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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.
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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.
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Reid N, Hughes MF, Hynes RA, Montgomery WI, Prodöhl PA. Bidirectional hybridisation and introgression between introduced European brown hare, Lepus europaeus and the endemic Irish hare, L. timidus hibernicus. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01471-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AbstractIntroduced non-native species can threaten native species through interspecific hybridisation and genetic introgression. We assessed the prevalence of hybridisation and introgression between introduced European brown hare, Lepus europaeus, and the endemic Irish hare, L. timidus hibernicus. Roadkill hares (n = 56) were sequenced for a 379bp section of the mitochondrial DNA D-loop and a 474bp segment of the nuclear transferrin (Tf) gene. A species-specific indel in the transferrin gene was present in L.t. hibernicus and absent in L. europaeus. Excluding three hares from which molecular data could not be recovered, 28 hares (53%) were native L.t. hibernicus, 7 (13%) were non-native L. europaeus and 18 (34%) were hybrids; of which 5 (28%) were first generation (F1) involving bidirectional crosses with mismatched nuclear and mtDNA (3 ♂ europaeus x ♀ hibernicus and 2 ♂ hibernicus x ♀ europaeus). Mixed nuclear transferrin sequences suggested 13 (72%) of hybrids were at least 2nd generation (F2) with 9 (69%) possessing L.t. hibernicus and 4 (31%) L. europaeus mtDNA (the latter indicative of hybrid backcrossing with the non-native). The prevalence of hybridisation at similar mountain-brown hare contact zones throughout Europe is notably lower (4–16%) and typically unidirectional (♂ europaeus x ♀ timidus). A high prevalence of bidirectional hybridisation and introgression (in association with projected climate change) may favour the introduced species over the native. Genetic surveillance and population monitoring are needed to further explore the potential conservation implications of European brown hare in Ireland.
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Cui N, Chen W, Li X, Wang P. Comparative chloroplast genomes and phylogenetic analyses of Pinellia. Mol Biol Rep 2022; 49:7873-7885. [PMID: 35689783 PMCID: PMC9304046 DOI: 10.1007/s11033-022-07617-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 05/18/2022] [Indexed: 11/30/2022]
Abstract
Background Pinellia Tenore (Araceae) is a genus of perennial herbaceous plants, all of which have medicinal value. The chloroplast (cp) genome data of Pinellia are scarce, and the phylogenetic relationship and gene evolution remain unclear. Methods and results We sequenced and annotated the Pinellia pedatisecta cp genome and combined it with previously published genomes for other Pinellia species. We used bioinformatics methods to analyse the genomic structure, repetitive sequences, interspecific variation, divergence hotspots, phylogenetic relationships, divergence time estimation and selective pressure of four Pinellia plastomes. Results showed that the cp genomes of Pinellia varied in length between 168,178 (P. pedatisecta MN046890) and 164,013 bp (P. ternata KR270823). A total of 68–111 SSR loci were identified as candidate molecular markers for further genetic diversity study. Eight mutational hotspot regions were determined, including psbI-trnG-UCC, psbM-rpoB, ndhJ-trnT-UGU, trnP-UGG-trnW-CCA, ndhF-trnN-GUU, ndhG-ndhE, ycf1-rps15 and trnR-ycf1. Gene selection pressure suggested that four genes were subjected to positive selection. Phylogenetic inferences based on the complete cp genomes revealed a sister relationship between Pinellia and Arisaema plants whose divergence was estimated to occur around 22.48 million years ago. All Pinellia species formed a monophyletic evolutionary clade in which P. peltata, rather than P. pedatisecta, earlier diverged, indicating that P. pedatisecta is not the basal taxon of Pinellia but P. peltata may be. Conclusions The cp genomes of Pinellia will provide valuable information for species classification, identification, molecular breeding and evolutionary exploration of the genus Pinellia. Supplementary Information The online version of this article (10.1007/s11033-022-07617-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ning Cui
- Central Laboratory, Shandong Academy of Chinese Medicine, Ji'nan, China
| | - Weixu Chen
- Shang Yao Hua Yu (LinYi) Traditional Chinese Medicine Resources Co., Ltd, Linyi, China
| | - Xiwen Li
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.
| | - Ping Wang
- Central Laboratory, Shandong Academy of Chinese Medicine, Ji'nan, China.
