1
|
Thompson KA, Brandvain Y, Coughlan JM, Delmore KE, Justen H, Linnen CR, Ortiz-Barrientos D, Rushworth CA, Schneemann H, Schumer M, Stelkens R. The Ecology of Hybrid Incompatibilities. Cold Spring Harb Perspect Biol 2024; 16:a041440. [PMID: 38151331 PMCID: PMC11368197 DOI: 10.1101/cshperspect.a041440] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
Ecologically mediated selection against hybrids, caused by hybrid phenotypes fitting poorly into available niches, is typically viewed as distinct from selection caused by epistatic Dobzhansky-Muller hybrid incompatibilities. Here, we show how selection against transgressive phenotypes in hybrids manifests as incompatibility. After outlining our logic, we summarize current approaches for studying ecology-based selection on hybrids. We then quantitatively review QTL-mapping studies and find traits differing between parent taxa are typically polygenic. Next, we describe how verbal models of selection on hybrids translate to phenotypic and genetic fitness landscapes, highlighting emerging approaches for detecting polygenic incompatibilities. Finally, in a synthesis of published data, we report that trait transgression-and thus possibly extrinsic hybrid incompatibility in hybrids-escalates with the phenotypic divergence between parents. We discuss conceptual implications and conclude that studying the ecological basis of hybrid incompatibility will facilitate new discoveries about mechanisms of speciation.
Collapse
Affiliation(s)
- Ken A Thompson
- Department of Biology, Stanford University, Stanford, California 94305, USA
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305, USA
| | - Yaniv Brandvain
- Department of Plant and Microbial Biology, University of Minnesota - Twin Cities, St Paul, Minnesota 55108, USA
| | - Jenn M Coughlan
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, Connecticut 06511, USA
| | - Kira E Delmore
- Department of Biology, Texas A&M University, College Station, Texas 77843, USA
| | - Hannah Justen
- Department of Biology, Texas A&M University, College Station, Texas 77843, USA
| | - Catherine R Linnen
- Department of Biology, University of Kentucky, Lexington, Kentucky 40506, USA
| | - Daniel Ortiz-Barrientos
- School of Biological Sciences, The University of Queensland, Centre of Excellence for Plant Success in Nature and Agriculture, St Lucia, Queensland 4072, Australia
| | - Catherine A Rushworth
- Department of Biology and Ecology Center, Utah State University, Logan, Utah 84322, USA
| | - Hilde Schneemann
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Molly Schumer
- Department of Biology, Stanford University, Stanford, California 94305, USA
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca," A.C., Calnali 43240, Mexico
- Hanna H. Gray Fellow, Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Rike Stelkens
- Division of Population Genetics, Department of Zoology, Stockholm University, 106 91 Stockholm, Sweden
| |
Collapse
|
2
|
Dong CM, Aponte Rolón B, Sullivan JK, Tataru D, Deleon M, Dennis R, Dutton S, Machado Perez FJ, Montano L, Ferris KG. Short-term fluctuating and long-term divergent selection on sympatric Monkeyflowers: insights from decade-spanning reciprocal transplants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.26.600870. [PMID: 38979251 PMCID: PMC11230446 DOI: 10.1101/2024.06.26.600870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Sympatric species are often locally adapted to distinct microhabitats. However, temporal variation may cause local maladaptation and species boundary breakdown, especially during extreme climatic events leading to episodic selection. Repeated reciprocal transplants can reveal the interplay between short and long-term patterns of natural selection. To examine evolutionary trajectories of sympatric Monkeyflowers adapted to different niches, Mimulus guttatus and M. laciniatus, we performed three replicated transplants and combined them with previous experiments to leverage a dataset of five transplants spanning 10 years. We performed phenotypic selection analyses on parents and hybrids in parental habitats in Yosemite NP, CA during years of drastically differing snowpack. If there is ecological isolation, then we predicted divergent phenotypic selection between habitats in line with species' differences and local adaptation. We found interannual fluctuations in phenotypic selection, often in unpredicted directions. However, a combined-year analysis detected longer-term divergent selection on flowering time, a key temporally isolating and adaptative trait, suggesting that selection may reinforce species boundaries despite short-term fluctuations. Finally, we found temporal variation in local adaptation with M. laciniatus locally adapted in low snowpack years, while an extremely high snowpack year contributed to average local maladaptation of M. guttatus .
