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Calixto-Rojas M, Lira-Noriega A, Rubio-Godoy M, Pérez-Ponce de León G, Pinacho-Pinacho CD. Delimitation and species discovery in the Profundulidae fish family: Using genetic, environmental and morphologic data to address taxonomic uncertainty. Mol Phylogenet Evol 2023:107856. [PMID: 37327830 DOI: 10.1016/j.ympev.2023.107856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 06/18/2023]
Abstract
The family Profundulidae includes some one of the most enigmatic freshwater fishes of Mesoamerica: despite many attempts, a robust phylogenetic framework to delimit species is lacking, mainly due to limited morphological variation within the group. The accumulation of molecular data of profundulid fishes has led to advances in the description of new taxa, but relatively less progress has been made estimating evolutionary and phylogenetic relationships for this fish family. Here, we adopt an integrative taxonomy approach including the use of nuclear and mitochondrial DNA sequences, morphometric and ecological data, to test species boundaries in profundulid fishes in the westernmost area of their known distribution range in the states of Guerrero and Oaxaca, Mexico. Using a combination of methods for species discovery and validation based on Bayesian gene tree topologies, our analyses support the delimitation of 15 valid species of profundulid fishes - a combination of previously described species validated by this study, the synonymy of unsupported taxa, and the description of two new species. Using species delimitation methods, examination of phenotypic variation, and ecological niche characterization, we also identify five potentially new lineages which require further evidence to be erected as new species. We demonstrate that the use of an integrative taxonomy approach provides a robust methodology to delimit species in a taxonomically complex group like Profundulidae. Accurate taxonomic and ecological information is crucial for the conservation of these microendemic fishes, as several species are endangered.
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Affiliation(s)
- Miguel Calixto-Rojas
- Doctorado en Ciencias, Instituto de Ecología, A.C., Red de Estudios Moleculares Avanzados, Carretera Antigua a Coatepec 351, El Haya, Xalapa, Veracruz 91073, Mexico.
| | - Andrés Lira-Noriega
- CONACyT Research Fellow, Instituto de Ecología A.C., Red de Estudios Moleculares Avanzados, Carretera Antigua a Coatepec 351, El Haya, Xalapa, Veracruz 91073, Mexico
| | - Miguel Rubio-Godoy
- Instituto de Ecología, A.C., Red de Biología Evolutiva, Carretera Antigua a Coatepec 351, El Haya, Xalapa, Veracruz 91073, Mexico
| | - Gerardo Pérez-Ponce de León
- Escuela Nacional de Estudios Superiores unidad Mérida, Universidad Nacional Autónoma de México, Km 4.5 Carretera Mérida-Tetiz, Municipio de Ucú, Yucatán 97357, Mexico
| | - Carlos D Pinacho-Pinacho
- CONACyT Research Fellow, Instituto de Ecología A.C., Red de Estudios Moleculares Avanzados, Carretera Antigua a Coatepec 351, El Haya, Xalapa, Veracruz 91073, Mexico
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2
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MacPherson N, Champion CP, Weir LK, Dalziel AC. Reproductive isolating mechanisms contributing to asymmetric hybridization in Killifishes (Fundulus spp.). J Evol Biol 2023; 36:605-621. [PMID: 36636892 DOI: 10.1111/jeb.14148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 10/27/2022] [Accepted: 11/26/2022] [Indexed: 01/14/2023]
Abstract
When species hybridize, one F1 hybrid cross type often predominates. Such asymmetry can arise from differences in a variety of reproductive barriers, but the relative roles and concordance of pre-mating, post-mating prezygotic, and post-zygotic barriers in producing these biases in natural animal populations have not been widely investigated. Here, we study a population of predominantly F1 hybrids between two killifish species (Fundulus heteroclitus and F. diaphanus) in which >95% of F1 hybrids have F. diaphanus mothers and F. heteroclitus fathers (D♀ × H♂). To determine why F. heteroclitus × F. diaphanus F1 hybrids (H♀ × D♂) are so rare, we tested for asymmetry in pre-mating reproductive barriers (female preference and male aggression) at a common salinity (10 ppt) and post-mating, pre-zygotic (fertilization success) and post-zygotic (embryonic development time and hatching success) reproductive barriers at a range of ecologically relevant salinities (0, 5, 10, and 15 ppt). We found that F. heteroclitus females preferred conspecific males, whereas F. diaphanus females did not, matching the observed cross bias in the wild. Naturally rare H♀ × D♂ crosses also had lower fertilization success than all other cross types, and a lower hatching success than the prevalent D♀ × H♂ crosses at the salinity found in the hybrid zone centre (10 ppt). Furthermore, the naturally predominant D♀ × H♂ crosses had a higher hatching success than F. diaphanus crosses at 10 ppt, which may further increase their relative abundance. The present study suggests that a combination of incomplete mating, post-mating pre-zygotic and post-zygotic reproductive isolating mechanisms act in concert to produce hybrid asymmetry in this system.
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Affiliation(s)
- Nathalie MacPherson
- Department of Biology, Saint Mary's University, Halifax, Nova Scotia, Canada
| | - Chloe P Champion
- Department of Biology, Saint Mary's University, Halifax, Nova Scotia, Canada
| | - Laura K Weir
- Department of Biology, Saint Mary's University, Halifax, Nova Scotia, Canada
| | - Anne C Dalziel
- Department of Biology, Saint Mary's University, Halifax, Nova Scotia, Canada
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3
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Dedić N, Vetešník L, Šimková A. Monogeneans in intergeneric hybrids of leuciscid fish: Is parasite infection driven by hybrid heterosis, genetic incompatibilities, or host-parasite coevolutionary interactions? Front Zool 2023; 20:5. [PMID: 36703186 PMCID: PMC9881282 DOI: 10.1186/s12983-022-00481-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 12/21/2022] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Several hypotheses have been proposed to explain parasite infection in parental species and their hybrids. Hybrid heterosis is generally applied to explain the advantage for F1 generations of hybrids exhibiting a lower level of parasite infection when compared to parental species. Post-F1 generations often suffer from genetic incompatibilities potentially reflected in the higher level of parasite infection when compared to parental species. However, the presence of specific parasites in an associated host is also limited by close coevolutionary genetic host-parasite associations. This study focused on monogenean parasites closely associated with two leuciscid fish species-common bream and roach-with the aim of comparing the level of monogenean infection between parental species and hybrids representing two F1 generations with different mtDNA and two backcross generations with different cyto-nuclear compositions. RESULTS Monogenean infection in F1 generations of hybrids was lower when compared to parental species, in line with the hybrid heterosis hypothesis. Monogenean infection in backcross generations exhibited similarities with the parental species whose genes contributed more to the backcross genotype. The distribution of monogeneans associated with one or the other parental species showed the same asymmetry with a higher proportion of roach-associated monogeneans in both F1 generations and backcross generation with roach in the paternal position. A higher proportion of common bream-associated monogeneans was found in backcross generation with common bream in the paternal position. CONCLUSIONS Our study indicated that cyto-nuclear incompatibilities in hybrids do not induce higher monogenean infection in backcross generations when compared to parental species. However, as backcross hybrids with a higher proportion of the genes of one parental taxon also exhibited high level of this parental taxon-associated parasites, host-parasite coevolutionary interactions seem to play an obvious role in determining the level of infection of host-specific monogeneans in hybrids.
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Affiliation(s)
- Neira Dedić
- grid.10267.320000 0001 2194 0956Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Lukáš Vetešník
- grid.10267.320000 0001 2194 0956Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic ,grid.418095.10000 0001 1015 3316Institute of Vertebrate Biology, Czech Academy of Sciences, Květná 8, 603 65 Brno, Czech Republic
| | - Andrea Šimková
- grid.10267.320000 0001 2194 0956Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
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Lewanski AL, Golcher-Benavides J, Rick JA, Wagner CE. Variable hybridization between two Lake Tanganyikan cichlid species in recent secondary contact. Mol Ecol 2022; 31:5041-5059. [PMID: 35913373 DOI: 10.1111/mec.16636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 07/22/2022] [Accepted: 07/26/2022] [Indexed: 12/01/2022]
Abstract
Closely related taxa frequently exist in sympatry before the evolution of robust reproductive barriers, which can lead to substantial gene flow. Post-divergence gene flow can promote several disparate trajectories of divergence ranging from the erosion of distinctiveness and eventual collapse of the taxa to the strengthening of reproductive isolation. Among many relevant factors, understanding the demographic history of divergence (e.g. divergence time, extent of historical gene flow) can be particularly informative when examining contemporary gene flow between closely related taxa because this history can influence gene flow's prevalence and consequences. Here, we used genotyping-by-sequencing data to investigate speciation and contemporary hybridization in two closely related and sympatrically distributed Lake Tanganyikan cichlid species in the genus Petrochromis. Demographic modeling supported a speciation scenario involving divergence in isolation followed by secondary contact with bidirectional gene flow. Further investigation of this recent gene flow found evidence of ongoing hybridization between the species that varied in extent between different co-occurring populations. Relationships between abundance and the degree of admixture across populations suggest that the availability of conspecific mates may influence patterns of hybridization. These results, together with the observation that sets of recently diverged cichlid taxa are generally geographically separated in the lake, suggest that ongoing speciation in Lake Tanganyikan cichlids relies on initial spatial isolation. Additionally, the spatially heterogeneous patterns of admixture between the Petrochromis species illustrates the complexities of hybridization when species are in recent secondary contact.
