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Tapanainen R, Aasumets K, Fekete Z, Goffart S, Dufour E, L O Pohjoismäki J. Species-specific variation in mitochondrial genome tandem repeat polymorphisms in hares (Lepus spp., Lagomorpha, Leporidae) provides insight into their evolution. Gene 2024; 926:148644. [PMID: 38851366 DOI: 10.1016/j.gene.2024.148644] [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: 03/09/2024] [Revised: 04/23/2024] [Accepted: 06/03/2024] [Indexed: 06/10/2024]
Abstract
The non-coding regions of the mitochondrial DNAs (mtDNAs) of hares, rabbits, and pikas (Lagomorpha) contain short (∼20 bp) and long (130-160 bp) tandem repeats, absent in related mammalian orders. In the presented study, we provide in-depth analysis for mountain hare (Lepus timidus) and brown hare (L. europaeus) mtDNA non-coding regions, together with a species- and population-level analysis of tandem repeat variation. Mountain hare short tandem repeats (SRs) as well as other analyzed hare species consist of two conserved 10 bp motifs, with only brown hares exhibiting a single, more variable motif. Long tandem repeats (LRs) also differ in sequence and copy number between species. Mountain hares have four to seven LRs, median value five, while brown hares exhibit five to nine LRs, median value six. Interestingly, introgressed mountain hare mtDNA in brown hares obtained an intermediate LR length distribution, with median copy number being the same as with conspecific brown hare mtDNA. In contrast, transfer of brown hare mtDNA into cultured mtDNA-less mountain hare cells maintained the original LR number, whereas the reciprocal transfer caused copy number instability, suggesting that cellular environment rather than the nuclear genomic background plays a role in the LR maintenance. Due to their dynamic nature and separation from other known conserved sequence elements on the non-coding region of hare mitochondrial genomes, the tandem repeat elements likely to represent signatures of ancient genetic rearrangements. clarifying the nature and dynamics of these rearrangements may shed light on the possible role of NCR repeated elements in mitochondria and in species evolution.
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Affiliation(s)
- Riikka Tapanainen
- University of Eastern Finland, Department of Environmental and Biological Sciences, Joensuu, Finland
| | - Koit Aasumets
- University of Eastern Finland, Department of Environmental and Biological Sciences, Joensuu, Finland
| | - Zsófia Fekete
- University of Eastern Finland, Department of Environmental and Biological Sciences, Joensuu, Finland; Hungarian University of Agriculture and Life Sciences, Institute of Genetics and Biotechnology, Gödöllő, Hungary
| | - Steffi Goffart
- University of Eastern Finland, Department of Environmental and Biological Sciences, Joensuu, Finland
| | - Eric Dufour
- Mitochondrial Bioenergetics and Metabolism, Faculty of Medicine and Health Technology, FI-33014 Tampere University, Finland
| | - Jaakko L O Pohjoismäki
- University of Eastern Finland, Department of Environmental and Biological Sciences, Joensuu, Finland.
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2
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Potter S, Moritz C, Piggott MP, Bragg JG, Afonso Silva AC, Bi K, McDonald-Spicer C, Turakulov R, Eldridge MDB. Museum Skins Enable Identification of Introgression Associated with Cytonuclear Discordance. Syst Biol 2024; 73:579-593. [PMID: 38577768 DOI: 10.1093/sysbio/syae016] [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: 03/10/2022] [Revised: 03/14/2024] [Accepted: 04/03/2024] [Indexed: 04/06/2024] Open
Abstract
Increased sampling of genomes and populations across closely related species has revealed that levels of genetic exchange during and after speciation are higher than previously thought. One obvious manifestation of such exchange is strong cytonuclear discordance, where the divergence in mitochondrial DNA (mtDNA) differs from that for nuclear genes more (or less) than expected from differences between mtDNA and nuclear DNA (nDNA) in population size and mutation rate. Given genome-scale data sets and coalescent modeling, we can now confidently identify cases of strong discordance and test specifically for historical or recent introgression as the cause. Using population sampling, combining exon capture data from historical museum specimens and recently collected tissues we showcase how genomic tools can resolve complex evolutionary histories in the brachyotis group of rock-wallabies (Petrogale). In particular, applying population and phylogenomic approaches we can assess the role of demographic processes in driving complex evolutionary patterns and assess a role of ancient introgression and hybridization. We find that described species are well supported as monophyletic taxa for nDNA genes, but not for mtDNA, with cytonuclear discordance involving at least 4 operational taxonomic units across 4 species which diverged 183-278 kya. ABC modeling of nDNA gene trees supports introgression during or after speciation for some taxon pairs with cytonuclear discordance. Given substantial differences in body size between the species involved, this evidence for gene flow is surprising. Heterogenous patterns of introgression were identified but do not appear to be associated with chromosome differences between species. These and previous results suggest that dynamic past climates across the monsoonal tropics could have promoted reticulation among related species.
