1
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Johnson SB, Winnikoff JR, Schultz DT, Christianson LM, Patry WL, Mills CE, Haddock SHD. Speciation of pelagic zooplankton: Invisible boundaries can drive isolation of oceanic ctenophores. Front Genet 2022; 13:970314. [PMID: 36276958 PMCID: PMC9585324 DOI: 10.3389/fgene.2022.970314] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022] Open
Abstract
The study of evolution and speciation in non-model systems provides us with an opportunity to expand our understanding of biodiversity in nature. Connectivity studies generally focus on species with obvious boundaries to gene flow, but in open-ocean environments, such boundaries are difficult to identify. Due to the lack of obvious boundaries, speciation and population subdivision in the pelagic environment remain largely unexplained. Comb jellies (Phylum Ctenophora) are mostly planktonic gelatinous invertebrates, many of which are considered to have freely interbreeding distributions worldwide. It is thought that the lobate ctenophore Bolinopsis infundibulum is distributed throughout cooler northern latitudes and B. vitrea warmer. Here, we examined the global population structure for species of Bolinopsis with genetic and morphological data. We found distinct evolutionary patterns within the genus, where B. infundibulum had a broad distribution from northern Pacific to Atlantic waters despite many physical barriers, while other species were geographically segregated despite few barriers. Divergent patterns of speciation within the genus suggest that oceanic currents, sea-level, and geological changes over time can act as either barriers or aids to dispersal in the pelagic environment. Further, we used population genomic data to examine evolution in the open ocean of a distinct lineage of Bolinopsis ctenophores from the North Eastern Pacific. Genetic information and morphological observations validated this as a separate species, Bolinopsis microptera, which was previously described but has recently been called B. infundibulum. We found that populations of B. microptera from California were in cytonuclear discordance, which indicates a secondary contact zone for previously isolated populations. Discordance at this scale is rare, especially in a continuous setting.
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Affiliation(s)
- Shannon B. Johnson
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, United States
- *Correspondence: Shannon B. Johnson, ; Steven H. D. Haddock,
| | - Jacob R. Winnikoff
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, United States
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Darrin T. Schultz
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, United States
- Department of Neurosciences and Developmental Biology, University of Vienna, Vienna, Austria
- Department of Biomolecular Engineering and Bioinformatics, University of California, Santa Cruz, Santa Cruz, CA, United States
| | | | - Wyatt L. Patry
- Animal Care Division, Monterey Bay Aquarium, Monterey, CA, United States
| | - Claudia E. Mills
- Friday Harbor Laboratories and the Department of Biology, University of Washington, Friday Harbor, WA, United States
| | - Steven H. D. Haddock
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, United States
- *Correspondence: Shannon B. Johnson, ; Steven H. D. Haddock,
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2
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Marshall TL, Chambers EA, Matz MV, Hillis DM. How mitonuclear discordance and geographic variation have confounded species boundaries in a widely studied snake. Mol Phylogenet Evol 2021; 162:107194. [PMID: 33940060 DOI: 10.1016/j.ympev.2021.107194] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 03/12/2021] [Accepted: 04/28/2021] [Indexed: 12/15/2022]
Abstract
As DNA sequencing technologies and methods for delimiting species with genomic data become more accessible and numerous, researchers have more tools than ever to investigate questions in systematics and phylogeography. However, easy access to sophisticated computational tools is not without its drawbacks. Choosing the right approach for one's question can be challenging when presented with multitudinous options, some of which fail to distinguish between species and intraspecific population structure. Here, we employ a methodology that emphasizes intensive geographic sampling, particularly at contact zones between populations, with a focus on differentiating intraspecific genetic clusters from species in the Pantherophis guttatus complex, a group of North American ratsnakes. Using a mitochondrial marker as well as ddRADseq data, we find evidence of mitonuclear discordance which has contributed to historical confusion about the relationships within this group. Additionally, we identify geographically and genetically structured populations within the species Pantherophis emoryi that are congruent with previously described morphological variation. Importantly, we find that these structured populations within P. emoryi are highly admixed throughout the range of the species and show no evidence of any reproductive isolation. Our data support a revision of the taxonomy of this group, and we recognize two species within the complex and three subspecies within P. emoryi. This study illustrates the importance of thorough sampling of contact zones and consideration of gene flow when delimiting species in widespread complexes containing parapatric lineages.
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Affiliation(s)
- Thomas L Marshall
- Department of Integrative Biology and Biodiversity Center, The University of Texas at Austin, Austin, TX 78712, USA.
| | - E Anne Chambers
- Department of Integrative Biology and Biodiversity Center, The University of Texas at Austin, Austin, TX 78712, USA
| | - Mikhail V Matz
- Department of Integrative Biology and Biodiversity Center, The University of Texas at Austin, Austin, TX 78712, USA
| | - David M Hillis
- Department of Integrative Biology and Biodiversity Center, The University of Texas at Austin, Austin, TX 78712, USA
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3
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Sadanandan KR, Low GW, Sridharan S, Gwee CY, Ng EYX, Yuda P, Prawiradilaga DM, Lee JGH, Tritto A, Rheindt FE. The conservation value of admixed phenotypes in a critically endangered species complex. Sci Rep 2020; 10:15549. [PMID: 32968132 PMCID: PMC7511927 DOI: 10.1038/s41598-020-72428-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 08/17/2020] [Indexed: 11/19/2022] Open
Abstract
In today's environmental crisis, conservationists are increasingly confronted with terminally endangered species whose last few surviving populations may be affected by allelic introgression from closely related species. Yet there is a worrying lack of evidence-based recommendations and solutions for this emerging problem. We analyzed genome-wide DNA markers and plumage variability in a critically endangered insular songbird, the Black-winged Myna (BWM, Acridotheres melanopterus). This species is highly threatened by the illegal wildlife trade, with its wild population numbering in the low hundreds, and its continued survival urgently depending on ex-situ breeding. Its three subspecies occur along a geographic gradient of melanism and are variably interpreted as three species. However, our integrative approach revealed that melanism poorly reflects the pattern of limited genomic differentiation across BWM subspecies. We also uncovered allelic introgression into the most melanistic subspecies, tertius, from the all-black congeneric Javan Myna (A. javanicus), which is native to the same islands. Based on our results, we recommend the establishment of three separate breeding programs to maintain subspecific traits that may confer local adaptation, but with the option of occasional cross-breeding between insurance populations in order to boost genetic diversity and increase overall viability prospects of each breeding program. Our results underscore the importance of evidence-based integrative approaches when determining appropriate conservation units. Given the rapid increase of terminally endangered organisms in need of ex-situ conservation, this study provides an important blueprint for similar programs dealing with phenotypically variable species.
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Affiliation(s)
- Keren R Sadanandan
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore
- Max Planck Institute for Ornithology, 82319, Seewiesen, Germany
| | - Gabriel W Low
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore
- School of Biological Sciences, Monash University, Clayton, VIC, 3800, Australia
| | - Sheeraja Sridharan
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore
- Department of Biological Sciences, University of Alberta, 116 St & 85 Ave, Edmonton, AB, T6G 2R3, Canada
| | - Chyi Yin Gwee
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore
| | - Elize Y X Ng
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore
| | - Pramana Yuda
- Universitas Atma Jaya, Jl. Babarsari 44, Janti, Caturtunggal, Kec. Depok, Kabupaten Sleman, Daerah Istimewa Yogyakarta, 55281, Indonesia
| | - Dewi M Prawiradilaga
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jalan Raya Jakarta Bogor KM 46, Cibinong Science Center, Cibinong, 16911, Indonesia
| | - Jessica G H Lee
- Wildlife Reserves Singapore, 80 Mandai Lake Road, Singapore, 729826, Singapore
| | - Anaïs Tritto
- Wildlife Reserves Singapore, 80 Mandai Lake Road, Singapore, 729826, Singapore
| | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore.
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4
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Mao X, Rossiter SJ. Genome-wide data reveal discordant mitonuclear introgression in the intermediate horseshoe bat (Rhinolophus affinis). Mol Phylogenet Evol 2020; 150:106886. [PMID: 32534185 DOI: 10.1016/j.ympev.2020.106886] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 06/01/2020] [Accepted: 06/03/2020] [Indexed: 10/24/2022]
Abstract
Closely related taxa often exhibit mitonuclear discordance attributed to introgression of mitochondrial DNA (mtDNA), yet few studies have considered the underlying causes of mtDNA introgression. Here we test for demographic versus adaptive processes as explanations for mtDNA introgression in three subspecies of the intermediate horseshoe bat (Rhinolophus affinis). We generated sequences of 1692 nuclear genes and 13 mitochondrial protein-coding genes for 48 individuals. Phylogenetic reconstructions based on 320 exon sequences and 2217 single nucleotide polymorphisms (SNPs) both revealed conflicts between the species tree and mtDNA tree. These results, together with geographic patterns of mitonuclear discordance, and shared identical or near-identical mtDNA sequences, suggest extensive introgression of mtDNA between the two parapatric mainland subspecies. Under demographic hypotheses, we would also expect to uncover traces of ncDNA introgression, however, population structure and gene flow analyses revealed little nuclear admixture. Furthermore, we found inconsistent estimates of the timing of population expansion and that of the most recent common ancestor for the clade containing introgressed haplotypes. Without a clear demographic explanation, we also examined whether introgression likely arises from adaptation. We found that five mtDNA genes contained fixed amino acid differences between introgressed and non-introgressed individuals, including putative positive selection found in one codon, although this did not show introgression. While our evidence for rejecting demographic hypotheses is arguably stronger than that for rejecting adaptation, we find no definitive support for either explanation. Future efforts will focus on larger-scale resequencing to decipher the underlying causes of discordant mitonuclear introgression in this system.
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Affiliation(s)
- Xiuguang Mao
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200062, China; Institute of Eco-Chongming (IEC), East China Normal University, Shanghai 200062, China.
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK.
