1
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Josić D, Çoraman E, Waurick I, Franzenburg S, Ancillotto L, Bajić B, Budinski I, Dietz C, Görföl T, Hayden Bofill SI, Presetnik P, Russo D, Spada M, Zrnčić V, Blom MPK, Mayer F. Cryptic hybridization between the ancient lineages of Natterer's bat (Myotis nattereri). Mol Ecol 2024; 33:e17411. [PMID: 38785347 DOI: 10.1111/mec.17411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 04/16/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024]
Abstract
Studying hybrid zones that form between morphologically cryptic taxa offers valuable insights into the mechanisms of cryptic speciation and the evolution of reproductive barriers. Although hybrid zones have long been the focus of evolutionary studies, the awareness of cryptic hybrid zones increased recently due to rapidly growing evidence of biological diversity lacking obvious phenotypic differentiation. The characterization of cryptic hybrid zones with genome-wide analysis is in its early stages and offers new perspectives for studying population admixture and thus the impact of gene flow. In this study, we investigate the population genomics of the Myotis nattereri complex in one of its secondary contact zones, where a putative hybrid zone is formed between two of its cryptic lineages. By utilizing a whole-genome shotgun sequencing approach, we aim to characterize this cryptic hybrid zone in detail. Demographic analysis suggests that the cryptic lineages diverged during the Pliocene, c. 3.6 million years ago. Despite this ancient separation, the populations in the contact zone exhibit mitochondrial introgression and a considerable amount of mixing in nuclear genomes. The genomic structure of the populations corresponds to geographic locations and the genomic admixture changes along a geographic gradient. These findings suggest that there is no effective hybridization barrier between both lineages, nevertheless, their population structure is shaped by dispersal barriers. Our findings highlight how such deeply diverged cryptic lineages can still readily hybridize in secondary contact.
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Affiliation(s)
- Darija Josić
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Emrah Çoraman
- Department of Ecology and Evolution, Eurasia Institute of Earth Sciences, Istanbul Technical University, İstanbul, Türkiye
| | - Isabelle Waurick
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Sören Franzenburg
- IKMB, Institute of Clinical Molecular Biology, University of Kiel, Kiel, Germany
| | - Leonardo Ancillotto
- Laboratory of Animal Ecology and Evolution (AnEcoEvo), Dipartimento di Agraria, Universita degli Studi di Napoli Federico II, Portici, Italy
| | - Branka Bajić
- Department of Genetic Research, Institute for Biological Research 'Siniša Stanković' - National Institute of Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Ivana Budinski
- Department of Genetic Research, Institute for Biological Research 'Siniša Stanković' - National Institute of Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | | | - Tamás Görföl
- Department of Zoology, Hungarian Natural History Museum, Budapest, Hungary
- National Laboratory of Virology, University of Pécs, Pécs, Hungary
| | - Sofia I Hayden Bofill
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Primož Presetnik
- Centre for Cartography of Fauna and Flora, Miklavž na Dravskem Polju, Slovenia
| | - Danilo Russo
- Laboratory of Animal Ecology and Evolution (AnEcoEvo), Dipartimento di Agraria, Universita degli Studi di Napoli Federico II, Portici, Italy
| | - Martina Spada
- Dipartimento Ambiente-Salute-Sicurezza, Universita degli Studi dell'Insubria, Varese, Italy
| | - Vida Zrnčić
- Croatian Biospeleogical Society Zagreb, Zagreb, Croatia
| | - Mozes P K Blom
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Frieder Mayer
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
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2
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Firneno TJ, Semenov G, Dopman EB, Taylor SA, Larson EL, Gompert Z. Quantitative Analyses of Coupling in Hybrid Zones. Cold Spring Harb Perspect Biol 2023; 15:a041434. [PMID: 37739809 PMCID: PMC10691479 DOI: 10.1101/cshperspect.a041434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
In hybrid zones, whether barrier loci experience selection mostly independently or as a unit depends on the ratio of selection to recombination as captured by the coupling coefficient. Theory predicts a sharper transition between an uncoupled and coupled system when more loci affect hybrid fitness. However, the extent of coupling in hybrid zones has rarely been quantified. Here, we use simulations to characterize the relationship between the coupling coefficient and variance in clines across genetic loci. We then reanalyze 25 hybrid zone data sets and find that cline variances and estimated coupling coefficients form a smooth continuum from high variance and weak coupling to low variance and strong coupling. Our results are consistent with low rates of hybridization and a strong genome-wide barrier to gene flow when the coupling coefficient is much greater than 1, but also suggest that this boundary might be approached gradually and at a near constant rate over time.