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Affiliation(s)
| | - Jimena Golcher-Benavides
- Department of Botany, University of Wyoming, Laramie, WY, USA.,Program in Ecology, University of Wyoming, Laramie, WY, USA
| | - Jessica A Rick
- Department of Botany, University of Wyoming, Laramie, WY, USA.,Program in Ecology, University of Wyoming, Laramie, WY, USA
| | - Catherine E Wagner
- Department of Botany, University of Wyoming, Laramie, WY, USA.,Program in Ecology, University of Wyoming, Laramie, WY, USA.,Biodiversity Institute, University of Wyoming, Laramie, WY, USA
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5
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Zamani A, Dal Pos D, Fric ZF, Orfinger AB, Scherz MD, Bartoňová AS, Gante HF. The future of zoological taxonomy is integrative, not minimalist. SYST BIODIVERS 2022. [DOI: 10.1080/14772000.2022.2063964] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Alireza Zamani
- Zoological Museum, Biodiversity Unit, University of Turku, 20500 Turku, Finland
| | - Davide Dal Pos
- Department of Biology, University of Central Florida, 4110 Libra dr. Rm 442, Orlando, FL 32816, USA
| | - Zdenek Faltýnek Fric
- Department of Biodiversity and Conservation Biology, Institute of Entomology, Biology Centre of the Czech Academy of Sciences, Branisovska 31, Ceske Budejovice, CZ-37005, Czech Republic
| | - Alexander B. Orfinger
- Department of Entomology and Nematology, University of Florida, Gainesville, FL 32611, USA
- Center for Water Resources, Florida A&M University, Tallahassee, FL 32301, USA
| | - Mark D. Scherz
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, 1350, Denmark
| | - Alena Sucháčková Bartoňová
- Department of Biodiversity and Conservation Biology, Institute of Entomology, Biology Centre of the Czech Academy of Sciences, Branisovska 31, Ceske Budejovice, CZ-37005, Czech Republic
| | - Hugo F. Gante
- cE3c—Center for Ecology, Evolution and Environmental Changes, Universidade de Lisboa, Lisboa, Portugal
- Department of Biology, KU Leuven, Section Ecology, Evolution and Biodiversity Conservation, Charles Deberiotstraat 32 box 2439, Leuven, B-3000, Belgium
- Royal Museum for Central Africa, Leuvensesteenweg 17, Tervuren, 3080, Belgium
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6
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Silliman K, Zhao H, Justice M, Thongda W, Bowen B, Peatman E. Complex introgression among three diverged largemouth bass lineages. Evol Appl 2021; 14:2815-2830. [PMID: 34950231 PMCID: PMC8674896 DOI: 10.1111/eva.13314] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 09/21/2021] [Accepted: 10/14/2021] [Indexed: 12/30/2022] Open
Abstract
Hybrid zones between diverged lineages offer a unique opportunity to study evolutionary processes related to speciation. Natural and anthropogenic hybridization in the black basses (Micropterus spp.) is well documented, including an extensive intergrade zone between the widespread northern Largemouth Bass (M. salmoides) and the Florida Bass (M. floridanus). Phenotypic surveys have identified an estuarine population of Largemouth Bass (M. salmoides) in the Mobile-Tensaw Delta, with larger relative weight and smaller adult size compared to inland populations, suggesting a potential third lineage of largemouth bass. To determine the evolutionary relationships among these Mobile Delta bass populations, M. salmoides and M. floridanus, putative pure and intergrade populations of all three groups were sampled across the eastern United States. Phylogenetic analyses of 8582 nuclear SNPs derived from genotype-by-sequencing and the ND2 mitochondrial gene determined that Delta bass populations stem from a recently diverged lineage of Largemouth Bass. Using a novel quantitative pipeline, a panel of 73 diagnostic SNPs was developed for the three lineages, evaluated for accuracy, and then used to screen 881 samples from 52 sites for genetic integrity and hybridization on the Agena MassARRAY platform. These results strongly support a redrawing of native ranges for both the intergrade zone and M. floridanus, which has significant implications for current fisheries management. Furthermore, Delta bass ancestry was shown to contribute significantly to the previously described intergrade zone between northern Largemouth Bass and Florida Bass, suggesting a more complex pattern of secondary contact and introgression among these diverged Micropterus lineages.
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Affiliation(s)
- Katherine Silliman
- School of Fisheries, Aquaculture, and Aquatic SciencesAuburn UniversityAuburnAlabamaUSA
| | - Honggang Zhao
- Department of Natural ResourcesCornell UniversityIthacaNew YorkUSA
| | - Megan Justice
- School of Fisheries, Aquaculture, and Aquatic SciencesAuburn UniversityAuburnAlabamaUSA
| | - Wilawan Thongda
- Center of Excellence for Shrimp Molecular Biology and Biology (CENTEX Shrimp)Faculty of ScienceMahidol UniversityBangkokThailand
- National Center for Genetic Engineering and Biotechnology (BIOTEC)National Science and Technology Development Agency (NSTDA)Pathum ThaniThailand
| | - Bryant Bowen
- Georgia Department of Natural ResourcesSocial CircleGeorgiaUSA
| | - Eric Peatman
- School of Fisheries, Aquaculture, and Aquatic SciencesAuburn UniversityAuburnAlabamaUSA
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7
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Kartavtsev YP. Some Examples of the Use of Molecular Markers for Needs of Basic Biology and Modern Society. Animals (Basel) 2021; 11:1473. [PMID: 34065552 PMCID: PMC8160991 DOI: 10.3390/ani11051473] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/13/2021] [Accepted: 05/15/2021] [Indexed: 01/27/2023] Open
Abstract
Application of molecular genetic markers appeared to be very fruitful in achieving many goals, including (i) proving the theoretic basements of general biology and (ii) assessment of worldwide biodiversity. Both are provided in the present meta-analysis and a review as the main signal. One of the basic current challenges in modern biology in the face of new demands in the 21st century is the validation of its paradigms such as the synthetic theory of evolution (STE) and biological species concept (BSC). Another of most valuable goals is the biodiversity assessment for a variety of social needs including free web-based information resources about any living being, renovation of museum collections, nature conservation that recognized as a global project, iBOL, as well as resolving global trading problems such as false labeling of species specimens used as food, drug components, entertainment, etc. The main issues of the review are focused on animals and combine four items. (1) A combination of nDNA and mtDNA markers best suits the identification of hybrids and estimation of genetic introgression. (2) The available facts on nDNA and mtDNA diversity seemingly make introgression among many taxa obvious, although it is evident, that introgression may be quite restricted or asymmetric, thus, leaving at least the "source" taxon (taxa) intact. (3) If we consider sexually reproducing species in marine and terrestrial realms introgressed, as it is still evident in many cases, then we should recognize that the BSC, in view of the complete lack of gene flow among species, is inadequate because many zoological species are not biological ones yet. However, vast modern molecular data have proven that sooner or later they definitely become biological species. (4) An investigation into the fish taxa divergence using the BOLD database shows that most gene trees are basically monophyletic and interspecies reticulations are quite rare.
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Affiliation(s)
- Yuri Phedorovich Kartavtsev
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, 690041 Vladivostok, Russia
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8
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Gueuning M, Frey JE, Praz C. Ultraconserved yet informative for species delimitation: Ultraconserved elements resolve long-standing systematic enigma in Central European bees. Mol Ecol 2020; 29:4203-4220. [PMID: 32916006 DOI: 10.1111/mec.15629] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 08/21/2020] [Accepted: 08/24/2020] [Indexed: 12/21/2022]
Abstract
Accurate and testable species hypotheses are essential for measuring, surveying and managing biodiversity. Taxonomists often rely on mitochondrial DNA barcoding to complement morphological species delimitations. Although COI-barcoding has largely proven successful in assisting identifications for most animal taxa, there are nevertheless numerous cases where mitochondrial barcodes do not reflect species hypotheses. For instance, what is regarded as a single species can be associated with two distinct DNA barcodes, which can point either to cryptic diversity or to within-species mitochondrial divergences without reproductive isolation. In contrast, two or more species can share barcodes, for instance due to mitochondrial introgression. These intrinsic limitations of DNA barcoding are commonly addressed with nuclear genomic markers, which are expensive, may have low repeatability and often require high-quality DNA. To overcome these limitations, we examined the use of ultraconserved elements (UCEs) as a quick and robust genomic approach to address such problematic cases of species delimitation in bees. This genomic method was assessed using six different species complexes suspected to harbour cryptic diversity, mitochondrial introgression or mitochondrial paraphyly. The sequencing of UCEs recovered between 686 and 1,860 homologous nuclear loci and provided explicit species delimitation in all investigated species complexes. These results provide strong evidence for the suitability of UCEs as a fast method for species delimitation even in recently diverged lineages. Furthermore, we provide the first evidence for both mitochondrial introgression among distinct bee species, and mitochondrial paraphyly within a single bee species.
