1
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Burban E, Tenaillon MI, Glémin S. RIDGE, a tool tailored to detect gene flow barriers across species pairs. Mol Ecol Resour 2024; 24:e13944. [PMID: 38419376 DOI: 10.1111/1755-0998.13944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 01/19/2024] [Accepted: 02/05/2024] [Indexed: 03/02/2024]
Abstract
Characterizing the processes underlying reproductive isolation between diverging lineages is central to understanding speciation. Here, we present RIDGE-Reproductive Isolation Detection using Genomic polymorphisms-a tool tailored for quantifying gene flow barrier proportion and identifying the relevant genomic regions. RIDGE relies on an Approximate Bayesian Computation with a model-averaging approach to accommodate diverse scenarios of lineage divergence. It captures heterogeneity in effective migration rate along the genome while accounting for variation in linked selection and recombination. The barrier detection test relies on numerous summary statistics to compute a Bayes factor, offering a robust statistical framework that facilitates cross-species comparisons. Simulations revealed RIDGE's efficiency in capturing signals of ongoing migration. Model averaging proved particularly valuable in scenarios of high model uncertainty where no migration or migration homogeneity can be wrongly assumed, typically for recent divergence times <0.1 2Ne generations. Applying RIDGE to four published crow data sets, we first validated our tool by identifying a well-known large genomic region associated with mate choice patterns. Second, while we identified a significant overlap of outlier loci using RIDGE and traditional genomic scans, our results suggest that a substantial portion of previously identified outliers are likely false positives. Outlier detection relies on allele differentiation, relative measures of divergence and the count of shared polymorphisms and fixed differences. Our analyses also highlight the value of incorporating multiple summary statistics including our newly developed outlier ones that can be useful in challenging detection conditions.
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Affiliation(s)
- Ewen Burban
- University of Rennes, CNRS, ECOBIO-UMR 6553, Rennes, France
| | - Maud I Tenaillon
- University Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette, France
| | - Sylvain Glémin
- University of Rennes, CNRS, ECOBIO-UMR 6553, Rennes, France
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
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2
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Abou Zeid F, Morelli F, Ibáñez-Álamo JD, Díaz M, Reif J, Jokimäki J, Suhonen J, Kaisanlahti-Jokimäki ML, Markó G, Bussière R, Mägi M, Tryjanowski P, Kominos T, Galanaki A, Bukas N, Pruscini F, Jerzak L, Ciebiera O, Benedetti Y. Spatial Overlap and Habitat Selection of Corvid Species in European Cities. Animals (Basel) 2023; 13:ani13071192. [PMID: 37048448 PMCID: PMC10093487 DOI: 10.3390/ani13071192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 03/22/2023] [Accepted: 03/27/2023] [Indexed: 04/01/2023] Open
Abstract
Understanding habitat and spatial overlap in sympatric species of urban areas would aid in predicting species and community modifications in response to global change. Habitat overlap has been widely investigated for specialist species but neglected for generalists living in urban settings. Many corvid species are generalists and are adapted to urban areas. This work aimed to determine the urban habitat requirements and spatial overlap of five corvid species in sixteen European cities during the breeding season. All five studied corvid species had high overlap in their habitat selection while still having particular tendencies. We found three species, the Carrion/Hooded Crow, Rook, and Eurasian Magpie, selected open habitats. The Western Jackdaw avoided areas with bare soil cover, and the Eurasian Jay chose more forested areas. The species with similar habitat selection also had congruent spatial distributions. Our results indicate that although the corvids had some tendencies regarding habitat selection, as generalists, they still tolerated a wide range of urban habitats, which resulted in high overlap in their habitat niches and spatial distributions.
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Affiliation(s)
- Farah Abou Zeid
- Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Prague, Czech Republic; (F.M.); (Y.B.)
- Correspondence:
| | - Federico Morelli
- Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Prague, Czech Republic; (F.M.); (Y.B.)
- Institute of Biological Sciences, University of Zielona Góra, Prof. Z. Szafrana St. 1, 65-516 Zielona Góra, Poland; (L.J.); (O.C.)
| | | | - Mario Díaz
- Department of Biogeography and Global Change, Museo Nacional de Ciencias Naturales (BGC-MNCN-CSIC), 28006 Madrid, Spain;
| | - Jiří Reif
- Institute for Environmental Studies, Faculty of Science, Charles University, Prague, Benatska 2, 128 01 Praha, Czech Republic;
- Department of Zoology, Faculty of Science, Palacky University in Olomouc, 17. Listopadu 50, 771 46 Olomouc, Czech Republic
| | - Jukka Jokimäki
- Nature Inventory and EIA-Services, Arctic Centre, University of Lapland, P.O. Box 122, 96101 Rovaniemi, Finland; (J.J.); (M.-L.K.-J.)
| | - Jukka Suhonen
- Department of Biology, University of Turku, 20014 Turku, Finland;
| | - Marja-Liisa Kaisanlahti-Jokimäki
- Nature Inventory and EIA-Services, Arctic Centre, University of Lapland, P.O. Box 122, 96101 Rovaniemi, Finland; (J.J.); (M.-L.K.-J.)
| | - Gábor Markó
- Department of Plant Pathology, Institute of Plant Protection, Hungarian University of Agriculture and Life Sciences, Ménesi út 44, 1118 Budapest, Hungary;
| | | | - Marko Mägi
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, 50409 Tartu, Estonia;
| | - Piotr Tryjanowski
- Institute of Zoology, Poznań University of Life Sciences, Wojska Polskiego 71C, 60-625 Poznań, Poland;
| | - Theodoros Kominos
- Department of Zoology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (T.K.); (A.G.)
| | - Antonia Galanaki
- Department of Zoology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (T.K.); (A.G.)
| | - Nikos Bukas
- Plegadis, Riga Feraiou 6A, 45444 Ioannina, Greece;
| | | | - Leszek Jerzak
- Institute of Biological Sciences, University of Zielona Góra, Prof. Z. Szafrana St. 1, 65-516 Zielona Góra, Poland; (L.J.); (O.C.)
| | - Olaf Ciebiera
- Institute of Biological Sciences, University of Zielona Góra, Prof. Z. Szafrana St. 1, 65-516 Zielona Góra, Poland; (L.J.); (O.C.)
| | - Yanina Benedetti
- Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Prague, Czech Republic; (F.M.); (Y.B.)