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Affiliation(s)
- Thomas J Firneno
- Department of Biology, University of Denver, Denver, Colorado 80208, USA
| | - Georgy Semenov
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado 80211, USA
| | - Erik B Dopman
- Department of Biology, Tufts University, Medford, Massachusetts 02155, USA
| | - Scott A Taylor
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado 80211, USA
| | - Erica L Larson
- Department of Biology, University of Denver, Denver, Colorado 80208, USA
| | - Zachariah Gompert
- Department of Biology, Utah State University, Logan, Utah 84321, USA
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3
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Bailey N, Ruiz C, Tosi A, Stevison L. Genomic analysis of the rhesus macaque ( Macaca mulatta) and the cynomolgus macaque ( Macaca fascicularis) uncover polygenic signatures of reinforcement speciation. Ecol Evol 2023; 13:e10571. [PMID: 37849934 PMCID: PMC10577069 DOI: 10.1002/ece3.10571] [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: 06/21/2023] [Revised: 09/11/2023] [Accepted: 09/12/2023] [Indexed: 10/19/2023] Open
Abstract
Speciation can involve phases of divergent adaptation in allopatry and ecological/reproductive character displacement in sympatry or parapatry. Reproductive character displacement can result as a means of preventing hybridization, a process known as reinforcement speciation. In this study, we use whole-genome sequencing (WGS) of two closely related primate species that have experienced introgression in their history, the rhesus (Macaca mulatta) and cynomolgus (M. fascicularis) macaques, to identify genes exhibiting reproductive character displacement and other patterns consistent with reinforcement speciation. Using windowed scans of various population genetic statistics to identify signatures of reinforcement, we find 184 candidate genes associated with a variety of functions, including an overrepresentation of multiple neurological functions and several genes involved in sexual development and gametogenesis. These results are consistent with a variety of genes acting in a reinforcement process between these species. We also find signatures of introgression of the Y-chromosome that confirm previous studies suggesting male-driven introgression of M. mulatta into M. fascicularis populations. This study uses WGS to find evidence of the process of reinforcement in primates that have medical and conservation relevance.
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Affiliation(s)
- Nick Bailey
- Department of Biological SciencesAuburn UniversityAuburnAlabamaUSA
| | - Cody Ruiz
- Department of AnthropologyKent State UniversityKentOhioUSA
| | - Anthony Tosi
- Department of AnthropologyKent State UniversityKentOhioUSA
| | - Laurie Stevison
- Department of Biological SciencesAuburn UniversityAuburnAlabamaUSA
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4
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Hirst MA, Rodas-Martínez AZ, Milich KM, Cortés-Ortiz L. Differences in sperm morphology between Alouatta palliata and Alouatta pigra are consistent with the intensity of sperm competition in each species. Am J Primatol 2023; 85:e23538. [PMID: 37487624 PMCID: PMC10528854 DOI: 10.1002/ajp.23538] [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: 11/22/2022] [Revised: 07/03/2023] [Accepted: 07/08/2023] [Indexed: 07/26/2023]
Abstract
The intensity of sperm competition, in which sperm compete within the female reproductive tract to reach and fertilize her eggs, varies in species with different mating systems. Sperm competition is more intense in species where males cannot monopolize access to reproductive females and females mate with multiple males. In this scenario, a morphological change that increases the ability of sperm to reach and fertilize eggs should rapidly spread in the population, leading to sperm morphological differences between closely related species. Differences in sperm morphology have been reported among primate species with different mating systems. However, due to the inherent logistical and ethical difficulties to sample sperm from wild primates, the extent of variation in sperm morphology within species and among closely related species remains understudied. Here, we compared sperm morphological traits from two sister howler monkey species (Alouatta palliata and Alouatta pigra) that have different mating systems to investigate the effect of sperm competition on sperm morphological traits. We predicted that sperm from A. palliata, where females have more opportunities to mate with multiple males, would show differences in traits associated with increase sperm competitiveness compared to A. pigra where females mostly mate with the central male. We used linear mixed models to determine species differences in sperm morphology, controlling for individual variation. We found that midpieces and heads in A. palliata sperm were on average 26.2% and 11.0% longer, respectively, than those of A. pigra. Differences in these traits are important for sperm speed and hydrodynamic movement in other species and can affect fertilization success. This study provides empirical evidence of sperm morphological traits that evolved through sexual selection in sister primate species with different mating systems.
