1
|
Chen J, Wang S, Wang D, Chiu Y, Yang N, Lian X, Zhao Z, Wei Q. Uncovering rearrangements in the Tibetan antelope via population-derived genome refinement and comparative analysis with homologous species. Front Genet 2024; 15:1302554. [PMID: 38425715 PMCID: PMC10902437 DOI: 10.3389/fgene.2024.1302554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 01/24/2024] [Indexed: 03/02/2024] Open
Abstract
Introduction: The Tibetan antelope (Pantholops hodgsonii) is a remarkable mammal thriving in the extreme Qinghai-Tibet Plateau conditions. Despite the availability of its genome sequence, limitations in the scaffold-level assembly have hindered a comprehensive understanding of its genomics. Moreover, comparative analyses with other Bovidae species are lacking, along with insights into genome rearrangements in the Tibetan antelope. Methods: Addressing these gaps, we present a multifaceted approach by refining the Tibetan Antelope genome through linkage disequilibrium analysis with data from 15 newly sequenced samples. Results: The scaffold N50 of the refined reference is 3.2 Mbp, surpassing the previous version by 1.15-fold. Our annotation analysis resulted in 50,750 genes, encompassing 29,324 novel genes not previously study. Comparative analyses reveal 182 unique rearrangements within the scaffolds, contributing to our understanding of evolutionary dynamics and species-specific adaptations. Furthermore, by conducting detailed genomic comparisons and reconstructing rearrangements, we have successfully pioneered the reconstruction of the X-chromosome in the Tibetan antelope. Discussion: This effort enhances our comprehension of the genomic landscape of this species.
Collapse
Affiliation(s)
- Jiarui Chen
- College of Eco‐Environmental Engineering, Qinghai University, Xining, Qinghai, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
| | - Shuwen Wang
- College of Eco‐Environmental Engineering, Qinghai University, Xining, Qinghai, China
| | - Dong Wang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, China
- School of Geographical Science, Qinghai Normal University, Xining, Qinghai, China
| | - Yunkang Chiu
- Shenzhen Byoryn Technology Co., Ltd., Shenzhen, China
| | - Nan Yang
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Xinming Lian
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, Qinghai, China
| | - Zicheng Zhao
- Shenzhen Byoryn Technology Co., Ltd., Shenzhen, China
| | - Qing Wei
- College of Eco‐Environmental Engineering, Qinghai University, Xining, Qinghai, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
| |
Collapse
|
2
|
Piatkowski B, Weston DJ, Aguero B, Duffy A, Imwattana K, Healey AL, Schmutz J, Shaw AJ. Divergent selection and climate adaptation fuel genomic differentiation between sister species of Sphagnum (peat moss). ANNALS OF BOTANY 2023; 132:499-512. [PMID: 37478307 PMCID: PMC10666999 DOI: 10.1093/aob/mcad104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 07/24/2023] [Indexed: 07/23/2023]
Abstract
BACKGROUND AND AIMS New plant species can evolve through the reinforcement of reproductive isolation via local adaptation along habitat gradients. Peat mosses (Sphagnaceae) are an emerging model system for the study of evolutionary genomics and have well-documented niche differentiation among species. Recent molecular studies have demonstrated that the globally distributed species Sphagnum magellanicum is a complex of morphologically cryptic lineages that are phylogenetically and ecologically distinct. Here, we describe the architecture of genomic differentiation between two sister species in this complex known from eastern North America: the northern S. diabolicum and the largely southern S. magniae. METHODS We sampled plant populations from across a latitudinal gradient in eastern North America and performed whole genome and restriction-site associated DNA sequencing. These sequencing data were then analyzed computationally. KEY RESULTS Using sliding-window population genetic analyses we find that differentiation is concentrated within 'islands' of the genome spanning up to 400 kb that are characterized by elevated genetic divergence, suppressed recombination, reduced nucleotide diversity and increased rates of non-synonymous substitution. Sequence variants that are significantly associated with genetic structure and bioclimatic variables occur within genes that have functional enrichment for biological processes including abiotic stress response, photoperiodism and hormone-mediated signalling. Demographic modelling demonstrates that these two species diverged no more than 225 000 generations ago with secondary contact occurring where their ranges overlap. CONCLUSIONS We suggest that this heterogeneity of genomic differentiation is a result of linked selection and reflects the role of local adaptation to contrasting climatic zones in driving speciation. This research provides insight into the process of speciation in a group of ecologically important plants and strengthens our predictive understanding of how plant populations will respond as Earth's climate rapidly changes.
Collapse
Affiliation(s)
- Bryan Piatkowski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Blanka Aguero
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Aaron Duffy
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Karn Imwattana
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Adam L Healey
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - A Jonathan Shaw
- Department of Biology, Duke University, Durham, NC 27708, USA
| |
Collapse
|
3
|
de Mestier A, Lücking R, Gutierrez J, Brokamp G, Celis M, Borsch T. Nested singletons in molecular trees: Utility of adding morphological and geographical data from digitized herbarium specimens to test taxon concepts at species level in the case of Casearia (Salicaceae). Ecol Evol 2023; 13:e9736. [PMID: 36694555 PMCID: PMC9843533 DOI: 10.1002/ece3.9736] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 12/21/2022] [Accepted: 12/23/2022] [Indexed: 01/19/2023] Open
Abstract
Using the genus Casearia, we assessed the status of nested singletons: individual specimens corresponding to accepted species but in molecular trees appearing nested within clades of closely related species. Normally, such cases would be left undecided, while on the other hand, timely taxonomic decisions are required. We argue that morphological, chorological, and ecological data can be informative to illuminate patterns of speciation. Their use can provide a first step in testing taxon concepts at species level. We focused on five cases of nested singletons in trees of the genus Casearia. We employed PCA and cluster analysis to assess phenotypic differentiation. Using geocoordinates, we calculated niche space differentiation based on 19 bioclim variables, by means of PCA and niche equivalency and similarity tests and generated dot maps. We found that the singletons were morphologically distinctive in two of the five cases (Casearia selloana and C. manausensis), relatively distinctive in two other cases (C. zizyphoides and C. mariquitensis), and partially overlapping in the last case (C. grandiflora). For two cases (C. mariquitensis and C. selloana), ecological niche space was broadly overlapping, in two cases it was found broadly nested (C. grandiflora and C. zizyphoides), and in one case narrowly nested (C. manausensis), but in no case niche differentiation was observed. Niche overlap, similarity and equivalency showed corresponding patterns. Given these data, one would interpret C. selloana and C. manausensis as presumably well-distinguished taxa, their narrow distribution ranges suggesting recently emerging lineages. The other three cases are not clearcut. Morphological data would suggest particularly C. grandiflora conspecific with C. arborea, but differences in the distribution are intriguing. Our approach would reject the notion of potential synonymy based on nested phylogenetic placement for at least two of the five cases. The other case also shows no complete lack of differentiation which would support synonymy.
Collapse
Affiliation(s)
- Astrid de Mestier
- Botanischer GartenFreie Universität BerlinBerlinGermany,Institut für Biologie – Systematische Botanik und PflanzengeographieFreie Universität BerlinBerlinGermany
| | | | - Jorge Gutierrez
- Jardín Botánico Nacional CalabazarUniversidad de La HabanaBoyerosCuba
| | - Grischa Brokamp
- Botanischer GartenFreie Universität BerlinBerlinGermany,Fachbereich Wald und UmweltHochschule für Nachhaltige Entwicklung EberswaldeEberswaldeGermany
| | - Marcela Celis
- Departamento de Química y BiologíaUniversidad del NorteBarranquillaColombia
| | - Thomas Borsch
- Botanischer GartenFreie Universität BerlinBerlinGermany,Institut für Biologie – Systematische Botanik und PflanzengeographieFreie Universität BerlinBerlinGermany
| |
Collapse
|
4
|
Boza Espinoza TE, Kessler M. A monograph of the genus Polylepis (Rosaceae). PHYTOKEYS 2022; 203:1-274. [PMID: 36761034 PMCID: PMC9849045 DOI: 10.3897/phytokeys.203.83529] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 05/13/2022] [Indexed: 05/27/2023]
Abstract
We present a monograph of the high Andean tree genus Polylepis (Rosaceae), based on a species concept considering morphological, climatic and biogeographic distinctness as indicators of evolutionary independence. In total, we recognize 45 species of Polylepis, grouped in five sections. Polylepissect.Sericeae is represented by 15 species in four subsections, P.sect.Reticulatae by seven species, P.sect.Subsericantes by three species, P.sect.Australes by two species and P.sect.Incanaee by three subsections with 18 species. We describe seven new species, one from Colombia (P.frontinensis), one from Ecuador (P.simpsoniae) and five from Peru (P.acomayensis, P.fjeldsaoi, P.occidentalis, P.pilosissima and P.sacra). Three species from Peru (P.albicans, P.pallidistigma and P.serrata) are re-instated as valid species. Two taxa from Bolivia (P.incanoides and P.nana) are elevated from subspecies to species rank. The morphology, habitat, distribution, ecology and conservation status of each species are documented. We also provide an identification key to the species of the genus and general introductions on taxonomic history, morphology, evolution, ecology and conservation.
Collapse
Affiliation(s)
- Tatiana Erika Boza Espinoza
- Institute for Nature, Earth and Energy (INTE), Pontificia Universidad Católica del Perú (PUCP), Av. Universitaria 1801, Lima 15088, PeruPontificia Universidad Católica del Perú (PUCP)LimaPeru
| | - Michael Kessler
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, CH-8008 Zurich, SwitzerlandUniversity of ZurichZürichSwitzerland
| |
Collapse
|
5
|
Yang F, Wan H, Li J, Wang Q, Yang N, Zhu X, Liu Z, Yang Y, Ma W, Fan X, Yang W, Zhou Y. Pentaploidization Enriches the Genetic Diversity of Wheat by Enhancing the Recombination of AB Genomes. FRONTIERS IN PLANT SCIENCE 2022; 13:883868. [PMID: 35845672 PMCID: PMC9281561 DOI: 10.3389/fpls.2022.883868] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 06/06/2022] [Indexed: 06/15/2023]
Abstract
Allohexaploidization and continuous introgression play a key role in the origin and evolution of bread wheat. The genetic bottleneck of bread wheat resulting from limited germplasms involved in the origin and modern breeding may be compensated by gene flow from tetraploid wheat through introgressive hybridization. The inter-ploidy hybridization between hexaploid and tetraploid wheat generates pentaploid hybrids first, which absorbed genetic variations both from hexaploid and tetraploid wheat and have great potential for re-evolution and improvement in bread wheat. Therefore, understanding the effects of the pentaploid hybrid is of apparent significance in our understanding of the historic introgression and in informing breeding. In the current study, two sets of F2 populations of synthetic pentaploid wheat (SPW1 and SPW2) and synthetic hexaploid wheat (SHW1 and SHW2) were created to analyze differences in recombination frequency (RF) of AB genomes and distorted segregation of polymorphic SNP markers through SNP genotyping. Results suggested that (1) the recombination of AB genomes in the SPW populations was about 3- to 4-fold higher than that in the SHW populations, resulting from the significantly (P < 0.01) increased RF between adjacent and linked SNP loci, especially the variations that occurred in a pericentromeric region which would further enrich genetic diversity; (2) the crosses of hexaploid × tetraploid wheat could be an efficient way to produce pentaploid derivatives than the crosses of tetraploid × hexaploid wheat according to the higher germination rate found in the former crosses; (3) the high proportion of distorted segregation loci that skewed in favor of the female parent genotype/allele in the SPW populations might associate with the fitness and survival of the offspring. Based on the presented data, we propose that pentaploid hybrids should increasingly be used in wheat breeding. In addition, the contribution of gene flow from tetraploid wheat to bread wheat mediated by pentaploid introgressive hybridization also was discussed in the re-evolution of bread wheat.
