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Vangestel C, Swaegers J, De Corte Z, Dekoninck W, Gharbi K, Gillespie R, Vandekerckhove M, Van Belleghem SM, Hendrickx F. Chromosomal inversions from an initial ecotypic divergence drive a gradual repeated radiation of Galápagos beetles. SCIENCE ADVANCES 2024; 10:eadk7906. [PMID: 38820159 PMCID: PMC11141621 DOI: 10.1126/sciadv.adk7906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 04/30/2024] [Indexed: 06/02/2024]
Abstract
Island faunas exhibit some of the most iconic examples where similar forms repeatedly evolve within different islands. Yet, whether these deterministic evolutionary trajectories within islands are driven by an initial, singular divergence and the subsequent exchange of individuals and adaptive genetic variation between islands remains unclear. Here, we study a gradual, repeated evolution of low-dispersive highland ecotypes from a dispersive lowland ecotype of Calosoma beetles along the island progression of the Galápagos. We show that repeated highland adaptation involved selection on multiple shared alleles within extensive chromosomal inversions that originated from an initial adaptation event on the oldest island. These highland inversions first spread through dispersal of highland individuals. Subsequent admixture with the lowland ecotype resulted in polymorphic dispersive populations from which the highland populations evolved on the youngest islands. Our findings emphasize the significance of an ancient divergence in driving repeated evolution and highlight how a mixed contribution of inter-island colonization and within-island evolution can shape parallel species communities.
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Affiliation(s)
- Carl Vangestel
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium
- Terrestrial Ecology Unit, Biology Department, Ghent University, Gent, Belgium
| | - Janne Swaegers
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium
- Ecology, Evolution and Conservation Biology, Biology Department, University of Leuven, Leuven, Belgium
| | - Zoë De Corte
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium
- Terrestrial Ecology Unit, Biology Department, Ghent University, Gent, Belgium
| | | | - Karim Gharbi
- Earlham Institute, Norwich Research Park, Norfolk, United Kingdom
| | - Rosemary Gillespie
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, USA
| | - Matthias Vandekerckhove
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium
- Terrestrial Ecology Unit, Biology Department, Ghent University, Gent, Belgium
| | - Steven M. Van Belleghem
- Ecology, Evolution and Conservation Biology, Biology Department, University of Leuven, Leuven, Belgium
| | - Frederik Hendrickx
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium
- Terrestrial Ecology Unit, Biology Department, Ghent University, Gent, Belgium
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2
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3
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Snead AA, Clark RD. The Biological Hierarchy, Time, and Temporal 'Omics in Evolutionary Biology: A Perspective. Integr Comp Biol 2022; 62:1872-1886. [PMID: 36057775 DOI: 10.1093/icb/icac138] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/28/2022] [Accepted: 08/29/2022] [Indexed: 01/05/2023] Open
Abstract
Sequencing data-genomics, transcriptomics, epigenomics, proteomics, and metabolomics-have revolutionized biological research, enabling a more detailed study of processes, ranging from subcellular to evolutionary, that drive biological organization. These processes, collectively, are responsible for generating patterns of phenotypic variation and can operate over dramatically different timescales (milliseconds to billions of years). While researchers often study phenotypic variation at specific levels of biological organization to isolate processes operating at that particular scale, the varying types of sequence data, or 'omics, can also provide complementary inferences to link molecular and phenotypic variation to produce an integrated view of evolutionary biology, ranging from molecular pathways to speciation. We briefly describe how 'omics has been used across biological levels and then demonstrate the utility of integrating different types of sequencing data across multiple biological levels within the same study to better understand biological phenomena. However, single-time-point studies cannot evaluate the temporal dynamics of these biological processes. Therefore, we put forward temporal 'omics as a framework that can better enable researchers to study the temporal dynamics of target processes. Temporal 'omics is not infallible, as the temporal sampling regime directly impacts inferential ability. Thus, we also discuss the role the temporal sampling regime plays in deriving inferences about the environmental conditions driving biological processes and provide examples that demonstrate the impact of the sampling regime on biological inference. Finally, we forecast the future of temporal 'omics by highlighting current methodological advancements that will enable temporal 'omics to be extended across species and timescales. We extend this discussion to using temporal multi-omics to integrate across the biological hierarchy to evaluate and link the temporal dynamics of processes that generate phenotypic variation.
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Affiliation(s)
- Anthony A Snead
- Department of Biological Sciences, University of Alabama, 300 Hackberry Lane, Tuscaloosa, AL 35487, USA
| | - René D Clark
- Department of Ecology, Evolution and Natural Resources, Rutgers University, 14 College Farm Road, New Brunswick, NJ 08901, USA
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4
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Wang X, He Z, Guo Z, Yang M, Xu S, Chen Q, Shao S, Li S, Zhong C, Duke NC, Shi S. Extensive gene flow in secondary sympatry after allopatric speciation. Natl Sci Rev 2022; 9:nwac280. [PMID: 36694801 PMCID: PMC9869077 DOI: 10.1093/nsr/nwac280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 12/04/2022] [Accepted: 12/10/2022] [Indexed: 12/15/2022] Open
Abstract
In the conventional view, species are separate gene pools delineated by reproductive isolation (RI). In an alternative view, species may also be delineated by a small set of 'speciation genes' without full RI, a view that has gained broad acceptance. A recent survey, however, suggested that the extensive literature on 'speciation with gene flow' is mostly (if not all) about exchanges in the early stages of speciation. There is no definitive evidence that the observed gene flow actually happened after speciation is completed. Here, we wish to know whether 'good species' (defined by the 'secondary sympatry' test) do continue to exchange genes and, importantly, under what conditions such exchanges can be observed. De novo whole-genome assembly and re-sequencing of individuals across the range of two closely related mangrove species (Rhizophora mucronata and R. stylosa) reveal the genomes to be well delineated in allopatry. They became sympatric in northeastern Australia but remain distinct species. Nevertheless, their genomes harbor ∼4000-10 000 introgression blocks averaging only about 3-4 Kb. These fine-grained introgressions indicate continual gene flow long after speciation as non-introgressable 'genomic islets,' ∼1.4 Kb in size, often harbor diverging genes of flower or gamete development. The fine-grained introgression in secondary sympatry may help settle the debate about sympatric vs. micro-allopatric speciation. In conclusion, true 'good species' may often continue to exchange genes but the opportunity for detection is highly constrained.