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5
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Reynolds RG, Kolbe JJ, Glor RE, López-Darias M, Gómez Pourroy CV, Harrison AS, de Queiroz K, Revell LJ, Losos JB. Phylogeographic and phenotypic outcomes of brown anole colonization across the Caribbean provide insight into the beginning stages of an adaptive radiation. J Evol Biol 2020; 33:468-494. [PMID: 31872929 DOI: 10.1111/jeb.13581] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Accepted: 12/18/2019] [Indexed: 01/15/2023]
Abstract
Some of the most important insights into the ecological and evolutionary processes of diversification and speciation have come from studies of island adaptive radiations, yet relatively little research has examined how these radiations initiate. We suggest that Anolis sagrei is a candidate for understanding the origins of the Caribbean Anolis adaptive radiation and how a colonizing anole species begins to undergo allopatric diversification, phenotypic divergence and, potentially, speciation. We undertook a genomic and morphological analysis of representative populations across the entire native range of A. sagrei, finding that the species originated in the early Pliocene, with the deepest divergence occurring between western and eastern Cuba. Lineages from these two regions subsequently colonized the northern Caribbean. We find that at the broadest scale, populations colonizing areas with fewer closely related competitors tend to evolve larger body size and more lamellae on their toepads. This trend follows expectations for post-colonization divergence from progenitors and convergence in allopatry, whereby populations freed from competition with close relatives evolve towards common morphological and ecological optima. Taken together, our results show a complex history of ancient and recent Cuban diaspora with populations on competitor-poor islands evolving away from their ancestral Cuban populations regardless of their phylogenetic relationships, thus providing insight into the original diversification of colonist anoles at the beginning of the radiation. Our research also supplies an evolutionary framework for the many studies of this increasingly important species in ecological and evolutionary research.
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Affiliation(s)
| | - Jason J Kolbe
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, USA
| | - Richard E Glor
- Herpetology Division, Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KA, USA
| | | | | | - Alexis S Harrison
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Kevin de Queiroz
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Liam J Revell
- Department of Biology, University of Massachusetts Boston, Boston, MA, USA.,Departamento de Ecología, Facultad de Ciencias, Universidad Católica de la Santísima Concepción, Concepción, Chile
| | - Jonathan B Losos
- Department of Biology, Washington University in Saint Louis, Saint Louis, MO, USA
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6
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Gürün K, Furman A, Juste J, Ramos Pereira MJ, Palmeirim JM, Puechmaille SJ, Hulva P, Presetnik P, Hamidovic D, Ibáñez C, Karataş A, Allegrini B, Georgiakakis P, Scaravelli D, Uhrin M, Nicolaou H, Abi-Said MR, Nagy ZL, Gazaryan S, Bilgin R. A continent-scale study of the social structure and phylogeography of the bent-wing bat, Miniopterus schreibersii (Mammalia: Chiroptera), using new microsatellite data. J Mammal 2019. [DOI: 10.1093/jmammal/gyz153] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
AbstractMiniopterus schreibersii is a cave-dwelling bat species with a wide distribution in the western Palearctic spanning southern and central Europe, North Africa, Anatolia, the Middle East, and the Caucasus. We investigated the social structure and its effects on the genetic makeup of this species, using 10 nuclear microsatellite markers and a partial fragment of the mitochondrial cytochrome b gene. Samples were examined from the species' entire circum-Mediterranean range. Local structuring that was previously detected among populations of M. schreibersii using mitochondrial markers was not observed for microsatellite markers, indicating male-biased dispersal for the species. Some support was found for postglacial expansions in Europe, with Anatolia potentially acting as the primary refugium during the Last Glacial Maximum (LGM). However, support for this hypothesis is not as strong as that previously detected using mitochondrial DNA markers. This is likely due to the diminishing effect of male-mediated dispersal, replenishing the nuclear diversity faster than the mitochondrial diversity in regions that are relatively far from the glacial refugia.
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Affiliation(s)
- Kanat Gürün
- Institute of Environmental Sciences, Boğaziçi University, Bebek, Istanbul 34342, Turkey
| | - Andrzej Furman
- Institute of Environmental Sciences, Boğaziçi University, Bebek, Istanbul 34342, Turkey
| | - Javier Juste
- Estación Biológica de Doñana (CSIC), Avda. Américo Vespucio s/n, Seville 41092, Spain
| | - Maria J Ramos Pereira
- CIBER of Epidemiology and Public Health (CIBERESP), Madrid 28029, Spain
- Department of Zoology, Institute of Biosciences, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, Porto Alegre, RS 91540-000, Brazil
- Centre for Environmental and Marine Studies, Wildlife Research Unit, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Jorge M Palmeirim
- Center for Ecology, Evolution and Environmental Change, Dept. Biologia Animal, Faculdade de Ciencias, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Sebastien J Puechmaille
- University College Dublin, School of Biological and Environmental Sciences, Belfield, Dublin 4, Ireland
- Zoology Institute, University of Greifswald, 17489 Greifswald, Germany
- Chauves-souris Aveyron (CSA), 12310, Vimenet, France
| | - Pavel Hulva
- Department of Zoology, Faculty of Science, Charles University in Prague, Viničná 7, CZ-128 44 Praha 2, Czech Republic
- Department of Biology and Ecology, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic
| | - Primoz Presetnik
- Centre for Cartography of Fauna and Flora, Ljubljana Office, Klunova 3, SI-1000, Ljubljana, Slovenia
| | - Daniela Hamidovic
- Croatian Biospeleological Society, Zagreb, Demetrova 1, 10000 Zagreb, Croatia
| | - Carlos Ibáñez
- Estación Biológica de Doñana (CSIC), Avda. Américo Vespucio s/n, Seville 41092, Spain
| | - Ahmet Karataş
- Department of Biology, Niğde University, Niğde 51100, Turkey
| | | | - Panagiotis Georgiakakis
- Natural History Museum of Crete, University of Crete, Knossos Ave., P.O. Box: 2208, GR71 409 Irakleion, Crete, Greece
| | - Dino Scaravelli
- Department Veterinary Medical Sciences, University of Bologna, via Tolara di Sopra 50, 40064 Ozzano dell'Emilia (BO), Italy
| | - Marcel Uhrin
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Moyzesova 11, SK-040 01 Košice, Slovakia
- Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Kamycká 1176, 165 21 Praha 6, Czech Republic
| | - Haris Nicolaou
- Parks and Environment Sector, Forestry Department, Ministry of Agriculture, Natural Resources and Environment, 1414 Nicosia, Cyprus
| | - Mounir R Abi-Said
- Animal Encounter, Aley, Lebanon
- Faculty of Sciences II, Lebanese University, Al Fanar, 90656 Jdeidet, Lebanon
| | | | - Suren Gazaryan
- Institute of Ecology of Mountain Territories RAS, Armand 37A360000, Nalchik, Russia
| | - Raşit Bilgin
- Institute of Environmental Sciences, Boğaziçi University, Bebek, Istanbul 34342, Turkey
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7
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McKenzie JL, Chung DJ, Healy TM, Brennan RS, Bryant HJ, Whitehead A, Schulte PM. Mitochondrial Ecophysiology: Assessing the Evolutionary Forces That Shape Mitochondrial Variation. Integr Comp Biol 2019; 59:925-937. [PMID: 31282925 DOI: 10.1093/icb/icz124] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The mitonuclear species concept hypothesizes that incompatibilities between interacting gene products of the nuclear and mitochondrial genomes are a major factor establishing and maintaining species boundaries. However, most of the data available to test this concept come from studies of genetic variation in mitochondrial DNA, and clines in the mitochondrial genome across contact zones can be produced by a variety of forces. Here, we show that using a combination of population genomic analyses of the nuclear and mitochondrial genomes and studies of mitochondrial function can provide insight into the relative roles of neutral processes, adaptive evolution, and mitonuclear incompatibility in establishing and maintaining mitochondrial clines, using Atlantic killifish (Fundulus heteroclitus) as a case study. There is strong evidence for a role of secondary contact following the last glaciation in shaping a steep mitochondrial cline across a contact zone between northern and southern subspecies of killifish, but there is also evidence for a role of adaptive evolution in driving differentiation between the subspecies in a variety of traits from the level of the whole organism to the level of mitochondrial function. In addition, studies are beginning to address the potential for mitonuclear incompatibilities in admixed populations. However, population genomic studies have failed to detect evidence for a strong and pervasive influence of mitonuclear incompatibilities, and we suggest that polygenic selection may be responsible for the complex patterns observed. This case study demonstrates that multiple forces can act together in shaping mitochondrial clines, and illustrates the challenge of disentangling their relative roles.
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Affiliation(s)
- Jessica L McKenzie
- Department of Zoology and Biodiversity Research Centre, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Dillon J Chung
- Department of Zoology and Biodiversity Research Centre, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Timothy M Healy
- Department of Zoology and Biodiversity Research Centre, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Reid S Brennan
- Department of Environmental Toxicology, University of California-Davis, 4138 Meyer Hall, 1 Shields Avenue, Davis, CA 95616, USA
| | - Heather J Bryant
- Department of Zoology and Biodiversity Research Centre, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Andrew Whitehead
- Department of Environmental Toxicology, University of California-Davis, 4138 Meyer Hall, 1 Shields Avenue, Davis, CA 95616, USA
| | - Patricia M Schulte
- Department of Zoology and Biodiversity Research Centre, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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8
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Zhang D, Tang L, Cheng Y, Hao Y, Xiong Y, Song G, Qu Y, Rheindt FE, Alström P, Jia C, Lei F. 'Ghost introgression' as a cause of deep mitochondrial divergence in a bird species complex. Mol Biol Evol 2019; 36:2375-2386. [PMID: 31364717 DOI: 10.1093/molbev/msz170] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Revised: 05/15/2019] [Accepted: 07/08/2019] [Indexed: 12/19/2022] Open
Abstract
In the absence of nuclear-genomic differentiation between two populations, deep mitochondrial divergence (DMD) is a form of mito-nuclear discordance. Such instances of DMD are rare and might variably be explained by unusual cases of female-linked selection, by male-biased dispersal, by 'speciation reversal' or by mitochondrial capture through genetic introgression. Here we analyze DMD in an Asian Phylloscopus leaf warbler (Aves: Phylloscopidae) complex. Bioacoustic, morphological and genomic data demonstrate close similarity between the taxa affinis and occisinensis, even though DMD previously led to their classification as two distinct species. Using population genomic and comparative genomic methods on 45 whole genomes, including historical reconstructions of effective population size, genomic peaks of differentiation and genomic linkage, we infer that the form affinis is likely the product of a westward expansion in which it replaced a now-extinct congener that was the donor of its mtDNA and small portions of its nuclear genome. This study provides strong evidence of 'ghost introgression' as the cause of DMD, and we suggest that 'ghost introgression' may be a widely overlooked phenomenon in nature.