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Introgression at the emerging secondary contact zone of magpie Pica pica subspecies (Aves: Corvidae): integrating data on nuclear and mitochondrial markers, vocalizations, and field observations. ORG DIVERS EVOL 2022. [DOI: 10.1007/s13127-022-00568-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Abstract
Zones of secondary contact provide a good opportunity to investigate the origin and dynamics of reproductive isolation between related populations. We analyzed genetic and phenotypic patterns and gene flow between two subspecies of the Eurasian magpie Pica pica s.l. which recently came into contact after presumably long periods of isolation. We describe the distribution of subspecies in a young contact zone at Argun’ river basin in southern Siberia where populations occur in parapatry and an older hybrid population in eastern Mongolia. Based on genome-wide SNP data, we analyzed patterns and strength of gene flow between the subspecies. Our results indicate occasional hybridization with backcrossing and asymmetric introgression along a wide range in Transbaikalia and locally in eastern Mongolia. Males of P. p. jankowskii apparently exhibit higher dispersal ability towards the west compared to P. p. leucoptera (towards the east). The former occasionally migrates to eastern Mongolia and Transbaikalia where introgression of nuclear, but not mitochondrial DNA was evident. Bioacoustic investigations showed differences between the subspecies in speed and structure of vocalization. We discovered intermediate calls of hybrid magpies and bilingual birds alternating calls that are typical for the two taxa. Furthermore, we found dramatically decreased reproductive success in hybridogeneous populations. By complementing our results with established phylogeographic patterns of P. pica s.l. based on a mitochondrial marker sequence, and considering indications of sterility of hybrids in the contact zone, we propose to elevate the two corresponding subspecies to species level: P. pica for the western form and P. serica for the eastern form.
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Kraatz B, Belabbas R, Fostowicz-Frelik Ł, Ge DY, Kuznetsov AN, Lang MM, López-Torres S, Mohammadi Z, Racicot RA, Ravosa MJ, Sharp AC, Sherratt E, Silcox MT, Słowiak J, Winkler AJ, Ruf I. Lagomorpha as a Model Morphological System. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.636402] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Due to their global distribution, invasive history, and unique characteristics, European rabbits are recognizable almost anywhere on our planet. Although they are members of a much larger group of living and extinct mammals [Mammalia, Lagomorpha (rabbits, hares, and pikas)], the group is often characterized by several well-known genera (e.g., Oryctolagus, Sylvilagus, Lepus, and Ochotona). This representation does not capture the extraordinary diversity of behavior and form found throughout the order. Model organisms are commonly used as exemplars for biological research, but there are a limited number of model clades or lineages that have been used to study evolutionary morphology in a more explicitly comparative way. We present this review paper to show that lagomorphs are a strong system in which to study macro- and micro-scale patterns of morphological change within a clade that offers underappreciated levels of diversity. To this end, we offer a summary of the status of relevant aspects of lagomorph biology.