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Affiliation(s)
| | | | | | - Ming Yang
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA98195, USA
| | - Shaohua Xu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou510275, China
| | - Qipian Chen
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou510275, China
| | - Shao Shao
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou510275, China
| | - Sen Li
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou510275, China
| | - Cairong Zhong
- Hainan Academy of Forestry (Hainan Academy of Mangrove), Haikou571100, China
| | - Norman C Duke
- Centre for Tropical Water and Aquatic Ecosystem Research, James Cook University, Townsville, QLD 4811, Australia
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5
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Rodriguez AK, Krug PJ. Ecological speciation by sympatric host shifts in a clade of herbivorous sea slugs, with introgression and localized mitochondrial capture between species. Mol Phylogenet Evol 2022; 174:107523. [PMID: 35589054 DOI: 10.1016/j.ympev.2022.107523] [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: 11/11/2021] [Revised: 03/30/2022] [Accepted: 05/06/2022] [Indexed: 11/25/2022]
Abstract
Host shifting in insect-plant systems was historically important to the development of ecological speciation theory, yet surprisingly few studies have examined whether host shifting drives diversification of marine herbivores. When small-bodied consumers feed and also mate on a preferred host, disruptive selection can split a population into host races despite gene flow. Support for host shifts is notably lacking for invertebrates associated with macroalgae, where the scale of dispersal by planktonic larvae often far exceeds the grain of host patchiness, and adults are typically less specialized than terrestrial herbivores. Here, we present a candidate example of ecological speciation in a clade of sea slugs that primarily consume green algae in the genus Caulerpa, including highly invasive species. Ancestral character state reconstructions supported 'sea grapes' (C. racemosa, C. lentillifera) as the ancestral host for a tropical radiation of 12 Elysia spp., with one shift onto alternative Caulerpa spp. in the Indo-Pacific. A Caribbean radiation of three species included symaptric host shifts to Rhipocephalus brevicaulis in the ancestor of E. pratensis Ortea & Espinosa, 1996, and to C. prolifera in E. hamanni Krug, Vendetti & Valdes 2016, plus a niche expansion to a range of Caulerpa spp. in E. subornata Verrill, 1901. All three species are broadly sympatric across the Caribbean but are host-partitioned at a fine grain, and distinct by morphology and at nuclear loci. However, non-recombining mtDNA revealed a history of gene flow between E. pratensis and E. subornata: COI haplotypes from E. subornata were 10.4% divergent from E. pratensis haplotypes from four sites, but closely related to all E. pratensis haplotypes sampled from six Bahamian islands, indicating historical introgression and localized "mitochondrial capture." Disruptive selective likely fueled divergence and adaptation to distinct host environments, indicating ecological speciation may be an under-appreciated driver of diversification for marine herbivores as well as epibionts and other resource specialists.
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Affiliation(s)
- Albert K Rodriguez
- Department of Biological Sciences, California State University, Los Angeles, CA 90032-8201, U.S.A
| | - Patrick J Krug
- Department of Biological Sciences, California State University, Los Angeles, CA 90032-8201, U.S.A.
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Tamaki I, Obora T, Ohsawa T, Matsumoto A, Saito Y, Ide Y. Different population size change and migration histories created genetic diversity of three oaks in Tokai region, central Japan. JOURNAL OF PLANT RESEARCH 2021; 134:933-946. [PMID: 34155542 DOI: 10.1007/s10265-021-01323-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/14/2021] [Indexed: 06/13/2023]
Abstract
To understand genetic diversity in focal species, it is important to consider the possibility of speciation with gene flow, especially in species with porous genomes such as oaks. We studied genetic diversity and structure in three oaks, Quercus mongolica var. mongolicoides (QM), Q. mongolica var. crispula (QC) and Q. serrata (QS), growing in the Tokai region, central Japan. QM is semi-endemic to the region while the others are common taxa. We also conducted demographic modeling to infer their population size change and migration histories using an approximate Bayesian computation (ABC) approach. The three taxa showed distinct genetic structures but there was genetic admixture among the taxa, especially between QM and QC. ABC analysis of population size change revealed that the population size of QM was stable during and after the last glacial period, while QC and QS showed population expansion after the last glacial maximum. ABC analysis of population divergence and migration revealed that continuous gene flow between QM and QC after their divergence was supported, while between QM and QS, and between QC and QS, secondary contact after sufficient isolation was supported. These historical migration patterns among the three taxa indicate that QM and QC are currently in the early stage or gray zone of speciation, whereas speciation of the other two taxon pairs is considered to have almost been established. Observed gene flow patterns and strength between QM and QC, and between QM and QS, were explained by both flowering patterns and historical distributions, but those between QC and QS were not.
