1
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Owens GL, Huang K, Todesco M, Rieseberg LH. Re-evaluating Homoploid Reticulate Evolution in Helianthus Sunflowers. Mol Biol Evol 2023; 40:6989481. [PMID: 36648104 PMCID: PMC9907532 DOI: 10.1093/molbev/msad013] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 01/03/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
Sunflowers of the genus Helianthus are models for hybridization research and contain three of the best-studied examples of homoploid hybrid speciation. To understand a broader picture of hybridization within the annual sunflowers, we used whole-genome resequencing to conduct a phylogenomic analysis and test for gene flow between lineages. We find that all annual sunflower species tested have evidence of admixture, suggesting hybridization was common during the radiation of the genus. Support for the major species tree decreases with increasing recombination rate, consistent with hybridization and introgression contributing to discordant topologies. Admixture graphs found hybridization to be associated with the origins of the three putative hybrid species (Helianthus anomalus, Helianthus deserticola, and Helianthus paradoxus). However, the hybridization events are more ancient than suggested by previous work. Furthermore, H. anomalus and H. deserticola appear to have arisen from a single hybridization event involving an unexpected donor, rather than through multiple independent events as previously proposed. This means our results are consistent with, but not definitive proof of, two ancient independent homoploid hybrid speciation events in the genus. Using a broader data set that covers the whole Helianthus genus, including perennial species, we find that signals of introgression span the genus and beyond, suggesting highly divergent introgression and/or the sorting of ancient haplotypes. Thus, Helianthus can be viewed as a syngameon in which largely reproductively isolated species are linked together by occasional or frequent gene flow.
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Affiliation(s)
| | - Kaichi Huang
- Department of Botany and Beaty Biodiversity Center, University of British Columbia, Vancouver, BC, Canada
| | - Marco Todesco
- Department of Botany and Beaty Biodiversity Center, University of British Columbia, Vancouver, BC, Canada
| | - Loren H Rieseberg
- Department of Botany and Beaty Biodiversity Center, University of British Columbia, Vancouver, BC, Canada
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2
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Alexander A, Robbins MB, Holmes J, Moyle RG, Peterson AT. Limited movement of an avian hybrid zone in relation to regional variation in magnitude of climate change. Mol Ecol 2022; 31:6634-6648. [PMID: 36210655 PMCID: PMC9729445 DOI: 10.1111/mec.16727] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 09/26/2022] [Accepted: 09/28/2022] [Indexed: 01/13/2023]
Abstract
Studies of natural hybrid zones can provide documentation of range shifts in response to climate change and identify loci important to reproductive isolation. Using a temporal (36-38 years) comparison of the black-capped (Poecile atricapillus) and Carolina (P. carolinensis) chickadee hybrid zone, we investigated movement of the western portion of the zone (western Missouri) and assessed whether loci and pathways underpinning reproductive isolation were similar to those in the eastern portion of the hybrid zone. Using 92 birds sampled along the hybrid zone transect in 2016 and 68 birds sampled between 1978 and 1980, we generated 11,669 SNPs via ddRADseq. These SNPs were used to assess movement of the hybrid zone through time and to evaluate variation in introgression among loci. We demonstrate that the interface has moved ~5 km to the northwest over the last 36-38 years, that is, at only one-fifth the rate at which the eastern portion (e.g., Pennsylvania, Ohio) of the hybrid zone has moved. Temperature trends over the last 38 years reveal that eastern areas have warmed 50% more than western areas in terms of annual mean temperature, possibly providing an explanation for the slower movement of the hybrid zone in Missouri. Our results suggest hybrid zone movement in broadly distributed species, such as chickadees, will vary between areas in response to local differences in the impacts of climate change.
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Affiliation(s)
- Alana Alexander
- Biodiversity Institute, University of Kansas, Lawrence, Kansas 66045, USA.,Department of Anatomy, University of Otago, Dunedin 9016, New Zealand.,Corresponding author.
| | - Mark B. Robbins
- Biodiversity Institute, University of Kansas, Lawrence, Kansas 66045, USA
| | - Jesse Holmes
- Biodiversity Institute, University of Kansas, Lawrence, Kansas 66045, USA.,Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas 66045, USA
| | - Robert G. Moyle
- Biodiversity Institute, University of Kansas, Lawrence, Kansas 66045, USA.,Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas 66045, USA
| | - A. Townsend Peterson
- Biodiversity Institute, University of Kansas, Lawrence, Kansas 66045, USA.,Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas 66045, USA
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3
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Ranathunge C, Chimahusky ME, Welch ME. A comparative study of population genetic structure reveals patterns consistent with selection at functional microsatellites in common sunflower. Mol Genet Genomics 2022; 297:1329-1342. [PMID: 35786764 DOI: 10.1007/s00438-022-01920-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 06/16/2022] [Indexed: 10/17/2022]
Abstract
Microsatellites, also known as short tandem repeats (STRs), have long been considered non-functional, neutrally evolving regions of the genome. Recent findings suggest that they can function as drivers of rapid adaptive evolution. Previous work on the common sunflower identified 479 transcribed microsatellites where allele length significantly correlates with gene expression (eSTRs) in a stepwise manner. Here, a population genetic approach is used to test whether eSTR allele length variation is under selection. Genotypic variation among and within populations at 13 eSTRs was compared with that at 19 anonymous microsatellites in 672 individuals from 17 natural populations of sunflower from across a cline running from Saskatchewan to Oklahoma (distance of approximately 1600 km). Expected heterozygosity, allelic richness, and allelic diversity were significantly lower at eSTRs, a pattern consistent with higher relative rates of purifying selection. Further, an analysis of variation in microsatellite allele lengths (lnRV), and heterozygosities (lnRH), indicate recent selective sweeps at the eSTRs. Mean microsatellite allele lengths at four eSTRs within populations are significantly correlated with latitude consistent with the predictions of the tuning-knob model which predicts stepwise relationships between microsatellite allele length and phenotypes. This finding suggests that shorter or longer alleles at eSTRs may be favored in climatic extremes. Collectively, our results imply that eSTRs are likely under selection and that they may be playing a role in facilitating local adaptation across a well-defined cline in the common sunflower.
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Affiliation(s)
- Chathurani Ranathunge
- Department of Biological Sciences, Mississippi State University, Starkville, MS, 39762, USA.
- School of Health Professions, Eastern Virginia Medical School, Norfolk, VA, 23507, USA.
| | - Melody E Chimahusky
- Department of Biological Sciences, Mississippi State University, Starkville, MS, 39762, USA
| | - Mark E Welch
- Department of Biological Sciences, Mississippi State University, Starkville, MS, 39762, USA
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4
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Goebl AM, Doak DF, Kane NC. Empirical test of increasing genetic variation via inter‐population crossing for native plant restoration in variable environments. Restor Ecol 2022. [DOI: 10.1111/rec.13648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- April M. Goebl
- Department of Ecology & Evolutionary Biology University of Colorado Boulder CO USA 80302
| | - Daniel F. Doak
- Environmental Studies Program University of Colorado Boulder CO USA 80303
| | - Nolan C. Kane
- Department of Ecology & Evolutionary Biology University of Colorado Boulder CO USA 80302
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5
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Guo M, Pang X, Xu Y, Jiang W, Liao B, Yu J, Xu J, Song J, Chen S. Plastid genome data provide new insights into the phylogeny and evolution of the genus Epimedium. J Adv Res 2022; 36:175-185. [PMID: 35127172 PMCID: PMC8799909 DOI: 10.1016/j.jare.2021.06.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 05/14/2021] [Accepted: 06/26/2021] [Indexed: 10/25/2022] Open
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6
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Nagasawa K, Setoguchi H, Maki M, Sawa K, Horie K, Sakaguchi S. Species cohesion of an extremophyte (Carex angustisquama, Cyperaceae) in solfatara fields maintained under interspecific natural hybridization. ANNALS OF BOTANY 2021; 128:343-356. [PMID: 34104952 PMCID: PMC8389175 DOI: 10.1093/aob/mcab069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 05/30/2021] [Indexed: 05/28/2023]
Abstract
BACKGROUND AND AIMS Hybridization is the main driver of plant diversification, and gene flow via hybridization has multifaceted effects on plant evolution. Carex angustisquama is an extremophyte that grows on soils heavily acidified by volcanism. Despite its habitat distinct from that of other species, this species is known to form interspecific hybrids, implying interspecific gene flow. It is crucial to verify the extent and direction of interspecific gene flow between C. angustisquama and closely related species to understand the evolutionary process of an extremophyte in solfatara fields. METHODS In this study, expressed sequence tag-simple sequence repeat markers were utilized to infer the extent and direction of interspecific gene flow between C. angustisquama and closely related species. KEY RESULTS Bayesian clustering and simulation analyses revealed that all individuals of the three hybrid species were classified into the first hybrid generation or first backcross to C. angustisquama; therefore, current interspecific gene flow is limited. Moreover, in the Bayesian inference of historical gene flow based on multispecies samples, the model that assumed no interspecific gene flow was the most strongly supported across all species pairs, including phylogenetically close but ecologically distinctive species pairs. CONCLUSIONS Our results revealed that interspecific gene flow between C. angustisquama and its related species has been limited both currently and historically. Moreover, our results of Bayesian inference of historical gene flow indicated that extrinsic, rather than intrinsic, factors probably act as isolating barriers between Carex species, with hybrid breakdown via microhabitat segregation being the probable potential barrier. Overall, our findings provide insights into the evolutionary process of an extremophyte in solfatara fields and offer an important example of the mechanisms of diversification of the speciose genus Carex.
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Affiliation(s)
- Koki Nagasawa
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-nihonmatsu-cho, Sakyo-ku, Kyoto, Japan
| | - Hiroaki Setoguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-nihonmatsu-cho, Sakyo-ku, Kyoto, Japan
| | - Masayuki Maki
- Botanical Gardens, Tohoku University, Kawauchi, Sendai, Japan
| | | | - Kenji Horie
- Asahikawa City Northern Wild Plants Garden, Asahikawa, Japan
| | - Shota Sakaguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-nihonmatsu-cho, Sakyo-ku, Kyoto, Japan
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7
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Owens GL, Todesco M, Bercovich N, Légaré JS, Mitchell N, Whitney KD, Rieseberg LH. Standing variation rather than recent adaptive introgression probably underlies differentiation of the texanus subspecies of Helianthus annuus. Mol Ecol 2021; 30:6229-6245. [PMID: 34080243 DOI: 10.1111/mec.16008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 05/17/2021] [Accepted: 05/26/2021] [Indexed: 12/24/2022]
Abstract
The origins of geographic races in wide-ranging species are poorly understood. In Texas, the texanus subspecies of Helianthus annuus has long been thought to have acquired its defining phenotypic traits via introgression from a local congener, H. debilis, but previous tests of this hypothesis were inconclusive. Here, we explore the origins of H. a. texanus using whole genome sequencing data from across the entire range of H. annuus and possible donor species, as well as phenotypic data from a common garden study. We found that although it is morphologically convergent with H. debilis, H. a. texanus has conflicting signals of introgression. Genome wide tests (Patterson's D and TreeMix) only found evidence of introgression from H. argophyllus (sister species to H. annuus and also sympatric), but not H. debilis, with the exception of one individual of 109 analysed. We further scanned the genome for localized signals of introgression using PCAdmix and found minimal but nonzero introgression from H. debilis and significant introgression from H. argophyllus in some populations. Given the paucity of introgression from H. debilis, we argue that the morphological convergence observed in Texas is probably from standing genetic variation. We also found that genomic differentiation in H. a. texanus is mostly driven by large segregating inversions, several of which have signatures of natural selection based on haplotype frequencies.