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Ferreira MS, Jones MR, Callahan CM, Farelo L, Tolesa Z, Suchentrunk F, Boursot P, Mills LS, Alves PC, Good JM, Melo-Ferreira J. The Legacy of Recurrent Introgression during the Radiation of Hares. Syst Biol 2021; 70:593-607. [PMID: 33263746 PMCID: PMC8048390 DOI: 10.1093/sysbio/syaa088] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 11/06/2020] [Accepted: 11/13/2020] [Indexed: 12/30/2022] Open
Abstract
Hybridization may often be an important source of adaptive variation, but the extent and long-term impacts of introgression have seldom been evaluated in the phylogenetic context of a radiation. Hares (Lepus) represent a widespread mammalian radiation of 32 extant species characterized by striking ecological adaptations and recurrent admixture. To understand the relevance of introgressive hybridization during the diversification of Lepus, we analyzed whole exome sequences (61.7 Mb) from 15 species of hares (1-4 individuals per species), spanning the global distribution of the genus, and two outgroups. We used a coalescent framework to infer species relationships and divergence times, despite extensive genealogical discordance. We found high levels of allele sharing among species and show that this reflects extensive incomplete lineage sorting and temporally layered hybridization. Our results revealed recurrent introgression at all stages along the Lepus radiation, including recent gene flow between extant species since the last glacial maximum but also pervasive ancient introgression occurring since near the origin of the hare lineages. We show that ancient hybridization between northern hemisphere species has resulted in shared variation of potential adaptive relevance to highly seasonal environments, including genes involved in circadian rhythm regulation, pigmentation, and thermoregulation. Our results illustrate how the genetic legacy of ancestral hybridization may persist across a radiation, leaving a long-lasting signature of shared genetic variation that may contribute to adaptation. [Adaptation; ancient introgression; hybridization; Lepus; phylogenomics.].
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Affiliation(s)
- Mafalda S Ferreira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - Matthew R Jones
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - Colin M Callahan
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - Liliana Farelo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
| | - Zelalem Tolesa
- Department of Biology, Hawassa University, Hawassa, Ethiopia
| | - Franz Suchentrunk
- Department for Interdisciplinary Life Sciences, Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Pierre Boursot
- Institut des Sciences de l’Évolution Montpellier (ISEM), Université de Montpellier, CNRS, IRD, EPHE, France
| | - L Scott Mills
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, Montana, United States of America
- Office of Research and Creative Scholarship, University of Montana, Missoula, Montana, United States of America; Jeffrey M. Good and José Melo-Ferreira shared the senior authorship
| | - Paulo C Alves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, Montana, United States of America
| | - Jeffrey M Good
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, Montana, United States of America
| | - José Melo-Ferreira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
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Colella JP, Frederick LM, Talbot SL, Cook JA. Extrinsically reinforced hybrid speciation within Holarctic ermine (
Mustela
spp.) produces an insular endemic. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13234] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
- Jocelyn P. Colella
- Department of Biology and Museum of Southwestern Biology University of New Mexico Albuquerque NM USA
- Biodiversity Institute University of Kansas Lawrence KS USA
| | - Lindsey M. Frederick
- Department of Biology and Museum of Southwestern Biology University of New Mexico Albuquerque NM USA
- New Mexico Museum of Natural History and Science Albuquerque NM USA
| | | | - Joseph A. Cook
- Department of Biology and Museum of Southwestern Biology University of New Mexico Albuquerque NM USA
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Ye B, Saito T, Hirano T, Dong Z, Do VT, Chiba S. Human-geographic effects on variations in the population genetics of Sinotaia quadrata (Gastropoda: Viviparidae) that historically migrated from continental East Asia to Japan. Ecol Evol 2020; 10:8055-8072. [PMID: 32788961 PMCID: PMC7417235 DOI: 10.1002/ece3.6456] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 05/06/2020] [Accepted: 05/11/2020] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Anthropogenic factors potentially affect observed biogeographical patterns in population genetics, but the effects of ancient human activities on the original patterns created by natural processes are unknown. Sinotaia quadrata, a widely distributed freshwater snail species in East Asia, was used to investigate this issue. It is unclear whether S. quadrata in Japan was introduced from China and how different human uses and varying geographic patterns affect the contemporary population genetics between the two regions. Thus, we investigated the demography of S. quadrata and detected its genetic structure in Japan and continental East Asia. RESULTS Sinotaia quadrata populations first naturally migrated from continental East Asia to Japan, which is associated with the ancient period in Japanese geohistory (about 70,000 years ago). They were then artificially introduced in association with agriculture expansion by human movements in two recent periods (about 8,000 and 1,200 years ago). Populations in different parts of Japan have their own sources. Natural migration in the ancient period and artificial introduction in the recent period suggest that the population distribution is affected by both the geohistory of East Asia and the history of human expansion. In the background of the historical migration and introduction, contemporary populations in the two regions show different genetic patterns. Population divergence levels were significantly correlated with geographical patterns in Japan and significantly correlated with human interventions variables in continental East Asia, suggesting that long-term geographical isolation is likely the major factor that shaped the contemporary population genetics in Japan, while modern human uses are likely the major factor in continental East Asia. CONCLUSIONS Our preliminary results show a complex demography and unusual genetic patterns in the contemporary populations for a common freshwater snail and are of significance to determine the historical formation and contemporary patterns of biogeography in Japan and continental East Asia.