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Affiliation(s)
- Sally Potter
- School of Natural Sciences, 14 Eastern Road, Macquarie University, Macquarie Park, NSW 2109, Australia
- Division of Ecology and Evolution, Research School of Biology, 134 Linnaeus Way, The Australian National University, Acton, ACT 2601, Australia
- Australian Museum Research Institute, Australian Museum, 1 William St, Sydney, NSW 2010, Australia
| | - Craig Moritz
- Division of Ecology and Evolution, Research School of Biology, 134 Linnaeus Way, The Australian National University, Acton, ACT 2601, Australia
| | - Maxine P Piggott
- Division of Ecology and Evolution, Research School of Biology, 134 Linnaeus Way, The Australian National University, Acton, ACT 2601, Australia
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Casuarina, NT 0811, Australia
| | - Jason G Bragg
- National Herbarium of New South Wales, The Royal Botanical Gardens and Domain Trust, Mrs Macquaries Road, Sydney, NSW 2000, Australia
| | | | - Ke Bi
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Christiana McDonald-Spicer
- Division of Ecology and Evolution, Research School of Biology, 134 Linnaeus Way, The Australian National University, Acton, ACT 2601, Australia
| | - Rustamzhon Turakulov
- Australian Genome Research Facility, Victorian Comprehensive Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia
- Earth Sciences, College of Science and Engineering, Flinders University GPO Box 2100, Adelaide, SA 5001, Australia
| | - Mark D B Eldridge
- Australian Museum Research Institute, Australian Museum, 1 William St, Sydney, NSW 2010, Australia
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3
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Myers EA, Rautsaw RM, Borja M, Jones J, Grünwald CI, Holding ML, Grazziotin F, Parkinson CL. Phylogenomic discordance is driven by wide-spread introgression and incomplete lineage sorting during rapid species diversification within rattlesnakes (Viperidae: Crotalus and Sistrurus). Syst Biol 2024:syae018. [PMID: 38695290 DOI: 10.1093/sysbio/syae018] [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: 05/10/2023] [Indexed: 08/11/2024] Open
Abstract
Phylogenomics allows us to uncover the historical signal of evolutionary processes through time and estimate phylogenetic networks accounting for these signals. Insight from genome-wide data further allows us to pinpoint the contributions to phylogenetic signal from hybridization, introgression, and ancestral polymorphism across the genome. Here we focus on how these processes have contributed to phylogenetic discordance among rattlesnakes (genera Crotalus and Sistrurus), a group for which there are numerous conflicting phylogenetic hypotheses based on a diverse array of molecular datasets and analytical methods. We address the instability of the rattlesnake phylogeny using genomic data generated from transcriptomes sampled from nearly all known species. These genomic data, analyzed with coalescent and network-based approaches, reveal numerous instances of rapid speciation where individual gene trees conflict with the species tree. Moreover, the evolutionary history of rattlesnakes is dominated by incomplete speciation and frequent hybridization, both of which have likely influenced past interpretations of phylogeny. We present a new framework in which the evolutionary relationships of this group can only be understood in light of genome-wide data and network-based analytical methods. Our data suggest that network radiations, like seen within the rattlesnakes, can only be understood in a phylogenomic context, necessitating similar approaches in our attempts to understand evolutionary history in other rapidly radiating species.
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Affiliation(s)
- Edward A Myers
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
- Department of Herpetology, California Academy of Sciences, San Francisco, CA 94118, USA
| | - Rhett M Rautsaw
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
| | - Miguel Borja
- Facultad de Ciencias Biológicas, Universdad Juárez del Estado de Durango, Av. Universidad s/n. Fracc. Filadelfia, Gómez Palacio, Durango., Mex
| | - Jason Jones
- Herp.mx A.C. C.P. 28989, Villa de Álvarez, Colima, Mexico
| | - Christoph I Grünwald
- Herp.mx A.C. C.P. 28989, Villa de Álvarez, Colima, Mexico
- Biodiversa A.C., Avenida de la Ribera #203, C.P. 45900, Chapala, Jalisco, Mexico
| | - Matthew L Holding
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Felipe Grazziotin
- Laboratório Especial de Coleções Zoológicas, Instituto Butantan, Avenida Vital Brasil, São Paulo, 05503-900, Brazil
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4
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Stone BW, Wessinger CA. Ecological Diversification in an Adaptive Radiation of Plants: The Role of De Novo Mutation and Introgression. Mol Biol Evol 2024; 41:msae007. [PMID: 38232726 PMCID: PMC10826641 DOI: 10.1093/molbev/msae007] [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: 11/01/2023] [Revised: 01/01/2024] [Accepted: 01/10/2024] [Indexed: 01/19/2024] Open
Abstract
Adaptive radiations are characterized by rapid ecological diversification and speciation events, leading to fuzzy species boundaries between ecologically differentiated species. Adaptive radiations are therefore key systems for understanding how species are formed and maintained, including the role of de novo mutations versus preexisting variation in ecological adaptation and the genome-wide consequences of hybridization events. For example, adaptive introgression, where beneficial alleles are transferred between lineages through hybridization, may fuel diversification in adaptive radiations and facilitate adaptation to new environments. In this study, we employed whole-genome resequencing data to investigate the evolutionary origin of hummingbird-pollinated flowers and to characterize genome-wide patterns of phylogenetic discordance and introgression in Penstemon subgenus Dasanthera, a small and diverse adaptive radiation of plants. We found that magenta hummingbird-adapted flowers have apparently evolved twice from ancestral blue-violet bee-pollinated flowers within this radiation. These shifts in flower color are accompanied by a variety of inactivating mutations to a key anthocyanin pathway enzyme, suggesting that independent de novo loss-of-function mutations underlie the parallel evolution of this trait. Although patterns of introgression and phylogenetic discordance were heterogenous across the genome, a strong effect of gene density suggests that, in general, natural selection opposes introgression and maintains genetic differentiation in gene-rich genomic regions. Our results highlight the importance of both de novo mutation and introgression as sources of evolutionary change and indicate a role for de novo mutation in driving parallel evolution in adaptive radiations.
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Affiliation(s)
- Benjamin W Stone
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208-3401, USA
| | - Carolyn A Wessinger
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208-3401, USA
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5
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Stone BW, Wessinger CA. Ecological diversification in an adaptive radiation of plants: the role of de novo mutation and introgression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.01.565185. [PMID: 37961506 PMCID: PMC10635055 DOI: 10.1101/2023.11.01.565185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Adaptive radiations are characterized by rapid ecological diversification and speciation events, leading to fuzzy species boundaries between ecologically differentiated species. Adaptive radiations are therefore key systems for understanding how species are formed and maintained, including the role of de novo mutations vs. pre-existing variation in ecological adaptation and the genome-wide consequences of hybridization events. For example, adaptive introgression, where beneficial alleles are transferred between lineages through hybridization, may fuel diversification in adaptive radiations and facilitate adaptation to new environments. In this study, we employed whole-genome resequencing data to investigate the evolutionary origin of hummingbird-pollinated flowers and to characterize genome-wide patterns of phylogenetic discordance and introgression in Penstemon subgenus Dasanthera, a small and diverse adaptive radiation of plants. We found that magenta hummingbird-adapted flowers have apparently evolved twice from ancestral blue-violet bee-pollinated flowers within this radiation. These shifts in flower color are accompanied by a variety of inactivating mutations to a key anthocyanin pathway enzyme, suggesting that independent de novo loss-of-function mutations underlie parallel evolution of this trait. Although patterns of introgression and phylogenetic discordance were heterogenous across the genome, a strong effect of gene density suggests that, in general, natural selection opposes introgression and maintains genetic differentiation in gene-rich genomic regions. Our results highlight the importance of both de novo mutation and introgression as sources of evolutionary change and indicate a role for de novo mutation in driving parallel evolution in adaptive radiations.
