1
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Sianta SA, Moeller DA, Brandvain Y. The extent of introgression between incipient Clarkia species is determined by temporal environmental variation and mating system. Proc Natl Acad Sci U S A 2024; 121:e2316008121. [PMID: 38466849 PMCID: PMC10963018 DOI: 10.1073/pnas.2316008121] [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: 09/18/2023] [Accepted: 02/07/2024] [Indexed: 03/13/2024] Open
Abstract
Introgression is pervasive across the tree of life but varies across taxa, geography, and genomic regions. However, the factors modulating this variation and how they may be affected by global change are not well understood. Here, we used 200 genomes and a 15-y site-specific environmental dataset to investigate the effects of environmental variation and mating system divergence on the magnitude of introgression between a recently diverged outcrosser-selfer pair of annual plants in the genus Clarkia. These sister taxa diverged very recently and subsequently came into secondary sympatry where they form replicated contact zones. Consistent with observations of other outcrosser-selfer pairs, we found that introgression was asymmetric between taxa, with substantially more introgression from the selfer to the outcrosser. This asymmetry was caused by a bias in the direction of initial F1 hybrid formation and subsequent backcrossing. We also found extensive variation in the outcrosser's admixture proportion among contact zones, which was predicted nearly entirely by interannual variance in spring precipitation. Greater fluctuations in spring precipitation resulted in higher admixture proportions, likely mediated by the effects of spring precipitation on the expression of traits that determine premating reproductive isolation. Climate-driven hybridization dynamics may be particularly affected by global change, potentially reshaping species boundaries and adaptation to novel environments.
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Affiliation(s)
- Shelley A. Sianta
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN55108
| | - David A. Moeller
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN55108
| | - Yaniv Brandvain
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN55108
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2
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Garrick RC. Genetic signatures of lineage fusion closely resemble population decline. Ecol Evol 2023; 13:e10725. [PMID: 37964788 PMCID: PMC10641302 DOI: 10.1002/ece3.10725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/24/2023] [Accepted: 10/27/2023] [Indexed: 11/16/2023] Open
Abstract
Accurate interpretation of the genetic signatures of past demographic events is crucial for reconstructing evolutionary history. Lineage fusion (complete merging, resulting in a single panmictic population) is a special case of secondary contact that is seldom considered. Here, the circumstances under which lineage fusion can be distinguished from population size constancy, growth, bottleneck, and decline were investigated. Multi-locus haplotype data were simulated under models of lineage fusion with different divergence versus sampling lag times (D:L ratios). These pseudo-observed datasets also differed in their allocation of a fixed amount of sequencing resources (number of sampled alleles, haplotype length, number of loci). Distinguishability of lineage fusion versus each of 10 untrue non-fusion scenarios was quantified based on six summary statistics (neutrality tests). Some datasets were also analyzed using extended Bayesian skyline plots. Results showed that signatures of lineage fusion very closely resemble those of decline-high distinguishability was generally limited to the most favorable scenario (D:L = 9), using the most sensitive summary statistics (F S and Z nS), coupled with the optimal sequencing resource allocation (maximizing number of loci). Also, extended Bayesian skyline plots often erroneously inferred population decline. Awareness of the potential for lineage fusion to carry the hallmarks of population decline is critical.
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Affiliation(s)
- Ryan C. Garrick
- Department of BiologyUniversity of MississippiOxfordMississippiUSA
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3
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Slovák M, Melichárková A, Štubňová EG, Kučera J, Mandáková T, Smyčka J, Lavergne S, Passalacqua NG, Vďačný P, Paun O. Pervasive Introgression During Rapid Diversification of the European Mountain Genus Soldanella (L.) (Primulaceae). Syst Biol 2023; 72:491-504. [PMID: 36331548 PMCID: PMC10276626 DOI: 10.1093/sysbio/syac071] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 10/26/2022] [Accepted: 10/31/2022] [Indexed: 03/19/2024] Open
Abstract
Hybridization is a key mechanism involved in lineage diversification and speciation, especially in ecosystems that experienced repeated environmental oscillations. Recently radiated plant groups, which have evolved in mountain ecosystems impacted by historical climate change provide an excellent model system for studying the impact of gene flow on speciation. We combined organellar (whole-plastome) and nuclear genomic data (RAD-seq) with a cytogenetic approach (rDNA FISH) to investigate the effects of hybridization and introgression on evolution and speciation in the genus Soldanella (snowbells, Primulaceae). Pervasive introgression has already occurred among ancestral lineages of snowbells and has persisted throughout the entire evolutionary history of the genus, regardless of the ecology, cytotype, or distribution range size of the affected species. The highest extent of introgression has been detected in the Carpathian species, which is also reflected in their extensive karyotype variation. Introgression occurred even between species with dysploid and euploid cytotypes, which were considered to be reproductively isolated. The magnitude of introgression detected in snowbells is unprecedented in other mountain genera of the European Alpine System investigated hitherto. Our study stresses the prominent evolutionary role of hybridization in facilitating speciation and diversification on the one hand, but also enriching previously isolated genetic pools. [chloroplast capture; diversification; dysploidy; European Alpine system; introgression; nuclear-cytoplasmic discordance; ribosomal DNA.].
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Affiliation(s)
- Marek Slovák
- Department of Evolution and Systematics, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Institute of Botany, Bratislava, Slovakia
- Department of Botany, Charles University, Prague, Czech Republic
| | - Andrea Melichárková
- Department of Evolution and Systematics, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Institute of Botany, Bratislava, Slovakia
| | - Eliška Gbúrová Štubňová
- Department of Evolution and Systematics, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Institute of Botany, Bratislava, Slovakia
- Slovak National Museum, Natural History Museum, Bratislava, Slovakia
| | - Jaromír Kučera
- Department of Evolution and Systematics, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Institute of Botany, Bratislava, Slovakia
| | - Terezie Mandáková
- Central European Institute of Technology, Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 753/5, CZ-625 00 Brno, Czech Republic
| | - Jan Smyčka
- Department of Botany, Charles University, Prague, Czech Republic
- Center for Theoretical Study, Charles University and the Academy of Sciences of the Czech Republic, Jilská 1, 110 00 Praha, Czech Republic
- Université Grenoble Alpes, University of Savoie Mont Blanc, CNRS, Grenoble, France
| | - Sébastien Lavergne
- Université Grenoble Alpes, University of Savoie Mont Blanc, CNRS, Grenoble, France
| | | | - Peter Vďačný
- Department of Zoology, Comenius University in Bratislava, Bratislava, Slovakia
| | - Ovidiu Paun
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
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4
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Liu G, Xue G, Zhao T, Li Y, Yue L, Song H, Liu Q. Population structure and phylogeography of three closely related tree peonies. Ecol Evol 2023; 13:e10073. [PMID: 37274151 PMCID: PMC10234759 DOI: 10.1002/ece3.10073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/23/2023] [Accepted: 04/25/2023] [Indexed: 06/06/2023] Open
Abstract
Paeonia decomposita, Paeonia rotundiloba, and Paeonia rockii are three closely related species of Sect. Moutan is distributed in the montane area of the Eastern Hengduan Mountain region. Understanding the population history of these three tree peony species could contribute to unraveling the evolutionary patterns of undergrowth species in this hotspot area. We used one nuclear DNA marker (internal transcribed spacer region, ITS) and two chloroplast DNA markers (matK, ycf1) to reconstruct the phylogeographic pattern of the populations. In total, 228 individuals from 17 populations of the three species were analyzed in this study. Three nuclear clades (Clade I - Clade III) and four maternal clades (Clade A - Clade D) were reconstructed. Molecular dating suggested that young lineages diverged during the late Pliocene and early Pleistocene, younger than the uplift of the Hengduan Mountains but older than the last glacial maximum (LGM). Significant population and phylogeographic structures were detected at both markers. Furthermore, the populations of these tree peonies were overall at equilibrium during the climatic oscillations of the Pleistocene. The simulated palaeoranges of the three species during the LGM period mostly overlapped, which could have led to cross-breeding events. We propose an evolutionary scenario in which mountain orogenesis around the Hengduan Mountain area triggered parapatric isolation between maternal lineages of tree peonies. Subsequent climatic fluctuations drove migration and range recontact of these populations along the valleys. This detailed evolutionary history provides new insights into the phylogeographic pattern of species from mountain-valley systems.
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Affiliation(s)
- Guangli Liu
- College of Landscape ArchitectureSichuan Agricultural UniversityChengduChina
| | - Ge Xue
- College of Landscape ArchitectureSichuan Agricultural UniversityChengduChina
| | - Tingting Zhao
- College of Landscape ArchitectureSichuan Agricultural UniversityChengduChina
| | - Yang Li
- College of Landscape ArchitectureSichuan Agricultural UniversityChengduChina
| | - Liangliang Yue
- National Plateau Wetlands Research Center, College of WetlandsSouthwest Forestry UniversityKunmingChina
| | - Huixing Song
- College of Landscape ArchitectureSichuan Agricultural UniversityChengduChina
| | - Qinglin Liu
- College of Landscape ArchitectureSichuan Agricultural UniversityChengduChina
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5
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Stiller J, Wilson NG, Rouse GW. Range-wide population genomics of common seadragons shows secondary contact over a former barrier and insights on illegal capture. BMC Biol 2023; 21:129. [PMID: 37248474 DOI: 10.1186/s12915-023-01628-9] [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: 01/26/2023] [Accepted: 05/16/2023] [Indexed: 05/31/2023] Open
Abstract
BACKGROUND Common seadragons (Phyllopteryx taeniolatus, Syngnathidae) are an emblem of the diverse endemic fauna of Australia's southern rocky reefs, the newly recognized "Great Southern Reef." A lack of assessments spanning this global biodiversity hotspot in its entirety is currently hampering an understanding of the factors that have contributed to its diversity. The common seadragon has a wide range across Australia's entire temperate south and includes a geogenetic break over a former land bridge, which has called its status as a single species into question. As a popular aquarium display that sells for high prices, common seadragons are also vulnerable to illegal capture. RESULTS Here, we provide range-wide nuclear sequences (986 variable Ultraconserved Elements) for 198 individuals and mitochondrial genomes for 140 individuals to assess species status, identify genetic units and their diversity, and trace the source of two poached individuals. Using published data of the other two seadragon species, we found that lineages of common seadragons have diverged relatively recently (< 0.63 Ma). Within common seadragons, we found pronounced genetic structure, falling into three major groups in the western, central, and eastern parts of the range. While populations across the Bassian Isthmus were divergent, there is also evidence for secondary contact since the passage opened. We found a strong cline of genetic diversity from the range center tapering symmetrically towards the range peripheries. Based on their genetic similarities, the poached individuals were inferred to have originated from around Albany in southwestern Australia. CONCLUSIONS We conclude that common seadragons constitute a single species with strong geographic structure but coherence through gene flow. The low genetic diversity on the east and west coasts is concerning given that these areas are projected to face fast climate change. Our results suggest that in addition to their life history, geological events and demographic expansions have all played a role in shaping populations in the temperate south. These insights are an important step towards understanding the historical determinants of the diversity of species endemic to the Great Southern Reef.
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Affiliation(s)
- Josefin Stiller
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, 92093 , USA.
- Centre for Biodiversity Genomics, University of Copenhagen, 2100, Copenhagen, Denmark.
| | - Nerida G Wilson
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, 92093 , USA
- Research & Collections, Western Australian Museum, Perth, Western Australia, 6106, Australia
- School of Biological Sciences, University of Western Australia, Perth, Western Australia, 6009, Australia
| | - Greg W Rouse
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, 92093 , USA.