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Affiliation(s)
- Bin Ye
- Graduate School of Life SciencesTohoku UniversitySendaiJapan
| | - Takumi Saito
- Department of BiologyFaculty of ScienceToho UniversityFunabashiJapan
| | - Takahiro Hirano
- Graduate School of Life SciencesTohoku UniversitySendaiJapan
- Center for Northeast Asian StudiesTohoku UniversitySendaiJapan
| | - Zhengzhong Dong
- Agricultural Experiment StationZhejiang UniversityHangzhouChina
| | - Van Tu Do
- Institute of Ecology and Biological ResourcesVietnam Academy of Science and TechnologyHa NoiVietnam
- Graduate University of Science and TechnologyVietnam Academy of Science and TechnologyHa NoiVietnam
| | - Satoshi Chiba
- Graduate School of Life SciencesTohoku UniversitySendaiJapan
- Center for Northeast Asian StudiesTohoku UniversitySendaiJapan
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Mynhardt S, Bennett NC, Bloomer P. New insights from RADseq data on differentiation in the Hottentot golden mole species complex from South Africa. Mol Phylogenet Evol 2019; 143:106667. [PMID: 31676418 DOI: 10.1016/j.ympev.2019.106667] [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: 03/15/2019] [Revised: 10/28/2019] [Accepted: 10/28/2019] [Indexed: 10/25/2022]
Abstract
Golden moles (Family Chrysochloridae) are small subterranean mammals, endemic to sub-Saharan Africa, and many of the 21 species are listed as threatened on the IUCN Red List. Most species have highly restricted ranges; however two species, the Hottentot golden mole (Amblysomus hottentotus) and the Cape golden mole (Chrysochloris asiatica) have relatively wide ranges. We recently uncovered cryptic diversity within A. hottentotus, through a phylogeographic analysis of this taxon using two mitochondrial gene regions and a nuclear intron. To further investigate this cryptic diversity, we generated nuclear SNP data from across the genome of A. hottentotus, by means of double-digest restriction-site associated DNA sequencing (ddRADSeq), and mapped reads to the Cape golden mole genome. We conducted a phylogenetic analysis and investigated population differentiation. Our results support the distinctiveness of A. h. meesteri. Furthermore, we provide evidence from nuclear SNPs in support of our previous finding that Central coastal samples represent a unique cryptic lineage that is highly divergent from A. h. pondoliae farther south. Although mtDNA suggests that Umtata may represent a unique lineage sister to A. h. longiceps, mito-nuclear discordance from our RADseq data indicate that these samples may instead be closer to A. h. pondoliae, and therefore may not represent a distinct lineage. We stress the importance of recognizing that understudied populations, such as that of Umtata, may represent populations or ESUs under threat and in need of conservation attention. We present a high-quality filtered SNP dataset, comprising thousands of SNPs, which may serve as a useful resource for future golden mole studies. We have thus added to the growing body of research demonstrating the power and utility of RADseq to investigate population differentiation.
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Affiliation(s)
- Samantha Mynhardt
- Molecular Ecology and Evolution Programme, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa; Department of Zoology and Entomology, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa.
| | - Nigel C Bennett
- Department of Zoology and Entomology, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa; Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa.
| | - Paulette Bloomer
- Molecular Ecology and Evolution Programme, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa; Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa.
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