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Affiliation(s)
- Benjamin W. Stone
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208-3401, USA
| | - Carolyn A. Wessinger
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208-3401, USA
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6
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Cerca J. Understanding natural selection and similarity: Convergent, parallel and repeated evolution. Mol Ecol 2023; 32:5451-5462. [PMID: 37724599 DOI: 10.1111/mec.17132] [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: 04/13/2023] [Revised: 08/26/2023] [Accepted: 08/30/2023] [Indexed: 09/21/2023]
Abstract
Parallel and convergent evolution offer some of the most compelling evidence for the significance of natural selection in evolution, as the emergence of similar adaptive solutions is unlikely to occur by random chance alone. However, these terms are often employed inconsistently, leading to misinterpretation and confusion, and recently proposed definitions have unintentionally diminished the emphasis on the evolution of similar adaptive solutions. Here, I examine various conceptual frameworks and definitions related to parallel and convergent evolution and propose a consolidated framework that enhances our comprehension of these evolutionary patterns. The primary aim of this framework is to harmonize the concepts of parallel and convergent evolution together with natural selection and the idea of similarity. Both concepts involve the evolution of similar adaptive solutions as a result of environmental challenges. The distinction lies in ancestral phenotypes. Parallel evolution takes place when the ancestral phenotypes (before selection) of the lineages are similar. Convergent evolution happens when the lineages have distinct ancestral phenotypes (before selection). Because an ancestral-based distinction will inevitably lead to cases where uncertainty in the distinction may arise, the framework includes a general term, repeated evolution, which can be used as a term applying to the evolution of similar phenotypes and genotypes as well as similar responses to environmental pressures. Based on the argument that genetic similarity may frequently arise without selection, the framework posits that the similarity of genetic sequences is not of great interest unless linked to the actions of natural selection or to the origins (mutation, standing genetic variation, gene flow) and locations of the similar sequences.
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Affiliation(s)
- José Cerca
- CEES - Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
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7
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Pinheiro A, de Sousa-Pereira P, Esteves PJ. The IgA of hares ( Lepus sp.) and rabbit confirms that the leporids IgA explosion is old and reveals a new case of trans-species polymorphism. Front Immunol 2023; 14:1192460. [PMID: 37600766 PMCID: PMC10435986 DOI: 10.3389/fimmu.2023.1192460] [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: 03/23/2023] [Accepted: 07/10/2023] [Indexed: 08/22/2023] Open
Abstract
Background Immunoglobulin A (IgA) is the mammalian mucosal antibody, providing an important line of defense against pathogens. With 15 IgA subclasses, the European rabbit has an extremely complex IgA system, strikingly more complex than most other mammals, which have only one IgA or, in the case of hominoids, two IgA subclasses. Similar to the two hominoid primate IGHA genes, the expansion of the rabbit IGHA genes appears to have begun in an ancestral lagomorph since multiple IgA copies were found by Southern blot analysis for the genera Sylvilagus, Lepus, and Ochotona. Results To gain a better insight into the extraordinary lagomorph IgA evolution, we sequenced, for the first time, expressed IgA genes for two Lepus species, L. europaeus and L. granatensis. These were aligned with the 15 rabbit IgA isotypes, and evolutionary analyses were conducted. The obtained phylogenetic tree shows that the Lepus IgA sequences cluster with and among the rabbit IgA isotypes, and the interspecies and intraspecies nucleotide genetic distances are similar. A comparison of the amino acid sequences of the Lepus and rabbit IgA confirms that there are two trans-species polymorphisms and that the rabbit and Lepus sequences share a common genetic pool. In fact, the main differences between the studied leporids IgAs reside in the characteristics of the hinge region. Conclusion The Lepus IgA sequences we have obtained strongly suggest that the great expansion of the leporid IGHA genes occurred in a common ancestral species and was then maintained in the descendants. A strong selective pressure caused the extraordinary expansion of the IGHA genes but then subsided, leading to the maintenance of the acquired polymorphisms in the descendants, with little subsequent divergence. This is a unique evolutionary pattern in which an ancient gene expansion has been maintained for approximately 18 million years.
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Affiliation(s)
- Ana Pinheiro
- Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto (CIBIO-UP), InBIO, Laboratório Associado, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Patrícia de Sousa-Pereira
- Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto (CIBIO-UP), InBIO, Laboratório Associado, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Pedro J. Esteves
- Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto (CIBIO-UP), InBIO, Laboratório Associado, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- Centro de Investigação em Tecnologias de Saúde (CITS), CESPU, Gandra, Portugal
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8
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L Rocha J, Silva P, Santos N, Nakamura M, Afonso S, Qninba A, Boratynski Z, Sudmant PH, Brito JC, Nielsen R, Godinho R. North African fox genomes show signatures of repeated introgression and adaptation to life in deserts. Nat Ecol Evol 2023; 7:1267-1286. [PMID: 37308700 PMCID: PMC10527534 DOI: 10.1038/s41559-023-02094-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 04/26/2023] [Indexed: 06/14/2023]
Abstract
Elucidating the evolutionary process of animal adaptation to deserts is key to understanding adaptive responses to climate change. Here we generated 82 individual whole genomes of four fox species (genus Vulpes) inhabiting the Sahara Desert at different evolutionary times. We show that adaptation of new colonizing species to a hot arid environment has probably been facilitated by introgression and trans-species polymorphisms shared with older desert resident species, including a putatively adaptive 25 Mb genomic region. Scans for signatures of selection implicated genes affecting temperature perception, non-renal water loss and heat production in the recent adaptation of North African red foxes (Vulpes vulpes), after divergence from Eurasian populations approximately 78 thousand years ago. In the extreme desert specialists, Rueppell's fox (V. rueppellii) and fennec (V. zerda), we identified repeated signatures of selection in genes affecting renal water homeostasis supported by gene expression and physiological differences. Our study provides insights into the mechanisms and genetic underpinnings of a natural experiment of repeated adaptation to extreme conditions.
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Affiliation(s)
- Joana L Rocha
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal.
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal.
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal.