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Affiliation(s)
- Molly A. Hirst
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105 N. University Ave., Ann Arbor, MI, USA 48109
| | - Alba Z. Rodas-Martínez
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco, km 0.5 Carr. Villahermosa-Cárdenas S/N, entroque a Bosques de Saloya, 86039 Villahermosa, Tabasco, México
| | - Krista M. Milich
- Department of Anthropology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, USA 63130
| | - Liliana Cortés-Ortiz
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105 N. University Ave., Ann Arbor, MI, USA 48109
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Lajmi A, Glinka F, Privman E. Optimizing ddRAD sequencing for population genomic studies with ddgRADer. Mol Ecol Resour 2023. [PMID: 37732396 DOI: 10.1111/1755-0998.13870] [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: 10/27/2022] [Revised: 08/04/2023] [Accepted: 08/31/2023] [Indexed: 09/22/2023]
Abstract
Double-digest Restriction-site Associated DNA sequencing (ddRADseq) is widely used to generate genomic data for non-model organisms in evolutionary and ecological studies. Along with affordable paired-end sequencing, this method makes population genomic analyses more accessible. However, multiple factors should be considered when designing a ddRADseq experiment, which can be challenging for new users. The generated data often suffer from substantial read overlaps and adaptor contamination, severely reducing sequencing efficiency and affecting data quality. Here, we analyse diverse datasets from the literature and carry out controlled experiments to understand the effects of enzyme choice and size selection on sequencing efficiency. The empirical data reveal that size selection is imprecise and has limited efficacy. In certain scenarios, a substantial proportion of short fragments pass below the lower size-selection cut-off resulting in low sequencing efficiency. However, enzyme choice can considerably mitigate inadvertent inclusion of these shorter fragments. A simple model based on these experiments is implemented to predict the number of genomic fragments generated after digestion and size selection, number of SNPs genotyped, number of samples that can be multiplexed and the expected sequencing efficiency. We developed ddgRADer - http://ddgrader.haifa.ac.il/ - a user-friendly webtool and incorporated these calculations to aid in ddRADseq experimental design while optimizing sequencing efficiency. This tool can also be used for single enzyme protocols such as Genotyping-by-Sequencing. Given user-defined study goals, ddgRADer recommends enzyme pairs and allows users to compare and choose enzymes and size-selection criteria. ddgRADer improves the accessibility and ease of designing ddRADseq experiments and increases the probability of success of the first population genomic study conducted in labs with no prior experience in genomics.
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Affiliation(s)
- Aparna Lajmi
- Department of Evolutionary and Environmental Biology, Institute of Evolution, University of Haifa, Haifa, Israel
| | - Felix Glinka
- Department of Evolutionary and Environmental Biology, Institute of Evolution, University of Haifa, Haifa, Israel
| | - Eyal Privman
- Department of Evolutionary and Environmental Biology, Institute of Evolution, University of Haifa, Haifa, Israel
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6
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Nikolakis ZL, Schield DR, Westfall AK, Perry BW, Ivey KN, Orton RW, Hales NR, Adams RH, Meik JM, Parker JM, Smith CF, Gompert Z, Mackessy SP, Castoe TA. Evidence that genomic incompatibilities and other multilocus processes impact hybrid fitness in a rattlesnake hybrid zone. Evolution 2022; 76:2513-2530. [PMID: 36111705 DOI: 10.1111/evo.14612] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 06/24/2022] [Accepted: 08/15/2022] [Indexed: 01/22/2023]
Abstract
Hybrid zones provide valuable opportunities to understand the genomic mechanisms that promote speciation by providing insight into factors involved in intermediate stages of speciation. Here, we investigate introgression in a hybrid zone between two rattlesnake species (Crotalus viridis and Crotalus oreganus concolor) that have undergone historical allopatric divergence and recent range expansion and secondary contact. We use Bayesian genomic cline models to characterize genomic patterns of introgression between these lineages and identify loci potentially subject to selection in hybrids. We find evidence for a large number of genomic regions with biased ancestry that deviate from the genomic background in hybrids (i.e., excess ancestry loci), which tend to be associated with genomic regions with higher recombination rates. We also identify suites of excess ancestry loci that show highly correlated allele frequencies (including conspecific and heterospecific combinations) across physically unlinked genomic regions in hybrids. Our findings provide evidence for multiple multilocus evolutionary processes impacting hybrid fitness in this system.