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Affiliation(s)
- Morgan Gueuning
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics, Wädenswil, Switzerland.,Institute of Biology, University of Neuchatel, Neuchatel, Switzerland
| | - Juerg E Frey
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics, Wädenswil, Switzerland
| | - Christophe Praz
- Institute of Biology, University of Neuchatel, Neuchatel, Switzerland
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9
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Tobler M, Barts N, Greenway R. Mitochondria and the Origin of Species: Bridging Genetic and Ecological Perspectives on Speciation Processes. Integr Comp Biol 2020; 59:900-911. [PMID: 31004483 DOI: 10.1093/icb/icz025] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Mitochondria have been known to be involved in speciation through the generation of Dobzhansky-Muller incompatibilities, where functionally neutral co-evolution between mitochondrial and nuclear genomes can cause dysfunction when alleles are recombined in hybrids. We propose that adaptive mitochondrial divergence between populations can not only produce intrinsic (Dobzhansky-Muller) incompatibilities, but could also contribute to reproductive isolation through natural and sexual selection against migrants, post-mating prezygotic isolation, as well as by causing extrinsic reductions in hybrid fitness. We describe how these reproductive isolating barriers can potentially arise through adaptive divergence of mitochondrial function in the absence of mito-nuclear coevolution, a departure from more established views. While a role for mitochondria in the speciation process appears promising, we also highlight critical gaps of knowledge: (1) many systems with a potential for mitochondrially-mediated reproductive isolation lack crucial evidence directly linking reproductive isolation and mitochondrial function; (2) it often remains to be seen if mitochondrial barriers are a driver or a consequence of reproductive isolation; (3) the presence of substantial gene flow in the presence of mito-nuclear incompatibilities raises questions whether such incompatibilities are strong enough to drive speciation to completion; and (4) it remains to be tested how mitochondrial effects on reproductive isolation compare when multiple mechanisms of reproductive isolation coincide. We hope this perspective and the proposed research plans help to inform future studies of mitochondrial adaptation in a manner that links genotypic changes to phenotypic adaptations, fitness, and reproductive isolation in natural systems, helping to clarify the importance of mitochondria in the formation and maintenance of biological diversity.
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Affiliation(s)
- M Tobler
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - N Barts
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - R Greenway
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
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10
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Diversification and gene flow of tilapia species driven by ecological changes in lowland and mountain areas of southern Mauritania. Evol Ecol 2019. [DOI: 10.1007/s10682-019-10017-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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11
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Ford AG, Bullen TR, Pang L, Genner MJ, Bills R, Flouri T, Ngatunga BP, Rüber L, Schliewen UK, Seehausen O, Shechonge A, Stiassny ML, Turner GF, Day JJ. Molecular phylogeny of Oreochromis (Cichlidae: Oreochromini) reveals mito-nuclear discordance and multiple colonisation of adverse aquatic environments. Mol Phylogenet Evol 2019; 136:215-226. [DOI: 10.1016/j.ympev.2019.04.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 03/26/2019] [Accepted: 04/06/2019] [Indexed: 12/15/2022]
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12
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Sefc KM, Mattersdorfer K, Hermann CM, Koblmüller S. Past lake shore dynamics explain present pattern of unidirectional introgression across a habitat barrier. HYDROBIOLOGIA 2019; 791:69-82. [PMID: 31186578 PMCID: PMC6557712 DOI: 10.1007/s10750-016-2791-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Introgression patterns between divergent lineages are often characterized by asymmetry in the direction and among-marker variation in the extent of gene flow, and therefore inform on the mechanisms involved in differentiation and speciation. In the present study, we test the hypothesis that unidirectional introgression between two phenotypically and genetically distinct lineages of the littoral, rock-dwelling cichlid fish Tropheus moorii across a wide sandy bay is linked to observed differences in mate preferences between the two lineages. This hypothesis predicts bi-directional nuclear gene flow and was rejected by congruent patterns of introgression in mtDNA, AFLP and microsatellite markers, with admixture confined to the populations west of the bay. This pattern can be explained on the basis of habitat changes in the course of lake level fluctuations, which first facilitated the development of a symmetric admixture zone including the area corresponding to the present sand bay and then shaped asymmetry by causing local extinctions and cessation of gene flow when this area became once more inhabitable. This conforms with previous assumptions that habitat dynamics are a primary determinant of population-level evolution in Tropheus. In this respect, Tropheus may be representative of species whose preferred habitat is subject to frequent re-structuring.
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13
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Salzburger W. Understanding explosive diversification through cichlid fish genomics. Nat Rev Genet 2018; 19:705-717. [DOI: 10.1038/s41576-018-0043-9] [Citation(s) in RCA: 138] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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14
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Pauquet G, Salzburger W, Egger B. The puzzling phylogeography of the haplochromine cichlid fish Astatotilapia burtoni. Ecol Evol 2018; 8:5637-5648. [PMID: 29938080 PMCID: PMC6010872 DOI: 10.1002/ece3.4092] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 03/15/2018] [Accepted: 03/27/2018] [Indexed: 12/14/2022] Open
Abstract
Astatotilapia burtoni is a member of the "modern haplochromines," the most species-rich lineage within the family of cichlid fishes. Although the species has been in use as research model in various fields of research since almost seven decades, including developmental biology, neurobiology, genetics and genomics, and behavioral biology, little is known about its spatial distribution and phylogeography. Here, we examine the population structure and phylogeographic history of A. burtoni throughout its entire distribution range in the Lake Tanganyika basin. In addition, we include several A. burtoni laboratory strains to trace back their origin from wild populations. To this end, we reconstruct phylogenetic relationships based on sequences of the mitochondrial DNA (mtDNA) control region (d-loop) as well as thousands of genomewide single nucleotide polymorphisms (SNPs) derived from restriction-associated DNA sequencing. Our analyses reveal high population structure and deep divergence among several lineages, however, with discordant nuclear and mtDNA phylogenetic inferences. Whereas the SNP-based phylogenetic hypothesis uncovers an unexpectedly deep split in A. burtoni, separating the populations in the southern part of the Lake Tanganyika basin from those in the northern part, analyses of the mtDNA control region suggest deep divergence between populations from the southwestern shoreline and populations from the northern and southeastern shorelines of Lake Tanganyika. This phylogeographic pattern and mitochondrial haplotype sharing between populations from the very North and the very South of Lake Tanganyika can only partly be explained by introgression linked to lake-level fluctuations leading to past contact zones between otherwise isolated populations and large-scale migration events.
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Affiliation(s)
| | | | - Bernd Egger
- Zoological InstituteUniversity of BaselBaselSwitzerland
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15
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Derycke S, Kéver L, Herten K, Van den Berge K, Van Steenberge M, Van Houdt J, Clement L, Poncin P, Parmentier E, Verheyen E. Neurogenomic Profiling Reveals Distinct Gene Expression Profiles Between Brain Parts That Are Consistent in Ophthalmotilapia Cichlids. Front Neurosci 2018; 12:136. [PMID: 29593484 PMCID: PMC5855355 DOI: 10.3389/fnins.2018.00136] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 02/20/2018] [Indexed: 01/22/2023] Open
Abstract
The detection of external and internal cues alters gene expression in the brain which in turn may affect neural networks that underly behavioral responses. Previous studies have shown that gene expression profiles differ between major brain regions within individuals and between species with different morphologies, cognitive abilities and/or behaviors. A detailed description of gene expression in all macroanatomical brain regions and in species with similar morphologies and behaviors is however lacking. Here, we dissected the brain of two cichlid species into six macroanatomical regions. Ophthalmotilapia nasuta and O. ventralis have similar morphology and behavior and occasionally hybridize in the wild. We use 3′ mRNA sequencing and a stage-wise statistical testing procedure to identify differential gene expression between females that were kept in a social setting with other females. Our results show that gene expression differs substantially between all six brain parts within species: out of 11,577 assessed genes, 8,748 are differentially expressed (DE) in at least one brain part compared to the average expression of the other brain parts. At most 16% of these DE genes have |log2FC| significantly higher than two. Functional differences between brain parts were consistent between species. The majority (61–79%) of genes that are DE in a particular brain part were shared between both species. Only 32 genes show significant differences in fold change across brain parts between species. These genes are mainly linked to transport, transmembrane transport, transcription (and its regulation) and signal transduction. Moreover, statistical equivalence testing reveals that within each comparison, on average 89% of the genes show an equivalent fold change between both species. The pronounced differences in gene expression between brain parts and the conserved patterns between closely related species with similar morphologies and behavior suggest that unraveling the interactions between genes and behavior will benefit from neurogenomic profiling of distinct brain regions.