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Affiliation(s)
- Dezhi Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Linfang Tang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yalin Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yan Hao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Ying Xiong
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, Singapore, Republic of Singapore
| | - Per Alström
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18 D, Uppsala, Sweden.,Swedish Species Information Centre, Swedish University of Agricultural Sciences, Box 7007, Uppsala, Sweden
| | - Chenxi Jia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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9
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Hinojosa JC, Koubínová D, Szenteczki MA, Pitteloud C, Dincă V, Alvarez N, Vila R. A mirage of cryptic species: Genomics uncover striking mitonuclear discordance in the butterfly Thymelicus sylvestris. Mol Ecol 2019; 28:3857-3868. [PMID: 31233646 DOI: 10.1111/mec.15153] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 06/07/2019] [Indexed: 10/26/2022]
Abstract
Mitochondrial DNA (mtDNA) sequencing has led to an unprecedented rise in the identification of cryptic species. However, it is widely acknowledged that nuclear DNA (nuDNA) sequence data are also necessary to properly define species boundaries. Next generation sequencing techniques provide a wealth of nuclear genomic data, which can be used to ascertain both the evolutionary history and taxonomic status of putative cryptic species. Here, we focus on the intriguing case of the butterfly Thymelicus sylvestris (Lepidoptera: Hesperiidae). We identified six deeply diverged mitochondrial lineages; three distributed all across Europe and found in sympatry, suggesting a potential case of cryptic species. We then sequenced these six lineages using double-digest restriction-site associated DNA sequencing (ddRADseq). Nuclear genomic loci contradicted mtDNA patterns and genotypes generally clustered according to geography, i.e., a pattern expected under the assumption of postglacial recolonization from different refugia. Further analyses indicated that this strong mtDNA/nuDNA discrepancy cannot be explained by incomplete lineage sorting, sex-biased asymmetries, NUMTs, natural selection, introgression or Wolbachia-mediated genetic sweeps. We suggest that this mitonuclear discordance was caused by long periods of geographic isolation followed by range expansions, homogenizing the nuclear but not the mitochondrial genome. These results highlight T. sylvestris as a potential case of multiple despeciation and/or lineage fusion events. We finally argue, since mtDNA and nuDNA do not necessarily follow the same mechanisms of evolution, their respective evolutionary history reflects complementary aspects of past demographic and biogeographic events.
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Affiliation(s)
| | - Darina Koubínová
- Unit of Research and Collection, Museum of Natural History, Geneva, Switzerland
| | - Mark A Szenteczki
- Laboratory of Functional Ecology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Camille Pitteloud
- Department of Environmental Systems Sciences, Institute of Terrestrial Ecosystems, ETHZ, Zürich, Switzerland
| | - Vlad Dincă
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Nadir Alvarez
- Unit of Research and Collection, Museum of Natural History, Geneva, Switzerland
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-UPF), Barcelona, Spain
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10
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García-Verdugo C, Caujapé-Castells J, Mairal M, Monroy P. How repeatable is microevolution on islands? Patterns of dispersal and colonization-related plant traits in a phylogeographical context. ANNALS OF BOTANY 2019; 123:557-568. [PMID: 30380011 PMCID: PMC6377097 DOI: 10.1093/aob/mcy191] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 10/04/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND AND AIMS Archipelagos provide a valuable framework for investigating phenotypic evolution under different levels of geographical isolation. Here, we analysed two co-distributed, widespread plant lineages to examine if incipient island differentiation follows parallel patterns of variation in traits related to dispersal and colonization. METHODS Twenty-one populations of two anemochorous Canarian endemics, Kleinia neriifolia and Periploca laevigata, were sampled to represent mainland congeners and two contrasting exposures across all the main islands. Leaf size, seed size and dispersability (estimated as diaspore terminal velocity) were characterized in each population. For comparison, dispersability was also measured in four additional anemochorous island species. Plastid DNA data were used to infer genetic structure and to reconstruct the phylogeographical pattern of our focal species. KEY RESULTS In both lineages, mainland-island phenotypic divergence probably started within a similar time frame (i.e. Plio-Pleistocene). Island colonization implied parallel increases in leaf size and dispersability, but seed size showed opposite patterns of variation between Kleinia and Periploca species pairs. Furthermore, dispersability in our focal species was low when compared with other island plants, mostly due to large diaspore sizes. At the archipelago scale, island exposure explained a significant variation in leaf size across islands, but not in dispersability or seed size. Combined analyses of genetic and phenotypic data revealed two consistent patterns: (1) extensive within-island but very limited among-island dispersal, and (2) recurrent phenotypic differentiation between older (central) and younger (peripheral) island populations. CONCLUSIONS Leaf size follows a more predictable pattern than dispersability, which is affected by stochastic shifts in seed size. Increased dispersability is associated with high population connectivity at the island scale, but does not preclude allopatric divergence among islands. In sum, phenotypic convergent patterns between species suggest a major role of selection, but deviating traits also indicate the potential contribution of random processes, particularly on peripheral islands.
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Affiliation(s)
- Carlos García-Verdugo
- Departamento de Biodiversidad Molecular y Banco de ADN, Jardín Botánico Canario ‘Viera y Clavijo’ – Unidad Asociada CSIC, Cabildo de Gran Canaria, Camino del Palmeral 15 de Tafira Alta, Las Palmas de Gran Canaria, Spain
- Institut Mediterrani d’Estudis Avançats (CSIC-UIB), C/Miquel Marqués, Esporles, Balearic Islands, Spain
| | - Juli Caujapé-Castells
- Departamento de Biodiversidad Molecular y Banco de ADN, Jardín Botánico Canario ‘Viera y Clavijo’ – Unidad Asociada CSIC, Cabildo de Gran Canaria, Camino del Palmeral 15 de Tafira Alta, Las Palmas de Gran Canaria, Spain
| | - Mario Mairal
- Department of Botany, Charles University Faculty of Science, Albertov, Praha, Czech Republic
| | - Pedro Monroy
- Departamento de Biodiversidad Molecular y Banco de ADN, Jardín Botánico Canario ‘Viera y Clavijo’ – Unidad Asociada CSIC, Cabildo de Gran Canaria, Camino del Palmeral 15 de Tafira Alta, Las Palmas de Gran Canaria, Spain
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11
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Lee-Yaw JA, Grassa CJ, Joly S, Andrew RL, Rieseberg LH. An evaluation of alternative explanations for widespread cytonuclear discordance in annual sunflowers (Helianthus). THE NEW PHYTOLOGIST 2019; 221:515-526. [PMID: 30136727 DOI: 10.1111/nph.15386] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Accepted: 07/05/2018] [Indexed: 05/03/2023]
Abstract
Cytonuclear discordance is commonly observed in phylogenetic studies, yet few studies have tested whether these patterns reflect incomplete lineage sorting or organellar introgression. Here, we used whole-chloroplast sequence data in combination with over 1000 nuclear single-nucleotide polymorphisms to clarify the extent of cytonuclear discordance in wild annual sunflowers (Helianthus), and to test alternative explanations for such discordance. Our phylogenetic analyses indicate that cytonuclear discordance is widespread within this group, both in terms of the relationships among species and among individuals within species. Simulations of chloroplast evolution show that incomplete lineage sorting cannot explain these patterns in most cases. Instead, most of the observed discordance is better explained by cytoplasmic introgression. Molecular tests of evolution further indicate that selection may have played a role in driving patterns of plastid variation - although additional experimental work is needed to fully evaluate the importance of selection on organellar variants in different parts of the geographic range. Overall, this study represents one of the most comprehensive tests of the drivers of cytonuclear discordance and highlights the potential for gene flow to lead to extensive organellar introgression in hybridizing taxa.
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Affiliation(s)
- Julie A Lee-Yaw
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Christopher J Grassa
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Harvard University Herbaria, Cambridge, MA, 02138, USA
| | - Simon Joly
- Institut Recherche en Biologie Végétale, QC, H1X 2B2, Canada
- Jardin botanique de Montréal, Department Sciences Biologiques, Université de Montréal, Montréal, QC, H1X 2B2, Canada
| | - Rose L Andrew
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- School of Environmental and Rural Science, University of New England, Armidale, NSW, 2351, Australia
| | - Loren H Rieseberg
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
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12
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Testing Hypotheses of Diversification in Panamanian Frogs and Freshwater Fishes Using Hierarchical Approximate Bayesian Computation with Model Averaging. DIVERSITY 2018. [DOI: 10.3390/d10040120] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Most Neotropical frog and freshwater fish species sampled to date show phylogeographic breaks along the Pacific coast of the Isthmus of Panama, with lineages in Costa Rica and western Panama isolated from central Panama. We examine temporal patterns of diversification of taxa across this ‘western Panama isthmus’ (WPI) break to test hypotheses about the origin of species geographical distributions and genetic structuring in this region. We tested for synchronous diversification of four codistributed frog taxon-pairs and three fish taxon-pairs sharing the WPI break using hierarchical approximate Bayesian computation with model averaging based on mitochondrial DNA sequences. We also estimated lineage divergence times using full-Bayesian models. Several of our results supported synchronous divergences within the frog and freshwater fish assemblages; however, Bayes factor support was equivocal for or against synchronous or asynchronous diversification. Nevertheless, we infer that frog populations were likely isolated by one or multiple Pliocene–Pleistocene events more recently than predicted by previous models, while fish genetic diversity was structured by Pleistocene events. By integrating our results with external information from geology and elevational sea level modeling, we discuss the implications of our findings for understanding the biogeographical scenario of the diversification of Panamanian frogs and fishes. Consistent with the ‘Bermingham/Martin model’ (Molecular Ecology 1998, 7, 499–517), we conclude that the regional fish assemblage was fractured by processes shaping isthmian landscapes during the Pleistocene glaciations, including drainage basin isolation during lowered sea levels.
