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Mendoza-Maya E, Giles-Pérez GI, Vargas-Hernández JJ, Sáenz-Romero C, Martínez-Trujillo M, de Los Angeles Beltrán-Nambo M, Hernández-Díaz JC, Prieto-Ruíz JÁ, Jaramillo-Correa JP, Wehenkel C. Evolutionary drivers of reproductive fitness in two endangered forest trees. THE NEW PHYTOLOGIST 2024. [PMID: 39187985 DOI: 10.1111/nph.20073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Accepted: 08/06/2024] [Indexed: 08/28/2024]
Abstract
Population genetics theory predicts a relationship between fitness, genetic diversity (H0) and effective population size (Ne), which is often tested through heterozygosity-fitness correlations (HFCs). We tested whether population and individual fertility and heterozygosity are correlated in two endangered Mexican spruces (Picea martinezii and Picea mexicana) by combining genomic, demographic and reproductive data (seed development and germination traits). For both species, there was a positive correlation between population size and seed development traits, but not germination rate. Individual genome-wide heterozygosity and seed traits were only correlated in P. martinezii (general-effects HFC), and none of the candidate single nucleotide polymorphisms (SNPs) associated with individual fertility showed heterozygote advantage in any species (no local-effects HFC). We observed a single and recent (c. 30 thousand years ago (ka)) population decline for P. martinezii; the collapse of P. mexicana occurred in two phases separated by a long period of stability (c. 800 ka). Recruitment always contributed more to total population census than adult trees in P. mexicana, while this was only the case in the largest populations of P. martinezii. Equating fitness to either H0 or Ne, as traditionally proposed in conservation biology, might not always be adequate, as species-specific evolutionary factors can decouple the expected correlation between these parameters.
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Affiliation(s)
- Eduardo Mendoza-Maya
- Programa Institucional de Doctorado en Ciencias Agropecuarias y Forestales, Universidad Juárez del Estado de Durango, 34000, Durango, Mexico
| | - Gustavo Ibrahim Giles-Pérez
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, 04510, Ciudad de Mexico, Mexico
| | - J Jesús Vargas-Hernández
- Postgrado en Ciencias Forestales, Colegio de Postgraduados, Montecillo, Texcoco, 56264, Estado de México, Mexico
| | - Cuauhtémoc Sáenz-Romero
- Instituto de Investigaciones sobre los Recursos Naturales, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, 58330, Michoacán, Mexico
| | - Miguel Martínez-Trujillo
- Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, 58030, Michoacán, Mexico
| | | | - José Ciro Hernández-Díaz
- Instituto de Silvicultura e Industria de la Madera, Universidad Juárez del Estado de Durango, 34120, Durango, Mexico
| | - José Ángel Prieto-Ruíz
- Facultad de Ciencias Forestales y Ambientales, Universidad Juárez del Estado de Durango, 34120, Durango, Mexico
| | - Juan P Jaramillo-Correa
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, 04510, Ciudad de Mexico, Mexico
| | - Christian Wehenkel
- Instituto de Silvicultura e Industria de la Madera, Universidad Juárez del Estado de Durango, 34120, Durango, Mexico
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Katsuhara KR, Ushimaru A, Miyazaki Y. Does a coexisting congener of a mixed mating species affect the genetic structure and selfing rate via reproductive interference? Oecologia 2024:10.1007/s00442-024-05607-x. [PMID: 39174734 DOI: 10.1007/s00442-024-05607-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 08/03/2024] [Indexed: 08/24/2024]
Abstract
Reproductive interference is defined as an interspecific interaction that reduces fitness via mating processes. Although its ecological and evolutionary consequences have attracted much attention, how reproductive interference affects the population genetic structures of interacting species is still unclear. In flowering plants, recent studies found that self-pollination can mitigate the negative effects of reproductive interference. Selfing-biased seed production is expected to increase population-level inbreeding and the selfing rate, and limits gene flow via pollinator outcrossing among populations. We examined the population genetics of the mixed-mating annual herb Commelina communis f. ciliata, focusing on reproductive interference by the sympatric competing congener C. communis using microsatellite markers. First, we found that almost all C. c. f. ciliata populations had relatively high inbreeding coefficients. Then, comparing sympatric and allopatric populations, we found evidence that reproductive interference from a competing congener increased the inbreeding coefficient and selfing rate. Allopatric populations exhibit varied selfing rates while almost all sympatric populations exhibit extremely high selfing rates, suggesting that population selfing rates were also influenced by unexamined factors, such as pollinator limitation. Besides, our findings revealed that reproductive interference from a competing congener did not limit gene flow among populations. We present the first report on how reproductive interference affects the genetic aspects of populations. Our results suggested that the high selfing rate of C. c. f. ciliata promotes its sympatric distribution with C. communis, even in the presence of reproductive interference, although it is not clear whether reproductive interference directly causes the high selfing rate.
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Affiliation(s)
- Koki R Katsuhara
- Faculty of Environmental, Life, Natural Science and Technology, Okayama University, Tsushima-Naka 1-1-1, Kita-ku, Okayama, 700-8530, Japan.
- Graduate School of Human Development and Environment, Kobe University, 3-11 Tsurukabuto, Kobe, 657-8501, Japan.
| | - Atushi Ushimaru
- Graduate School of Human Development and Environment, Kobe University, 3-11 Tsurukabuto, Kobe, 657-8501, Japan
| | - Yuko Miyazaki
- Faculty of Environmental, Life, Natural Science and Technology, Okayama University, Tsushima-Naka 1-1-1, Kita-ku, Okayama, 700-8530, Japan
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Çetin C, Jokela J, Feulner PGD, Schlegel T, Tardent N, Seppälä O. Population genetic structure in a self-compatible hermaphroditic snail is driven by drift independently of its contemporary mating system. Ecol Evol 2024; 14:e70162. [PMID: 39139911 PMCID: PMC11319733 DOI: 10.1002/ece3.70162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 07/19/2024] [Accepted: 07/30/2024] [Indexed: 08/15/2024] Open
Abstract
Genetic drift, gene flow, and natural selection commonly influence population genetic diversity. In populations of self-compatible hermaphrodites, the mating system (e.g., self-fertilization) further reduces individual heterozygosity. Furthermore, selfing, as a form of inbreeding, significantly impacts genetic drift by reducing effective population size (N e). This can potentially accelerate genetic drift, particularly in small populations where self-fertilization is likely during founder events. To investigate the roles of genetic drift and contemporary mating system in populations of the freshwater snail Lymnaea stagnalis, we examined their effective population sizes (N e) and Tajima's D values, which reflect genetic drift over extended time periods, as well as estimates of within-population selfing rates and pairwise relatedness reflecting contemporary mating system. We used 4054 SNP markers obtained using restriction site associated DNA (RAD) sequencing from individuals in five snail populations originating from geographically closely located ponds. We found strong population genetic structure and differences in genetic diversity among populations. Covariation between genetic diversity and N e estimates and Tajima's D values suggested drift being an important determinant of genetic diversity and structure in these populations. However, this effect was independent of the contemporary mating system, as indicated by the similarity of selfing rates and relatedness estimates among populations. Thus, founder events (possibly including historical inbreeding) and/or drift due to small sizes of L. stagnalis populations are likely to explain their genetic structure and limit within-population genetic diversity.
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Affiliation(s)
- Cansu Çetin
- Department of Aquatic EcologySwiss Federal Institute of Aquatic Science and TechnologyDübendorfSwitzerland
- Institute of Integrative BiologyETH ZurichZurichSwitzerland
- Institute of Environmental Sciences, Faculty of BiologyJagiellonian UniversityKrakówPoland
| | - Jukka Jokela
- Department of Aquatic EcologySwiss Federal Institute of Aquatic Science and TechnologyDübendorfSwitzerland
- Institute of Integrative BiologyETH ZurichZurichSwitzerland
| | - Philine G. D. Feulner
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and BiogeochemistryEAWAG Swiss Federal Institute of Aquatic Science and TechnologyKastanienbaumSwitzerland
- Division of Aquatic Ecology and Evolution, Institute of Ecology and EvolutionUniversity of BernBernSwitzerland
| | - Tamara Schlegel
- Department of Aquatic EcologySwiss Federal Institute of Aquatic Science and TechnologyDübendorfSwitzerland
- Institute of Integrative BiologyETH ZurichZurichSwitzerland
| | - Nadine Tardent
- Department of Aquatic EcologySwiss Federal Institute of Aquatic Science and TechnologyDübendorfSwitzerland
- Institute of Integrative BiologyETH ZurichZurichSwitzerland
| | - Otto Seppälä
- Department of Aquatic EcologySwiss Federal Institute of Aquatic Science and TechnologyDübendorfSwitzerland
- Institute of Integrative BiologyETH ZurichZurichSwitzerland
- Research Department for LimnologyUniversität InnsbruckMondseeAustria
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4
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Zeitler L, Gilbert KJ. Using Runs of Homozygosity and Machine Learning to Disentangle Sources of Inbreeding and Infer Self-Fertilization Rates. Genome Biol Evol 2024; 16:evae139. [PMID: 38935434 PMCID: PMC11245710 DOI: 10.1093/gbe/evae139] [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: 02/27/2024] [Revised: 06/07/2024] [Accepted: 06/18/2024] [Indexed: 06/29/2024] Open
Abstract
Runs of homozygosity (ROHs) are indicative of elevated homozygosity and inbreeding due to mating of closely related individuals. Self-fertilization can be a major source of inbreeding which elevates genome-wide homozygosity and thus should also create long ROHs. While ROHs are frequently used to understand inbreeding in the context of conservation and selective breeding, as well as for consanguinity of populations and their demographic history, it remains unclear how ROH characteristics are altered by selfing and if this confounds expected signatures of inbreeding due to demographic change. Using simulations, we study the impact of the mode of reproduction and demographic history on ROHs. We apply random forests to identify unique characteristics of ROHs, indicative of different sources of inbreeding. We pinpoint distinct features of ROHs that can be used to better characterize the type of inbreeding the population was subjected to and to predict outcrossing rates and complex demographic histories. Using additional simulations and four empirical datasets, two from highly selfing species and two from mixed-maters, we predict the selfing rate and validate our estimations. We find that self-fertilization rates are successfully identified even with complex demography. Population genetic summary statistics improve algorithm accuracy particularly in the presence of additional inbreeding, e.g. from population bottlenecks. Our findings highlight the importance of ROHs in disentangling confounding factors related to various sources of inbreeding and demonstrate situations where such sources cannot be differentiated. Additionally, our random forest models provide a novel tool to the community for inferring selfing rates using genomic data.
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Affiliation(s)
- Leo Zeitler
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg 1700, Switzerland
| | - Kimberly J Gilbert
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg 1700, Switzerland
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Paijmans AJ, Berthelsen AL, Nagel R, Christaller F, Kröcker N, Forcada J, Hoffman JI. Little evidence of inbreeding depression for birth mass, survival and growth in Antarctic fur seal pups. Sci Rep 2024; 14:12610. [PMID: 38824161 PMCID: PMC11144264 DOI: 10.1038/s41598-024-62290-x] [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: 01/12/2024] [Accepted: 05/15/2024] [Indexed: 06/03/2024] Open
Abstract
Inbreeding depression, the loss of offspring fitness due to consanguineous mating, is generally detrimental for individual performance and population viability. We investigated inbreeding effects in a declining population of Antarctic fur seals (Arctocephalus gazella) at Bird Island, South Georgia. Here, localised warming has reduced the availability of the seal's staple diet, Antarctic krill, leading to a temporal increase in the strength of selection against inbred offspring, which are increasingly failing to recruit into the adult breeding population. However, it remains unclear whether selection operates before or after nutritional independence at weaning. We therefore used microsatellite data from 885 pups and their mothers, and SNP array data from 98 mother-offspring pairs, to quantify the effects of individual and maternal inbreeding on three important neonatal fitness traits: birth mass, survival and growth. We did not find any clear or consistent effects of offspring or maternal inbreeding on any of these traits. This suggests that selection filters inbred individuals out of the population as juveniles during the time window between weaning and recruitment. Our study brings into focus a poorly understood life-history stage and emphasises the importance of understanding the ecology and threats facing juvenile pinnipeds.
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Affiliation(s)
- A J Paijmans
- Department of Evolutionary Population Genetics, Bielefeld University, 33615, Bielefeld, Germany.
- Department of Animal Behaviour, Bielefeld University, 33501, Bielefeld, Germany.
| | - A L Berthelsen
- Department of Evolutionary Population Genetics, Bielefeld University, 33615, Bielefeld, Germany
- Department of Animal Behaviour, Bielefeld University, 33501, Bielefeld, Germany
| | - R Nagel
- Department of Evolutionary Population Genetics, Bielefeld University, 33615, Bielefeld, Germany
- Department of Animal Behaviour, Bielefeld University, 33501, Bielefeld, Germany
- Centre for Biological Diversity, University of St. Andrews, St Andrews, KY16 9TH, UK
| | - F Christaller
- Department of Evolutionary Population Genetics, Bielefeld University, 33615, Bielefeld, Germany
- Department of Animal Behaviour, Bielefeld University, 33501, Bielefeld, Germany
| | - N Kröcker
- Department of Evolutionary Population Genetics, Bielefeld University, 33615, Bielefeld, Germany
- Department of Animal Behaviour, Bielefeld University, 33501, Bielefeld, Germany
| | - J Forcada
- British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 OET, UK
| | - J I Hoffman
- Department of Evolutionary Population Genetics, Bielefeld University, 33615, Bielefeld, Germany
- Department of Animal Behaviour, Bielefeld University, 33501, Bielefeld, Germany
- British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 OET, UK
- Joint Institute for Individualisation in a Changing Environment (JICE), Bielefeld University and University of Münster, Bielefeld, Germany
- Center for Biotechnology (CeBiTec), Faculty of Biology, Bielefeld University, 33615, Bielefeld, Germany
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Huang JP, Wu SP, Chen WY, Pham GJ, Kuan YH. Genomic data revealed inbreeding despite a geographically connected stable effective population size since the Holocene in the protected Formosan Long-Arm Scarab beetle, Cheirotonus formosanus. J Hered 2024; 115:292-301. [PMID: 38364316 DOI: 10.1093/jhered/esae006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 02/08/2024] [Indexed: 02/18/2024] Open
Abstract
Biodiversity conservation is a top priority in the face of global environmental change, and the practical restoration of biodiversity has emerged as a key objective. Nevertheless, the question of how to effectively contribute to biodiversity restoration and identify suitable systems for such efforts continues to present major challenges. By using genome-wide SNP data, our study revealed that populations from different mountain ranges of the Formosan Long-Arm Scarab beetle, a flagship species that receives strict protection, exhibited a single genetic cluster with no subdivision. Additionally, our result implied an association between the demographic history and historical fluctuations in climate and environmental conditions. Furthermore, we showed that, despite a stable and moderately sized effective population over recent history, all the individuals we studied exhibited signs of genetic inbreeding. We argued that the current practice of protecting the species as one evolutionarily significant unit remains the best conservation plan and that recent habitat change may have led to the pattern of significant inbreeding. We closed by emphasizing the importance of conservation genetic studies in guiding policy decisions and highlighting the potential of genomic data for identifying ideal empirical systems for genetic rescue, or assisted gene flow studies.