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Affiliation(s)
- Sofie Derycke
- Operational Direction Taxonomy and Phylogeny, Royal Belgian Institute for Natural Sciences, Brussels, Belgium.,Department of Biology, Ghent University, Ghent, Belgium
| | - Loic Kéver
- Laboratory of Functional and Evolutionary Morphology, University of Liège, Liège, Belgium.,Behavioural Biology Unit, Ethology and Animal Psychology, University of Liège, Liège, Belgium
| | - Koen Herten
- Department of Human Genetics, Genomics Core Facility, KU Leuven, Leuven, Belgium
| | - Koen Van den Berge
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Maarten Van Steenberge
- Operational Direction Taxonomy and Phylogeny, Royal Belgian Institute for Natural Sciences, Brussels, Belgium.,Section Vertebrates, Ichthyology, Royal Museum for Central Africa, Tervuren, Belgium
| | - Jeroen Van Houdt
- Department of Human Genetics, Genomics Core Facility, KU Leuven, Leuven, Belgium
| | - Lieven Clement
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Pascal Poncin
- Behavioural Biology Unit, Ethology and Animal Psychology, University of Liège, Liège, Belgium
| | - Eric Parmentier
- Laboratory of Functional and Evolutionary Morphology, University of Liège, Liège, Belgium
| | - Erik Verheyen
- Operational Direction Taxonomy and Phylogeny, Royal Belgian Institute for Natural Sciences, Brussels, Belgium
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16
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Kéver L, Parmentier E, Derycke S, Verheyen E, Snoeks J, Van Steenberge M, Poncin P. Limited possibilities for prezygotic barriers in the reproductive behaviour of sympatric Ophthalmotilapia species (Teleostei, Cichlidae). ZOOLOGY 2018; 126:71-81. [PMID: 29307727 DOI: 10.1016/j.zool.2017.12.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 11/30/2017] [Accepted: 12/02/2017] [Indexed: 10/18/2022]
Abstract
Since prezygotic rather than postzygotic barriers are believed to maintain the diversity of closely related sympatric cichlids, differences in phenotypic traits and reproductive behaviours are likely involved in maintaining species boundaries. Here, we focused on the reproductive behaviour of three Ophthalmotilapia species with distributions that only overlap on a small stretch of the shore line of Lake Tanganyika. Repeated introgression of mitochondrial DNA between these species was previously reported, which suggested they can hybridise. Our aim is to test the hypothesis that reproductive behaviour acts as a prezygotic barrier that prevents frequent hybridisation in sympatric Ophthalmotilapia species. We performed a quantitative analysis of twelve reproductions (four for O. ventralis, six for O. nasuta, one for O. boops, and one between a female O. ventralis and a male O. nasuta). Although similar ethograms were obtained for these reproductions, the O. ventralis and O. boops males displayed a behaviour that was never performed by O. nasuta males. This behaviour was displayed during courtship and we called it 'invite'. In O. ventralis, we could show that it was associated with the emission of a single pulse sound. The comparison of O. nasuta and O. ventralis reproductive behaviours also revealed some quantitative differences: O. ventralis males showed the location of the bower more often to the female, whereas O. ventralis females followed the male more often. The similarity between the reproductive behaviours in O. ventralis and O. nasuta could explain the occurrence of the heterospecific spawning event recorded between an O. nasuta male and an O. ventralis female. Importantly, few eggs were laid and the maternal mouthbrooding that resulted from this heterospecific reproduction only lasted for two days, which suggested the abortion of egg development. Hence, in the absence of conspecifics, courtship and mating behaviours alone do not constitute perfect prezygotic barriers between these two species.
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Affiliation(s)
- Loïc Kéver
- Laboratory of Fish and Amphibian Ethology, Behavioural Biology Unit, Liège University, 4000 Liège, Belgium; Laboratory of Functional and Evolutionary Morphology, Liège University, 4000 Liège, Belgium.
| | - Eric Parmentier
- Laboratory of Functional and Evolutionary Morphology, Liège University, 4000 Liège, Belgium
| | - Sofie Derycke
- Operational Directorate Taxonomy and phylogeny, Royal Belgian Institute of Natural Sciences, 1000 Brussels, Belgium; Department of Biology, Ghent University, 9000 Ghent, Belgium
| | - Erik Verheyen
- Operational Directorate Taxonomy and phylogeny, Royal Belgian Institute of Natural Sciences, 1000 Brussels, Belgium
| | - Jos Snoeks
- Section Vertebrates, Ichthyology, Royal Museum for Central Africa, 3080 Tervuren, Belgium; Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven, 3000 Leuven, Belgium
| | - Maarten Van Steenberge
- Operational Directorate Taxonomy and phylogeny, Royal Belgian Institute of Natural Sciences, 1000 Brussels, Belgium; Section Vertebrates, Ichthyology, Royal Museum for Central Africa, 3080 Tervuren, Belgium; Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven, 3000 Leuven, Belgium
| | - Pascal Poncin
- Laboratory of Fish and Amphibian Ethology, Behavioural Biology Unit, Liège University, 4000 Liège, Belgium
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17
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Rahmouni C, Vanhove MPM, Šimková A. Underexplored diversity of gill monogeneans in cichlids from Lake Tanganyika: eight new species of Cichlidogyrus Paperna, 1960 (Monogenea: Dactylogyridae) from the northern basin of the lake, with remarks on the vagina and the heel of the male copulatory organ. Parasit Vectors 2017; 10:591. [PMID: 29197419 PMCID: PMC5712084 DOI: 10.1186/s13071-017-2460-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 10/09/2017] [Indexed: 11/17/2022] Open
Abstract
Background Lake Tanganyika harbours the most diverse cichlid assemblage of the Great African Lakes. Considering its cichlid flocks consist of approximately 250 endemic species, we can hypothesize a high species-richness in their often quite host-specific monogenean ectoparasites belonging to Cichlidogyrus Paperna, 1960. Yet, only 24 species were described from Tanganyikan hosts and some host tribes have never been investigated for monogeneans. This study presents the first parasitological examination of species of the tribes Cyprichromini (Cyprichromis microlepidotus (Poll, 1956)), Eretmodini (Eretmodus marksmithi Burgess, 2012 and Tanganicodus irsacae Poll, 1950) and Ectodini (Aulonocranus dewindti (Boulenger, 1899)). Specimens of the ectodine Ophthalmotilapia nasuta (Poll & Matthes, 1962) from which four Cichlidogyrus spp. have been previously described from more southern localities were also studied. Further, we discuss the haptor configuration in Tanganyikan Cichlidogyrus spp. and highlight the morphological diversity of the vagina, and that of the heel, a sclerotized part of the male copulatory organ, absent in some species of Cichlidogyrus. Methods Cichlidogyrus spp. were isolated from gills and fixed using GAP. Haptoral and genital hard parts were measured and drawn by means of a phase contrast microscopic examination. Results We describe eight new species: Cichlidogyrus milangelnari n. sp. on C. microlepidotus; C. jeanloujustinei n. sp. on E. marksmithi; C. evikae n. sp. on T. irsacae; C. aspiralis n. sp., C. glacicremoratus n. sp. and C. rectangulus n. sp. on O. nasuta; and C. pseudoaspiralis n. sp. and C. discophonum n. sp. on A. dewindti. Three haptoral morphotypes were recognized among the new species. Species of Cichlidogyrus from closely related hosts exhibited the same morphotypes. Geographical variation in Cichlidogyrus spp. fauna as observed in O. nasuta and three morphotypes were distinguished. Finally, we listed 111 Cichlidogyrus species, of which 27 and three Tanganyikan species lack sclerotized vagina and heel, respectively, just like 19 and seven species outside of the lake. Conclusions Haptoral and genital features in the Tanganyikan Cichlidogyrus fauna reflect the phylogenetic relationships of their cichlid hosts. It seems that several lineages of Cichlidogyrus spp. exist in Lake Tanganyika but further studies are necessary to confirm this hypothesis and answer questions related to Lake Tanganyika and its cichlids. Electronic supplementary material The online version of this article (10.1186/s13071-017-2460-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chahrazed Rahmouni
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, CZ-611 37, Brno, Czech Republic.
| | - Maarten P M Vanhove
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, CZ-611 37, Brno, Czech Republic.,Capacities for Biodiversity and Sustainable Development (CEBioS), Operational Directorate Natural Environment, Royal Belgian Institute of Natural Sciences, Vautierstraat 29, B-1000, Brussels, Belgium.,Laboratory of Biodiversity and Evolutionary Genomics, Department of Biology, University of Leuven, Charles Deberiotstraat 32, B-3000, Leuven, Belgium.,Centre for Environmental Sciences, Research Group Zoology: Biodiversity & Toxicology, Hasselt University, Agoralaan Gebouw D, B-3590, Diepenbeek, Belgium
| | - Andrea Šimková
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, CZ-611 37, Brno, Czech Republic
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18
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Pabijan M, Zieliński P, Dudek K, Stuglik M, Babik W. Isolation and gene flow in a speciation continuum in newts. Mol Phylogenet Evol 2017; 116:1-12. [PMID: 28797693 DOI: 10.1016/j.ympev.2017.08.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 08/04/2017] [Accepted: 08/06/2017] [Indexed: 02/06/2023]
Abstract
Because reproductive isolation often evolves gradually, differentiating lineages may retain the potential for genetic exchange for prolonged periods, providing an opportunity to quantify and to understand the fundamental role of gene flow during speciation. Here we delimit evolutionary lineages, reconstruct the phylogeny and infer gene flow in newts of the Lissotriton vulgaris species complex based on 74 nuclear markers sampled from 127 localities. We demonstrate that distinct lineages along the speciation continuum in newts exchange nontrivial amounts of genes, affecting their evolutionary trajectories. By integrating a wide array of methods, we delimit nine evolutionary lineages and show that two principal factors have driven their genetic differentiation: time since the last common ancestor determining levels of shared ancestral polymorphism, and shifts in geographic distributions determining the extent of secondary contact. Post-divergence gene flow, indicative of evolutionary non-independence, has been most extensive in Central Europe, while four southern European lineages have acquired the population-genetic hallmarks of independent species (L. graecus, L. kosswigi, L. lantzi, L. schmidtleri). We obtained strong statistical support for widespread mtDNA introgression following secondary contact, previously suggested by discordance between mtDNA phylogeny and morphology. Our study reveals long-term evolutionary persistence of evolutionary lineages that may periodically exchange genes with one another: although some of these lineages may become extinct or fuse, others will acquire complete reproductive isolation and will carry signatures of this complex history in their genomes.