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13
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Wang GD, Zhang BL, Zhou WW, Li YX, Jin JQ, Shao Y, Yang HC, Liu YH, Yan F, Chen HM, Jin L, Gao F, Zhang Y, Li H, Mao B, Murphy RW, Wake DB, Zhang YP, Che J. Selection and environmental adaptation along a path to speciation in the Tibetan frog Nanorana parkeri. Proc Natl Acad Sci U S A 2018; 115:E5056-E5065. [PMID: 29760079 PMCID: PMC5984489 DOI: 10.1073/pnas.1716257115] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Tibetan frogs, Nanorana parkeri, are differentiated genetically but not morphologically along geographical and elevational gradients in a challenging environment, presenting a unique opportunity to investigate processes leading to speciation. Analyses of whole genomes of 63 frogs reveal population structuring and historical demography, characterized by highly restricted gene flow in a narrow geographic zone lying between matrilines West (W) and East (E). A population found only along a single tributary of the Yalu Zangbu River has the mitogenome only of E, whereas nuclear genes of W comprise 89-95% of the nuclear genome. Selection accounts for 579 broadly scattered, highly divergent regions (HDRs) of the genome, which involve 365 genes. These genes fall into 51 gene ontology (GO) functional classes, 14 of which are likely to be important in driving reproductive isolation. GO enrichment analyses of E reveal many overrepresented functional categories associated with adaptation to high elevations, including blood circulation, response to hypoxia, and UV radiation. Four genes, including DNAJC8 in the brain, TNNC1 and ADORA1 in the heart, and LAMB3 in the lung, differ in levels of expression between low- and high-elevation populations. High-altitude adaptation plays an important role in maintaining and driving continuing divergence and reproductive isolation. Use of total genomes enabled recognition of selection and adaptation in and between populations, as well as documentation of evolution along a stepped cline toward speciation.
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Affiliation(s)
- Guo-Dong Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Bao-Lin Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, Yunnan, China
| | - Wei-Wei Zhou
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, 05282 Nay Pyi Taw, Myanmar
| | - Yong-Xin Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, Yunnan, China
| | - Jie-Qiong Jin
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - He-Chuan Yang
- Human Genetics, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore 138672, Singapore
| | - Yan-Hu Liu
- Laboratory for Conservation and Utilization of Bio-Resources & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, China
| | - Fang Yan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Hong-Man Chen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Li Jin
- Key Laboratory of Freshwater Fish Reproduction and Development of the Ministry of Education and Key Laboratory of Aquatic Science of Chongqing, Southwest University School of Life Sciences, Chongqing 400715, China
| | - Feng Gao
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yaoguang Zhang
- Key Laboratory of Freshwater Fish Reproduction and Development of the Ministry of Education and Key Laboratory of Aquatic Science of Chongqing, Southwest University School of Life Sciences, Chongqing 400715, China
| | - Haipeng Li
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Bingyu Mao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Robert W Murphy
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, ON, Canada M5S 2C6
| | - David B Wake
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720-3160
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China;
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Jing Che
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China;
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, 05282 Nay Pyi Taw, Myanmar
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Irwin DE. Sex chromosomes and speciation in birds and other ZW systems. Mol Ecol 2018; 27:3831-3851. [PMID: 29443419 DOI: 10.1111/mec.14537] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 02/03/2018] [Accepted: 02/06/2018] [Indexed: 01/01/2023]
Abstract
Theory and empirical patterns suggest a disproportionate role for sex chromosomes in evolution and speciation. Focusing on ZW sex determination (females ZW, males ZZ; the system in birds, many snakes, and lepidopterans), I review how evolutionary dynamics are expected to differ between the Z, W and the autosomes, discuss how these differences may lead to a greater role of the sex chromosomes in speciation and use data from birds to compare relative evolutionary rates of sex chromosomes and autosomes. Neutral mutations, partially or completely recessive beneficial mutations, and deleterious mutations under many conditions are expected to accumulate faster on the Z than on autosomes. Sexually antagonistic polymorphisms are expected to arise on the Z, raising the possibility of the spread of preference alleles. The faster accumulation of many types of mutations and the potential for complex evolutionary dynamics of sexually antagonistic traits and preferences contribute to a role for the Z chromosome in speciation. A quantitative comparison among a wide variety of bird species shows that the Z tends to have less within-population diversity and greater between-species differentiation than the autosomes, likely due to both adaptive evolution and a greater rate of fixation of deleterious alleles. The W chromosome also shows strong potential to be involved in speciation, in part because of its co-inheritance with the mitochondrial genome. While theory and empirical evidence suggest a disproportionate role for sex chromosomes in speciation, the importance of sex chromosomes is moderated by their small size compared to the whole genome.
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Affiliation(s)
- Darren E Irwin
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
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15
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Marcus JM. Our love-hate relationship with DNA barcodes, the Y2K problem, and the search for next generation barcodes. AIMS GENETICS 2018; 5:1-23. [PMID: 31435510 PMCID: PMC6690253 DOI: 10.3934/genet.2018.1.1] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 01/11/2018] [Indexed: 01/27/2023]
Abstract
DNA barcodes are very useful for species identification especially when identification by traditional morphological characters is difficult. However, the short mitochondrial and chloroplast barcodes currently in use often fail to distinguish between closely related species, are prone to lateral transfer, and provide inadequate phylogenetic resolution, particularly at deeper nodes. The deficiencies of short barcode identifiers are similar to the deficiencies of the short year identifiers that caused the Y2K problem in computer science. The resolution of the Y2K problem was to increase the size of the year identifiers. The performance of conventional mitochondrial COI barcodes for phylogenetics was compared with the performance of complete mitochondrial genomes and nuclear ribosomal RNA repeats obtained by genome skimming for a set of caddisfly taxa (Insect Order Trichoptera). The analysis focused on Trichoptera Family Hydropsychidae, the net-spinning caddisflies, which demonstrates many of the frustrating limitations of current barcodes. To conduct phylogenetic comparisons, complete mitochondrial genomes (15 kb each) and nuclear ribosomal repeats (9 kb each) from six caddisfly species were sequenced, assembled, and are reported for the first time. These sequences were analyzed in comparison with eight previously published trichopteran mitochondrial genomes and two triochopteran rRNA repeats, plus outgroup sequences from sister clade Lepidoptera (butterflies and moths). COI trees were not well-resolved, had low bootstrap support, and differed in topology from prior phylogenetic analyses of the Trichoptera. Phylogenetic trees based on mitochondrial genomes or rRNA repeats were well-resolved with high bootstrap support and were largely congruent with each other. Because they are easily sequenced by genome skimming, provide robust phylogenetic resolution at various phylogenetic depths, can better distinguish between closely related species, and (in the case of mitochondrial genomes), are backwards compatible with existing mitochondrial barcodes, it is proposed that mitochondrial genomes and rRNA repeats be used as next generation DNA barcodes.
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Affiliation(s)
- Jeffrey M. Marcus
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, Canada, R3T 2N2
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16
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Thielsch A, Knell A, Mohammadyari A, Petrusek A, Schwenk K. Divergent clades or cryptic species? Mito-nuclear discordance in a Daphnia species complex. BMC Evol Biol 2017; 17:227. [PMID: 29166859 PMCID: PMC5700674 DOI: 10.1186/s12862-017-1070-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 11/08/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genetically divergent cryptic species are frequently detected by molecular methods. These discoveries are often a byproduct of molecular barcoding studies in which fragments of a selected marker are used for species identification. Highly divergent mitochondrial lineages and putative cryptic species are even detected in intensively studied animal taxa, such as the crustacean genus Daphnia. Recently, eleven such lineages, exhibiting genetic distances comparable to levels observed among well-defined species, were recorded in the D. longispina species complex, a group that contains several key taxa of freshwater ecosystems. We tested if three of those lineages represent indeed distinct species, by analyzing patterns of variation of ten nuclear microsatellite markers in six populations. RESULTS We observed a discordant pattern between mitochondrial and nuclear DNA, as all individuals carrying one of the divergent mitochondrial lineages grouped at the nuclear level with widespread, well-recognized species coexisting at the same localities (Daphnia galeata, D. longispina, and D. cucullata). CONCLUSIONS A likely explanation for this pattern is the introgression of the mitochondrial genome of undescribed taxa into the common species, either in the distant past or after long-distance dispersal. The occurrence of highly divergent but rare mtDNA lineages in the gene pool of widespread species would suggest that hybridization and introgression in the D. longispina species complex is frequent even across large phylogenetic distances, and that discoveries of such distinct clades must be interpreted with caution. However, maintenance of ancient polymorphisms through selection is another plausible alternative that may cause the observed discordance and cannot be entirely excluded.
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Affiliation(s)
- Anne Thielsch
- Institute for Environmental Sciences, Molecular Ecology, University of Koblenz-Landau, Landau in der Pfalz, Germany.
| | - Alexis Knell
- Institute for Environmental Sciences, Molecular Ecology, University of Koblenz-Landau, Landau in der Pfalz, Germany
| | - Ali Mohammadyari
- Faculty of Science, Department of Biology, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Adam Petrusek
- Faculty of Science, Department of Ecology, Charles University, Prague, Czechia
| | - Klaus Schwenk
- Institute for Environmental Sciences, Molecular Ecology, University of Koblenz-Landau, Landau in der Pfalz, Germany
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17
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Salvi D, Pinho C, Harris DJ. Digging up the roots of an insular hotspot of genetic diversity: decoupled mito-nuclear histories in the evolution of the Corsican-Sardinian endemic lizard Podarcis tiliguerta. BMC Evol Biol 2017; 17:63. [PMID: 28253846 PMCID: PMC5335832 DOI: 10.1186/s12862-017-0899-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Accepted: 01/31/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mediterranean islands host a disproportionately high level of biodiversity and endemisms. Growing phylogeographic evidence on island endemics has unveiled unexpectedly complex patterns of intra-island diversification, which originated at diverse spatial and temporal scales. We investigated multilocus genetic variation of the Corsican-Sardinian endemic lizard Podarcis tiliguerta with the aim of shedding more light on the evolutionary processes underlying the origin of Mediterranean island biodiversity. RESULTS We analysed DNA sequences of mitochondrial (12S and nd4) and nuclear (acm4 and mc1r) gene fragments in 174 individuals of P. tiliguerta from 81 localities across the full range of the species in a geographic and genealogical framework. We found surprisingly high genetic diversity both at mitochondrial and nuclear loci. Seventeen reciprocally monophyletic allopatric mitochondrial haplogroups were sharply divided into four main mitochondrial lineages (two in Corsica and two in Sardinia) of Miocene origin. In contrast, shallow divergence and shared diversity within and between islands was observed at the nuclear loci. We evaluated alternative biogeographic and evolutionary scenarios to explain such profound discordance in spatial and phylogenetic patterning between mitochondrial and nuclear genomes. While neutral models provided unparsimonious explanations for the observed pattern, the hypothesis of environmental selection driving mitochondrial divergence in the presence of nuclear gene flow is favoured. CONCLUSIONS Our study on the genetic variation of P. tiliguerta reveals surprising levels of diversity underlining a complex phylogeographic pattern with a striking example of mito-nuclear discordance. These findings have profound implications, not only for the taxonomy and conservation of P. tiliguerta. Growing evidence on deep mitochondrial breaks in absence of geographic barriers and of climatic factors associated to genetic variation of Corsican-Sardinian endemics warrants additional investigation on the potential role of environmental selection driving the evolution of diversity hotspots within Mediterranean islands.