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Affiliation(s)
- Zachary L Nikolakis
- Department of Biology, University of Texas at Arlington, Arlington, Texas, 76019
| | - Drew R Schield
- Department of Biology, University of Texas at Arlington, Arlington, Texas, 76019.,Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, 80309
| | - Aundrea K Westfall
- Department of Biology, University of Texas at Arlington, Arlington, Texas, 76019
| | - Blair W Perry
- Department of Biology, University of Texas at Arlington, Arlington, Texas, 76019
| | - Kathleen N Ivey
- Department of Biology, University of Texas at Arlington, Arlington, Texas, 76019
| | - Richard W Orton
- Department of Biology, University of Texas at Arlington, Arlington, Texas, 76019
| | - Nicole R Hales
- Department of Biology, University of Texas at Arlington, Arlington, Texas, 76019
| | - Richard H Adams
- Department of Biological and Environmental Sciences, Georgia College and State University, Milledgeville, Georgia, 31061
| | - Jesse M Meik
- Department of Biological Sciences, Tarleton State University, Stephenville, Texas, 76402
| | - Joshua M Parker
- Department of Life Sciences, Fresno City College, Fresno, California, 93741
| | - Cara F Smith
- School of Biological Sciences, University of Northern Colorado, Greeley, Colorado, 80639
| | | | - Stephen P Mackessy
- School of Biological Sciences, University of Northern Colorado, Greeley, Colorado, 80639
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington, Arlington, Texas, 76019
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7
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Horta P, Raposeira H, Baños A, Ibáñez C, Razgour O, Rebelo H, Juste J. Counteracting forces of introgressive hybridization and interspecific competition shape the morphological traits of cryptic Iberian Eptesicus bats. Sci Rep 2022; 12:11695. [PMID: 35803997 PMCID: PMC9270368 DOI: 10.1038/s41598-022-15412-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 06/23/2022] [Indexed: 11/30/2022] Open
Abstract
Cryptic species that coexist in sympatry are likely to simultaneously experience strong competition and hybridization. The first phenomenon would lead to character displacement, whereas the second can potentially promote morphological similarity through adaptive introgression. The main goal of this work was to investigate the effect of introgressive hybridization on the morphology of cryptic Iberian Eptesicus bats when facing counteracting evolutionary forces from interspecific competition. We found substantial overlap both in dentition and in wing morphology traits, though mainly in individuals in sympatry. The presence of hybrids contributes to a fifth of this overlap, with hybrids showing traits with intermediate morphometry. Thus, introgressive hybridization may contribute to species adaptation to trophic and ecological space responding directly to the macro-habitats characteristics of the sympatric zone and to local prey availability. On the other hand, fur shade tended to be browner and brighter in hybrids than parental species. Colour differences could result from partitioning of resources as an adaptation to environmental factors such as roost and microhabitats. We argue that a balance between adaptive introgression and niche partitioning shapes species interactions with the environment through affecting morphological traits under selection.