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Affiliation(s)
- Maciej Pabijan
- Institute of Environmental Sciences, Jagiellonian University, ul. Gronostajowa 7, 30-387 Kraków, Poland.
| | - Piotr Zieliński
- Institute of Environmental Sciences, Jagiellonian University, ul. Gronostajowa 7, 30-387 Kraków, Poland.
| | - Katarzyna Dudek
- Institute of Environmental Sciences, Jagiellonian University, ul. Gronostajowa 7, 30-387 Kraków, Poland.
| | - Michał Stuglik
- Institute of Environmental Sciences, Jagiellonian University, ul. Gronostajowa 7, 30-387 Kraków, Poland; Scotland's Rural College, Integrative Animal Sciences, Easter Bush Campus, Midlothian EH25 9RG, Scotland, UK.
| | - Wiesław Babik
- Institute of Environmental Sciences, Jagiellonian University, ul. Gronostajowa 7, 30-387 Kraków, Poland.
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19
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Whole genome comparative analysis of four Georgian grape cultivars. Mol Genet Genomics 2017; 292:1377-1389. [PMID: 28785866 DOI: 10.1007/s00438-017-1353-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 07/27/2017] [Indexed: 10/19/2022]
Abstract
Grapevine is the one of the most important fruit species in the world. Comparative genome sequencing of grape cultivars is very important for the interpretation of the grape genome and understanding its evolution. The genomes of four Georgian grape cultivars-Chkhaveri, Saperavi, Meskhetian green, and Rkatsiteli, belonging to different haplogroups, were resequenced. The shotgun genomic libraries of grape cultivars were sequenced on an Illumina HiSeq. Pinot Noir nuclear, mitochondrial, and chloroplast DNA were used as reference. Mitochondrial DNA of Chkhaveri closely matches that of the reference Pinot noir mitochondrial DNA, with the exception of 16 SNPs found in the Chkhaveri mitochondrial DNA. The number of SNPs in mitochondrial DNA from Saperavi, Meskhetian green, and Rkatsiteli was 764, 702, and 822, respectively. Nuclear DNA differs from the reference by 1,800,675 nt in Chkhaveri, 1,063,063 nt in Meskhetian green, 2,174,995 in Saperavi, and 5,011,513 in Rkatsiteli. Unlike mtDNA Pinot noir, chromosomal DNA is closer to the Meskhetian green than to other cultivars. Substantial differences in the number of SNPs in mitochondrial and nuclear DNA of Chkhaveri and Pinot noir cultivars are explained by backcrossing or introgression of their wild predecessors before or during the process of domestication. Annotation of chromosomal DNA of Georgian grape cultivars by MEGANTE, a web-based annotation system, shows 66,745 predicted genes (Chkhaveri-17,409; Saperavi-17,021; Meskhetian green-18,355; and Rkatsiteli-13,960). Among them, 106 predicted genes and 43 pseudogenes of terpene synthase genes were found in chromosomes 12, 18 random (18R), and 19. Four novel TPS genes not present in reference Pinot noir DNA were detected. Two of them-germacrene A synthase (Chromosome 18R) and (-) germacrene D synthase (Chromosome 19) can be identified as putatively full-length proteins. This work performs the first attempt of the comparative whole genome analysis of different haplogroups of Vitis vinifera cultivars. Based on complete nuclear and mitochondrial DNA sequence analysis, hypothetical phylogeny scheme of formation of grape cultivars is presented.
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20
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Kartavtsev YP. Barcode index number, taxonomic rank and modes of speciation: examples from fish. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:535-542. [PMID: 28481646 DOI: 10.1080/24701394.2017.1315570] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Species delimitation by DNA sequence data or DNA barcoding is successful, as confirmed by the vast BOLD data base. However, the theory that would explain this fact has not been developed yet. An approach based on Barcoding Index Number (BIN), suggested in the assignment, allows delimiting of taxa of three ranks (species, genera, and families) and statistical validation with a high precision of delimiting (over 80%), as well as shows for majority of Co-1-based single gene trees good correspondence between their topology and conventional taxa content for analyzed fish species (R2 ≈ 0.84-0.98). Knowledge of deviations from these data can help to find out new taxa and improve biodiversity description. It is concluded that delimiting is successful for bulk of cases because the geographic mode of speciation prevails in nature. It takes a long time for new taxa to form in isolation, which allows accumulation of random mutations and many different nucleotide substitutions between them that can be detected by molecular markers and give unique DNA barcodes. The use of BIN approach, described here, can aid greatly in making this important question clearer especially under wider examination of other organisms.
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Affiliation(s)
- Yuri Phedorovich Kartavtsev
- a Laboratory of Molecular Systematics, A.V. Zhirmunsky Institute of Marine Biology , National Scientific Center of Marine Biology, Russian Academy of Sciences , Vladivostok , Russia.,b Chair of Biodiversity and Marine Bioresources, Far Eastern Federal University , Vladivostok , Russia
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21
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Kmentová N, Gelnar M, Mendlová M, Van Steenberge M, Koblmüller S, Vanhove MPM. Reduced host-specificity in a parasite infecting non-littoral Lake Tanganyika cichlids evidenced by intraspecific morphological and genetic diversity. Sci Rep 2016; 6:39605. [PMID: 28004766 PMCID: PMC5177900 DOI: 10.1038/srep39605] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 11/24/2016] [Indexed: 12/27/2022] Open
Abstract
Lake Tanganyika is well-known for its high species-richness and rapid radiation processes. Its assemblage of cichlid fishes recently gained momentum as a framework to study parasite ecology and evolution. It offers a rare chance to investigate the influence of a deepwater lifestyle in a freshwater fish-parasite system. Our study represents the first investigation of parasite intraspecific genetic structure related to host specificity in the lake. It focused on the monogenean flatworm Cichlidogyrus casuarinus infecting deepwater cichlids belonging to Bathybates and Hemibates. Morphological examination of C. casuarinus had previously suggested a broad host range, while the lake's other Cichlidogyrus species are usually host specific. However, ongoing speciation or cryptic diversity could not be excluded. To distinguish between these hypotheses, we analysed intraspecific diversity of C. casuarinus. Monogeneans from nearly all representatives of the host genera were examined using morphometrics, geomorphometrics and genetics. We confirmed the low host-specificity of C. casuarinus based on morphology and nuclear DNA. Yet, intraspecific variation of sclerotized structures was observed. Nevertheless, the highly variable mitochondrial DNA indicated recent population expansion, but no ongoing parasite speciation, confirming, for the first time in freshwater, reduced parasite host specificity in the deepwater realm, probably an adaptation to low host availability.
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Affiliation(s)
- Nikol Kmentová
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Milan Gelnar
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Monika Mendlová
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Maarten Van Steenberge
- Biology Department, Royal Museum for Central Africa, Leuvensesteenweg 13, B-3080 Tervuren, Belgium.,Institute of Zoology, University of Graz, Universitätsplatz 2, A-8010 Graz, Austria.,Laboratory of Biodiversity and Evolutionary Genomics, Department of Biology, University of Leuven, Ch. Deberiotstraat 32, B-3000 Leuven, Belgium
| | - Stephan Koblmüller
- Institute of Zoology, University of Graz, Universitätsplatz 2, A-8010 Graz, Austria.,Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Květná 8, 603 65 Brno, Czech Republic
| | - Maarten P M Vanhove
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic.,Biology Department, Royal Museum for Central Africa, Leuvensesteenweg 13, B-3080 Tervuren, Belgium.,Laboratory of Biodiversity and Evolutionary Genomics, Department of Biology, University of Leuven, Ch. Deberiotstraat 32, B-3000 Leuven, Belgium.,Hasselt University, Centre for Environmental Sciences, Research Group Zoology: Biodiversity &Toxicology, Agoralaan Gebouw D, B-3590 Diepenbeek, Belgium
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22
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Osborne OG, Chapman MA, Nevado B, Filatov DA. Maintenance of Species Boundaries Despite Ongoing Gene Flow in Ragworts. Genome Biol Evol 2016; 8:1038-47. [PMID: 26979797 PMCID: PMC4860686 DOI: 10.1093/gbe/evw053] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/07/2016] [Indexed: 12/22/2022] Open
Abstract
The role of hybridization between diversifying species has been the focus of a huge amount of recent evolutionary research. While gene flow can prevent speciation or initiate species collapse, it can also generate new hybrid species. Similarly, while adaptive divergence can be wiped out by gene flow, new adaptive variation can be introduced via introgression. The relative frequency of these outcomes, and indeed the frequency of hybridization and introgression in general are largely unknown. One group of closely-related species with several documented cases of hybridization is the Mediterranean ragwort (genus: Senecio) species-complex. Examples of both polyploid and homoploid hybrid speciation are known in the clade, although their evolutionary relationships and the general frequency of introgressive hybridization among them remain unknown. Using a whole genome gene-space dataset comprising eight Senecio species we fully resolve the phylogeny of these species for the first time despite phylogenetic incongruence across the genome. Using a D-statistic approach, we demonstrate previously unknown cases of introgressive hybridization between multiple pairs of taxa across the species tree. This is an important step in establishing these species as a study system for diversification with gene flow, and suggests that introgressive hybridization may be a widespread and important process in plant evolution.