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Affiliation(s)
- Daniele Salvi
- Department of Health, Life and Environmental Sciences, University of L'Aquila, 67100 Coppito, L'Aquila, Italy. .,CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661, Vairão, Portugal.
| | - Catarina Pinho
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
| | - D James Harris
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
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18
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Ball SE, Bovero S, Sotgiu G, Tessa G, Angelini C, Bielby J, Durrant C, Favelli M, Gazzaniga E, Garner TWJ. Islands within an island: Population genetic structure of the endemic Sardinian newt, Euproctus platycephalus. Ecol Evol 2017; 7:1190-1211. [PMID: 28303189 PMCID: PMC5306002 DOI: 10.1002/ece3.2665] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 10/21/2016] [Indexed: 12/04/2022] Open
Abstract
The identification of historic and contemporary barriers to dispersal is central to the conservation of endangered amphibians, but may be hindered by their complex life history and elusive nature. The complementary information generated by mitochondrial (mtDNA) and microsatellite markers generates a valuable tool in elucidating population structure and the impact of habitat fragmentation. We applied this approach to the study of an endangered montane newt, Euproctus platycephalus. Endemic to the Mediterranean island of Sardinia, it is threatened by anthropogenic activity, disease, and climate change. We have demonstrated a clear hierarchy of structure across genetically divergent and spatially distinct subpopulations. Divergence between three main mountain regions dominated genetic partitioning with both markers. Mitochondrial phylogeography revealed a deep division dating to ca. 1 million years ago (Mya), isolating the northern region, and further differentiation between the central and southern regions ca. 0.5 Mya, suggesting an association with Pleistocene severe glacial oscillations. Our findings are consistent with a model of southward range expansion during glacial periods, with postglacial range retraction to montane habitat and subsequent genetic isolation. Microsatellite markers revealed further strong population structure, demonstrating significant divergence within the central region, and partial differentiation within the south. The northern population showed reduced genetic diversity. Discordance between mitochondrial and microsatellite markers at this scale indicated a further complexity of population structure, in keeping with male-biased dispersal and female philopatry. Our study underscores the need to elucidate cryptic population structure in the ecology and conservation strategies for endangered island-restricted amphibians, especially in the context of disease and climate change.
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Affiliation(s)
- Sarah E. Ball
- Institute of ZoologyThe Zoological Society of LondonLondonUK
| | - Stefano Bovero
- Zirichiltaggi S. W. C. Non‐profit Association for Wildlife ConservationSassariItaly
| | - Giuseppe Sotgiu
- Zirichiltaggi S. W. C. Non‐profit Association for Wildlife ConservationSassariItaly
| | - Giulia Tessa
- Zirichiltaggi S. W. C. Non‐profit Association for Wildlife ConservationSassariItaly
- Dipartimento di Scienze della Vita e Biologia dei SistemiUniversita degli Studi di TorinoTorinoItaly
| | - Claudio Angelini
- Zirichiltaggi S. W. C. Non‐profit Association for Wildlife ConservationSassariItaly
| | - Jon Bielby
- Institute of ZoologyThe Zoological Society of LondonLondonUK
- Zirichiltaggi S. W. C. Non‐profit Association for Wildlife ConservationSassariItaly
| | | | - Marco Favelli
- Zirichiltaggi S. W. C. Non‐profit Association for Wildlife ConservationSassariItaly
| | - Enrico Gazzaniga
- Zirichiltaggi S. W. C. Non‐profit Association for Wildlife ConservationSassariItaly
| | - Trenton W. J. Garner
- Institute of ZoologyThe Zoological Society of LondonLondonUK
- Zirichiltaggi S. W. C. Non‐profit Association for Wildlife ConservationSassariItaly
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Bagley JC, Matamoros WA, McMahan CD, Tobler M, Chakrabarty P, Johnson JB. Phylogeography and species delimitation in convict cichlids (Cichlidae:Amatitlania): implications for taxonomy and Plio-Pleistocene evolutionary history in Central America. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12845] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Justin C. Bagley
- Evolutionary Ecology Laboratories; Department of Biology; Brigham Young University; Provo UT 84602 USA
| | - Wilfredo A. Matamoros
- Facultad de Ciencias Biológicas, Museo de Zoología; Colección de Ictiología; Universidad de Ciencias y Artes de Chiapas; CP 29039 Tuxtla Gutierrez Chiapas México
| | - Caleb D. McMahan
- Museum of Natural Science (Ichthyology); Department of Biological Sciences; Louisiana State University; Baton Rouge LA 70803 USA
- The Field Museum of Natural History; 1400 S. Lake Shore Drive Chicago IL 60605 USA
| | - Michael Tobler
- Division of Biology; Kansas State University; Manhattan KS 66506 USA
| | - Prosanta Chakrabarty
- Museum of Natural Science (Ichthyology); Department of Biological Sciences; Louisiana State University; Baton Rouge LA 70803 USA
| | - Jerald B. Johnson
- Evolutionary Ecology Laboratories; Department of Biology; Brigham Young University; Provo UT 84602 USA
- Monte L. Bean Life Science Museum; Brigham Young University; Provo UT 84602 USA
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20
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Sun Y, Surget-Groba Y, Gao S. Divergence maintained by climatic selection despite recurrent gene flow: a case study of Castanopsis carlesii (Fagaceae). Mol Ecol 2016; 25:4580-92. [PMID: 27447352 DOI: 10.1111/mec.13764] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Revised: 06/18/2016] [Accepted: 07/02/2016] [Indexed: 01/20/2023]
Abstract
Local adaptation to different environments has the potential to maintain divergence between populations despite recurrent gene flow and is an important driver for generating biological diversity. In this study, we investigate the role of adaptation in the maintenance of two parapatric varieties of a forest tree. We used sequence variation of chloroplastic DNA and restriction site-associated DNA to investigate the genetic structure of two varieties of Castanopsis carlesii in subtropical China and relate it to climatic variation. We used niche reconstruction methods to investigate niche differentiation between the two varieties and to estimate the past distribution of this species. A deep divergence was observed between the two varieties, but evidence of introgression and genetic admixture was detected in two phenotypically and geographically intermediate populations. Niche reconstruction suggests that the distribution of the two varieties was disjunct during periods of global cooling and that the two varieties occupy significantly different niches. The genetic structure was mainly driven by environmental factors, and 13 outlier loci under divergent selection were correlated with climatic variation. These results suggest that the two varieties evolved in allopatry and came back into secondary contact after the last glacial maximum and that they are an evolutionary example of divergence maintained by climatic selection despite recurrent gene flow.
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Affiliation(s)
- Ye Sun
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China. , .,Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China. ,
| | - Yann Surget-Groba
- Institut des Sciences de la Forêt Tempérée, Université du Québec en Outaouais, 58 rue Principale, Ripon, Quebec, J0V 1V0, Canada.,Quebec Centre for Biodiversity Science, McGill University, 1205 Dr. Penfield Avenue, Montreal, Quebec, H3A 1B1, Canada
| | - Shaoxiong Gao
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
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21
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Mende MB, Bartel M, Hundsdoerfer AK. A comprehensive phylogeography of the Hyles euphorbiae complex (Lepidoptera: Sphingidae) indicates a 'glacial refuge belt'. Sci Rep 2016; 6:29527. [PMID: 27439775 PMCID: PMC4954964 DOI: 10.1038/srep29527] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 06/08/2016] [Indexed: 12/20/2022] Open
Abstract
We test the morphology based hypothesis that the Western Palaearctic spurge hawkmoths represent two species, the Eurasian H. euphorbiae and Afro-Macaronesian H. tithymali. It has been suggested that these species merged into several hybrid swarm populations, although a mitochondrial phylogeography revealed substructure with local differentiation. We analysed a three-gene mt-dataset (889 individuals) and 12 microsatellite loci (892 individuals). Microsatellite analyses revealed an overall weak differentiation and corroborated the superordinate division into two clusters. The data indicate that the populations studied belong to only one species according to the biological species concept, refuting the opening hypothesis. A future taxonomic revision appears necessary to reflect the division into two subgroups. Ancestral mitochondrial polymorphisms are retained in H. euphorbiae, indicating gene flow within a broad 'glacial refuge belt' and ongoing postglacial gene flow. Diverse patterns of extensive mito-nuclear discordance in the Mediterranean and the Middle East presumably evolved by more recent processes. This discordance indicates introgression of H. tithymali-related mitochondrial haplogroups, accompanied (to a lesser degree) by nuclear alleles, into Italian and Aegean H. euphorbiae populations as recently as the late Holocene. The complex mosaic of divergence and reintegration is assumed to have been influenced by locally differing environmental barriers to gene flow.