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6
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Yu J, Niu Y, You Y, Cox CJ, Barrett RL, Trias-Blasi A, Guo J, Wen J, Lu L, Chen Z. Integrated phylogenomic analyses unveil reticulate evolution in Parthenocissus (Vitaceae), highlighting speciation dynamics in the Himalayan-Hengduan Mountains. THE NEW PHYTOLOGIST 2023; 238:888-903. [PMID: 36305244 DOI: 10.1111/nph.18580] [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: 08/09/2022] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
Hybridization caused by frequent environmental changes can lead both to species diversification (speciation) and to speciation reversal (despeciation), but the latter has rarely been demonstrated. Parthenocissus, a genus with its trifoliolate lineage in the Himalayan-Hengduan Mountains (HHM) region showing perplexing phylogenetic relationships, provides an opportunity for investigating speciation dynamics based on integrated evidence. We investigated phylogenetic discordance and reticulate evolution in Parthenocissus based on rigorous analyses of plastome and transcriptome data. We focused on reticulations in the trifoliolate lineage in the HHM region using a population-level genome resequencing dataset, incorporating evidence from morphology, distribution, and elevation. Comprehensive analyses confirmed multiple introgressions within Parthenocissus in a robust temporal-spatial framework. Around the HHM region, at least three hybridization hot spots were identified, one of which showed evidence of ongoing speciation reversal. We present a solid case study using an integrative methodological approach to investigate reticulate evolutionary history and its underlying mechanisms in plants. It demonstrates an example of speciation reversal through frequent hybridizations in the HHM region, which provides new perspectives on speciation dynamics in mountainous areas with strong topographic and environmental heterogeneity.
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Affiliation(s)
- Jinren Yu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanting Niu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- China National Botanical Garden, Beijing, 100093, China
| | - Yichen You
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Cymon J Cox
- Centro de Ciências do Mar, Universidade do Algarve, Gambelas, Faro, 8005-319, Portugal
| | - Russell L Barrett
- National Herbarium of New South Wales, Australian Botanic Garden, Locked Bag 6002, Mount Annan, 2567, NSW, Australia
| | | | - Jing Guo
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Jun Wen
- Department of Botany, National Museum of Natural History, MRC-166, Smithsonian Institution, Washington, DC, 20013-7012, USA
| | - Limin Lu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Zhiduan Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
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7
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Dai C, Feng P. Multiple concordant cytonuclear divergences and potential hybrid speciation within a species complex in Asia. Mol Phylogenet Evol 2023; 180:107709. [PMID: 36657627 DOI: 10.1016/j.ympev.2023.107709] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 12/29/2022] [Accepted: 01/12/2023] [Indexed: 01/19/2023]
Abstract
Various environmental factors impact the distribution, population structure, demography and evolutionary trajectory of a bird species, leading to genetic and morphological divergences between populations across its distribution. The Paradoxornis webbianus species complex is found throughout much of East Asia, where its geographically distinct populations exhibit dramatic morphological variation. This has resulted in a hotly debated taxonomy. This study intended to identify genetic divergence patterns and their underlying contributing factors for this species complex. We collected 243 birds, whose data was combined with those available in GenBank to perform phylogeographic analyses using one mitochondrial and six nuclear loci. Six mitochondrial clades were observed in the species complex, while individual-based Bayesian clustering using nuclear markers showed multiple congruent breaks. Overall, the six molecular lineages could be recognized as independent species under the lineage species concept in view of genetic divergence, clade-specific morphological changes and distribution: P. webbianus, P. w. bulomachus, P. alphonsianus, P. a. ganluoensis, P. brunneus brunneus and P. b. ricketti. The estimated divergence times range from 0.46 to 3.36 million years ago, suggesting it was likely impacted by paleoclimatic changes. Interestingly, P. alphonsianus carries two divergent mitochondrial lineages shared with P. webbianus and P. a. ganluoensis, respectively, and analyses based on nuclear loci found a similar pattern. We discussed the various hypotheses for this pattern and argued that P. alphonsianus was likely the result of hybridization between P. webbianus and P. a. ganluoensis. Further data on genome, transcriptome and breeding ecology are needed to address the hypothesis of hybrid speciation and its underlying mechanisms.
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Affiliation(s)
- Chuanyin Dai
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin 541006, China; Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin 541006, China.
| | - Ping Feng
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin 541006, China; Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin 541006, China
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8
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Obert T, Zhang T, Rurik I, Vďačný P. First molecular evidence of hybridization in endosymbiotic ciliates (Protista, Ciliophora). Front Microbiol 2022; 13:1067315. [PMID: 36569075 PMCID: PMC9772525 DOI: 10.3389/fmicb.2022.1067315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/14/2022] [Indexed: 12/13/2022] Open
Abstract
Hybridization is an important evolutionary process that can fuel diversification via formation of hybrid species or can lead to fusion of previously separated lineages by forming highly diverse species complexes. We provide here the first molecular evidence of hybridization in wild populations of ciliates, a highly diverse group of free-living and symbiotic eukaryotic microbes. The impact of hybridization was studied on the model of Plagiotoma, an obligate endosymbiont of the digestive tube of earthworms, using split decomposition analyses and species networks, 2D modeling of the nuclear rRNA molecules and compensatory base change analyses as well as multidimensional morphometrics. Gene flow slowed down and eventually hampered the diversification of Lumbricus-dwelling plagiotomids, which collapsed into a single highly variable biological entity, the P. lumbrici complex. Disruption of the species boundaries was suggested also by the continuum of morphological variability in the phenotypic space. On the other hand, hybridization conspicuously increased diversity in the nuclear rDNA cistron and somewhat weakened the host structural specificity of the P. lumbrici complex, whose members colonize a variety of phylogenetically closely related anecic and epigeic earthworms. By contrast, another recorded species, P. aporrectodeae sp. n., showed no signs of introgression, no variability in the rDNA cistron, and very high host specificity. These contrasting eco-evolutionary patterns indicate that hybridization might decrease the alpha-diversity by dissolving species boundaries, weaken the structural host specificity by broadening ecological amplitudes, and increase the nuclear rDNA variability by overcoming concerted evolution within the P. lumbrici species complex.
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9
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Princepe D, de Aguiar MAM, Plotkin JB. Mito-nuclear selection induces a trade-off between species ecological dominance and evolutionary lifespan. Nat Ecol Evol 2022; 6:1992-2002. [PMID: 36216905 DOI: 10.1038/s41559-022-01901-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 09/02/2022] [Indexed: 12/15/2022]
Abstract
Mitochondrial and nuclear genomes must be co-adapted to ensure proper cellular respiration and energy production. Mito-nuclear incompatibility reduces individual fitness and induces hybrid infertility, which can drive reproductive barriers and speciation. Here, we develop a birth-death model for evolution in spatially extended populations under selection for mito-nuclear co-adaptation. Mating is constrained by physical and genetic proximity, and offspring inherit nuclear genomes from both parents, with recombination. The model predicts macroscopic patterns including a community's species diversity, species abundance distribution, speciation and extinction rates, as well as intraspecific and interspecific genetic variation. We explore how these long-term outcomes depend upon the parameters of reproduction: individual fitness governed by mito-nuclear compatibility, constraints on mating compatibility and ecological carrying capacity. We find that strong selection for mito-nuclear compatibility reduces the equilibrium number of species after a radiation, increasing species' abundances and simultaneously increasing both speciation and extinction rates. The negative correlation between species diversity and diversification rates in our model agrees with the broad empirical pattern of lower diversity and higher speciation/extinction rates in temperate regions, compared to the tropics. We conclude that these empirical patterns may be caused in part by latitudinal variation in metabolic demands and corresponding variation in selection for mito-nuclear function.
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Affiliation(s)
- Débora Princepe
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas, Campinas, Brazil.
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.
| | - Marcus A M de Aguiar
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas, Campinas, Brazil
| | - Joshua B Plotkin
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
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10
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Noguerales V, Ortego J. Genomic evidence of speciation by fusion in a recent radiation of grasshoppers. Evolution 2022; 76:2618-2633. [PMID: 35695020 PMCID: PMC9796961 DOI: 10.1111/evo.14508] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 03/22/2022] [Accepted: 04/02/2022] [Indexed: 01/22/2023]
Abstract
Postdivergence gene flow can trigger a number of creative evolutionary outcomes, ranging from the transfer of beneficial alleles across species boundaries (i.e., adaptive introgression) to the formation of new species (i.e., hybrid speciation). Although neutral and adaptive introgression has been broadly documented in nature, hybrid speciation is assumed to be rare and the evolutionary and ecological context facilitating this phenomenon still remains controversial. Through combining genomic and phenotypic data, we evaluate the hypothesis that the dual feeding regime (based on both scrub legumes and gramineous herbs) of the taxonomically controversial grasshopper Chorthippus saulcyi algoaldensis resulted from hybridization between the sister taxa C. binotatus (that exclusively feeds on scrub legumes) and C. saulcyi (that only feeds on gramineous herbs). Genetic clustering analyses and inferences from coalescent-based demographic simulations confirm that C. s. algoaldensis represents an independently evolving lineage and support the ancient hybrid origin of this taxon (about 1.4 Ma), which sheds light on its uncertain phylogenetic position and might explain its broader trophic niche. We propose a Pleistocene hybrid speciation model where range shifts resulting from climatic oscillations can promote the formation of hybrid swarms and facilitate their long-term persistence through geographic isolation from parental forms in topographically complex landscapes.
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Affiliation(s)
- Víctor Noguerales
- Department of Biological SciencesUniversity of CyprusNicosia1678Cyprus,Island Ecology and Evolution GroupInstituto de Productos Naturales y Agrobiología (IPNA‐CSIC)San Cristóbal de La Laguna38206Spain
| | - Joaquín Ortego
- Department of Integrative EcologyEstación Biológica de Doñana (EBD‐CSIC)Sevilla41092Spain
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11
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Ng EYX, Li S, Zhang D, Garg KM, Song G, Martinez J, Hung LM, Tu VT, Fuchs J, Dong L, Olsson U, Huang Y, Alström P, Rheindt FE, Lei F. Genome‐wide
SNPs
confirm plumage polymorphism and hybridisation within a
Cyornis
flycatcher species complex. ZOOL SCR 2022. [DOI: 10.1111/zsc.12568] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Elize Y. X. Ng
- Department of Biological Sciences National University of Singapore Singapore Singapore
- Discipline of Biological Science, School of Natural Sciences University of Tasmania Hobart Tasmania Australia
| | - Siqi Li
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology Chinese Academy of Sciences Beijing China
- College of Life Sciences Shaanxi Normal University Xi'an China
| | - Dezhi Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Kritika M. Garg
- Department of Biological Sciences National University of Singapore Singapore Singapore
- Centre for Interdisciplinary Archaeological Research Ashoka University Sonipat India
- Department of Biology Ashoka University Sonipat India
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology Chinese Academy of Sciences Beijing China
| | | | - Le Manh Hung
- Institute of Ecology and Biological Resources, Graduate University of Science and Technology Vietnam Academy of Science and Technology Hanoi Vietnam
| | - Vuong Tan Tu
- Institute of Ecology and Biological Resources, Graduate University of Science and Technology Vietnam Academy of Science and Technology Hanoi Vietnam
| | - Jérôme Fuchs
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle CNRS, 22 S U, EPHE, UA CP51 Paris France
| | - Lu Dong
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences Beijing Normal University Beijing China
| | - Urban Olsson
- Systematics and Biodiversity, Department of Biology and Environmental Sciences University of Gothenburg Gothenburg Sweden
- Gothenburg Global Biodiversity Center Göteborg Sweden
| | - Yuan Huang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Per Alström
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology Chinese Academy of Sciences Beijing China
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre Uppsala University Uppsala Sweden
| | - Frank E. Rheindt
- Department of Biological Sciences National University of Singapore Singapore Singapore
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
- Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Kunming China
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12
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Rubin CJ, Enbody ED, Dobreva MP, Abzhanov A, Davis BW, Lamichhaney S, Pettersson M, Sendell-Price AT, Sprehn CG, Valle CA, Vasco K, Wallerman O, Grant BR, Grant PR, Andersson L. Rapid adaptive radiation of Darwin's finches depends on ancestral genetic modules. SCIENCE ADVANCES 2022; 8:eabm5982. [PMID: 35857449 PMCID: PMC9269886 DOI: 10.1126/sciadv.abm5982] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 05/25/2022] [Indexed: 05/21/2023]
Abstract
Recent adaptive radiations are models for investigating mechanisms contributing to the evolution of biodiversity. An unresolved question is the relative importance of new mutations, ancestral variants, and introgressive hybridization for phenotypic evolution and speciation. Here, we address this issue using Darwin's finches and investigate the genomic architecture underlying their phenotypic diversity. Admixture mapping for beak and body size in the small, medium, and large ground finches revealed 28 loci showing strong genetic differentiation. These loci represent ancestral haplotype blocks with origins predating speciation events during the Darwin's finch radiation. Genes expressed in the developing beak are overrepresented in these genomic regions. Ancestral haplotypes constitute genetic modules for selection and act as key determinants of the unusual phenotypic diversity of Darwin's finches. Such ancestral haplotype blocks can be critical for how species adapt to environmental variability and change.