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Affiliation(s)
- Jen-Pan Huang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Shu-Ping Wu
- Department of Earth and Life Science, University of Taipei, Taipei, Taiwan
| | - Wei-Yun Chen
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Guan Jie Pham
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yi-Hsiu Kuan
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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7
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Zeng ZH, Zhong L, Sun HY, Wu ZK, Wang X, Wang H, Li DZ, Barrett SCH, Zhou W. Parallel evolution of morphological and genomic selfing syndromes accompany the breakdown of heterostyly. THE NEW PHYTOLOGIST 2024; 242:302-316. [PMID: 38214455 DOI: 10.1111/nph.19522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 12/18/2023] [Indexed: 01/13/2024]
Abstract
Evolutionary transitions from outcrossing to selfing in flowering plants have convergent morphological and genomic signatures and can involve parallel evolution within related lineages. Adaptive evolution of morphological traits is often assumed to evolve faster than nonadaptive features of the genomic selfing syndrome. We investigated phenotypic and genomic changes associated with transitions from distyly to homostyly in the Primula oreodoxa complex. We determined whether the transition to selfing occurred more than once and investigated stages in the evolution of morphological and genomic selfing syndromes using 22 floral traits and both nuclear and plastid genomic data from 25 populations. Two independent transitions were detected representing an earlier and a more recently derived selfing lineage. The older lineage exhibited classic features of the morphological and genomic selfing syndrome. Although features of both selfing syndromes were less developed in the younger selfing lineage, they exhibited parallel development with the older selfing lineage. This finding contrasts with the prediction that some genomic changes should lag behind adaptive changes to morphological traits. Our findings highlight the value of comparative studies on the timing and extent of transitions from outcrossing to selfing between related lineages for investigating the tempo of morphological and molecular evolution.
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Affiliation(s)
- Zhi-Hua Zeng
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li Zhong
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hua-Ying Sun
- School of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming, Yunnan, 650500, China
| | - Zhi-Kun Wu
- Department of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, 550002, China
| | - Xin Wang
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Hong Wang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Spencer C H Barrett
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Wei Zhou
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- Lijiang Forest Biodiversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, Yunnan, 674100, China
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8
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Colangelo P, Di Civita M, Bento CM, Franchini P, Meyer A, Orel N, das Neves LCBG, Mulandane FC, Almeida JS, Senczuk G, Pilla F, Sabatelli S. Genome-wide diversity, population structure and signatures of inbreeding in the African buffalo in Mozambique. BMC Ecol Evol 2024; 24:29. [PMID: 38433185 PMCID: PMC10910738 DOI: 10.1186/s12862-024-02209-2] [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: 10/30/2023] [Accepted: 02/01/2024] [Indexed: 03/05/2024] Open
Abstract
The African buffalo, Syncerus caffer, is a key species in African ecosystems. Like other large herbivores, it plays a fundamental role in its habitat acting as an ecosystem engineer. Over the last few centuries, African buffalo populations have declined because of range contraction and demographic decline caused by direct or indirect human activities. In Mozambique, historically home to large buffalo herds, the combined effect of colonialism and subsequent civil wars has created a critical situation that urgently needs to be addressed. In this study, we focused on the analysis of genetic diversity of Syncerus caffer caffer populations from six areas of Mozambique. Using genome-wide SNPs obtained from ddRAD sequencing, we examined the population structure across the country, estimated gene flow between areas under conservation management, including national reserves, and assessed the inbreeding coefficients. Our results indicate that all studied populations of Syncerus caffer caffer are genetically depauperate, with a high level of inbreeding. Moreover, buffaloes in Mozambique present a significant population differentiation between southern and central areas. We found an unexpected genotype in the Gorongosa National Park, where buffaloes experienced a dramatic population size reduction, that shares a common ancestry with southern populations of Catuane and Namaacha. This could suggest the past occurrence of a connection between southern and central Mozambique and that the observed population structuring could reflect recent events of anthropogenic origin. All the populations analysed showed high levels of homozygosity, likely due to extensive inbreeding over the last few decades, which could have increased the frequency of recessive deleterious alleles. Improving the resilience of Syncerus caffer caffer in Mozambique is essential for preserving the ecosystem integrity. The most viable approach appears to be facilitating translocations and re-establishing connectivity between isolated herds. However, our results also highlight the importance of assessing intraspecific genetic diversity when considering interventions aimed at enhancing population viability such as selecting suitable source populations.
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Affiliation(s)
- Paolo Colangelo
- National Research Council, Research Institute on Terrestrial Ecosystems, Via Salaria km 29.300, 00015, Montelibretti (Roma), Italy
| | - Marika Di Civita
- Department of Agricultural, Environmental and Food Sciences, University of Molise, 86100, Campobasso, Italy
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University, Viale dell'Università 32, 00185, Roma, Italy
| | - Carlos M Bento
- Natural History Museum, Eduardo Mondlane University, Travessia do Zambeze 104, 1100, Maputo, Mozambique
| | - Paolo Franchini
- Department of Biology, University of Konstanz, Konstanz, Germany.
- Department of Ecological and Biological Sciences, University of Tuscia, Viale dell'Università s.n.c, 01100, Viterbo, Italy.
| | - Axel Meyer
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Nadiya Orel
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Luis C B G das Neves
- Biotechnology Centre of Eduardo Mondlane University, Maputo, Mozambique
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Sciences, University of Pretoria, Pretoria, South Africa
| | | | | | - Gabriele Senczuk
- Department of Agricultural, Environmental and Food Sciences, University of Molise, 86100, Campobasso, Italy
| | - Fabio Pilla
- Department of Agricultural, Environmental and Food Sciences, University of Molise, 86100, Campobasso, Italy
| | - Simone Sabatelli
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University, Viale dell'Università 32, 00185, Roma, Italy
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Osborne MJ, Archdeacon TP, Yackulic CB, Dudley RK, Caeiro-Dias G, Turner TF. Genetic erosion in an endangered desert fish during a megadrought despite long-term supportive breeding. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2024; 38:e14154. [PMID: 37489292 DOI: 10.1111/cobi.14154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 06/08/2023] [Accepted: 07/05/2023] [Indexed: 07/26/2023]
Abstract
Human water use combined with a recent megadrought have reduced river and stream flow through the southwest United States and led to periodic drying of formerly perennial river segments. Reductions in snowmelt runoff and increased extent of drying collectively threaten short-lived, obligate aquatic species, including the endangered Rio Grande silvery minnow (Hybognathus amarus). This species is subject to boom-and-bust population dynamics, under which large fluctuations in abundance are expected to lower estimates of effective population size and erode genetic diversity over time. Rates of diversity loss are also affected by additions of hatchery-origin fish used to supplement the wild population. We used demographic and genetic data from wild and hatchery individuals to examine the relationship of genetic diversity and effective population size to abundance over the last two decades. Genetic diversity was low during the early 2000s, but diversity and demographic metrics stabilized after the hatchery program was initiated and environmental conditions improved. Yet, from 2017 onward, allelic diversity declined (Cohen's d = 1.34) and remained low despite hatchery stocking and brief wild population recovery. Across the time series, single-sample estimates of effective population size based on linkage disequilibrium (LD Ne ) were positively associated (r = 0.53) with wild abundance and total abundance, but as the proportion of hatchery-origin spawners increased, LD Ne declined (r = -0.55). Megadrought limited wild spawner abundance and precluded refreshment of hatchery brood stocks with wild fish; hence, we predict a riverine population increasingly dominated by hatchery-origin individuals and accelerated loss of genetic diversity despite supplementation. We recommend an adaptive and accelerated management plan that integrates river flow management and hatchery operations to slow the pace of genetic diversity loss exacerbated by megadrought.
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Affiliation(s)
- Megan J Osborne
- Department of Biology and Museum of Southwestern Biology, MSC 03-2020, University of New Mexico, Albuquerque, New Mexico, USA
| | - Thomas P Archdeacon
- U.S. Fish and Wildlife Service, New Mexico Fish and Wildlife Conservation Office, Albuquerque, New Mexico, USA
| | - Charles B Yackulic
- U.S. Geological Survey, Southwest Biological Science Center, Flagstaff, Arizona, USA
| | - Robert K Dudley
- Department of Biology and Museum of Southwestern Biology, MSC 03-2020, University of New Mexico, Albuquerque, New Mexico, USA
- American Southwest Ichthyological Researchers, Albuquerque, New Mexico, USA
| | - Guilherme Caeiro-Dias
- Department of Biology and Museum of Southwestern Biology, MSC 03-2020, University of New Mexico, Albuquerque, New Mexico, USA
| | - Thomas F Turner
- Department of Biology and Museum of Southwestern Biology, MSC 03-2020, University of New Mexico, Albuquerque, New Mexico, USA
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10
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Afonso RO, Pina-Martins F, Friesen V, Sun Z, Campioni L, Madeiros J, Silva MC. No evidence of inbreeding depression despite a historical severe bottleneck in the endangered Bermuda petrel (Pterodroma cahow). J Hered 2023; 114:459-469. [PMID: 37162284 DOI: 10.1093/jhered/esad030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 05/08/2023] [Indexed: 05/11/2023] Open
Abstract
The Bermuda petrel Pterodroma cahow is an island endemic seabird that belongs to the Procellariiformes, one of the most endangered orders of birds. Historical records suggest a significant population size decline following human settlement in Bermuda, bringing the species to near extinction. Since the 1950s, the population has been recovering aided by the implementation of an ongoing conservation plan. However, it still faces several threats, and negative genetic effects resulting from that drastic decline are to be expected, including inbreeding and genetic drift. We studied genetic diversity and levels of inbreeding, and their effects on individual fitness and mating choice. We also tested for a genetic signature of the recent demographic bottleneck. For this, we analyzed variation in thousands of nuclear single-nucleotide polymorphisms derived from double digest restriction site-associated DNA sequencing and 1 mitochondrial gene (cytochrome oxidase I). The results revealed that the Bermuda petrel suffered a recent genetic bottleneck and shows low mitochondrial diversity compared with other petrel species. Conversely, nuclear diversity was similar to that of other endangered petrels. Inbreeding levels were not high overall, although some individuals were highly inbred. However, we found no evidence that individual inbreeding or relatedness between mates affected hatching success, or that mate choice is influenced by kinship in this very small population.
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Affiliation(s)
- Rita O Afonso
- cE3c-Centre for Ecology, Evolution and Environmental Changes & CHANGE-Global Change and Sustainability Institute, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Francisco Pina-Martins
- cE3c-Centre for Ecology, Evolution and Environmental Changes & CHANGE-Global Change and Sustainability Institute, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Vicki Friesen
- Department of Biology, Queen's University, Kingston, ON, Canada
| | - Zhengxin Sun
- Department of Biology, Queen's University, Kingston, ON, Canada
| | - Letizia Campioni
- MARE-Marine and Environmental Sciences Centre, Ispa-Instituto Universitário, Lisboa, Portugal
| | - Jeremy Madeiros
- Department of Environment and Natural Resources, Government of Bermuda, Hamilton, Bermuda
| | - Mónica C Silva
- cE3c-Centre for Ecology, Evolution and Environmental Changes & CHANGE-Global Change and Sustainability Institute, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
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11
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Teterina AA, Willis JH, Lukac M, Jovelin R, Cutter AD, Phillips PC. Genomic diversity landscapes in outcrossing and selfing Caenorhabditis nematodes. PLoS Genet 2023; 19:e1010879. [PMID: 37585484 PMCID: PMC10461856 DOI: 10.1371/journal.pgen.1010879] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 08/28/2023] [Accepted: 07/21/2023] [Indexed: 08/18/2023] Open
Abstract
Caenorhabditis nematodes form an excellent model for studying how the mode of reproduction affects genetic diversity, as some species reproduce via outcrossing whereas others can self-fertilize. Currently, chromosome-level patterns of diversity and recombination are only available for self-reproducing Caenorhabditis, making the generality of genomic patterns across the genus unclear given the profound potential influence of reproductive mode. Here we present a whole-genome diversity landscape, coupled with a new genetic map, for the outcrossing nematode C. remanei. We demonstrate that the genomic distribution of recombination in C. remanei, like the model nematode C. elegans, shows high recombination rates on chromosome arms and low rates toward the central regions. Patterns of genetic variation across the genome are also similar between these species, but differ dramatically in scale, being tenfold greater for C. remanei. Historical reconstructions of variation in effective population size over the past million generations echo this difference in polymorphism. Evolutionary simulations demonstrate how selection, recombination, mutation, and selfing shape variation along the genome, and that multiple drivers can produce patterns similar to those observed in natural populations. The results illustrate how genome organization and selection play a crucial role in shaping the genomic pattern of diversity whereas demographic processes scale the level of diversity across the genome as a whole.