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Affiliation(s)
- Gregory L Owens
- Department of Biology, University of Victoria, Victoria, BC, Canada
| | - Marco Todesco
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Natalia Bercovich
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Jean-Sébastien Légaré
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Nora Mitchell
- Department of Biology, University of Wisconsin - Eau Claire, Eau Claire, WI, USA.,Department of Biology, University of New Mexico, Albuquerque, NM, USA
| | - Kenneth D Whitney
- Department of Biology, University of New Mexico, Albuquerque, NM, USA
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
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8
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Bangs MR, Douglas MR, Brunner PC, Douglas ME. Reticulate evolution as a management challenge: Patterns of admixture with phylogenetic distance in endemic fishes of western North America. Evol Appl 2020; 13:1400-1419. [PMID: 32684966 PMCID: PMC7359839 DOI: 10.1111/eva.13042] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 05/20/2020] [Accepted: 05/26/2020] [Indexed: 12/12/2022] Open
Abstract
Admixture in natural populations is a long-standing management challenge, with population genomic approaches offering means for adjudication. We now more clearly understand the permeability of species boundaries and the potential of admixture for promoting adaptive evolution. These issues particularly resonate in western North America, where tectonism and aridity have fragmented and reshuffled rivers over millennia, in turn promoting reticulation among endemic fishes, a situation compounded by anthropogenic habitat modifications and non-native introductions. The melding of historic and contemporary admixture has both confused and stymied management. We underscore this situation with a case study that quantifies basin-wide admixture among a group of native and introduced fishes by employing double-digest restriction site-associated DNA (ddRAD) sequencing. Our approach: (a) quantifies the admixed history of 343 suckers (10 species of Catostomidae) across the Colorado River Basin; (b) gauges admixture within the context of phylogenetic distance and "ecological specialization"; and (c) extrapolates potential drivers of introgression across hybrid crosses that involve endemic as well as invasive species. Our study extends across an entire freshwater basin and expands previous studies more limited in scope both geographically and taxonomically. Our results detected admixture involving all 10 species, with habitat alterations not only accelerating the breakdown of reproductive isolation, but also promoting introgression. Hybridization occurred across the genus despite phylogenetic distance, whereas introgression was only detected within subgenera, implicating phylogenetic distance and/or ecological specialization as drivers of reproductive isolation. Understanding the extent of admixture and reproductive isolation across multiple species serves to disentangle their reticulate evolutionary histories and provides a broadscale perspective for basin-wide conservation and management.
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Affiliation(s)
- Max R. Bangs
- Department of Biological SciencesUniversity of ArkansasFayettevilleARUSA
- Department of Biological SciencesFlorida State UniversityTallahasseeFLUSA
| | - Marlis R. Douglas
- Department of Biological SciencesUniversity of ArkansasFayettevilleARUSA
| | - Patrick C. Brunner
- Integrative BiologySwiss Federal Institute of Technology (ETH)ZürichSwitzerland
| | - Michael E. Douglas
- Department of Biological SciencesUniversity of ArkansasFayettevilleARUSA
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9
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Unraveling the Chloroplast Genomes of Two Prosopis Species to Identify Its Genomic Information, Comparative Analyses and Phylogenetic Relationship. Int J Mol Sci 2020; 21:ijms21093280. [PMID: 32384622 PMCID: PMC7247323 DOI: 10.3390/ijms21093280] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 04/14/2020] [Accepted: 04/23/2020] [Indexed: 12/18/2022] Open
Abstract
Genus Prosopis (family Fabaceae) are shrubby trees, native to arid and semi-arid regions of Asia, Africa, and America and known for nitrogen fixation. Here, we have sequenced the complete chloroplast (cp) genomes of two Prosopis species (P. juliflora and P. cineraria) and compared them with previously sequenced P. glandulosa, Adenanthera microsperma, and Parkia javanica belonging to the same family. The complete genome sequences of Prosopis species and related species ranged from 159,389 bp (A. microsperma) to 163,677 bp (P. cineraria). The overall GC contents of the genomes were almost the similar (35.9–36.6%). The P. juliflora and P. cineraria genomes encoded 132 and 131 genes, respectively, whereas both the species comprised of 85 protein-coding genes higher than other compared species. About 140, 134, and 129 repeats were identified in P. juliflora, P. cineraria and P. glandulosa cp genomes, respectively. Similarly, the maximum number of simple sequence repeats were determined in P. juliflora (88), P. cineraria (84), and P. glandulosa (78). Moreover, complete cp genome comparison determined a high degree of sequence similarity among P. juliflora, P. cineraria, and P. glandulosa, however some divergence in the intergenic spacers of A. microsperma and Parkia javanica were observed. The phylogenetic analysis showed that P. juliflora is closer to P. cineraria than P. glandulosa.
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10
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Mason NA, Fletcher NK, Gill BA, Funk WC, Zamudio KR. Coalescent-based species delimitation is sensitive to geographic sampling and isolation by distance. SYST BIODIVERS 2020. [DOI: 10.1080/14772000.2020.1730475] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Nicholas A. Mason
- Department of Ecology and Evolutionary Biology, Cornell University, Corson Hall, Ithaca, New York 14853, USA
| | - Nicholas K. Fletcher
- Department of Ecology and Evolutionary Biology, Cornell University, Corson Hall, Ithaca, New York 14853, USA
| | - Brian A. Gill
- Department of Biology, Colorado State University, Fort Collins, Colorado 80523, USA
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - W. Chris Funk
- Department of Biology, Colorado State University, Fort Collins, Colorado 80523, USA
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Kelly R. Zamudio
- Department of Ecology and Evolutionary Biology, Cornell University, Corson Hall, Ithaca, New York 14853, USA
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11
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Alwadani KG, Janes JK, Andrew RL. Chloroplast genome analysis of box-ironbark Eucalyptus. Mol Phylogenet Evol 2019; 136:76-86. [PMID: 30954587 DOI: 10.1016/j.ympev.2019.04.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 03/25/2019] [Accepted: 04/01/2019] [Indexed: 11/17/2022]
Abstract
Eucalyptus L'Hérit. (Myrtaceae) is a taxonomically complex and highly speciose genus that dominates much of Australia's woody vegetation. However, very little information is available about the molecular biology and chloroplast diversity of certain groups, such as Eucalyptus section Adnataria, which is found in many woodland habitats of eastern Australia. We report four new complete chloroplast genomes of Eucalyptus, including three genomes from species previously lacking any chloroplast reference sequences. Plastomes of E. albens, E. conica, E. crebra and E. melliodora assembled using a de novo approach were shown to be largely identical to each other, and similar in size and structure to previously published chloroplast genomes from Eucalyptus. A total of 132 genes (114 single-copy genes and 18 duplicated genes in the IR regions) were identified, and shown to be highly conserved in terms of gene order, content and organization. Slightly higher divergence in the intergenic spacers was identified through comparative genomic analyses. Chloroplast sequences of 35 additional individuals representing 12 species were assembled using a reference guided approach. Rates of nucleotide substitution varied among the protein coding genes, with 17 genes under possible positive selection, and 29 invariant genes. Phylogenetic analysis of either the whole reconstructed plastome sequences or the individual genes revealed extreme discordance with expected species boundaries or higher-level relationships. Plastome relationships were better predicted by geography than by nuclear DNA or taxonomic relationships, suggesting a substantial influence of gene flow over and above the effects of incomplete lineage sorting. These results provide resources for future research and valuable insights into the prevalence of interspecific gene flow among Eucalyptus species.
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Affiliation(s)
- Khawla G Alwadani
- School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia; Biology Department, Faculty of Science, Jazan University, Saudi Arabia
| | - Jasmine K Janes
- School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia; Biology Department, Faculty of Science and Technology, Vancouver Island University, British Columbia, Canada
| | - Rose L Andrew
- School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia.
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12
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Hübner S, Bercovich N, Todesco M, Mandel JR, Odenheimer J, Ziegler E, Lee JS, Baute GJ, Owens GL, Grassa CJ, Ebert DP, Ostevik KL, Moyers BT, Yakimowski S, Masalia RR, Gao L, Ćalić I, Bowers JE, Kane NC, Swanevelder DZH, Kubach T, Muños S, Langlade NB, Burke JM, Rieseberg LH. Sunflower pan-genome analysis shows that hybridization altered gene content and disease resistance. NATURE PLANTS 2019; 5:54-62. [PMID: 30598532 DOI: 10.1038/s41477-018-0329-0] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 11/15/2018] [Indexed: 05/22/2023]
Abstract
Domesticated plants and animals often display dramatic responses to selection, but the origins of the genetic diversity underlying these responses remain poorly understood. Despite domestication and improvement bottlenecks, the cultivated sunflower remains highly variable genetically, possibly due to hybridization with wild relatives. To characterize genetic diversity in the sunflower and to quantify contributions from wild relatives, we sequenced 287 cultivated lines, 17 Native American landraces and 189 wild accessions representing 11 compatible wild species. Cultivar sequences failing to map to the sunflower reference were assembled de novo for each genotype to determine the gene repertoire, or 'pan-genome', of the cultivated sunflower. Assembled genes were then compared to the wild species to estimate origins. Results indicate that the cultivated sunflower pan-genome comprises 61,205 genes, of which 27% vary across genotypes. Approximately 10% of the cultivated sunflower pan-genome is derived through introgression from wild sunflower species, and 1.5% of genes originated solely through introgression. Gene ontology functional analyses further indicate that genes associated with biotic resistance are over-represented among introgressed regions, an observation consistent with breeding records. Analyses of allelic variation associated with downy mildew resistance provide an example in which such introgressions have contributed to resistance to a globally challenging disease.
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Affiliation(s)
- Sariel Hübner
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada.
- Department of Biotechnology, Tel-Hai Academic College, Upper Galilee, Israel.
- MIGAL-Galilee Research Institute, Kiryat Shmona, Israel.
| | - Natalia Bercovich
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Marco Todesco
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jennifer R Mandel
- Department of Biological Sciences, University of Memphis, Memphis, TN, USA
| | | | | | - Joon S Lee
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Gregory J Baute
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Gregory L Owens
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Christopher J Grassa
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Harvard University Herbaria , Cambridge, MA, USA
| | - Daniel P Ebert
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- The Beef Industry Centre, University of New England, Armidale, New South Wales, Australia
| | - Katherine L Ostevik
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Biology , Duke University, Durham, NC, USA
| | - Brook T Moyers
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, USA
| | - Sarah Yakimowski
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Rishi R Masalia
- Department of Plant Biology, Miller Plant Sciences, University of Georgia, Athens, Georgia, USA
| | - Lexuan Gao
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Irina Ćalić
- Department of Plant Biology, Miller Plant Sciences, University of Georgia, Athens, Georgia, USA
| | - John E Bowers
- Department of Plant Biology, Miller Plant Sciences, University of Georgia, Athens, Georgia, USA
| | - Nolan C Kane
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Dirk Z H Swanevelder
- Agricultural Research Council, Biotechnology Platform, Private Bag X05, Onderstepoort, South Africa
| | - Timo Kubach
- SAP SE, Dietmar-Hopp-Allee 16, Walldorf, Germany
| | - Stephane Muños
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | | | - John M Burke
- Department of Plant Biology, Miller Plant Sciences, University of Georgia, Athens, Georgia, USA
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
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13
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Mota MR, Pinheiro F, Leal BSS, Wendt T, Palma-Silva C. The role of hybridization and introgression in maintaining species integrity and cohesion in naturally isolated inselberg bromeliad populations. PLANT BIOLOGY (STUTTGART, GERMANY) 2019; 21:122-132. [PMID: 30195257 DOI: 10.1111/plb.12909] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 09/06/2018] [Indexed: 05/02/2023]
Abstract
Hybridization is a widespread phenomenon present in numerous lineages across the tree of life. Its evolutionary consequences range from effects on the origin and maintenance, to the loss of biodiversity. We studied genetic diversity and intra- and interspecific gene flow between two sympatric populations of closely-related species, Pitcairnia flammea and P. corcovadensis (Bromeliaceae), which are adapted to naturally fragmented Neotropical inselbergs, based on nuclear and plastidial DNA. Our main results indicate a strong reproductive isolation barrier, although low levels of interspecific gene flow were observed in both sympatric populations. The low rates of intraspecific gene flow observed for both P. corcovadensis and P. flammea populations corroborate the increasing body of evidence that inselberg bromeliad species are maintained as discrete evolutionary units despite the presence of low genetic connectivity. Nuclear patterns of genetic diversity and gene flow revealed that hybridization and introgression might not cause species extinction via genetic assimilation of the rare P. corcovadensis. In the face of reduced intraspecific gene exchange, hybridization and introgression may be important aspects of the Pitcairnia diversification process, with a positive evolutionary impact at the bromeliad community level, and thus contribute to increasing and maintaining genetic diversity in local isolated inselberg populations.