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Affiliation(s)
- Ichiro Tamaki
- Gifu Academy of Forest Science and Culture, 88 Sodai, Mino, Gifu, 501-3714, Japan.
| | - Tomohiro Obora
- Gifu Academy of Forest Science and Culture, 88 Sodai, Mino, Gifu, 501-3714, Japan
| | - Takafumi Ohsawa
- Ministry of the Environment, 1-2-2 Kasumigaseki, Chiyoda-ku, Tokyo, 100-8975, Japan
| | - Asako Matsumoto
- Forestry and Forest Products Research Institute, 1 Matsunosato, Tsukuba, Ibaraki, 305-8687, Japan
| | - Yoko Saito
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yuji Ide
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
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7
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Gompert Z, Springer A, Brady M, Chaturvedi S, Lucas LK. Genomic time-series data show that gene flow maintains high genetic diversity despite substantial genetic drift in a butterfly species. Mol Ecol 2021; 30:4991-5008. [PMID: 34379852 DOI: 10.1111/mec.16111] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 07/09/2021] [Accepted: 07/19/2021] [Indexed: 11/29/2022]
Abstract
Effective population size affects the efficacy of selection, rate of evolution by drift, and neutral diversity levels. When species are subdivided into multiple populations connected by gene flow, evolutionary processes can depend on global or local effective population sizes. Theory predicts that high levels of diversity might be maintained by gene flow, even very low levels of gene flow, consistent with species long-term effective population size, but tests of this idea are mostly lacking. Here, we show that Lycaeides buttery populations maintain low contemporary (variance) effective population sizes (e.g., ~200 individuals) and thus evolve rapidly by genetic drift. In contrast, populations harbored high levels of genetic diversity consistent with an effective population size several orders of magnitude larger. We hypothesized that the differences in the magnitude and variability of contemporary versus long-term effective population sizes were caused by gene flow of sufficient magnitude to maintain diversity but only subtly affect evolution on generational time scales. Consistent with this hypothesis, we detected low but non-trivial gene flow among populations. Furthermore, using short-term population-genomic time-series data, we documented patterns consistent with predictions from this hypothesis, including a weak but detectable excess of evolutionary change in the direction of the mean (migrant gene pool) allele frequencies across populations, and consistency in the direction of allele frequency change over time. The documented decoupling of diversity levels and short-term change by drift in Lycaeides has implications for our understanding of contemporary evolution and the maintenance of genetic variation in the wild.
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Affiliation(s)
- Zachariah Gompert
- Department of Biology, Utah State University, Logan, UT, 84322, USA.,Ecology Center, Utah State University, Logan, UT, 84322, USA
| | - Amy Springer
- Department of Biology, Utah State University, Logan, UT, 84322, USA
| | - Megan Brady
- Department of Biology, Utah State University, Logan, UT, 84322, USA
| | - Samridhi Chaturvedi
- Department of Biology, Utah State University, Logan, UT, 84322, USA.,Department of Organismic & Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Lauren K Lucas
- Department of Biology, Utah State University, Logan, UT, 84322, USA
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8
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Ortego J, Gutiérrez-Rodríguez J, Noguerales V. Demographic consequences of dispersal-related trait shift in two recently diverged taxa of montane grasshoppers. Evolution 2021; 75:1998-2013. [PMID: 33646593 DOI: 10.1111/evo.14205] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 02/03/2021] [Accepted: 02/17/2021] [Indexed: 12/19/2022]
Abstract
Although the pervasiveness of intraspecific wing-size polymorphism and transitions to flightlessness have long captivated biologists, the demographic outcomes of shifts in dispersal ability are not yet well understood and have been seldom studied at early stages of diversification. Here, we use genomic data to infer the consequences of dispersal-related trait variation in the taxonomically controversial short-winged (Chorthippus corsicus corsicus) and long-winged (Chorthippus corsicus pascuorum) Corsican grasshoppers. Our analyses revealed lack of contemporary hybridization between sympatric long- and short-winged forms and phylogenomic reconstructions supported their taxonomic distinctiveness, rejecting the hypothesis of intraspecific wing polymorphism. Statistical evaluation of alternative models of speciation strongly supported a scenario of Pleistocene divergence (<1.5 Ma) with ancestral gene flow. According to neutral expectations from differences in dispersal capacity, historical effective migration rates from the long- to the short-winged taxon were threefold higher than in the opposite direction. Although populations of the two taxa present a marked genetic structure and have experienced parallel demographic histories, our coalescent-based analyses suggest that reduced dispersal has fueled diversification in the short-winged C. c. corsicus. Collectively, our study illustrates how dispersal reduction can speed up geographical diversification and increase the opportunity for allopatric speciation in topographically complex landscapes.
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Affiliation(s)
- Joaquín Ortego
- Department of Integrative Ecology, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
| | | | - Víctor Noguerales
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), La Laguna, Tenerife, Canarias, Spain
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9
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Prada C, Hellberg ME. Speciation-by-depth on coral reefs: Sympatric divergence with gene flow or cryptic transient isolation? J Evol Biol 2021; 34:128-137. [PMID: 33140895 PMCID: PMC7894305 DOI: 10.1111/jeb.13731] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 07/21/2020] [Accepted: 09/29/2020] [Indexed: 12/30/2022]
Abstract
The distributions of many sister species in the sea overlap geographically but are partitioned along depth gradients. The genetic changes leading to depth segregation may evolve in geographic isolation as a prerequisite to coexistence or may emerge during primary divergence leading to new species. These alternatives can now be distinguished via the power endowed by the thousands of scorable loci provided by second-generation sequence data. Here, we revisit the case of two depth-segregated, genetically isolated ecotypes of the nominal Caribbean candelabrum coral Eunicea flexuosa. Previous analyses based on a handful of markers could not distinguish between models of genetic exchange after a period of isolation (consistent with secondary contact) and divergence with gene flow (consistent with primary divergence). Analyses of the history of isolation, genetic exchange and population size based on 15,640 new SNP markers derived from RNAseq data best support models where divergence began 800K BP and include epochs of divergence with gene flow, but with an intermediate period of transient isolation. Results also supported the previous conclusion that recent exchange between the ecotypes occurs asymmetrically from the Shallow lineage to the Deep. Parallel analyses of data from two other corals with depth-segregated populations (Agaricia fragilis and Pocillopora damicornis) suggest divergence leading to depth-segregated populations may begin with a period of symmetric exchange, but that an epoch of population isolation precedes more complete isolation marked by asymmetric introgression. Thus, while divergence-with-gene flow may account for much of the differentiation that separates closely related, depth-segregated species, it remains to be seen whether any critical steps in the speciation process only occur when populations are isolated.