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Affiliation(s)
- Pedro Horta
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal. .,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002, Porto, Portugal. .,OII - Observatório Inovação Investigação, Seia, Portugal. .,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal.
| | - Helena Raposeira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002, Porto, Portugal.,OII - Observatório Inovação Investigação, Seia, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
| | | | - Carlos Ibáñez
- Departmento de Ecología Evolutiva, Estación Biológica de Doñana (CSIC), Avda. Américo Vespucio 26, 41092, Sevilla, Spain.,CIBER de Epidemiología y Salud Pública, CIBERESP, Madrid, Spain
| | | | - Hugo Rebelo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal.,ESS, Polytechnic Institute of Setúbal, Setúbal, Portugal, Campus do IPS - Estefanilha, 2910-761 Setúbal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Javier Juste
- Departmento de Ecología Evolutiva, Estación Biológica de Doñana (CSIC), Avda. Américo Vespucio 26, 41092, Sevilla, Spain.,CIBER de Epidemiología y Salud Pública, CIBERESP, Madrid, Spain
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8
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Zheng W, Yan LJ, Burgess KS, Luo YH, Zou JY, Qin HT, Wang JH, Gao LM. Natural hybridization among three Rhododendron species (Ericaceae) revealed by morphological and genomic evidence. BMC PLANT BIOLOGY 2021; 21:529. [PMID: 34763662 PMCID: PMC8582147 DOI: 10.1186/s12870-021-03312-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Accepted: 11/02/2021] [Indexed: 06/08/2023]
Abstract
BACKGROUND Natural hybridization can influence the adaptive response to selection and accelerate species diversification. Understanding the composition and structure of hybrid zones may elucidate patterns of hybridization processes that are important to the formation and maintenance of species, especially for taxa that have experienced rapidly adaptive radiation. Here, we used morphological traits, ddRAD-seq and plastid DNA sequence data to investigate the structure of a Rhododendron hybrid zone and uncover the hybridization patterns among three sympatric and closely related species. RESULTS Our results show that the hybrid zone is complex, where bi-directional hybridization takes place among the three sympatric parental species: R. spinuliferum, R. scabrifolium, and R. spiciferum. Hybrids between R. spinuliferum and R. spiciferum (R. ×duclouxii) comprise multiple hybrid classes and a high proportion of F1 generation hybrids, while a novel hybrid taxon between R. spinuliferum and R. scabrifolium dominated the F2 generation, but no backcross individuals were detected. The hybrid zone showed basically coincident patterns of population structure between genomic and morphological data. CONCLUSIONS Natural hybridization exists among the three Rhododendron species in the hybrid zone, although patterns of hybrid formation vary between hybrid taxa, which may result in different evolutionary outcomes. This study represents a unique opportunity to dissect the ecological and evolutionary mechanisms associated with adaptive radiation of Rhododendron species in a biodiversity hotspot.
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Affiliation(s)
- Wei Zheng
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, China
- University of Chinese Academy of Sciences, 10049, Beijing, China
| | - Li-Jun Yan
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, China
- University of Chinese Academy of Sciences, 10049, Beijing, China
- College of Vocational and Technical Education, Yunnan Normal University, 650092, Kunming, Yunnan, China
| | - Kevin S Burgess
- Department of Biology, Columbus State University, University System of Georgia, 31907-5645, Columbus, GA, USA
| | - Ya-Huang Luo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, China
| | - Jia-Yun Zou
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, China
- University of Chinese Academy of Sciences, 10049, Beijing, China
| | - Han-Tao Qin
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, China
- University of Chinese Academy of Sciences, 10049, Beijing, China
| | - Ji-Hua Wang
- The Flower Research Institute, Yunnan Academy of Agricultural Sciences, 650205, Kunming, China.
| | - Lian-Ming Gao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, China.
- Lijiang Forest Biodiversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, 674100, Lijiang, Yunnan, China.