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Affiliation(s)
- M R Mota
- Departamento de Ecologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, Brazil
| | - F Pinheiro
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil
| | - B S S Leal
- Departamento de Ecologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, Brazil
| | - T Wendt
- Departamento de Botânica, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - C Palma-Silva
- Departamento de Ecologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, Brazil
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil
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14
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Andriollo T, Ashrafi S, Arlettaz R, Ruedi M. Porous barriers? Assessment of gene flow within and among sympatric long-eared bat species. Ecol Evol 2018; 8:12841-12854. [PMID: 30619587 PMCID: PMC6309003 DOI: 10.1002/ece3.4714] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 10/18/2018] [Accepted: 10/30/2018] [Indexed: 11/11/2022] Open
Abstract
Species are the basic units for measuring biodiversity and for comprehending biological interactions. Yet, their delineation is often contentious, especially in groups that are both diverse and phenotypically conservative. Three cryptic species of long-eared bats, Plecotus auritus, P. austriacus, and P. macrobullaris, co-occur over extensive areas of Western Europe. The latter is a fairly recent discovery, questioning the overall diversity of the entire Plecotus complex. Yet, high morphological and acoustic similarities compromise the reliable identification of long-eared bats in the field. We postulate that such extensive phenotypic overlap, along with the recurrent observation of morphologically intermediate individuals, may hide rampant interspecific hybridization. Based on a geographic sampling centered on areas of sympatry in the Alps and Corsica, we assessed the level of reproductive isolation of these three Plecotus species with mitochondrial and nuclear markers, looking at both inter- and intraspecific genetic population structuring. No sign of hybridization was detected between these three species that appear well separated biologically. Genetic structuring of populations, however, reflected different species-specific responses to environmental connectivity, that is, to the presence of orographic or sea barriers. While the Alpine range and the Ligurian Sea coincided with sharp genetic discontinuities in P. macrobullaris and P. austriacus, the more ubiquitous P. auritus showed no significant population structuration. There were clear phylogeographic discrepancies between microsatellite and mitochondrial markers at the intraspecific level, however, which challenges the reliance on simple barcoding approaches for the delineation of sound conservation units.
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Affiliation(s)
- Tommy Andriollo
- Department of Mammalogy and OrnithologyNatural History Museum of GenevaGenevaSwitzerland
- Section of Biology, Faculty of SciencesUniversity of GenevaGenevaSwitzerland
| | - Sohrab Ashrafi
- Department of Environmental Sciences, Faculty of Natural ResourcesUniversity of TehranKarajIran
| | - Raphaël Arlettaz
- Division of Conservation Biology, Institute of Ecology and EvolutionUniversity of BernBernSwitzerland
| | - Manuel Ruedi
- Department of Mammalogy and OrnithologyNatural History Museum of GenevaGenevaSwitzerland
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15
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Walsh J, Kovach AI, Olsen BJ, Shriver WG, Lovette IJ. Bidirectional adaptive introgression between two ecologically divergent sparrow species. Evolution 2018; 72:2076-2089. [PMID: 30101975 DOI: 10.1111/evo.13581] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 07/10/2018] [Accepted: 07/31/2018] [Indexed: 12/24/2022]
Abstract
Natural hybrid zones can be used to dissect the mechanisms driving key evolutionary processes by allowing us to identify genomic regions important for establishing reproductive isolation and that allow for transfer of adaptive variation. We leverage whole-genome data in a system where two bird species, the saltmarsh (Ammospiza caudacuta) and Nelson's (A. nelsoni) sparrow, hybridize despite their relatively high background genetic differentiation and past ecological divergence. Adaptive introgression is plausible in this system because Nelson's sparrows are recent colonists of saltwater marshes, compared to the specialized saltmarsh sparrow that has a longer history of saltmarsh adaptation. Comparisons among whole-genome sequences of 34 individuals from allopatric and sympatric populations show that ongoing gene flow is shaping the genomic landscape, with allopatric populations exhibiting genome-wide FST estimates close to double of that observed in sympatry. We characterized patterns of introgression across the genome and identify regions that exhibit biased introgression into hybrids from one parental species. These regions offer compelling candidates for genes related to tidal marsh adaptations suggesting that adaptive introgression may be an important consequence of hybridization. These findings highlight the value of considering the landscapes of both genome-wide introgression and divergence when characterizing the evolutionary forces that drive speciation.
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Affiliation(s)
- Jennifer Walsh
- Fuller Evolutionary Biology Program, Cornell Laboratory of Ornithology, Ithaca, New York 14850.,Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York 14853
| | - Adrienne I Kovach
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, New Hampshire 03824
| | - Brian J Olsen
- School of Biology and Ecology, University of Maine, Orono, Maine 04469
| | - W Gregory Shriver
- Department of Entomology and Wildlife Ecology, University of Delaware, Newark, Delaware 19716
| | - Irby J Lovette
- Fuller Evolutionary Biology Program, Cornell Laboratory of Ornithology, Ithaca, New York 14850.,Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York 14853
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16
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Lee S, Kim B, Kim Y. Genetic diagnosis of a rare myrmecochorous species, Plagiorhegma dubium (Berberidaceae): Historical genetic bottlenecks and strong spatial structures among populations. Ecol Evol 2018; 8:8791-8802. [PMID: 30271546 PMCID: PMC6157670 DOI: 10.1002/ece3.4362] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 06/15/2018] [Accepted: 06/20/2018] [Indexed: 11/17/2022] Open
Abstract
Distribution of genetic variation over time and space is relevant to demographic histories and tightly linked to ecological disturbances as well as evolutionary potential of an organism. Therefore, understanding the pattern of genetic diversity is a primary step in conservation and management projects for rare and threatened plant species. We used eight microsatellite markers to examine the level of genetic diversity, spatial structure, and demographic history of Plagiorhegma dubium, a rare myrmecochorous herb, populations sampled across northeast Asia and Siberia. We found low within-population genetic variation associated with historical bottlenecks. Although pairwise F ST values were not much higher than the ones found in similar life form species, STRUCTURE and PCoA revealed a clear broadscale spatial pattern of genetic structure. Bayesian clustering (best K = 6) and PCoA identified three populations that are distinctive from neighboring populations in the Korean peninsula, which suggests potential units for conservation and management plans in Korea. MIGRATE-N and BAYESASS showed that both contemporary (0.003-0.045) and historical migration rates (2 × e-5-4.6 × e-4) were low. Our findings provide a good example, where genetic considerations should be integrated for conservation and management plans of rare and threatened species.
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Affiliation(s)
- Soo‐Rang Lee
- Multidisciplinary Genome InstituteHallym UniversityChuncheon‐siKorea
| | - Bo‐Yun Kim
- Multidisciplinary Genome InstituteHallym UniversityChuncheon‐siKorea
| | - Young‐Dong Kim
- Department of Life SciencesHallym UniversityChuncheon‐siKorea
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17
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Bangs MR, Douglas MR, Mussmann SM, Douglas ME. Unraveling historical introgression and resolving phylogenetic discord within Catostomus (Osteichthys: Catostomidae). BMC Evol Biol 2018; 18:86. [PMID: 29879898 PMCID: PMC5992631 DOI: 10.1186/s12862-018-1197-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 05/18/2018] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Porous species boundaries can be a source of conflicting hypotheses, particularly when coupled with variable data and/or methodological approaches. Their impacts can often be magnified when non-model organisms with complex histories of reticulation are investigated. One such example is the genus Catostomus (Osteichthys, Catostomidae), a freshwater fish clade with conflicting morphological and mitochondrial phylogenies. The former is hypothesized as reflecting the presence of admixed genotypes within morphologically distinct lineages, whereas the latter is interpreted as the presence of distinct morphologies that emerged multiple times through convergent evolution. We tested these hypotheses using multiple methods, to including multispecies coalescent and concatenated approaches. Patterson's D-statistic was applied to resolve potential discord, examine introgression, and test the putative hybrid origin of two species. We also applied naïve binning to explore potential effects of concatenation. RESULTS We employed 14,007 loci generated from ddRAD sequencing of 184 individuals to derive the first highly supported nuclear phylogeny for Catostomus. Our phylogenomic analyses largely agreed with a morphological interpretation,with the exception of the placement of Xyrauchen texanus, which differs from both morphological and mitochondrial phylogenies. Additionally, our evaluation of the putative hybrid species C. columbianus revealed a lack introgression and instead matched the mitochondrial phylogeny. Furthermore, D-statistic tests clarified all discrepancies based solely on mitochondrial data, with agreement among topologies derived from concatenation and multispecies coalescent approaches. Extensive historic introgression was detected across six species-pairs. Potential endemism in the Virgin and Little Colorado Rivers was also apparent, and the former genus Pantosteus was derived as monophyletic, save for C. columbianus. CONCLUSIONS Complex reticulated histories detected herein support the hypothesis that introgression was responsible for conflicts that occurred within the mitochondrial phylogeny, and explains discrepancies found between it and previous morphological phylogenies. Additionally, the hybrid origin of C. columbianus was refuted, but with the caveat that more fine-grain sampling is still needed. Our diverse phylogenomic approaches provided largely concordant results, with naïve binning useful in exploring the single conflict. Considerable diversity was found within Catostomus across southwestern North America, with two drainages [Virgin River (UT) and Little Colorado River (AZ)] reflecting unique composition.
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Affiliation(s)
- Max R Bangs
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, 72701, USA. .,School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA.
| | - Marlis R Douglas
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Steven M Mussmann
- 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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18
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Menon M, Bagley JC, Friedline CJ, Whipple AV, Schoettle AW, Leal‐Sàenz A, Wehenkel C, Molina‐Freaner F, Flores‐Rentería L, Gonzalez‐Elizondo MS, Sniezko RA, Cushman SA, Waring KM, Eckert AJ. The role of hybridization during ecological divergence of southwestern white pine (
Pinus strobiformis
) and limber pine (
P. flexilis
). Mol Ecol 2018; 27:1245-1260. [DOI: 10.1111/mec.14505] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 12/19/2017] [Accepted: 12/21/2017] [Indexed: 12/11/2022]
Affiliation(s)
- Mitra Menon
- Integrative Life Sciences Virginia Commonwealth University Richmond VA USA
- Department of Biology Virginia Commonwealth University Richmond VA USA
| | - Justin C. Bagley
- Department of Biology Virginia Commonwealth University Richmond VA USA
- Departamento de Zoologia Universidade de Brasília Brasília DF Brazil
| | | | - Amy V. Whipple
- Department of Biological Sciences and Merriam Powel Center for Environmental Research Northern Arizona University Flagstaff AZ USA
| | - Anna W. Schoettle
- Rocky Mountain Research Station USDA Forest Service Ft. Collins CO USA
| | - Alejandro Leal‐Sàenz
- Programa Institucional de Doctorado en Ciencias Agropecuarias y Forestales Universidad Juárez del Estado de Durango Durango Mexico
| | - Christian Wehenkel
- Instituto de Silvicultura e Industria de la Madera Universidad Juarez del Estado de Durango Durango Mexico
| | - Francisco Molina‐Freaner
- Institutos de Geologia y Ecologia Universidad Nacional Autónoma de Mexico, Estación Regional del Noroeste Hermosillo Sonora Mexico
| | | | | | | | - Samuel A. Cushman
- Rocky Mountain Research Station USDA Forest Service Flagstaff AZ USA
| | | | - Andrew J. Eckert
- Department of Biology Virginia Commonwealth University Richmond VA USA
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19
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Schmidt L, Fischer M, Oja T. Two closely related species differ in their regional genetic differentiation despite admixing. AOB PLANTS 2018; 10:ply007. [PMID: 29479408 PMCID: PMC5817946 DOI: 10.1093/aobpla/ply007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 01/09/2018] [Indexed: 06/08/2023]
Abstract
Regional genetic differentiation within species is often addressed in evolutionary ecology and conservation biology. Here, we address regional differentiation in two closely related hybridizing taxa, the perennial sedges Carex flava and C. viridula and their hybrid C. × subviridula in 37 populations in the north and centre of their distribution range in Europe (Estonia, Lowland (<1000 m a.s.l.) and Highland Switzerland) using 10 putative microsatellite loci. We ask whether regional differentiation was larger in the less common taxon C. viridula or whether, possibly due to hybridization, it was similar between taxa. Our results showed similar, low to moderate genetic diversity for the three studied taxa. In total, we found 12 regional species-specific alleles. Analysis of molecular variance (AMOVA), STRUCTURE and multidimensional scaling analysis showed regional structure in genetic variation, where intraspecific differentiation between regions was lower for C. flava (AMOVA: 6.84 %) than for C. viridula (20.77 %) or C. × subviridula (18.27 %) populations. Hybrids differed from the parental taxa in the two regions where they occurred, i.e. in Estonia and Lowland Switzerland. We conclude that C. flava and C. viridula clearly differ from each other genetically, that there is pronounced regional differentiation and that, despite hybridization, this regional differentiation is more pronounced in the less common taxon, C. viridula. We encourage future studies on hybridizing taxa to work with plant populations from more than one region.