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Affiliation(s)
- Owen G Osborne
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom Department of Life Sciences, Imperial College London - Silwood Park Campus, Berkshire, United Kingdom
| | - Mark A Chapman
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom Department of Life Sciences, Imperial College London - Silwood Park Campus, Berkshire, United Kingdom Centre for Biological Sciences, Faculty of Natural & Environmental Sciences, University of Southampton, Southampton, United Kingdom
| | - Bruno Nevado
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Dmitry A Filatov
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
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23
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Breman FC, Loix S, Jordaens K, Snoeks J, Van Steenberge M. Testing the potential of DNA barcoding in vertebrate radiations: the case of the littoral cichlids (Pisces, Perciformes, Cichlidae) from Lake Tanganyika. Mol Ecol Resour 2016; 16:1455-1464. [DOI: 10.1111/1755-0998.12523] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 02/26/2016] [Accepted: 02/26/2016] [Indexed: 11/28/2022]
Affiliation(s)
- Floris C. Breman
- Biology Department; Royal Museum for Central Africa; Leuvensesteenweg 13 B-3080 Tervuren Belgium
| | - Sara Loix
- Laboratory of Biodiversity and Evolutionary Genomics; KU Leuven; Charles Debériotstraat 32 B-3000 Leuven Belgium
| | - Kurt Jordaens
- Biology Department; Royal Museum for Central Africa; Leuvensesteenweg 13 B-3080 Tervuren Belgium
| | - Jos Snoeks
- Biology Department; Royal Museum for Central Africa; Leuvensesteenweg 13 B-3080 Tervuren Belgium
- Laboratory of Biodiversity and Evolutionary Genomics; KU Leuven; Charles Debériotstraat 32 B-3000 Leuven Belgium
| | - Maarten Van Steenberge
- Biology Department; Royal Museum for Central Africa; Leuvensesteenweg 13 B-3080 Tervuren Belgium
- Laboratory of Biodiversity and Evolutionary Genomics; KU Leuven; Charles Debériotstraat 32 B-3000 Leuven Belgium
- Institute of Zoology; University of Graz; Universitätsplatz 2 8010 Graz Austria
- Operational Directorate Taxonomy and Phylogeny; Royal Belgian Institute of Natural Sciences; Vautierstraat 29 1000 Brussels Belgium
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24
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Alric B, Möst M, Domaizon I, Pignol C, Spaak P, Perga ME. Local human pressures influence gene flow in a hybridizing Daphnia
species complex. J Evol Biol 2016; 29:720-35. [DOI: 10.1111/jeb.12820] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 12/22/2015] [Accepted: 12/22/2015] [Indexed: 11/28/2022]
Affiliation(s)
- B. Alric
- INRA; UMR 0042 CARRTEL; Thonon-les-Bains France
- University of Savoie; Le Bourget du Lac France
- CNRS; UMR 5558; Laboratory of Biometry and Evolutionary Biology; University of Lyon; University Lyon 1; Villeurbanne France
| | - M. Möst
- Eawag; Swiss Federal Institute of Aquatic Science and Technology; Dübendorf Switzerland
- Institute of Integrative Biology; ETH Zurich; Zurich Switzerland
- Department of Zoology; University of Cambridge; Cambridge UK
| | - I. Domaizon
- INRA; UMR 0042 CARRTEL; Thonon-les-Bains France
- University of Savoie; Le Bourget du Lac France
| | - C. Pignol
- UMR 5204 EDYTEM; University of Savoie; Le Bourget du Lac France
| | - P. Spaak
- Eawag; Swiss Federal Institute of Aquatic Science and Technology; Dübendorf Switzerland
- Institute of Integrative Biology; ETH Zurich; Zurich Switzerland
| | - M.-E. Perga
- INRA; UMR 0042 CARRTEL; Thonon-les-Bains France
- University of Savoie; Le Bourget du Lac France
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25
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Dong F, Zou FS, Lei FM, Liang W, Li SH, Yang XJ. Testing hypotheses of mitochondrial gene-tree paraphyly: unravelling mitochondrial capture of the Streak-breasted Scimitar Babbler (Pomatorhinus ruficollis) by the Taiwan Scimitar Babbler (Pomatorhinus musicus). Mol Ecol 2014; 23:5855-67. [DOI: 10.1111/mec.12981] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 10/02/2014] [Accepted: 10/14/2014] [Indexed: 01/08/2023]
Affiliation(s)
- Feng Dong
- State Key Laboratory of Genetic Resources and Evolution; Kunming Institute of Zoology; Chinese Academy of Sciences; Kunming 650223 China
| | - Fa-Sheng Zou
- South China Institute of Endangered Animals; Guangzhou 510260 China
| | - Fu-Min Lei
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
| | - Wei Liang
- Ministry of Education Key Laboratory for Tropical Plant and Animal Ecology; College of Life Sciences; Hainan Normal University; Haikou 571158 China
| | - Shou-Hsien Li
- Department of Life Science; National Taiwan Normal University; Taipei 116 Taiwan
| | - Xiao-Jun Yang
- State Key Laboratory of Genetic Resources and Evolution; Kunming Institute of Zoology; Chinese Academy of Sciences; Kunming 650223 China
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Dong J, Mao X, Sun H, Irwin DM, Zhang S, Hua P. Introgression of mitochondrial DNA promoted by natural selection in the Japanese pipistrelle bat (Pipistrellus abramus). Genetica 2014; 142:483-94. [DOI: 10.1007/s10709-014-9794-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 09/23/2014] [Indexed: 10/24/2022]
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An important natural genetic resource of Oreochromis niloticus (Linnaeus, 1758) threatened by aquaculture activities in Loboi drainage, Kenya. PLoS One 2014; 9:e106972. [PMID: 25222491 PMCID: PMC4164595 DOI: 10.1371/journal.pone.0106972] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 08/04/2014] [Indexed: 11/19/2022] Open
Abstract
The need to improve food security in Africa through culture of tilapias has led to transfer of different species from their natural ranges causing negative impacts on wild fish genetic resources. Loboi swamp in Kenya is fed by three hot springs: Lake Bogoria Hotel, Chelaba and Turtle Springs, hosting natural populations of Oreochromis niloticus. The present study aimed at better genetic characterization of these threatened populations. Partial mtDNA sequences of the D-loop region and variations at 16 microsatellite loci were assessed in the three hot spring populations and compared with three other natural populations of O. niloticus in the region. Results obtained indicated that the hot spring populations had mitochondrial and nuclear genetic variability similar to or higher than the large closely related populations. This may be attributed to the perennial nature of the hot springs, which do not depend on rainfall but rather receive permanent water supply from deep aquifers. The study also revealed that gene flow between the three different hot spring populations was sufficiently low thus allowing their differentiation. This differentiation was unexpected considering the very close proximity of the springs to each other. It is possible that the swamp creates a barrier to free movement of fish from one spring to the other thereby diminishing gene flow. Finally, the most surprising and worrying results were that the three hot spring populations are introgressed by mtDNA genes of O. leucostictus, while microsatellite analysis suggested that some nuclear genes may also have crossed the species barrier. It is very likely that the recent intensification of aquaculture activities in the Loboi drainage may be responsible for these introgressions. Taking into account the importance of these new genetic resources, protection and management actions of the Loboi swamp should be accorded top priority to prevent the loss of these spring populations.