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9
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Divergence and introgression in small apes, the genus Hylobates, revealed by reduced representation sequencing. Heredity (Edinb) 2021; 127:312-322. [PMID: 34188193 PMCID: PMC8405704 DOI: 10.1038/s41437-021-00452-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 06/15/2021] [Accepted: 06/15/2021] [Indexed: 02/06/2023] Open
Abstract
Gibbons of the genus Hylobates, which inhabit Southeast Asia, show great diversity and comprise seven to nine species. Natural hybridisation has been observed in several species contact zones, but the history and extent of hybridisation and introgression in possibly historical and the current contact zones remain unclear. To uncover Hylobates species phylogeny and the extent of introgression in their evolution, genotyping by random amplicon sequencing-direct (GRAS-Di) was applied to 47 gibbons, representing seven Hylobates species/subspecies and two outgroup gibbon species. Over 200,000 autosomal single-nucleotide variant sites were identified. The autosomal phylogeny supported that divergence from the mainland species began ~3.5 million years ago, and subsequently occurred among the Sundaic island species. Significant introgression signals were detected between H. lar and H. pileatus, H. lar and H. agilis and H. albibarbis and H. muelleri, which all are parapatric and form ongoing hybrid zones. Furthermore, the introgression signals were detected in every analysed individual of these species, indicating a relatively long history of hybridisation, which might have affected the entire gene pool. By contrast, signals of introgression were either not detected or doubtful in other species pairs living on different islands, indicating the rarity of hybridisation and introgression, even though the Sundaic islands were connected during the Pliocene and Pleistocene glacial events.
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10
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Fraïsse C, Sachdeva H. The rates of introgression and barriers to genetic exchange between hybridizing species: sex chromosomes vs autosomes. Genetics 2021; 217:6042694. [PMID: 33724409 DOI: 10.1093/genetics/iyaa025] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 11/23/2020] [Indexed: 12/14/2022] Open
Abstract
Interspecific crossing experiments have shown that sex chromosomes play a major role in reproductive isolation between many pairs of species. However, their ability to act as reproductive barriers, which hamper interspecific genetic exchange, has rarely been evaluated quantitatively compared to Autosomes. This genome-wide limitation of gene flow is essential for understanding the complete separation of species, and thus speciation. Here, we develop a mainland-island model of secondary contact between hybridizing species of an XY (or ZW) sexual system. We obtain theoretical predictions for the frequency of introgressed alleles, and the strength of the barrier to neutral gene flow for the two types of chromosomes carrying multiple interspecific barrier loci. Theoretical predictions are obtained for scenarios where introgressed alleles are rare. We show that the same analytical expressions apply for sex chromosomes and autosomes, but with different sex-averaged effective parameters. The specific features of sex chromosomes (hemizygosity and absence of recombination in the heterogametic sex) lead to reduced levels of introgression on the X (or Z) compared to autosomes. This effect can be enhanced by certain types of sex-biased forces, but it remains overall small (except when alleles causing incompatibilities are recessive). We discuss these predictions in the light of empirical data comprising model-based tests of introgression and cline surveys in various biological systems.
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Affiliation(s)
- Christelle Fraïsse
- Institute of Science and Technology Austria, Klosterneuburg 3400, Austria.,CNRS, Univ. Lille, UMR 8198 - Evo-Eco-Paleo, F-59000 Lille, France
| | - Himani Sachdeva
- Institute of Science and Technology Austria, Klosterneuburg 3400, Austria.,Mathematics and BioSciences Group, Faculty of Mathematics, University of Vienna, A-1090 Vienna, Austria
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11
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Baiz MD, Tucker PK, Mueller JL, Cortés-Ortiz L. X-Linked Signature of Reproductive Isolation in Humans is Mirrored in a Howler Monkey Hybrid Zone. J Hered 2021; 111:419-428. [PMID: 32725191 PMCID: PMC7525826 DOI: 10.1093/jhered/esaa021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Indexed: 12/13/2022] Open
Abstract
Reproductive isolation is a fundamental step in speciation. While sex chromosomes have been linked to reproductive isolation in many model systems, including hominids, genetic studies of the contribution of sex chromosome loci to speciation for natural populations are relatively sparse. Natural hybrid zones can help identify genomic regions contributing to reproductive isolation, like hybrid incompatibility loci, since these regions exhibit reduced introgression between parental species. Here, we use a primate hybrid zone (Alouatta palliata × Alouatta pigra) to test for reduced introgression of X-linked SNPs compared to autosomal SNPs. To identify X-linked sequence in A. palliata, we used a sex-biased mapping approach with whole-genome re-sequencing data. We then used genomic cline analysis with reduced-representation sequence data for parental A. palliata and A. pigra individuals and hybrids (n = 88) to identify regions with non-neutral introgression. We identified ~26 Mb of non-repetitive, putatively X-linked genomic sequence in A. palliata, most of which mapped collinearly to the marmoset and human X chromosomes. We found that X-linked SNPs had reduced introgression and an excess of ancestry from A. palliata as compared to autosomal SNPs. One outlier region with reduced introgression overlaps a previously described "desert" of archaic hominin ancestry on the human X chromosome. These results are consistent with a large role for the X chromosome in speciation across animal taxa and further, suggest shared features in the genomic basis of the evolution of reproductive isolation in primates.