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Affiliation(s)
- Michael B Mende
- Senckenberg Naturhistorische Sammlungen Dresden, Museum für Tierkunde, Königsbrücker Landstraße 159, D-01109 Dresden, Germany.,Georg-August-Universität Göttingen, Johann-Friedrich-Blumenbach-Institut für Zoologie und Anthropologie, Abteilung für Morphologie, Systematik und Evolutionsbiologie, Berliner Str. 28, D-37073 Göttingen, Germany.,Biodiversität und Klima Forschungszentrum (BiK-F), Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
| | - Manuela Bartel
- Senckenberg Naturhistorische Sammlungen Dresden, Museum für Tierkunde, Königsbrücker Landstraße 159, D-01109 Dresden, Germany
| | - Anna K Hundsdoerfer
- Senckenberg Naturhistorische Sammlungen Dresden, Museum für Tierkunde, Königsbrücker Landstraße 159, D-01109 Dresden, Germany.,Biodiversität und Klima Forschungszentrum (BiK-F), Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
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22
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Simonato M, Martinez-Sañudo I, Cavaletto G, Santoiemma G, Saltarin A, Mazzon L. High genetic diversity in the Culex pipiens complex from a West Nile Virus epidemic area in Southern Europe. Parasit Vectors 2016; 9:150. [PMID: 26979749 PMCID: PMC4791856 DOI: 10.1186/s13071-016-1429-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 03/05/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Culex pipiens complex includes the most widespread mosquito species in the world. Cx. pipiens is the primary vector of the West Nile Virus (WNV) in Europe and North America. Cases of WNV have been recorded in Italy since 1998. In particular, wet areas along the Po River are considered some of the most WNV affected areas in Italy. Here, we analyzed the genetic structure of ten Cx. pipiens populations collected in the last part of the Po River including the Delta area. METHODS We assessed the genetic variability of two mitochondrial markers, cytochrome oxidase 1 (COI) and 2 (COII), for a total of 1200 bp, and one nuclear marker, a fragment of acetylcholinesterase-2 (ace-2), 502 bp long. The effect of the landscape features was evaluated comparing haplotype and nucleotide diversity with the landscape composition. RESULTS The analysis showed a high genetic diversity in both COI and COII gene fragments mainly shared by the populations in the Delta area. The COI-COII network showed that the set of haplotypes found was grouped into three main supported lineages with the higher genetic variability gathered in two of the three lineages. By contrast, ace-2 fragment did not show the same differentiation, displaying alleles grouped in a single clade. Finally, a positive correlation between mitochondrial diversity and natural wetland areas was found. CONCLUSIONS The high mitochondrial genetic diversity found in Cx. pipiens populations from the Po River Delta contrasts with the low variability of inland populations. The different patterns of genetic diversity found comparing mitochondrial and nuclear markers could be explained by factors such as differences in effective population size between markers, sex biased dispersal or lower fitness of dispersing females. Moreover, the correlation between genetic diversity and wetland areas is consistent with ecosystem stability and lack of insecticide pressure characteristic of this habitat. The mtDNA polymorphism found in the Po River Delta is even more interesting due to possible linkages between the mitochondrial lineages and different biting behaviors of the mosquitoes influencing their vector ability of arboviral infections.
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Affiliation(s)
- Mauro Simonato
- Department of Agronomy, Food, Natural Resources, Animals, & Environment (DAFNAE), University of Padua, Viale dell'Università 16, 35020, Legnaro, PD, Italy
| | - Isabel Martinez-Sañudo
- Department of Agronomy, Food, Natural Resources, Animals, & Environment (DAFNAE), University of Padua, Viale dell'Università 16, 35020, Legnaro, PD, Italy
| | - Giacomo Cavaletto
- Department of Agronomy, Food, Natural Resources, Animals, & Environment (DAFNAE), University of Padua, Viale dell'Università 16, 35020, Legnaro, PD, Italy
| | - Giacomo Santoiemma
- Department of Agronomy, Food, Natural Resources, Animals, & Environment (DAFNAE), University of Padua, Viale dell'Università 16, 35020, Legnaro, PD, Italy
| | - Andrea Saltarin
- Istituto Tecnico Agrario "O. Munerati", Via Capello 10, 45010, Sant'Apollinare, RO, Italy
| | - Luca Mazzon
- Department of Agronomy, Food, Natural Resources, Animals, & Environment (DAFNAE), University of Padua, Viale dell'Università 16, 35020, Legnaro, PD, Italy.
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23
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Garnica S, Schön ME, Abarenkov K, Riess K, Liimatainen K, Niskanen T, Dima B, Soop K, Frøslev TG, Jeppesen TS, Peintner U, Kuhnert-Finkernagel R, Brandrud TE, Saar G, Oertel B, Ammirati JF. Determining threshold values for barcoding fungi: lessons from Cortinarius (Basidiomycota), a highly diverse and widespread ectomycorrhizal genus. FEMS Microbiol Ecol 2016; 92:fiw045. [PMID: 26929438 DOI: 10.1093/femsec/fiw045] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Indexed: 11/14/2022] Open
Abstract
Different distance-based threshold selection approaches were used to assess and compare use of the internal transcribed spacer (ITS) region to distinguish among 901 Cortinarius species represented by >3000 collections. Sources of error associated with genetic markers and selection approaches were explored and evaluated using MOTUs from genus and lineage based-alignments. Our study indicates that 1%-2% more species can be distinguished by using the full-length ITS barcode as compared to either the ITS1 or ITS2 regions alone. Optimal threshold values for different picking approaches and genetic marker lengths inferred from a subset of species containing major lineages ranged from 97.0% to 99.5% sequence similarity using clustering optimization and UNITE SH, and from 1% to 2% sequence dissimilarity with CROP. Errors for the optimal cutoff ranged from 0% to 70%, and these can be reduced to a maximum of 22% when excluding species lacking a barcode gap. A threshold value of 99% is suitable for distinguishing species in the majority of lineages in the genus using the entire ITS region but only 90% of the species could be identified using just the ITS1 or ITS2 region. Prior identification of species, lacking barcode gaps and their subsequent separate analyses, maximized the accuracy of threshold approaches.
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Affiliation(s)
- Sigisfredo Garnica
- Institute of Evolution and Ecology, Plant Evolutionary Ecology, University of Tübingen, Auf der Morgenstelle 5, D-72076 Tübingen, Germany
| | - Max Emil Schön
- Institute of Evolution and Ecology, Plant Evolutionary Ecology, University of Tübingen, Auf der Morgenstelle 5, D-72076 Tübingen, Germany
| | - Kessy Abarenkov
- Institute of Ecology and Earth Sciences, University of Tartu, 51005 Tartu, Estonia
| | - Kai Riess
- Institute of Evolution and Ecology, Plant Evolutionary Ecology, University of Tübingen, Auf der Morgenstelle 5, D-72076 Tübingen, Germany
| | - Kare Liimatainen
- Department of Biosciences, Plant Biology, University of Helsinki, PO Box 65, 00014 Lahti, Finland
| | - Tuula Niskanen
- Jodrell Laboratory, Royal Botanic Gardens, Kew, TW9 3DS, UK
| | - Bálint Dima
- Department of Biosciences, Plant Biology, University of Helsinki, PO Box 65, 00014 Lahti, Finland
| | - Karl Soop
- Honorary Research Associate, Swedish Museum of Natural History, Department of Cryptogamic Botany, Naturhistoriska riksmuseet, 104 05 Stockholm, Sweden
| | - Tobias Guldberg Frøslev
- Natural History Museum of Denmark, Center for Geogenetics, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark
| | - Thomas Stjernegaard Jeppesen
- Natural History Museum of Denmark, Collections, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, Denmark
| | - Ursula Peintner
- Institute of Microbiology, University Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | | | - Tor Erik Brandrud
- Department of Landscape Ecology (Oslo), Norwegian Institute for Nature Research, N-Oslo 5, Norway
| | | | - Bernhard Oertel
- INRES, University of Bonn, Auf dem Hügel 6, D-53121 Bonn, Germany
| | - Joseph F Ammirati
- Department of Biology, University of Washington, Seattle, Washington 98195, USA
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24
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Gemmell AP, Marcus JM. A tale of two haplotype groups: Evaluating the New World Junonia ring species hypothesis using the distribution of divergent COI haplotypes. SYSTEMATIC ENTOMOLOGY 2015; 40:532-546. [PMID: 26279602 PMCID: PMC4532355 DOI: 10.1111/syen.12120] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The New World Junonia butterflies are a possible ring species with a circum-Caribbean distribution. Previous reports suggest a steady transition between North and South American forms in Mesoamerica, but in Cuba the forms were thought to co-exist without interbreeding representing the overlapping ends of the ring. Three criteria establish the existence of a ring species: a ring-shaped geographic distribution, gene flow among intervening forms, and genetic isolation in the region of range overlap. We evaluated mitochondrial cytochrome oxidase I haplotypes in Junonia from 9 species in the Western Hemisphere to test the Junonia ring species hypothesis. Junonia species are generally not monophyletic with respect to COI haplotypes, which are shared across species. However, two major COI haplotype groups exist. Group A predominates in South America, and Group B predominates in North and Central America. Therefore, COI haplotypes can be used to assess the degree of genetic influence a population receives from each continent. Junonia shows a ring-shaped distribution around the Caribbean, and evidence is consistent with gene flow among forms of Junonia, including those from Mesoamerica. However, we detected no discontinuity in gene flow in Cuba or elsewhere in the Caribbean consistent with genetic isolation in the region of overlap. Though sampling is still very limited in the critical region, the only remaining possiblity for a circum-Caribbean discontinuity in gene flow is at the Isthmus of Panama, where there may be a transition from 98% Group B haplotypes in Costa Rica to 85-100% Group A haplotypes in South America.
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Affiliation(s)
| | - Jeffrey M. Marcus
- Correspondence: Jeffrey M. Marcus, Department of Biological Sciences, 208 Biological Sciences Building, University of Manitoba, Winnipeg, MB, R3T 2N2 Canada.
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25
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Shum P, Pampoulie C, Kristinsson K, Mariani S. Three-dimensional post-glacial expansion and diversification of an exploited oceanic fish. Mol Ecol 2015; 24:3652-67. [PMID: 26073046 PMCID: PMC4744735 DOI: 10.1111/mec.13262] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 05/22/2015] [Accepted: 05/29/2015] [Indexed: 01/27/2023]
Abstract
Vertical divergence in marine organisms is being increasingly documented, yet much remains to be carried out to understand the role of depth in the context of phylogeographic reconstruction and the identification of management units. An ideal study system to address this issue is the beaked redfish, Sebastes mentella – one of four species of ‘redfish’ occurring in the North Atlantic – which is known for a widely distributed ‘shallow‐pelagic’ oceanic type inhabiting waters between 250 and 550 m, and a more localized ‘deep‐pelagic’ population dwelling between 550 and 800 m, in the oceanic habitat of the Irminger Sea. Here, we investigate the extent of population structure in relation to both depth and geographic spread of oceanic beaked redfish throughout most of its distribution range. By sequencing the mitochondrial control region of 261 redfish collected over a decadal interval, and combining 160 rhodopsin coding nuclear sequences and previously genotyped microsatellite data, we map the existence of two strongly divergent evolutionary lineages with significantly different distribution patterns and historical demography, and whose genetic variance is mostly explained by depth. Combined genetic data, analysed via independent approaches, are consistent with a Late Pleistocene lineage split, where segregation by depth probably resulted from the interplay of climatic and oceanographic processes with life history and behavioural traits. The ongoing process of diversification in North Atlantic S. mentella may serve as an ‘hourglass’ to understand speciation and adaptive radiation in Sebastes and in other marine taxa distributed across a depth gradient.