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Affiliation(s)
- Anastasia A. Teterina
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
- Center of Parasitology, Severtsov Institute of Ecology and Evolution RAS, Moscow, Russia
| | - John H. Willis
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Matt Lukac
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Richard Jovelin
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Asher D. Cutter
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Patrick C. Phillips
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
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12
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Han EK, Tamaki I, Oh SH, Park JS, Cho WB, Jin DP, Kim BY, Yang S, Son DC, Choi HJ, Gantsetseg A, Isagi Y, Lee JH. Genetic and demographic signatures accompanying the evolution of the selfing syndrome in Daphne kiusiana, an evergreen shrub. ANNALS OF BOTANY 2023; 131:751-767. [PMID: 36469429 PMCID: PMC10184445 DOI: 10.1093/aob/mcac142] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 11/23/2022] [Indexed: 05/16/2023]
Abstract
BACKGROUND AND AIMS The evolution of mating systems from outcrossing to self-fertilization is a common transition in flowering plants. This shift is often associated with the 'selfing syndrome', which is characterized by less visible flowers with functional changes to control outcrossing. In most cases, the evolutionary history and demographic dynamics underlying the evolution of the selfing syndrome remain poorly understood. METHODS Here, we characterize differences in the demographic genetic consequences and associated floral-specific traits between two distinct geographical groups of a wild shrub, Daphne kiusiana, endemic to East Asia; plants in the eastern region (southeastern Korea and Kyushu, Japan) exhibit smaller and fewer flowers compared to those of plants in the western region (southwestern Korea). Genetic analyses were conducted using nuclear microsatellites and chloroplast DNA (multiplexed phylogenetic marker sequencing) datasets. KEY RESULTS A high selfing rate with significantly increased homozygosity characterized the eastern lineage, associated with lower levels of visibility and herkogamy in the floral traits. The two lineages harboured independent phylogeographical histories. In contrast to the western lineage, the eastern lineage showed a gradual reduction in the effective population size with no signs of a severe bottleneck despite its extreme range contraction during the last glacial period. CONCLUSIONS Our results suggest that the selfing-associated morphological changes in D. kiusiana are of relatively old origin (at least 100 000 years ago) and were driven by directional selection for efficient self-pollination. We provide evidence that the evolution of the selfing syndrome in D. kiusiana is not strongly associated with a severe population bottleneck.
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Affiliation(s)
- Eun-Kyeong Han
- Department of Biology Education, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Ichiro Tamaki
- Gifu Academy of Forest Science and Culture, 88 Sodai, Mino, Gifu 501-3714, Japan
| | - Sang-Hun Oh
- Department of Biology, Daejeon University, Daejeon 34520, Republic of Korea
| | - Jong-Soo Park
- Department of Botany, Honam National Institute of Biological Resources, Mokpo 58762, Republic of Korea
| | - Won-Bum Cho
- Department of Plant Variety Protection, National Forest Seed and Variety Center, Chungju 27495, Republic of Korea
| | - Dong-Pil Jin
- Urban Biodiversity Research Division, Sejong National Arboretum, Sejong 30106, Republic of Korea
| | - Bo-Yun Kim
- Plant Resources Division, National Institute of Biological Resources, Incheon 22689, Republic of Korea
| | - Sungyu Yang
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju 58245, Republic of Korea
| | - Dong Chan Son
- Division of Forest Biodiversity and Herbarium, Korea National Arboretum, Pocheon 11186, Republic of Korea
| | - Hyeok-Jae Choi
- Department of Biology and Chemistry, Changwon National University, Changwon 51140, Republic of Korea
| | - Amarsanaa Gantsetseg
- Department of Biology Education, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Yuji Isagi
- Division of Forest and Biomaterials Science, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Jung-Hyun Lee
- Department of Biology Education, Chonnam National University, Gwangju 61186, Republic of Korea
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13
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Hulke JM, Criscione CD. Characterization of 21 microsatellite loci for the precocious, grass-shrimp trematode Alloglossidium renale. Mol Biochem Parasitol 2023; 254:111563. [PMID: 37086899 DOI: 10.1016/j.molbiopara.2023.111563] [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: 01/31/2023] [Revised: 04/04/2023] [Accepted: 04/19/2023] [Indexed: 04/24/2023]
Abstract
We developed microsatellite markers to use in studying the population genetics of the trematode Alloglossidium renale, a fluke with a precocious life cycle where sexual maturation occurs in a grass shrimp. Among 21 tested loci in a Mississippi population sample, 14 were polymorphic, 12 of which significantly deviated from Hardy-Weinberg Equilibrium (HWE). We estimated identity disequilibrium (ID) to confirm whether the deviations from HWE were due to significant amounts of selfing or due to technical factors. The selfing rate derived from FIS was 86.6%, whereas the selfing rate obtained by ID was 83.9%, indicating that the deviation in HWE was due to a high amount of selfing within the population. These markers will be useful for ecological and evolutionary studies of A. renale especially in relation to the interplay of hermaphroditic mating systems, inbreeding depression, and transmission dynamics.
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Affiliation(s)
- Jenna M Hulke
- Department of Biology, Texas A&M University, 3258 TAMU, College Station, Texas 77843.
| | - Charles D Criscione
- Department of Biology, Texas A&M University, 3258 TAMU, College Station, Texas 77843
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14
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Medinas D, Ribeiro V, Barbosa S, Valerio F, Marques JT, Rebelo H, Paupério J, Santos S, Mira A. Fine scale genetics reveals the subtle negative effects of roads on an endangered bat. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 869:161705. [PMID: 36682566 DOI: 10.1016/j.scitotenv.2023.161705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 01/14/2023] [Accepted: 01/15/2023] [Indexed: 06/17/2023]
Abstract
The effective management of species with small and fragmented populations requires an in-depth understanding of how the effects of human-induced habitat disturbance shape the structure and gene flow at fine spatial scales. Identification of putative environmental barriers that affect individual exchange among subpopulations is imperative to prevent extinction risks. Here, we investigated how landscape affects the gene flow and relatedness structure of a population of the endangered lesser horseshoe bat (Rhinolophus hipposideros). We also assessed the effects of sexbiased dispersal on genetic relatedness. We genotyped 287 bat samples collected across southern Portugal and developed resistance surfaces for landscape variables hypothesized to affect gene flow. Then, we used spatially explicit models to fit relatedness distance through the resistance surfaces. We found genetic evidence of sex-biased dispersal and identified a significant fine scale structuring in the relatedness regarding females, the philopatric sex. Males displayed uniform levels of relatedness throughout the landscape. The results indicated less relatedness between the female´ from roosts located on proximity of roads than in roosts away from roads. Also, when analysing the sexes together the relatedness on roosts separated by highway were subtly less related in comparison to those occurring on the same side. Roads seem to be major shapers of the contemporary population structure of females, regardless of being relatively recent structures in the landscape. Furthermore, the relatedness patterns detected suggested that high tree density among roosts and continuity of forest patches in broader surrounding areas, promotes the relatedness among individuals. Landscape heterogeneity among roosts slightly decreases genetic relatedness. Nevertheless, those relationships are still weak, suggesting that population structuring driven by those factors is slowly ongoing. Thus, effective management measures should focus on issues for promoting safe road passages and suitable habitat corridors, allowing for the exchange of individuals and gene flow among lesser horseshoe bat roosts.
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Affiliation(s)
- Denis Medinas
- CIBIO/InBIO, Research Centre in Biodiversity and Genetic Resources, Pole of Évora, Research Network in Biodiversity and Evolutionary Biology, University of Évora, Mitra, 7002-554 Évora, Portugal; UBC, Conservation Biology Lab, Department of Biology, University of Évora, Mitra, 7002-554 Évora, Portugal.
| | - Vera Ribeiro
- UBC, Conservation Biology Lab, Department of Biology, University of Évora, Mitra, 7002-554 Évora, Portugal.
| | - Soraia Barbosa
- CIBIO/InBIO-UP, Research Centre in Biodiversity and Genetic Resources, University of Porto, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal.
| | - Francesco Valerio
- UBC, Conservation Biology Lab, Department of Biology, University of Évora, Mitra, 7002-554 Évora, Portugal; MED - Mediterranean Institute for Agriculture, Environment and Development, University of Évora, Mitra, 7002-554 Évora, Portugal; EaRSLab-Earth Remote Sensing Laboratory, University of Évora, 7000-671 Évora, Portugal.
| | - João Tiago Marques
- UBC, Conservation Biology Lab, Department of Biology, University of Évora, Mitra, 7002-554 Évora, Portugal; MED - Mediterranean Institute for Agriculture, Environment and Development, University of Évora, Mitra, 7002-554 Évora, Portugal.
| | - Hugo Rebelo
- CIBIO/InBIO-UP, Research Centre in Biodiversity and Genetic Resources, University of Porto, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal; CEABN-InBIO, Centre for Applied Ecology "Prof. Baeta Neves", Institute of Agronomy, University of Lisbon, Tapada da Ajuda, 1349-017 Lisbon, Portugal.
| | - Joana Paupério
- CIBIO/InBIO-UP, Research Centre in Biodiversity and Genetic Resources, University of Porto, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal.
| | - Sara Santos
- UBC, Conservation Biology Lab, Department of Biology, University of Évora, Mitra, 7002-554 Évora, Portugal; MED - Mediterranean Institute for Agriculture, Environment and Development, University of Évora, Mitra, 7002-554 Évora, Portugal.
| | - António Mira
- UBC, Conservation Biology Lab, Department of Biology, University of Évora, Mitra, 7002-554 Évora, Portugal; MED - Mediterranean Institute for Agriculture, Environment and Development, University of Évora, Mitra, 7002-554 Évora, Portugal.
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15
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Smith RD. Digenic genotypes: The interface of inbreeding, linkage, and linkage disequilibrium. Theor Popul Biol 2023; 151:1-18. [PMID: 36948254 DOI: 10.1016/j.tpb.2023.03.003] [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: 10/18/2021] [Revised: 03/07/2023] [Accepted: 03/15/2023] [Indexed: 03/24/2023]
Abstract
Many traits in populations are well understood as being Mendelian effects at single loci or additive polygenic effects across numerous loci. However, there are important phenomena and traits that are intermediate between these two extremes and are known as oligogenic traits. Here we investigate digenic, or two-locus, traits and how their frequencies in populations are affected by non-random mating, specifically inbreeding, linkage disequilibrium, and selection. These effects are examined both separately and in combination to demonstrate how many digenic traits, especially double homozygous ones, can show significant, sometimes unexpected, changes in population frequency with inbreeding, linkage, and linkage disequilibrium. The effects of selection on deleterious digenic traits are also detailed. These results are applied to both digenic traits of medical significance as well as measuring inbreeding in natural populations.
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Affiliation(s)
- Reginald D Smith
- Ronin Institute 127 Haddon Pl, Montclair, NJ 07043, USA; Supreme Vinegar LLC, 3430 Progress Dr. Suite D, Bensalem, PA 19020, USA.
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16
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Powell JH, Kalinowski ST, Taper ML, Rotella JJ, Davis CS, Garrott RA. Evidence of an Absence of Inbreeding Depression in a Wild Population of Weddell Seals ( Leptonychotes weddellii). ENTROPY (BASEL, SWITZERLAND) 2023; 25:403. [PMID: 36981292 PMCID: PMC10047074 DOI: 10.3390/e25030403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 02/17/2023] [Accepted: 02/18/2023] [Indexed: 06/18/2023]
Abstract
Inbreeding depression can reduce the viability of wild populations. Detecting inbreeding depression in the wild is difficult; developing accurate estimates of inbreeding can be time and labor intensive. In this study, we used a two-step modeling procedure to incorporate uncertainty inherent in estimating individual inbreeding coefficients from multilocus genotypes into estimates of inbreeding depression in a population of Weddell seals (Leptonychotes weddellii). The two-step modeling procedure presented in this paper provides a method for estimating the magnitude of a known source of error, which is assumed absent in classic regression models, and incorporating this error into inferences about inbreeding depression. The method is essentially an errors-in-variables regression with non-normal errors in both the dependent and independent variables. These models, therefore, allow for a better evaluation of the uncertainty surrounding the biological importance of inbreeding depression in non-pedigreed wild populations. For this study we genotyped 154 adult female seals from the population in Erebus Bay, Antarctica, at 29 microsatellite loci, 12 of which are novel. We used a statistical evidence approach to inference rather than hypothesis testing because the discovery of both low and high levels of inbreeding are of scientific interest. We found evidence for an absence of inbreeding depression in lifetime reproductive success, adult survival, age at maturity, and the reproductive interval of female seals in this population.
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Affiliation(s)
- John H. Powell
- Department of Ecology, Montana State University, P.O. Box 173460, Bozeman, MT 59717, USA
| | - Steven T. Kalinowski
- Department of Ecology, Montana State University, P.O. Box 173460, Bozeman, MT 59717, USA
| | - Mark L. Taper
- Department of Ecology, Montana State University, P.O. Box 173460, Bozeman, MT 59717, USA
| | - Jay J. Rotella
- Department of Ecology, Montana State University, P.O. Box 173460, Bozeman, MT 59717, USA
| | - Corey S. Davis
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Robert A. Garrott
- Department of Ecology, Montana State University, P.O. Box 173460, Bozeman, MT 59717, USA
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17
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Mora‐Carrera E, Stubbs RL, Keller B, Léveillé‐Bourret É, de Vos JM, Szövényi P, Conti E. Different molecular changes underlie the same phenotypic transition: Origins and consequences of independent shifts to homostyly within species. Mol Ecol 2023; 32:61-78. [PMID: 34761469 PMCID: PMC10078681 DOI: 10.1111/mec.16270] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 10/29/2021] [Accepted: 11/02/2021] [Indexed: 12/29/2022]
Abstract
The repeated transition from outcrossing to selfing is a key topic in evolutionary biology. However, the molecular basis of such shifts has been rarely examined due to lack of knowledge of the genes controlling these transitions. A classic example of mating system transition is the repeated shift from heterostyly to homostyly. Occurring in 28 angiosperm families, heterostyly is characterized by the reciprocal position of male and female sexual organs in two (or three) distinct, usually self-incompatible floral morphs. Conversely, homostyly is characterized by a single, self-compatible floral morph with reduced separation of male and female organs, facilitating selfing. Here, we investigate the origins of homostyly in Primula vulgaris and its microevolutionary consequences by integrating surveys of the frequency of homostyles in natural populations, DNA sequence analyses of the gene controlling the position of female sexual organs (CYPᵀ), and microsatellite genotyping of both progeny arrays and natural populations characterized by varying frequencies of homostyles. As expected, we found that homostyles displace short-styled individuals, but long-style morphs are maintained at low frequencies within populations. We also demonstrated that homostyles repeatedly evolved from short-styled individuals in association with different types of loss-of-function mutations in CYPᵀ. Additionally, homostyly triggers a shift to selfing, promoting increased inbreeding within and genetic differentiation among populations. Our results elucidate the causes and consequences of repeated transitions to homostyly within species, and the putative mechanisms precluding its fixation in P. vulgaris. This study represents a benchmark for future analyses of losses of heterostyly in other angiosperms.