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Affiliation(s)
- Carlos Prada
- Department of Biological SciencesUniversity of Rhode IslandKingstonRIUSA
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10
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Garcia-Erill G, Kjaer MM, Albrechtsen A, Siegismund HR, Heller R. Vicariance followed by secondary gene flow in a young gazelle species complex. Mol Ecol 2020; 30:528-544. [PMID: 33226701 PMCID: PMC7898927 DOI: 10.1111/mec.15738] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 11/03/2020] [Accepted: 11/11/2020] [Indexed: 01/03/2023]
Abstract
Grant's gazelles have recently been proposed to be a species complex comprising three highly divergent mtDNA lineages (Nanger granti, N. notata and N. petersii). The three lineages have nonoverlapping distributions in East Africa, but without any obvious geographical divisions, making them an interesting model for studying the early‐stage evolutionary dynamics of allopatric speciation in detail. Here, we use genomic data obtained by restriction site‐associated (RAD) sequencing of 106 gazelle individuals to shed light on the evolutionary processes underlying Grant's gazelle divergence, to characterize their genetic structure and to assess the presence of gene flow between the main lineages in the species complex. We date the species divergence to 134,000 years ago, which is recent in evolutionary terms. We find population subdivision within N. granti, which coincides with the previously suggested two subspecies, N. g. granti and N. g. robertsii. Moreover, these two lineages seem to have hybridized in Masai Mara. Perhaps more surprisingly given their extreme genetic differentiation, N. granti and N. petersii also show signs of prolonged admixture in Mkomazi, which we identified as a hybrid population most likely founded by allopatric lineages coming into secondary contact. Despite the admixed composition of this population, elevated X chromosomal differentiation suggests that selection may be shaping the outcome of hybridization in this population. Our results therefore provide detailed insights into the processes of allopatric speciation and secondary contact in a recently radiated species complex.
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Affiliation(s)
- Genís Garcia-Erill
- Department of Biology, Section for Computational and RNA Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Michael Munkholm Kjaer
- Department of Biology, Section for Computational and RNA Biology, University of Copenhagen, Copenhagen N, Denmark.,Norwegian College of Fishery Science, UiT The Arctic University of Norway, Tromsø, Norway
| | - Anders Albrechtsen
- Department of Biology, Section for Computational and RNA Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Hans Redlef Siegismund
- Department of Biology, Section for Computational and RNA Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Rasmus Heller
- Department of Biology, Section for Computational and RNA Biology, University of Copenhagen, Copenhagen N, Denmark
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11
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Breusing C, Johnson SB, Tunnicliffe V, Clague DA, Vrijenhoek RC, Beinart RA. Allopatric and Sympatric Drivers of Speciation in Alviniconcha Hydrothermal Vent Snails. Mol Biol Evol 2020; 37:3469-3484. [PMID: 32658967 PMCID: PMC7743903 DOI: 10.1093/molbev/msaa177] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Despite significant advances in our understanding of speciation in the marine environment, the mechanisms underlying evolutionary diversification in deep-sea habitats remain poorly investigated. Here, we used multigene molecular clocks and population genetic inferences to examine processes that led to the emergence of the six extant lineages of Alviniconcha snails, a key taxon inhabiting deep-sea hydrothermal vents in the Indo-Pacific Ocean. We show that both allopatric divergence through historical vicariance and ecological isolation due to niche segregation contributed to speciation in this genus. The split between the two major Alviniconcha clades (separating A. boucheti and A. marisindica from A. kojimai, A. hessleri, and A. strummeri) probably resulted from tectonic processes leading to geographic separation, whereas the splits between co-occurring species might have been influenced by ecological factors, such as the availability of specific chemosynthetic symbionts. Phylogenetic origin of the sixth species, Alviniconcha adamantis, remains uncertain, although its sister position to other extant Alviniconcha lineages indicates a possible ancestral relationship. This study lays a foundation for future genomic studies aimed at deciphering the roles of local adaptation, reproductive biology, and host–symbiont compatibility in speciation of these vent-restricted snails.