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Affiliation(s)
- Carl-Johan Rubin
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Institute of Marine Research, Nordnesgaten 50, 5005 Bergen, Norway
| | - Erik D. Enbody
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Mariya P. Dobreva
- Department of Life Sciences, Imperial College London, Silwood Park Campus, SL5 7PY Ascot, UK
| | - Arhat Abzhanov
- Department of Life Sciences, Imperial College London, Silwood Park Campus, SL5 7PY Ascot, UK
| | - Brian W. Davis
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | | | - Mats Pettersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Ashley T. Sendell-Price
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Edward Grey Institute, Department of Zoology, University of Oxford, Oxford, UK
| | - C. Grace Sprehn
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Carlos A. Valle
- Colegio de Ciencias Biológicas y Ambientales, Galápagos Science Center GSC, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Karla Vasco
- Colegio de Ciencias Biológicas y Ambientales, Galápagos Science Center GSC, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Ola Wallerman
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - B. Rosemary Grant
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Peter R. Grant
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Leif Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Corresponding author.
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13
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Burbrink FT, Crother BI, Murray CM, Smith BT, Ruane S, Myers EA, Pyron RA. Empirical and philosophical problems with the subspecies rank. Ecol Evol 2022; 12:e9069. [PMID: 35845367 PMCID: PMC9271888 DOI: 10.1002/ece3.9069] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 06/01/2022] [Accepted: 06/10/2022] [Indexed: 11/12/2022] Open
Abstract
Species‐level taxonomy derives from empirical sources (data and techniques) that assess the existence of spatiotemporal evolutionary lineages via various species “concepts.” These concepts determine if observed lineages are independent given a particular methodology and ontology, which relates the metaphysical species concept to what “kind” of thing a species is in reality. Often, species concepts fail to link epistemology back to ontology. This lack of coherence is in part responsible for the persistence of the subspecies rank, which in modern usage often functions as a placeholder between the evolutionary events of divergence or collapse of incipient species. Thus, prospective events like lineages merging or diverging require information from unknowable future information. This is also conditioned on evidence that the lineage already has a detectably distinct evolutionary history. Ranking these lineages as subspecies can seem attractive given that many lineages do not exhibit intrinsic reproductive isolation. We argue that using subspecies is indefensible on philosophical and empirical grounds. Ontologically, the rank of subspecies is either identical to that of species or undefined in the context of evolutionary lineages representing spatiotemporally defined individuals. Some species concepts more inclined to consider subspecies, like the Biological Species Concept, are disconnected from evolutionary ontology and do not consider genealogy. Even if ontology is ignored, methods addressing reproductive isolation are often indirect and fail to capture the range of scenarios linking gene flow to species identity over space and time. The use of subspecies and reliance on reproductive isolation as a basis for an operational species concept can also conflict with ethical issues governing the protection of species. We provide a way forward for recognizing and naming species that links theoretical and operational species concepts regardless of the magnitude of reproductive isolation.
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Affiliation(s)
- Frank T Burbrink
- Department of Herpetology American Museum of Natural History New York New York USA
| | - Brian I Crother
- Department of Biological Sciences Southeastern Louisiana University Hammond Louisiana USA
| | - Christopher M Murray
- Department of Biological Sciences Southeastern Louisiana University Hammond Louisiana USA
| | - Brian Tilston Smith
- Department of Ornithology American Museum of Natural History New York New York USA
| | - Sara Ruane
- Life Sciences Section, Negaunee Integrative Research Center Field Museum of Natural History Chicago Illinois USA
| | - Edward A Myers
- Department of Herpetology American Museum of Natural History New York New York USA.,Department of Biological Sciences Clemson University Clemson South Carolina USA.,Department of Vertebrate Zoology Smithsonian Institution, National Museum of Natural History Washington District of Columbia USA
| | - Robert Alexander Pyron
- Department of Vertebrate Zoology Smithsonian Institution, National Museum of Natural History Washington District of Columbia USA.,Department of Biological Sciences The George Washington University Washington District of Columbia USA
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14
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Chen K, Moravec JÍC, Gavryushkin A, Welch D, Drummond AJ. Accounting for errors in data improves divergence time estimates in single-cell cancer evolution. Mol Biol Evol 2022; 39:6613463. [PMID: 35733333 PMCID: PMC9356729 DOI: 10.1093/molbev/msac143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Single-cell sequencing provides a new way to explore the evolutionary history of cells. Compared to traditional bulk sequencing, where a population of heterogeneous cells is pooled to form a single observation, single-cell sequencing isolates and amplifies genetic material from individual cells, thereby preserving the information about the origin of the sequences. However, single-cell data is more error-prone than bulk sequencing data due to the limited genomic material available per cell. Here, we present error and mutation models for evolutionary inference of single-cell data within a mature and extensible Bayesian framework, BEAST2. Our framework enables integration with biologically informative models such as relaxed molecular clocks and population dynamic models. Our simulations show that modeling errors increase the accuracy of relative divergence times and substitution parameters. We reconstruct the phylogenetic history of a colorectal cancer patient and a healthy patient from single-cell DNA sequencing data. We find that the estimated times of terminal splitting events are shifted forward in time compared to models which ignore errors. We observed that not accounting for errors can overestimate the phylogenetic diversity in single-cell DNA sequencing data. We estimate that 30-50% of the apparent diversity can be attributed to error. Our work enables a full Bayesian approach capable of accounting for errors in the data within the integrative Bayesian software framework BEAST2.
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Affiliation(s)
- Kylie Chen
- School of Computer Science, University of Auckland, Auckland, New Zealand
| | - Jiř Í C Moravec
- Department of Computer Science, University of Otago, Dunedin, New Zealand.,School of Mathematics and Statistics, University of Canterbury, Christchurch, New Zealand
| | - Alex Gavryushkin
- School of Mathematics and Statistics, University of Canterbury, Christchurch, New Zealand
| | - David Welch
- School of Computer Science, University of Auckland, Auckland, New Zealand
| | - Alexei J Drummond
- School of Computer Science, University of Auckland, Auckland, New Zealand.,School of Biological Sciences, University of Auckland, Auckland, New Zealand
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15
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Smith WJ, Quilodrán CS, Jezierski MT, Sendell-Price AT, Clegg SM. The wild ancestors of domestic animals as a neglected and threatened component of biodiversity. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2022; 36:e13867. [PMID: 34811819 DOI: 10.1111/cobi.13867] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/27/2021] [Accepted: 11/12/2021] [Indexed: 06/13/2023]
Abstract
Domestic animals have immense economic, cultural, and practical value and have played pivotal roles in the development of human civilization. Many domesticates have, among their wild relatives, undomesticated forms representative of their ancestors. Resurgent interest in these ancestral forms has highlighted the unclear genetic status of many, and some are threatened with extinction by hybridization with domestic conspecifics. We considered the contemporary status of these ancestral forms relative to their scientific, practical, and ecological importance; the varied impacts of wild-domestic hybridization; and the challenges and potential resolutions involved in conservation efforts. Identifying and conserving ancestral forms, particularly with respect to disentangling patterns of gene flow from domesticates, is complex because of the lack of available genomic and phenotypic baselines. Comparative behavioral, ecological, and genetic studies of ancestral-type, feral, and domestic animals should be prioritized to establish the contemporary status of the former. Such baseline information will be fundamental in ensuring successful conservation efforts.
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Affiliation(s)
- William J Smith
- Edward Grey Institute of Field Ornithology, Department of Zoology, University of Oxford, Oxford, UK
| | - Claudio S Quilodrán
- Edward Grey Institute of Field Ornithology, Department of Zoology, University of Oxford, Oxford, UK
- Department of Biology and Biochemistry, University of Fribourg, Fribourg, Switzerland
| | - Michał T Jezierski
- Edward Grey Institute of Field Ornithology, Department of Zoology, University of Oxford, Oxford, UK
| | - Ashley T Sendell-Price
- Edward Grey Institute of Field Ornithology, Department of Zoology, University of Oxford, Oxford, UK
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Sonya M Clegg
- Edward Grey Institute of Field Ornithology, Department of Zoology, University of Oxford, Oxford, UK
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16
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Frei D, De-Kayne R, Selz OM, Seehausen O, Feulner PGD. Genomic variation from an extinct species is retained in the extant radiation following speciation reversal. Nat Ecol Evol 2022; 6:461-468. [PMID: 35210577 DOI: 10.1038/s41559-022-01665-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 01/10/2022] [Indexed: 11/09/2022]
Abstract
Ecosystem degradation and biodiversity loss are major global challenges. When reproductive isolation between species is contingent on the interaction of intrinsic lineage traits with features of the environment, environmental change can weaken reproductive isolation and result in extinction through hybridization. By this process called speciation reversal, extinct species can leave traces in genomes of extant species through introgressive hybridization. Using historical and contemporary samples, we sequenced all four species of an Alpine whitefish radiation before and after anthropogenic lake eutrophication and the associated loss of one species through speciation reversal. Despite the extinction of this taxon, substantial fractions of its genome, including regions shaped by positive selection before eutrophication, persist within surviving species as a consequence of introgressive hybridization during eutrophication. Given the prevalence of environmental change, studying speciation reversal and its genomic consequences provides fundamental insights into evolutionary processes and informs biodiversity conservation.
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Affiliation(s)
- David Frei
- Department of Fish Ecology and Evolution, Center for Ecology, Evolution and Biogeochemistry, Eawag-Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland.,Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Rishi De-Kayne
- Department of Fish Ecology and Evolution, Center for Ecology, Evolution and Biogeochemistry, Eawag-Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland.,Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Oliver M Selz
- Department of Fish Ecology and Evolution, Center for Ecology, Evolution and Biogeochemistry, Eawag-Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland.,Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Ole Seehausen
- Department of Fish Ecology and Evolution, Center for Ecology, Evolution and Biogeochemistry, Eawag-Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland.,Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Philine G D Feulner
- Department of Fish Ecology and Evolution, Center for Ecology, Evolution and Biogeochemistry, Eawag-Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland. .,Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.
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17
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Urfer K, Spasojevic T, Klopfstein S, Baur H, Lasut L, Kropf C. Incongruent molecular and morphological variation in the crab spider Synemaglobosum (Araneae, Thomisidae) in Europe. Zookeys 2021; 1078:107-134. [PMID: 35068955 PMCID: PMC8709837 DOI: 10.3897/zookeys.1078.64116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 10/29/2021] [Indexed: 11/12/2022] Open
Abstract
Establishing species boundaries is one of the challenges taxonomists around the world have been tackling for centuries. The relation between intraspecific and interspecific variability is still under discussion and in many taxa it remains understudied. Here the hypothesis of single versus multiple species of the crab spider Synemaglobosum (Fabricius) is tested. The wide distribution range as well as its high morphological variability makes this species an interesting candidate for re-evaluation using an integrative approach. This study combines information from barcoding, phylogenetic reconstruction based on mitochondrial CO1 and ITS2 of more than 60 specimens collected over a wide range of European localities, and morphology. The findings show deep clades with up to 6% mean pairwise distance in the CO1 barcode without any biogeographical pattern. The nuclear ITS2 gene did not support the CO1 clades. Morphological assessment of somatic and genital characters in males and females and a morphometric analysis of the male palp uncovered high intraspecific variation that does not match the CO1 or ITS2 phylogenies or biogeography either. Screening for endosymbiotic Wolbachia bacteria was conducted and only a single infected specimen was found. Several scenarios might explain these inconsistent patterns. While the deep divergences in the barcoding marker might suggest cryptic or ongoing speciation or geographical isolation in the past, the lack of congruent variation in the nuclear ITS2 gene or the studied morphological character systems, especially the male palp, indicates that S.globosum might simply be highly polymorphic both in terms of its mtDNA and morphology. Therefore, more data on ecology and behaviour and full genome sequences are necessary to ultimately resolve this taxonomically intriguing case.