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Affiliation(s)
- Emiliano Mora‐Carrera
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZurichSwitzerland
| | - Rebecca L. Stubbs
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZurichSwitzerland
| | - Barbara Keller
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZurichSwitzerland
| | - Étienne Léveillé‐Bourret
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZurichSwitzerland
- Département de Sciences BiologiquesInstitut de Recherche en Biologie VégétaleUniversité de MontréalMontréalQuébecCanada
| | - Jurriaan M. de Vos
- Department of Environmental Sciences – BotanyUniversity of BaselBaselSwitzerland
| | - Peter Szövényi
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZurichSwitzerland
| | - Elena Conti
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZurichSwitzerland
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18
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Keeney DB, Cobb SA, Jadin RC, Orlofske SA. Atypical life cycle does not lead to inbreeding or selfing in parasites despite clonemate accumulation in intermediate hosts. Mol Ecol 2022; 32:1777-1790. [PMID: 36579456 DOI: 10.1111/mec.16837] [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: 09/21/2022] [Revised: 12/16/2022] [Accepted: 12/19/2022] [Indexed: 12/30/2022]
Abstract
Many parasites utilize asexual and sexual reproduction and multiple hosts to complete their life cycles. How these taxa avoid inbreeding is an essential question for understanding parasite evolution and ecology. Aquatic trematodes that require multiple host species may benefit from diverse genetic parasite assemblages accumulating within second intermediate hosts prior to sexual reproduction in definitive hosts. However, Cotylurus species are able to utilize the same snail species as first and second intermediate hosts, potentially resulting in the accumulation of genetically identical clones (clonemates) prior to sexual reproduction. In this study, we developed and analysed novel microsatellite loci to determine if clones are accumulating within snail hosts prior to ingestion by bird hosts and the effects this could have on parasite inbreeding. Contrary to previous studies of aquatic trematodes, significantly large numbers of clonemates were present within snails, but full-sibs were not. Genetic structure was present over a relatively small geographical scale despite the use of vagile definitive hosts. Phylogenetic analysis identified the Cotylurus sp. clones as belonging to a single species. Despite the presence of clones within snails, mating between clones/selfing was not common and heterozygosity is maintained within individuals. Potential issues with clones mating may be mitigated by the presence of snails with numerous clones, the consumption of many snails by bird hosts and parasite clone recognition/avoidance. Use of the same host species for multiple life stages may have advantages when parasites are able to avoid inbreeding and the required hosts are common.
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Affiliation(s)
- Devon B Keeney
- Department of Biological and Environmental Sciences, Le Moyne College, Syracuse, New York, USA
| | - Sarah A Cobb
- Department of Biological and Environmental Sciences, Le Moyne College, Syracuse, New York, USA.,Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Robert C Jadin
- Department of Biology, Northeastern Illinois University, Chicago, Illinois, USA.,Department of Biology, Museum of Natural History, University of Wisconsin - Stevens Point, Stevens Point, Wisconsin, USA
| | - Sarah A Orlofske
- Department of Biology, Northeastern Illinois University, Chicago, Illinois, USA.,Department of Biology, Museum of Natural History, University of Wisconsin - Stevens Point, Stevens Point, Wisconsin, USA
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19
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Olsson M, Bererhi B, Miller E, Schwartz T, Rollings N, Lindsay W, Wapstra E. Inbreeding effects on telomeres in hatchling sand lizards (Lacerta agilis): An optimal family affair? Mol Ecol 2022; 31:6605-6616. [PMID: 36208022 PMCID: PMC10092626 DOI: 10.1111/mec.16723] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 09/15/2022] [Accepted: 09/21/2022] [Indexed: 01/13/2023]
Abstract
Telomeres are nucleotide-protein caps, predominantly at the ends of Metazoan linear chromosomes, showing complex dynamics with regard to their lengthening and shortening through life. Their complexity has entertained the idea that net telomere length and attrition could be valuable biomarkers of phenotypic and genetic quality of their bearer. Intuitively, those individuals could be more heterozygous and, hence, less inbred. However, some inbred taxa have longer, not shorter, telomeres. To understand the role of inbreeding in this complex scenario we need large samples across a range of genotypes with known maternity and paternity in telomere-screened organisms under natural conditions. We assessed the effects of parental and hatchling inbreeding on telomere length in >1300 offspring from >500 sires and dams in a population of sand lizards (Lacerta agilis). Maternal and paternal ID and their interactions predict hatchling telomere length at substantial effect sizes (R2 > .50). Deviation from mean maternal heterozygosity statistically predicts shorter offspring telomeres but this only when sibship is controlled for by paternal ID, and then is still limited (R2 = .06). Raw maternal heterozygosity scores, ignoring absolute deviation from the mean, explained 0.07% of the variance in hatchling telomere length. In conclusion, inbreeding is not a driver of telomere dynamics in the sand lizard (Lacerta agilis) study system.
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Affiliation(s)
- Mats Olsson
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.,School of Biological Sciences, University of Wollongong, Wollongong, New South Wales, Australia
| | - Badreddine Bererhi
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Emily Miller
- Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Tonia Schwartz
- Biological Sciences, Auburn University, Auburn, Alabama, USA
| | - Nicky Rollings
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Willow Lindsay
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Erik Wapstra
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
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20
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Criscione CD, Hulke JM, Goater CP. Trematode Clone Abundance Distributions: An Eco-Evolutionary Link between Parasite Transmission and Parasite Mating Systems. J Parasitol 2022; 108:565-576. [DOI: 10.1645/22-68] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Charles D. Criscione
- Department of Biology, Texas A&M University, 3258 TAMU, College Station, Texas 77843
| | - Jenna M. Hulke
- Department of Biology, Texas A&M University, 3258 TAMU, College Station, Texas 77843
| | - Cameron P. Goater
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, T1K 3M4, Canada
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21
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Cheptou PO, Imbert E, Thomann M. Rapid evolution of selfing syndrome traits in Viola arvensis revealed by resurrection ecology. AMERICAN JOURNAL OF BOTANY 2022; 109:1838-1846. [PMID: 35929747 DOI: 10.1002/ajb2.16028] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 05/13/2022] [Accepted: 05/13/2022] [Indexed: 06/15/2023]
Abstract
PREMISE As part of global change, climate warming and pollinator decline are expected to affect plant phenology and plant-pollinator interactions. This paper aims at characterizing rapid evolution of life history traits and floral traits over two decades in the wild pansy (Viola arvensis), a common weed in agrosystems. METHODS We used a resurrection ecology approach with genotypes sampled in 1991 and 2012 from a population in Burgundy (France). The species has a mixed mating system (hereafter: mixed selfer) and presents a floral polymorphism. To correct for maternal effects, we measured plant traits in the second generation in a common garden (after a refreshing generation) to characterize plant evolution during the two decades. In addition, historical population selfing rates in 1991 and 2012 were inferred from microsatellites markers through heterozygote deficiency and identity disequilibrium. RESULTS Phenotypic data revealed a significant advance in flowering date, reduced flower sizes and a higher propensity of plants to set seed by autonomous selfing. Moreover, we detected a change in color morph frequency with an increase of the pale morph frequency. In accordance with phenotypic data, the neutral genetic data revealed an increase in historical selfing rates from 0.68 in 1991 to 0.86 in 2012. CONCLUSIONS Taken together, such data suggest that the wild pansy, a mixed selfer, is evolving a selfing syndrome that may be the consequence of reduced pollinator activity in agrosystems.
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Affiliation(s)
- Pierre-Olivier Cheptou
- CEFE UMR 5175, CNRS, Université de Montpellier, Université Paul-Valery Montpellier, EPHE, Montpellier, Cedex, 05, France
| | - Eric Imbert
- ISEM, University of Montpellier-Montpellier, France
| | - Michel Thomann
- CEFE UMR 5175, CNRS, Université de Montpellier, Université Paul-Valery Montpellier, EPHE, Montpellier, Cedex, 05, France
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22
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Surendranadh P, Arathoon L, Baskett CA, Field DL, Pickup M, Barton NH. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. Genetics 2022; 221:iyac083. [PMID: 35639938 PMCID: PMC9252276 DOI: 10.1093/genetics/iyac083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 05/05/2022] [Indexed: 11/13/2022] Open
Abstract
Many studies have quantified the distribution of heterozygosity and relatedness in natural populations, but few have examined the demographic processes driving these patterns. In this study, we take a novel approach by studying how population structure affects both pairwise identity and the distribution of heterozygosity in a natural population of the self-incompatible plant Antirrhinum majus. Excess variance in heterozygosity between individuals is due to identity disequilibrium, which reflects the variance in inbreeding between individuals; it is measured by the statistic g2. We calculated g2 together with FST and pairwise relatedness (Fij) using 91 SNPs in 22,353 individuals collected over 11 years. We find that pairwise Fij declines rapidly over short spatial scales, and the excess variance in heterozygosity between individuals reflects significant variation in inbreeding. Additionally, we detect an excess of individuals with around half the average heterozygosity, indicating either selfing or matings between close relatives. We use 2 types of simulation to ask whether variation in heterozygosity is consistent with fine-scale spatial population structure. First, by simulating offspring using parents drawn from a range of spatial scales, we show that the known pollen dispersal kernel explains g2. Second, we simulate a 1,000-generation pedigree using the known dispersal and spatial distribution and find that the resulting g2 is consistent with that observed from the field data. In contrast, a simulated population with uniform density underestimates g2, indicating that heterogeneous density promotes identity disequilibrium. Our study shows that heterogeneous density and leptokurtic dispersal can together explain the distribution of heterozygosity.
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Affiliation(s)
| | | | | | - David L Field
- School of Science, Edith Cowan University, Joondalup WA 6027, Australia
| | - Melinda Pickup
- IST Austria, 3400 Klosterneuburg, Austria
- Greening Australia, Perth, WA 6000, Australia
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23
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Cisternas‐Fuentes A, Jogesh T, Broadhead GT, Raguso RA, Skogen KA, Fant JB. Evolution of selfing syndrome and its influence on genetic diversity and inbreeding: A range-wide study in Oenothera primiveris. AMERICAN JOURNAL OF BOTANY 2022; 109:789-805. [PMID: 35596689 PMCID: PMC9320852 DOI: 10.1002/ajb2.1861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 03/09/2022] [Accepted: 03/11/2022] [Indexed: 06/15/2023]
Abstract
PREMISE To avoid inbreeding depression, plants have evolved diverse breeding systems to favor outcrossing, such as self-incompatibility. However, changes in biotic and abiotic conditions can result in selective pressures that lead to a breakdown in self-incompatibility. The shift to increased selfing is commonly associated with reduced floral features, lower attractiveness to pollinators, and increased inbreeding. We tested the hypothesis that the loss of self-incompatibility, a shift to self-fertilization (autogamy), and concomitant evolution of the selfing syndrome (reduction in floral traits associated with cross-fertilization) will lead to increased inbreeding and population differentiation in Oenothera primiveris. Across its range, this species exhibits a shift in its breeding system and floral traits from a self-incompatible population with large flowers to self-compatible populations with smaller flowers. METHODS We conducted a breeding system assessment, evaluated floral traits in the field and under controlled conditions, and measured population genetic parameters using RADseq data. RESULTS Our results reveal a bimodal transition to the selfing syndrome from the west to the east of the range of O. primiveris. This shift includes variation in the breeding system and the mating system, a reduction in floral traits (flower diameter, herkogamy, and scent production), a shift to greater autogamy, reduced genetic diversity, and increased inbreeding. CONCLUSIONS The observed variation highlights the importance of range-wide studies to understand breeding system variation and the evolution of the selfing syndrome within populations and species.
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Affiliation(s)
- Anita Cisternas‐Fuentes
- Negaunee Institute for Plant Conservation Science and ActionChicago Botanic Garden1000 Lake Cook RoadGlencoeIllinois60035USA
- Plant Biology and ConservationNorthwestern University2205 Tech DriveEvanstonIllinois60208USA
- Department of Biological ScienceClemson University132 Long HallClemsonSouth Carolina29631USA
| | - Tania Jogesh
- Negaunee Institute for Plant Conservation Science and ActionChicago Botanic Garden1000 Lake Cook RoadGlencoeIllinois60035USA
| | - Geoffrey T. Broadhead
- Department of Entomology and NematologyUniversity of Florida1881 Natural Area DriveGainesvilleFlorida32611USA
| | - Robert A. Raguso
- Department of Neurobiology and BehaviorCornell UniversityW361 Mudd HallIthacaNew York14853USA
| | - Krissa A. Skogen
- Negaunee Institute for Plant Conservation Science and ActionChicago Botanic Garden1000 Lake Cook RoadGlencoeIllinois60035USA
- Plant Biology and ConservationNorthwestern University2205 Tech DriveEvanstonIllinois60208USA
| | - Jeremie B. Fant
- Negaunee Institute for Plant Conservation Science and ActionChicago Botanic Garden1000 Lake Cook RoadGlencoeIllinois60035USA
- Plant Biology and ConservationNorthwestern University2205 Tech DriveEvanstonIllinois60208USA
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24
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Rodríguez-Rodríguez P, Fernández de Castro AG, Pérez de Paz PL, Curbelo L, Palomares Á, Mesa R, Acevedo A, Sosa PA. Evolution and conservation genetics of an insular hemiparasitic plant lineage at the limit of survival: the case of Thesium sect. Kunkeliella in the Canary Islands. AMERICAN JOURNAL OF BOTANY 2022; 109:419-436. [PMID: 35289923 PMCID: PMC9415105 DOI: 10.1002/ajb2.1830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 11/25/2021] [Accepted: 11/30/2021] [Indexed: 06/14/2023]
Abstract
PREMISE The diversification of island flora has been widely studied. However, the role of environmental niches in insular radiation processes has been less investigated. We combined population genetic analyses with species distribution modelling to clarify the genetic relationships, diversification patterns, species niche requirements, and conservation of Thesium sect. Kunkeliella, a clade of rare hemiparasitic plants endemic to the Canaries. METHODS We studied the three extant Thesium species and a new taxon from La Palma Island. We developed 12 microsatellites and performed population genetic analysis and studied the demographic history of the group. To evaluate the role of niche conservatism in the diversification of the group, we performed species distribution modelling (ESM) with four algorithms. RESULTS All species presented moderate genetic diversity values for rare endemics. Thesium canariense (Gran Canaria) showed high differentiation, whereas T. subsucculentum, T. retamoides (Tenerife), and La Palma populations are closely related. The lineage may have undergone a recent diversification with colonization proceeding east to west, with T. canariense as sister to the others. We detected a climatic niche shift, as taxa showed different distributions across the temperature gradient. There is enough evidence to describe La Palma populations as a new species. CONCLUSIONS We characterized the evolutionary history of Thesium sect. Kunkeliella by integrating genetic and ecological assessments. Our results indicate that this clade has undergone a recent radiation process with niche differentiation among species. The results increase our knowledge about insular radiations and will inform the conservation management of the study species.