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Affiliation(s)
- Corinna Breusing
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI
| | | | - Verena Tunnicliffe
- Department of Biology and School of Earth and Ocean Sciences, University of Victoria, Victoria, BC, Canada
| | - David A Clague
- Monterey Bay Aquarium Research Institute, Moss Landing, CA
| | | | - Roxanne A Beinart
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI
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Wu CI, Wang X, He Z, Shi S. Replies to the commentaries on the question of 'Is it time to abandon the biological species concept?'. Natl Sci Rev 2020; 7:1407-1409. [PMID: 34692170 PMCID: PMC8289014 DOI: 10.1093/nsr/nwaa117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- Chung-I Wu
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Sun Yat-Sen University, China
| | - Xinfeng Wang
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Sun Yat-Sen University, China
| | - Ziwen He
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Sun Yat-Sen University, China
| | - Suhua Shi
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Sun Yat-Sen University, China
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13
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Wang X, He Z, Shi S, Wu CI. Genes and speciation: is it time to abandon the biological species concept? Natl Sci Rev 2020; 7:1387-1397. [PMID: 34692166 PMCID: PMC8288927 DOI: 10.1093/nsr/nwz220] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 12/17/2019] [Accepted: 12/31/2019] [Indexed: 01/04/2023] Open
Abstract
The biological species concept (BSC) is the cornerstone of neo-Darwinian thinking. In BSC, species do not exchange genes either during or after speciation. However, as gene flow during speciation is increasingly being reported in a substantial literature, it seems time to reassess the revered, but often doubted, BSC. Contrary to the common perception, BSC should expect substantial gene flow at the onset of speciation, not least because geographical isolation develops gradually. Although BSC does not stipulate how speciation begins, it does require a sustained period of isolation for speciation to complete its course. Evidence against BSC must demonstrate that the observed gene flow does not merely occur at the onset of speciation but continues until its completion. Importantly, recent genomic analyses cannot reject this more realistic version of BSC, although future analyses may still prove it wrong. The ultimate acceptance or rejection of BSC is not merely about a historical debate; rather, it is about the fundamental nature of species - are species (and, hence, divergent adaptations) driven by a relatively small number of genes, or by thousands of them? Many levels of biology, ranging from taxonomy to biodiversity, depend on this resolution.
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Affiliation(s)
- Xinfeng Wang
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Ziwen He
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Suhua Shi
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Chung-I Wu
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
- Department of Ecology and Evolution, University of Chicago, Illinois 60637, USA
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14
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Blanckaert A, Bank C, Hermisson J. The limits to parapatric speciation 3: evolution of strong reproductive isolation in presence of gene flow despite limited ecological differentiation. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190532. [PMID: 32654650 PMCID: PMC7423268 DOI: 10.1098/rstb.2019.0532] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Gene flow tends to impede the accumulation of genetic divergence. Here, we determine the limits for the evolution of postzygotic reproductive isolation in a model of two populations that are connected by gene flow. We consider two selective mechanisms for the creation and maintenance of a genetic barrier: local adaptation leads to divergence among incipient species due to selection against migrants, and Dobzhansky–Muller incompatibilities (DMIs) reinforce the genetic barrier through selection against hybrids. In particular, we are interested in the maximum strength of the barrier under a limited amount of local adaptation, a challenge that many incipient species may initially face. We first confirm that with classical two-locus DMIs, the maximum amount of local adaptation is indeed a limit to the strength of a genetic barrier. However, with three or more loci and cryptic epistasis, this limit holds no longer. In particular, we identify a minimal configuration of three epistatically interacting mutations that is sufficient to confer strong reproductive isolation. 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)
- Alexandre Blanckaert
- Department of Mathematics, University of Vienna, 1090 Vienna, Austria.,Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
| | - Claudia Bank
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
| | - Joachim Hermisson
- Department of Mathematics, University of Vienna, 1090 Vienna, Austria.,Mathematics and Biosciences Group, Max Perutz Lab, 1030 Vienna, Austria
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15
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Feng L, Ruhsam M, Wang YH, Li ZH, Wang XM. Using demographic model selection to untangle allopatric divergence and diversification mechanisms in the Rheum palmatum complex in the Eastern Asiatic Region. Mol Ecol 2020; 29:1791-1805. [PMID: 32306487 DOI: 10.1111/mec.15448] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 03/30/2020] [Accepted: 04/08/2020] [Indexed: 12/22/2022]
Abstract
Allopatric divergence is often initiated by geological uplift and restriction to sky-islands, climate oscillations, or river capture. However, it can be difficult to establish which mechanism was the most likely to generate the current phylogeographical structure of a species. Recently, genomic data in conjunction with a model testing framework have been applied to address this issue in animals. To test whether such an approach is also likely to be successful in plants, we used population genomic data of the Rheum palmatum complex from the Eastern Asiatic Region, in conjunction with biogeographical reconstruction and demographic model selection, to identify the potential mechanism(s) which have led to the current level of divergence. Our results indicate that the R. palmatum complex originated in the central Hengduan Mts and possibly in regions further east, and then dispersed westward and eastward resulting in genetically distinct lineages. Populations are likely to have diverged in refugia during climate oscillations followed by subsequent expansion and secondary contact. However, model simulations within the western lineage of the R. palmatum complex cannot reject a restriction to sky-islands as a possible mechanism of diversification due to the genetically ambiguous position of one population. This highlights that genetically mixed populations might introduce ambiguity regarding the best diversification model in some cases. Although it might be possible to resolve this ambiguity using other data, sometimes this could prove to be difficult in complex biogeographical areas.