Collapse
Affiliation(s)
- Fan Yang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Wheat Biology and Genetic Improvement in Southwestern China (Ministry of Agriculture and Rural Affairs of P.R.C.), Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Hongshen Wan
- Key Laboratory of Wheat Biology and Genetic Improvement in Southwestern China (Ministry of Agriculture and Rural Affairs of P.R.C.), Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Jun Li
- Key Laboratory of Wheat Biology and Genetic Improvement in Southwestern China (Ministry of Agriculture and Rural Affairs of P.R.C.), Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Qin Wang
- Key Laboratory of Wheat Biology and Genetic Improvement in Southwestern China (Ministry of Agriculture and Rural Affairs of P.R.C.), Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Ning Yang
- Key Laboratory of Wheat Biology and Genetic Improvement in Southwestern China (Ministry of Agriculture and Rural Affairs of P.R.C.), Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Xinguo Zhu
- Key Laboratory of Wheat Biology and Genetic Improvement in Southwestern China (Ministry of Agriculture and Rural Affairs of P.R.C.), Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Zehou Liu
- Key Laboratory of Wheat Biology and Genetic Improvement in Southwestern China (Ministry of Agriculture and Rural Affairs of P.R.C.), Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Yumin Yang
- Institute of Agricultural Resources and Environment, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Wujun Ma
- Australia-China Joint Centre for Wheat Improvement, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, Australia
| | - Xing Fan
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Wuyun Yang
- Key Laboratory of Wheat Biology and Genetic Improvement in Southwestern China (Ministry of Agriculture and Rural Affairs of P.R.C.), Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Yonghong Zhou
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| |
Collapse
|
6
|
da Rocha RH, Fernandes CA, Bignotto TS, Margarido VP, Tencatt LFC, da Graça WJ, Gubiani ÉA. Integrated analysis reveals a new species of Corydoras Lacépède, 1803 (Siluriformes: Callichthyidae) in the lower Iguassu River, Brazil. ORG DIVERS EVOL 2022. [DOI: 10.1007/s13127-021-00534-8] [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]
|
7
|
Chang JT, Chao CT, Nakamura K, Liu HL, Luo MX, Liao PC. Divergence With Gene Flow and Contrasting Population Size Blur the Species Boundary in Cycas Sect. Asiorientales, as Inferred From Morphology and RAD-Seq Data. FRONTIERS IN PLANT SCIENCE 2022; 13:824158. [PMID: 35615129 PMCID: PMC9125193 DOI: 10.3389/fpls.2022.824158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 03/15/2022] [Indexed: 06/15/2023]
Abstract
The divergence process of incipient species is fascinating but elusive by incomplete lineage sorting or gene flow. Species delimitation is also challenging among those morphologically similar allopatric species, especially when lacking comprehensive data. Cycas sect. Asiorientales, comprised of C. taitungensis and C. revoluta in the Ryukyu Archipelago and Taiwan, diverged recently with continuous gene flow, resulting in a reciprocal paraphyletic relationship. Their previous evolutionary inferences are questioned from few genetic markers, incomplete sampling, and incomprehensive morphological comparison by a long-term taxonomic misconception. By whole range sampling, this study tests the geographic mode of speciation in the two species of Asiorientales by approximate Bayesian computation (ABC) using genome-wide single nucleotide polymorphisms (SNPs). The individual tree was reconstructed to delimit the species and track the gene-flow trajectory. With the comparison of diagnostic morphological traits and genetic data, the allopatric speciation was rejected. Alternatively, continuous but spatially heterogeneous gene flow driven by transoceanic vegetative dispersal and pollen flow with contrasting population sizes blurred their species boundary. On the basis of morphological, genetic, and evolutionary evidence, we synonymized these two Cycas species. This study highlights not only the importance of the Kuroshio Current to species evolution but also the disadvantage of using species with geographically structured genealogies as conservation units.
Collapse
Affiliation(s)
- Jui-Tse Chang
- School of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Chien-Ti Chao
- School of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Koh Nakamura
- Botanic Garden, Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Japan
| | - Hsiao-Lei Liu
- Department of Anthropology, Smithsonian Institution, National Museum of Natural History, Washington, DC, United States
| | - Min-Xin Luo
- School of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Pei-Chun Liao
- School of Life Science, National Taiwan Normal University, Taipei, Taiwan
| |
Collapse
|
8
|
Wong ELY, Hiscock SJ, Filatov DA. The Role of Interspecific Hybridisation in Adaptation and Speciation: Insights From Studies in Senecio. FRONTIERS IN PLANT SCIENCE 2022; 13:907363. [PMID: 35812981 PMCID: PMC9260247 DOI: 10.3389/fpls.2022.907363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 06/03/2022] [Indexed: 05/08/2023]
Abstract
Hybridisation is well documented in many species, especially plants. Although hybrid populations might be short-lived and do not evolve into new lineages, hybridisaiton could lead to evolutionary novelty, promoting adaptation and speciation. The genus Senecio (Asteraceae) has been actively used to unravel the role of hybridisation in adaptation and speciation. In this article, we first briefly describe the process of hybridisation and the state of hybridisation research over the years. We then discuss various roles of hybridisation in plant adaptation and speciation illustrated with examples from different Senecio species, but also mention other groups of organisms whenever necessary. In particular, we focus on the genomic and transcriptomic consequences of hybridisation, as well as the ecological and physiological aspects from the hybrids' point of view. Overall, this article aims to showcase the roles of hybridisation in speciation and adaptation, and the research potential of Senecio, which is part of the ecologically and economically important family, Asteraceae.
Collapse
Affiliation(s)
- Edgar L. Y. Wong
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
- *Correspondence: Edgar L. Y. Wong,
| | - Simon J. Hiscock
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
- Oxford Botanic Garden and Arboretum, Oxford, United Kingdom
| | - Dmitry A. Filatov
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| |
Collapse
|
9
|
Tamaki I, Obora T, Ohsawa T, Matsumoto A, Saito Y, Ide Y. Different population size change and migration histories created genetic diversity of three oaks in Tokai region, central Japan. JOURNAL OF PLANT RESEARCH 2021; 134:933-946. [PMID: 34155542 DOI: 10.1007/s10265-021-01323-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/14/2021] [Indexed: 06/13/2023]
Abstract
To understand genetic diversity in focal species, it is important to consider the possibility of speciation with gene flow, especially in species with porous genomes such as oaks. We studied genetic diversity and structure in three oaks, Quercus mongolica var. mongolicoides (QM), Q. mongolica var. crispula (QC) and Q. serrata (QS), growing in the Tokai region, central Japan. QM is semi-endemic to the region while the others are common taxa. We also conducted demographic modeling to infer their population size change and migration histories using an approximate Bayesian computation (ABC) approach. The three taxa showed distinct genetic structures but there was genetic admixture among the taxa, especially between QM and QC. ABC analysis of population size change revealed that the population size of QM was stable during and after the last glacial period, while QC and QS showed population expansion after the last glacial maximum. ABC analysis of population divergence and migration revealed that continuous gene flow between QM and QC after their divergence was supported, while between QM and QS, and between QC and QS, secondary contact after sufficient isolation was supported. These historical migration patterns among the three taxa indicate that QM and QC are currently in the early stage or gray zone of speciation, whereas speciation of the other two taxon pairs is considered to have almost been established. Observed gene flow patterns and strength between QM and QC, and between QM and QS, were explained by both flowering patterns and historical distributions, but those between QC and QS were not.
Collapse
Affiliation(s)
- Ichiro Tamaki
- Gifu Academy of Forest Science and Culture, 88 Sodai, Mino, Gifu, 501-3714, Japan.
| | - Tomohiro Obora
- Gifu Academy of Forest Science and Culture, 88 Sodai, Mino, Gifu, 501-3714, Japan
| | - Takafumi Ohsawa
- Ministry of the Environment, 1-2-2 Kasumigaseki, Chiyoda-ku, Tokyo, 100-8975, Japan
| | - Asako Matsumoto
- Forestry and Forest Products Research Institute, 1 Matsunosato, Tsukuba, Ibaraki, 305-8687, Japan
| | - Yoko Saito
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yuji Ide
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| |
Collapse
|
10
|
Wen G, Fu J. Isolation and reconnection: Demographic history and multiple contact zones of the green odorous frog (Odorrana margaretae) around the Sichuan Basin. Mol Ecol 2021; 30:4103-4117. [PMID: 34145663 DOI: 10.1111/mec.16021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 05/27/2021] [Accepted: 06/10/2021] [Indexed: 01/25/2023]
Abstract
The green odorous frog (Odorrana margaretae) displays a circular distribution around the Sichuan Basin of western China and possesses multiple replicate hybrid zones between lineages with high levels of divergence. To gain an understanding of the speciation process, we obtained 1540 SNPs from 29 populations and 227 individuals using ddRAD sequencing. Population structure analysis revealed three groups within the species: the West, North & South, and East groups. Demographic inference showed that they were initially isolated at ~2 million years ago, and subsequent post-glacial expansion produced the current circular distribution with four secondary contact zones. Hybridization in those zones involved lineages with various levels of divergence and produced greatly different patterns of introgression. Contact zones between the East and North & South groups (E-S and E-N) had contrast admixture levels but both showed a general lack of potential barrier loci. Meanwhile, the reconnection of the West and North & South groups produced two contact zones along the rim of the Basin. The S-W zone had extensive admixture while the N-W zone had limited admixture within a narrow geographic distance. Both showed substantial barrier effects, and a large number of potential barrier loci were shared. We also detected strong coupling among these loci. The N-W hybrid zone involved two highly-diverged lineages (FST = 0.704) and many loci have reached fixation around the hybrid zone. This study system offers a unique opportunity to understand the dynamics of introgression in contact zones and the architecture of reproductive isolation at different stages of speciation.
Collapse
Affiliation(s)
- Guannan Wen
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jinzhong Fu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China.,Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| |
Collapse
|
11
|
Bamberger S, Xu J, Hausdorf B. Evaluating Species Delimitation Methods in Radiations: The Land Snail Albinaria cretensis Complex on Crete. Syst Biol 2021; 71:439-460. [PMID: 34181027 DOI: 10.1093/sysbio/syab050] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 06/11/2021] [Accepted: 06/26/2021] [Indexed: 01/25/2023] Open
Abstract
Delimiting species in radiations is notoriously difficult because of the small differences between the incipient species, the star-like tree with short branches between species, incomplete lineage sorting, and the possibility of introgression between several of the incipient species. Next generation sequencing data may help to overcome some of these problems. We evaluated methods for species delimitation based on genome-wide markers in a land snail radiation on Crete. Species delimitation in the Albinaria cretensis group was based exclusively on shell characters until now and resulted in classifications distinguishing 3-9 species. We generated sequences of 4270 loci for 140 specimens of the Albinaria cretensis group from 48 populations by double-digest restriction site-associated DNA sequencing. We evaluated three methods for species discovery. The multispecies coalescent approach implemented in the program Bayesian Phylogenetics and Phylogeography resulted in a drastic overestimating of the number of species, whereas Gaussian clustering resulted in an overlumping. Primary species hypotheses based on the maximum percentage of the genome of the individuals derived from ancestral populations as estimated with the program ADMIXTURE moderately overestimated the number of species, but this was the only approach that provided information about gene flow between groups. Two of the methods for species validation that we applied, BFD* and delimitR, resulted in an acceptance of almost all primary species hypotheses, even such based on arbitrary subdivisions of hypotheses based on ADMIXTURE. In contrast, secondary species hypotheses, resulting from an evaluation of primary species hypotheses based on ADMIXTURE with isolation by distance tests, approached the morphological classification, but also uncovered two cryptic species and indicated that some of the previously delimited units should be combined. Thus, we recommend this combination of approaches that provided more detailed insights in the distinctness of barriers between the taxa of a species complex and the spatial distribution of admixture between them than the other methods. The recognition and delimitation of undersampled species remained a major challenge.