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Affiliation(s)
- Priscila Rodríguez-Rodríguez
- Instituto Universitario de Estudios Ambientales y Recursos Naturales (IUNAT), Universidad de Las Palmas de Gran Canaria, Campus Universitario de Tafira, 35017 Las Palmas de Gran Canaria, Canary Islands, Spain
| | | | - Pedro Luis Pérez de Paz
- Departamento de Botánica, Ecología y Fisiología Vegetal, Universidad de La Laguna, 38071 La Laguna, Canary Islands, Spain
| | - Leticia Curbelo
- Instituto Universitario de Estudios Ambientales y Recursos Naturales (IUNAT), Universidad de Las Palmas de Gran Canaria, Campus Universitario de Tafira, 35017 Las Palmas de Gran Canaria, Canary Islands, Spain
| | - Ángel Palomares
- Parque Nacional de la Caldera de Taburiente. Carretera de Padrón, 47. 38750 El Paso (La Palma), Canary Islands, Spain
| | - Ricardo Mesa
- Calle Francisco Bermúdez 6, 38500 Güímar. Santa Cruz de Tenerife, Canary Islands, Spain
| | - Aurelio Acevedo
- Calle Barrial de Abajo N13A, 38750 El Paso, La Palma, Canary Islands, Spain
| | - Pedro A Sosa
- Instituto Universitario de Estudios Ambientales y Recursos Naturales (IUNAT), Universidad de Las Palmas de Gran Canaria, Campus Universitario de Tafira, 35017 Las Palmas de Gran Canaria, Canary Islands, Spain
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25
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Gay L, Dhinaut J, Jullien M, Vitalis R, Navascués M, Ranwez V, Ronfort J. Evolution of flowering time in a selfing annual plant: Roles of adaptation and genetic drift. Ecol Evol 2022; 12:e8555. [PMID: 35127051 PMCID: PMC8794724 DOI: 10.1002/ece3.8555] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 12/10/2021] [Indexed: 11/10/2022] Open
Abstract
Resurrection studies are a useful tool to measure how phenotypic traits have changed in populations through time. If these trait modifications correlate with the environmental changes that occurred during the time period, it suggests that the phenotypic changes could be a response to selection. Selfing, through its reduction of effective size, could challenge the ability of a population to adapt to environmental changes. Here, we used a resurrection study to test for adaptation in a selfing population of Medicago truncatula, by comparing the genetic composition and flowering times across 22 generations. We found evidence for evolution toward earlier flowering times by about two days and a peculiar genetic structure, typical of highly selfing populations, where some multilocus genotypes (MLGs) are persistent through time. We used the change in frequency of the MLGs through time as a multilocus fitness measure and built a selection gradient that suggests evolution toward earlier flowering times. Yet, a simulation model revealed that the observed change in flowering time could be explained by drift alone, provided the effective size of the population is small enough (<150). These analyses suffer from the difficulty to estimate the effective size in a highly selfing population, where effective recombination is severely reduced.
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Affiliation(s)
- Laurène Gay
- CIRADINRAEInstitut AgroUMR AGAP InstitutUniv MontpellierMontpellierFrance
| | - Julien Dhinaut
- CIRADINRAEInstitut AgroUMR AGAP InstitutUniv MontpellierMontpellierFrance
- Present address:
Evolutionary Biology and Ecology of AlgaeUPMCUniversity of Paris VI, UC, UACH, UMI 3614CNRSSorbonne UniversitésRoscoffFrance
| | - Margaux Jullien
- CIRADINRAEInstitut AgroUMR AGAP InstitutUniv MontpellierMontpellierFrance
- Present address:
INRAUniv. Paris‐SudCNRSAgroParisTechGQE – Le MoulonUniversité Paris‐SaclayGif‐sur‐YvetteFrance
| | - Renaud Vitalis
- CIRADINRAEInstitut AgroIRDCBGPUniv MontpellierMontpellierFrance
| | | | - Vincent Ranwez
- CIRADINRAEInstitut AgroUMR AGAP InstitutUniv MontpellierMontpellierFrance
| | - Joëlle Ronfort
- CIRADINRAEInstitut AgroUMR AGAP InstitutUniv MontpellierMontpellierFrance
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26
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Metapopulation management of a critically endangered marsupial in the age of genomics. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01869] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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27
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Lettoof DC, Thomson VA, Cornelis J, Bateman PW, Aubret F, Gagnon MM, von Takach B. Bioindicator snake shows genomic signatures of natural and anthropogenic barriers to gene flow. PLoS One 2021; 16:e0259124. [PMID: 34714831 PMCID: PMC8555784 DOI: 10.1371/journal.pone.0259124] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 10/12/2021] [Indexed: 11/18/2022] Open
Abstract
Urbanisation alters landscapes, introduces wildlife to novel stressors, and fragments habitats into remnant 'islands'. Within these islands, isolated wildlife populations can experience genetic drift and subsequently suffer from inbreeding depression and reduced adaptive potential. The Western tiger snake (Notechis scutatus occidentalis) is a predator of wetlands in the Swan Coastal Plain, a unique bioregion that has suffered substantial degradation through the development of the city of Perth, Western Australia. Within the urban matrix, tiger snakes now only persist in a handful of wetlands where they are known to bioaccumulate a suite of contaminants, and have recently been suggested as a relevant bioindicator of ecosystem health. Here, we used genome-wide single nucleotide polymorphism (SNP) data to explore the contemporary population genomics of seven tiger snake populations across the urban matrix. Specifically, we used population genomic structure and diversity, effective population sizes (Ne), and heterozygosity-fitness correlations to assess fitness of each population with respect to urbanisation. We found that population genomic structure was strongest across the northern and southern sides of a major river system, with the northern cluster of populations exhibiting lower heterozygosities than the southern cluster, likely due to a lack of historical gene flow. We also observed an increasing signal of inbreeding and genetic drift with increasing geographic isolation due to urbanisation. Effective population sizes (Ne) at most sites were small (< 100), with Ne appearing to reflect the area of available habitat rather than the degree of adjacent urbanisation. This suggests that ecosystem management and restoration may be the best method to buffer the further loss of genetic diversity in urban wetlands. If tiger snake populations continue to decline in urban areas, our results provide a baseline measure of genomic diversity, as well as highlighting which 'islands' of habitat are most in need of management and protection.
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Affiliation(s)
- Damian C. Lettoof
- Behavioural Ecology Lab, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Vicki A. Thomson
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Jari Cornelis
- Behavioural Ecology Lab, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Philip W. Bateman
- Behavioural Ecology Lab, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Fabien Aubret
- Station d’Ecologie Théorique et Expérimentale, CNRS, Moulis, France
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Marthe M. Gagnon
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Brenton von Takach
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory, Australia
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28
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Janicke T, Chapuis E, Meconcelli S, Bonel N, Delahaie B, David P. Environmental effects on the genetic architecture of fitness components in a simultaneous hermaphrodite. J Anim Ecol 2021; 91:124-137. [PMID: 34652857 DOI: 10.1111/1365-2656.13607] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 10/04/2021] [Indexed: 12/01/2022]
Abstract
Understanding how environmental change affects genetic variances and covariances of reproductive traits is key to formulate firm predictions on evolutionary responses. This is particularly true for sex-specific variance in reproductive success, which has been argued to affect how populations can adapt to environmental change. Our current knowledge on the impact of environmental stress on sex-specific genetic architecture of fitness components is still limited and restricted to separate-sexed organisms. However, hermaphroditism is widespread across animals and may entail interesting peculiarities with respect to genetic constraints imposed on the evolution of male and female reproduction. We explored how food restriction affects the genetic variance-covariance (G) matrix of body size and reproductive success of the simultaneously hermaphroditic freshwater snail Physa acuta. Our results provide strong evidence that the imposed environmental stress elevated the opportunity for selection in both sex functions. However, the G-matrix remained largely stable across the tested food treatments. Importantly, our results provide no support for cross-sex genetic correlations suggesting no strong evolutionary coupling of male and female reproductive traits. We discuss potential implications for the adaptation to changing environments and highlight the need for more quantitative genetic studies on male and female fitness components in simultaneous hermaphrodites.
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Affiliation(s)
- Tim Janicke
- Centre d'Écologie Fonctionnelle et Évolutive, CNRS, Univ Montpellier, EPHE, IRD, Montpellier, France.,Applied Zoology, Technical University Dresden, Dresden, Germany
| | - Elodie Chapuis
- MIVEGEC, Univ Montpellier, CNRS, IRD, Montpellier, France
| | - Stefania Meconcelli
- Centre d'Écologie Fonctionnelle et Évolutive, CNRS, Univ Montpellier, EPHE, IRD, Montpellier, France.,Department of Life Sciences and Systems Biology, Università di Torino, Torino, Italy
| | - Nicolas Bonel
- Centre d'Écologie Fonctionnelle et Évolutive, CNRS, Univ Montpellier, EPHE, IRD, Montpellier, France.,Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS-CCT-CONICET Bahía Blanca), Bahía Blanca, Argentina
| | - Boris Delahaie
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Patrice David
- Centre d'Écologie Fonctionnelle et Évolutive, CNRS, Univ Montpellier, EPHE, IRD, Montpellier, France
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29
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Hellwig T, Abbo S, Sherman A, Ophir R. Prospects for the natural distribution of crop wild-relatives with limited adaptability: The case of the wild pea Pisum fulvum. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 310:110957. [PMID: 34315583 DOI: 10.1016/j.plantsci.2021.110957] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 04/12/2021] [Accepted: 05/22/2021] [Indexed: 06/13/2023]
Abstract
Plant breeders and conservationist depend on knowledge about the genetic variation of their species of interest. Pisum fulvum, a wild relative of domesticated pea, has attracted attention as a genetic resource for crop improvement, yet little information about its diversity in the wild has been published hitherto. We sampled 15 populations of P. fulvum from Israeli natural habitats and conducted genotyping by sequencing to analyse their genetic diversity and adaptive state. We also attempted to evaluate the species past demography and the prospects of its future reaction to environmental changes. The results suggest that genetic diversity of P. fulvum is low to medium and is distributed between well diverged populations. Surprisingly, with 56 % in the total population the selfing rate was found to be significantly lower than expected from a species that is commonly assumed to be a predominant selfer. We found a strong genetic bottleneck during the last glacial period and only limited patterns of isolation by distance and environment, which explained 13 %-18 % of the genetic variation. Despite the weak signatures of genome-wide IBE, 1,354 markers were significantly correlated with environmental factors, 1,233 of which were located within known genes with a nonsynonymous to synonymous ratio of 0.382. Species distribution modelling depicted an ongoing fragmentation and decreased habitable area over the next 80 years under two different socio-economic pathways. Our results suggest that complex interactions of substantial drift and selection shaped the genome of P. fulvum. Climate changeis likely to cause further erosion of genetic diversity in P. fulvum. Systematic ex-situ conservation may be advisable to safeguard genetic variability for future utilization of this species.
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Affiliation(s)
- Timo Hellwig
- R.H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, POB 12, Rehovot, 761001, Israel; Institute of Plant Sciences, Agricultural Research Organization - Volcani Center, P.O.B 15159, Rishon LeZion, 7505101, Israel
| | - Shahal Abbo
- R.H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, POB 12, Rehovot, 761001, Israel
| | - Amir Sherman
- Institute of Plant Sciences, Agricultural Research Organization - Volcani Center, P.O.B 15159, Rishon LeZion, 7505101, Israel
| | - Ron Ophir
- Institute of Plant Sciences, Agricultural Research Organization - Volcani Center, P.O.B 15159, Rishon LeZion, 7505101, Israel.
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30
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Phillips KP, Cable J, Mohammed RS, Chmielewski S, Przesmycka KJ, van Oosterhout C, Radwan J. Functional immunogenetic variation, rather than local adaptation, predicts ectoparasite infection intensity in a model fish species. Mol Ecol 2021; 30:5588-5604. [PMID: 34415650 PMCID: PMC9292977 DOI: 10.1111/mec.16135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 07/07/2021] [Accepted: 08/11/2021] [Indexed: 11/28/2022]
Abstract
Natural host populations differ in their susceptibility to infection by parasites, and these intrapopulation differences are still an incompletely understood component of host‐parasite dynamics. In this study, we used controlled infection experiments with wild‐caught guppies (Poecilia reticulata) and their ectoparasite Gyrodactylus turnbulli to investigate the roles of local adaptation and host genetic composition (immunogenetic and neutral) in explaining differences in susceptibility to infection. We found differences between our four study host populations that were consistent between two parasite source populations, with no indication of local adaptation by either host or parasite at two tested spatial scales. Greater values of host population genetic variability metrics broadly aligned with lower population mean infection intensity, with the best alignments associated with major histocompatibility complex (MHC) “supertypes”. Controlling for intrapopulation differences and potential inbreeding variance, we found a significant negative relationship between individual‐level functional MHC variability and infection: fish carrying more MHC supertypes experienced infections of lower severity, with limited evidence for supertype‐specific effects. We conclude that population‐level differences in host infection susceptibility probably reflect variation in parasite selective pressure and/or host evolutionary potential, underpinned by functional immunogenetic variation.