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Affiliation(s)
- Li Feng
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, China.,Key Laboratory of Qiyao Resources and Anti-tumor Activities, Shaanxi Administration of Traditional Chinese Medicine, School of Pharmacy, Xi'an Jiaotong University, Xi'an, China
| | | | - Yi-Han Wang
- College of Life Sciences, Henan Agriculture University, Zhengzhou, China
| | - Zhong-Hu Li
- College of Life Sciences, Northwest University, Xi'an, China
| | - Xu-Mei Wang
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, China.,Key Laboratory of Qiyao Resources and Anti-tumor Activities, Shaanxi Administration of Traditional Chinese Medicine, School of Pharmacy, Xi'an Jiaotong University, Xi'an, China
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16
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Papadopulos AST, Igea J, Smith TP, Hutton I, Baker WJ, Butlin RK, Savolainen V. Ecological speciation in sympatric palms: 4. Demographic analyses support speciation of
Howea
in the face of high gene flow. Evolution 2019; 73:1996-2002. [DOI: 10.1111/evo.13813] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 07/04/2019] [Accepted: 07/16/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Alexander S. T. Papadopulos
- Department of Life SciencesSilwood Park CampusImperial College London Ascot SL5 7PY United Kingdom
- Molecular Ecology and Fisheries Genetics LaboratoryEnvironment Centre WalesSchool of Natural SciencesBangor University Bangor LL57 2UW United Kingdom
| | - Javier Igea
- Department of Life SciencesSilwood Park CampusImperial College London Ascot SL5 7PY United Kingdom
- Department of Plant SciencesUniversity of Cambridge Cambridge CB2 3EA United Kingdom
| | - Thomas P. Smith
- Department of Life SciencesSilwood Park CampusImperial College London Ascot SL5 7PY United Kingdom
| | - Ian Hutton
- Lord Howe Island Museum Lord Howe Island New South Wales Australia
| | | | - Roger K. Butlin
- Department of Animal and Plant SciencesUniversity of Sheffield Sheffield S10 2TN United Kingdom
- Department of Marine SciencesUniversity of Gothenburg Gothenburg SE‐405 30 Sweden
| | - Vincent Savolainen
- Department of Life SciencesSilwood Park CampusImperial College London Ascot SL5 7PY United Kingdom
- Royal Botanic Gardens, Kew Richmond TW9 3AB United Kingdom
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17
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Wang X, Que P, Heckel G, Hu J, Zhang X, Chiang CY, Zhang N, Huang Q, Liu S, Martinez J, Pagani-Núñez E, Dingle C, Leung YY, Székely T, Zhang Z, Liu Y. Genetic, phenotypic and ecological differentiation suggests incipient speciation in two Charadrius plovers along the Chinese coast. BMC Evol Biol 2019; 19:135. [PMID: 31248363 PMCID: PMC6598359 DOI: 10.1186/s12862-019-1449-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 05/29/2019] [Indexed: 02/01/2023] Open
Abstract
Background Speciation with gene flow is an alternative to the nascence of new taxa in strict allopatric separation. Indeed, many taxa have parapatric distributions at present. It is often unclear if these are secondary contacts, e.g. caused by past glaciation cycles or the manifestation of speciation with gene flow, which hampers our understanding of how different forces drive diversification. Here we studied genetic, phenotypic and ecological aspects of divergence in a pair of incipient shorebird species, the Kentish (Charadrius alexandrinus) and the White-faced Plovers (C. dealbatus), shorebirds with parapatric breeding ranges along the Chinese coast. We assessed divergence based on molecular markers with different modes of inheritance and quantified phenotypic and ecological divergence in aspects of morphometric, dietary and climatic niches. Results Our integrative analyses revealed small to moderate levels of genetic and phenotypic distinctiveness with symmetric gene flow across the contact area at the Chinese coast. The two species diverged approximately half a million years ago in dynamic isolation with secondary contact occurring due to cycling sea level changes between the Eastern and Southern China Sea in the mid-late Pleistocene. We found evidence of character displacement and ecological niche differentiation between the two species, invoking the role of selection in facilitating divergence despite gene flow. Conclusion These findings imply that ecology can indeed counter gene flow through divergent selection and thus contributes to incipient speciation in these plovers. Furthermore, our study highlights the importance of using integrative datasets to reveal the evolutionary history and assist the inference of mechanisms of speciation. Electronic supplementary material The online version of this article (10.1186/s12862-019-1449-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xuejing Wang
- State Key Laboratory of Biocontrol, Department of Ecology, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.,Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012, Bern, Switzerland
| | - Pinjia Que
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Gerald Heckel
- Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012, Bern, Switzerland.,Swiss Institute of Bioinformatics, Genopode, 1015, Lausanne, Switzerland
| | - Junhua Hu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Xuecong Zhang
- State Key Laboratory of Biocontrol, Department of Ecology, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Chung-Yu Chiang
- Department of Environmental Science, Tunhai University, Taichun, Taiwan
| | - Nan Zhang
- State Key Laboratory of Biocontrol, Department of Ecology, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Qin Huang
- State Key Laboratory of Biocontrol, Department of Ecology, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Simin Liu
- State Key Laboratory of Biocontrol, Department of Ecology, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | | | - Emilio Pagani-Núñez
- State Key Laboratory of Biocontrol, Department of Ecology, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Caroline Dingle
- School of Biological Sciences, The University of Hong Kong, Hong Kong, SAR, China
| | - Yu Yan Leung
- School of Biological Sciences, The University of Hong Kong, Hong Kong, SAR, China
| | - Tamás Székely
- State Key Laboratory of Biocontrol, Department of Ecology, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.,Milner Center for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, BA1 7AY, UK
| | - Zhengwang Zhang
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Yang Liu
- State Key Laboratory of Biocontrol, Department of Ecology, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
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18
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Feng S, Ru D, Sun Y, Mao K, Milne R, Liu J. Trans-lineage polymorphism and nonbifurcating diversification of the genus Picea. THE NEW PHYTOLOGIST 2019; 222:576-587. [PMID: 30415488 DOI: 10.1111/nph.15590] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Accepted: 11/02/2018] [Indexed: 06/09/2023]
Abstract
Nonbifurcating divergence caused by introgressive hybridization is continuously reported for groups of closely related species. In this study, we aimed to reconstruct the genome-scale classification of deep lineages of the conifer genus Picea, establish their phylogenetic relationships and test the bifurcating hypothesis between deeply branching lineages based on genomic data. We sequenced the transcriptomes of 35 individuals of 27 taxa covering all main lineages of the genus. Four major lineages, comprising three to 12 taxa each, largely consistent with morphological evidence, were recovered across the coalescent and integrated nuclear phylogeny. However, many of the individual gene trees recovered contradict one another. Moreover, the well-supported coalescent tree inferred here differs from previous studies based on various DNA markers, with respect to topology and inter-lineage relationships. We identified the shared polymorphisms between four major lineages. ABBA-BABA tests confirmed the inter-lineage gene flow and thus violated the bifurcating divergence model. Gene flow occurred more frequently between lineages distributed in the same continent than those disjunct between continents. Our results indicate that introgression and nonbifurcating diversification apply, even between deeply branching lineages of the conifer genus Picea.