Collapse
Affiliation(s)
- Sonja Bamberger
- Center of Natural History, Zoological Museum, University of Hamburg, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
| | - Jie Xu
- Center of Natural History, Zoological Museum, University of Hamburg, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
| | - Bernhard Hausdorf
- Center of Natural History, Zoological Museum, University of Hamburg, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
| |
Collapse
|
12
|
Song Y, Jiang C, Li KH, Li J, Qiu H, Price M, Fan ZX, Li J. Genome-wide analysis reveals signatures of complex introgressive gene flow in macaques (genus Macaca). Zool Res 2021; 42:433-449. [PMID: 34114757 PMCID: PMC8317189 DOI: 10.24272/j.issn.2095-8137.2021.038] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The genus Macaca serves as an ideal research model for speciation and introgressive gene flow due to its short period of diversification (about five million years ago) and rapid radiation of constituent species. To understand evolutionary gene flow in macaques, we sequenced four whole genomes (two M. arctoides and two M. thibetana) and combined them with publicly available macaque genome data for genome-wide analyses. We analyzed 14 individuals from nine Macaca species covering all Asian macaque species groups and detected extensive gene flow signals, with the strongest signals between the fascicularis and silenus species groups. Notably, we detected bidirectional gene flow between M. fascicularis and M. nemestrina. The estimated proportion of the genome inherited via gene flow between the two species was 6.19%. However, the introgression signals found among studied island species, such as Sulawesi macaques and M. fuscata, and other species were largely attributed to the genomic similarity of closely related species or ancestral introgression. Furthermore, gene flow signals varied in individuals of the same species (M. arctoides, M. fascicularis, M. mulatta, M. nemestrina and M. thibetana), suggesting very recent gene flow after the populations split. Pairwise sequentially Markovian coalescence (PSMC) analysis showed all macaques experienced a bottleneck five million years ago, after which different species exhibited different fluctuations in demographic history trajectories, implying they have experienced complicated environmental variation and climate change. These results should help improve our understanding of the complicated evolutionary history of macaques, particularly introgressive gene flow.
Collapse
Affiliation(s)
- Yang Song
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
| | - Cong Jiang
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
| | - Kun-Hua Li
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
| | - Jing Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Hong Qiu
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
| | - Megan Price
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
| | - Zhen-Xin Fan
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China.,Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
| | - Jing Li
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China.,Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China. E-mail:
| |
Collapse
|
13
|
Menon M, Bagley JC, Page GFM, Whipple AV, Schoettle AW, Still CJ, Wehenkel C, Waring KM, Flores-Renteria L, Cushman SA, Eckert AJ. Adaptive evolution in a conifer hybrid zone is driven by a mosaic of recently introgressed and background genetic variants. Commun Biol 2021; 4:160. [PMID: 33547394 PMCID: PMC7864969 DOI: 10.1038/s42003-020-01632-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 11/18/2020] [Indexed: 01/30/2023] Open
Abstract
Extant conifer species may be susceptible to rapid environmental change owing to their long generation times, but could also be resilient due to high levels of standing genetic diversity. Hybridisation between closely related species can increase genetic diversity and generate novel allelic combinations capable of fuelling adaptive evolution. Our study unravelled the genetic architecture of adaptive evolution in a conifer hybrid zone formed between Pinus strobiformis and P. flexilis. Using a multifaceted approach emphasising the spatial and environmental patterns of linkage disequilibrium and ancestry enrichment, we identified recently introgressed and background genetic variants to be driving adaptive evolution along different environmental gradients. Specifically, recently introgressed variants from P. flexilis were favoured along freeze-related environmental gradients, while background variants were favoured along water availability-related gradients. We posit that such mosaics of allelic variants within conifer hybrid zones will confer upon them greater resilience to ongoing and future environmental change and can be a key resource for conservation efforts.
Collapse
Affiliation(s)
- Mitra Menon
- grid.27860.3b0000 0004 1936 9684Department of Evolution and Ecology, University of California, Davis, CA USA
| | - Justin C. Bagley
- grid.257992.20000 0001 0019 1845Department of Biology, Jacksonville State University, Jacksonville, AL USA
| | - Gerald F. M. Page
- grid.4391.f0000 0001 2112 1969Forest Ecosystems and Society, Oregon State University, Corvallis, OR USA
| | - Amy V. Whipple
- grid.261120.60000 0004 1936 8040Department of Biological Sciences and Merriam Powel Center for Environmental Research, Northern Arizona University, Flagstaff, AZ USA
| | - Anna W. Schoettle
- grid.497401.f0000 0001 2286 5230Rocky Mountain Research Station, USDA Forest Service, Fort Collins, CO USA
| | - Christopher J. Still
- grid.4391.f0000 0001 2112 1969Forest Ecosystems and Society, Oregon State University, Corvallis, OR USA
| | - Christian Wehenkel
- grid.412198.70000 0000 8724 8383Instituto de Silvicultura e Industria de la Madera, Universidad Juarez del Estado de Durango, Durango, Mexico
| | - Kristen M. Waring
- grid.261120.60000 0004 1936 8040School of Forestry, Northern Arizona University, Flagstaff, AZ USA
| | - Lluvia Flores-Renteria
- grid.263081.e0000 0001 0790 1491Department of Biology, San Diego State University, San Diego, CA USA
| | - Samuel A. Cushman
- grid.472551.00000 0004 0404 3120Rocky Mountain Research Station, USDA Forest Service, Flagstaff, AZ USA
| | - Andrew J. Eckert
- grid.224260.00000 0004 0458 8737Department of Biology, Virginia Commonwealth University, Richmond, VA USA
| |
Collapse
|
14
|
Choi JY, Purugganan M, Stacy EA. Divergent Selection and Primary Gene Flow Shape Incipient Speciation of a Riparian Tree on Hawaii Island. Mol Biol Evol 2020; 37:695-710. [PMID: 31693149 PMCID: PMC7038655 DOI: 10.1093/molbev/msz259] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
A long-standing goal of evolutionary biology is to understand the mechanisms underlying the formation of species. Of particular interest is whether or not speciation can occur in the presence of gene flow and without a period of physical isolation. Here, we investigated this process within Hawaiian Metrosideros, a hypervariable and highly dispersible woody species complex that dominates the Hawaiian Islands in continuous stands. Specifically, we investigated the origin of Metrosideros polymorpha var. newellii (newellii), a riparian ecotype endemic to Hawaii Island that is purportedly derived from the archipelago-wide M. polymorpha var. glaberrima (glaberrima). Disruptive selection across a sharp forest-riparian ecotone contributes to the isolation of these varieties and is a likely driver of newellii's origin. We examined genome-wide variation of 42 trees from Hawaii Island and older islands. Results revealed a split between glaberrima and newellii within the past 0.3-1.2 My. Admixture was extensive between lineages within Hawaii Island and between islands, but introgression from populations on older islands (i.e., secondary gene flow) did not appear to contribute to the emergence of newellii. In contrast, recurrent gene flow (i.e., primary gene flow) between glaberrima and newellii contributed to the formation of genomic islands of elevated absolute and relative divergence. These regions were enriched for genes with regulatory functions as well as for signals of positive selection, especially in newellii, consistent with divergent selection underlying their formation. In sum, our results support riparian newellii as a rare case of incipient ecological speciation with primary gene flow in trees.
Collapse
Affiliation(s)
- Jae Young Choi
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY
| | - Michael Purugganan
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY.,Center for Genomics and Systems Biology, NYU Abu Dhabi Research Institute, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Elizabeth A Stacy
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV
| |
Collapse
|
15
|
Binelli G, Montaigne W, Sabatier D, Scotti‐Saintagne C, Scotti I. Discrepancies between genetic and ecological divergence patterns suggest a complex biogeographic history in a Neotropical genus. Ecol Evol 2020; 10:4726-4738. [PMID: 32551056 PMCID: PMC7297752 DOI: 10.1002/ece3.6227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 03/04/2020] [Indexed: 11/19/2022] Open
Abstract
Phylogenetic patterns and the underlying speciation processes can be deduced from morphological, functional, and ecological patterns of species similarity and divergence. In some cases, though, species retain multiple similarities and remain almost indistinguishable; in other cases, evolutionary convergence can make such patterns misleading; very often in such cases, the "true" picture only emerges from carefully built molecular phylogenies, which may come with major surprises. In addition, closely related species may experience gene flow after divergence, thus potentially blurring species delimitation. By means of advanced inferential methods, we studied molecular divergence between species of the Virola genus (Myristicaceae): widespread Virola michelii and recently described, endemic V. kwatae, using widespread V. surinamensis as a more distantly related outgroup with different ecology and morphology-although with overlapping range. Contrary to expectations, we found that the latter, and not V. michelii, was sister to V. kwatae. Therefore, V. kwatae probably diverged from V. surinamensis through a recent morphological and ecological shift, which brought it close to distantly related V. michelii. Through the modeling of the divergence process, we inferred that gene flow between V. surinamensis and V. kwatae stopped soon after their divergence and resumed later, in a classical secondary contact event which did not erase their ecological and morphological differences. While we cannot exclude that initial divergence occurred in allopatry, current species distribution and the absence of geographical barriers make complete isolation during speciation unlikely. We tentatively conclude that (a) it is possible that divergence occurred in allopatry/parapatry and (b) secondary contact did not suppress divergence.
Collapse
Affiliation(s)
| | - William Montaigne
- UMR EcoFoGUniversité des Antilles et de la GuyaneKourouFrench Guiana
| | - Daniel Sabatier
- AMAPIRDCIRADCNRSINRAEUniversité de MontpellierMontpellierFrance
| | | | | |
Collapse
|
16
|
Baena-Díaz F, Zemp N, Widmer A. Insights into the genetic architecture of sexual dimorphism from an interspecific cross between two diverging Silene (Caryophyllaceae) species. Mol Ecol 2019; 28:5052-5067. [PMID: 31605646 DOI: 10.1111/mec.15271] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 08/15/2019] [Accepted: 09/23/2019] [Indexed: 12/15/2022]
Abstract
The evolution of sexual dimorphism in species with separate sexes is influenced by the resolution of sexual conflicts creating sex differences through genetic linkage or sex-biased expression. Plants with different degrees of sexual dimorphism are thus ideal to study the genetic basis of sexual dimorphism. In this study we explore the genetic architecture of sexual dimorphism between Silene latifolia and Silene dioica. These species have chromosomal sex determination and differ in the extent of sexual dimorphism. To test whether QTL for sexually dimorphic traits have accumulated on the sex chromosomes and to quantify their contribution to species differences, we create a linkage map and performed QTL analysis of life history, flower and vegetative traits using an unidirectional interspecific F2 hybrid cross. We found support for an accumulation of QTL on the sex chromosomes and that sex differences explained a large proportion of the variance between species, suggesting that both natural and sexual selection contributed to species divergence. Sexually dimorphic traits that also differed between species displayed transgressive segregation. We observed a reversal in sexual dimorphism in the F2 population, where males tended to be larger than females, indicating that sexual dimorphism is constrained within populations but not in recombinant hybrids. This study contributes to the understanding of the genetic basis of sexual dimorphism and its evolution in Silene.