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Affiliation(s)
- Karin Urfer
- Natural History Museum Bern, Bernastrasse 15, 3005 Bern, SwitzerlandNatural History Museum BernBernSwitzerland
- University of Bern, Institute of Ecology and Evolution, Baltzerstrasse 6, 3012 Bern, SwitzerlandUniversity of BernBernSwitzerland
- Natural History Museum St.Gallen, Rorschacher Strasse 263, 9016 St.Gallen, SwitzerlandNatural History Museum BaselBaselSwitzerland
- Natural History Museum Basel, Augustinergasse 2, 4051 Basel, SwitzerlandNatural History Museum St.GallenSt.GallenSwitzerland
| | - Tamara Spasojevic
- University of Bern, Institute of Ecology and Evolution, Baltzerstrasse 6, 3012 Bern, SwitzerlandUniversity of BernBernSwitzerland
- Natural History Museum Basel, Augustinergasse 2, 4051 Basel, SwitzerlandNatural History Museum St.GallenSt.GallenSwitzerland
| | - Seraina Klopfstein
- University of Bern, Institute of Ecology and Evolution, Baltzerstrasse 6, 3012 Bern, SwitzerlandUniversity of BernBernSwitzerland
- Natural History Museum Basel, Augustinergasse 2, 4051 Basel, SwitzerlandNatural History Museum St.GallenSt.GallenSwitzerland
| | - Hannes Baur
- Natural History Museum Bern, Bernastrasse 15, 3005 Bern, SwitzerlandNatural History Museum BernBernSwitzerland
- University of Bern, Institute of Ecology and Evolution, Baltzerstrasse 6, 3012 Bern, SwitzerlandUniversity of BernBernSwitzerland
| | - Liana Lasut
- Natural History Museum Bern, Bernastrasse 15, 3005 Bern, SwitzerlandNatural History Museum BernBernSwitzerland
- University of Bern, Institute of Ecology and Evolution, Baltzerstrasse 6, 3012 Bern, SwitzerlandUniversity of BernBernSwitzerland
| | - Christian Kropf
- Natural History Museum Bern, Bernastrasse 15, 3005 Bern, SwitzerlandNatural History Museum BernBernSwitzerland
- University of Bern, Institute of Ecology and Evolution, Baltzerstrasse 6, 3012 Bern, SwitzerlandUniversity of BernBernSwitzerland
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18
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Campana MG, Hawkins MTR, Caballero S. Editorial: Assessing Biodiversity in the Phylogenomic Era. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.803188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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19
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Larson DA, Vargas OM, Vicentini A, Dick CW. Admixture may be extensive among hyperdominant Amazon rainforest tree species. THE NEW PHYTOLOGIST 2021; 232:2520-2534. [PMID: 34389989 PMCID: PMC9292926 DOI: 10.1111/nph.17675] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 08/04/2021] [Indexed: 05/25/2023]
Abstract
Admixture is a mechanism by which species of long-lived plants may acquire novel alleles. However, the potential role of admixture in the origin and maintenance of tropical plant diversity is unclear. We ask whether admixture occurs in an ecologically important clade of Eschweilera (Parvifolia clade, Lecythidaceae), which includes some of the most widespread and abundant tree species in Amazonian forests. Using target capture sequencing, we conducted a detailed phylogenomic investigation of 33 species in the Parvifolia clade and investigated specific hypotheses of admixture within a robust phylogenetic framework. We found strong evidence of admixture among three ecologically dominant species, E. coriacea, E. wachenheimii and E. parviflora, but a lack of evidence for admixture among other lineages. Accepted species were largely distinguishable from one another, as was geographic structure within species. We show that hybridization may play a role in the evolution of the most widespread and ecologically variable Amazonian tree species. While admixture occurs among some species of Eschweilera, it has not led to widespread erosion of most species' genetic or morphological identities. Therefore, current morphological based species circumscriptions appear to provide a useful characterization of the clade's lineage diversity.
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Affiliation(s)
- Drew A. Larson
- Department of Ecology & Evolutionary BiologyUniversity of MichiganAnn ArborMI48109USA
| | - Oscar M. Vargas
- Department of Biological SciencesHumboldt State UniversityArcataCA95521USA
| | - Alberto Vicentini
- Instituto Nacional de Pesquisas da Amazônia (INPA)ManausAMCEP 69067‐375Brazil
| | - Christopher W. Dick
- Department of Ecology & Evolutionary BiologyUniversity of MichiganAnn ArborMI48109USA
- Smithsonian Tropical Research InstitutePanama CityRepublic of Panama
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20
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Hibbins MS, Hahn MW. Phylogenomic approaches to detecting and characterizing introgression. Genetics 2021; 220:6425633. [PMID: 34788444 PMCID: PMC9208645 DOI: 10.1093/genetics/iyab173] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 10/02/2021] [Indexed: 12/26/2022] Open
Abstract
Phylogenomics has revealed the remarkable frequency with which introgression occurs across the tree of life. These discoveries have been enabled by the rapid growth of methods designed to detect and characterize introgression from whole-genome sequencing data. A large class of phylogenomic methods makes use of data across species to infer and characterize introgression based on expectations from the multispecies coalescent. These methods range from simple tests, such as the D-statistic, to model-based approaches for inferring phylogenetic networks. Here, we provide a detailed overview of the various signals that different modes of introgression are expected leave in the genome, and how current methods are designed to detect them. We discuss the strengths and pitfalls of these approaches and identify areas for future development, highlighting the different signals of introgression, and the power of each method to detect them. We conclude with a discussion of current challenges in inferring introgression and how they could potentially be addressed.
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Affiliation(s)
- Mark S Hibbins
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Matthew W Hahn
- Department of Biology, Indiana University, Bloomington, IN 47405, USA.,Department of Computer Science, Indiana University, Bloomington, IN 47405, USA
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21
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Tang Q, Burri R, Liu Y, Suh A, Sundev G, Heckel G, Schweizer M. Seasonal migration patterns and the maintenance of evolutionary diversity in a cryptic bird radiation. Mol Ecol 2021; 31:632-645. [PMID: 34674334 PMCID: PMC9298432 DOI: 10.1111/mec.16241] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 10/07/2021] [Accepted: 10/12/2021] [Indexed: 02/03/2023]
Abstract
Morphological differentiation associated with evolutionary diversification is often explained with adaptive benefits but the processes and mechanisms maintaining cryptic diversity are still poorly understood. Using genome‐wide data, we show here that the pale sand martin Riparia diluta in Central and East Asia consists of three genetically deeply differentiated lineages which vary only gradually in morphology but broadly reflect traditional taxonomy. We detected no signs of gene flow along the eastern edge of the Qinghai‐Tibetan plateau between lowland south‐eastern Chinese R. d. fohkienensis and high‐altitude R. d. tibetana. Largely different breeding and migration timing between these low and high altitude populations as indicated by phenology data suggests that allochrony might act as prezygotic isolation mechanism in the area where their ranges abut. Mongolian populations of R. d. tibetana, however, displayed signs of limited mixed ancestries with Central Asian R. d. diluta. Their ranges meet in the area of a well‐known avian migratory divide, where western lineages take a western migration route around the Qinghai‐Tibetan plateau to winter quarters in South Asia, and eastern lineages take an eastern route to Southeast Asia. This might also be the case between western R. d. diluta and eastern R. d. tibetana as indicated by differing wintering grounds. We hypothesize that hybrids might have nonoptimal intermediate migration routes and selection against them might restrict gene flow. Although further potential isolation mechanisms might exist in the pale sand martin, our study points towards contrasting migration behaviour as an important factor in maintaining evolutionary diversity under morphological stasis.
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Affiliation(s)
- Qindong Tang
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Natural History Museum, Bern, Switzerland
| | - Reto Burri
- Schweizerische Vogelwarte, Sempach, Switzerland
| | - Yang Liu
- State Key Laboratory of Biocontrol, College of Ecology School of Life Science, Sun Yat-sen University, Guangzhou, China
| | - Alexander Suh
- School of Biological Sciences-Organisms and the Environment, University of East Anglia, Norwich, UK.,Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden
| | - Gombobaatar Sundev
- National University of Mongolia and Mongolian Ornithological Society, Ulaanbaatar, Mongolia
| | - Gerald Heckel
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Manuel Schweizer
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Natural History Museum, Bern, Switzerland
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22
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Hernández F, Brown JI, Kaminski M, Harvey MG, Lavretsky P. Genomic Evidence for Rare Hybridization and Large Demographic Changes in the Evolutionary Histories of Four North American Dove Species. Animals (Basel) 2021; 11:ani11092677. [PMID: 34573643 PMCID: PMC8468798 DOI: 10.3390/ani11092677] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/07/2021] [Accepted: 09/08/2021] [Indexed: 12/31/2022] Open
Abstract
Introductions and invasions provide opportunities for interaction and hybridization between colonists and closely related native species. We investigate this phenomenon using the mitochondrial DNA COI and 81,416 base-pairs of overlapping nuclear variation to examine the evolutionary histories and signatures of hybridization among introduced feral Rock Pigeon and Eurasian Collared-Dove and native White-winged and Mourning doves in southwestern North America. First, we report all four species to be highly divergent across loci (overall pair-wise species ΦST range = 0.17-0.70) and provide little evidence for gene flow at evolutionary timescales. Despite this, evidence from multiple population genetics analyses supports the presence of six putative contemporary late-stage hybrids among the 182 sampled individuals. These putative hybrids contain various ancestry combinations, but all involve the most populous species, the Mourning Dove. Next, we use a novel method to reconstruct demographic changes through time using partial genome sequence data. We identify recent, species-specific fluctuations in population size that are likely associated with changing environments since the Miocene and suggest that these fluctuations have influenced the genetic diversity of each dove species in ways that may impact their future persistence. Finally, we discuss the importance of using multiple marker types when attempting to infer complex evolutionary histories and propose important considerations when analyzing populations that were recently established or of domestic origins.
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23
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E Luzuriaga-Aveiga V, Ugarte M, Weir JT. Distinguishing genomic homogenization from parapatric speciation in an elevationally replacing pair of Ramphocelus tanagers. Mol Ecol 2021; 30:5517-5529. [PMID: 34403554 DOI: 10.1111/mec.16128] [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: 08/05/2020] [Revised: 07/30/2021] [Accepted: 08/11/2021] [Indexed: 12/14/2022]
Abstract
Geographically connected species pairs with weakly differentiated genomes could either represent cases of genomic homogenization in progress or of incipient parapatric speciation. Discriminating between these processes is difficult because intermediate stages of either may produce weakly differentiated genomes that diverge at few locations. We used coalescent modelling applied to a genome-wide sample of SNPs to discriminate between speciation with gene flow and genomic homogenization in two phenotypically distinct but genomically weakly diverged species of elevationally replacing Ramphocelus tanagers, forming a hybrid zone in the Andean foothills. We found overwhelming support for a model of genomic homogenization following secondary contact. Simulating under this model suggested that our species pair was differentiated (FST = 0.30) at secondary contact but that most of the genome has rapidly homogenized during 254 Ky of high gene flow towards the present (FST = 0.02). Despite extensive genome-wide homogenization, plumage remains distinctive with a narrower than expected geographic cline width, indicating divergent selection on colour. We found two SNPs significantly associated with plumage colour, which retain moderately high FST . We conclude that the majority of the genome has fused, but that divergent selection on select loci probably maintains the geographically structured colour differences between these incipient species.