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Affiliation(s)
- Shuo Feng
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Dafu Ru
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610064, China
| | - Yongshuai Sun
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610064, China
| | - Kangshan Mao
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610064, China
| | - Richard Milne
- Institute of Molecular Plant Sciences, School of Biological Sciences, The University of Edinburgh, Daniel Rutherford Building, The King's Buildings, Mayfield Road, Edinburgh, EH9 3JH, UK
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610064, China
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19
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Abbott RJ. A mixing-isolation-mixing model of speciation can potentially explain hotspots of species diversity. Natl Sci Rev 2019; 6:290-291. [PMID: 34691866 PMCID: PMC8291541 DOI: 10.1093/nsr/nwy112] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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20
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Peñalba JV, Joseph L, Moritz C. Current geography masks dynamic history of gene flow during speciation in northern Australian birds. Mol Ecol 2019; 28:630-643. [PMID: 30561150 DOI: 10.1111/mec.14978] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 12/11/2018] [Accepted: 12/12/2018] [Indexed: 12/25/2022]
Abstract
Genome divergence is greatly influenced by gene flow during early stages of speciation. As populations differentiate, geographic barriers can constrain gene flow and so affect the dynamics of divergence and speciation. Current geography, specifically disjunction and continuity of ranges, is often used to predict the historical gene flow during the divergence process. We test this prediction in eight meliphagoid bird species complexes codistributed in four regions. These regions are separated by known biogeographical barriers across northern Australia and Papua New Guinea. We find that bird populations currently separated by terrestrial habitat barriers within Australia and marine barriers between Australia and Papua New Guinea have a range of divergence levels and probability of gene flow not associated with current range connectivity. Instead, geographic distance and historical range connectivity better predict divergence and probability of gene flow. In this dynamic environmental context, we also find support for a nonlinear decrease of the probability of gene flow during the divergence process. The probability of gene flow initially decreases gradually after a certain level of divergence is reached. Its decrease then accelerates until the probability is close to zero. This implies that although geographic connectivity may have more of an effect early in speciation, other factors associated with higher divergence may play a more important role in influencing gene flow midway through and later in speciation. Current geographic connectivity may then mislead inferences regarding potential for gene flow during speciation under a complex and dynamic history of geographic and reproductive isolation.
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Affiliation(s)
- Joshua V Peñalba
- Ecology and Evolution, Australian National University, Acton, ACT, Australia.,Centre for Biodiversity Analysis, Acton, ACT, Australia.,Australian National Wildlife Collection, CSIRO National Research Collections Australia, Canberra, Canberra, ACT, Australia.,Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität Munich, Planegg-Martinsried, Germany
| | - Leo Joseph
- Centre for Biodiversity Analysis, Acton, ACT, Australia.,Australian National Wildlife Collection, CSIRO National Research Collections Australia, Canberra, Canberra, ACT, Australia
| | - Craig Moritz
- Ecology and Evolution, Australian National University, Acton, ACT, Australia.,Centre for Biodiversity Analysis, Acton, ACT, Australia
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21
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Myers EA, Bryson RW, Hansen RW, Aardema ML, Lazcano D, Burbrink FT. Exploring Chihuahuan Desert diversification in the gray-banded kingsnake, Lampropeltis alterna (Serpentes: Colubridae). Mol Phylogenet Evol 2019; 131:211-218. [DOI: 10.1016/j.ympev.2018.10.031] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 10/23/2018] [Accepted: 10/23/2018] [Indexed: 12/20/2022]
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22
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He Z, Li X, Yang M, Wang X, Zhong C, Duke NC, Wu CI, Shi S. Speciation with gene flow via cycles of isolation and migration: insights from multiple mangrove taxa. Natl Sci Rev 2018; 6:275-288. [PMID: 31258952 PMCID: PMC6599600 DOI: 10.1093/nsr/nwy078] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Allopatric speciation requiring an unbroken period of geographical isolation has been the standard model of neo-Darwinism. While doubts have been repeatedly raised, strict allopatry without any gene flow remains a plausible mechanism in most cases. To rigorously reject strict allopatry, genomic sequences superimposed on the geological records of a well-delineated geographical barrier are necessary. The Strait of Malacca, narrowly connecting the Pacific and Indian Ocean coasts, serves at different times either as a geographical barrier or a conduit of gene flow for coastal/marine species. We surveyed 1700 plants from 29 populations of 5 common mangrove species by large-scale DNA sequencing and added several whole-genome assemblies. Speciation between the two oceans is driven by cycles of isolation and gene flow due to the fluctuations in sea level leading to the opening/closing of the Strait to ocean currents. Because the time required for speciation in mangroves is longer than the isolation phases, speciation in these mangroves has proceeded through many cycles of mixing-isolation-mixing, or MIM, cycles. The MIM mechanism, by relaxing the condition of no gene flow, can promote speciation in many more geographical features than strict allopatry can. Finally, the MIM mechanism of speciation is also efficient, potentially yielding mn (m > 1) species after n cycles.