Collapse
Affiliation(s)
| | | | - Alex Widmer
- Institute of Integrative Biology, ETH Zurich, Zürich, Switzerland
| |
Collapse
|
17
|
Loiseau O, Olivares I, Paris M, de La Harpe M, Weigand A, Koubínová D, Rolland J, Bacon CD, Balslev H, Borchsenius F, Cano A, Couvreur TLP, Delnatte C, Fardin F, Gayot M, Mejía F, Mota-Machado T, Perret M, Roncal J, Sanin MJ, Stauffer F, Lexer C, Kessler M, Salamin N. Targeted Capture of Hundreds of Nuclear Genes Unravels Phylogenetic Relationships of the Diverse Neotropical Palm Tribe Geonomateae. FRONTIERS IN PLANT SCIENCE 2019; 10:864. [PMID: 31396244 PMCID: PMC6640726 DOI: 10.3389/fpls.2019.00864] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 06/17/2019] [Indexed: 05/11/2023]
Abstract
The tribe Geonomateae is a widely distributed group of 103 species of Neotropical palms which contains six ecologically important understory or subcanopy genera. Although it has been the focus of many studies, our understanding of the evolutionary history of this group, and in particular of the taxonomically complex genus Geonoma, is far from complete due to a lack of molecular data. Specifically, the previous Sanger sequencing-based studies used a few informative characters and partial sampling. To overcome these limitations, we used a recently developed Arecaceae-specific target capture bait set to undertake a phylogenomic analysis of the tribe Geonomateae. We sequenced 3,988 genomic regions for 85% of the species of the tribe, including 84% of the species of the largest genus, Geonoma. Phylogenetic relationships were inferred using both concatenation and coalescent methods. Overall, our phylogenetic tree is highly supported and congruent with taxonomic delimitations although several morphological taxa were revealed to be non-monophyletic. It is the first time that such a large genomic dataset is provided for an entire tribe within the Arecaceae. Our study lays the groundwork not only for detailed macro- and micro-evolutionary studies within the group, but also sets a workflow for understanding other species complexes across the tree of life.
Collapse
Affiliation(s)
- Oriane Loiseau
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Ingrid Olivares
- Department for Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
- Centre for Biodiversity and Environment Research, University College London, London, United Kingdom
| | - Margot Paris
- Department of Biology, Unit Ecology and Evolution, University of Fribourg, Fribourg, Switzerland
| | - Marylaure de La Harpe
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Anna Weigand
- Department for Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
| | - Darina Koubínová
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Natural History Museum of Geneva, Geneva, Switzerland
| | - Jonathan Rolland
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
| | - Christine D. Bacon
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Henrik Balslev
- Department of Bioscience, Biodiversity and Ecoinformatics, Aarhus University, Aarhus, Denmark
| | | | - Angela Cano
- Cambridge University Botanic Garden, Cambridge, United Kingdom
| | | | | | | | - Marc Gayot
- National Forestry Office, Guadeloupe, France
| | - Fabian Mejía
- Facultad de Ciencias y Biotecnología, Universidad CES, Medellin, Colombia
| | - Talita Mota-Machado
- Programa de Pós-Graduação em Biologia Vegetal, Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Mathieu Perret
- Department of Botany and Plant Biology, Conservatory and Botanical Garden of the City of Geneva, University of Geneva, Geneva, Switzerland
| | - Julissa Roncal
- Department of Biology, Memorial University of Newfoundland, St. John’s, NL, Canada
| | - Maria José Sanin
- Facultad de Ciencias y Biotecnología, Universidad CES, Medellin, Colombia
| | - Fred Stauffer
- Department of Botany and Plant Biology, Conservatory and Botanical Garden of the City of Geneva, University of Geneva, Geneva, Switzerland
| | - Christian Lexer
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Michael Kessler
- Department for Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
| | - Nicolas Salamin
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| |
Collapse
|
18
|
Abstract
Introgression is emerging as an important source of novel genetic variation, alongside standing variation and mutation. It is adaptive when such introgressed alleles are maintained by natural selection. Recently, there has been an explosion in the number of studies on adaptive introgression. In this review, we take a plant perspective centred on four lines of evidence: (i) introgression, (ii) selection, (iii) phenotype and (iv) fitness. While advances in genomics have contributed to our understanding of introgression and porous species boundaries (task 1), and the detection of signatures of selection in introgression (task 2), the investigation of adaptive introgression critically requires links to phenotypic variation and fitness (tasks 3 and 4). We also discuss the conservation implications of adaptive introgression in the face of climate change. Adaptive introgression is particularly important in rapidly changing environments, when standing genetic variation and mutation alone may only offer limited potential for adaptation. We conclude that clarifying the magnitude and fitness effects of introgression with improved statistical techniques, coupled with phenotypic evidence, has great potential for conservation and management efforts.
Collapse
Affiliation(s)
| | - Christian Lexer
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Quentin C B Cronk
- Department of Botany, University of British Columbia, Vancouver, Canada
| |
Collapse
|
19
|
He T, Lamont BB, Enright NJ, D'Agui HM, Stock W. Environmental drivers and genomic architecture of trait differentiation in fire-adapted Banksia attenuata ecotypes. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:417-432. [PMID: 29993190 DOI: 10.1111/jipb.12697] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 07/10/2018] [Indexed: 06/08/2023]
Abstract
Trait divergence between populations is considered an adaptive response to different environments, but to what extent this response is accompanied by genetic differentiation is less clear since it may be phenotypic plasticity. In this study, we analyzed phenotypic variation between two Banksia attenuata growth forms, lignotuberous (shrub) and epicormic resprouting (tree), in fire-prone environments to identify the environmental factors that have driven this phenotypic divergence. We linked genotype with phenotype and traced candidate genes using differential gene expression analysis. Fire intervals determined the phenotypic divergence between growth forms in B. attenuata. A genome-wide association study identified 69 single nucleotide polymorphisms, putatively associated with growth form, whereas no growth form- or phenotype-specific genotypes were identified. Genomic differentiation between the two growth forms was low (Fst = 0.024). Differential gene expression analysis identified 37 genes/transcripts that were differentially expressed in the two growth forms. A small heat-shock protein gene, associated with lignotuber presence, was differentially expressed in the two forms. We conclude that different fire regimes induce phenotypic polymorphism in B. attenuata, whereas phenotypic trait divergence involves the differential expression of a small fraction of genes that interact strongly with the disturbance regime. Thus, phenotypic plasticity among resprouters is the general strategy for surviving varying fire regimes.
Collapse
Affiliation(s)
- Tianhua He
- School of Molecular and Life Sciences, Curtin University, GPO Box U1987, Perth WA 6845, Australia
| | - Byron B Lamont
- School of Molecular and Life Sciences, Curtin University, GPO Box U1987, Perth WA 6845, Australia
| | - Neal J Enright
- School of Veterinary and Life Sciences, Murdoch University, Perth WA 6150, Australia
| | - Haylee M D'Agui
- School of Molecular and Life Sciences, Curtin University, GPO Box U1987, Perth WA 6845, Australia
| | - William Stock
- Centre for Ecosystem Management, Edith Cowan University, Joondalup WA 6027, Australia
| |
Collapse
|
20
|
Karrenberg S, Liu X, Hallander E, Favre A, Herforth-Rahmé J, Widmer A. Ecological divergence plays an important role in strong but complex reproductive isolation in campions (Silene). Evolution 2018; 73:245-261. [PMID: 30499144 DOI: 10.1111/evo.13652] [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: 06/12/2018] [Revised: 11/13/2018] [Accepted: 01/16/2018] [Indexed: 12/27/2022]
Abstract
New species arise through the evolution of reproductive barriers between formerly interbreeding lineages. Yet, comprehensive assessments of potential reproductive barriers, which are needed to make inferences on processes driving speciation, are only available for a limited number of systems. In this study, we estimated individual and cumulative strengths of seven prezygotic and six postzygotic reproductive barriers between the recently diverged taxa Silene dioica (L.) Clairv. and S. latifolia Poiret using both published and new data. A combination of multiple partial reproductive barriers resulted in near-complete reproductive isolation between S. dioica and S. latifolia, consistent with earlier estimates of gene flow between the taxa. Extrinsic barriers associated with adaptive ecological divergence were most important, while intrinsic postzygotic barriers had moderate individual strength but contributed only little to total reproductive isolation. These findings are in line with ecological divergence as driver of speciation. We further found extensive variation in extrinsic reproductive isolation, ranging from sites with very strong selection against migrants and hybrids to intermediate sites where substantial hybridization is possible. This situation may allow for, or even promote, heterogeneous genetic divergence.
Collapse
Affiliation(s)
- Sophie Karrenberg
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18 D, 75236, Uppsala, Sweden
| | - Xiaodong Liu
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18 D, 75236, Uppsala, Sweden
| | - Emelie Hallander
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18 D, 75236, Uppsala, Sweden.,Current Address: Swedish Board of Agriculture, Vallgatan 8, 551 82, Jönköping, Sweden
| | - Adrien Favre
- Department of Diversity and Evolution of Higher Plants, Institute of Ecology, Evolution and Diversity, Goethe-University, 60439, Frankfurt am Main, Germany.,Senckenberg Research Institute and Natural History Museum, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Joelle Herforth-Rahmé
- ETH Zurich, Institute of Integrative Biology, Universitätstrasse 16, 8092, Zürich, Switzerland.,Current Address: Research Institute of Organic Agriculture FiBL, Department of Soil Sciences, Ackerstrasse 113, Box 219, 5070, Frick, Switzerland
| | - Alex Widmer
- ETH Zurich, Institute of Integrative Biology, Universitätstrasse 16, 8092, Zürich, Switzerland
| |
Collapse
|
21
|
Gramlich S, Wagner ND, Hörandl E. RAD-seq reveals genetic structure of the F 2-generation of natural willow hybrids (Salix L.) and a great potential for interspecific introgression. BMC PLANT BIOLOGY 2018; 18:317. [PMID: 30509159 PMCID: PMC6276181 DOI: 10.1186/s12870-018-1552-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 11/21/2018] [Indexed: 05/23/2023]
Abstract
BACKGROUND Hybridization of species with porous genomes can eventually lead to introgression via repeated backcrossing. The potential for introgression between species is reflected by the extent of segregation distortion in later generation hybrids. Here we studied a population of hybrids between Salix purpurea and S. helvetica that has emerged within the last 30 years on a glacier forefield in the European Alps due to secondary contact of the parental species. We used 5758 biallelic SNPs produced by RAD sequencing with the aim to ascertain the predominance of backcrosses (F1 hybrid x parent) or F2 hybrids (F1 hybrid x F1 hybrid) among hybrid offspring. Further, the SNPs were used to study segregation distortion in the second hybrid generation. RESULTS The analyses in STRUCTURE and NewHybrids revealed that the population consisted of parents and F1 hybrids, whereas hybrid offspring consisted mainly of backcrosses to either parental species, but also some F2 hybrids. Although there was a clear genetic differentiation between S. purpurea and S. helvetica (FST = 0.24), there was no significant segregation distortion in the backcrosses or the F2 hybrids. Plant height of the backcrosses resembled the respective parental species, whereas F2 hybrids were more similar to the subalpine S. helvetica. CONCLUSIONS The co-occurrence of the parental species and the hybrids on the glacier forefield, the high frequency of backcrossing, and the low resistance to gene flow via backcrossing make a scenario of introgression in this young hybrid population highly likely, potentially leading to the transfer of adaptive traits. We further suggest that this willow hybrid population may serve as a model for the evolutionary processes initiated by recent global warming.