- Department of Integrative Biology and Department of Statistics, University of California Berkeley, Berkeley, CA, USA.
| | - Pedro Silva
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Nuno Santos
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Mónia Nakamura
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Sandra Afonso
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Abdeljebbar Qninba
- Laboratory of Geophysics and Natural Hazards, Geophysics, Natural Patrimony and Green Chemistry Research Center (GEOPAC), Institut Scientifique, Mohammed V University of Rabat, Rabat, Morocco
| | - Zbyszek Boratynski
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Peter H Sudmant
- Department of Integrative Biology and Department of Statistics, University of California Berkeley, Berkeley, CA, USA
- Center for Computational Biology, University of California, Berkeley, CA, USA
| | - José C Brito
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Rasmus Nielsen
- Department of Integrative Biology and Department of Statistics, University of California Berkeley, Berkeley, CA, USA.
- Center for Computational Biology, University of California, Berkeley, CA, USA.
- Globe Institute, University of Copenhagen, Copenhagen, Denmark.
| | - Raquel Godinho
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal.
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal.
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal.
- Department of Zoology, University of Johannesburg, Auckland Park, South Africa.
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9
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Zhou W, Furey NM, Soisook P, Thong VD, Lim BK, Rossiter SJ, Mao X. Diversification and introgression in four chromosomal taxa of the Pearson's horseshoe bat (Rhinolophus pearsoni) group. Mol Phylogenet Evol 2023; 183:107784. [PMID: 37040825 DOI: 10.1016/j.ympev.2023.107784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 03/11/2023] [Accepted: 04/07/2023] [Indexed: 04/13/2023]
Abstract
Chromosomal variation among closely related taxa is common in both plants and animals, and can reduce rates of introgression as well as promote reproductive isolation and speciation. In mammals, studies relating introgression to chromosomal variation have tended to focus on a few model systems and typically characterized levels of introgression using small numbers of loci. Here we took a genome-wide approach to examine how introgression rates vary among four closely related horseshoe bats (Rhinolophus pearsoni group) that possess different diploid chromosome numbers (2n = 42, 44, 46, and 60) resulting from Robertsonian (Rb) changes (fissions/fusions). Using a sequence capture we obtained orthologous loci for thousands of nuclear loci, as well as mitogenomes, and performed phylogenetic and population genetic analyses. We found that the taxon with 2n = 60 was the first to diverge in this group, and that the relationships among the three other taxa (2n = 42, 44 and 46) showed discordance across our different analyses. Our results revealed signatures of multiple ancient introgression events between the four taxa, with evidence of mitonuclar discordance in phylogenetic trees and reticulation events in their evolutionary history. Despite this, we found no evidence of recent and/or ongoing introgression between taxa. Overall, our results indicate that the effects of Rb changes on the reduction of introgression are complicated and that these may contribute to reproductive isolation and speciation in concert with other factors (e.g. phenotypic and genic divergence).
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Affiliation(s)
- Weiwei Zhou
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200062, China
| | - Neil M Furey
- Fauna & Flora International (Cambodia), PO Box 1380, No. 19, Street 360, Boeng Keng Kong 1, Phnom Penh 12000, Cambodia
| | - Pipat Soisook
- Princess Maha Chakri Sirindhorn Natural History Museum, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand
| | - Vu D Thong
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet Road, Cau Giay District, Hanoi, Viet Nam; Graduate University of Science and Technology, VAST, Viet Nam
| | - Burton K Lim
- Department of Natural History, Royal Ontario Museum, Toronto, Ontario M5S 2C6, Canada
| | - Stephen J Rossiter
- School of Biological and Behavioural Sciences, Queen Mary University of London, London E1 4NS, UK.
| | - Xiuguang Mao
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200062, China.
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10
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Yu J, Niu Y, You Y, Cox CJ, Barrett RL, Trias-Blasi A, Guo J, Wen J, Lu L, Chen Z. Integrated phylogenomic analyses unveil reticulate evolution in Parthenocissus (Vitaceae), highlighting speciation dynamics in the Himalayan-Hengduan Mountains. THE NEW PHYTOLOGIST 2023; 238:888-903. [PMID: 36305244 DOI: 10.1111/nph.18580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
Hybridization caused by frequent environmental changes can lead both to species diversification (speciation) and to speciation reversal (despeciation), but the latter has rarely been demonstrated. Parthenocissus, a genus with its trifoliolate lineage in the Himalayan-Hengduan Mountains (HHM) region showing perplexing phylogenetic relationships, provides an opportunity for investigating speciation dynamics based on integrated evidence. We investigated phylogenetic discordance and reticulate evolution in Parthenocissus based on rigorous analyses of plastome and transcriptome data. We focused on reticulations in the trifoliolate lineage in the HHM region using a population-level genome resequencing dataset, incorporating evidence from morphology, distribution, and elevation. Comprehensive analyses confirmed multiple introgressions within Parthenocissus in a robust temporal-spatial framework. Around the HHM region, at least three hybridization hot spots were identified, one of which showed evidence of ongoing speciation reversal. We present a solid case study using an integrative methodological approach to investigate reticulate evolutionary history and its underlying mechanisms in plants. It demonstrates an example of speciation reversal through frequent hybridizations in the HHM region, which provides new perspectives on speciation dynamics in mountainous areas with strong topographic and environmental heterogeneity.
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Affiliation(s)
- Jinren Yu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanting Niu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- China National Botanical Garden, Beijing, 100093, China
| | - Yichen You
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Cymon J Cox
- Centro de Ciências do Mar, Universidade do Algarve, Gambelas, Faro, 8005-319, Portugal
| | - Russell L Barrett
- National Herbarium of New South Wales, Australian Botanic Garden, Locked Bag 6002, Mount Annan, 2567, NSW, Australia
| | | | - Jing Guo
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Jun Wen
- Department of Botany, National Museum of Natural History, MRC-166, Smithsonian Institution, Washington, DC, 20013-7012, USA
| | - Limin Lu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Zhiduan Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
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11
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Ferreira MS, Thurman TJ, Jones MR, Farelo L, Kumar AV, Mortimer SME, Demboski JR, Mills LS, Alves PC, Melo-Ferreira J, Good JM. The evolution of white-tailed jackrabbit camouflage in response to past and future seasonal climates. Science 2023; 379:1238-1242. [PMID: 36952420 DOI: 10.1126/science.ade3984] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Abstract
The genetic basis of adaptive traits has rarely been used to predict future vulnerability of populations to climate change. We show that light versus dark seasonal pelage in white-tailed jackrabbits (Lepus townsendii) tracks snow cover and is primarily determined by genetic variation at endothelin receptor type B (EDNRB), corin serine peptidase (CORIN), and agouti signaling protein (ASIP). Winter color variation was associated with deeply divergent alleles at these genes, reflecting selection on both ancestral and introgressed variation. Forecasted reductions in snow cover are likely to induce widespread camouflage mismatch. However, simulated populations with variation for darker winter pelage are predicted to adapt rapidly, providing a trait-based genetic framework to facilitate evolutionary rescue. These discoveries demonstrate how the genetic basis of climate change adaptation can inform conservation.