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Affiliation(s)
- Marcella D Baiz
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI.,Department of Biology, Pennsylvania State University, University Park, PA
| | - Priscilla K Tucker
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI
| | - Jacob L Mueller
- Department of Human Genetics, University of Michigan, Ann Arbor, MI
| | - Liliana Cortés-Ortiz
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI
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12
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Jahner JP, Parchman TL, Matocq MD. Multigenerational backcrossing and introgression between two woodrat species at an abrupt ecological transition. Mol Ecol 2021; 30:4245-4258. [PMID: 34219316 DOI: 10.1111/mec.16056] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 06/28/2021] [Indexed: 12/27/2022]
Abstract
When organisms experience secondary contact after allopatric divergence, genomic regions can introgress differentially depending on their relationships with adaptation, reproductive isolation, recombination, and drift. Analyses of genome-wide patterns of divergence and introgression could provide insight into the outcomes of hybridization and the potential relationship between allopatric divergence and reproductive isolation. Here, we generate population genetic data (26,262 SNPs; 353 individuals) using a reduced-representation sequencing approach to quantify patterns of ancestry, differentiation, and introgression between a pair of ecologically distinct mammals-the desert woodrat (N. lepida) and Bryant's woodrat (N. bryanti)-that hybridize at a sharp ecotone in southern California. Individual ancestry estimates confirmed that hybrids were rare in this bimodal hybrid zone, and entirely consisted of a few F1 individuals and a broad range of multigenerational backcrosses. Genomic cline analyses indicated more than half of loci had elevated introgression from one genomic background into the other. However, introgression was not associated with relative or absolute measures of divergence, and loci with extreme values for both were not typically found near detoxification enzymes previously implicated in dietary specialization for woodrats. The decoupling of differentiation and introgression suggests that processes other than adaptation, such as drift, may underlie the extreme clines at this contact zone.
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Affiliation(s)
- Joshua P Jahner
- Department of Biology, University of Nevada, Reno, Nevada, USA.,Department of Botany, University of Wyoming, Laramie, Wyoming, USA
| | - Thomas L Parchman
- Department of Biology, University of Nevada, Reno, Nevada, USA.,Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, Nevada, USA
| | - Marjorie D Matocq
- Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, Nevada, USA.,Department of Natural Resources and Environmental Science, University of Nevada, Reno, Nevada, USA
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13
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Melo-Carrillo A, Dunn JC, Cortés-Ortiz L. Low genetic diversity and limited genetic structure across the range of the critically endangered Mexican howler monkey (Alouatta palliata mexicana). Am J Primatol 2020; 82:e23160. [PMID: 32557717 DOI: 10.1002/ajp.23160] [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] [Received: 02/14/2020] [Revised: 06/01/2020] [Accepted: 06/07/2020] [Indexed: 11/08/2022]
Abstract
Genetic diversity provides populations with the possibility to persist in ever-changing environments, where selective regimes change over time. Therefore, the long-term survival of a population may be affected by its level of genetic diversity. The Mexican howler monkey (Alouatta palliata mexicana) is a critically endangered primate restricted to southeast Mexico. Here, we evaluate the genetic diversity and population structure of this subspecies based on 83 individuals from 31 groups sampled across the distribution range of the subspecies, using 29 microsatellite loci. Our results revealed extremely low genetic diversity (HO = 0.21, HE = 0.29) compared to studies of other A. palliata populations and to other Alouatta species. Principal component analysis, a Bayesian clustering method, and analyses of molecular variance did not detect strong signatures of genetic differentiation among geographic populations of this subspecies. Although we detect small but significant FST values between populations, they can be explained by a pattern of isolation by distance. These results and the presence of unique alleles in different populations highlight the importance of implementing conservation efforts in multiple populations across the distribution range of A. p. mexicana to preserve its already low genetic diversity. This is especially important given current levels of population isolation due to the extreme habitat fragmentation across the distribution range of this primate.