Collapse
Affiliation(s)
- Susanne Gramlich
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University Goettingen, Untere Karspüle 2, 37073 Goettingen, Germany
| | - Natascha Dorothea Wagner
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University Goettingen, Untere Karspüle 2, 37073 Goettingen, Germany
| | - Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University Goettingen, Untere Karspüle 2, 37073 Goettingen, Germany
| |
Collapse
|
22
|
Liu X, Karrenberg S. Genetic architecture of traits associated with reproductive barriers in Silene: Coupling, sex chromosomes and variation. Mol Ecol 2018; 27:3889-3904. [PMID: 29577481 DOI: 10.1111/mec.14562] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 01/22/2018] [Accepted: 01/31/2018] [Indexed: 01/02/2023]
Abstract
The evolution of reproductive barriers and their underlying genetic architecture is of central importance for the formation of new species. Reproductive barriers can be controlled either by few large-effect loci suggesting strong selection on key traits, or by many small-effect loci, consistent with gradual divergence or with selection on polygenic or multiple traits. Genetic coupling between reproductive barrier loci further promotes divergence, particularly divergence with ongoing gene flow. In this study, we investigated the genetic architectures of ten morphological, phenological and life history traits associated with reproductive barriers between the hybridizing sister species Silene dioica and S. latifolia; both are dioecious with XY-sex determination. We used quantitative trait locus (QTL) mapping in two reciprocal F2 crosses. One to six QTLs per trait, including nine major QTLs (PVE > 20%), were detected on 11 of the 12 linkage groups. We found strong evidence for coupling of QTLs for uncorrelated traits and for an important role of sex chromosomes in the genetic architectures of reproductive barrier traits. Unexpectedly, QTLs detected in the two F2 crosses differed largely, despite limited phenotypic differences between them and sufficient statistical power. The widely dispersed genetic architectures of traits associated with reproductive barriers suggest gradual divergence or multifarious selection. Coupling of the underlying QTLs likely promoted divergence with gene flow in this system. The low congruence of QTLs between the two crosses further points to variable and possibly redundant genetic architectures of traits associated with reproductive barriers, with important implications for the evolutionary dynamics of divergence and speciation.
Collapse
Affiliation(s)
- Xiaodong Liu
- Department of Ecology and Genetics, Evolutionary Biology Center, Uppsala University, Uppsala, Sweden
| | - Sophie Karrenberg
- Department of Ecology and Genetics, Evolutionary Biology Center, Uppsala University, Uppsala, Sweden
| |
Collapse
|
23
|
Rutherford S, Rossetto M, Bragg JG, McPherson H, Benson D, Bonser SP, Wilson PG. Speciation in the presence of gene flow: population genomics of closely related and diverging Eucalyptus species. Heredity (Edinb) 2018; 121:126-141. [PMID: 29632325 DOI: 10.1038/s41437-018-0073-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 03/12/2018] [Accepted: 03/12/2018] [Indexed: 01/22/2023] Open
Abstract
Speciation is a complex process that is fundamental to the origins of biological diversity. While there has been considerable progress in our understanding of speciation, there are still many unanswered questions, especially regarding barriers to gene flow in diverging populations. Eucalyptus is an appropriate system for investigating speciation mechanisms since it comprises species that are rapidly evolving across heterogeneous environments. We examined patterns of genetic variation within and among six closely related Eucalyptus species in subgenus Eucalyptus section Eucalyptus in south-eastern Australia (commonly known as the "green ashes"). We used reduced representation genome sequencing to genotype samples from populations across altitudinal and latitudinal gradients. We found one species, Eucalyptus cunninghamii, to be highly genetically differentiated from the others, and a population of mallees from Mount Banks to be genetically distinct and therefore likely to be a new undescribed species. Only modest levels of differentiation were found between all other species in the study. There was population structure within some species (e.g., E. obstans) corresponding to geographical factors, indicating that vicariance may have played a role in the evolution of the group. Overall, we found that lineages within the green ashes are differentiated to varying extents, from strongly diverged to much earlier stages of the speciation continuum. Furthermore, our results suggest the green ashes represent a group where a range of mechanisms (e.g., reticulate evolution and vicariance) have been operating in concert. These findings not only offer insights into recent speciation mechanisms in Eucalyptus, but also other species complexes.
Collapse
Affiliation(s)
- Susan Rutherford
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW, Kensington, Sydney, Australia. .,National Herbarium of NSW, Royal Botanic Garden Sydney, Sydney, Australia.
| | - Maurizio Rossetto
- National Herbarium of NSW, Royal Botanic Garden Sydney, Sydney, Australia
| | - Jason G Bragg
- National Herbarium of NSW, Royal Botanic Garden Sydney, Sydney, Australia
| | - Hannah McPherson
- National Herbarium of NSW, Royal Botanic Garden Sydney, Sydney, Australia
| | - Doug Benson
- National Herbarium of NSW, Royal Botanic Garden Sydney, Sydney, Australia
| | - Stephen P Bonser
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW, Kensington, Sydney, Australia
| | - Peter G Wilson
- National Herbarium of NSW, Royal Botanic Garden Sydney, Sydney, Australia
| |
Collapse
|
24
|
Sung C, Bell KL, Nice CC, Martin NH. Integrating Bayesian genomic cline analyses and association mapping of morphological and ecological traits to dissect reproductive isolation and introgression in a Louisiana Iris hybrid zone. Mol Ecol 2018; 27:959-978. [DOI: 10.1111/mec.14481] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 12/14/2017] [Indexed: 01/01/2023]
Affiliation(s)
- Cheng‐Jung Sung
- Population and Conservation Biology Program Department of Biology Texas State University San Marcos TX USA
| | - Katherine L. Bell
- Population and Conservation Biology Program Department of Biology Texas State University San Marcos TX USA
| | - Chris C. Nice
- Population and Conservation Biology Program Department of Biology Texas State University San Marcos TX USA
| | - Noland H. Martin
- Population and Conservation Biology Program Department of Biology Texas State University San Marcos TX USA
| |
Collapse
|
25
|
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.
Collapse
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.
| |
Collapse
|
26
|
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.
Collapse
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
| |
Collapse
|
27
|
Leroy T, Roux C, Villate L, Bodénès C, Romiguier J, Paiva JAP, Dossat C, Aury JM, Plomion C, Kremer A. Extensive recent secondary contacts between four European white oak species. THE NEW PHYTOLOGIST 2017; 214:865-878. [PMID: 28085203 PMCID: PMC5624484 DOI: 10.1111/nph.14413] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 11/21/2016] [Indexed: 05/04/2023]
Abstract
Historical trajectories of tree species during the late Quaternary have been well reconstructed through genetic and palaeobotanical studies. However, many congeneric tree species are interfertile, and the timing and contribution of introgression to species divergence during their evolutionary history remains largely unknown. We quantified past and current gene flow events between four morphologically divergent oak species (Quercus petraea, Q. robur, Q. pyrenaica, Q. pubescens), by two independent inference methods: diffusion approximation to the joint frequency spectrum (∂a∂i) and approximate Bayesian computation (ABC). For each pair of species, alternative scenarios of speciation allowing gene flow over different timescales were evaluated. Analyses of 3524 single nucleotide polymorphisms (SNPs) randomly distributed in the genome, showed that these species evolved in complete isolation for most of their history, but recently came into secondary contact, probably facilitated by the most recent period of postglacial warming. We demonstrated that: there was sufficient genetic differentiation before secondary contact for the accumulation of barriers to gene flow; and current European white oak genomes are a mosaic of genes that have crossed species boundaries and genes impermeable to gene flow.
Collapse
Affiliation(s)
- Thibault Leroy
- BIOGECO, INRA, Université de Bordeaux, Cestas, 33610, France
| | - Camille Roux
- Department of Ecology and Evolution, University of Lausanne, Lausanne, 1015, Switzerland
| | - Laure Villate
- BIOGECO, INRA, Université de Bordeaux, Cestas, 33610, France
| | | | - Jonathan Romiguier
- Department of Ecology and Evolution, University of Lausanne, Lausanne, 1015, Switzerland
| | - Jorge A P Paiva
- Instituto de Biologia Experimental e Tecnológica, iBET, Apartado 12, Oeiras, 2780-901, Portugal
- Institute of Plant Genetics, Polish Academy of Sciences, 34 Strzeszynska street, Poznań, PL-60-479, Poland
| | - Carole Dossat
- Institut de Genomique (IG), Commissariat à l'Energie Atomique (CEA), Genoscope, Evry, 91057, France
| | - Jean-Marc Aury
- Institut de Genomique (IG), Commissariat à l'Energie Atomique (CEA), Genoscope, Evry, 91057, France
| | | | - Antoine Kremer
- BIOGECO, INRA, Université de Bordeaux, Cestas, 33610, France
| |
Collapse
|
28
|
Serrano-Serrano ML, Marcionetti A, Perret M, Salamin N. Transcriptomic resources for an endemic Neotropical plant lineage (Gesneriaceae). APPLICATIONS IN PLANT SCIENCES 2017; 5:apps1600135. [PMID: 28439475 PMCID: PMC5400431 DOI: 10.3732/apps.1600135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 03/06/2017] [Indexed: 06/07/2023]
Abstract
PREMISE OF THE STUDY Despite the extensive phenotypic variation that characterizes the Gesneriaceae family, there is a lack of genomic resources to investigate the molecular basis of their diversity. We developed and compared the transcriptomes for two species of the Neotropical lineage of the Gesneriaceae. METHODS AND RESULTS Illumina sequencing and de novo assembly of floral and leaf samples were used to generate multigene sequence data for Sinningia eumorpha and S. magnifica, two species endemic to the Brazilian Atlantic Forest. A total of 300 million reads were used to assemble the transcriptomes, with an average of 92,038 transcripts and 43,506 genes per species. The transcriptomes showed good quality metrics, with the presence of all eukaryotic core genes, and an equal representation of clusters of orthologous groups (COG) classifications between species. The orthologous search produced 8602 groups, with 15-20% of them annotated using BLAST tools. DISCUSSION This study provides the first step toward a comprehensive multispecies transcriptome characterization of the Gesneriaceae family. These resources are the basis for comparative analyses in this species-rich Neotropical plant group; they will also allow the investigation of the evolutionary importance of multiple metabolic pathways and phenotypic diversity, as well as developmental programs in these nonmodel species.