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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, MT, USA
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Timothy J Thurman
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Matthew R Jones
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Liliana Farelo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Alexander V Kumar
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, MT, USA
- US Fish and Wildlife Service, Fort Collins, CO, USA
| | | | - John R Demboski
- Zoology Department, Denver Museum of Nature & Science, Denver, CO, USA
| | - L Scott Mills
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, MT, USA
- Office of Research and Creative Scholarship, University of Montana, Missoula, MT, USA
| | - 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
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, MT, USA
| | - 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
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Jeffrey M Good
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, MT, USA
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12
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Sharko F, Slobodova N, Boulygina E, Cheprasov M, Gladysheva-Azgari M, Tsygankova S, Rastorguev S, Novgorodov G, Boeskorov G, Grigorieva L, Hwang WS, Tikhonov A, Nedoluzhko A. Ancient DNA of the Don-Hares Assumes the Existence of Two Distinct Mitochondrial Clades in Northeast Asia. Genes (Basel) 2023; 14:genes14030700. [PMID: 36980972 PMCID: PMC10047931 DOI: 10.3390/genes14030700] [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: 02/08/2023] [Revised: 03/09/2023] [Accepted: 03/11/2023] [Indexed: 03/14/2023] Open
Abstract
Paleoclimatic changes during the Pleistocene–Holocene transition is suggested as a main factor that led to species extinction, including the woolly mammoth (Mammuthus primigenius), Steller’s sea cow (Hydrodamalis gigas) and the Don-hare (Lepus tanaiticus). These species inhabited the territory of Eurasia during the Holocene, but eventually went extinct. The Don-hare is an extinct species of the genus Lepus (Leporidae, Lagomorpha), which lived in the Late Pleistocene–Early Holocene in Eastern Europe and Northern Asia. For a long time, the Don-hare was considered a separate species, but at the same time, its species status was disputed, taking into account both morphological data and mitochondrial DNA. In this study, mitochondrial genomes of five Don-hares, whose remains were found on the territory of Northeastern Eurasia were reconstructed. Firstly, we confirm the phylogenetic proximity of the “young” specimens of Don-hare and mountain or white hare, and secondly, that samples older than 39 Kya form a completely distinct mitochondrial clade.
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Affiliation(s)
- Fedor Sharko
- Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
- Kurchatov Center for Genomic Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | - Natalia Slobodova
- Kurchatov Center for Genomic Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
- Faculty of Biology and Biotechnology, HSE University, 101000 Moscow, Russia
| | - Eugenia Boulygina
- Kurchatov Center for Genomic Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | - Maksim Cheprasov
- Lazarev Mammoth Museum, M.K. Ammosov North-Eastern Federal University, 677000 Yakutsk, Russia
- Federal Research Centre “The Yakut Scientific Centre of the Siberian Branch of the Russian Academy of Sciences”, 677980 Yakutsk, Russia
| | - Maria Gladysheva-Azgari
- Kurchatov Center for Genomic Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | - Svetlana Tsygankova
- Kurchatov Center for Genomic Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | - Sergey Rastorguev
- Laboratory of Experimental Embryology, Institute of Translational Medicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Gavril Novgorodov
- Lazarev Mammoth Museum, M.K. Ammosov North-Eastern Federal University, 677000 Yakutsk, Russia
| | - Gennady Boeskorov
- Institute of Diamond and Precious Metals Geology, Siberian Branch of the Russian Academy of Sciences, 677007 Yakutsk, Russia
| | - Lena Grigorieva
- Center of Molecular Paleontology, M.K. Ammosov North-Eastern Federal University, 677000 Yakutsk, Russia
| | - Woo Suk Hwang
- UAE Biotech Research Center, Abu Dhabi 30310, United Arab Emirates
- Department of Biology, North-Eastern Federal University, 677000 Yakutsk, Russia
| | - Alexei Tikhonov
- Lazarev Mammoth Museum, M.K. Ammosov North-Eastern Federal University, 677000 Yakutsk, Russia
- Zoological Institute of the Russian Academy of Sciences, 190121 Saint Petersburg, Russia
| | - Artem Nedoluzhko
- Paleogenomics Laboratory, European University at Saint Petersburg, 191187 Saint Petersburg, Russia
- Correspondence:
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13
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Ye Z, Damgaard J, Hädicke CW, Zhu X, Mazzucconi SA, Hebsgaard MB, Xie T, Yang H, Bu W. Phylogeny and historical biogeography of the water boatmen (Insecta: Hemiptera: Heteroptera: Nepomorpha: Corixoidea). Mol Phylogenet Evol 2023; 180:107698. [PMID: 36587885 DOI: 10.1016/j.ympev.2022.107698] [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: 09/03/2022] [Revised: 12/27/2022] [Accepted: 12/27/2022] [Indexed: 12/31/2022]
Abstract
The water boatmen of Corixoidea, a group of aquatic bugs with more than 600 extant species, is one of the largest superfamilies of Nepomorpha. Contrary to the other nepomorphan lineages, the Corixoidea are most diverse in the Laurasian remnant Holarctic region. To explicitly test whether the present-day Holarctic distribution of diverse corixids is associated with the arising of the Laurasian landmass that was separated from Gondwana, we investigated the phylogeny, divergence times and historical biogeography of Corixoidea based on morphological and molecular characters sampled from 122 taxa representing all families, subfamilies, tribes and approximately 54 % of the genera. Our results were largely congruent with the phylogenetic relationships within the established nepomorphan phylogenetic context. The fossil calibrated chronogram, diversification analysis and ancestral ranges reconstruction indicated that Corixoidea began to diversify in Gondwana in the late Triassic approximately at 224 Ma and the arising of the most diverse subfamily Corixinae in Corixidae in the Holarctic region was largely congruent with the time of separation of Laurasia from Gondwana. The large-scale expansion of the temperate and cold zones on the northward-moving Laurasian landmass after the breakup of the Pangea provided new aquatic niches and ecological opportunities for promoting rapid diversification for the Holarctic corixid lineage.