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Affiliation(s)
- Peter Shum
- Ecosystems and Environment Research Centre, School of Environment and Life Sciences, University of Salford, Salford, M5 4WT, UK
| | | | | | - Stefano Mariani
- Ecosystems and Environment Research Centre, School of Environment and Life Sciences, University of Salford, Salford, M5 4WT, UK
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26
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Affiliation(s)
- Amanda E. Glazier
- Biology Department; University of Massachusetts; 100 Morrissey Blvd Boston MA 02125 USA
| | - Ron J. Etter
- Biology Department; University of Massachusetts; 100 Morrissey Blvd Boston MA 02125 USA
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27
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Bock DG, Andrew RL, Rieseberg LH. On the adaptive value of cytoplasmic genomes in plants. Mol Ecol 2014; 23:4899-911. [PMID: 25223488 DOI: 10.1111/mec.12920] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 09/08/2014] [Accepted: 09/10/2014] [Indexed: 01/30/2023]
Abstract
Is DNA variation maintained in organelle genomes selectively neutral? The answer to this question has important implications for many aspects of ecology and evolution. While traditionally the answer has been 'yes', recent studies in animals have shown that, on the contrary, mitochondrial DNA polymorphism is frequently adaptive. In plants, however, the neutrality assumption has not been strongly challenged. Here, we begin with a critical evaluation of arguments in favour of this long-held view. We then discuss the latest empirical evidence for the opposing prediction that sequence variation in plant cytoplasmic genomes is frequently adaptive. While outstanding research progress is being made towards understanding this fundamental topic, we highlight the need for studies that combine information ranging from field experiments to physiology to molecular evolutionary biology. Such an interdisciplinary approach provides a means for determining the frequency, drivers and evolutionary significance of adaptive organelle DNA variation.
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Affiliation(s)
- Dan G Bock
- Department of Botany, Biodiversity Research Centre, University of British Columbia, 3529-6270 University Blvd., Vancouver, British Columbia, Canada, V6T 1Z4
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28
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Giri F, Collins P. Clinal variation in carapace shape in the South American freshwater crab,Aegla uruguayana(Anomura: Aeglidae). Biol J Linn Soc Lond 2014. [DOI: 10.1111/bij.12382] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Federico Giri
- Instituto Nacional de Limnología (CONICET-UNL); Pje El Pozo s/n CP3000 Santa Fe Argentina
- Facultad de Humanidades y Ciencias; Universidad Nacional del Litoral; Pje El Pozo s/n CP3000 Santa Fe Argentina
| | - Pablo Collins
- Instituto Nacional de Limnología (CONICET-UNL); Pje El Pozo s/n CP3000 Santa Fe Argentina
- Facultad de Bioquímica y Ciencias Biológicas; Universidad Nacional del Litoral; Pje El Pozo s/n CP3000 Santa Fe Argentina
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29
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Lee-Yaw JA, Jacobs CGC, Irwin DE. Individual performance in relation to cytonuclear discordance in a northern contact zone between long-toed salamander (Ambystoma macrodactylum) lineages. Mol Ecol 2014; 23:4590-602. [DOI: 10.1111/mec.12878] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2014] [Revised: 07/01/2014] [Accepted: 07/10/2014] [Indexed: 01/29/2023]
Affiliation(s)
- Julie A. Lee-Yaw
- Department of Zoology; University of British Columbia; 6270 University Blvd. Vancouver British Columbia Canada V6T 1Z4
| | - Chris G. C. Jacobs
- Institute of Biology Leiden; Leiden University; Sylviusweg 72 2333 BE Leiden The Netherlands
| | - Darren E. Irwin
- Department of Zoology; University of British Columbia; 6270 University Blvd. Vancouver British Columbia Canada V6T 1Z4
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30
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31
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Hung CM, Hung HY, Yeh CF, Fu YQ, Chen D, Lei F, Yao CT, Yao CJ, Yang XJ, Lai YT, Li SH. Species delimitation in the Chinese bamboo partridgeBambusicola thoracica(Phasianidae; Aves). ZOOL SCR 2014. [DOI: 10.1111/zsc.12071] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Chih-Ming Hung
- Department of Life Science; National Taiwan Normal University; Taipei 11677 Taiwan
| | - Hsin-Yi Hung
- Department of Life Science; National Taiwan Normal University; Taipei 11677 Taiwan
| | - Chia-Fen Yeh
- Department of Life Science; National Taiwan Normal University; Taipei 11677 Taiwan
| | - Yi-Qiang Fu
- College of Life Science; Leshan Normal University; Leshan 614000 China
| | - De Chen
- Department of Life Science; College of Life Sciences; Beijing Normal University; Beijing 100875 China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
| | - Cheng-Te Yao
- Division of Zoology; Endemic Species Research Institute; Chi-chi Nantou 55244 Taiwan
| | - Chiou-Ju Yao
- Department of Biology; National Museum of Natural Science; Taichung 40453 Taiwan
| | - Xiao-Jun Yang
- Kunming Institute Zoology; Chinese Academy of Sciences; Kunming Yunnan China
| | - Yu-Ting Lai
- Department of Life Science; National Taiwan Normal University; Taipei 11677 Taiwan
| | - Shou-Hsien Li
- Department of Life Science; National Taiwan Normal University; Taipei 11677 Taiwan
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32
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Alcaide M, Scordato ESC, Price TD, Irwin DE. Genomic divergence in a ring species complex. Nature 2014; 511:83-5. [DOI: 10.1038/nature13285] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 03/26/2014] [Indexed: 11/09/2022]
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Jennings RM, Etter RJ, Ficarra L. Population differentiation and species formation in the deep sea: the potential role of environmental gradients and depth. PLoS One 2013; 8:e77594. [PMID: 24098590 PMCID: PMC3788136 DOI: 10.1371/journal.pone.0077594] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 09/12/2013] [Indexed: 11/19/2022] Open
Abstract
Ecological speciation probably plays a more prominent role in diversification than previously thought, particularly in marine ecosystems where dispersal potential is great and where few obvious barriers to gene flow exist. This may be especially true in the deep sea where allopatric speciation seems insufficient to account for the rich and largely endemic fauna. Ecologically driven population differentiation and speciation are likely to be most prevalent along environmental gradients, such as those attending changes in depth. We quantified patterns of genetic variation along a depth gradient (1600-3800m) in the western North Atlantic for a protobranch bivalve (Nuculaatacellana) to test for population divergence. Multilocus analyses indicated a sharp discontinuity across a narrow depth range, with extremely low gene flow inferred between shallow and deep populations for thousands of generations. Phylogeographical discordance occurred between nuclear and mitochondrial loci as might be expected during the early stages of species formation. Because the geographic distance between divergent populations is small and no obvious dispersal barriers exist in this region, we suggest the divergence might reflect ecologically driven selection mediated by environmental correlates of the depth gradient. As inferred for numerous shallow-water species, environmental gradients that parallel changes in depth may play a key role in the genesis and adaptive radiation of the deep-water fauna.
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Affiliation(s)
- Robert M. Jennings
- Biology Department, University of Massachusetts Boston, Boston, Massachusetts, United States of America
| | - Ron J. Etter
- Biology Department, University of Massachusetts Boston, Boston, Massachusetts, United States of America
| | - Lynn Ficarra
- Biology Department, University of Massachusetts Boston, Boston, Massachusetts, United States of America
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34
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Toews DPL, Mandic M, Richards JG, Irwin DE. MIGRATION, MITOCHONDRIA, AND THE YELLOW-RUMPED WARBLER. Evolution 2013; 68:241-55. [DOI: 10.1111/evo.12260] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Accepted: 08/15/2013] [Indexed: 01/05/2023]
Affiliation(s)
- David P. L. Toews
- Department of Zoology and Biodiversity Research Centre; University of British Columbia; 6270 University Blvd. Vancouver BC V6T 1Z4 Canada
| | - Milica Mandic
- Department of Zoology and Biodiversity Research Centre; University of British Columbia; 6270 University Blvd. Vancouver BC V6T 1Z4 Canada
| | - Jeffrey G. Richards
- Department of Zoology and Biodiversity Research Centre; University of British Columbia; 6270 University Blvd. Vancouver BC V6T 1Z4 Canada
| | - Darren E. Irwin
- Department of Zoology and Biodiversity Research Centre; University of British Columbia; 6270 University Blvd. Vancouver BC V6T 1Z4 Canada
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35
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Haller BC, Mazzucco R, Dieckmann U. Evolutionary branching in complex landscapes. Am Nat 2013; 182:E127-41. [PMID: 24021409 DOI: 10.1086/671907] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Divergent adaptation to different environments can promote speciation, and it is thus important to consider spatial structure in models of speciation. Earlier theoretical work, however, has been limited to particularly simple types of spatial structure (linear environmental gradients and spatially discrete metapopulations), leaving unaddressed the effects of more realistic patterns of landscape heterogeneity, such as nonlinear gradients and spatially continuous patchiness. To elucidate the consequences of such complex landscapes, we adapt an established spatially explicit individual-based model of evolutionary branching. We show that branching is most probable at intermediate levels of various types of heterogeneity and that different types of heterogeneity have, to some extent, additive effects in promoting branching. In contrast to such additivity, we find a novel refugium effect in which refugia in hostile environments provide opportunities for colonization, thus increasing the probability of branching in patchy landscapes. Effects of patchiness depend on the scale of patches relative to dispersal. Providing a needed connection to empirical research on biodiversity and conservation policy, we introduce empirically accessible spatial environmental metrics that quantitatively predict a landscape's branching propensity.