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Affiliation(s)
- Lisanna Schmidt
- Institute of Ecology and Earth Sciences, Department of Botany, University of Tartu, Tartu, Estonia
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Markus Fischer
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
- Botanical Garden, University of Bern, Bern, Switzerland
- Oeschger Centre for Climate Change Research, University of Bern, Bern, Switzerland
| | - Tatjana Oja
- Institute of Ecology and Earth Sciences, Department of Botany, University of Tartu, Tartu, Estonia
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20
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Yang Y, Moore MJ, Brockington SF, Mikenas J, Olivieri J, Walker JF, Smith SA. Improved transcriptome sampling pinpoints 26 ancient and more recent polyploidy events in Caryophyllales, including two allopolyploidy events. THE NEW PHYTOLOGIST 2018; 217:855-870. [PMID: 28944472 DOI: 10.1111/nph.14812] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 08/09/2017] [Indexed: 05/14/2023]
Abstract
Studies of the macroevolutionary legacy of polyploidy are limited by an incomplete sampling of these events across the tree of life. To better locate and understand these events, we need comprehensive taxonomic sampling as well as homology inference methods that accurately reconstruct the frequency and location of gene duplications. We assembled a data set of transcriptomes and genomes from 168 species in Caryophyllales, of which 43 transcriptomes were newly generated for this study, representing one of the most densely sampled genomic-scale data sets available. We carried out phylogenomic analyses using a modified phylome strategy to reconstruct the species tree. We mapped the phylogenetic distribution of polyploidy events by both tree-based and distance-based methods, and explicitly tested scenarios for allopolyploidy. We identified 26 ancient and more recent polyploidy events distributed throughout Caryophyllales. Two of these events were inferred to be allopolyploidy. Through dense phylogenomic sampling, we show the propensity of polyploidy throughout the evolutionary history of Caryophyllales. We also provide a framework for utilizing transcriptome data to detect allopolyploidy, which is important as it may have different macroevolutionary implications compared with autopolyploidy.
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Affiliation(s)
- Ya Yang
- Department of Ecology & Evolutionary Biology, University of Michigan, 830 North University Avenue, Ann Arbor, MI, 48109-1048, USA
| | - Michael J Moore
- Department of Biology, Oberlin College, 119 Woodland St, Oberlin, OH, 44074-1097, USA
| | | | - Jessica Mikenas
- Department of Biology, Oberlin College, 119 Woodland St, Oberlin, OH, 44074-1097, USA
| | - Julia Olivieri
- Department of Biology, Oberlin College, 119 Woodland St, Oberlin, OH, 44074-1097, USA
| | - Joseph F Walker
- Department of Ecology & Evolutionary Biology, University of Michigan, 830 North University Avenue, Ann Arbor, MI, 48109-1048, USA
| | - Stephen A Smith
- Department of Ecology & Evolutionary Biology, University of Michigan, 830 North University Avenue, Ann Arbor, MI, 48109-1048, USA
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21
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Mondon A, Owens GL, Poverene M, Cantamutto M, Rieseberg LH. Gene flow in Argentinian sunflowers as revealed by genotyping-by-sequencing data. Evol Appl 2017; 11:193-204. [PMID: 29387155 PMCID: PMC5775495 DOI: 10.1111/eva.12527] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 07/26/2017] [Indexed: 01/04/2023] Open
Abstract
Gene flow can have several different applied consequences, ranging from extinction to the escape of transgenes to the evolution of weedy or invasive lineages. Here, we describe patterns of hybridization and gene flow involving domesticated and wild sunflowers in Argentina. To address the risks of introgression of variants from the cultivated sunflower into invasive wild Helianthus, we used genotyping‐by‐sequencing (GBS) to genotype 182 samples from 11 sites in Argentina, along with previously published data from samples from the native range (North America), to determine the native source populations of the Argentinian samples and to detect admixture. We unexpectedly discovered two distinctive forms of H. petiolaris in Argentina, one from H. petiolaris subsp. petiolaris as expected, but the other from an unknown source. Extensive admixture was observed among Argentinian sunflowers, largely confirming phenotypic predictions. While many hybrids are F1s, there were signals consistent with introgression from the domesticated sunflower into H. petiolaris. Whether this introgression is incidental or a causal driver of invasiveness is not yet clear, but it seems likely that genes found in the domesticated sunflower genome (whether engineered or not) will quickly find their way into wild Argentinian sunflower populations.
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Affiliation(s)
- Ana Mondon
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS) CCT Bahía Blanca Provincia de Buenos Aires Argentina
| | - Gregory L Owens
- Department of Botany and Biodiversity Research Centre University of British Columbia Vancouver BC Canada
| | - Mónica Poverene
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS) CCT Bahía Blanca Provincia de Buenos Aires Argentina.,Dpto. Agronomía Universidad Nacional del Sur (UNS) Bahía Blanca Argentina
| | - Miguel Cantamutto
- Estación Experimental Agropecuaria Instituto Nacional de Tecnología Agropecuaria (INTA) Hilario Ascasubi Argentina
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre University of British Columbia Vancouver BC Canada
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22
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Gong X, Hung KH, Ting YW, Hsu TW, Malikova L, Tran HT, Huang CL, Liu SH, Chiang TY. Frequent gene flow blurred taxonomic boundaries of sections in Lilium L. (Liliaceae). PLoS One 2017; 12:e0183209. [PMID: 28841664 PMCID: PMC5571923 DOI: 10.1371/journal.pone.0183209] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 08/01/2017] [Indexed: 12/13/2022] Open
Abstract
Gene flow between species may last a long time in plants. Reticulation inevitably causes difficulties in phylogenetic reconstruction. In this study, we looked into the genetic divergence and phylogeny of 20 Lilium species based on multilocus analyses of 8 genes of chloroplast DNA (cpDNA), the internally transcribed nuclear ribosomal DNA (nrITS) spacer and 20 loci extracted from the expressed sequence tag (EST) libraries of L. longiflorum Thunb. and L. formosanum Wallace. The phylogeny based on the combined data of the maternally inherited cpDNA and nrITS was largely consistent with the taxonomy of Lilium sections. This phylogeny was deemed the hypothetical species tree and uncovered three groups, i.e., Cluster A consisting of 4 taxa from the sections Pseudolirium and Liriotypus, Cluster B consisting of the 4 taxa from the sections Leucolirion, Archelirion and Daurolirion, and Cluster C comprising 10 taxa mostly from the sections Martagon and Sinomartagon. In contrast, systematic inconsistency occurred across the EST loci, with up to 19 genes (95%) displaying tree topologies deviating from the hypothetical species tree. The phylogenetic incongruence was likely attributable to the frequent genetic exchanges between species/sections, as indicated by the high levels of genetic recombination and the IMa analyses with the EST loci. Nevertheless, multilocus analysis could provide complementary information among the loci on the species split and the extent of gene flow between the species. In conclusion, this study not only detected frequent gene flow among Lilium sections that resulted in phylogenetic incongruence but also reconstructed a hypothetical species tree that gave insights into the nature of the complex relationships among Lilium species.
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Affiliation(s)
- Xun Gong
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Kuo-Hsiang Hung
- Graduate Institute of Bioresources, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Yu-Wei Ting
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Tsai-Wen Hsu
- Endemic Species Research Institute, Nantou, Taiwan
| | - Lenka Malikova
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
- Institute of Botany CAS, Třeboň, Czech Republic
| | - Huyen Trang Tran
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
- Institute of Natural Science Education, Vinh University, Vinh, Nghe An, Vietnam
| | - Chao-Li Huang
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, Taiwan
- * E-mail: (TYC); (SHL); (CLH)
| | - Shih-Hui Liu
- Department of Biology, Saint Louis University, Saint Louis, Missouri, United States of America
- Missouri Botanical Garden, Saint Louis, Missouri, United States of America
- * E-mail: (TYC); (SHL); (CLH)
| | - Tzen-Yuh Chiang
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
- University Center for Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan
- * E-mail: (TYC); (SHL); (CLH)
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23
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Catanese G, Watteaux R, Montes I, Barra M, Rumolo P, Borme D, Buongiorno Nardelli B, Botte V, Mazzocchi MG, Genovese S, Di Capua I, Iriondo M, Estonba A, Ruggeri P, Tirelli V, Caputo-Barucchi V, Basilone G, Bonanno A, Iudicone D, Procaccini G. Insights on the drivers of genetic divergence in the European anchovy. Sci Rep 2017. [PMID: 28646131 PMCID: PMC5482869 DOI: 10.1038/s41598-017-03926-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Anchovies represent the largest world's marine fish catches and the current threats on their populations impose a sustainable exploitment based on sound scientific information. In the European anchovy (Engraulis encrasicolus), the existence of several populations has been proposed but a global view is missing. Using a multidisciplinary approach, here we assessed the divergence among different ecotypes and its possible causes. SNPs have revealed two functionally distinct ecotypes overlapping in the Central Mediterranean, with one ecotype confined near the river estuaries. The same SNPs outliers also segregated two distinct populations in the near Atlantic, despite their large spatial distance. In addition, while most studies suggested that adaptation to low salinity is key to divergence, here we show that the offshore ecotype has higher environmental tolerance and an opportunistic feeding behaviour, as assessed by the study of environmental conditions, anchovy diet and trophic levels, and passive egg dispersal. These results provide insights into the anchovy evolutionary history, stressing the importance of behaviour in shaping ecotypes.
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Affiliation(s)
- Gaetano Catanese
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy.,Laboratorio de Investigaciones Marinas y Acuicultura (LIMIA) Govern de les Illes Balears, Av. Gabriel Roca 69, 07158, Port d'Andratx - Mallorca, Spain
| | - Romain Watteaux
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy
| | - Iratxe Montes
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Sarriena auzoa z/g, Leioa - Bizkaia, Spain
| | - Marco Barra
- Institute for Coastal and Marine Environment (IAMC), Consiglio Nazionale delle Ricerche (CNR), Detached Units of Capo Granitola (TP) and Naples, Napoli, Italy
| | - Paola Rumolo
- Institute for Coastal and Marine Environment (IAMC), Consiglio Nazionale delle Ricerche (CNR), Detached Units of Capo Granitola (TP) and Naples, Napoli, Italy
| | - Diego Borme
- Department of Oceanography, Istituto Nazionale di Oceanografia e di Geofisica Sperimentale (OGS), Via A. Piccard 54, 34151, Trieste, Italy
| | - Bruno Buongiorno Nardelli
- Institute for Coastal and Marine Environment (IAMC), Consiglio Nazionale delle Ricerche (CNR), Detached Units of Capo Granitola (TP) and Naples, Napoli, Italy
| | - Vincenzo Botte
- Institute for Coastal and Marine Environment (IAMC), Consiglio Nazionale delle Ricerche (CNR), Detached Units of Capo Granitola (TP) and Naples, Napoli, Italy
| | - Maria Grazia Mazzocchi
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy
| | - Simona Genovese
- Institute for Coastal and Marine Environment (IAMC), Consiglio Nazionale delle Ricerche (CNR), Detached Units of Capo Granitola (TP) and Naples, Napoli, Italy
| | - Iole Di Capua
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy
| | - Mikel Iriondo
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Sarriena auzoa z/g, Leioa - Bizkaia, Spain
| | - Andone Estonba
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Sarriena auzoa z/g, Leioa - Bizkaia, Spain
| | - Paolo Ruggeri
- Dipartimento di Scienze della Vita e dell'Ambiente (DiSVA), Università Politecnica delle Marche, via Brecce Bianche, 60131, Ancona, Italy.,University of Miami, RSMAS, 4600 Rickenbacker Causeway, 33149, Miami, Florida, USA
| | - Valentina Tirelli
- Department of Oceanography, Istituto Nazionale di Oceanografia e di Geofisica Sperimentale (OGS), Via A. Piccard 54, 34151, Trieste, Italy
| | - Vincenzo Caputo-Barucchi
- Dipartimento di Scienze della Vita e dell'Ambiente (DiSVA), Università Politecnica delle Marche, via Brecce Bianche, 60131, Ancona, Italy
| | - Gualtiero Basilone
- Institute for Coastal and Marine Environment (IAMC), Consiglio Nazionale delle Ricerche (CNR), Detached Units of Capo Granitola (TP) and Naples, Napoli, Italy
| | - Angelo Bonanno
- Institute for Coastal and Marine Environment (IAMC), Consiglio Nazionale delle Ricerche (CNR), Detached Units of Capo Granitola (TP) and Naples, Napoli, Italy.
| | - Daniele Iudicone
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy.
| | - Gabriele Procaccini
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy.