Collapse
Affiliation(s)
- Martha L. Serrano-Serrano
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland
| | - Anna Marcionetti
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland
| | - Mathieu Perret
- Conservatoire et Jardin botaniques de la Ville de Genève and Laboratory of Plant Systematics and Biodiversity, University of Geneva, Chemin de l’Impératrice 1, 1292 Chambésy, Geneva, Switzerland
| | - Nicolas Salamin
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland
| |
Collapse
|
29
|
Smith JF, Clark JL, Amaya-Márquez M, Marín-Gómez OH. Resolving incongruence: Species of hybrid origin in Columnea (Gesneriaceae). Mol Phylogenet Evol 2017; 106:228-240. [DOI: 10.1016/j.ympev.2016.10.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 09/30/2016] [Accepted: 10/03/2016] [Indexed: 01/19/2023]
|
30
|
Dowling TE, Markle DF, Tranah GJ, Carson EW, Wagman DW, May BP. Introgressive Hybridization and the Evolution of Lake-Adapted Catostomid Fishes. PLoS One 2016; 11:e0149884. [PMID: 26959681 PMCID: PMC4784955 DOI: 10.1371/journal.pone.0149884] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 02/06/2016] [Indexed: 12/13/2022] Open
Abstract
Hybridization has been identified as a significant factor in the evolution of plants as groups of interbreeding species retain their phenotypic integrity despite gene exchange among forms. Recent studies have identified similar interactions in animals; however, the role of hybridization in the evolution of animals has been contested. Here we examine patterns of gene flow among four species of catostomid fishes from the Klamath and Rogue rivers using molecular and morphological traits. Catostomus rimiculus from the Rogue and Klamath basins represent a monophyletic group for nuclear and morphological traits; however, the Klamath form shares mtDNA lineages with other Klamath Basin species (C. snyderi, Chasmistes brevirostris, Deltistes luxatus). Within other Klamath Basin taxa, D. luxatus was largely fixed for alternate nuclear alleles relative to C. rimiculus, while Ch. brevirostris and C. snyderi exhibited a mixture of these alleles. Deltistes luxatus was the only Klamath Basin species that exhibited consistent covariation of nuclear and mitochondrial traits and was the primary source of mismatched mtDNA in Ch. brevirostris and C. snyderi, suggesting asymmetrical introgression into the latter species. In Upper Klamath Lake, D. luxatus spawning was more likely to overlap spatially and temporally with C. snyderi and Ch. brevirostris than either of those two with each other. The latter two species could not be distinguished with any molecular markers but were morphologically diagnosable in Upper Klamath Lake, where they were largely spatially and temporally segregated during spawning. We examine parallel evolution and syngameon hypotheses and conclude that observed patterns are most easily explained by introgressive hybridization among Klamath Basin catostomids.
Collapse
Affiliation(s)
- Thomas E. Dowling
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
- * E-mail:
| | - Douglas F. Markle
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, Oregon, United States of America
| | - Greg J. Tranah
- Department of Animal Science, University of California Davis, Davis, California, United States of America
| | - Evan W. Carson
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - David W. Wagman
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, Oregon, United States of America
| | - Bernard P. May
- Department of Animal Science, University of California Davis, Davis, California, United States of America
| |
Collapse
|
31
|
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.
Collapse
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
| |
Collapse
|
32
|
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
| |
Collapse
|
33
|
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.
Collapse
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
| |
Collapse
|
34
|
Liu J, Zhou W, Gong X. Species delimitation, genetic diversity and population historical dynamics of Cycas diannanensis (Cycadaceae) occurring sympatrically in the Red River region of China. FRONTIERS IN PLANT SCIENCE 2015; 6:696. [PMID: 26442013 PMCID: PMC4562272 DOI: 10.3389/fpls.2015.00696] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 08/21/2015] [Indexed: 06/02/2023]
Abstract
Delimitating species boundaries could be of critical importance when evaluating the species' evolving process and providing guidelines for conservation genetics. Here, species delimitation was carried out on three endemic and endangered Cycas species with resembling morphology and overlapped distribution range along the Red River (Yuanjiang) in China: Cycas diananensis Z. T. Guan et G. D. Tao, Cycas parvula S. L. Yang and Cycas multiovula D. Y. Wang. A total of 137 individuals from 15 populations were genotyped by using three chloroplastic (psbA-trnH, atpI-atpH, and trnL-rps4) and two single copy nuclear (RPB1 and SmHP) DNA sequences. Basing on the carefully morphological comparison and cladistic haplotype aggregation (CHA) analysis, we propose all the populations as one species, with the rest two incorporated into C. diannanensis. Genetic diversity and structure analysis of the conflated C. diannanensis revealed this species possessed a relative lower genetic diversity than estimates of other Cycas species. The higher genetic diversity among populations and relative lower genetic diversity within populations, as well as obvious genetic differentiation among populations inferred from chloroplastic DNA (cpDNA) suggested a recent genetic loss within this protected species. Additionally, a clear genetic structure of C. diannanensis corresponding with geography was detected based on cpDNA, dividing its population ranges into "Yuanjiang-Nanhun" basin and "Ejia-Jiepai" basin groups. Demographical history analyses based on combined cpDNA and one nuclear DNA (nDNA) SmHP both showed the population size of C. diannanensis began to decrease in Quaternary glaciation with no subsequent expansion, while another nDNA RPB1 revealed a more recent sudden expansion after long-term population size contraction, suggesting its probable bottleneck events in history. Our findings offer grounded views for clarifying species boundaries of C. diannanensis when determining the conservation objectives. For operational guidelines, the downstream populations which occupy high and peculiar haplotypes should be given prior in-situ conservation. In addition, ex-situ conservation and reintroduction measures for decades of generations are supplemented for improving the population size and genetic diversity of the endemic and endangered species.
Collapse
Affiliation(s)
- Jian Liu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- University of Chinese Academy of SciencesBeijing, China
| | - Wei Zhou
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
| | - Xun Gong
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- Yunnan Key Laboratory for Wild Plant ResourcesKunming, China
| |
Collapse
|
35
|
Pinheiro F, Cafasso D, Cozzolino S, Scopece G. Transitions between self-compatibility and self-incompatibility and the evolution of reproductive isolation in the large and diverse tropical genus Dendrobium (Orchidaceae). ANNALS OF BOTANY 2015; 116:457-67. [PMID: 25953040 PMCID: PMC4549954 DOI: 10.1093/aob/mcv057] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 03/30/2015] [Indexed: 05/09/2023]
Abstract
BACKGROUND AND AIMS The evolution of interspecific reproductive barriers is crucial to understanding species evolution. This study examines the contribution of transitions between self-compatibility (SC) and self-incompatibility (SI) and genetic divergence in the evolution of reproductive barriers in Dendrobium, one of the largest orchid genera. Specifically, it investigates the evolution of pre- and postzygotic isolation and the effects of transitions between compatibility states on interspecific reproductive isolation within the genus. METHODS The role of SC and SI changes in reproductive compatibility among species was examined using fruit set and seed viability data available in the literature from 86 species and ∼2500 hand pollinations. The evolution of SC and SI in Dendrobium species was investigated within a phylogenetic framework using internal transcribed spacer sequences available in GenBank. KEY RESULTS Based on data from crossing experiments, estimations of genetic distance and the results of a literature survey, it was found that changes in SC and SI significantly influenced the compatibility between species in interspecific crosses. The number of fruits produced was significantly higher in crosses in which self-incompatible species acted as pollen donor for self-compatible species, following the SI × SC rule. Maximum likelihood and Bayesian tests did not reject transitions from SI to SC and from SC to SI across the Dendrobium phylogeny. In addition, postzygotic isolation (embryo mortality) was found to evolve gradually with genetic divergence, in agreement with previous results observed for other plant species, including orchids. CONCLUSIONS Transitions between SC and SI and the gradual accumulation of genetic incompatibilities affecting postzygotic isolation are important mechanisms preventing gene flow among Dendrobium species, and may constitute important evolutionary processes contributing to the high levels of species diversity in this tropical orchid group.
Collapse
Affiliation(s)
- Fabio Pinheiro
- Departamento de Botânica, Instituto de Biociências, Universidade Estadual Paulista, 13506-900, Rio Claro, SP, Brazil,
| | - Donata Cafasso
- Università degli Studi di Napoli Federico II, Department of Biology, via Cinthia, I-80126, Naples, Italy and
| | - Salvatore Cozzolino
- Università degli Studi di Napoli Federico II, Department of Biology, via Cinthia, I-80126, Naples, Italy and
| | - Giovanni Scopece
- Università degli Studi di Napoli Federico II, Department of Biology, via Cinthia, I-80126, Naples, Italy and Institute for Plant Protection, Consiglio Nazionale delle Ricerche, Via Madonna del Piano, 10, I-50019, Sesto Fiorentino (FI), Italy
| |
Collapse
|
36
|
Mosaic genetic differentiation along environmental and geographic gradients indicate divergent selection in a white pine species complex. Evol Ecol 2015. [DOI: 10.1007/s10682-015-9785-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
37
|
Hamlin JAP, Arnold ML. Neutral and Selective Processes Drive Population Differentiation for Iris hexagona. J Hered 2015; 106:628-36. [PMID: 26163584 DOI: 10.1093/jhered/esv045] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 06/11/2015] [Indexed: 11/15/2022] Open
Abstract
Gene flow among widespread populations can be reduced by geographical distance or by divergent selection resulting from local adaptation. In this study, we tested for the divergence of phenotypes and genotypes among 8 populations of Iris hexagona. Using a genotyping-by-sequencing approach, we generated a panel of 750 single nucleotide polymorphisms (SNPs) and used population genetic analyses to determine what may affect patterns of divergence across I. hexagona populations. Specifically, genetic differentiation was compared between populations at neutral and nonneutral SNPs and detected significant differences between the 2 types of markers. We then asked whether loci with the strongest degree of population genetic differentiation were also the loci with the strongest association to morphology or climate differences, allowing us to test if pollinators or climate drive population differentiation or some combination of both. We found 2 markers that were associated with morphology and 1 marker associated with 2 of the environmental variables, which were also identified in the outlier analysis. We then show that the SNPs putatively under selection were positively correlated with both geographic distance and phenotypic distance, albeit weakly to phenotypic distance. Moreover, neutral SNPs were only correlated with geographic distance and thus isolation-by-distance was observed for neutral SNPs. Our data suggest that both deterministic and neutral processes have contributed to the evolutionary trajectory of I. hexagona populations.
Collapse
Affiliation(s)
- Jennafer A P Hamlin
- From the Department of Genetics, University of Georgia, 120 East Green St., Davison Life Sciences Building, Athens, GA (Arnold) and the Department of Biology, Indiana University, Bloomington, IN 47405, USA (Hamlin).
| | - Michael L Arnold
- From the Department of Genetics, University of Georgia, 120 East Green St., Davison Life Sciences Building, Athens, GA (Arnold) and the Department of Biology, Indiana University, Bloomington, IN 47405, USA (Hamlin)
| |
Collapse
|
38
|
Marczewski T, Chamberlain DF, Milne RI. Hybridization in closely related Rhododendron species: half of all species-differentiating markers experience serious transmission ratio distortion. Ecol Evol 2015; 5:3003-22. [PMID: 26357534 PMCID: PMC4559045 DOI: 10.1002/ece3.1570] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 05/18/2015] [Accepted: 05/19/2015] [Indexed: 01/29/2023] Open
Abstract
An increasing number of studies of hybridization in recent years have revealed that complete reproductive isolation between species is frequently not finalized in more or less closely related organisms. Most of these species do, however, seem to retain their phenotypical characteristics despite the implication of gene flow, highlighting the remaining gap in our knowledge of how much of an organism’s genome is permeable to gene flow, and which factors promote or prevent hybridization. We used AFLP markers to investigate the genetic composition of three populations involving two interfertile Rhododendron species: two sympatric populations, of which only one contained hybrids, and a further hybrid-dominated population. No fixed differences between the species were found, and only 5.8% of the markers showed some degree of species differentiation. Additionally, 45.5% of highly species-differentiating markers experienced significant transmission distortion in the hybrids, which was most pronounced in F1 hybrids, suggesting that factors conveying incompatibilities are still segregating within the species. Furthermore, the two hybrid populations showed stark contrasting composition of hybrids; one was an asymmetrically backcrossing hybrid swarm, while in the other, backcrosses were absent, thus preventing gene flow.