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Affiliation(s)
- Zhen Ye
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China.
| | - Jakob Damgaard
- Natural History Museum of Denmark, Zoological Museum, Universitetsparken 15, 2100 Ø, Denmark.
| | | | - Xiuxiu Zhu
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Silvia A Mazzucconi
- Laboratorio de Entomología, IBBEA, CONICET-UBA., DBBE-FCEN, Universidad de Buenos Aires, C1428EHA Buenos Aires, Argentina
| | - Martin B Hebsgaard
- Natural History Museum of Denmark, Zoological Museum, Universitetsparken 15, 2100 Ø, Denmark
| | - Tongyin Xie
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Huanhuan Yang
- School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong 250353, China
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China.
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14
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Characterising Mitochondrial Capture in an Iberian Shrew. Genes (Basel) 2022; 13:genes13122228. [PMID: 36553495 PMCID: PMC9777731 DOI: 10.3390/genes13122228] [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: 10/07/2022] [Revised: 11/08/2022] [Accepted: 11/19/2022] [Indexed: 11/29/2022] Open
Abstract
Mitochondrial introgression raises questions of biogeography and of the extent of reproductive isolation and natural selection. Previous phylogenetic work on the Sorex araneus complex revealed apparent mitonuclear discordance in Iberian shrews, indicating past hybridisation of Sorex granarius and the Carlit chromosomal race of S. araneus, enabling introgression of the S. araneus mitochondrial genome into S. granarius. To further study this, we genetically typed 61 Sorex araneus/coronatus/granarius from localities in Portugal, Spain, France, and Andorra at mitochondrial, autosomal, and sex-linked loci and combined our data with the previously published sequences. Our data are consistent with earlier data indicating that S. coronatus and S. granarius are the most closely related of the three species, confirming that S. granarius from the Central System mountain range in Spain captured the mitochondrial genome from a population of S. araneus. This mitochondrial capture event can be explained by invoking a biogeographical scenario whereby S. araneus was in contact with S. granarius during the Younger Dryas in central Iberia, despite the two species currently having disjunct distributions. We discuss whether selection favoured S. granarius with an introgressed mitochondrial genome. Our data also suggest recent hybridisation and introgression between S. coronatus and S. granarius, as well as between S. araneus and S. coronatus.
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15
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Gaertner K, Michell C, Tapanainen R, Goffart S, Saari S, Soininmäki M, Dufour E, Pohjoismäki JLO. Molecular phenotyping uncovers differences in basic housekeeping functions among closely related species of hares (
Lepus
spp., Lagomorpha: Leporidae). Mol Ecol 2022. [PMID: 36320183 DOI: 10.1111/mec.16755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 09/16/2022] [Accepted: 10/06/2022] [Indexed: 11/15/2022]
Abstract
Speciation is a fundamental evolutionary process, which results in genetic differentiation of populations and manifests as discrete morphological, physiological and behavioural differences. Each species has travelled its own evolutionary trajectory, influenced by random drift and driven by various types of natural selection, making the association of genetic differences between the species with the phenotypic differences extremely complex to dissect. In the present study, we have used an in vitro model to analyse in depth the genetic and gene regulation differences between fibroblasts of two closely related mammals, the arctic/subarctic mountain hare (Lepus timidus Linnaeus) and the temperate steppe-climate adapted brown hare (Lepus europaeus Pallas). We discovered the existence of a species-specific expression pattern of 1623 genes, manifesting in differences in cell growth, cell cycle control, respiration, and metabolism. Interspecific differences in the housekeeping functions of fibroblast cells suggest that speciation acts on fundamental cellular processes, even in these two interfertile species. Our results help to understand the molecular constituents of a species difference on a cellular level, which could contribute to the maintenance of the species boundary.
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Affiliation(s)
- Kateryna Gaertner
- Mitochondrial Bioenergetics and Metabolism, Faculty of Medicine and Health Technology FI‐33014 Tampere University Tampere Finland
| | - Craig Michell
- Department of Environmental and Biological Sciences FI‐80101 University of Eastern Finland Kuopio Finland
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering King Abdullah University of Science and Technology (KAUST) Thuwal Saudi Arabia
| | - Riikka Tapanainen
- Department of Environmental and Biological Sciences FI‐80101 University of Eastern Finland Kuopio Finland
| | - Steffi Goffart
- Department of Environmental and Biological Sciences FI‐80101 University of Eastern Finland Kuopio Finland
| | - Sina Saari
- Mitochondrial Bioenergetics and Metabolism, Faculty of Medicine and Health Technology FI‐33014 Tampere University Tampere Finland
| | - Manu Soininmäki
- Department of Environmental and Biological Sciences FI‐80101 University of Eastern Finland Kuopio Finland
| | - Eric Dufour
- Mitochondrial Bioenergetics and Metabolism, Faculty of Medicine and Health Technology FI‐33014 Tampere University Tampere Finland
| | - Jaakko L. O. Pohjoismäki
- Department of Environmental and Biological Sciences FI‐80101 University of Eastern Finland Kuopio Finland
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16
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Michell CT, Pohjoismäki JLO, Spong G, Thulin CG. Mountain- and brown hare genetic polymorphisms to survey local adaptations and conservation status of the heath hare (Lepus timidus sylvaticus, Nilsson 1831). Sci Data 2022; 9:667. [PMID: 36329035 PMCID: PMC9633808 DOI: 10.1038/s41597-022-01794-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 10/20/2022] [Indexed: 11/06/2022] Open
Abstract
We provide the first whole genome sequences from three specimens of the mountain hare subspecies the heath hare (Lepus timidus sylvaticus), along with samples from two mountain hares (Lepus timidus timidus) and two brown hares (Lepus europaeus) from Sweden. The heath hare has a unique grey winter pelage as compared to other mountain hares (white) and brown hares (mostly brown), and face regional extinction, likely due to competitive exclusion from the non-native brown hare. Whole genome resequencing from the seven hare specimens were mapped to the Lepus timidus pseudoreference genome and used for detection of 11,363,883 polymorphic nucleotide positions. The data presented here could be useful for addressing local adaptations and conservation status of mountain hares and brown hares in Sweden, including unique subspecies. Measurement(s) | whole genome sequencing | Technology Type(s) | Illumina HiSeq X | Factor Type(s) | Species | Sample Characteristic - Organism | Lepus timidus • Lepus europaeus • Lepus timidus sylvaticus | Sample Characteristic - Location | Sweden |
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Affiliation(s)
- Craig T Michell
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 111, FI-80101, Joensuu, Finland. .,Red Sea Research Center, King Abdullah University of Science and Technology, Box 4700, 23955-6900, Thuwal, Kingdom of Saudi Arabia.