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24
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de Lafontaine G, Bousquet J. Asymmetry matters: A genomic assessment of directional biases in gene flow between hybridizing spruces. Ecol Evol 2017; 7:3883-3893. [PMID: 28616185 PMCID: PMC5468134 DOI: 10.1002/ece3.2682] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 11/16/2016] [Accepted: 11/20/2016] [Indexed: 01/08/2023] Open
Abstract
Assessing directional bias in interspecific gene flow might be important in determining the evolutionary trajectory of closely related species pairs. Using a set of 300 single nucleotide polymorphisms (SNPs) having variable propensity to cross species boundary, we evaluated the genomic extent and direction of interspecific gene flow in a progenitor‐derivative spruce species pair (black spruce and red spruce). A higher rate of gene flow was found from black spruce toward red spruce purebreds than vice versa. This asymmetry could reflect the historical gene flow between the two taxa at the time of species inception and during postglacial colonization. A clear asymmetry in introgression was depicted by a greater gene flow between red spruce and hybrids than between black spruce and hybrids. While backcrossing toward red spruce was invariably high across the genome, the actual species boundary is between hybrids and black spruce where gene flow is impeded at those genomic regions impermeable to introgression. Associations between hybrid index and climatic variables (total annual precipitation and mean annual temperature) were tested, as these might indicate a role for exogenous selection in maintaining the species boundary. While an apparent association was found between the hybrid index and precipitation, it collapsed when considered in light of the directional bias in interspecific gene flow. Hence, considering asymmetrical patterns of introgression allowed us to falsify an apparent role for exogenous selection. Although this was not formerly tested here, we suggest that this pattern could result from asymmetrical endogenous selection, a contention that deserves further investigations.
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Affiliation(s)
- Guillaume de Lafontaine
- Canada Research Chair in Forest Genomics Centre for Forest Research and Institute of Systems and Integrative Biology Université Laval Québec QC Canada.,Department of Plant Biology University of Illinois Urbana IL USA
| | - Jean Bousquet
- Canada Research Chair in Forest Genomics Centre for Forest Research and Institute of Systems and Integrative Biology Université Laval Québec QC Canada
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25
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Hoban S, Kelley JL, Lotterhos KE, Antolin MF, Bradburd G, Lowry DB, Poss ML, Reed LK, Storfer A, Whitlock MC. Finding the Genomic Basis of Local Adaptation: Pitfalls, Practical Solutions, and Future Directions. Am Nat 2016; 188:379-97. [PMID: 27622873 PMCID: PMC5457800 DOI: 10.1086/688018] [Citation(s) in RCA: 438] [Impact Index Per Article: 54.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Uncovering the genetic and evolutionary basis of local adaptation is a major focus of evolutionary biology. The recent development of cost-effective methods for obtaining high-quality genome-scale data makes it possible to identify some of the loci responsible for adaptive differences among populations. Two basic approaches for identifying putatively locally adaptive loci have been developed and are broadly used: one that identifies loci with unusually high genetic differentiation among populations (differentiation outlier methods) and one that searches for correlations between local population allele frequencies and local environments (genetic-environment association methods). Here, we review the promises and challenges of these genome scan methods, including correcting for the confounding influence of a species' demographic history, biases caused by missing aspects of the genome, matching scales of environmental data with population structure, and other statistical considerations. In each case, we make suggestions for best practices for maximizing the accuracy and efficiency of genome scans to detect the underlying genetic basis of local adaptation. With attention to their current limitations, genome scan methods can be an important tool in finding the genetic basis of adaptive evolutionary change.
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Affiliation(s)
- Sean Hoban
- Morton Arboretum, Lisle, Illinois 60532; and National Institute for Mathematical and Biological Synthesis (NIMBioS), Knoxville, Tennessee 37966
| | - Joanna L. Kelley
- School of Biological Sciences, Washington State University, Pullman, Washington 99164
| | - Katie E. Lotterhos
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Nahant, Massachusetts 01908
| | - Michael F. Antolin
- Department of Biology, Colorado State University, Fort Collins, Colorado 80523
| | - Gideon Bradburd
- Museum of Vertebrate Zoology and Department of Environmental Science, Policy, and Management, University of California, Berkeley, California 94720
| | - David B. Lowry
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Mary L. Poss
- Department of Biology and Veterinary and Biomedical Sciences, Penn State University, University Park, Pennsylvania 16802
| | - Laura K. Reed
- Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama 35406
| | - Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, Washington 99164
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26
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Ye Z, Chen P, Bu W. Terrestrial mountain islands and Pleistocene climate fluctuations as motors for speciation: A case study on the genus Pseudovelia (Hemiptera: Veliidae). Sci Rep 2016; 6:33625. [PMID: 27650911 PMCID: PMC5030487 DOI: 10.1038/srep33625] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Accepted: 08/31/2016] [Indexed: 11/08/2022] Open
Abstract
This study investigated the influences of geographic isolation and climate fluctuation on the genetic diversity, speciation, and biogeography of the genus Pseudovelia (Hemiptera: Veliidae) in subtropical China and tropic Indo-China Peninsula. Species nucleotide and haplotype diversities decreased with reduction in species distribution limits. The gene tree was congruent with the taxonomy of monophyly, except for four species, P. contorta, P. extensa, P. tibialis tibialis, and P. vittiformis. The conflicts between the genes and species tree could be due to long-term isolation and incomplete lineage sorting. Diversification analysis showed that the diversification rate (0.08 sp/My shifted to 0.5 sp/My) changed at 2.1 Ma, which occurred in the early Pleistocene period. Ancestral area reconstruction suggested that subtropical species possibly evolved from the tropics region (i.e., Indo-China Peninsula). Results implied that narrow endemics harbored relatively low genetic diversity because of small effective population and genetic drift. Radiation of subtropical Pseudovelia species was rapidly promoted by Pleistocene climate fluctuations and geographic isolation. The acute rising of the Hengduan Mountain with the entire uplift of the Qinghai-Tibet Plateau induced the initial differentiation of Pseudovelia species. These results highlighted the importance of geographical isolation and climate changes in promoting speciation in mountain habitat islands.
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Affiliation(s)
- Zhen Ye
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071,China
- College of Environmental Science and Engineering, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Pingping Chen
- Netherlands Biodiversity Centre – Naturalis, 2300 RA Leiden, The Netherlands
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071,China
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27
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The invasion of Senecio pterophorus across continents: multiple, independent introductions, admixture and hybridization. Biol Invasions 2016. [DOI: 10.1007/s10530-016-1150-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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28
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Bodénès C, Chancerel E, Ehrenmann F, Kremer A, Plomion C. High-density linkage mapping and distribution of segregation distortion regions in the oak genome. DNA Res 2016; 23:115-24. [PMID: 27013549 PMCID: PMC4833419 DOI: 10.1093/dnares/dsw001] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 01/05/2016] [Indexed: 11/14/2022] Open
Abstract
We developed the densest single-nucleotide polymorphism (SNP)-based linkage genetic map to date for the genus Quercus An 8k gene-based SNP array was used to genotype more than 1,000 full-sibs from two intraspecific and two interspecific full-sib families of Quercus petraea and Quercus robur A high degree of collinearity was observed between the eight parental maps of the two species. A composite map was then established with 4,261 SNP markers spanning 742 cM over the 12 linkage groups (LGs) of the oak genome. Nine genomic regions from six LGs displayed highly significant distortions of segregation. Two main hypotheses concerning the mechanisms underlying segregation distortion are discussed: genetic load vs. reproductive barriers. Our findings suggest a predominance of pre-zygotic to post-zygotic barriers.
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Affiliation(s)
- Catherine Bodénès
- INRA, UMR1202 BIOGECO, F-33610 Cestas, France Université de Bordeaux, UMR1202 BIOGECO, F-33610 Talence, France
| | - Emilie Chancerel
- INRA, UMR1202 BIOGECO, F-33610 Cestas, France Université de Bordeaux, UMR1202 BIOGECO, F-33610 Talence, France
| | - François Ehrenmann
- INRA, UMR1202 BIOGECO, F-33610 Cestas, France Université de Bordeaux, UMR1202 BIOGECO, F-33610 Talence, France
| | - Antoine Kremer
- INRA, UMR1202 BIOGECO, F-33610 Cestas, France Université de Bordeaux, UMR1202 BIOGECO, F-33610 Talence, France
| | - Christophe Plomion
- INRA, UMR1202 BIOGECO, F-33610 Cestas, France Université de Bordeaux, UMR1202 BIOGECO, F-33610 Talence, France
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29
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Walsh J, Shriver WG, Olsen BJ, Kovach AI. Differential introgression and the maintenance of species boundaries in an advanced generation avian hybrid zone. BMC Evol Biol 2016; 16:65. [PMID: 27000833 PMCID: PMC4802838 DOI: 10.1186/s12862-016-0635-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 03/10/2016] [Indexed: 12/31/2022] Open
Abstract
Background Evolutionary processes, including selection and differential fitness, shape the introgression of genetic material across a hybrid zone, resulting in the exchange of some genes but not others. Differential introgression of molecular or phenotypic markers can thus provide insight into factors contributing to reproductive isolation. We characterized patterns of genetic variation across a hybrid zone between two tidal marsh birds, Saltmarsh (Ammodramus caudacutus) and Nelson’s (A. nelsoni) sparrows (n = 286), and compared patterns of introgression among multiple genetic markers and phenotypic traits. Results Geographic and genomic cline analyses revealed variable patterns of introgression among marker types. Most markers exhibited gradual clines and indicated that introgression exceeds the spatial extent of the previously documented hybrid zone. We found steeper clines, indicating strong selection for loci associated with traits related to tidal marsh adaptations, including for a marker linked to a gene region associated with metabolic functions, including an osmotic regulatory pathway, as well as for a marker related to melanin-based pigmentation, supporting an adaptive role of darker plumage (salt marsh melanism) in tidal marshes. Narrow clines at mitochondrial and sex-linked markers also offer support for Haldane’s rule. We detected patterns of asymmetrical introgression toward A. caudacutus, which may be driven by differences in mating strategy or differences in population density between the two species. Conclusions Our findings offer insight into the dynamics of a hybrid zone traversing a unique environmental gradient and provide evidence for a role of ecological divergence in the maintenance of pure species boundaries despite ongoing gene flow. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0635-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jennifer Walsh
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH, USA. .,Cornell Lab of Ornithology, Cornell University, Ithaca, NY, USA.
| | - W Gregory Shriver
- Department of Entomology and Wildlife Ecology, University of Delaware, Newark, DE, USA
| | - Brian J Olsen
- School of Biology and Ecology, University of Maine, Orono, ME, USA
| | - Adrienne I Kovach
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH, USA
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30
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Chapman MA, Hiscock SJ, Filatov DA. The genomic bases of morphological divergence and reproductive isolation driven by ecological speciation in Senecio (Asteraceae). J Evol Biol 2015; 29:98-113. [PMID: 26414668 DOI: 10.1111/jeb.12765] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 08/18/2015] [Accepted: 09/18/2015] [Indexed: 12/18/2022]
Abstract
Ecological speciation, driven by adaptation to contrasting environments, provides an attractive opportunity to study the formation of distinct species, and the role of selection and genomic divergence in this process. Here, we focus on a particularly clear-cut case of ecological speciation to reveal the genomic bases of reproductive isolation and morphological differences between closely related Senecio species, whose recent divergence within the last ~200,000 years was likely driven by the uplift of Mt. Etna (Sicily). These species form a hybrid zone, yet remain morphologically and ecologically distinct, despite active gene exchange. Here, we report a high-density genetic map of the Senecio genome and map hybrid breakdown to one large and several small quantitative trait loci (QTL). Loci under diversifying selection cluster in three 5 cM regions which are characterized by a significant increase in relative (F(ST)), but not absolute (d(XY)), interspecific differentiation. They also correspond to some of the regions of greatest marker density, possibly corresponding to 'cold-spots' of recombination, such as centromeres or chromosomal inversions. Morphological QTL for leaf and floral traits overlap these clusters. We also detected three genomic regions with significant transmission ratio distortion (TRD), possibly indicating accumulation of intrinsic genetic incompatibilities between these recently diverged species. One of the TRD regions overlapped with a cluster of high species differentiation, and another overlaps the large QTL for hybrid breakdown, indicating that divergence of these species may have occurred due to a complex interplay of ecological divergence and accumulation of intrinsic genetic incompatibilities.