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Affiliation(s)
- Vanessa E Luzuriaga-Aveiga
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada.,Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Mauricio Ugarte
- Área de Ornitología, Universidad Nacional de San Agustín de Arequipa, Museo de Historia Natural Arequipa, Peru
| | - Jason T Weir
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada.,Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada.,Department of Ornithology, Royal Ontario Museum, Toronto, Ontario, Canada
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24
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Pazhenkova EA, Lukhtanov VA. Genomic introgression from a distant congener in the Levant fritillary butterfly, Melitaea acentria. Mol Ecol 2021; 30:4819-4832. [PMID: 34288183 DOI: 10.1111/mec.16085] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 12/12/2022]
Abstract
Introgressive hybridization is more common in nature than previously thought, and its role and creative power in evolution is hotly discussed but not completely understood. Introgression occurs more frequently in sympatry between recently diverged taxa, or when the speciation process has not yet been completed. However, there are relatively few documented cases of hybridization that erodes reproductive barriers between distantly related species. Here, we use whole genome and mitochondrial data to examine how introgression from a distant congener affects pattern of genetic differentiation in the Levant fritillary butterfly Melitaea acentria. We show that this local taxon has evolved as a peripatric geographic isolate of the widespread Melitaea persea, and that there has been significant unidirectional gene flow from the sympatric, nonclosely related Melitaea didyma to M. acentria. We found direct evidence of ongoing sporadic hybridization between M. didyma and M. acentria, which are separated by at least 5 million years of independent evolution. Elevated differentiation and lower level of introgression on the sex Z chromosome compared to autosomes suggest that the Z chromosome has accumulated loci acting as intrinsic postzygotic barriers. Our results show that introgression from M. didyma has been an additional source of nucleotide diversity in the M. acentria population, providing material for drift and selection.
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Affiliation(s)
- Elena A Pazhenkova
- Department of Entomology, St. Petersburg State University, St. Petersburg, Russia.,Department of Karyosystematics, Zoological Institute of Russian Academy of Sciences, St. Petersburg, Russia
| | - Vladimir A Lukhtanov
- Department of Karyosystematics, Zoological Institute of Russian Academy of Sciences, St. Petersburg, Russia
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25
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Palmer A, Sommer V, Msindai JN. Hybrid apes in the Anthropocene: Burden or asset for conservation? PEOPLE AND NATURE 2021; 3:573-586. [PMID: 34805779 PMCID: PMC8581989 DOI: 10.1002/pan3.10214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 04/01/2021] [Indexed: 11/08/2022] Open
Abstract
Conservationists often view hybrid animals as problematic, at least if anthropogenic influence caused the intermixing to occur. However, critics propose that humans should respect non-human autonomy, reject and accept the creatures they have helped to create.Based on two case studies of our own ethological, genetic and ethnographic research about chimpanzee and orangutan subspecies hybrids, we assess what, if anything, should be done about such animals. We consider problems posed by cross-bred apes relating to: (a) Breeding-Do hybrids really experience reduced reproductive success? How are population-level concerns and welfare of individual animals balanced in conservation breeding? (b) Essentialism-Are anti-hybrid arguments based on essentialist or purist thinking? Does essentialism vary by conservation context? (c) Pragmatism-How do socio-economic circumstances influence whether hybrids are embraced or ignored? Does the erosion of 'untouched nature' render hybrids more important?We show that answers to these questions are complex and context-specific, and that therefore decisions should be made on a case-by-case basis. For example, we find that anti-hybrid arguments are essentialist in some cases (e.g. ape management in zoos) but not in others (e.g. ape reintroduction). Thus, rather than present recommendations, we conclude by posing nine questions that conservationists should ask themselves when making decisions about taxonomic hybrids. A free Plain Language Summary can be found within the Supporting Information of this article.
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Affiliation(s)
- Alexandra Palmer
- School of Geography and the EnvironmentUniversity of OxfordOxfordUK
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26
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Freeman BG, Pennell MW. The latitudinal taxonomy gradient. Trends Ecol Evol 2021; 36:778-786. [PMID: 34074540 DOI: 10.1016/j.tree.2021.05.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/03/2021] [Accepted: 05/06/2021] [Indexed: 10/21/2022]
Abstract
Emerging large-scale datasets coupled with statistical advances have provided new insights into the processes that generate the latitudinal diversity gradient (LDG). But many of these studies run into an old, if often underappreciated, problem: The interpretation of the data critically depends on the consistent application of criteria to define what constitutes a species. This is particularly pernicious for the LDG because good species have been easier to recognize in temperate than in tropical regions. We provide evidence that this latitudinal taxonomy gradient exists, discuss how this potentially impacts inferences about latitudinal variation in ecoevolutionary processes such as population differentiation and speciation, and provide a roadmap for how to mitigate taxonomic biases in the study of biodiversity patterns.
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Affiliation(s)
- Benjamin G Freeman
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada, V6T1Z4; Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada.
| | - Matthew W Pennell
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada, V6T1Z4; Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
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27
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Velo-Antón G, Lourenço A, Galán P, Nicieza A, Tarroso P. Landscape resistance constrains hybridization across contact zones in a reproductively and morphologically polymorphic salamander. Sci Rep 2021; 11:9259. [PMID: 33927228 PMCID: PMC8085075 DOI: 10.1038/s41598-021-88349-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 04/07/2021] [Indexed: 02/02/2023] Open
Abstract
Explicitly accounting for phenotypic differentiation together with environmental heterogeneity is crucial to understand the evolutionary dynamics in hybrid zones. Species showing intra-specific variation in phenotypic traits that meet across environmentally heterogeneous regions constitute excellent natural settings to study the role of phenotypic differentiation and environmental factors in shaping the spatial extent and patterns of admixture in hybrid zones. We studied three environmentally distinct contact zones where morphologically and reproductively divergent subspecies of Salamandra salamandra co-occur: the pueriparous S. s. bernardezi that is mostly parapatric to its three larviparous subspecies neighbours. We used a landscape genetics framework to: (i) characterise the spatial location and extent of each contact zone; (ii) assess patterns of introgression and hybridization between subspecies pairs; and (iii) examine the role of environmental heterogeneity in the evolutionary dynamics of hybrid zones. We found high levels of introgression between parity modes, and between distinct phenotypes, thus demonstrating the evolution to pueriparity alone or morphological differentiation do not lead to reproductive isolation between these highly divergent S. salamandra morphotypes. However, we detected substantial variation in patterns of hybridization across contact zones, being lower in the contact zone located on a topographically complex area. We highlight the importance of accounting for spatial environmental heterogeneity when studying evolutionary dynamics of hybrid zones.
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Affiliation(s)
- Guillermo Velo-Antón
- grid.5808.50000 0001 1503 7226CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Instituto de Ciências Agrárias de Vairão. R. Padre Armando Quintas, 4485-661 Vairão, Portugal ,grid.6312.60000 0001 2097 6738Universidade de Vigo, Grupo de Ecoloxía Animal, Departamento de Ecoloxía e Bioloxía Animal, Torre Cacti (Lab 97), 36310 Vigo, Spain
| | - André Lourenço
- grid.5808.50000 0001 1503 7226CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Instituto de Ciências Agrárias de Vairão. R. Padre Armando Quintas, 4485-661 Vairão, Portugal ,grid.5808.50000 0001 1503 7226Departamento de Biologia da Faculdade de Ciências, Universidade do Porto. Rua Campo Alegre, 4169-007 Porto, Portugal
| | - Pedro Galán
- grid.8073.c0000 0001 2176 8535Grupo de Investigación en Bioloxía Evolutiva (GIBE), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, Campus da Zapateira, s/n, 15071 A Coruña, Spain
| | - Alfredo Nicieza
- grid.10863.3c0000 0001 2164 6351Departamento de Biologıa de Organismos y Sistemas, Universidad de Oviedo, Oviedo, Spain ,grid.10863.3c0000 0001 2164 6351Unidad Mixta de Investigacion en Biodiversidad (UMIB), CSIC-Universidad de Oviedo-Principado de Asturias, Mieres, Spain
| | - Pedro Tarroso
- grid.5808.50000 0001 1503 7226CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Instituto de Ciências Agrárias de Vairão. R. Padre Armando Quintas, 4485-661 Vairão, Portugal
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28
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Schmickl R, Yant L. Adaptive introgression: how polyploidy reshapes gene flow landscapes. THE NEW PHYTOLOGIST 2021; 230:457-461. [PMID: 33454987 DOI: 10.1111/nph.17204] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 12/09/2020] [Indexed: 06/12/2023]
Abstract
Rare yet accumulating evidence in both plants and animals shows that whole genome duplication (WGD, leading to polyploidy) can break down reproductive barriers, facilitating gene flow between otherwise isolated species. Recent population genomic studies in wild, outcrossing Arabidopsis arenosa and Arabidopsis lyrata indicate that this WGD-potentiated gene flow can be adaptive and highly specific in response to particular environmental and intracellular challenges. The mechanistic basis of WGD-mediated easing of species barrier strength seems to primarily lie in the relative dosage of each parental genome in the endosperm. While generalisations about polyploids can be fraught, this evidence indicates that the breakdown of these barriers, combined with diploid to polyploid gene flow and gene flow between polyploids, allows some polyploids to act as adaptable 'allelic sponges', enjoying increased potential to respond to challenging environments.
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Affiliation(s)
- Roswitha Schmickl
- Department of Botany, Faculty of Science, Charles University, Benátská 2, Prague, 128 01, Czech Republic
- Institute of Botany, The Czech Academy of Sciences, Zámek 1, Průhonice, 252 43, Czech Republic
| | - Levi Yant
- Future Food Beacon and School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
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29
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Lavretsky P, Wilson RE, Talbot SL, Sonsthagen SA. Phylogenomics reveals ancient and contemporary gene flow contributing to the evolutionary history of sea ducks (Tribe Mergini). Mol Phylogenet Evol 2021; 161:107164. [PMID: 33798675 DOI: 10.1016/j.ympev.2021.107164] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 02/05/2021] [Accepted: 03/25/2021] [Indexed: 12/26/2022]
Abstract
Insight into complex evolutionary histories continues to build through broad comparative phylogenomic and population genomic studies. In particular, there is a need to understand the extent and scale that gene flow contributes to standing genomic diversity and the role introgression has played in evolutionary processes such as hybrid speciation. Here, we investigate the evolutionary history of the Mergini tribe (sea ducks) by coupling multi-species comparisons with phylogenomic analyses of thousands of nuclear ddRAD-seq loci, including Z-sex chromosome and autosomal linked loci, and the mitogenome assayed across all extant sea duck species in North America. All sea duck species are strongly structured across all sampled marker types (pair-wise species ΦST > 0.2), with clear genetic assignments of individuals to their respective species, and phylogenetic relationships recapitulate known relationships. Despite strong species integrity, we identify at least 18 putative hybrids; with all but one being late generational backcrosses. Most interesting, we provide the first evidence that an ancestral gene flow event between long-tailed ducks (Clangula hyemalis) and true Eiders (Somateria spp.) not only moved genetic material into the former species, but likely generated a novel species - the Steller's eider (Polysticta stelleri) - via hybrid speciation. Despite generally low contemporary levels of gene flow, we conclude that hybridization has and continues to be an important process that shifts novel genetic variation between species within the tribe Mergini. Finally, we outline methods that permit researchers to contrast genomic patterns of contemporary versus ancestral gene flow when attempting to reconstruct potentially complex evolutionary histories.
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Affiliation(s)
- Philip Lavretsky
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX 79668, USA; US Geological Survey, Alaska Science Center, 4210 University Dr., Anchorage, AK 99508, USA.
| | - Robert E Wilson
- US Geological Survey, Alaska Science Center, 4210 University Dr., Anchorage, AK 99508, USA
| | - Sandra L Talbot
- US Geological Survey, Alaska Science Center, 4210 University Dr., Anchorage, AK 99508, USA
| | - Sarah A Sonsthagen
- US Geological Survey, Alaska Science Center, 4210 University Dr., Anchorage, AK 99508, USA
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30
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Pfennig KS. Biased Hybridization and Its Impact on Adaptive Introgression. Trends Ecol Evol 2021; 36:488-497. [PMID: 33752896 DOI: 10.1016/j.tree.2021.02.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 02/20/2021] [Accepted: 02/22/2021] [Indexed: 02/07/2023]
Abstract
Gene exchange between species can influence ecological and evolutionary processes ranging from population rescue to adaptive radiation. Genomic tools have provided new insights into the prevalence and nature of gene exchange between species. However, much remains unknown of how ecological, behavioral, and evolutionary factors determine what genetic variation moves between species in the first place. In particular, more research is needed that evaluates whether such factors bias gene flow from one species to another, and whether any such biases affect how genetic variation from another species is ultimately retained in the genome of a given species. Addressing this issue is crucial in a changing world where hybridization and introgression might determine which species succeed and which become extinct.