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Affiliation(s)
- Karl P Phillips
- Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland.,School of Biological Earth & Environmental Sciences, University College Cork, Cork, Ireland.,Marine Institute, Newport, Co. Mayo, Ireland
| | - Joanne Cable
- School of Biosciences, Cardiff University, Cardiff, UK
| | - Ryan S Mohammed
- Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland.,Department of Life Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Sebastian Chmielewski
- Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Karolina J Przesmycka
- Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Cock van Oosterhout
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Jacek Radwan
- Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
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31
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Riquet F, De Kuyper CA, Fauvelot C, Airoldi L, Planes S, Fraschetti S, Mačić V, Milchakova N, Mangialajo L, Bottin L. Highly restricted dispersal in habitat-forming seaweed may impede natural recovery of disturbed populations. Sci Rep 2021; 11:16792. [PMID: 34408197 PMCID: PMC8373921 DOI: 10.1038/s41598-021-96027-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 07/14/2021] [Indexed: 02/07/2023] Open
Abstract
Cystoseira sensu lato (Class Phaeophyceae, Order Fucales, Family Sargassaceae) forests play a central role in marine Mediterranean ecosystems. Over the last decades, Cystoseira s.l. suffered from a severe loss as a result of multiple anthropogenic stressors. In particular, Gongolaria barbata has faced multiple human-induced threats, and, despite its ecological importance in structuring rocky communities and hosting a large number of species, the natural recovery of G. barbata depleted populations is uncertain. Here, we used nine microsatellite loci specifically developed for G. barbata to assess the genetic diversity of this species and its genetic connectivity among fifteen sites located in the Ionian, the Adriatic and the Black Seas. In line with strong and significant heterozygosity deficiencies across loci, likely explained by Wahlund effect, high genetic structure was observed among the three seas (ENA corrected FST = 0.355, IC = [0.283, 0.440]), with an estimated dispersal distance per generation smaller than 600 m, both in the Adriatic and Black Sea. This strong genetic structure likely results from restricted gene flow driven by geographic distances and limited dispersal abilities, along with genetic drift within isolated populations. The presence of genetically disconnected populations at small spatial scales (< 10 km) has important implications for the identification of relevant conservation and management measures for G. barbata: each population should be considered as separated evolutionary units with dedicated conservation efforts.
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Affiliation(s)
- Florentine Riquet
- Institut de Recherche pour le Développement (IRD), UMR ENTROPIE, Nouméa, New Caledonia.
- Sorbonne Université, CNRS, UMR LOV, Villefranche‑sur‑Mer, France.
| | | | - Cécile Fauvelot
- Institut de Recherche pour le Développement (IRD), UMR ENTROPIE, Nouméa, New Caledonia
- Sorbonne Université, CNRS, UMR LOV, Villefranche‑sur‑Mer, France
| | - Laura Airoldi
- Department of Biology, Chioggia Hydrobiological Station Umberto D'Ancona, University of Padova, Chioggia, Italy
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, UO CoNISMa, Ravenna, Italy
| | - Serge Planes
- PSL Research University, EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan, France
| | - Simonetta Fraschetti
- Department of Biology, University of Naples Federico II, Naples, Italy
- Stazione Zoologica Anton Dohrn, Naples, Italy
- CoNISMa, Rome, Italy
| | - Vesna Mačić
- Institut za biologiju mora, Univerzitet Crne Gore, Kotor, Montenegro
| | - Nataliya Milchakova
- Laboratory of Phytoresources, Kovalevsky Institute of Biology of the Southern Seas of RAS (IBSS), Sevastopol, Russia
| | | | - Lorraine Bottin
- Université Côte d'Azur, CNRS, UMR 7035 ECOSEAS, Nice, France
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Adhikari S, Revolinski SR, Eigenbrode SD, Burke IC. Genetic diversity and population structure of a global invader Mayweed chamomile ( Anthemis cotula): management implications. AOB PLANTS 2021; 13:plab049. [PMID: 34466213 PMCID: PMC8403231 DOI: 10.1093/aobpla/plab049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 07/26/2021] [Indexed: 06/13/2023]
Abstract
Mayweed chamomile (Anthemis cotula) is a globally invasive, troublesome annual weed but knowledge of its genetic diversity, population structure in invaded regions and invasion patterns remains unstudied. Therefore, germplasm from 19 A. cotula populations (sites) from three geographically distinct invaded regions: the Walla Walla Basin (located in southern Washington) and the Palouse (located in both northern Idaho and eastern Washington), Pacific Northwest, USA and Kashmir Valley, India were grown in the greenhouse for DNA extraction and sequencing. A total of 18 829 single-nucleotide polymorphisms were called and filtered for each of 89 samples. Pairwise F ST, Nei's genetic distance, heterozygosity, Wright's inbreeding coefficient (F) and self-fertilization rates were estimated for populations within and among the three regions with a total of 19 populations comprised of 89 individuals. Overall measurements of genetic variation were low but significant among regions, populations and individuals. Despite the weak genetic structure, two main genetic clusters were evident, one comprised of populations from Palouse and Kashmir Valley, the other comprised of populations from the Walla Walla Basin. Significant selfing was observed in populations from the Walla Walla Basin and Palouse but not from Kashmir Valley, indicating that Mayweed chamomile in the Pacific Northwest, USA could persist with low pollinator or pollen donor densities. Although F ST values between the regions indicate Palouse populations are more closely related to Kashmir Valley than to Walla Walla Basin populations, based on Migrate-n analysis, panmixis was the most likely model, suggesting an unrestricted gene flow among all three regions. Our study indicated that Kashmir Valley populations either originated from or shared the origin with the Palouse populations, suggesting human-mediated migration of A. cotula between regions.
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Affiliation(s)
- Subodh Adhikari
- Department of Entomology, Plant Pathology and Nematology, University of Idaho, 875 Perimeter Drive MS 2329, Moscow, ID 83844, USA
- Department of Crop and Soil Sciences, Washington State University, Johnson Hall Rm. 115, PO Box 646420, Pullman, WA 99164, USA
| | - Samuel R Revolinski
- Department of Crop and Soil Sciences, Washington State University, Johnson Hall Rm. 115, PO Box 646420, Pullman, WA 99164, USA
| | - Sanford D Eigenbrode
- Department of Entomology, Plant Pathology and Nematology, University of Idaho, 875 Perimeter Drive MS 2329, Moscow, ID 83844, USA
| | - Ian C Burke
- Department of Crop and Soil Sciences, Washington State University, Johnson Hall Rm. 115, PO Box 646420, Pullman, WA 99164, USA
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Sin SYW, Hoover BA, Nevitt GA, Edwards SV. Demographic History, Not Mating System, Explains Signatures of Inbreeding and Inbreeding Depression in a Large Outbred Population. Am Nat 2021; 197:658-676. [PMID: 33989142 DOI: 10.1086/714079] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractInbreeding depression is often found in small, inbred populations, but whether it can be detected in and have evolutionary consequences for large, wide-ranging populations is poorly known. Here, we investigate the possibility of inbreeding in a large population to determine whether mild levels of inbreeding can still have genetic and phenotypic consequences and how genomically widespread these effects can be. We apply genome-wide methods to investigate whether individual and parental heterozygosity is related to morphological, growth, or life-history traits in a pelagic seabird, Leach's storm-petrel (Oceanodroma leucorhoa). Examining 560 individuals as part of a multiyear study, we found a substantial effect of maternal heterozygosity on chick traits: chicks from less heterozygous (relatively inbred) mothers were significantly smaller than chicks from more heterozygous (noninbred) mothers. We show that these heterozygosity-fitness correlations were due to general genome-wide effects and demonstrate a correlation between heterozygosity and inbreeding, suggesting inbreeding depression. We used population genetic models to further show that the variance in inbreeding was probably due to past demographic events rather than the current mating system and ongoing mate choice. Our findings demonstrate that inbreeding depression can be observed in large populations and illustrate how the integration of genomic techniques and fieldwork can elucidate its underlying causes.
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Mongue AJ, Michaelides S, Coombe O, Tena A, Kim DS, Normark BB, Gardner A, Hoddle MS, Ross L. Sex, males, and hermaphrodites in the scale insect Icerya purchasi. Evolution 2021; 75:2972-2983. [PMID: 33844310 DOI: 10.1111/evo.14233] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 03/25/2021] [Accepted: 03/27/2021] [Indexed: 11/30/2022]
Abstract
Androdioecy (the coexistence of males and hermaphrodites) is a rare mating system for which the evolutionary dynamics are poorly understood. Here, we investigate the cottony cushion scale, Icerya purchasi, one of only three reported cases of androdioecy in insects. In this species, female-like hermaphrodites have been shown to produce sperm and self-fertilize. However, males are ocassionally observed as well. In a large genetic analysis, we show for the first time that, although self-fertilization appears to be the primary mode of reproduction, rare outbreeding events do occur in natural populations, supporting the hypothesis that hermaphrodites mate with males and hence androdioecy is the mating system of I. purchasi. Thus, this globally invasive pest insect appears to enjoy the colonization advantages of a selfing organism while also benefitting from periodic reintroduction of genetic variation through outbreeding with males.
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Affiliation(s)
- Andrew J Mongue
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JT, United Kingdom
| | - Sozos Michaelides
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, United Kingdom.,Department of Biology, Concordia University, Montreal, Quebec, H4B 1R6, Canada
| | - Oliver Coombe
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, United Kingdom
| | - Alejandro Tena
- Institut Valencià d'Investigacions Agràries (IVIA), Centre de Protecció Vegetal i Biotecnologia, Unitat d'Entomologia, Moncada, 46113, Spain
| | - Dong-Soon Kim
- Majors in Plant Resource Sciences and Environment, College of Applied Life Science, SARI, Jeju National University, Jeju, 63243, Republic of Korea
| | - Benjamin B Normark
- Department of Biology and Graduate Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst, Massachusetts, 01003
| | - Andy Gardner
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, United Kingdom.,School of Biology, University of St Andrews, Fife, KY16 9TH, United Kingdom
| | - Mark S Hoddle
- Department of Entomology, University of California, Riverside, California, 92521
| | - Laura Ross
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JT, United Kingdom.,Department of Zoology, University of Oxford, Oxford, OX1 3PS, United Kingdom.,Department of Biology and Graduate Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst, Massachusetts, 01003
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Vanden Abeele S, Janssens SB, Piñeiro R, Hardy OJ. Evidence of past forest fragmentation in the Congo Basin from the phylogeography of a shade-tolerant tree with limited seed dispersal: Scorodophloeus zenkeri (Fabaceae, Detarioideae). BMC Ecol Evol 2021; 21:50. [PMID: 33784979 PMCID: PMC8011194 DOI: 10.1186/s12862-021-01781-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 03/15/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Comparative phylogeographic studies on rainforest species that are widespread in Central Africa often reveal genetic discontinuities within and between biogeographic regions, indicating (historical) barriers to gene flow, possibly due to repeated and/or long-lasting population fragmentation during glacial periods according to the forest refuge hypothesis. The impact of forest fragmentation seems to be modulated by the ecological amplitude and dispersal capacities of each species, resulting in different demographic histories. Moreover, while multiple studies investigated the western part of Central Africa (Lower Guinea), few have sufficiently sampled the heart of the Congo Basin (Congolia). In this study, we look for genetic discontinuities between populations of the widespread tropical tree Scorodophloeus zenkeri Harms (Fabaceae, Detarioideae) in Central Africa. Additionally, we characterize genetic diversity, selfing rate and fine-scale spatial genetic structure within populations to estimate the gene dispersal capacity of the species. RESULTS Clear intraspecific genetic discontinuities occur throughout the species' distribution range, with two genetic clusters in Congolia and four in Lower Guinea, and highest differentiation occurring between these bioregions. Genetic diversity is higher in Lower Guinea than Congolia. A spatial genetic structure characteristic of isolation by distance occurs within the genetic clusters. This allowed us to estimate gene dispersal distances (σg) for this outcrossing species with ballistic seed dispersal, which range between 100 and 250 m in areas where S. zenkeri occurs in high densities, and are in the low range of σg values compared to other tropical trees. Gene dispersal distances are larger in low density populations, probably due to extensive pollen dispersal capacity. CONCLUSIONS Fragmentation of S. zenkeri populations seems to have occurred not only in Lower Guinea but also in the Congo Basin, though not necessarily according to previously postulated forest refuge areas. The lower genetic diversity in Congolia compared to Lower Guinea parallels the known gradient of species diversity, possibly reflecting a stronger impact of past climate changes on the forest cover in Congolia. Despite its bisexual flowers, S. zenkeri appears to be mostly outcrossing. The limited dispersal observed in this species implies that genetic discontinuities resulting from past forest fragmentation can persist for a long time before being erased by gene flow.
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Affiliation(s)
- Samuel Vanden Abeele
- Meise Botanic Garden, Nieuwelaan 38, 1860, Meise, Belgium.
- Evolutionary Biology and Ecology, Faculté Des Sciences, Université Libre de Bruxelles, Av. F.D. Roosevelt 50, 1050, Brussels, Belgium.
- School of Integrative Plant Sciences, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, 14853, USA.
| | - Steven B Janssens
- Meise Botanic Garden, Nieuwelaan 38, 1860, Meise, Belgium
- Plant Conservation and Population Biology, KU, Leuven, Belgium
| | - Rosalía Piñeiro
- Geography, College of Life and Environmental Sciences, University of Exeter, Laver Building, North Park Road, Exeter, EX4 4QE, UK
| | - Olivier J Hardy
- Evolutionary Biology and Ecology, Faculté Des Sciences, Université Libre de Bruxelles, Av. F.D. Roosevelt 50, 1050, Brussels, Belgium
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The rapid dissolution of dioecy by experimental evolution. Curr Biol 2021; 31:1277-1283.e5. [PMID: 33472050 DOI: 10.1016/j.cub.2020.12.028] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/10/2020] [Accepted: 12/18/2020] [Indexed: 11/20/2022]
Abstract
Evolutionary transitions from hermaphroditism to dioecy have been common in flowering plants,1,2 but recent analysis also points to frequent reversions from dioecy to hermaphroditism.2-4 Here, we use experimental evolution to expose a mechanism for such reversions, validating an explanation for the scattered phylogenetic distribution of dioecy. We removed males from dioecious populations of the wind-pollinated plant Mercurialis annua and allowed natural selection to act on the remaining females that occasionally produced male flowers; such "leaky" sex expression is common in both males and females of dioecious plants.5 Over the course of four generations, females evolved a 23-fold increase in average male flower production. This phenotypic masculinization of females coincided with the evolution of partial self-fertilization, high average seed set in the continued absence of males, and a capacity to sire progeny when males were re-introduced into their populations. Our study thus validates a mechanism for the rapid dissolution of dioecy and the evolution of functional hermaphroditism under conditions that may frequently occur during periods of low population density, repeated colonization, or range expansion.6,7 Our results illustrate the power of natural selection, acting in replicated experimental populations, to bring about transitions in the mating behavior of plants.