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Affiliation(s)
- Adrián Melo-Carrillo
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan
| | - Jacob C Dunn
- Behavioural Ecology Research Group, School of Life Sciences, Anglia Ruskin University, Cambridge, UK.,Biological Anthropology, Department of Archaeology, University of Cambridge, Cambridge, UK.,Department of Cognitive Biology, University of Vienna, Vienna, Austria
| | - Liliana Cortés-Ortiz
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan
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14
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Tonzo V, Papadopoulou A, Ortego J. Genomic footprints of an old affair: Single nucleotide polymorphism data reveal historical hybridization and the subsequent evolution of reproductive barriers in two recently diverged grasshoppers with partly overlapping distributions. Mol Ecol 2020; 29:2254-2268. [DOI: 10.1111/mec.15475] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 05/10/2020] [Accepted: 05/11/2020] [Indexed: 12/17/2022]
Affiliation(s)
- Vanina Tonzo
- Department of Integrative Ecology Estación Biológica de Doñana (EBD‐CSIC) Seville Spain
| | - Anna Papadopoulou
- Department of Biological Sciences University of Cyprus Nicosia Cyprus
| | - Joaquín Ortego
- Department of Integrative Ecology Estación Biológica de Doñana (EBD‐CSIC) Seville Spain
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15
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Wells CP, Lavretsky P, Sorenson MD, Peters JL, DaCosta JM, Turnbull S, Uyehara KJ, Malachowski CP, Dugger BD, Eadie JM, Engilis A. Persistence of an endangered native duck, feral mallards, and multiple hybrid swarms across the main Hawaiian Islands. Mol Ecol 2019; 28:5203-5216. [DOI: 10.1111/mec.15286] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 10/14/2019] [Accepted: 10/15/2019] [Indexed: 12/26/2022]
Affiliation(s)
- Caitlin P. Wells
- Department of Wildlife, Fish, and Conservation Biology University of California Davis CA USA
| | - Philip Lavretsky
- Department of Biological Sciences University of Texas El Paso TX USA
| | | | - Jeffrey L. Peters
- Department of Biological Sciences Wright State University Dayton OH USA
| | | | - Stephen Turnbull
- Division of Forestry and Wildlife Department of Land and Natural Resources Honolulu HI USA
| | - Kimberly J. Uyehara
- Kauaʻi National Wildlife Refuge Complex U.S. Fish and Wildlife Service Kīlauea HI USA
| | | | - Bruce D. Dugger
- Department of Fisheries and Wildlife Oregon State University Corvallis OR USA
| | - John M. Eadie
- Department of Wildlife, Fish, and Conservation Biology University of California Davis CA USA
| | - Andrew Engilis
- Department of Wildlife, Fish, and Conservation Biology University of California Davis CA USA
- Museum of Wildlife and Fish Biology University of California Davis CA USA
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16
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Tonzo V, Papadopoulou A, Ortego J. Genomic data reveal deep genetic structure but no support for current taxonomic designation in a grasshopper species complex. Mol Ecol 2019; 28:3869-3886. [DOI: 10.1111/mec.15189] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 07/14/2019] [Accepted: 07/15/2019] [Indexed: 01/04/2023]
Affiliation(s)
- Vanina Tonzo
- Department of Integrative Ecology Estación Biológica de Doñana (EBD‐CSIC) Seville Spain
| | - Anna Papadopoulou
- Department of Biological Sciences University of Cyprus Nicosia Cyprus
| | - Joaquín Ortego
- Department of Integrative Ecology Estación Biológica de Doñana (EBD‐CSIC) Seville Spain
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17
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Cortés-Ortiz L, Roos C, Zinner D. Introduction to Special Issue on Primate Hybridization and Hybrid Zones. INT J PRIMATOL 2019. [DOI: 10.1007/s10764-019-00076-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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