Collapse
Affiliation(s)
- Tobias Marczewski
- Royal Botanic Garden Edinburgh 20A Inverleith Row, Edinburgh, EH3 5LR, UK ; Institute of Molecular Plant Sciences, University of Edinburgh Mayfield Road, Edinburgh, EH9 3JH, UK
| | | | - Richard I Milne
- Royal Botanic Garden Edinburgh 20A Inverleith Row, Edinburgh, EH3 5LR, UK ; Institute of Molecular Plant Sciences, University of Edinburgh Mayfield Road, Edinburgh, EH9 3JH, UK
| |
Collapse
|
39
|
Breitkopf H, Onstein RE, Cafasso D, Schlüter PM, Cozzolino S. Multiple shifts to different pollinators fuelled rapid diversification in sexually deceptive Ophrys orchids. THE NEW PHYTOLOGIST 2015; 207:377-389. [PMID: 25521237 DOI: 10.1111/nph.13219] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 10/31/2014] [Indexed: 05/03/2023]
Abstract
Episodes of rapid speciation provide unique insights into evolutionary processes underlying species radiations and patterns of biodiversity. Here we investigated the radiation of sexually deceptive bee orchids (Ophrys). Based on a time-calibrated phylogeny and by means of ancestral character reconstruction and divergence time estimation, we estimated the tempo and mode of this radiation within a state-dependent evolutionary framework. It appears that, in the Pleistocene, the evolution of Ophrys was marked by episodes of rapid diversification coinciding with shifts to different pollinator types: from wasps to Eucera bees to Andrena and other bees. An abrupt increase in net diversification rate was detected in three clades. Among these, two phylogenetically distant lineages switched from Eucera to Andrena and other bees in a parallel fashion and at about the same time in their evolutionary history. Lack of early radiation associated with the evolution of the key innovation of sexual deception suggests that Ophrys diversification was mainly driven by subsequent ecological opportunities provided by the exploitation of novel pollinator groups, encompassing many bee species slightly differing in their sex pheromone communication systems, and by spatiotemporal fluctuations in the pollinator mosaic.
Collapse
Affiliation(s)
- Hendrik Breitkopf
- Department of Biology, University of Naples Federico II, Naples, Italy
- Institute of Biochemistry and Biology, Biodiversity Research/Systematic Botany, University of Potsdam, Potsdam, Germany
| | - Renske E Onstein
- Institute of Systematic Botany, University of Zurich, Zurich, Switzerland
| | - Donata Cafasso
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Philipp M Schlüter
- Institute of Systematic Botany, University of Zurich, Zurich, Switzerland
| | | |
Collapse
|
40
|
Smouse PE, Whitehead MR, Peakall R. An informational diversity framework, illustrated with sexually deceptive orchids in early stages of speciation. Mol Ecol Resour 2015; 15:1375-84. [PMID: 25916981 DOI: 10.1111/1755-0998.12422] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 04/20/2015] [Accepted: 04/23/2015] [Indexed: 11/30/2022]
Abstract
Reconstructing evolutionary history for emerging species complexes is notoriously difficult, with newly isolated taxa often morphologically cryptic and the signature of reproductive isolation often restricted to a few genes. Evidence from multiple loci and genomes is highly desirable, but multiple inputs require 'common currency' translation. Here we deploy a Shannon information framework, converting into diversity analogue, which provides a common currency analysis for maternally inherited haploid and bi-parentally inherited diploid nuclear markers, and then extend that analysis to construction of minimum-spanning networks for both genomes. The new approach is illustrated with a quartet of cryptic congeners from the sexually deceptive Australian orchid genus Chiloglottis, still in the early stages of speciation. Divergence is more rapid for haploid plastids than for nuclear markers, consistent with the effective population size differential (N(ep) < (N(en)), but divergence patterns are broadly correlated for the two genomes. There are nevertheless intriguing discrepancies between the emerging plastid and nuclear signals of early phylogenetic radiation of these taxa, and neither pattern is entirely consistent with the available information on the sexual cues used by the orchids to lure the pollinators enforcing reproductive isolation. We describe possible extensions of this methodology to multiple ploidy levels and other types of markers, which should increase the range of application to any taxonomic assemblage in the very early stages of reproductive isolation and speciation.
Collapse
Affiliation(s)
- Peter E Smouse
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ, 08901-8551, USA
| | - Michael R Whitehead
- Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, ACT, 0200, Australia
| | - Rod Peakall
- Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, ACT, 0200, Australia
| |
Collapse
|
41
|
Xu S, Schlüter PM. Modeling the two-locus architecture of divergent pollinator adaptation: how variation in SAD paralogs affects fitness and evolutionary divergence in sexually deceptive orchids. Ecol Evol 2015; 5:493-502. [PMID: 25691974 PMCID: PMC4314279 DOI: 10.1002/ece3.1378] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 12/01/2014] [Indexed: 01/26/2023] Open
Abstract
Divergent selection by pollinators can bring about strong reproductive isolation via changes at few genes of large effect. This has recently been demonstrated in sexually deceptive orchids, where studies (1) quantified the strength of reproductive isolation in the field; (2) identified genes that appear to be causal for reproductive isolation; and (3) demonstrated selection by analysis of natural variation in gene sequence and expression. In a group of closely related Ophrys orchids, specific floral scent components, namely n-alkenes, are the key floral traits that control specific pollinator attraction by chemical mimicry of insect sex pheromones. The genetic basis of species-specific differences in alkene production mainly lies in two biosynthetic genes encoding stearoyl–acyl carrier protein desaturases (SAD) that are associated with floral scent variation and reproductive isolation between closely related species, and evolve under pollinator-mediated selection. However, the implications of this genetic architecture of key floral traits on the evolutionary processes of pollinator adaptation and speciation in this plant group remain unclear. Here, we expand on these recent findings to model scenarios of adaptive evolutionary change at SAD2 and SAD5, their effects on plant fitness (i.e., offspring number), and the dynamics of speciation. Our model suggests that the two-locus architecture of reproductive isolation allows for rapid sympatric speciation by pollinator shift; however, the likelihood of such pollinator-mediated speciation is asymmetric between the two orchid species O. sphegodes and O. exaltata due to different fitness effects of their predominant SAD2 and SAD5 alleles. Our study not only provides insight into pollinator adaptation and speciation mechanisms of sexually deceptive orchids but also demonstrates the power of applying a modeling approach to the study of pollinator-driven ecological speciation.
Collapse
Affiliation(s)
- Shuqing Xu
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology Hans-Knöll-Straße 8, D-07745, Jena, Germany
| | - Philipp M Schlüter
- Institute of Systematic Botany, University of Zurich Zollikerstrasse 107, CH-8008, Zürich, Switzerland
| |
Collapse
|
42
|
Sedeek KEM, Scopece G, Staedler YM, Schönenberger J, Cozzolino S, Schiestl FP, Schlüter PM. Genic rather than genome‐wide differences between sexually deceptive
O
phrys
orchids with different pollinators. Mol Ecol 2014; 23:6192-205. [DOI: 10.1111/mec.12992] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 10/25/2014] [Accepted: 10/29/2014] [Indexed: 01/12/2023]
Affiliation(s)
- Khalid E. M. Sedeek
- Institute of Systematic Botany University of Zurich Zollikerstr. 107 CH‐8008 Zurich Switzerland
| | - Giovanni Scopece
- Department of Biology University of Naples Federico II Complesso Universitario MSA Via Cinthia I‐80126 Naples Italy
| | - Yannick M. Staedler
- Department of Botany and Biodiversity Research University of Vienna Rennweg 14 A‐1030 Vienna Austria
| | - Jürg Schönenberger
- Department of Botany and Biodiversity Research University of Vienna Rennweg 14 A‐1030 Vienna Austria
| | - Salvatore Cozzolino
- Department of Biology University of Naples Federico II Complesso Universitario MSA Via Cinthia I‐80126 Naples Italy
| | - Florian P. Schiestl
- Institute of Systematic Botany University of Zurich Zollikerstr. 107 CH‐8008 Zurich Switzerland
| | - Philipp M. Schlüter
- Institute of Systematic Botany University of Zurich Zollikerstr. 107 CH‐8008 Zurich Switzerland
| |
Collapse
|
43
|
Crawford DJ, Doyle JJ, Soltis DE, Soltis PS, Wendel JF. Contemporary and future studies in plant speciation, morphological/floral evolution and polyploidy: honouring the scientific contributions of Leslie D. Gottlieb to plant evolutionary biology. Philos Trans R Soc Lond B Biol Sci 2014; 369:20130341. [PMID: 24958916 PMCID: PMC4071516 DOI: 10.1098/rstb.2013.0341] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- Daniel J Crawford
- Department of Ecology and Evolutionary Biology, and Biodiversity Institute, University of Kansas, Lawrence, KS 66045, USA
| | - Jeffrey J Doyle
- L. H. Bailey Hortorium, Department of Plant Biology, Cornell University, Ithaca, NY 14853, USA
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, FL 17 32611, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 17 32611, USA
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| |
Collapse
|
44
|
Morrison KR, Stacy EA. Intraspecific divergence and evolution of a life-history trade-off along a successional gradient in Hawaii's Metrosideros polymorpha. J Evol Biol 2014; 27:1192-204. [PMID: 24848688 DOI: 10.1111/jeb.12393] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Revised: 03/21/2014] [Accepted: 03/31/2014] [Indexed: 01/16/2023]
Abstract
The importance of environmental gradients in the diversification of long-lived tree species is poorly understood. Two morphologically distinct varieties of the endemic Hawaiian tree, 'ōhi'a lehua (Metrosideros polymorpha), are the canopy dominants at alternate extremes of a successional gradient formed by the recurring disturbance of lava flows on east Hawai'i Island. The maintenance of these varieties despite hybridization may be due to disruptive selection at either end of the successional gradient. To test this hypothesis, seeds from three, replicate monotypic stands of each variety on east Hawai'i Island were germinated and the resulting seedlings grown under four combinations of light and nitrogen levels in a greenhouse, and at early- and late-successional field sites. Growth and survivorship measures revealed differential fitness of these varieties in high- and low-light environments in the greenhouse with corresponding differential fitness in early- and late-successional field sites. Unique light-by-nitrogen interaction effects on growth were observed in each variety, and only the late-successional variety appeared to be nitrogen limited. These two varieties exhibit the classic plant life-history trade-off between fast growth in high light and high survivorship in shade, but notably within a single tree species. These findings strongly implicate a role for Hawaii's striking environmental heterogeneity in the emergence of at least two endemic forms of this woody genus.
Collapse
Affiliation(s)
- K R Morrison
- Department of Tropical Conservation Biology & Environmental Science, University of Hawai'i Hilo, Hilo, HI, USA
| | | |
Collapse
|
45
|
Genetics of cryptic speciation within an Arctic mustard, Draba nivalis. PLoS One 2014; 9:e93834. [PMID: 24691072 PMCID: PMC3972243 DOI: 10.1371/journal.pone.0093834] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 03/09/2014] [Indexed: 01/13/2023] Open
Abstract
Crossing experiments indicate that hybrid sterility barriers frequently have developed within diploid, circumpolar plant species of the genus Draba. To gain insight into the rapid evolution of postzygotic reproductive isolation in this system, we augmented the linkage map of one of these species, D. nivalis, and searched for quantitative trait loci (QTLs) associated with reproductive isolation. The map adds 63 new dominant markers to a previously published dataset of 31 co-dominant microsatellites. These markers include 52 amplified fragment length polymorphisms (AFLPs) and 11 sequence-specific amplified polymorphisms (SSAPs) based on retrotransposon sequence. 22 markers displaying transmission ratio distortion were further included in the map. We resolved eight linkage groups with a total map length of 894 cM. Significant genotype-trait associations, or quantitative trait loci (QTL), were detected for reproductive phenotypes including pollen fertility (4 QTLs), seed set (3 QTLs), flowering time (3 QTLs) and number of flowers (4 QTLs). Observed patterns of inheritance were consistent with the influence of both nuclear-nuclear interactions and chromosomal changes on these traits. All seed set QTLs and one pollen fertility QTL displayed underdominant effects suggestive of the involvement of chromosomal rearrangements in hybrid sterility. Interestingly, D. nivalis is predominantly self-fertilizing, which may facilitate the establishment of underdominant loci and contribute to reproductive isolation.