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Affiliation(s)
- Karin S Pfennig
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA.
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31
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Sarver BAJ, Herrera ND, Sneddon D, Hunter SS, Settles ML, Kronenberg Z, Demboski JR, Good JM, Sullivan J. Diversification, Introgression, and Rampant Cytonuclear Discordance in Rocky Mountains Chipmunks (Sciuridae: Tamias). Syst Biol 2021; 70:908-921. [PMID: 33410870 DOI: 10.1093/sysbio/syaa085] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 11/02/2020] [Accepted: 11/03/2020] [Indexed: 12/18/2022] Open
Abstract
Evidence from natural systems suggests that hybridization between animal species is more common than traditionally thought, but the overall contribution of introgression to standing genetic variation within species remains unclear for most animal systems. Here, we use targeted exon-capture to sequence thousands of nuclear loci and complete mitochondrial genomes from closely related chipmunk species in the Tamias quadrivittatus group that are distributed across the Great Basin and the central and southern Rocky Mountains of North America. This recent radiation includes six overlapping, ecologically distinct species (T. canipes, T. cinereicollis, T. dorsalis, T. quadrivittatus, T. rufus, and T. umbrinus) that show evidence for widespread introgression across species boundaries. Such evidence has historically been derived from a handful of markers, typically focused on mitochondrial loci, to describe patterns of introgression; consequently, the extent of introgression of nuclear genes is less well characterized. We conducted a series of phylogenomic and species-tree analyses to resolve the phylogeny of six species in this group. In addition, we performed several population genomic analyses to characterize nuclear genomes and infer coancestry among individuals. Furthermore, we used emerging quartets-based approaches to simultaneously infer the species tree (SVDquartets) and identify introgression (HyDe). We found that, in spite of rampant introgression of mitochondrial genomes between some species pairs (and sometimes involving up to three species), there appears to be little to no evidence for nuclear introgression. These findings mirror other genomic results where complete mitochondrial capture has occurred between chipmunk species in the absence of appreciable nuclear gene flow. The underlying causes of recurrent massive cytonuclear discordance remain unresolved in this group but mitochondrial DNA appears highly misleading of population histories as a whole. Collectively, it appears that chipmunk species boundaries are largely impermeable to nuclear gene flow and that hybridization, while pervasive with respect to mtDNA, has likely played a relatively minor role in the evolutionary history of this group.
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Affiliation(s)
- Brice A J Sarver
- Department of Biological Sciences, University of Idaho, Moscow, Idaho.,Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow Idaho
| | | | - David Sneddon
- Department of Biological Sciences, University of Idaho, Moscow, Idaho
| | - Samuel S Hunter
- Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow Idaho.,UC-Davis Genome Center, Davis, California
| | | | | | - John R Demboski
- Department of Zoology, Denver Museum of Nature & Sciences, Denver, Colorado
| | - Jeffrey M Good
- Division of Biological Sciences, University of Montana, Missoula, Montana.,Wildlife Biology Program, University of Montana, Missoula, Montana
| | - Jack Sullivan
- Department of Biological Sciences, University of Idaho, Moscow, Idaho.,Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow Idaho
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32
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Kirschel ANG, Nwankwo EC, Pierce DK, Lukhele SM, Moysi M, Ogolowa BO, Hayes SC, Monadjem A, Brelsford A. CYP2J19 mediates carotenoid colour introgression across a natural avian hybrid zone. Mol Ecol 2020; 29:4970-4984. [PMID: 33058329 DOI: 10.1111/mec.15691] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 10/02/2020] [Accepted: 10/05/2020] [Indexed: 02/06/2023]
Abstract
It has long been of interest to identify the phenotypic traits that mediate reproductive isolation between related species, and more recently, the genes that underpin them. Much work has focused on identifying genes associated with animal colour, with the candidate gene CYP2J19 identified in laboratory studies as the ketolase converting yellow dietary carotenoids to red ketocarotenoids in birds with red pigments. However, evidence that CYP2J19 explains variation between red and yellow feather coloration in wild populations of birds is lacking. Hybrid zones provide the opportunity to identify genes associated with specific traits. Here we investigate genomic regions associated with colour in red-fronted and yellow-fronted tinkerbirds across a hybrid zone in southern Africa. We sampled 85 individuals, measuring spectral reflectance of forecrown feathers and scoring colours from photographs, while testing for carotenoid presence with Raman spectroscopy. We performed a genome-wide association study to identify associations with carotenoid-based coloration, using double-digest RAD sequencing aligned to a short-read whole genome of a Pogoniulus tinkerbird. Admixture mapping using 104,933 single nucleotide polymorphisms (SNPs) identified a region of chromosome 8 that includes CYP2J19 as the only locus with more than two SNPs significantly associated with both crown hue and crown score, while Raman spectra provided evidence of ketocarotenoids in red feathers. Asymmetric backcrossing in the hybrid zone suggests that yellow-fronted females mate more often with red-fronted males than vice versa. Female red-fronted tinkerbirds mating assortatively with red-crowned males is consistent with the hypothesis that converted carotenoids are an honest signal of quality.
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Affiliation(s)
| | - Emmanuel C Nwankwo
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Daniel K Pierce
- Department of Evolution, Ecology, and Organismal Biology, University of California Riverside, Riverside, CA, USA
| | - Sifiso M Lukhele
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Michaella Moysi
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Bridget O Ogolowa
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Sophia C Hayes
- Department of Chemistry, University of Cyprus, Nicosia, Cyprus
| | - Ara Monadjem
- Department of Biological Sciences, University of Eswatini, Kwaluseni, Eswatini.,Department of Zoology & Entomology, Mammal Research Institute, University of Pretoria, Hatfield, South Africa
| | - Alan Brelsford
- Department of Evolution, Ecology, and Organismal Biology, University of California Riverside, Riverside, CA, USA
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33
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Tobias JA, Ottenburghs J, Pigot AL. Avian Diversity: Speciation, Macroevolution, and Ecological Function. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2020. [DOI: 10.1146/annurev-ecolsys-110218-025023] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The origin, distribution, and function of biological diversity are fundamental themes of ecology and evolutionary biology. Research on birds has played a major role in the history and development of these ideas, yet progress was for many decades limited by a focus on patterns of current diversity, often restricted to particular clades or regions. Deeper insight is now emerging from a recent wave of integrative studies combining comprehensive phylogenetic, environmental, and functional trait data at unprecedented scales. We review these empirical advances and describe how they are reshaping our understanding of global patterns of bird diversity and the processes by which it arises, with implications for avian biogeography and functional ecology. Further expansion and integration of data sets may help to resolve longstanding debates about the evolutionary origins of biodiversity and offer a framework for understanding and predicting the response of ecosystems to environmental change.
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Affiliation(s)
- Joseph A. Tobias
- Department of Life Sciences, Imperial College London, Silwood Park, Ascot SL5 7PY, United Kingdom
| | - Jente Ottenburghs
- Department of Evolutionary Biology, Uppsala University, 752 36 Uppsala, Sweden
| | - Alex L. Pigot
- Centre for Biodiversity and Environment Research, Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, United Kingdom
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34
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Schley RJ, Pennington RT, Pérez-Escobar OA, Helmstetter AJ, de la Estrella M, Larridon I, Sabino Kikuchi IAB, Barraclough TG, Forest F, Klitgård B. Introgression across evolutionary scales suggests reticulation contributes to Amazonian tree diversity. Mol Ecol 2020; 29:4170-4185. [PMID: 32881172 DOI: 10.1111/mec.15616] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 08/14/2020] [Accepted: 08/17/2020] [Indexed: 01/03/2023]
Abstract
Hybridization has the potential to generate or homogenize biodiversity and is a particularly common phenomenon in plants, with an estimated 25% of plant species undergoing interspecific gene flow. However, hybridization in Amazonia's megadiverse tree flora was assumed to be extremely rare despite extensive sympatry between closely related species, and its role in diversification remains enigmatic because it has not yet been examined empirically. Using members of a dominant Amazonian tree family (Brownea, Fabaceae) as a model to address this knowledge gap, our study recovered extensive evidence of hybridization among multiple lineages across phylogenetic scales. More specifically, using targeted sequence capture our results uncovered several historical introgression events between Brownea lineages and indicated that gene tree incongruence in Brownea is best explained by reticulation, rather than solely by incomplete lineage sorting. Furthermore, investigation of recent hybridization using ~19,000 ddRAD loci recovered a high degree of shared variation between two Brownea species that co-occur in the Ecuadorian Amazon. Our analyses also showed that these sympatric lineages exhibit homogeneous rates of introgression among loci relative to the genome-wide average, implying a lack of selection against hybrid genotypes and persistent hybridization. Our results demonstrate that gene flow between multiple Amazonian tree species has occurred across temporal scales, and contrasts with the prevailing view of hybridization's rarity in Amazonia. Overall, our results provide novel evidence that reticulate evolution influenced diversification in part of the Amazonian tree flora, which is the most diverse on Earth.
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Affiliation(s)
- Rowan J Schley
- Royal Botanic Gardens, Kew, Richmond, UK.,Department of Life Sciences, Imperial College London, Ascot, Berkshire, London, UK
| | - R Toby Pennington
- Geography, University of Exeter, Exeter, UK.,Royal Botanic Garden Edinburgh, Edinburgh, UK
| | | | - Andrew J Helmstetter
- Institut de Recherche pour le Développement (IRD), UMR-DIADE, Montpellier, France
| | - Manuel de la Estrella
- Departamento de Botánica, Ecología y Fisiología Vegetal, Facultad de Ciencias, Universidad de Córdoba, Córdoba, Spain
| | - Isabel Larridon
- Royal Botanic Gardens, Kew, Richmond, UK.,Systematic and Evolutionary Botany Lab, Department of Biology, Ghent University, K.L, Gent, Belgium
| | | | - Timothy G Barraclough
- Department of Life Sciences, Imperial College London, Ascot, Berkshire, London, UK.,Department of Zoology, University of Oxford, Oxford, UK
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35
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Martin BT, Douglas MR, Chafin TK, Placyk JS, Birkhead RD, Phillips CA, Douglas ME. Contrasting signatures of introgression in North American box turtle (
Terrapene
spp.) contact zones. Mol Ecol 2020; 29:4186-4202. [DOI: 10.1111/mec.15622] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 08/19/2020] [Accepted: 08/24/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Bradley T. Martin
- Department of Biological Sciences University of Arkansas Fayetteville AR USA
| | - Marlis R. Douglas
- Department of Biological Sciences University of Arkansas Fayetteville AR USA
| | - Tyler K. Chafin
- Department of Biological Sciences University of Arkansas Fayetteville AR USA
| | - John S. Placyk
- Department of Biology University of Texas Tyler TX USA
- Science Division Trinity Valley Community College Athens TX USA
| | | | - Christopher A. Phillips
- Illinois Natural History Survey Prairie Research Institute University of Illinois Champaign IL USA
| | - Michael E. Douglas
- Department of Biological Sciences University of Arkansas Fayetteville AR USA
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36
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The Genomic Landscape of Divergence Across the Speciation Continuum in Island-Colonising Silvereyes ( Zosterops lateralis). G3-GENES GENOMES GENETICS 2020; 10:3147-3163. [PMID: 32660974 PMCID: PMC7466963 DOI: 10.1534/g3.120.401352] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Inferring the evolutionary dynamics at play during the process of speciation by analyzing the genomic landscape of divergence is a major pursuit in population genomics. However, empirical assessments of genomic landscapes under varying evolutionary scenarios that are known a priori are few, thereby limiting our ability to achieve this goal. Here we combine RAD-sequencing and individual-based simulations to evaluate the genomic landscape of divergence in the silvereye (Zosterops lateralis). Using pairwise comparisons that differ in divergence timeframe and the presence or absence of gene flow, we document how genomic patterns accumulate along the speciation continuum. In contrast to previous predictions, our results provide limited support for the idea that divergence accumulates around loci under divergent selection or that genomic islands widen with time. While a small number of genomic islands were found in populations diverging with and without gene flow, in few cases were SNPs putatively under selection tightly associated with genomic islands. The transition from localized to genome-wide levels of divergence was captured using individual-based simulations that considered only neutral processes. Our results challenge the ubiquity of existing verbal models that explain the accumulation of genomic differences across the speciation continuum and instead support the idea that divergence both within and outside of genomic islands is important during the speciation process.