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Botero-Delgadillo E, Quirici V, Vásquez RA, Kempenaers B. Heterozygosity-Fitness Correlations in a Continental Island Population of Thorn-Tailed Rayadito. J Hered 2020; 111:628-639. [PMID: 33277658 DOI: 10.1093/jhered/esaa056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 12/04/2020] [Indexed: 11/15/2022] Open
Abstract
Heterozygosity-fitness correlations (HFCs) have been used to monitor the effects of inbreeding in threatened populations. HFCs can also be useful to investigate the potential effects of inbreeding in isolated relict populations of long-term persistence and to better understand the role of inbreeding and outbreeding as drivers of changes in genetic diversity. We studied a continental island population of thorn-tailed rayadito (Aphrastura spinicauda) inhabiting the relict forest of Fray Jorge National Park, north-central Chile. This population has experienced a long-term, gradual process of isolation since the end of the Tertiary. Using 10 years of field data in combination with molecular techniques, we tested for HFCs to assess the importance of inbreeding depression. If inbreeding depression is important, we predict a positive relationship between individual heterozygosity and fitness-related traits. We genotyped 183 individuals at 12 polymorphic microsatellite loci and used 7 measures of reproductive success and estimates of apparent survival to calculate HFCs. We found weak to moderate statistical support (P-values between 0.05 and 0.01) for a linear effect of female multi-locus heterozygosity (MLH) on clutch size and nonlinear effects on laying date and fledging success. While more heterozygous females laid smaller clutches, nonlinear effects indicated that females with intermediate values of MLH started laying earlier and had higher fledging success. We found no evidence for effects of MLH on annual fecundity or on apparent survival. Our results along with the long-term demographic stability of the study population contradict the hypothesis that inbreeding depression occurs in this population.
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Affiliation(s)
- Esteban Botero-Delgadillo
- Department of Behavioural Ecology and Evolutionary Genetics, Max Plank Institute for Ornithology, Seewiesen, Germany
| | - Verónica Quirici
- Departamento de Ecología y Biodiversidad, Facultad de Ecología y Recursos Naturales, Universidad Andrés Bello, Santiago, Chile.,Centro de investigación para la sustentabilidad, Universidad Andrés Bello, Santiago, Chile
| | - Rodrigo A Vásquez
- Instituto de Ecología y Biodiversidad, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Bart Kempenaers
- Department of Behavioural Ecology and Evolutionary Genetics, Max Plank Institute for Ornithology, Seewiesen, Germany
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Gasca-Pineda J, Gutiérrez-Guerrero YT, Aguirre-Planter E, Eguiarte LE. The role of environment, local adaptation, and past climate fluctuation on the amount and distribution of genetic diversity in two subspecies of Mexican wild Zea mays. AMERICAN JOURNAL OF BOTANY 2020; 107:1542-1554. [PMID: 33205455 DOI: 10.1002/ajb2.1561] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/09/2020] [Indexed: 06/11/2023]
Abstract
PREMISE Past climate fluctuations during the Holocene and Pleistocene shaped the distribution of several plant species in temperate areas over the world. Wild maize, commonly known as teosinte, is a good system to evaluate the effects of historical climate fluctuations on genetic diversity due to its wide distribution in Mexico with contrasting environmental conditions. We explored the influence of contemporary factors and historical environmental shifts on genetic diversity, including present and three historical periods using neutral markers. METHODS We used 22 nuclear microsatellite loci to examine the genetic diversity of 14 populations of Zea mays subsp. parviglumis and 15 populations of Zea mays subsp. mexicana (527 individuals total). We implemented genetic structure analyses to evaluate genetic differentiation between and within subspecies. We applied coalescent-based demographic analysis and species distribution modeling to evaluate the effects of historical environmental shifts. RESULTS We found 355 alleles in total for the two subspecies and variable levels of diversity in each (Z. mays subsp. parviglumis expected heterozygosity HE = 0.3646-0.7699; Z. mays subsp. mexicana HE = 0.5885-0.7671). We detected significant genetic structure among populations (DEST = 0.4332) with significant heterozygote deficiency (FIS = 0.1796), and variable selfing rates (sg2 = 0.0-0.3090). The Bayesian assignment analysis differentiated four genetic groups. Demographic and species distribution modeling analysis suggested that environmental shifts were influential in the amount of genetic diversity. CONCLUSIONS Our analyses suggest that the current genetic diversity in teosinte is shaped by factors such as local adaptation and genetic isolation, along with historical environmental fluctuations.
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Affiliation(s)
- Jaime Gasca-Pineda
- Laboratorio de Evolución Molecular y Experimental, Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, AP, 70-275 Coyoacán 04510, Ciudad de México, México
| | - Yocelyn T Gutiérrez-Guerrero
- Laboratorio de Evolución Molecular y Experimental, Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, AP, 70-275 Coyoacán 04510, Ciudad de México, México
| | - Erika Aguirre-Planter
- Laboratorio de Evolución Molecular y Experimental, Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, AP, 70-275 Coyoacán 04510, Ciudad de México, México
| | - Luis E Eguiarte
- Laboratorio de Evolución Molecular y Experimental, Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, AP, 70-275 Coyoacán 04510, Ciudad de México, México
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Botero-Delgadillo E, Gilsenan C, Mueller JC, Kempenaers B. Negative effects of individual heterozygosity on reproductive success in a wild bird population. Mol Ecol 2020; 29:3196-3216. [PMID: 32668071 DOI: 10.1111/mec.15553] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 07/03/2020] [Indexed: 01/01/2023]
Abstract
The evolutionary consequences of individual genetic diversity are frequently studied by assessing heterozygosity-fitness correlations (HFCs). The prevalence of positive and negative HFCs and the predominance of general versus local effects in wild populations are far from understood, partly because comprehensive studies testing for both inbreeding and outbreeding depression are lacking. We studied a genetically diverse population of blue tits in southern Germany using a genome-wide set of 87 microsatellites to investigate the relationship between proxies of reproductive success and measures of multilocus and single-locus individual heterozygosity (MLH and SLH). We used complimentary measures of MLH and partitioned markers into functional categories according to their position in the blue tit genome. HFCs based on MLH were consistently negative for functional loci, whereas correlations were rather inconsistent for loci found in nonfunctional areas of the genome. Clutch size was the only reproductive variable showing a general effect. We found evidence for local effects for three measures of reproductive success: arrival date at the breeding site, the probability of breeding at the study site and male reproductive success. For these, we observed consistent, and relatively strong, negative effects at one functional locus. Remarkably, this marker had a similar effect in another blue tit population from Austria (~400 km to the east). We suggest that a genetic local effect on timing of arrival might be responsible for most negative HFCs detected, with carry-over effects on other reproductive traits. This effect could reflect individual differences in the distance between overwintering areas and breeding sites.
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Affiliation(s)
- Esteban Botero-Delgadillo
- Department of Behavioural Ecology and Evolutionary Genetics, Max Plank Institute for Ornithology, Seewiesen, Germany
| | - Carol Gilsenan
- Department of Behavioural Ecology and Evolutionary Genetics, Max Plank Institute for Ornithology, Seewiesen, Germany
| | - Jakob C Mueller
- Department of Behavioural Ecology and Evolutionary Genetics, Max Plank Institute for Ornithology, Seewiesen, Germany
| | - Bart Kempenaers
- Department of Behavioural Ecology and Evolutionary Genetics, Max Plank Institute for Ornithology, Seewiesen, Germany
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Hoffman JI, Nagel R, Litzke V, Wells DA, Amos W. Genetic analysis of Boletus edulis suggests that intra-specific competition may reduce local genetic diversity as a woodland ages. ROYAL SOCIETY OPEN SCIENCE 2020; 7:200419. [PMID: 32874636 PMCID: PMC7428248 DOI: 10.1098/rsos.200419] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 06/18/2020] [Indexed: 06/11/2023]
Abstract
Ectomycorrhizal fungi are key players in terrestrial ecosystems yet their mating systems and population dynamics remain poorly understood. We investigated the fine-scale relatedness structure and genetic diversity of Boletus edulis, one of the world's most commercially important wild mushrooms. Microsatellite genotyping of fruiting bodies from 14 different sites around Bielefeld in Germany revealed little in the way of population structure over a geographic scale of several kilometres. However, on a more local scale we found evidence for elevated relatedness as well as inbreeding. We also observed a significant negative association between the genetic diversity of fruit and the age of the trees under which they were sampled. Taken together, our results suggest that as genets mature, they compete and potentially create conditions under which further spores struggle to become established. By implication, even though this species is widely picked, propagules remain common enough to create strong competition when new habitats become available.
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Affiliation(s)
- J. I. Hoffman
- Department of Animal Behaviour, Bielefeld University, 33501 Bielefeld, Germany
- British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK
| | - R. Nagel
- Department of Animal Behaviour, Bielefeld University, 33501 Bielefeld, Germany
| | - V. Litzke
- Department of Animal Behaviour, Bielefeld University, 33501 Bielefeld, Germany
| | - D. A. Wells
- Department of Animal Behaviour, Bielefeld University, 33501 Bielefeld, Germany
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
- School of Natural Science and Psychology, Liverpool John Moores University, Liverpool, UK
| | - W. Amos
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
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Gooley RM, Hogg CJ, Fox S, Pemberton D, Belov K, Grueber CE. Inbreeding depression in one of the last DFTD-free wild populations of Tasmanian devils. PeerJ 2020; 8:e9220. [PMID: 32587794 PMCID: PMC7304431 DOI: 10.7717/peerj.9220] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 04/28/2020] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Vulnerable species experiencing inbreeding depression are prone to localised extinctions because of their reduced fitness. For Tasmanian devils, the rapid spread of devil facial tumour disease (DFTD) has led to population declines and fragmentation across the species' range. Here we show that one of the few remaining DFTD-free populations of Tasmanian devils is experiencing inbreeding depression. Moreover, this population has experienced a significant reduction in reproductive success over recent years. METHODS We used 32 microsatellite loci to examine changes in genetic diversity and inbreeding in the wild population at Woolnorth, alongside field data on breeding success from females to test for inbreeding depression. RESULTS Wefound that maternal internal relatedness has a negative impact on litter sizes. The results of this study imply that this population may be entering an extinction vortex and that to protect the population genetic rescue should be considered. This study provides conservation managers with useful information for managing wild devils and provides support for the "Wild Devil Recovery Program", which is currently augmenting small, isolated populations.
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Affiliation(s)
- Rebecca M. Gooley
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Carolyn J. Hogg
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Samantha Fox
- Save the Tasmanian Devil Program, Hobart, Tasmania, Australia
- Toledo Zoo, Toledo, OH, United States of America
| | - David Pemberton
- Save the Tasmanian Devil Program, Hobart, Tasmania, Australia
| | - Katherine Belov
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Catherine E. Grueber
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
- San Diego Zoo Global, San Diego, CA, United States of America
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Wilder AP, Navarro AY, King SND, Miller WB, Thomas SM, Steiner CC, Ryder OA, Shier DM. Fitness costs associated with ancestry to isolated populations of an endangered species. CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01272-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Cousseau L, Van de Loock D, Githiru M, Vangestel C, Lens L. Female need for paternal care shapes variation in extra-pair paternity in a cooperative breeder. Behav Ecol 2020. [DOI: 10.1093/beheco/arz215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Socially monogamous females regularly mate with males outside the pair bond. The prevailing explanation for this behavior is that females gain genetic benefits resulting from increased fitness of extra-pair offspring. Furthermore, because of the risk of reduced paternal care in response to cuckoldry, females are expected to seek extra-pair copulations when they can rear offspring with little help from their social partner (“constrained female” hypothesis). We tested these hypotheses and analyzed variation in paternal care in the Afrotropical, facultative cooperative breeding placid greenbul (Phyllastrephus placidus). Overall, approximately 50% of the offspring resulted from extra-pair (and extra-group) mating. Identified extra-pair males were in most cases neighboring dominant males, yet never within-group subordinates. As predicted by the constrained female hypothesis, the occurrence of extra-pair paternity (EPP) increased with the number of cooperative helpers (and not with total group size). However, dominant males did not adjust their food provisioning rates in response to EPP. Although extra-pair males were more strongly related to the dominant female and less heterozygous than the latter’s social mate, this did not result in more inbred extra-pair offspring, likely because identified extra-pair males were not representative of the extra-pair male population. While earlier studies on EPP mainly focused on male genetic quality, results from this study provide evidence that female’s social context may affect extra-pair strategies too.
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Affiliation(s)
- Laurence Cousseau
- Terrestrial Ecology Unit, Ghent University, K. L. Ledeganckstraat 35, Ghent, Belgium
| | - Dries Van de Loock
- Terrestrial Ecology Unit, Ghent University, K. L. Ledeganckstraat 35, Ghent, Belgium
- Evolutionary Ecology Group, University of Antwerp, Campus Drie Eiken, Universiteitsplein 1, Wilrijk, Belgium
- Ornithology Section, Department of Zoology, National Museums of Kenya, Nairobi, Kenya
| | - Mwangi Githiru
- Ornithology Section, Department of Zoology, National Museums of Kenya, Nairobi, Kenya
- Wildlife Works, Voi, Kenya
| | - Carl Vangestel
- Terrestrial Ecology Unit, Ghent University, K. L. Ledeganckstraat 35, Ghent, Belgium
- Royal Belgian Institute of Natural Sciences, Vautierstraat 26, Brussels, Belgium
| | - Luc Lens
- Terrestrial Ecology Unit, Ghent University, K. L. Ledeganckstraat 35, Ghent, Belgium
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Gkafas GA, de Jong M, Exadactylos A, Raga JA, Aznar FJ, Hoelzel AR. Sex-specific impact of inbreeding on pathogen load in the striped dolphin. Proc Biol Sci 2020; 287:20200195. [PMID: 32156218 DOI: 10.1098/rspb.2020.0195] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The impact of inbreeding on fitness has been widely studied and provides consequential inference about adaptive potential and the impact on survival for reduced and fragmented natural populations. Correlations between heterozygosity and fitness are common in the literature, but they rarely inform about the likely mechanisms. Here, we investigate a pathology with a clear impact on health in striped dolphin hosts (a nematode infection that compromises lung function). Dolphins varied with respect to their parasite burden of this highly pathogenic lung nematode (Skrjabinalius guevarai). Genetic diversity revealed by high-resolution restriction-associated DNA (43 018 RADseq single nucleotide polymorphisms) analyses showed a clear association between heterozygosity and pathogen load, but only for female dolphins, for which the more heterozygous individuals had lower Sk. guevarai burden. One locus identified by RADseq was a strong outlier in association with parasite load (heterozygous in all uninfected females, homozygous for 94% of infected females), found in an intron of the citron rho-interacting serine/threonine kinase locus (associated with milk production in mammals). Allelic variation at the Class II major histocompatability complex DQB locus was also assessed and found to be associated with both regional variation and with pathogen load. Both sex specificity and the identification of associating functional loci provide insight into the mechanisms by which more inbred individuals may be more susceptible to the infection of this parasite. This provides important insight towards our understanding of the impact of inbreeding in natural populations, relevant to both evolutionary and practical conservation considerations.