Collapse
|
46
|
Nybom H, Weising K, Rotter B. DNA fingerprinting in botany: past, present, future. INVESTIGATIVE GENETICS 2014; 5:1. [PMID: 24386986 PMCID: PMC3880010 DOI: 10.1186/2041-2223-5-1] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 12/02/2013] [Indexed: 12/20/2022]
Abstract
Almost three decades ago Alec Jeffreys published his seminal Nature papers on the use of minisatellite probes for DNA fingerprinting of humans (Jeffreys and colleagues Nature 1985, 314:67-73 and Nature 1985, 316:76-79). The new technology was soon adopted for many other organisms including plants, and when Hilde Nybom, Kurt Weising and Alec Jeffreys first met at the very First International Conference on DNA Fingerprinting in Berne, Switzerland, in 1990, everybody was enthusiastic about the novel method that allowed us for the first time to discriminate between humans, animals, plants and fungi on the individual level using DNA markers. A newsletter coined "Fingerprint News" was launched, T-shirts were sold, and the proceedings of the Berne conference filled a first book on "DNA fingerprinting: approaches and applications". Four more conferences were about to follow, one on each continent, and Alec Jeffreys of course was invited to all of them. Since these early days, methodologies have undergone a rapid evolution and diversification. A multitude of techniques have been developed, optimized, and eventually abandoned when novel and more efficient and/or more reliable methods appeared. Despite some overlap between the lifetimes of the different technologies, three phases can be defined that coincide with major technological advances. Whereas the first phase of DNA fingerprinting ("the past") was dominated by restriction fragment analysis in conjunction with Southern blot hybridization, the advent of the PCR in the late 1980s gave way to the development of PCR-based single- or multi-locus profiling techniques in the second phase. Given that many routine applications of plant DNA fingerprinting still rely on PCR-based markers, we here refer to these methods as "DNA fingerprinting in the present", and include numerous examples in the present review. The beginning of the third phase actually dates back to 2005, when several novel, highly parallel DNA sequencing strategies were developed that increased the throughput over current Sanger sequencing technology 1000-fold and more. High-speed DNA sequencing was soon also exploited for DNA fingerprinting in plants, either in terms of facilitated marker development, or directly in the sense of "genotyping-by-sequencing". Whereas these novel approaches are applied at an ever increasing rate also in non-model species, they are still far from routine, and we therefore treat them here as "DNA fingerprinting in the future".
Collapse
Affiliation(s)
- Hilde Nybom
- Department of Plant Breeding–Balsgård, Swedish University for Agricultural Sciences, Fjälkestadsvägen 459, Kristianstad 29194, Sweden
| | - Kurt Weising
- Plant Molecular Systematics, Institute of Biology, University of Kassel, Kassel 34109, Germany
| | - Björn Rotter
- GenXPro GmbH, Altenhöferallee 3, Frankfurt 60438, Germany
| |
Collapse
|
47
|
Peakall R, Whitehead MR. Floral odour chemistry defines species boundaries and underpins strong reproductive isolation in sexually deceptive orchids. ANNALS OF BOTANY 2014; 113:341-55. [PMID: 24052555 PMCID: PMC3890385 DOI: 10.1093/aob/mct199] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
BACKGROUND AND AIMS The events leading to speciation are best investigated in systems where speciation is ongoing or incomplete, such as incipient species. By examining reproductive barriers among incipient sister taxa and their congeners we can gain valuable insights into the relative timing and importance of the various barriers involved in the speciation process. The aim of this study was to identify the reproductive barriers among sexually deceptive orchid taxa in the genus Chiloglottis. METHODS The study targeted four closely related taxa with varying degrees of geographic overlap. Chemical, morphological and genetic evidence was combined to explore the basis of reproductive isolation. Of primary interest was the degree of genetic differentiation among taxa at both nuclear and chloroplast DNA markers. To objectively test whether or not species boundaries are defined by the chemistry that controls pollinator specificity, genetic analysis was restricted to samples of known odour chemistry. KEY RESULTS Floral odour chemical analysis was performed for 600+ flowers. The three sympatric taxa were defined by their specific chiloglottones, the semiochemicals responsible for pollinator attraction, and were found to be fully cross-compatible. Multivariate morphometric analysis could not reliably distinguish among the four taxa. Although varying from very low to moderate, significant levels of genetic differentiation were detected among all pairwise combinations of taxa at both nuclear and chloroplast loci. However, the levels of genetic differentiation were lower than expected for mature species. Critically, a lack of chloroplast DNA haplotype sharing among the morphologically indistinguishable and most closely related taxon pair confirmed that chemistry alone can define taxon boundaries. CONCLUSIONS The results confirmed that pollinator isolation, mediated by specific pollinator attraction, underpins strong reproductive isolation in these taxa. A combination of large effective population sizes, initial neutral mutations in the genes controlling floral scent, and a pool of available pollinators likely drives diversity in this system.
Collapse
|
48
|
Lindtke D, González-Martínez SC, Macaya-Sanz D, Lexer C. Admixture mapping of quantitative traits in Populus hybrid zones: power and limitations. Heredity (Edinb) 2013; 111:474-85. [PMID: 23860234 PMCID: PMC3833683 DOI: 10.1038/hdy.2013.69] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2013] [Revised: 06/06/2013] [Accepted: 06/12/2013] [Indexed: 01/30/2023] Open
Abstract
Uncovering the genetic architecture of species differences is of central importance for understanding the origin and maintenance of biological diversity. Admixture mapping can be used to identify the number and effect sizes of genes that contribute to the divergence of ecologically important traits, even in taxa that are not amenable to laboratory crosses because of their long generation time or other limitations. Here, we apply admixture mapping to naturally occurring hybrids between two ecologically divergent Populus species. We map quantitative trait loci for eight leaf morphological traits using 77 mapped microsatellite markers from all 19 chromosomes of Populus. We apply multivariate linear regression analysis allowing the modeling of additive and non-additive gene action and identify several candidate genomic regions associated with leaf morphology using an information-theoretic approach. We perform simulation studies to assess the power and limitations of admixture mapping of quantitative traits in natural hybrid populations for a variety of genetic architectures and modes of gene action. Our results indicate that (1) admixture mapping has considerable power to identify the genetic architecture of species differences if sample sizes and marker densities are sufficiently high, (2) modeling of non-additive gene action can help to elucidate the discrepancy between genotype and phenotype sometimes seen in interspecific hybrids, and (3) the genetic architecture of leaf morphological traits in the studied Populus species involves complementary and overdominant gene action, providing the basis for rapid adaptation of these ecologically important forest trees.
Collapse
Affiliation(s)
- D Lindtke
- Unit of Ecology and Evolution, Department of
Biology, University of Fribourg, Fribourg,
Switzerland
| | - S C González-Martínez
- INIA, Forest Research Centre, Department of
Forest Ecology and Genetics, Madrid, Spain
| | - D Macaya-Sanz
- INIA, Forest Research Centre, Department of
Forest Ecology and Genetics, Madrid, Spain
- Technical University of Madrid, ETS Forestry
Engineering, Department of Silviculture, Madrid, Spain
| | - C Lexer
- Unit of Ecology and Evolution, Department of
Biology, University of Fribourg, Fribourg,
Switzerland
- Jodrell Laboratory, Royal Botanic
Gardens, Kew, Richmond, Surrey, UK
| |
Collapse
|
49
|
Genetic differentiation and species cohesion in two widespread Central American Begonia species. Heredity (Edinb) 2013; 112:382-90. [PMID: 24220088 DOI: 10.1038/hdy.2013.116] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Revised: 08/20/2013] [Accepted: 09/19/2013] [Indexed: 11/08/2022] Open
Abstract
Begonia is one of the ten largest plant genera, with over 1500 species. This high species richness may in part be explained by weak species cohesion, which has allowed speciation by divergence in allopatry. In this study, we investigate species cohesion in the widespread Central American Begonia heracleifolia and Begonia nelumbiifolia, by genotyping populations at microsatellite loci. We then test for post-zygotic reproductive barriers using experimental crosses, and assess whether sterility barriers are related to intraspecific changes in genome size, indicating major genome restructuring between isolated populations. Strong population substructure was found for B. heracleifolia (FST=0.364, F'ST=0.506) and B. nelumbiifolia (FST=0.277, F'ST=0.439), and Bayesian admixture analysis supports the division of most populations into discrete genetic clusters. Moderate levels of inferred selfing (B. heracleifolia s=0.40, B. nelumbiifolia s=0.62) and dispersal limitation are likely to have contributed to significant genetic differentiation (B. heracleifolia Jost's D=0.274; B. nelumbiifolia D=0.294). Interpopulation crosses involving a divergent B. heracleifolia population with a genome size ∼10% larger than the species mean had a ∼20% reduction in pollen viability compared with other outcrosses, supporting reproductive isolation being polymorphic within the species. The population genetic data suggest that Begonia populations are only weakly connected by gene flow, allowing reproductive barriers to accumulate between the most isolated populations. This supports allopatric divergence in situ being the precursor of speciation in Begonia, and may also be a common speciation mechanism in other tropical herbaceous plant groups.
Collapse
|
50
|
Segatto ALA, Cazé ALR, Turchetto C, Klahre U, Kuhlemeier C, Bonatto SL, Freitas LB. Nuclear and plastid markers reveal the persistence of genetic identity: a new perspective on the evolutionary history of Petunia exserta. Mol Phylogenet Evol 2013; 70:504-12. [PMID: 24161675 DOI: 10.1016/j.ympev.2013.10.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 09/27/2013] [Accepted: 10/11/2013] [Indexed: 12/01/2022]
Abstract
Recently divergent species that can hybridize are ideal models for investigating the genetic exchanges that can occur while preserving the species boundaries. Petunia exserta is an endemic species from a very limited and specific area that grows exclusively in rocky shelters. These shaded spots are an inhospitable habitat for all other Petunia species, including the closely related and widely distributed species P. axillaris. Individuals with intermediate morphologic characteristics have been found near the rocky shelters and were believed to be putative hybrids between P. exserta and P. axillaris, suggesting a situation where Petunia exserta is losing its genetic identity. In the current study, we analyzed the plastid intergenic spacers trnS/trnG and trnH/psbA and six nuclear CAPS markers in a large sampling design of both species to understand the evolutionary process occurring in this biological system. Bayesian clustering methods, cpDNA haplotype networks, genetic diversity statistics, and coalescence-based analyses support a scenario where hybridization occurs while two genetic clusters corresponding to two species are maintained. Our results reinforce the importance of coupling differentially inherited markers with an extensive geographic sample to assess the evolutionary dynamics of recently diverged species that can hybridize.
Collapse
Affiliation(s)
- Ana Lúcia Anversa Segatto
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS 91501-970, Brazil
| | | | | | | | | | | | | |
Collapse
|