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37
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Quilodrán CS, Montoya-Burgos JI, Currat M. Harmonizing hybridization dissonance in conservation. Commun Biol 2020; 3:391. [PMID: 32694629 PMCID: PMC7374702 DOI: 10.1038/s42003-020-1116-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 06/25/2020] [Indexed: 12/24/2022] Open
Abstract
A dramatic increase in the hybridization between historically allopatric species has been induced by human activities. However, the notion of hybridization seems to lack consistency in two respects. On the one hand, it is inconsistent with the biological species concept, which does not allow for interbreeding between species, and on the other hand, it is considered either as an evolutionary process leading to the emergence of new biodiversity or as a cause of biodiversity loss, with conservation implications. In the first case, we argue that conservation biology should avoid the discussion around the species concept and delimit priorities of conservation units based on the impact on biodiversity if taxa are lost. In the second case, we show that this is not a paradox but an intrinsic property of hybridization, which should be considered in conservation programmes. We propose a novel view of conservation guidelines, in which human-induced hybridization may also be a tool to enhance the likelihood of adaptation to changing environmental conditions or to increase the genetic diversity of taxa affected by inbreeding depression. The conservation guidelines presented here represent a guide for the development of programmes aimed at protecting biodiversity as a dynamic evolutionary system.
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Affiliation(s)
- Claudio S Quilodrán
- Department of Zoology, University of Oxford, Oxford, United Kingdom.
- Laboratory of Anthropology, Genetics and Peopling History, Anthropology Unit, Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.
| | - Juan I Montoya-Burgos
- Laboratory of Vertebrate Evolution, Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (IGE3), Geneva, Switzerland
| | - Mathias Currat
- Laboratory of Anthropology, Genetics and Peopling History, Anthropology Unit, Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (IGE3), Geneva, Switzerland
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38
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Coughlan JM, Matute DR. The importance of intrinsic postzygotic barriers throughout the speciation process. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190533. [PMID: 32654642 DOI: 10.1098/rstb.2019.0533] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Intrinsic postzygotic barriers can play an important and multifaceted role in speciation, but their contribution is often thought to be reserved to the final stages of the speciation process. Here, we review how intrinsic postzygotic barriers can contribute to speciation, and how this role may change through time. We outline three major contributions of intrinsic postzygotic barriers to speciation. (i) reduction of gene flow: intrinsic postzygotic barriers can effectively reduce gene exchange between sympatric species pairs. We discuss the factors that influence how effective incompatibilities are in limiting gene flow. (ii) early onset of species boundaries via rapid evolution: intrinsic postzygotic barriers can evolve between recently diverged populations or incipient species, thereby influencing speciation relatively early in the process. We discuss why the early origination of incompatibilities is expected under some biological models, and detail how other (and often less obvious) incompatibilities may also serve as important barriers early on in speciation. (iii) reinforcement: intrinsic postzygotic barriers can promote the evolution of subsequent reproductive isolation through processes such as reinforcement, even between relatively recently diverged species pairs. We incorporate classic and recent empirical and theoretical work to explore these three facets of intrinsic postzygotic barriers, and provide our thoughts on recent challenges and areas in the field in which progress can be made. This article is part of the theme issue 'Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.
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Affiliation(s)
- Jenn M Coughlan
- Department of Biology, University of North Carolina, 120 South Road, Coker Hall, Chapel Hill, NC 27599, USA
| | - Daniel R Matute
- Department of Biology, University of North Carolina, 120 South Road, Coker Hall, Chapel Hill, NC 27599, USA
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39
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Wang E, Zhang D, Braun MS, Hotz-Wagenblatt A, Pärt T, Arlt D, Schmaljohann H, Bairlein F, Lei F, Wink M. Can Mitogenomes of the Northern Wheatear (Oenanthe oenanthe) Reconstruct Its Phylogeography and Reveal the Origin of Migrant Birds? Sci Rep 2020; 10:9290. [PMID: 32518318 PMCID: PMC7283232 DOI: 10.1038/s41598-020-66287-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 05/15/2020] [Indexed: 11/09/2022] Open
Abstract
The Northern Wheatear (Oenanthe oenanthe, including the nominate and the two subspecies O. o. leucorhoa and O. o. libanotica) and the Seebohm’s Wheatear (Oenanthe seebohmi) are today regarded as two distinct species. Before, all four taxa were regarded as four subspecies of the Northern Wheatear. Their classification has exclusively been based on ecological and morphological traits, while their molecular characterization is still missing. With this study, we used next-generation sequencing to assemble 117 complete mitochondrial genomes covering O. o. oenanthe, O. o. leucorhoa and O. seebohmi. We compared the resolution power of each individual mitochondrial marker and concatenated marker sets to reconstruct the phylogeny and estimate speciation times of three taxa. Moreover, we tried to identify the origin of migratory wheatears caught on Helgoland (Germany) and on Crete (Greece). Mitogenome analysis revealed two different ancient lineages that separated around 400,000 years ago. Both lineages consisted of a mix of subspecies and species. The phylogenetic trees, as well as haplotype networks are incongruent with the present morphology-based classification. Mitogenome could not distinguish these presumed species. The genetic panmixia among present populations and taxa might be the consequence of mitochondrial introgression between ancient wheatear populations.
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Affiliation(s)
- Erjia Wang
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany.
| | - Dezhi Zhang
- Key laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, UniversityMerops apiaster. J. Divers of Chinese Academy of Sciences, Beijing, China
| | - Markus Santhosh Braun
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany
| | - Agnes Hotz-Wagenblatt
- Omics IT and Data Management Core Facility, German Cancer Research Center, Heidelberg University, Heidelberg, Germany
| | - Tomas Pärt
- Department of Ecology, Swedish University of Agricultural Science, Uppsala, Sweden
| | - Debora Arlt
- Department of Ecology, Swedish University of Agricultural Science, Uppsala, Sweden
| | - Heiko Schmaljohann
- Institute of Avian Research "Vogelwarte Helgoland", Wilhelmshaven, Germany.,Institute for Biology und Environmental Sciences (IBU), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Franz Bairlein
- Institute of Avian Research "Vogelwarte Helgoland", Wilhelmshaven, Germany
| | - Fumin Lei
- Key laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, UniversityMerops apiaster. J. Divers of Chinese Academy of Sciences, Beijing, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Michael Wink
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany.
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40
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Princepe D, De Aguiar MAM. Modeling Mito-nuclear Compatibility and Its Role in Species Identification. Syst Biol 2020; 70:133-144. [PMID: 32497198 DOI: 10.1093/sysbio/syaa044] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 05/26/2020] [Accepted: 05/27/2020] [Indexed: 01/27/2023] Open
Abstract
Mitochondrial genetic material (mtDNA) is widely used for phylogenetic reconstruction and as a barcode for species identification. The utility of mtDNA in these contexts derives from its particular molecular properties, including its high evolutionary rate, uniparental inheritance, and small size. But mtDNA may also play a fundamental role in speciation-as suggested by recent observations of coevolution with the nuclear DNA, along with the fact that respiration depends on coordination of genes from both sources. Here, we study how mito-nuclear interactions affect the accuracy of species identification by mtDNA, as well as the speciation process itself. We simulate the evolution of a population of individuals who carry a recombining nuclear genome and a mitochondrial genome inherited maternally. We compare a null model fitness landscape that lacks any mito-nuclear interaction against a scenario in which interactions influence fitness. Fitness is assigned to individuals according to their mito-nuclear compatibility, which drives the coevolution of the nuclear and mitochondrial genomes. Depending on the model parameters, the population breaks into distinct species and the model output then allows us to analyze the accuracy of mtDNA barcode for species identification. Remarkably, we find that species identification by mtDNA is equally accurate in the presence or absence of mito-nuclear coupling and that the success of the DNA barcode derives mainly from population geographical isolation during speciation. Nevertheless, selection imposed by mito-nuclear compatibility influences the diversification process and leaves signatures in the genetic content and spatial distribution of the populations, in three ways. First, speciation is delayed and the resulting phylogenetic trees are more balanced. Second, clades in the resulting phylogenetic tree correlate more strongly with the spatial distribution of species and clusters of more similar mtDNA's. Third, there is a substantial increase in the intraspecies mtDNA similarity, decreasing the number of alleles substitutions per locus and promoting the conservation of genetic information. We compare the evolutionary patterns observed in our model to empirical data from copepods (Tigriopus californicus). We find good qualitative agreement in the geographic patterns and the topology of the phylogenetic tree, provided the model includes selection based on mito-nuclear interactions. These results highlight the role of mito-nuclear compatibility in the speciation process and its reconstruction from genetic data.[Mito-nuclear coevolution; mtDNA barcode; parapatry; phylogeny.].
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Affiliation(s)
| | - Marcus A M De Aguiar
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas - 13083-859, Campinas, SP, Brazil
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41
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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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42
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Lamichhaney S, Han F, Webster MT, Grant BR, Grant PR, Andersson L. Female-biased gene flow between two species of Darwin’s finches. Nat Ecol Evol 2020; 4:979-986. [DOI: 10.1038/s41559-020-1183-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 03/20/2020] [Indexed: 01/29/2023]
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43
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Wogan GOU, Voelker G, Oatley G, Bowie RCK. Biome stability predicts population structure of a southern African aridland bird species. Ecol Evol 2020; 10:4066-4081. [PMID: 32489631 PMCID: PMC7244808 DOI: 10.1002/ece3.6175] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 01/15/2020] [Indexed: 11/07/2022] Open
Abstract
Environments are heterogeneous in space and time, and the permeability of landscape and climatic barriers to gene flow may change over time. When barriers are present, they may start populations down the path toward speciation, but if they become permeable before the process of speciation is complete, populations may once more merge. In Southern Africa, aridland biomes play a central role in structuring the organization of biodiversity. These biomes were subject to substantial restructuring during Plio-Pleistocene climatic fluctuations, and the imprint of this changing environment should leave genetic signatures on the species living there. Here, we investigate the role of adjacent aridland biome boundaries in structuring the genetic diversity within a widespread generalist bird, the Cape Robin-chat (Cossypha caffra). We find evidence supporting a central role for aridland biomes in structuring populations across Southern Africa. Our findings support a scenario wherein populations were isolated in different biome refugia, due to separation by the exceptionally arid Nama Karoo biome. This biome barrier may have arisen through a combination of habitat instability and environmental unsuitability, and was highly unstable throughout the Plio-Pleistocene. However, we also recovered a pattern of extensive contemporary gene flow and admixture across the Nama Karoo, potentially driven by the establishment of homesteads over the past 200 years. Thus, the barrier has become permeable, and populations are currently merging. This represents an instance where initial formation of a barrier to gene flow enabled population differentiation, with subsequent gene flow and the merging of populations after the barrier became permeable.