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Quinzin MC, Mardulyn P. Multi-locus DNA sequence variation in a complex of four leaf beetle species with parapatric distributions: Mitochondrial and nuclear introgressions reveal recent hybridization. Mol Phylogenet Evol 2014; 78:14-24. [DOI: 10.1016/j.ympev.2014.05.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 04/05/2014] [Accepted: 05/02/2014] [Indexed: 11/30/2022]
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Bryson RW, Smith BT, Nieto-Montes de Oca A, García-Vázquez UO, Riddle BR. The role of mitochondrial introgression in illuminating the evolutionary history of Nearctic treefrogs. Zool J Linn Soc 2014. [DOI: 10.1111/zoj.12169] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Robert W. Bryson
- School of Life Sciences; University of Nevada Las Vegas; Las Vegas NV 89154-4004 USA
- Department of Biology and Burke Museum of Natural History and Culture; University of Washington; Seattle WA 98195-1800 USA
| | - Brian Tilston Smith
- Museum of Natural Science; Louisiana State University; Baton Rouge LA 70803 USA
| | - Adrian Nieto-Montes de Oca
- Museo de Zoología Alfonso L. Herrera; Facultad de Ciencias; Universidad Nacional Autónoma de México; Circuito exterior s/n, Cd. Universitaria México 04510 Distrito Federal Mexico
| | - Uri Omar García-Vázquez
- Museo de Zoología Alfonso L. Herrera; Facultad de Ciencias; Universidad Nacional Autónoma de México; Circuito exterior s/n, Cd. Universitaria México 04510 Distrito Federal Mexico
| | - Brett R. Riddle
- School of Life Sciences; University of Nevada Las Vegas; Las Vegas NV 89154-4004 USA
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Denton RD, Kenyon LJ, Greenwald KR, Gibbs HL. Evolutionary basis of mitonuclear discordance between sister species of mole salamanders (Ambystoma sp.). Mol Ecol 2014; 23:2811-24. [PMID: 24787951 DOI: 10.1111/mec.12775] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Revised: 04/07/2014] [Accepted: 04/16/2014] [Indexed: 11/29/2022]
Abstract
Distinct genetic markers should show similar patterns of differentiation between species reflecting their common evolutionary histories, yet there are increasing examples of differences in the biogeographic distribution of species-specific nuclear (nuDNA) and mitochondrial DNA (mtDNA) variants within and between species. Identifying the evolutionary processes that underlie these anomalous patterns of genetic differentiation is an important goal. Here, we analyse the putative mitonuclear discordance observed between sister species of mole salamanders (Ambystoma barbouri and A. texanum) in which A. barbouri-specific mtDNA is found in animals located within the range of A. texanum. We test three hypotheses for this discordance (undetected range expansion, mtDNA introgression, and hybridization) using nuDNA and mtDNA data analysed with methods that varied in the parameters estimated and the timescales measured. Results from a Bayesian clustering technique (structure), bidirectional estimates of gene flow (migrate-n and IMa2) and phylogeny-based methods (*beast, bucky) all support the conclusion that the discordance is due to geographically restricted mtDNA introgression from A. barbouri into A. texanum. Limited data on species-specific tooth morphology match this conclusion. Significant differences in environmental conditions exist between sites where A. texanum with and without A. barbouri-like mtDNA occur, suggesting a possible role for selection in the process of introgression. Overall, our study provides a general example of the value of using complimentary analyses to make inferences of the directionality, timescale, and source of mtDNA introgression in animals.
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Affiliation(s)
- Robert D Denton
- Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, OH, 43210, USA
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Ruane S, Bryson RW, Pyron RA, Burbrink FT. Coalescent Species Delimitation in Milksnakes (Genus Lampropeltis) and Impacts on Phylogenetic Comparative Analyses. Syst Biol 2013; 63:231-50. [DOI: 10.1093/sysbio/syt099] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Dufort MJ, Keith Barker F. Range dynamics, rather than convergent selection, explain the mosaic distribution of red-winged blackbird phenotypes. Ecol Evol 2013; 3:4910-24. [PMID: 24455125 PMCID: PMC3892357 DOI: 10.1002/ece3.859] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Revised: 09/26/2013] [Accepted: 09/30/2013] [Indexed: 11/24/2022] Open
Abstract
Geographic distributions of genetic and phenotypic characters can illuminate historical evolutionary processes. In particular, mosaic distributions of phenotypically similar populations can arise from parallel evolution or from irregular patterns of dispersal and colonization by divergent forms. Two phenotypically divergent forms of the red-winged blackbird (Agelaius phoeniceus) show a mosaic phenotypic distribution, with a "bicolored" form occurring disjunctly in California and Mexico. We analyzed the relationships among these bicolored populations and neighboring typical populations, using ∼600 bp of mitochondrial DNA sequence data and 10 nuclear short tandem repeat loci. We find that bicolored populations, although separated by ∼3000 km, are genetically more similar to one other than they are to typical populations separated by ∼400 km. We also find evidence of ongoing gene flow among populations, including some evidence of asymmetric gene flow. We conclude that the current distribution of bicolored forms represents incomplete speciation, where recent asymmetric hybridization with typical A. phoeniceus is dividing the range of a formerly widespread bicolored form. This hypothesis predicts that bicolored forms may suffer extinction by hybridization. Future work will use fine-scaled geographical sampling and nuclear sequence data to test for hybrid origins of currently typical populations and to more precisely quantify the directionality of gene flow.
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Affiliation(s)
- Matthew J Dufort
- Department of Ecology, Evolution and Behavior, University of Minnesota 100 Ecology Building, 1987 Upper Buford Circle, Saint Paul, Minnesota, 55108
| | - F Keith Barker
- Department of Ecology, Evolution and Behavior, University of Minnesota 100 Ecology Building, 1987 Upper Buford Circle, Saint Paul, Minnesota, 55108 ; Bell Museum of Natural History, University of Minnesota 100 Ecology Building, 1987 Upper Buford Circle, Saint Paul, Minnesota, 55108
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Burton RS, Pereira RJ, Barreto FS. Cytonuclear Genomic Interactions and Hybrid Breakdown. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2013. [DOI: 10.1146/annurev-ecolsys-110512-135758] [Citation(s) in RCA: 200] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ronald S. Burton
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093-0202; , ,
| | - Ricardo J. Pereira
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093-0202; , ,
| | - Felipe S. Barreto
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093-0202; , ,
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Rona LDP, Carvalho-Pinto CJ, Peixoto AA. Evidence for the occurrence of two sympatric sibling species within the Anopheles (Kerteszia) cruzii complex in southeast Brazil and the detection of asymmetric introgression between them using a multilocus analysis. BMC Evol Biol 2013; 13:207. [PMID: 24063651 PMCID: PMC3850420 DOI: 10.1186/1471-2148-13-207] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Accepted: 08/21/2013] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Anopheles (Kerteszia) cruzii (Diptera: Culicidae) is a primary vector of human and simian malaria parasites in southern and southeastern Brazil. Earlier studies using chromosome inversions, isoenzymes and a number of molecular markers have suggested that An. cruzii is a species complex. RESULTS In this study, a multilocus approach using six loci, three circadian clock genes and three encoding ribosomal proteins, was carried out to investigate in more detail the genetic differentiation between the An. cruzii populations from Florianópolis-Santa Catarina (southern Brazil) and Itatiaia-Rio de Janeiro States (southeastern Brazil). The analyses were performed first comparing Florianópolis and Itatiaia, and then comparing the two putative sympatric incipient species from Itatiaia (Itatiaia A and Itatiaia B). The analysis revealed high FST values between Florianópolis and Itatiaia (considering Itatiaia A and B together) and also between the sympatric Itatiaia A and Itatiaia B, irrespective of their function. Also, using the IM program, no strong indication of migration was found between Florianópolis and Itatiaia (considering Itatiaia A and B together) using all loci together, but between Itatiaia A and Itatiaia B, the results show evidence of migration only in the direction of Itatiaia B. CONCLUSIONS The results of the multilocus analysis indicate that Florianópolis and Itatiaia represent different species of the An. cruzii complex that diverged around 0.6 Mya, and also that the Itatiaia sample is composed of two sympatric incipient species A and B, which diverged around 0.2 Mya. Asymmetric introgression was found between the latter two species despite strong divergence in some loci.
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Affiliation(s)
- Luísa D P Rona
- Universidade Federal do Rio de Janeiro, Polo de Xerém, Estrada de Xerém 27, Duque de Caxias 25245-390, RJ, Brazil.