Collapse
|
3
|
Tataru D, De Leon M, Dutton S, Perez FM, Rendahl A, Ferris KG. Fluctuating selection in a Monkeyflower hybrid zone. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.14.599085. [PMID: 38948721 PMCID: PMC11212913 DOI: 10.1101/2024.06.14.599085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
While hybridization was viewed as a hindrance to adaptation and speciation by early evolutionary biologists, recent studies have demonstrated the importance of hybridization in facilitating evolutionary processes. However, it is still not well-known what role spatial and temporal variation in natural selection play in the maintenance of naturally occurring hybrid zones. To identify whether hybridization is adaptive between two closely related monkeyflower species, Mimulus guttatus and Mimulus laciniatus, we performed repeated reciprocal transplants between natural hybrid and pure species' populations. We planted parental genotypes along with multiple experimental hybrid generations in a dry (2021) and extremely wet (2023) year in the Sierra Nevada, CA. By taking fine scale environmental measurements, we found that the environment of the hybrid zone is more similar to M. laciniatus's seasonally dry rocky outcrop habitat than M. guttatus's moist meadows. In our transplants hybridization does not appear to be maintained by a consistent fitness advantage of hybrids over parental species in hybrid zones, but rather a lack of strong selection against hybrids. We also found higher fitness of the drought adapted species, M. laciniatus, than M. guttatus in both species' habitats, as well as phenotypic selection for M. laciniatus-like traits in the hybrid habitat in the dry year of our experiment. These findings suggest that in this system hybridization might function to introduce drought-adapted traits and genes from M. laciniatus into M. guttatus, specifically in years with limited soil moisture. However, we also find evidence of genetic incompatibilities in second generation hybrids in the wetter year, which may balance a selective advantage of M. laciniatus introgression. Therefore, we find that hybridization in this system is both potentially adaptive and costly, and that the interaction of positive and negative selection likely determines patterns of gene flow between these Mimulus species.
Collapse
Affiliation(s)
- Diana Tataru
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA
| | - Max De Leon
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA
| | - Spencer Dutton
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA
| | - Fidel Machado Perez
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA
- University of California Merced, Merced, CA
| | - Alexander Rendahl
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA
| | - Kathleen G Ferris
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA
| |
Collapse
|
4
|
Veltsos P, Kelly JK. The quantitative genetics of gene expression in Mimulus guttatus. PLoS Genet 2024; 20:e1011072. [PMID: 38603726 PMCID: PMC11060551 DOI: 10.1371/journal.pgen.1011072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 04/30/2024] [Accepted: 03/23/2024] [Indexed: 04/13/2024] Open
Abstract
Gene expression can be influenced by genetic variants that are closely linked to the expressed gene (cis eQTLs) and variants in other parts of the genome (trans eQTLs). We created a multiparental mapping population by sampling genotypes from a single natural population of Mimulus guttatus and scored gene expression in the leaves of 1,588 plants. We find that nearly every measured gene exhibits cis regulatory variation (91% have FDR < 0.05). cis eQTLs are usually allelic series with three or more functionally distinct alleles. The cis locus explains about two thirds of the standing genetic variance (on average) but varies among genes and tends to be greatest when there is high indel variation in the upstream regulatory region and high nucleotide diversity in the coding sequence. Despite mapping over 10,000 trans eQTL / affected gene pairs, most of the genetic variance generated by trans acting loci remains unexplained. This implies a large reservoir of trans acting genes with subtle or diffuse effects. Mapped trans eQTLs show lower allelic diversity but much higher genetic dominance than cis eQTLs. Several analyses also indicate that trans eQTLs make a substantial contribution to the genetic correlations in expression among different genes. They may thus be essential determinants of "gene expression modules," which has important implications for the evolution of gene expression and how it is studied by geneticists.