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Affiliation(s)
- Ziwen He
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Xinnian Li
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Ming Yang
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Xinfeng Wang
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Cairong Zhong
- Hainan Dongzhai Harbor National Nature Reserve Administration, Haikou 571129, China
| | - Norman C Duke
- Centre for Tropical Water and Aquatic Ecosystem Research, James Cook University, Townsville 4811, Australia
| | - Chung-I Wu
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,Department of Ecology and Evolution, University of Chicago, Chicago IL 60637, USA
| | - Suhua Shi
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
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23
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The Limits to Parapatric Speciation II: Strengthening a Preexisting Genetic Barrier to Gene Flow in Parapatry. Genetics 2018; 209:241-254. [PMID: 29496748 PMCID: PMC5937195 DOI: 10.1534/genetics.117.300652] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 02/27/2018] [Indexed: 11/25/2022] Open
Abstract
By encompassing the whole continuum between allopatric and sympatric scenarios, parapatric speciation includes many potential scenarios for the evolution of new species. Here, we investigate how a genetic barrier to gene flow, that relies on a single postzygotic genetic incompatibility, may further evolve under ongoing migration. We consider a continent island model with three loci involved in pairwise Dobzhansky–Muller incompatibilities (DMIs). Using an analytic approach, we derive the conditions for invasion of a new mutation and its consequences for the strength and stability of the initial genetic barrier. Our results show that the accumulation of genetic incompatibilities in the presence of gene flow is under strong selective constraints. In particular, preexisting incompatibilities do not always facilitate the invasion of further barrier genes. If new mutations do invade, they will often weaken or destroy the barrier rather than strengthening it. We conclude that migration is highly effective at disrupting the so-called “snowball effect”, the accelerated accumulation of DMIs that has been described for allopatric populations en route to reproductive isolation.
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24
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25
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Foote AD. Sympatric Speciation in the Genomic Era. Trends Ecol Evol 2017; 33:85-95. [PMID: 29198471 DOI: 10.1016/j.tree.2017.11.003] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 11/03/2017] [Accepted: 11/07/2017] [Indexed: 10/18/2022]
Abstract
Sympatric speciation has been of key interest to biologists investigating how natural and sexual selection drive speciation without the confounding variable of geographic isolation. The advent of the genomic era has provided a more nuanced and quantitative understanding of the different and often complex modes of speciation by which sympatric sister taxa arose, and a reassessment of some of the most compelling empirical case studies of sympatric speciation. However, I argue that genomic studies based on contemporary populations may never be able to provide unequivocal evidence of true primary sympatric speciation, and there is a need to incorporate palaeogenomic studies into this field. This inability to robustly distinguish cases of primary and secondary 'divergence with gene flow' may be inconsequential, as both are useful for understanding the role of large effect barrier loci in the progression from localised genic isolation to genome-wide reproductive isolation. I argue that they can be of equivalent interest due to shared underlying mechanisms driving divergence and potentially leaving similar patterns of coalescence.
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Affiliation(s)
- Andrew D Foote
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK.
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26
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Guerrero RF, Hahn MW. Speciation as a sieve for ancestral polymorphism. Mol Ecol 2017; 26:5362-5368. [DOI: 10.1111/mec.14290] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 07/27/2017] [Accepted: 08/02/2017] [Indexed: 12/12/2022]
Affiliation(s)
| | - Matthew W. Hahn
- Department of Biology Indiana University Bloomington IN USA
- Department of Computer Science Indiana University Bloomington IN USA
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27
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Xu S, He Z, Zhang Z, Guo Z, Guo W, Lyu H, Li J, Yang M, Du Z, Huang Y, Zhou R, Zhong C, Boufford DE, Lerdau M, Wu CI, Duke NC, Shi S. The origin, diversification and adaptation of a major mangrove clade (Rhizophoreae) revealed by whole-genome sequencing. Natl Sci Rev 2017; 4:721-734. [PMID: 31258950 DOI: 10.1093/nsr/nwx065] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Mangroves invade some very marginal habitats for woody plants-at the interface between land and sea. Since mangroves anchor tropical coastal communities globally, their origin, diversification and adaptation are of scientific significance, particularly at a time of global climate change. In this study, a combination of single-molecule long reads and the more conventional short reads are generated from Rhizophora apiculata for the de novo assembly of its genome to a near chromosome level. The longest scaffold, N50 and N90 for the R. apiculata genome, are 13.3 Mb, 5.4 Mb and 1.0 Mb, respectively. Short reads for the genomes and transcriptomes of eight related species are also generated. We find that the ancestor of Rhizophoreae experienced a whole-genome duplication ~70 Myrs ago, which is followed rather quickly by colonization and species diversification. Mangroves exhibit pan-exome modifications of amino acid (AA) usage as well as unusual AA substitutions among closely related species. The usage and substitution of AAs, unique among plants surveyed, is correlated with the rapid evolution of proteins in mangroves. A small subset of these substitutions is associated with mangroves' highly specialized traits (vivipary and red bark) thought to be adaptive in the intertidal habitats. Despite the many adaptive features, mangroves are among the least genetically diverse plants, likely the result of continual habitat turnovers caused by repeated rises and falls of sea level in the geologically recent past. Mangrove genomes thus inform about their past evolutionary success as well as portend a possibly difficult future.
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Affiliation(s)
- Shaohua Xu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Ziwen He
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Zhang Zhang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Zixiao Guo
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Wuxia Guo
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Haomin Lyu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Jianfang Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Ming Yang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Zhenglin Du
- Core Genomic Facility, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yelin Huang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Renchao Zhou
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Cairong Zhong
- Hainan Dongzhai Harbor National Nature Reserve, Haikou 571129, China
| | | | - Manuel Lerdau
- Departments of Environmental Sciences and of Biology, University of Virginia, Charlottesville, VA 22904-4123, USA
| | - Chung-I Wu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China.,Core Genomic Facility, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
| | - Norman C Duke
- Centre for Tropical Water and Aquatic Ecosystem Research, James Cook University, Townsville, QLD 4815, Australia
| | | | - Suhua Shi
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
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