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Affiliation(s)
- Guinevere O. U. Wogan
- Department of Integrative BiologyMuseum of Vertebrate ZoologyUniversity of CaliforniaBerkeleyCAUSA
| | - Gary Voelker
- Department of Wildlife and Fisheries SciencesBiodiversity Research and Teaching CollectionsTexas A&M UniversityCollege StationTXUSA
| | - Graeme Oatley
- Department of GeographyCollege of Life and Environmental SciencesUniversity of ExeterExeterUK
- DST/NRF Centre of Excellence at the Percy FitzPatrick InstituteUniversity of Cape TownRondeboschSouth Africa
| | - Rauri C. K. Bowie
- Department of Integrative BiologyMuseum of Vertebrate ZoologyUniversity of CaliforniaBerkeleyCAUSA
- DST/NRF Centre of Excellence at the Percy FitzPatrick InstituteUniversity of Cape TownRondeboschSouth Africa
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44
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Pulido‐Santacruz P, Aleixo A, Weir JT. Genomic data reveal a protracted window of introgression during the diversification of a neotropical woodcreeper radiation*. Evolution 2020; 74:842-858. [DOI: 10.1111/evo.13902] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 10/31/2019] [Accepted: 12/04/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Paola Pulido‐Santacruz
- Department of Ecology and Evolutionary BiologyUniversity of Toronto Toronto Canada
- Instituto de Investigación de Recursos Biológicos Alexander von Humboldt Bogotá Colombia
- Current address: Instituto de Investigación de Recursos Biológicos Alexander von Humboldt Calle 28A No. 15 – 09 Bogotá Colombia
| | | | - Jason T. Weir
- Department of Ecology and Evolutionary BiologyUniversity of Toronto Toronto Canada
- Department of Biological SciencesUniversity of Toronto Scarborough Toronto Canada
- Department of OrnithologyRoyal Ontario Museum Toronto Canada
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45
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Slager DL, Epperly KL, Ha RR, Rohwer S, Wood C, Van Hemert C, Klicka J. Cryptic and extensive hybridization between ancient lineages of American crows. Mol Ecol 2020; 29:956-969. [PMID: 32034818 DOI: 10.1111/mec.15377] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 12/30/2019] [Accepted: 02/05/2020] [Indexed: 01/02/2023]
Abstract
Most species and therefore most hybrid zones have historically been defined using phenotypic characters. However, both speciation and hybridization can occur with negligible morphological differentiation. Recently developed genomic tools provide the means to better understand cryptic speciation and hybridization. The Northwestern Crow (Corvus caurinus) and American Crow (Corvus brachyrhynchos) are continuously distributed sister taxa that lack reliable traditional characters for identification. In this first population genomic study of Northwestern and American crows, we use genomic SNPs (nuDNA) and mtDNA to investigate the degree of genetic differentiation between these crows and the extent to which they may hybridize. Our results indicate that American and Northwestern crows have distinct evolutionary histories, supported by two nuDNA ancestry clusters and two 1.1%-divergent mtDNA clades dating to the late Pleistocene, when glacial advances may have isolated crow populations in separate refugia. We document extensive hybridization, with geographic overlap of mtDNA clades and admixture of nuDNA across >900 km of western Washington and western British Columbia. This broad hybrid zone consists of late-generation hybrids and backcrosses, but not recent (e.g., F1) hybrids. Nuclear DNA and mtDNA clines had concordant widths and were both centred in southwestern British Columbia, farther north than previously postulated. Overall, our results suggest a history of reticulate evolution in American and Northwestern crows, perhaps due to recurring neutral expansion(s) from Pleistocene glacial refugia followed by lineage fusion(s). However, we do not rule out a contributing role for more recent potential drivers of hybridization, such as expansion into human-modified habitats.
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Affiliation(s)
- David L Slager
- Department of Biology, University of Washington, Seattle, WA, USA.,Burke Museum of Natural History and Culture, Seattle, WA, USA
| | - Kevin L Epperly
- Department of Biology, University of Washington, Seattle, WA, USA.,Burke Museum of Natural History and Culture, Seattle, WA, USA
| | - Renee R Ha
- Department of Psychology, University of Washington, Seattle, WA, USA
| | - Sievert Rohwer
- Department of Biology, University of Washington, Seattle, WA, USA.,Burke Museum of Natural History and Culture, Seattle, WA, USA
| | - Chris Wood
- Burke Museum of Natural History and Culture, Seattle, WA, USA
| | | | - John Klicka
- Department of Biology, University of Washington, Seattle, WA, USA.,Burke Museum of Natural History and Culture, Seattle, WA, USA
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46
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Zhou S, Ni S, Dai J, Zhou Q, Zhou R, Liu Y. Natural hybridization between Phyllagathis and Sporoxeia species produces a hybrid without reproductive organs. PLoS One 2020; 15:e0227625. [PMID: 31914145 PMCID: PMC6949006 DOI: 10.1371/journal.pone.0227625] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 12/22/2019] [Indexed: 01/05/2023] Open
Abstract
Natural hybridization plays important roles in plant evolution and speciation. In this study, we sequenced ribosomal internal transcribed spacer (nrITS), four low-copy nuclear genes (Dbr1, SOS4a, SOS4b and PCRF1) and the chloroplast intergenic spacer trnV-trnM to test the hypothesis of hybridization between two species of Phyllagathis and Sporoxeia (Sonerileae/Dissochaeteae, Melastomataceae). Our results provided compelling evidence for the hybridization hypothesis. All hybrid individuals sampled were first-generation hybrids. The failure of flower production in the F1 hybrid individuals may work as the barrier preventing later-generation hybridization or backcross. Analysis of the chloroplast trnV-trnM sequences showed that the hybridization is bidirectional with S. petelotii as the major maternal parent. Several factors, such as sympatry, similar habitat preference, overlapping flowering season and shared pollinators, might have contributed to this hybridization event. The "intergeneric" hybridization reported in this study suggests close relationship between P. longicalcarata and S. petelotii.
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Affiliation(s)
- Shuaixi Zhou
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Shuheng Ni
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jinhong Dai
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Qiujie Zhou
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Renchao Zhou
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
- * E-mail: (RZ); (YL)
| | - Ying Liu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
- * E-mail: (RZ); (YL)
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47
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Beausoleil MO, Frishkoff LO, M'Gonigle LK, Raeymaekers JAM, Knutie SA, De León LF, Huber SK, Chaves JA, Clayton DH, Koop JAH, Podos J, Sharpe DMT, Hendry AP, Barrett RDH. Temporally varying disruptive selection in the medium ground finch ( Geospiza fortis). Proc Biol Sci 2019; 286:20192290. [PMID: 31795872 DOI: 10.1098/rspb.2019.2290] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Disruptive natural selection within populations exploiting different resources is considered to be a major driver of adaptive radiation and the production of biodiversity. Fitness functions, which describe the relationships between trait variation and fitness, can help to illuminate how this disruptive selection leads to population differentiation. However, a single fitness function represents only a particular selection regime over a single specified time period (often a single season or a year), and therefore might not capture longer-term dynamics. Here, we build a series of annual fitness functions that quantify the relationships between phenotype and apparent survival. These functions are based on a 9-year mark-recapture dataset of over 600 medium ground finches (Geospiza fortis) within a population bimodal for beak size. We then relate changes in the shape of these functions to climate variables. We find that disruptive selection between small and large beak morphotypes, as reported previously for 2 years, is present throughout the study period, but that the intensity of this selection varies in association with the harshness of environment. In particular, we find that disruptive selection was strongest when precipitation was high during the dry season of the previous year. Our results shed light on climatic factors associated with disruptive selection in Darwin's finches, and highlight the role of temporally varying fitness functions in modulating the extent of population differentiation.
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Affiliation(s)
- Marc-Olivier Beausoleil
- Department of Biology and Redpath Museum, McGill University, 859 Rue Sherbrooke Ouest, Montréal, Québec, Canada H3A 0C4
| | - Luke O Frishkoff
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Leithen K M'Gonigle
- Department of Biological Sciences, Simon Fraser University, Burnaby BC V5A 1S6, Canada
| | | | - Sarah A Knutie
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Luis F De León
- Department of Biology, University of Massachusetts Boston, Boston, MA, USA.,Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología, Panama
| | - Sarah K Huber
- Virginia Institute of Marine Science, College of William and Mary, Gloucester Point, VA, USA
| | - Jaime A Chaves
- Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Pichincha, Ecuador.,Galápagos Science Center, Puerto Baquerizo Moreno, Galápagos, Ecuador
| | - Dale H Clayton
- School of Biological Sciences, University of Utah, 257 South 1400 East, Salt Lake City, 84112 UT, USA
| | - Jennifer A H Koop
- Department of Biological Sciences, Northern Illinois University, 1425 W. Lincoln Hwy., DeKalb, IL 60115, USA
| | - Jeffrey Podos
- Department of Biology, University of Massachusetts, 221 Morrill Science Center, Amherst, MA, USA
| | - Diana M T Sharpe
- Department of Biology, University of Massachusetts Boston, Boston, MA, USA
| | - Andrew P Hendry
- Department of Biology and Redpath Museum, McGill University, 859 Rue Sherbrooke Ouest, Montréal, Québec, Canada H3A 0C4
| | - Rowan D H Barrett
- Department of Biology and Redpath Museum, McGill University, 859 Rue Sherbrooke Ouest, Montréal, Québec, Canada H3A 0C4
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48
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Chafin TK, Douglas MR, Martin BT, Douglas ME. Hybridization drives genetic erosion in sympatric desert fishes of western North America. Heredity (Edinb) 2019; 123:759-773. [PMID: 31431737 PMCID: PMC6834602 DOI: 10.1038/s41437-019-0259-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/24/2019] [Accepted: 07/30/2019] [Indexed: 01/26/2023] Open
Abstract
Many species have evolved or currently coexist in sympatry due to differential adaptation in a heterogeneous environment. However, anthropogenic habitat modifications can either disrupt reproductive barriers or obscure environmental conditions which underlie fitness gradients. In this study, we evaluated the potential for an anthropogenically-mediated shift in reproductive boundaries that separate two historically sympatric fish species (Gila cypha and G. robusta) endemic to the Colorado River Basin using ddRAD sequencing of 368 individuals. We first examined the integrity of reproductive isolation while in sympatry and allopatry, then characterized hybrid ancestries using genealogical assignment tests. We tested for localized erosion of reproductive isolation by comparing site-wise genomic clines against global patterns and identified a breakdown in the drainage-wide pattern of selection against interspecific heterozygotes. This, in turn, allowed for the formation of a hybrid swarm in one tributary, and asymmetric introgression where species co-occur. We also detected a weak but significant relationship between genetic purity and degree of consumptive water removal, suggesting a role for anthropogenic habitat modifications in undermining species boundaries or expanding historically limited introgression. In addition, results from basin-wide genomic clines suggested that hybrids and parental forms are adaptively nonequivalent. If so, then a failure to manage for hybridization will exacerbate the long-term extinction risk in parental populations. These results reinforce the role of anthropogenic habitat modification in promoting interspecific introgression in sympatric species by relaxing divergent selection. This, in turn, underscores a broader role for hybridization in decreasing global biodiversity within rapidly deteriorating environments.
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Affiliation(s)
- Tyler K Chafin
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, 72701, USA.
| | - Marlis R Douglas
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Bradley T Martin
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Michael E Douglas
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
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49
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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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50
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Aubier TG, Kokko H, Joron M. Coevolution of male and female mate choice can destabilize reproductive isolation. Nat Commun 2019; 10:5122. [PMID: 31719522 PMCID: PMC6851176 DOI: 10.1038/s41467-019-12860-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 09/17/2019] [Indexed: 11/09/2022] Open
Abstract
Sexual interactions play an important role in the evolution of reproductive isolation, with important consequences for speciation. Theoretical studies have focused on the evolution of mate preferences in each sex separately. However, mounting empirical evidence suggests that premating isolation often involves mutual mate choice. Here, using a population genetic model, we investigate how female and male mate choice coevolve under a phenotype matching rule and how this affects reproductive isolation. We show that the evolution of female preferences increases the mating success of males with reciprocal preferences, favouring mutual mate choice. However, the evolution of male preferences weakens indirect selection on female preferences and, with weak genetic drift, the coevolution of female and male mate choice leads to periodic episodes of random mating with increased hybridization (deterministic 'preference cycling' triggered by stochasticity). Thus, counterintuitively, the process of establishing premating isolation proves rather fragile if both male and female mate choice contribute to assortative mating.
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Affiliation(s)
- Thomas G Aubier
- Centre d'Ecologie Fonctionnelle et Evolutive, CEFE - UMR 5175 - CNRS, Université de Montpellier, EPHE, Université Paul Valéry, 1919 route de Mende, F-34293, Montpellier 5, France.
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland.
| | - Hanna Kokko
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Mathieu Joron
- Centre d'Ecologie Fonctionnelle et Evolutive, CEFE - UMR 5175 - CNRS, Université de Montpellier, EPHE, Université Paul Valéry, 1919 route de Mende, F-34293, Montpellier 5, France.
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