| | - Jaakko L O Pohjoismäki
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 111, FI-80101, Joensuu, Finland
| | - Göran Spong
- Department of Wildlife, Fish, and Environmental Studies, Molecular Ecology Group, Swedish University of Agricultural Sciences, Skogmarksgränd, 901 83, Umeå, Sweden
| | - Carl-Gustaf Thulin
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Box 7011, 750 07, Uppsala, Sweden.
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17
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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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18
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Awadi A, Suchentrunk F, Knauer F, Smith S, Tolesa Z, Ben Slimen H. Spatial diversity of MHC class II DRB exon2 sequences in North African cape hares (Lepus capensis): positive selection and climatic adaptation signals. Mamm Biol 2022. [DOI: 10.1007/s42991-022-00258-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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19
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Andrea C. As fast as a hare: did intraspecific morphological change bring the Hallands Väderö Island population of Lepus timidus close to interspecific differences in less than 150 years? ZOOLOGY 2022; 152:126014. [DOI: 10.1016/j.zool.2022.126014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 04/15/2022] [Accepted: 04/18/2022] [Indexed: 11/28/2022]
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20
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Cano-Sánchez E, Rodríguez-Gómez F, Ruedas LA, Oyama K, León-Paniagua L, Mastretta-Yanes A, Velazquez A. Using Ultraconserved Elements to Unravel Lagomorph Phylogenetic Relationships. J MAMM EVOL 2022. [DOI: 10.1007/s10914-021-09595-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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21
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Giska I, Pimenta J, Farelo L, Boursot P, Hackländer K, Jenny H, Reid N, Montgomery WI, Prodöhl PA, Alves PC, Melo-Ferreira J. The evolutionary pathways for local adaptation in mountain hares. Mol Ecol 2022; 31:1487-1503. [PMID: 34995383 PMCID: PMC9303332 DOI: 10.1111/mec.16338] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 12/06/2021] [Accepted: 12/17/2021] [Indexed: 12/13/2022]
Abstract
Understanding the evolution of local adaptations is a central aim of evolutionary biology and key for the identification of unique populations and lineages of conservation relevance. By combining RAD sequencing and whole‐genome sequencing, we identify genetic signatures of local adaptation in mountain hares (Lepus timidus) from isolated and distinctive habitats of its wide distribution: Ireland, the Alps and Fennoscandia. Demographic modelling suggested that the split of these mountain hares occurred around 20 thousand years ago, providing the opportunity to study adaptive evolution over a short timescale. Using genome‐wide scans, we identified signatures of extreme differentiation among hares from distinct geographic areas that overlap with area‐specific selective sweeps, suggesting targets for local adaptation. Several identified candidate genes are associated with traits related to the uniqueness of the different environments inhabited by the three groups of mountain hares, including coat colour, ability to live at high altitudes and variation in body size. In Irish mountain hares, a variant of ASIP, a gene previously implicated in introgression‐driven winter coat colour variation in mountain and snowshoe hares (L. americanus), may underlie brown winter coats, reinforcing the repeated nature of evolution at ASIP moulding adaptive seasonal colouration. Comparative genomic analyses across several hare species suggested that mountain hares’ adaptive variants appear predominantly species‐specific. However, using coalescent simulations, we also show instances where the candidate adaptive variants have been introduced via introgressive hybridization. Our study shows that standing adaptive variation, including that introgressed from other species, was a crucial component of the post‐glacial dynamics of species.
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Affiliation(s)
- Iwona Giska
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
| | - João Pimenta
- 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.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Liliana Farelo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Pierre Boursot
- Institut des Sciences de l'Évolution Montpellier (ISEM), Université Montpellier, CNRS, IRD, Montpellier, France
| | - Klaus Hackländer
- Institute of Wildlife Biology and Game Management, University of Natural Resources and Life Sciences, Vienna, Austria.,Deutsche Wildtier Stiftung (German Wildlife Foundation), Hamburg, Germany
| | - Hannes Jenny
- Department of Wildlife and Fishery Service Grison, Chur, Switzerland
| | - Neil Reid
- Institute of Global Food Security (IGFS), School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - W Ian Montgomery
- Institute of Global Food Security (IGFS), School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - Paulo A Prodöhl
- Institute of Global Food Security (IGFS), School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - 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.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - 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.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
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22
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Adavoudi R, Pilot M. Consequences of Hybridization in Mammals: A Systematic Review. Genes (Basel) 2021; 13:50. [PMID: 35052393 PMCID: PMC8774782 DOI: 10.3390/genes13010050] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/14/2021] [Accepted: 12/20/2021] [Indexed: 12/18/2022] Open
Abstract
Hybridization, defined as breeding between two distinct taxonomic units, can have an important effect on the evolutionary patterns in cross-breeding taxa. Although interspecific hybridization has frequently been considered as a maladaptive process, which threatens species genetic integrity and survival via genetic swamping and outbreeding depression, in some cases hybridization can introduce novel adaptive variation and increase fitness. Most studies to date focused on documenting hybridization events and analyzing their causes, while relatively little is known about the consequences of hybridization and its impact on the parental species. To address this knowledge gap, we conducted a systematic review of studies on hybridization in mammals published in 2010-2021, and identified 115 relevant studies. Of 13 categories of hybridization consequences described in these studies, the most common negative consequence (21% of studies) was genetic swamping and the most common positive consequence (8%) was the gain of novel adaptive variation. The total frequency of negative consequences (49%) was higher than positive (13%) and neutral (38%) consequences. These frequencies are biased by the detection possibilities of microsatellite loci, the most common genetic markers used in the papers assessed. As negative outcomes are typically easier to demonstrate than positive ones (e.g., extinction vs hybrid speciation), they may be over-represented in publications. Transition towards genomic studies involving both neutral and adaptive variation will provide a better insight into the real impacts of hybridization.