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Affiliation(s)
- Benjamin C Haller
- Department of Biology and Redpath Museum, McGill University, 859 Sherbrooke Street West, Montreal, Quebec H3A 0C4, Canada
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36
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Pavlova A, Amos JN, Joseph L, Loynes K, Austin JJ, Keogh JS, Stone GN, Nicholls JA, Sunnucks P. PERCHED AT THE MITO-NUCLEAR CROSSROADS: DIVERGENT MITOCHONDRIAL LINEAGES CORRELATE WITH ENVIRONMENT IN THE FACE OF ONGOING NUCLEAR GENE FLOW IN AN AUSTRALIAN BIRD. Evolution 2013; 67:3412-28. [DOI: 10.1111/evo.12107] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2012] [Accepted: 03/04/2013] [Indexed: 12/29/2022]
Affiliation(s)
- Alexandra Pavlova
- School of Biological Sciences and Australian Centre for Biodiversity; Clayton Campus, Monash University; Wellington Road Clayton Victoria 3800 Australia
| | - J. Nevil Amos
- School of Biological Sciences and Australian Centre for Biodiversity; Clayton Campus, Monash University; Wellington Road Clayton Victoria 3800 Australia
| | - Leo Joseph
- Australian National Wildlife Collection; CSIRO Ecosystem Sciences; GPO Box 1700 Canberra Australian Capital Territory 2601 Australia
| | - Kate Loynes
- Division of Evolution; Ecology and Genetics, Building 116, Daley Road, Research School of Biology, The Australian National University; Canberra Australian Capital Territory 0200 Australia
| | - Jeremy J. Austin
- Australian Centre for Ancient DNA (ACAD); School of Earth & Environmental Sciences, The University of Adelaide; Darling Building North Terrace Campus South Australia 5005 Australia
- Sciences Department; Museum Victoria; Carlton Gardens Melbourne Victoria 3001 Australia
| | - J. Scott Keogh
- Division of Evolution; Ecology and Genetics, Building 116, Daley Road, Research School of Biology, The Australian National University; Canberra Australian Capital Territory 0200 Australia
| | - Graham N. Stone
- Institute of Evolutionary Biology; University of Edinburgh; The King's Buildings, West Mains Road Edinburgh EH9 3JT Scotland
| | - James A. Nicholls
- Institute of Evolutionary Biology; University of Edinburgh; The King's Buildings, West Mains Road Edinburgh EH9 3JT Scotland
| | - Paul Sunnucks
- School of Biological Sciences and Australian Centre for Biodiversity; Clayton Campus, Monash University; Wellington Road Clayton Victoria 3800 Australia
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Fuchs J, Parra JL, Goodman SM, Raherilalao MJ, Vanderwal J, Bowie RCK. Extending ecological niche models to the past 120 000 years corroborates the lack of strong phylogeographic structure in the Crested Drongo (Dicrurus forficatus forficatus) on Madagascar. Biol J Linn Soc Lond 2013. [DOI: 10.1111/j.1095-8312.2012.02022.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Jérôme Fuchs
- Museum of Vertebrate Zoology and Department of Integrative Biology; University of California; 3101 Valley Life Science Building Berkeley CA 94720-3160 USA
- Percy FitzPatrick Institute; DST/NRF Centre of Excellence; University of Cape Town; Rondebosch 7701 South Africa
| | - Juan L. Parra
- Instituto de Biología; Facultad de Ciencias Exactas y Naturales; Universidad de Antioquia; Medellín Colombia
| | - Steven M. Goodman
- Field Museum of Natural History; 1400 South Lake Shore Drive Chicago IL 60605 USA
- Association Vahatra; BP 3972 Antananarivo 101 Madagascar
| | - Marie Jeanne Raherilalao
- Association Vahatra; BP 3972 Antananarivo 101 Madagascar
- Département de Biologie Animale; Université d'Antananarivo; BP 906 Antananarivo 101 Madagascar
| | - Jeremy Vanderwal
- Centre for Tropical Biodiversity & Climate Change; School of Marine and Tropical Biology; James Cook University; Townsville QLD 4811 Australia
| | - Rauri C. K. Bowie
- Museum of Vertebrate Zoology and Department of Integrative Biology; University of California; 3101 Valley Life Science Building Berkeley CA 94720-3160 USA
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Quéré N, Desmarais E, Tsigenopoulos CS, Belkhir K, Bonhomme F, Guinand B. Gene flow at major transitional areas in sea bass (Dicentrarchus labrax) and the possible emergence of a hybrid swarm. Ecol Evol 2012; 2:3061-78. [PMID: 23301173 PMCID: PMC3539001 DOI: 10.1002/ece3.406] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Revised: 09/18/2012] [Accepted: 09/25/2012] [Indexed: 11/08/2022] Open
Abstract
The population genetic structure of sea bass (Dicentrarchus labrax) along a transect from the Atlantic Ocean (AO) to the Eastern Mediterranean (EM) Sea differs from that of most other marine taxa in this area. Three populations (AO, Western Mediterranean [WM], EM) are recognized today, which were originally two allopatric populations. How two ancestral genetic units have evolved into three distinct units has not been addressed yet. Therefore, to investigate mechanisms that lead to the emergence of the central WM population, its current status, and its connectivity with the two parental populations, we applied 20 nuclear loci that were either gene associated or gene independent. Results confirmed the existence of three distinct gene pools, with higher differentiation at two transitional areas, the Almeria-Oran Front (AOF) and of the Siculo-Tunisian Strait (STS), than within any population. Significant linkage disequilibrium and heterozygote excess indicated that the STS is probably another tension zone, as already described for the AOF. Neutrality tests fail to reveal marker loci that could be driven by selection within or among metapopulations, except for locus DLA0068. Collectively, results support that the central WM population arose by trapping two tensions zones at distinct geographic locations of limited connectivity. Population assignment further revealed that WM individuals were more introgressed than individuals from the other two metapopulations. This suggests that this population might result from hybrid swarming, and was or is still seeded by genes received through the filter of each tension zone.
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Affiliation(s)
- Nolwenn Quéré
- Institut des Sciences de l'Évolution de Montpellier, CNRS-UMR 5554, Université Montpellier 2cc63, 34095, Montpellier Cedex 5, France
- Station Méditerranéenne de l'Environnement Littoral2 Avenue des chantiers, 34200, Sète, France
| | - Erick Desmarais
- Institut des Sciences de l'Évolution de Montpellier, CNRS-UMR 5554, Université Montpellier 2cc63, 34095, Montpellier Cedex 5, France
- LabEx CeMEB, Université Montpellier IIplace E. Bataillon, cc63, 34095, Montpellier Cedex 5, France
| | - Costas S Tsigenopoulos
- Hellenic Center for Marine Research, Institute of Marine Biology and GeneticsPO Box 2214, Gournes Pediados, 71500, Heraklion, Crete, Greece
| | - Khalid Belkhir
- Institut des Sciences de l'Évolution de Montpellier, CNRS-UMR 5554, Université Montpellier 2cc63, 34095, Montpellier Cedex 5, France
| | - François Bonhomme
- Institut des Sciences de l'Évolution de Montpellier, CNRS-UMR 5554, Université Montpellier 2cc63, 34095, Montpellier Cedex 5, France
- Station Méditerranéenne de l'Environnement Littoral2 Avenue des chantiers, 34200, Sète, France
| | - Bruno Guinand
- Institut des Sciences de l'Évolution de Montpellier, CNRS-UMR 5554, Université Montpellier 2cc63, 34095, Montpellier Cedex 5, France
- Station Méditerranéenne de l'Environnement Littoral2 Avenue des chantiers, 34200, Sète, France
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Hogner S, Laskemoen T, Lifjeld JT, Porkert J, Kleven O, Albayrak T, Kabasakal B, Johnsen A. Deep sympatric mitochondrial divergence without reproductive isolation in the common redstart Phoenicurus phoenicurus. Ecol Evol 2012; 2:2974-88. [PMID: 23301165 PMCID: PMC3538993 DOI: 10.1002/ece3.398] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2012] [Accepted: 09/17/2012] [Indexed: 11/25/2022] Open
Abstract
Mitochondrial DNA usually shows low sequence variation within and high sequence divergence among species, which makes it a useful marker for phylogenetic inference and DNA barcoding. A previous study on the common redstart (Phoenicurus phoenicurus) revealed two very different mtDNA haplogroups (5% K2P distance). This divergence is comparable to that among many sister species; however, both haplogroups coexist and interbreed in Europe today. Herein, we describe the phylogeographic pattern of these lineages and test hypotheses for how such high diversity in mtDNA has evolved. We found no evidence for mitochondrial pseudogenes confirming that both haplotypes are of mitochondrial origin. When testing for possible reproductive barriers, we found no evidence for lineage-specific assortative mating and no difference in sperm morphology, indicating that they are not examples of cryptic species, nor likely to reflect the early stages of speciation. A gene tree based on a short fragment of cytochrome c oxidase subunit 1 from the common redstart and 10 other Phoenicurus species, showed no introgression from any of the extant congenerics. However, introgression from an extinct congeneric cannot be excluded. Sequences from two nuclear introns did not show a similar differentiation into two distinct groups. Mismatch distributions indicated that the lineages have undergone similar demographic changes. Taken together, these results confirm that deeply divergent mitochondrial lineages can coexist in biological species. Sympatric mtDNA divergences are relatively rare in birds, but the fact that they occur argues against the use of threshold mtDNA divergences in species delineation.
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Affiliation(s)
- Silje Hogner
- National Centre for Biosystematics, Natural History Museum, University of Oslo P.O. Box 1172, Blindern, NO-0318, Oslo, Norway
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Lee-Yaw JA, Irwin DE. Large geographic range size reflects a patchwork of divergent lineages in the long-toed salamander (Ambystoma macrodactylum). J Evol Biol 2012; 25:2276-87. [DOI: 10.1111/j.1420-9101.2012.02604.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 07/24/2012] [Accepted: 07/27/2012] [Indexed: 11/28/2022]
Affiliation(s)
- J. A. Lee-Yaw
- Department of Zoology; University of British Columbia; Vancouver; BC; Canada
| | - D. E. Irwin
- Department of Zoology; University of British Columbia; Vancouver; BC; Canada
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Affiliation(s)
- David P L Toews
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, 6270 University Blvd., Vancouver, BC V6T 1Z4, Canada.
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