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Affiliation(s)
- Georgios A Gkafas
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK.,Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Fytokou Street 384 46, Volos, Hellas, Greece
| | - Menno de Jong
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK
| | - Athanasios Exadactylos
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Fytokou Street 384 46, Volos, Hellas, Greece
| | - Juan Antonio Raga
- Unidad de Zoología Marina Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, Aptdo 22085, E-46071 Valencia, Spain
| | - Francisco J Aznar
- Unidad de Zoología Marina Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, Aptdo 22085, E-46071 Valencia, Spain
| | - A Rus Hoelzel
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK
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Le Cam S, Daguin‐Thiébaut C, Bouchemousse S, Engelen AH, Mieszkowska N, Viard F. A genome-wide investigation of the worldwide invader Sargassum muticum shows high success albeit (almost) no genetic diversity. Evol Appl 2020; 13:500-514. [PMID: 32431732 PMCID: PMC7045713 DOI: 10.1111/eva.12837] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 04/10/2019] [Accepted: 05/24/2019] [Indexed: 12/31/2022] Open
Abstract
Twenty years of genetic studies of marine invaders have shown that successful invaders are often characterized by native and introduced populations displaying similar levels of genetic diversity. This pattern is presumably due to high propagule pressure and repeated introductions. The opposite pattern is reported in this study of the brown seaweed, Sargassum muticum, an emblematic species for circumglobal invasions. Albeit demonstrating polymorphism in the native range, microsatellites failed to detect any genetic variation over 1,269 individuals sampled from 46 locations over the Pacific-Atlantic introduction range. Single-nucleotide polymorphisms (SNPs) obtained from ddRAD sequencing revealed some genetic variation, but confirmed severe founder events in both the Pacific and Atlantic introduction ranges. Our study thus exemplifies the need for extreme caution in interpreting neutral genetic diversity as a proxy for invasive potential. Our results confirm a previously hypothesized transoceanic secondary introduction from NE Pacific to Europe. However, the SNP panel unexpectedly revealed two additional distinct genetic origins of introductions. Also, conversely to scenarios based on historical records, southern rather than northern NE Pacific populations could have seeded most of the European populations. Finally, the most recently introduced populations showed the lowest selfing rates, suggesting higher levels of recombination might be beneficial at the early stage of the introduction process (i.e., facilitating evolutionary novelties), whereas uniparental reproduction might be favored later in sustainably established populations (i.e., sustaining local adaptation).
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Affiliation(s)
- Sabrina Le Cam
- Station Biologique de Roscoff, CNRSLaboratory Adaptation & Diversity in Marine Environments (UMR 7144 CNRS SU), Sorbonne UniversitéRoscoffFrance
| | - Claire Daguin‐Thiébaut
- Station Biologique de Roscoff, CNRSLaboratory Adaptation & Diversity in Marine Environments (UMR 7144 CNRS SU), Sorbonne UniversitéRoscoffFrance
| | - Sarah Bouchemousse
- Station Biologique de Roscoff, CNRSLaboratory Adaptation & Diversity in Marine Environments (UMR 7144 CNRS SU), Sorbonne UniversitéRoscoffFrance
| | | | - Nova Mieszkowska
- Marine Biological Association of the U.K. (MBA)PlymouthUK
- School of Environmental SciencesUniversity of LiverpoolLiverpoolUK
| | - Frédérique Viard
- Station Biologique de Roscoff, CNRSLaboratory Adaptation & Diversity in Marine Environments (UMR 7144 CNRS SU), Sorbonne UniversitéRoscoffFrance
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Donkpegan ASL, Piñeiro R, Heuertz M, Duminil J, Daïnou K, Doucet JL, Hardy OJ. Population genomics of the widespread African savannah trees Afzelia africana and Afzelia quanzensis reveals no significant past fragmentation of their distribution ranges. AMERICAN JOURNAL OF BOTANY 2020; 107:498-509. [PMID: 32200549 DOI: 10.1002/ajb2.1449] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 01/13/2020] [Indexed: 06/10/2023]
Abstract
PREMISE Few studies have addressed the evolutionary history of tree species from African savannahs. Afzelia contains economically important timber species, including two species widely distributed in African savannahs: A. africana in the Sudanian region and A. quanzensis in the Zambezian region. We aimed to infer whether these species underwent range fragmentation and/or demographic changes, possibly reflecting how savannahs responded to Quaternary climate changes. METHODS We characterized the genetic diversity and structure of these species across their distribution ranges using nuclear microsatellites (SSRs) and genotyping-by-sequencing (GBS) markers. Six SSR loci were genotyped in 241 A. africana and 113 A. quanzensis individuals, while 2800 high-quality single nucleotide polymorphisms (SNPs) were identified in 30 A. africana individuals. RESULTS Both species appeared to be mainly outcrossing. The kinship between individuals decayed with the logarithm of the distance at similar rates across species and markers, leading to relatively small Sp statistics (0.0056 for SSR and 0.0054 for SNP in A. africana, 0.0075 for SSR in A. quanzensis). The patterns were consistent with isolation by distance expectations in the absence of large-scale geographic gradients. Bayesian clustering of SSR genotypes did not detect genetic clusters within species. In contrast, SNP data resolved intraspecific genetic clusters in A. africana, illustrating the higher resolving power of GBS. However, these clusters revealed low levels of differentiation and no clear geographical entities, so that they were interpreted as resulting from the isolation by distance pattern rather than from past population fragmentation. CONCLUSIONS These results suggest that populations have remained connected throughout the large, continuous savannah landscapes. The absence of clear phylogeographic discontinuities, also found in a few other African savannah trees, indicates that their distribution ranges have not been significantly fragmented during the climatic oscillations of the Pleistocene, in contrast to patterns commonly found in African rainforest trees.
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Affiliation(s)
- Armel S L Donkpegan
- Forest is Life, TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liège, 2 Passage des Déportés, B-5030, Gembloux, Belgium
- Evolutionary Biology and Ecology Unit, CP 160/12, Faculté des Sciences, Université Libre de Bruxelles, 50 avenue F. D. Roosevelt, B-1050, Brussels, Belgium
- Univ. Bordeaux, INRAE, BFP, 71 Avenue Edouard Bourlaux, F-33882, Villenave d'Ornon, France
| | - Rosalía Piñeiro
- University of Exeter, Geography, College of Life and Environmental Sciences, Stocker road, EX44QD, Exeter, UK
- Evolutionary Genomics, Centre for Geogenetics - Natural History Museum of Denmark, Øster Voldgade 5-7, 1350, Copenhagen K, Denmark
| | - Myriam Heuertz
- Univ. Bordeaux, INRAE, BIOGECO, 69 route d'Arcachon, F-33610, Cestas, France
| | - Jérôme Duminil
- Evolutionary Biology and Ecology Unit, CP 160/12, Faculté des Sciences, Université Libre de Bruxelles, 50 avenue F. D. Roosevelt, B-1050, Brussels, Belgium
- DIADE, IRD, University of Montpellier, 911 Avenue Agropolis, BP 64501, 34394, Montpellier, France
- Bioversity International, Forest Genetic Resources and Restoration Programme, Sub-Regional Office for Central Africa, P.O. Box 2008, Messa, Yaoundé, Cameroon
| | - Kasso Daïnou
- Forest is Life, TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liège, 2 Passage des Déportés, B-5030, Gembloux, Belgium
- Evolutionary Biology and Ecology Unit, CP 160/12, Faculté des Sciences, Université Libre de Bruxelles, 50 avenue F. D. Roosevelt, B-1050, Brussels, Belgium
- Université d'Agriculture de Kétou, BP: 43, Kétou, Benin
| | - Jean-Louis Doucet
- Forest is Life, TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liège, 2 Passage des Déportés, B-5030, Gembloux, Belgium
| | - Olivier J Hardy
- Evolutionary Biology and Ecology Unit, CP 160/12, Faculté des Sciences, Université Libre de Bruxelles, 50 avenue F. D. Roosevelt, B-1050, Brussels, Belgium
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Development of 26 highly polymorphic microsatellite markers for the highly endangered fan mussel Pinna nobilis and cross-species amplification. Mol Biol Rep 2020; 47:2551-2559. [PMID: 32095986 DOI: 10.1007/s11033-020-05338-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 02/13/2020] [Accepted: 02/18/2020] [Indexed: 10/24/2022]
Abstract
The fan mussel, Pinna nobilis is a highly endangered bivalve species endemic to the Mediterranean Sea. During the last few decades, populations have been greatly reduced due to anthropic impacts and they are now under strict protection in most Mediterranean countries. Today, the species is facing a major crisis following the introduction of an haplosporidan parasite which is driving mass mortality in almost all P. nobilis populations throughout the Mediterranean Sea. Gathering additional knowledge regarding dynamics and connectivity patterns of P. nobilis populations is now more than ever critical. Here, we describe the development of 26 highly polymorphic microsatellite markers. Average allelic diversity of 10.9 alleles per locus was reported and heterozygosity ranged from 0.0294 to 0.9737. We tested cross-species amplification in four Pinna species for the new markers together with 10 already published markers, and analysed its success according to the genetic distances among species. Cross-species transferability success ranged from 3 to 38% and had a negative relationship with the genetic distance between the target species and the tested species. The establishment of this new set of high-resolution markers provides a useful tool to understand processes driving gene flow and genetic diversity in P. nobilis populations and the closest congeneric species.
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Latron M, Arnaud JF, Ferla H, Godé C, Duputié A. Effects of contemporary shifts of range margins on patterns of genetic structure and mating system in two coastal plant species. Heredity (Edinb) 2020; 124:336-350. [PMID: 31541203 PMCID: PMC6972893 DOI: 10.1038/s41437-019-0269-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 07/19/2019] [Accepted: 07/23/2019] [Indexed: 11/08/2022] Open
Abstract
Species' geographical ranges are often restricted due to niche limitation resulting in geographical isolation and reduced population size at range margins. Under the "abundant center" paradigm, static marginal populations are thus expected to show higher genetic differentiation and lower genetic diversity than core populations. Low mate availability may also drive shifts toward higher propensity for selfing in geographically marginal populations. However, these predictions remain to be validated for contemporary range shifts occurring under current environmental change. This study is devoted to bridging this gap and assesses the spatial patterns of genetic structure and mating system across the geographical range of two coastal plant species characterized by contrasting contemporary range dynamics: the receding myrmecochorous Dune pansy (Viola tricolor subsp. curtisii) and the widespread expanding hydrochorous Rock samphire (Crithmum maritimum). Both species exhibited high propensity for selfing, with indications of inbreeding depression acting at early life stages. In Dune pansy, a biogeographical break was observed between core and marginal populations, with trailing-edge populations showing higher levels of genetic differentiation, reduced genetic diversity, and higher levels of selfing estimated through progeny arrays. In contrast, genetic structuring was weak in Rock samphire and no clear spatial trends were observed in genetic diversity nor in mating system, likely the result of efficient long-distance seed dispersal by sea-surface currents. Our study highlights that key species differences in life-history traits related to dispersal and/or mate limitation modify the expectations of genetic diversity loss and mating system shift in contemporary range-expanding populations, as compared with historical core populations.
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Affiliation(s)
- Mathilde Latron
- University of Lille, CNRS, UMR 8198-Evo-Eco-Paleo, F-59000, Lille, France
| | | | - Héloïse Ferla
- University of Lille, CNRS, UMR 8198-Evo-Eco-Paleo, F-59000, Lille, France
| | - Cécile Godé
- University of Lille, CNRS, UMR 8198-Evo-Eco-Paleo, F-59000, Lille, France
| | - Anne Duputié
- University of Lille, CNRS, UMR 8198-Evo-Eco-Paleo, F-59000, Lille, France.
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50
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Saubin M, Devillers H, Proust L, Brier C, Grondin C, Pradal M, Legras JL, Neuvéglise C. Investigation of Genetic Relationships Between Hanseniaspora Species Found in Grape Musts Revealed Interspecific Hybrids With Dynamic Genome Structures. Front Microbiol 2020; 10:2960. [PMID: 32010076 PMCID: PMC6974558 DOI: 10.3389/fmicb.2019.02960] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 12/09/2019] [Indexed: 01/11/2023] Open
Abstract
Hanseniaspora, a predominant yeast genus of grape musts, includes sister species recently reported as fast evolving. The aim of this study was to investigate the genetic relationships between the four most closely related species, at the population level. A multi-locus sequence typing strategy based on five markers was applied on 107 strains, confirming the clear delineation of species H. uvarum, H. opuntiae, H. guilliermondii, and H. pseudoguilliermondii. Huge variations were observed in the level of intraspecific nucleotide diversity, and differences in heterozygosity between species indicate different life styles. No clear population structure was detected based on geographical or substrate origins. Instead, H. guilliermondii strains clustered into two distinct groups, which may reflect a recent step toward speciation. Interspecific hybrids were detected between H. opuntiae and H. pseudoguilliermondii. Their characterization using flow cytometry, karyotypes and genome sequencing showed different genome structures in different ploidy contexts: allodiploids, allotriploids, and allotetraploids. Subculturing of an allotriploid strain revealed chromosome loss equivalent to one chromosome set, followed by an auto-diploidization event, whereas another auto-diploidized tetraploid showed a segmental duplication. Altogether, these results suggest that Hanseniaspora genomes are not only fast evolving but also highly dynamic.
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Affiliation(s)
- Méline Saubin
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Hugo Devillers
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Lucas Proust
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Cathy Brier
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Cécile Grondin
- Micalis Institute, INRA, AgroParisTech, CIRM-Levures, Université Paris-Saclay, Jouy-en-Josas, France
| | - Martine Pradal
- SPO, Univ Montpellier, INRA, Montpellier SupAgro, Montpellier, France
| | - Jean-Luc Legras
- SPO, Univ Montpellier, INRA, Montpellier SupAgro, Montpellier, France
| | - Cécile Neuvéglise
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
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