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Affiliation(s)
| | - Małgorzata Pilot
- Museum and Institute of Zoology, Polish Academy of Sciences, ul. Nadwiślańska 108, 80-680 Gdańsk, Poland;
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23
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Singhal S, Derryberry GE, Bravo GA, Derryberry EP, Brumfield RT, Harvey MG. The dynamics of introgression across an avian radiation. Evol Lett 2021; 5:568-581. [PMID: 34917397 PMCID: PMC8645201 DOI: 10.1002/evl3.256] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 07/11/2021] [Accepted: 08/31/2021] [Indexed: 01/20/2023] Open
Abstract
Hybridization and resulting introgression can play both a destructive and a creative role in the evolution of diversity. Thus, characterizing when and where introgression is most likely to occur can help us understand the causes of diversification dynamics. Here, we examine the prevalence of and variation in introgression using phylogenomic data from a large (1300+ species), geographically widespread avian group, the suboscine birds. We first examine patterns of gene tree discordance across the geographic distribution of the entire clade. We then evaluate the signal of introgression in a subset of 206 species triads using Patterson's D‐statistic and test for associations between introgression signal and evolutionary, geographic, and environmental variables. We find that gene tree discordance varies across lineages and geographic regions. The signal of introgression is highest in cases where species occur in close geographic proximity and in regions with more dynamic climates since the Pleistocene. Our results highlight the potential of phylogenomic datasets for examining broad patterns of hybridization and suggest that the degree of introgression between diverging lineages might be predictable based on the setting in which they occur.
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Affiliation(s)
- Sonal Singhal
- Department of Biology California State University, Dominguez Hills Carson California 90747
| | - Graham E Derryberry
- Department of Ecology and Evolutionary Biology University of Tennessee Knoxville Tennessee 37996
| | - Gustavo A Bravo
- Department of Organismic and Evolutionary Biology Harvard University Cambridge Massachusetts 02138.,Museum of Comparative Zoology Harvard University Cambridge Massachusetts 02138
| | - Elizabeth P Derryberry
- Department of Ecology and Evolutionary Biology University of Tennessee Knoxville Tennessee 37996
| | - Robb T Brumfield
- Museum of Natural Science Louisiana State University Baton Rouge Louisiana 70803.,Department of Biological Sciences Louisiana State University Baton Rouge Louisiana 70803
| | - Michael G Harvey
- Department of Biological Sciences The University of Texas at El Paso El Paso Texas 79968.,Biodiversity Collections The University of Texas at El Paso El Paso Texas 79968
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24
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Hybridization with mountain hares increases the functional allelic repertoire in brown hares. Sci Rep 2021; 11:15771. [PMID: 34349207 PMCID: PMC8338973 DOI: 10.1038/s41598-021-95357-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 07/26/2021] [Indexed: 12/12/2022] Open
Abstract
Brown hares (Lepus europaeus Pallas) are able to hybridize with mountain hares (L. timidus Linnaeus) and produce fertile offspring, which results in cross-species gene flow. However, not much is known about the functional significance of this genetic introgression. Using targeted sequencing of candidate loci combined with mtDNA genotyping, we found the ancestral genetic diversity in the Finnish brown hare to be small, likely due to founder effect and range expansion, while gene flow from mountain hares constitutes an important source of functional genetic variability. Some of this variability, such as the alleles of the mountain hare thermogenin (uncoupling protein 1, UCP1), might have adaptive advantage for brown hares, whereas immunity-related MHC alleles are reciprocally exchanged and maintained via balancing selection. Our study offers a rare example where an expanding species can increase its allelic variability through hybridization with a congeneric native species, offering a route to shortcut evolutionary adaptation to the local environmental conditions.
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25
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Cerca J, Rivera-Colón AG, Ferreira MS, Ravinet M, Nowak MD, Catchen JM, Struck TH. Incomplete lineage sorting and ancient admixture, and speciation without morphological change in ghost-worm cryptic species. PeerJ 2021; 9:e10896. [PMID: 33614296 PMCID: PMC7879940 DOI: 10.7717/peerj.10896] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 01/13/2021] [Indexed: 12/14/2022] Open
Abstract
Morphologically similar species, that is cryptic species, may be similar or quasi-similar owing to the deceleration of morphological evolution and stasis. While the factors underlying the deceleration of morphological evolution or stasis in cryptic species remain unknown, decades of research in the field of paleontology on punctuated equilibrium have originated clear hypotheses. Species are expected to remain morphologically identical in scenarios of shared genetic variation, such as hybridization and incomplete lineage sorting, or in scenarios where bottlenecks reduce genetic variation and constrain the evolution of morphology. Here, focusing on three morphologically similar Stygocapitella species, we employ a whole-genome amplification method (WGA) coupled with double-digestion restriction-site associated DNA sequencing (ddRAD) to reconstruct the evolutionary history of the species complex. We explore population structure, use population-level statistics to determine the degree of connectivity between populations and species, and determine the most likely demographic scenarios which generally reject for recent hybridization. We find that the combination of WGA and ddRAD allowed us to obtain genomic-level data from microscopic eukaryotes (∼1 millimetre) opening up opportunities for those working with population genomics and phylogenomics in such taxa. The three species share genetic variance, likely from incomplete lineage sorting and ancient admixture. We speculate that the degree of shared variation might underlie morphological similarity in the Atlantic species complex.
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Affiliation(s)
- José Cerca
- Department of Environmental Science, Policy, and Management, University of California, University of California, Berkeley, Berkeley, CA, United States of America
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Angel G. Rivera-Colón
- Department of Evolution, Ecology, and Behavior, University of Illinois at Urbana-Champaign, Urbana Champaign, IL, United States of America
| | - Mafalda S. Ferreira
- Division of Biological Sciences, University of Montana, Missoula, MT, United States of America
- Departamento de Biologia, Universidade do Porto, Porto, Porto, Portugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Porto, Porto, Portugal
| | - Mark Ravinet
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway
| | | | - Julian M. Catchen
- Department of Evolution, Ecology, and Behavior, University of Illinois at Urbana-Champaign, Urbana Champaign, IL, United States of America
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