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3
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McDiarmid CS, Finch F, Peso M, van Rooij E, Hooper DM, Rowe M, Griffith SC. Experimentally testing mate preference in an avian system with unidirectional bill color introgression. Ecol Evol 2023; 13:e9812. [PMID: 36825134 PMCID: PMC9942114 DOI: 10.1002/ece3.9812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 01/16/2023] [Indexed: 02/23/2023] Open
Abstract
Mating behavior can play a key role in speciation by inhibiting or facilitating gene flow between closely related taxa. Hybrid zones facilitate a direct examination of mating behavior and the traits involved in establishing species barriers. The long-tailed finch (Poephila acuticauda) has two hybridizing subspecies that differ in bill color (red and yellow), and the yellow bill phenotype appears to have introgressed ~350 km eastward following secondary contact. To examine the role of mate choice on bill color introgression, we performed behavioral assays using natural and manipulated bill colors. We found an assortative female mating preference for males of their own subspecies when bill color was not manipulated. However, we did not find this assortative preference in trials based on artificially manipulated bill color. This could suggest that assortative preference is not fixed entirely on bill color and instead may be based on a different trait (e.g., song) or a combination of traits, or alternatively may be due to lower statistical power alongside the bill manipulations being unconvincing to the female choosers. Intriguingly, we find a bias in the inheritance of bill color in captive bred F1 hybrid females. Previous modeling suggests that assortative mate preference and this kind of partial dominance in the underlying genes may together contribute to introgression, making the genetic architecture of bill color in this system a priority for future research.
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Affiliation(s)
- Callum S. McDiarmid
- School of Natural SciencesMacquarie UniversitySydneyNew South WalesAustralia
| | - Fiona Finch
- School of Natural SciencesMacquarie UniversitySydneyNew South WalesAustralia
| | - Marianne Peso
- School of Natural SciencesMacquarie UniversitySydneyNew South WalesAustralia
| | - Erica van Rooij
- School of Natural SciencesMacquarie UniversitySydneyNew South WalesAustralia
| | - Daniel M. Hooper
- Department of Biological SciencesColumbia UniversityNew YorkNew YorkUSA,Institute for Comparative GenomicsAmerican Museum of Natural HistoryNew YorkNew YorkUSA
| | - Melissah Rowe
- Department of Animal EcologyNetherlands Institute of Ecology (NIOO‐KNAW)WageningenThe Netherlands
| | - Simon C. Griffith
- School of Natural SciencesMacquarie UniversitySydneyNew South WalesAustralia
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4
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Mallet J, Mullen SP. Reproductive isolation is a heuristic, not a measure: a commentary on Westram et al., 2022. J Evol Biol 2022; 35:1175-1182. [PMID: 36063161 DOI: 10.1111/jeb.14052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 12/17/2022]
Abstract
Reproductive isolation is the heuristic basis of the biological species concept, but what is it? Westram et al. (this issue) propose that it is a measurable quantity, "barrier strength," that prevents gene flow among populations. However, their attempt to make the concept of reproductive isolation more scientific is unlikely to satisfy the diverse opinions of all evolutionary biologists. There are many different opinions about the nature of species, even under the biological species concept. Complete reproductive isolation, where gene flow is effectively zero, is regarded by some biologists as an important end point of speciation. Others, including Westram et al., argue for a more nuanced approach, and they also suggest that reproductive isolation may differ in different parts of the genome due to variation in genetic linkage to divergently selected loci. In contrast to both these approaches, we favour as a key criterion of speciation the stable coexistence of divergent populations in sympatry. Obviously, such populations must be reproductively isolated in some sense, but neither the fraction of the genome that is exchanged, nor measures of overall barrier strength acting on neutral variation will yield very precise predictions as to species status. Although an overall measure of reproductive isolation is virtually unattainable for these reasons, its early generation components, such as assortative mating, divergent selection, or hybrid inviability and sterility are readily measurable and remain informative. For example, we can make the prediction that to remain divergent in sympatry, almost all sexual species will require strong assortative mating, as well as some sort of ecological or intrinsic selection against hybrids and introgressed variants.
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Affiliation(s)
- James Mallet
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Sean P Mullen
- Department of Biology, Boston University, Boston, Massachusetts, USA
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5
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Peñalba JV, Peters JL, Joseph L. Sustained plumage divergence despite weak genomic differentiation and broad sympatry in sister species of Australian woodswallows (
Artamus
spp.). Mol Ecol 2022; 31:5060-5073. [DOI: 10.1111/mec.16637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 07/13/2022] [Accepted: 07/21/2022] [Indexed: 11/29/2022]
Affiliation(s)
- Joshua V. Peñalba
- Museum für Naturkunde Berlin Leibniz Institute for Evolution and Biodiversity Science Center for Integrative Biodiversity Discovery, Invalidenstr. 43, D‐10115 Berlin Germany
| | - Jeffrey L. Peters
- Department of Biological Sciences Wright State University Dayton OH USA
| | - Leo Joseph
- Australian National Wildlife Collection, CSIRO National Research Collections Australia Canberra Australia
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