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Affiliation(s)
- M A Chapman
- Department of Plant Sciences, University of Oxford, Oxford, UK.,Centre for Biological Sciences, University of Southampton, Southampton, UK
| | - S J Hiscock
- University of Oxford Botanic Garden, Rose Lane, Oxford, UK
| | - D A Filatov
- Department of Plant Sciences, University of Oxford, Oxford, UK
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31
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de Lafontaine G, Prunier J, Gérardi S, Bousquet J. Tracking the progression of speciation: variable patterns of introgression across the genome provide insights on the species delimitation between progenitor-derivative spruces (Picea mariana×P. rubens). Mol Ecol 2015; 24:5229-47. [DOI: 10.1111/mec.13377] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 08/05/2015] [Accepted: 09/01/2015] [Indexed: 01/17/2023]
Affiliation(s)
- Guillaume de Lafontaine
- Canada Research Chair in Forest and Environmental Genomics; Centre for Forest Research and Institute of Systems and Integrative Biology; Université Laval; 1030 Avenue de la Médecine Québec QC G1V 0A6 Canada
| | - Julien Prunier
- Canada Research Chair in Forest and Environmental Genomics; Centre for Forest Research and Institute of Systems and Integrative Biology; Université Laval; 1030 Avenue de la Médecine Québec QC G1V 0A6 Canada
| | - Sébastien Gérardi
- Canada Research Chair in Forest and Environmental Genomics; Centre for Forest Research and Institute of Systems and Integrative Biology; Université Laval; 1030 Avenue de la Médecine Québec QC G1V 0A6 Canada
| | - Jean Bousquet
- Canada Research Chair in Forest and Environmental Genomics; Centre for Forest Research and Institute of Systems and Integrative Biology; Université Laval; 1030 Avenue de la Médecine Québec QC G1V 0A6 Canada
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32
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Paun O, Turner B, Trucchi E, Munzinger J, Chase MW, Samuel R. Processes Driving the Adaptive Radiation of a Tropical Tree (Diospyros, Ebenaceae) in New Caledonia, a Biodiversity Hotspot. Syst Biol 2015; 65:212-27. [PMID: 26430059 PMCID: PMC4748748 DOI: 10.1093/sysbio/syv076] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 09/25/2015] [Indexed: 11/12/2022] Open
Abstract
Due to its special geological history, the New Caledonian Archipelago is a mosaic of soil types, and in combination with climatic conditions this results in a heterogeneous environment across relatively small distances. A group of over 20 endemic species of Diospyros (Ebenaceae) has rapidly and recently radiated on the archipelago after a single long-distance dispersal event. Most of the Diospyros species in the radiating group are morphologically and ecologically well differentiated, but they exhibit low levels of DNA variability. To investigate the processes that shaped the diversification of this group we employed restriction site associated DNA sequencing (RADseq). Over 8400 filtered SNPs generally confirm species delimitations and produce a well-supported phylogenetic tree. Our analyses document local introgression, but only a limited potential for gene flow over longer distances. The phylogenetic relationships point to an early regional clustering among populations and species, indicating that allopatric speciation with respect to macrohabitat (i.e., climatic conditions) may have had a role in the initial differentiation within the group. A later, more rapid radiation involved divergence with respect to microhabitat (i.e., soil preference). Several sister species in the group show a parallel divergence in edaphic preference. Searches for genomic regions that are systematically differentiated in this replicated phenotypic divergence pointed to loci potentially involved in ion binding and cellular transport. These loci appear meaningful in the context of adaptations to soil types that differ in heavy-metal and mineral content. Identical nucleotide changes affected only two of these loci, indicating that introgression may have played a limited role in their evolution. Our results suggest that both allopatric diversification and (parapatric) ecological divergence shaped successive rounds of speciation in the Diospyros radiation on New Caledonia.
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Affiliation(s)
- Ovidiu Paun
- Department of Botany and Biodiversity Research, University of Vienna, 1030 Vienna, Austria
| | - Barbara Turner
- Department of Botany and Biodiversity Research, University of Vienna, 1030 Vienna, Austria;
| | - Emiliano Trucchi
- Department of Botany and Biodiversity Research, University of Vienna, 1030 Vienna, Austria
| | | | - Mark W Chase
- Jodrell Laboratory, Royal Botanic Gardens, Kew, TW9 3AB Surrey, UK; and School of Plant Biology, University of Western Australia, Crawley, WA 6009 Australia
| | - Rosabelle Samuel
- Department of Botany and Biodiversity Research, University of Vienna, 1030 Vienna, Austria
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33
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Eaton DAR, Hipp AL, González-Rodríguez A, Cavender-Bares J. Historical introgression among the American live oaks and the comparative nature of tests for introgression. Evolution 2015; 69:2587-601. [DOI: 10.1111/evo.12758] [Citation(s) in RCA: 153] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 07/09/2015] [Accepted: 08/03/2015] [Indexed: 12/29/2022]
Affiliation(s)
- Deren A. R. Eaton
- Department of Ecology and Evolutionary Biology; Yale University; New Haven Connecticut 06511
| | - Andrew L. Hipp
- The Morton Arboretum; Lisle Illinois 60532
- Department of Botany; The Field Museum; Chicago Illinois 60605
| | - Antonio González-Rodríguez
- Centro de Investigaciones en Ecosistemas; Universidad Nacional Autónoma de México; Morelia Michoacán 58190 Mexico
| | - Jeannine Cavender-Bares
- Department of Ecology, Evolution and Behavior; University of Minnesota; Saint Paul Minnesota 55108
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34
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Bragg JG, Supple MA, Andrew RL, Borevitz JO. Genomic variation across landscapes: insights and applications. THE NEW PHYTOLOGIST 2015; 207:953-67. [PMID: 25904408 DOI: 10.1111/nph.13410] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2014] [Accepted: 03/09/2015] [Indexed: 05/22/2023]
Abstract
The distribution of genomic variation across landscapes can provide insights into the complex interactions between the environment and the genome that influence the distribution of species, and mediate phenotypic adaptation to local conditions. High throughput sequencing technologies now offer unprecedented power to explore these interactions, allowing powerful inferences about historical processes of colonization, gene flow and divergence, as well as the identification of loci that mediate local adaptation. These 'landscape genomic' approaches have been validated in model species and are now being applied to nonmodel organisms, including foundation species that have substantial effects on ecosystem processes. Here we review the growing field of landscape genomics from a very broad perspective. In particular, we describe the inferential power that is gained by taking a genome-wide view of genetic variation, strategies for study design to best capture adaptive variation, and how to apply this information to practical challenges, such as restoration.
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Affiliation(s)
- Jason G Bragg
- Research School of Biology and Centre for Biodiversity Analysis, Australian National University, Canberra, ACT, 0200, Australia
| | - Megan A Supple
- Research School of Biology and Centre for Biodiversity Analysis, Australian National University, Canberra, ACT, 0200, Australia
| | - Rose L Andrew
- Research School of Biology and Centre for Biodiversity Analysis, Australian National University, Canberra, ACT, 0200, Australia
- School of Environmental and Rural Science, University of New England, Armidale, NSW, 2350, Australia
| | - Justin O Borevitz
- Research School of Biology and Centre for Biodiversity Analysis, Australian National University, Canberra, ACT, 0200, Australia
- ARC Centre of Excellence in Plant Energy Biology, Australian National University, Canberra, ACT, 0200, Australia
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35
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Gante HF, Doadrio I, Alves MJ, Dowling TE. Semi-permeable species boundaries in Iberian barbels (Barbus and Luciobarbus, Cyprinidae). BMC Evol Biol 2015; 15:111. [PMID: 26066794 PMCID: PMC4465174 DOI: 10.1186/s12862-015-0392-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Accepted: 05/28/2015] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND The evolution of species boundaries and the relative impact of selection and gene flow on genomic divergence are best studied in populations and species pairs exhibiting various levels of divergence along the speciation continuum. We studied species boundaries in Iberian barbels, Barbus and Luciobarbus, a system of populations and species spanning a wide degree of genetic relatedness, as well as geographic distribution and range overlap. We jointly analyze multiple types of molecular markers and morphological traits to gain a comprehensive perspective on the nature of species boundaries in these cyprinid fishes. RESULTS Intraspecific molecular and morphological differentiation is visible among many populations. Genomes of all sympatric species studied are porous to gene flow, even if they are not sister species. Compared to their allopatric counterparts, sympatric representatives of different species share alleles and show an increase in all measures of nucleotide polymorphism (S, Hd, K, π and θ). High molecular diversity is particularly striking in L. steindachneri from the Tejo and Guadiana rivers, which co-varies with other sympatric species. Interestingly, different nuclear markers introgress across species boundaries at various levels, with distinct impacts on population trees. As such, some loci exhibit limited introgression and population trees resemble the presumed species tree, while alleles at other loci introgress more freely and population trees reflect geographic affinities and interspecific gene flow. Additionally, extent of introgression decreases with increasing genetic divergence in hybridizing species pairs. CONCLUSIONS We show that reproductive isolation in Iberian Barbus and Luciobarbus is not complete and species boundaries are semi-permeable to (some) gene flow, as different species (including non-sister) are exchanging genes in areas of sympatry. Our results support a speciation-with-gene-flow scenario with heterogeneous barriers to gene flow across the genome, strengthening with genetic divergence. This is consistent with observations coming from other systems and supports the notion that speciation is not instantaneous but a gradual process, during which different species are still able to exchange some genes, while selection prevents gene flow at other loci. We also provide evidence for a hybrid origin of a barbel ecotype, L. steindachneri, suggesting that ecology plays a key role in species coexistence and hybridization in Iberian barbels. This ecotype with intermediate, yet variable, molecular, morphological, trophic and ecological characteristics is the local product of introgressive hybridization of L. comizo with up to three different species (with L. bocagei in the Tejo, with L. microcephalus and L. sclateri in the Guadiana). In spite of the homogenizing effects of ongoing gene flow, species can still be discriminated using a combination of morphological and molecular markers. Iberian barbels are thus an ideal system for the study of species boundaries, since they span a wide range of genetic divergences, with diverse ecologies and degrees of sympatry.
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Affiliation(s)
- Hugo F Gante
- School of Life Sciences, Arizona State University, 85287-4601, Tempe, AZ, USA.
- Museu Nacional de História Natural e da Ciência, Centre for Ecology, Evolution and Environmental Changes (Ce3C), Universidade de Lisboa, Rua da Escola Politécnica 58, 1250-102, Lisbon, Portugal.
- Current address: Zoological Institute, University of Basel, 4051, Basel, Switzerland.
| | - Ignacio Doadrio
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, CSIC, c/José Gutiérrez Abascal 2, 28006, Madrid, Spain.
| | - Maria Judite Alves
- Museu Nacional de História Natural e da Ciência, Centre for Ecology, Evolution and Environmental Changes (Ce3C), Universidade de Lisboa, Rua da Escola Politécnica 58, 1250-102, Lisbon, Portugal.
| | - Thomas E Dowling
- School of Life Sciences, Arizona State University, 85287-4601, Tempe, AZ, USA.
- Current address: Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, 48202, Detroit, MI, USA.
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36
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Renaut S, Rieseberg LH. The Accumulation of Deleterious Mutations as a Consequence of Domestication and Improvement in Sunflowers and Other Compositae Crops. Mol Biol Evol 2015; 32:2273-83. [PMID: 25939650 DOI: 10.1093/molbev/msv106] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
For populations to maintain optimal fitness, harmful mutations must be efficiently purged from the genome. Yet, under circumstances that diminish the effectiveness of natural selection, such as the process of plant and animal domestication, deleterious mutations are predicted to accumulate. Here, we compared the load of deleterious mutations in 21 accessions from natural populations and 19 domesticated accessions of the common sunflower using whole-transcriptome single nucleotide polymorphism data. Although we find that genetic diversity has been greatly reduced during domestication, the remaining mutations were disproportionally biased toward nonsynonymous substitutions. Bioinformatically predicted deleterious mutations affecting protein function were especially strongly over-represented. We also identify similar patterns in two other domesticated species of the sunflower family (globe artichoke and cardoon), indicating that this phenomenon is not due to idiosyncrasies of sunflower domestication or the sunflower genome. Finally, we provide unequivocal evidence that deleterious mutations accumulate in low recombining regions of the genome, due to the reduced efficacy of purifying selection. These results represent a conundrum for crop improvement efforts. Although the elimination of harmful mutations should be a long-term goal of plant and animal breeding programs, it will be difficult to weed them out because of limited recombination.