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Zieliński P, Nadachowska-Brzyska K, Wielstra B, Szkotak R, Covaciu-Marcov SD, Cogălniceanu D, Babik W. No evidence for nuclear introgression despite complete mtDNA replacement in the Carpathian newt (Lissotriton montandoni). Mol Ecol 2013; 22:1884-903. [DOI: 10.1111/mec.12225] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Revised: 12/11/2012] [Accepted: 12/13/2012] [Indexed: 11/26/2022]
Affiliation(s)
- P. Zieliński
- Institute of Environmental Sciences; Jagiellonian University; Gronostajowa 7 30-387 Kraków Poland
| | - K. Nadachowska-Brzyska
- Institute of Environmental Sciences; Jagiellonian University; Gronostajowa 7 30-387 Kraków Poland
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Norbyvägen 18D SE-75236 Uppsala Sweden
| | - B. Wielstra
- Netherlands Biodiversity Center; P. O. Box 9517 2300 RA Leiden The Netherlands
| | - R. Szkotak
- Institute of Environmental Sciences; Jagiellonian University; Gronostajowa 7 30-387 Kraków Poland
| | - S. D. Covaciu-Marcov
- University of Oradea; Faculty of Sciences; Department of Biology; Universităţii str. 1 410087 Oradea Romania
| | - D. Cogălniceanu
- Faculty of Natural Sciences and Agricultural Sciences; University Ovidius Constanţa; Aleea Universităţii nr. 1, corp B 900470 Constanţa Romania
| | - W. Babik
- Institute of Environmental Sciences; Jagiellonian University; Gronostajowa 7 30-387 Kraków Poland
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Mikulíček P, Horák A, Zavadil V, Kautman J, Piálek J. Hybridization between three crested newt species (Triturus cristatussuperspecies) in the Czech Republic and Slovakia: comparison of nuclear markers and mitochondrial DNA. FOLIA ZOOLOGICA 2012. [DOI: 10.25225/fozo.v61.i3.a4.2012] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Peter Mikulíček
- Comenius University, Faculty of Natural Sciences, Department of Zoology, Mlynská dolina B-1, 842 15 Bratislava, Slovak Republic
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, v.v.i., Květná 8, 603 65 Brno, Czech Republic
| | - Aleš Horák
- Biology Centre of Academy of Sciences of the Czech Republic, v.v.i., Institute of Parasitology, Branišovská 31, 370 05 České Budějovice, Czech Republic
- University of South Bohemia, Faculty of Sciences, Department of Molecular Biology, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Vít Zavadil
- ENKI, o.p.s., Dukelská 145, 379 01 Třeboň, Czech Republic
| | - Ján Kautman
- Slovak National Museum — Museum of Natural History, Department of Zoology, Vajanského nábrežie 2, 814 36 Bratislava, Slovak Republic
| | - Jaroslav Piálek
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, v.v.i., Květná 8, 603 65 Brno, Czech Republic
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38
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Burton RS, Barreto FS. A disproportionate role for mtDNA in Dobzhansky-Muller incompatibilities? Mol Ecol 2012; 21:4942-57. [PMID: 22994153 DOI: 10.1111/mec.12006] [Citation(s) in RCA: 203] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Revised: 07/18/2012] [Accepted: 07/25/2012] [Indexed: 01/07/2023]
Abstract
Evolution in allopatric populations can lead to incompatibilities that result in reduced hybrid fitness and ultimately reproductive isolation upon secondary contact. The Dobzhansky-Muller (DM) model nicely accounts for the evolution of such incompatibilities. Although DM incompatibilities were originally conceived as resulting of interactions between nuclear genes, recent studies have documented cases where incompatibilities have arisen between nuclear and mitochondrial genomes (mtDNA). Although mtDNA comprises only a tiny component (typically <<0.01%) of an organism's genetic material, several features of mtDNA may lead to a disproportionate contribution to the evolution of hybrid incompatibilities: (i) essentially all functions of mtDNA require interaction with nuclear gene products. All mtDNA-encoded proteins are components of the oxidative phosphorylation (OXPHOS) system and all mtDNA-encoded RNAs are part of the mitochondrial protein synthetic machinery; both processes require interaction with nuclear-encoded proteins for function. (ii) Transcription and replication of mtDNA also involve mitonuclear interactions as nuclear-encoded proteins must bind to regulatory motifs in the mtDNA to initiate these processes. (iii) Although features of mtDNA vary amongst taxa, metazoan mtDNA is typically characterized by high nucleotide substitution rates, lack of recombination and reduced effective population sizes that collectively lead to increased chance fixation of mildly deleterious mutations. Combined, these features create an evolutionary dynamic where rapid mtDNA evolution favours compensatory nuclear gene evolution, ultimately leading to co-adaptation of mitochondrial and nuclear genomes. When previously isolated lineages hybridize in nature or in the lab, intergenomic co-adaptation is disrupted and hybrid breakdown is observed; the role of intergenomic co-adaptation in hybrid breakdown and speciation will generally be most pronounced when rates of mtDNA evolution are high or when restricted gene flow results in significant population differentiation.
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Affiliation(s)
- Ronald S Burton
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093-0202, USA.
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Meyer BS, Salzburger W. A novel primer set for multilocus phylogenetic inference in East African cichlid fishes. Mol Ecol Resour 2012; 12:1097-104. [PMID: 22816488 DOI: 10.1111/j.1755-0998.2012.03169.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The cichlid fishes in the East African Great Lakes are a prime model system for the study of adaptive radiation. Therefore, the availability of an elaborate phylogenetic framework is an important prerequisite. Previous phylogenetic hypotheses on East African cichlids are mainly based on mitochondrial and/or fragment-based markers, and, to date, no taxon-rich phylogeny exists that is based on multilocus DNA sequence data. Here, we present the design of an extensive new primer set (24 nuclear makers) for East African cichlids that will be used for multilocus phylogenetic analyses in the future. The primers are designed to work for both Sanger sequencing and next-generation sequencing with the 454 technology. As a proof of principle, we validate these primers in a phylogenetically representative set of 16 cichlid species from Lake Tanganyika and main river systems in the area and provide a basic evaluation of the markers with respect to marker length and diversity indices.
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Affiliation(s)
- Britta S Meyer
- Zoological Institute, University of Basel, Basel, Switzerland
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40
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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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Wagner CE, McCune AR, Lovette IJ. Recent speciation between sympatric Tanganyikan cichlid colour morphs. Mol Ecol 2012; 21:3283-92. [PMID: 22612462 DOI: 10.1111/j.1365-294x.2012.05607.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Lake Tanganyika, Africa's oldest lake, harbours an impressive diversity of cichlid fishes. Although diversification in its radiating groups is thought to have been initially rapid, cichlids from Lake Tanganyika show little evidence for ongoing speciation. In contrast, examples of recent divergence among sympatric colour morphs are well known in haplochromine cichlids from Lakes Malawi and Victoria. Here, we report genetic evidence for recent divergence between two sympatric Tanganyikan cichlid colour morphs. These Petrochromis morphs share mitochondrial haplotypes, yet microsatellite loci reveal that their sympatric populations form distinct genetic groups. Nuclear divergence between the two morphs is equivalent to that which arises geographically within one of the morphs over short distances and is substantially smaller than that among other sympatric species in this genus. These patterns suggest that these morphs diverged only recently, yet that barriers to gene flow exist which prevent extensive admixture despite their sympatric distribution. The morphs studied here provide an unusual example of active diversification in Lake Tanganyika's generally ancient cichlid fauna and enable comparisons of speciation processes between Lake Tanganyika and other African lakes.
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Affiliation(s)
- Catherine E Wagner
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA.
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Lack JB, Greene DU, Conroy CJ, Hamilton MJ, Braun JK, Mares MA, Van Den Bussche RA. Invasion facilitates hybridization with introgression in the Rattus rattus species complex. Mol Ecol 2012; 21:3545-61. [PMID: 22607228 DOI: 10.1111/j.1365-294x.2012.05620.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Biological invasions result in novel species interactions, which can have significant evolutionary impacts on both native and invading taxa. One evolutionary concern with invasions is hybridization among lineages that were previously isolated, but make secondary contact in their invaded range(s). Black rats, consisting of several morphologically very similar but genetically distinct taxa that collectively have invaded six continents, are arguably the most successful mammalian invaders on the planet. We used mitochondrial cytochrome b sequences, two nuclear gene sequences (Atp5a1 and DHFR) and nine microsatellite loci to examine the distribution of three invasive black rat lineages (Rattus tanezumi, Rattus rattus I and R. rattus IV) in the United States and Asia and to determine the extent of hybridization among these taxa. Our analyses revealed two mitochondrial lineages that have spread to multiple continents, including a previously undiscovered population of R. tanezumi in the south-eastern United States, whereas the third lineage (R. rattus IV) appears to be confined to Southeast Asia. Analyses of nuclear DNA (both sequences and microsatellites) suggested significant hybridization is occurring among R. tanezumi and R. rattus I in the United States and also suggest hybridization between R. tanezumi and R. rattus IV in Asia, although further sampling of the latter species pair in Asia is required. Furthermore, microsatellite analyses suggest unidirectional introgression from both R. rattus I and R. rattus IV into R. tanezumi. Within the United States, introgression appears to be occurring to such a pronounced extent that we were unable to detect any nuclear genetic signal for R. tanezumi, and a similar pattern was detected in Asia.
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Affiliation(s)
- Justin B Lack
- Department of Zoology, 501 Life Sciences West, Oklahoma State University, Stillwater, OK 74078, USA.
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Evolutionary History of Lake Tanganyika's Predatory Deepwater Cichlids. INTERNATIONAL JOURNAL OF EVOLUTIONARY BIOLOGY 2012; 2012:716209. [PMID: 22675652 PMCID: PMC3362839 DOI: 10.1155/2012/716209] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Accepted: 03/05/2012] [Indexed: 11/23/2022]
Abstract
Hybridization among littoral cichlid species in Lake Tanganyika was inferred in several molecular phylogenetic studies. The phenomenon is generally attributed to the lake level-induced shoreline and habitat changes. These allow for allopatric divergence of geographically fragmented populations alternating with locally restricted secondary contact and introgression between incompletely isolated taxa. In contrast, the deepwater habitat is characterized by weak geographic structure and a high potential for gene flow, which may explain the lower species richness of deepwater than littoral lineages. For the same reason, divergent deepwater lineages should have evolved strong intrinsic reproductive isolation already in the incipient stages of diversification, and, consequently, hybridization among established lineages should have been less frequent than in littoral lineages. We test this hypothesis in the endemic Lake Tanganyika deepwater cichlid tribe Bathybatini by comparing phylogenetic trees of Hemibates and Bathybates species obtained with nuclear multilocus AFLP data with a phylogeny based on mitochondrial sequences. Consistent with our hypothesis, largely congruent tree topologies and negative tests for introgression provided no evidence for introgressive hybridization between the deepwater taxa. Together, the nuclear and mitochondrial data established a well-supported phylogeny and suggested ecological segregation during speciation.
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