify genetic units and their diversity, and trace the source of two poached individuals. Using published data of the other two seadragon species, we found that lineages of common seadragons have diverged relatively recently (< 0.63 Ma). Within common seadragons, we found pronounced genetic structure, falling into three major groups in the western, central, and eastern parts of the range. While populations across the Bassian Isthmus were divergent, there is also evidence for secondary contact since the passage opened. We found a strong cline of genetic diversity from the range center tapering symmetrically towards the range peripheries. Based on their genetic similarities, the poached individuals were inferred to have originated from around Albany in southwestern Australia. CONCLUSIONS We conclude that common seadragons constitute a single species with strong geographic structure but coherence through gene flow. The low genetic diversity on the east and west coasts is concerning given that these areas are projected to face fast climate change. Our results suggest that in addition to their life history, geological events and demographic expansions have all played a role in shaping populations in the temperate south. These insights are an important step towards understanding the historical determinants of the diversity of species endemic to the Great Southern Reef.
Collapse
Affiliation(s)
- Josefin Stiller
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, 92093 , USA.
- Centre for Biodiversity Genomics, University of Copenhagen, 2100, Copenhagen, Denmark.
| | - Nerida G Wilson
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, 92093 , USA
- Research & Collections, Western Australian Museum, Perth, Western Australia, 6106, Australia
- School of Biological Sciences, University of Western Australia, Perth, Western Australia, 6009, Australia
| | - Greg W Rouse
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, 92093 , USA.
| |
Collapse
|