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Affiliation(s)
- Sebastien Renaut
- Biodiversity Research Centre and Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Loren H Rieseberg
- Biodiversity Research Centre and Department of Botany, University of British Columbia, Vancouver, BC, Canada Department of Biology, Indiana University - Bloomington
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Huang CL, Ho CW, Chiang YC, Shigemoto Y, Hsu TW, Hwang CC, Ge XJ, Chen C, Wu TH, Chou CH, Huang HJ, Gojobori T, Osada N, Chiang TY. Adaptive divergence with gene flow in incipient speciation of Miscanthus floridulus/sinensis complex (Poaceae). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 80:834-847. [PMID: 25237766 DOI: 10.1111/tpj.12676] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 09/12/2014] [Accepted: 09/15/2014] [Indexed: 06/03/2023]
Abstract
Young incipient species provide ideal materials for untangling the process of ecological speciation in the presence of gene flow. The Miscanthus floridulus/sinensis complex exhibits diverse phenotypic and ecological differences despite recent divergence (approximately 1.59 million years ago). To elucidate the process of genetic differentiation during early stages of ecological speciation, we analyzed genomic divergence in the Miscanthus complex using 72 randomly selected genes from a newly assembled transcriptome. In this study, rampant gene flow was detected between species, estimated as M = 3.36 × 10(-9) to 1.20 × 10(-6) , resulting in contradicting phylogenies across loci. Nevertheless, beast analyses revealed the species identity and the effects of extrinsic cohesive forces that counteracted the non-stop introgression. As expected, early in speciation with gene flow, only 3-13 loci were highly diverged; two to five outliers (approximately 2.78-6.94% of the genome) were characterized by strong linkage disequilibrium, and asymmetrically distributed among ecotypes, indicating footprints of diversifying selection. In conclusion, ecological speciation of incipient species of Miscanthus probably followed the parapatric model, whereas allopatric speciation cannot be completely ruled out, especially between the geographically isolated northern and southern M. sinensis, for which no significant gene flow across oceanic barriers was detected. Divergence between local ecotypes in early-stage speciation began at a few genomic regions under the influence of natural selection and divergence hitchhiking that overcame gene flow.
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Affiliation(s)
- Chao-Li Huang
- Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan
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Harrison RG, Larson EL. Hybridization, Introgression, and the Nature of Species Boundaries. J Hered 2014; 105 Suppl 1:795-809. [DOI: 10.1093/jhered/esu033] [Citation(s) in RCA: 418] [Impact Index Per Article: 41.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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39
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Kantar MB, Baute GJ, Bock DG, Rieseberg LH. Genomic variation in Helianthus: learning from the past and looking to the future. Brief Funct Genomics 2014; 13:328-40. [DOI: 10.1093/bfgp/elu004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
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40
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Stuessy TF, Takayama K, López-Sepúlveda P, Crawford DJ. Interpretation of patterns of genetic variation in endemic plant species of oceanic islands. BOTANICAL JOURNAL OF THE LINNEAN SOCIETY. LINNEAN SOCIETY OF LONDON 2014; 174:276-288. [PMID: 26074627 PMCID: PMC4459035 DOI: 10.1111/boj.12088] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 04/18/2013] [Accepted: 07/07/2013] [Indexed: 05/07/2023]
Abstract
Oceanic islands offer special opportunities for understanding the patterns and processes of evolution. The availability of molecular markers in recent decades has enhanced these opportunities, facilitating the use of population genetics to reveal divergence and speciation in island systems. A common pattern seen in taxa on oceanic islands is a decreased level of genetic variation within and among populations, and the founder effect has often been invoked to explain this observation. Founder effects have a major impact on immigrant populations, but, over millions of years, the original genetic signature will normally be erased as a result of mutation, recombination, drift and selection. Therefore, the types and degrees of genetic modifications that occur must often be caused by other factors, which should be considered when explaining the patterns of genetic variation. The age of the island is extremely important because oceanic islands subside on their submarine plates over time. Erosion caused by wind, rain and wave action combine to grind down soft volcanic substrates. These geomorphological events can have a dramatic impact on population number and size, and hence levels of genetic diversity. The mode of speciation is also of significance. With anagenesis, genetic variation accumulates through time, whereas, with cladogenenesis, the gene pool splits into populations of adaptively radiating species. Breeding systems, population sizes and generation times are also important, as is hybridization between closely related taxa. Human disturbance has affected plant population number and size through the harvesting of forests and the introduction of invasive plants and animals. Therefore, the explanation of the observed levels of genetic variation in species of oceanic islands requires the consideration of many interconnected physical, biological and anthropomorphic factors.
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Affiliation(s)
- Tod F Stuessy
- Department of Systematic and Evolutionary Botany, Biodiversity Center, University of ViennaRennweg 14, A-1030, Vienna, Austria
- *Corresponding author. E-mail:
| | - Koji Takayama
- Department of Systematic and Evolutionary Botany, Biodiversity Center, University of ViennaRennweg 14, A-1030, Vienna, Austria
| | - Patricio López-Sepúlveda
- Department of Systematic and Evolutionary Botany, Biodiversity Center, University of ViennaRennweg 14, A-1030, Vienna, Austria
| | - Daniel J Crawford
- Department of Ecology & Evolutionary Biology and the Biodiversity Institute, University of KansasLawrence, KS, 66045, USA
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41
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Renaut S, Owens GL, Rieseberg LH. Shared selective pressure and local genomic landscape lead to repeatable patterns of genomic divergence in sunflowers. Mol Ecol 2013; 23:311-24. [DOI: 10.1111/mec.12600] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 11/15/2013] [Accepted: 11/18/2013] [Indexed: 01/28/2023]
Affiliation(s)
- Sebastien Renaut
- Department of Botany; Biodiversity Research Centre; University of British Columbia; Vancouver BC Canada V6T 1Z4
| | - Gregory L. Owens
- Department of Botany; Biodiversity Research Centre; University of British Columbia; Vancouver BC Canada V6T 1Z4
| | - Loren H. Rieseberg
- Department of Botany; Biodiversity Research Centre; University of British Columbia; Vancouver BC Canada V6T 1Z4
- Department of Biology; Indiana University; 1001 East Third Street Bloomington IN 47405 USA
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Turner B, Paun O, Munzinger J, Duangjai S, Chase MW, Samuel R. Analyses of amplified fragment length polymorphisms (AFLP) indicate rapid radiation of Diospyros species (Ebenaceae) endemic to New Caledonia. BMC Evol Biol 2013; 13:269. [PMID: 24330478 PMCID: PMC3881503 DOI: 10.1186/1471-2148-13-269] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 12/09/2013] [Indexed: 11/24/2022] Open
Abstract
Background Radiation in some plant groups has occurred on islands and due to the characteristic rapid pace of phenotypic evolution, standard molecular markers often provide insufficient variation for phylogenetic reconstruction. To resolve relationships within a clade of 21 closely related New Caledonian Diospyros species and evaluate species boundaries we analysed genome-wide DNA variation via amplified fragment length polymorphisms (AFLP). Results A neighbour-joining (NJ) dendrogram based on Dice distances shows all species except D. minimifolia, D. parviflora and D. vieillardii to form unique clusters of genetically similar accessions. However, there was little variation between these species clusters, resulting in unresolved species relationships and a star-like general NJ topology. Correspondingly, analyses of molecular variance showed more variation within species than between them. A Bayesian analysis with BEAST produced a similar result. Another Bayesian method, this time a clustering method, Structure, demonstrated the presence of two groups, highly congruent with those observed in a principal coordinate analysis (PCO). Molecular divergence between the two groups is low and does not correspond to any hypothesised taxonomic, ecological or geographical patterns. Conclusions We hypothesise that such a pattern could have been produced by rapid and complex evolution involving a widespread progenitor for which an initial split into two groups was followed by subsequent fragmentation into many diverging populations, which was followed by range expansion of then divergent entities. Overall, this process resulted in an opportunistic pattern of phenotypic diversification. The time since divergence was probably insufficient for some species to become genetically well-differentiated, resulting in progenitor/derivative relationships being exhibited in a few cases. In other cases, our analyses may have revealed evidence for the existence of cryptic species, for which more study of morphology and ecology are now required.
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Affiliation(s)
- Barbara Turner
- Department of Systematic and Evolutionary Botany, Faculty of Life Sciences, University Vienna, Rennweg 14, 1030 Wien, Austria.
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Darras H, Leniaud L, Aron S. Large-scale distribution of hybridogenetic lineages in a Spanish desert ant. Proc Biol Sci 2013; 281:20132396. [PMID: 24225458 DOI: 10.1098/rspb.2013.2396] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Recently, a unique case of hybridogenesis at a social level was reported in local populations of the desert ants Cataglyphis. Queens mate with males originating from a different genetic lineage than their own to produce hybrid workers, but they use parthenogenesis for the production of reproductive offspring (males and females). As a result, non-reproductive workers are all inter-lineage hybrids, whereas the sexual line is purely maternal. Here, we show that this unorthodox reproductive system occurs in all populations of the ant Cataglyphis hispanica. Remarkably, workers are hybrids of the same two genetic lineages along a 400 km transect crossing the whole distribution range of the species. These results indicate that social hybridogenesis in C. hispanica allows their maintenance over time and across a large geographical scale of two highly divergent genetic lineages, despite their constant hybridization. The widespread distribution of social hybridogenesis in C. hispanica supports that this reproductive strategy has been evolutionarily conserved over a long period.
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Affiliation(s)
- Hugo Darras
- Evolutionary Biology and Ecology, Université Libre de Bruxelles, , Avenue Franklin D. Roosevelt, 50, CP 160/12, Brussels 1050, Belgium, I.R.B.I. UMR CNRS 7261, Faculté des Sciences, Université François Rabelais Tours, 37200 Tours, France
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44
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Chapman MA, Hiscock SJ, Filatov DA. Genomic divergence during speciation driven by adaptation to altitude. Mol Biol Evol 2013; 30:2553-67. [PMID: 24077768 PMCID: PMC3840311 DOI: 10.1093/molbev/mst168] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Even though Darwin's "On the Origin of Species" implied selection being the main driver of species formation, the role of natural selection in speciation remains poorly understood. In particular, it remains unclear how selection at a few genes can lead to genomewide divergence and the formation of distinct species. We used a particularly attractive clear-cut case of recent plant ecological speciation to investigate the demography and genomic bases of species formation driven by adaptation to contrasting conditions. High-altitude Senecio aethnensis and low-altitude S. chrysanthemifolius live at the extremes of a mountain slope on Mt. Etna, Sicily, and form a hybrid zone at intermediate altitudes but remain morphologically distinct. Genetic differentiation of these species was analyzed at the DNA polymorphism and gene expression levels by high-throughput sequencing of transcriptomes from multiple individuals. Out of ≈ 18,000 genes analyzed, only a small number (90) displayed differential expression between the two species. These genes showed significantly elevated species differentiation (FST and Dxy), consistent with diversifying selection acting on these genes. Genomewide genetic differentiation of the species is surprisingly low (FST = 0.19), while ≈ 200 genes showed significantly higher (false discovery rate < 1%; mean outlier FST > 0.6) interspecific differentiation and evidence for local adaptation. Diversifying selection at only a handful of loci may be enough for the formation and maintenance of taxonomically well-defined species, despite ongoing gene flow. This provides an explanation of why many closely related species (in plants, in particular) remain phenotypically and ecologically distinct despite ongoing hybridization, a question that has long puzzled naturalists and geneticists alike.
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Affiliation(s)
- Mark A Chapman
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
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45
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Hodgins KA, Lai Z, Oliveira LO, Still DW, Scascitelli M, Barker MS, Kane NC, Dempewolf H, Kozik A, Kesseli RV, Burke JM, Michelmore RW, Rieseberg LH. Genomics of Compositae crops: reference transcriptome assemblies and evidence of hybridization with wild relatives. Mol Ecol Resour 2013; 14:166-77. [DOI: 10.1111/1755-0998.12163] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 08/14/2013] [Accepted: 08/15/2013] [Indexed: 11/30/2022]
Affiliation(s)
- Kathryn A. Hodgins
- Department of Botany and Biodiversity Research Centre; University of British Columbia; Vancouver BC V6T 1Z4 Canada
| | - Zhao Lai
- Department of Biology and Center for Genomics and Bioinformatics; Indiana University; Bloomington IN 47405 USA
| | - Luiz O. Oliveira
- Departamento de Bioquímica e Biologia Molecular; Universidade Federal de Viçosa; 36570-000 Viçosa Brazil
| | - David W. Still
- Department of Plant Sciences; Cal Poly Pomona; Pomona CA 91768 USA
| | - Moira Scascitelli
- Department of Botany and Biodiversity Research Centre; University of British Columbia; Vancouver BC V6T 1Z4 Canada
| | - Michael S. Barker
- Department of Ecology and Evolutionary Biology; University of Arizona; Tucson AZ 85721 USA
| | - Nolan C. Kane
- Department of Ecology and Evolutionary Biology; University of Colorado Boulder; Boulder CO 80309 USA
| | - Hannes Dempewolf
- Department of Botany and Biodiversity Research Centre; University of British Columbia; Vancouver BC V6T 1Z4 Canada
| | - Alex Kozik
- The Genome Center; University of California; Davis CA 95616 USA
| | | | - John M. Burke
- Department of Plant Biology; University of Georgia; Athens GA 30602 USA
| | - Richard W. Michelmore
- The Genome Center; University of California; Davis CA 95616 USA
- Departments of Plant Sciences, Molecular & Cellular Biology, and Medical Microbiology & Immunology; University of California; Davis CA 95616 USA
| | - Loren H. Rieseberg
- Department of Botany and Biodiversity Research Centre; University of British Columbia; Vancouver BC V6T 1Z4 Canada
- Department of Biology and Center for Genomics and Bioinformatics; Indiana University; Bloomington IN 47405 USA
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46
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Surget-Groba Y, Kay KM. Restricted gene flow within and between rapidly diverging Neotropical plant species. Mol Ecol 2013; 22:4931-42. [PMID: 23952304 DOI: 10.1111/mec.12442] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Revised: 07/02/2013] [Accepted: 07/04/2013] [Indexed: 11/30/2022]
Abstract
Speciation involves the evolution of traits and genetic differences that contribute to reproductive isolation and the cessation of gene flow, and studying closely related species and divergent populations gives insight into how these phenomena proceed. Here, we document patterns of gene flow within and between two members of a rapid Neotropical species radiation, Costus pulverulentus and Costus scaber (Costaceae). These species co-occur in the tropical rainforest and share pollinators, but are reproductively isolated by a series of prezygotic barriers, some of which show evidence of reinforcement at sympatric sites. Here, we genotype microsatellite markers in plants from eight sites that span the geographical range of both species, including four sympatric sites. We also genotype putative hybrids found at two sympatric sites. We find high levels of genetic isolation among populations within each species and low but detectable levels of introgression between species at sympatric sites. Putative hybrids identified by morphology are consistent with F1 or more advanced hybrids. Our results highlight the effectiveness of prezygotic isolating mechanisms at maintaining species boundaries in young radiations and provide empirical data on levels of gene flow consistent with reinforcement.
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Affiliation(s)
- Yann Surget-Groba
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Menglun, Yunnan, 666303, China
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47
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Feulner PGD, Gratten J, Kijas JW, Visscher PM, Pemberton JM, Slate J. Introgression and the fate of domesticated genes in a wild mammal population. Mol Ecol 2013; 22:4210-4221. [PMID: 23786437 DOI: 10.1111/mec.12378] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Revised: 04/28/2013] [Accepted: 04/29/2013] [Indexed: 01/23/2023]
Abstract
When domesticated species are not reproductively isolated from their wild relatives, the opportunity arises for artificially selected variants to be re-introduced into the wild. However, the evolutionary consequences of introgression of domesticated genes back into the wild are poorly understood. By combining high-throughput genotyping with 25 years of long-term ecological field data, we describe the occurrence and consequences of admixture between a primitive sheep breed, the free-living Soay sheep of St Kilda, and more modern breeds. Utilizing data from a 50 K ovine SNP chip, together with forward simulations of demographic scenarios, we show that admixture occurred between Soay sheep and a more modern breed, consistent with historical accounts, approximately 150 years ago. Haplotype-sharing analyses with other breeds revealed that polymorphisms in coat colour and pattern in Soay sheep arose as a result of introgression of genetic variants favoured by artificial selection. Because the haplotypes carrying the causative mutations are known to be under natural selection in free-living Soay sheep, the admixture event created an opportunity to observe the outcome of a 'natural laboratory' experiment where ancestral and domesticated genes competed with each other. The haplotype carrying the domesticated light coat colour allele was favoured by natural selection, while the haplotype associated with the domesticated self coat pattern allele was associated with decreased survival. Therefore, we demonstrate that introgression of domesticated alleles into wild populations can provide a novel source of variation capable of generating rapid evolutionary changes.
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Affiliation(s)
- Philine G D Feulner
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK.,Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, 24306, Ploen, Germany
| | - Jacob Gratten
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK.,The University of Queensland, Queensland Brain Institute, Brisbane, QLD 4072, Australia
| | - James W Kijas
- Livestock Industries, CSIRO 4067, Brisbane, QLD, Australia
| | - Peter M Visscher
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK.,The University of Queensland Diamantina Institute, Brisbane, QLD 4072, Australia
| | - Josephine M Pemberton
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JT, UK
| | - Jon Slate
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
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48
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Rowe HC, Rieseberg LH. Genome-scale transcriptional analyses of first-generation interspecific sunflower hybrids reveals broad regulatory compatibility. BMC Genomics 2013; 14:342. [PMID: 23701699 PMCID: PMC3679827 DOI: 10.1186/1471-2164-14-342] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Accepted: 04/15/2013] [Indexed: 12/26/2022] Open
Abstract
Background Interspecific hybridization creates individuals harboring diverged genomes. The interaction of these genomes can generate successful evolutionary novelty or disadvantageous genomic conflict. Annual sunflowers Helianthus annuus and H. petiolaris have a rich history of hybridization in natural populations. Although first-generation hybrids generally have low fertility, hybrid swarms that include later generation and fully fertile backcross plants have been identified, as well as at least three independently-originated stable hybrid taxa. We examine patterns of transcript accumulation in the earliest stages of hybridization of these species via analyses of transcriptome sequences from laboratory-derived F1 offspring of an inbred H. annuus cultivar and a wild H. petiolaris accession. Results While nearly 14% of the reference transcriptome showed significant accumulation differences between parental accessions, total F1 transcript levels showed little evidence of dominance, as midparent transcript levels were highly predictive of transcript accumulation in F1 plants. Allelic bias in F1 transcript accumulation was detected in 20% of transcripts containing sufficient polymorphism to distinguish parental alleles; however the magnitude of these biases were generally smaller than differences among parental accessions. Conclusions While analyses of allelic bias suggest that cis regulatory differences between H. annuus and H. petiolaris are common, their effect on transcript levels may be more subtle than trans-acting regulatory differences. Overall, these analyses found little evidence of regulatory incompatibility or dominance interactions between parental genomes within F1 hybrid individuals, although it is unclear whether this is a legacy or an enabler of introgression between species.
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Affiliation(s)
- Heather C Rowe
- Botany Department, University of British Columbia, Vancouver, BC, Canada
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49
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Andrew RL, Bernatchez L, Bonin A, Buerkle CA, Carstens BC, Emerson BC, Garant D, Giraud T, Kane NC, Rogers SM, Slate J, Smith H, Sork VL, Stone GN, Vines TH, Waits L, Widmer A, Rieseberg LH. A road map for molecular ecology. Mol Ecol 2013; 22:2605-26. [DOI: 10.1111/mec.12319] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 03/16/2013] [Indexed: 12/18/2022]
Affiliation(s)
- Rose L. Andrew
- Department of Botany; University of British Columbia; 3529-6270 University Blvd Vancouver BC V6T 1Z4 Canada
| | - Louis Bernatchez
- DInstitut de Biologie Intégrative et des Systémes; Département de Biologie; 1030, Avenue de la Médecine Université Laval; Québec QC G1V 0A6 Canada
| | - Aurélie Bonin
- Laboratoire d'Ecologie Alpine; CNRS UMR 5553 Université Joseph Fourier; BP 53, 38041 Grenoble Cedex 9 France
| | - C. Alex. Buerkle
- Department of Botany; University of Wyoming; 1000 E. University Ave. Laramie WY 82071 USA
| | - Bryan C. Carstens
- Department of Evolution, Ecology and Organismal Biology; 318 W. 12th Ave. The Ohio State University; Columbus OH 43210 USA
| | - Brent C. Emerson
- Island Ecology and Evolution Research Group; Instituto de Productos Naturales y Agrobiología (IPNA-CSIC) C/Astrofísico Francisco Sánchez 3 La Laguna Tenerife; Canary Islands 38206 Spain
| | - Dany Garant
- Département de Biologie; Université de Sherbrooke; Sherbrooke QC J1K 2R1 Canada
| | - Tatiana Giraud
- Laboratoire Ecologie, Systématique et Evolution; UMR 8079 CNRS-UPS-AgroParisTech, Bâtiment 360 Univ. Paris Sud; 91405 Orsay cedex France
| | - Nolan C. Kane
- Department of Botany; University of British Columbia; 3529-6270 University Blvd Vancouver BC V6T 1Z4 Canada
| | - Sean M. Rogers
- Department of Biological Sciences; University of Calgary; 2500 University Drive N.W., Calgary AB T2N 1N4 Canada
| | - Jon Slate
- Department of Animal and Plant Sciences; University of Sheffield; Sheffield S10 2TN UK
| | - Harry Smith
- 79 Melton Road Burton-on-the-Wolds Loughborough LE12 5TQ UK
| | - Victoria L. Sork
- Department of Ecology and Evolutionary Biology; University of California Los Angeles; 4139 Terasaki Life Sciences Building, 610 Charles E. Young Drive East Los Angeles CA 90095 USA
| | - Graham N. Stone
- Institute of Evolutionary Biology; University of Edinburgh; The King's Buildings, West Mains Road, Edinburgh EH9 3JT UK
| | - Timothy H. Vines
- Molecular Ecology Editorial Office; 6270 University Blvd Vancouver BC V6T 1Z4 Canada
| | - Lisette Waits
- Department of Fish and Wildlife Sciences; University of Idaho; 875 Perimeter Drive MS 1136 Moscow ID 83844 USA
| | - Alex Widmer
- ETH Zurich; Institute of Integrative Biology; Universitätstrasse 16 Zurich 8092 Switzerland
| | - Loren H. Rieseberg
- Department of Botany; University of British Columbia; 3529-6270 University Blvd Vancouver BC V6T 1Z4 Canada
- Department of Biology; Indiana University; 1001 E. 3 St., Bloomington IN 47405 USA
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50
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Hsieh YC, Chung JD, Wang CN, Chang CT, Chen CY, Hwang SY. Historical connectivity, contemporary isolation and local adaptation in a widespread but discontinuously distributed species endemic to Taiwan, Rhododendron oldhamii (Ericaceae). Heredity (Edinb) 2013; 111:147-56. [PMID: 23591517 DOI: 10.1038/hdy.2013.31] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Revised: 11/29/2012] [Accepted: 12/19/2012] [Indexed: 11/09/2022] Open
Abstract
Elucidation of the evolutionary processes that constrain or facilitate adaptive divergence is a central goal in evolutionary biology, especially in non-model organisms. We tested whether changes in dynamics of gene flow (historical vs contemporary) caused population isolation and examined local adaptation in response to environmental selective forces in fragmented Rhododendron oldhamii populations. Variation in 26 expressed sequence tag-simple sequence repeat loci from 18 populations in Taiwan was investigated by examining patterns of genetic diversity, inbreeding, geographic structure, recent bottlenecks, and historical and contemporary gene flow. Selection associated with environmental variables was also examined. Bayesian clustering analysis revealed four regional population groups of north, central, south and southeast with significant genetic differentiation. Historical bottlenecks beginning 9168-13,092 years ago and ending 1584-3504 years ago were revealed by estimates using approximate Bayesian computation for all four regional samples analyzed. Recent migration within and across geographic regions was limited. However, major dispersal sources were found within geographic regions. Altitudinal clines of allelic frequencies of environmentally associated positively selected outliers were found, indicating adaptive divergence. Our results point to a transition from historical population connectivity toward contemporary population isolation and divergence on a regional scale. Spatial and temporal dispersal differences may have resulted in regional population divergence and local adaptation associated with environmental variables, which may have played roles as selective forces at a regional scale.
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Affiliation(s)
- Y-C Hsieh
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
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