Collapse
Affiliation(s)
- Paris Veltsos
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
| | - John K. Kelly
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
| |
Collapse
|
5
|
Meng QL, Qiang CG, Li JL, Geng MF, Ren NN, Cai Z, Wang MX, Jiao ZH, Zhang FM, Song XJ, Ge S. Genetic architecture of ecological divergence between Oryza rufipogon and Oryza nivara. Mol Ecol 2024; 33:e17268. [PMID: 38230514 DOI: 10.1111/mec.17268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 01/04/2024] [Accepted: 01/08/2024] [Indexed: 01/18/2024]
Abstract
Ecological divergence due to habitat difference plays a prominent role in the formation of new species, but the genetic architecture during ecological speciation and the mechanism underlying phenotypic divergence remain less understood. Two wild ancestors of rice (Oryza rufipogon and Oryza nivara) are a progenitor-derivative species pair with ecological divergence and provide a unique system for studying ecological adaptation/speciation. Here, we constructed a high-resolution linkage map and conducted a quantitative trait locus (QTL) analysis of 19 phenotypic traits using an F2 population generated from a cross between the two Oryza species. We identified 113 QTLs associated with interspecific divergence of 16 quantitative traits, with effect sizes ranging from 1.61% to 34.1% in terms of the percentage of variation explained (PVE). The distribution of effect sizes of QTLs followed a negative exponential, suggesting that a few genes of large effect and many genes of small effect were responsible for the phenotypic divergence. We observed 18 clusters of QTLs (QTL hotspots) on 11 chromosomes, significantly more than that expected by chance, demonstrating the importance of coinheritance of loci/genes in ecological adaptation/speciation. Analysis of effect direction and v-test statistics revealed that interspecific differentiation of most traits was driven by divergent natural selection, supporting the argument that ecological adaptation/speciation would proceed rapidly under coordinated selection on multiple traits. Our findings provide new insights into the understanding of genetic architecture of ecological adaptation and speciation in plants and help effective manipulation of specific genes or gene cluster in rice breeding.
Collapse
Affiliation(s)
- Qing-Lin Meng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Cheng-Gen Qiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ji-Long Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mu-Fan Geng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ning-Ning Ren
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Zhe Cai
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Mei-Xia Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zi-Hui Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fu-Min Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xian-Jun Song
- Key Laboratory of Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
6
|
Merrill RM, Arenas-Castro H, Feller AF, Harenčár J, Rossi M, Streisfeld MA, Kay KM. Genetics and the Evolution of Prezygotic Isolation. Cold Spring Harb Perspect Biol 2024; 16:a041439. [PMID: 37848246 PMCID: PMC10835618 DOI: 10.1101/cshperspect.a041439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2023]
Abstract
The significance of prezygotic isolation for speciation has been recognized at least since the Modern Synthesis. However, fundamental questions remain. For example, how are genetic associations between traits that contribute to prezygotic isolation maintained? What is the source of genetic variation underlying the evolution of these traits? And how do prezygotic barriers affect patterns of gene flow? We address these questions by reviewing genetic features shared across plants and animals that influence prezygotic isolation. Emerging technologies increasingly enable the identification and functional characterization of the genes involved, allowing us to test established theoretical expectations. Embedding these genes in their developmental context will allow further predictions about what constrains the evolution of prezygotic isolation. Ongoing improvements in statistical and computational tools will reveal how pre- and postzygotic isolation may differ in how they influence gene flow across the genome. Finally, we highlight opportunities for progress by combining theory with appropriate data.
Collapse
Affiliation(s)
- Richard M Merrill
- Faculty of Biology, Division of Evolutionary Biology, LMU Munich, 82152 Planegg-Martinsried, Germany
| | - Henry Arenas-Castro
- School of Biological Sciences, University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Anna F Feller
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
- Arnold Arboretum of Harvard University, Boston, Massachusetts 02131, USA
| | - Julia Harenčár
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, California 95060, USA
| | - Matteo Rossi
- Faculty of Biology, Division of Evolutionary Biology, LMU Munich, 82152 Planegg-Martinsried, Germany
| | - Matthew A Streisfeld
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403-5289, USA
| | - Kathleen M Kay
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, California 95060, USA
| |
Collapse
|
7
|
Veltsos P, Kelly JK. The quantitative genetics of gene expression in Mimulus guttatus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.21.568003. [PMID: 38045261 PMCID: PMC10690227 DOI: 10.1101/2023.11.21.568003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Gene expression can be influenced by genetic variants that are closely linked to the expressed gene (cis eQTLs) and variants in other parts of the genome (trans eQTLs). We created a multiparental mapping population by sampling genotypes from a single natural population of Mimulus guttatus and scored gene expression in the leaves of 1,588 plants. We find that nearly every measured gene exhibits cis regulatory variation (91% have FDR < 0.05) and that cis eQTLs are usually allelic series with three or more functionally distinct alleles. The cis locus explains about two thirds of the standing genetic variance (on average) but varies among genes and tends to be greatest when there is high indel variation in the upstream regulatory region and high nucleotide diversity in the coding sequence. Despite mapping over 10,000 trans eQTL / affected gene pairs, most of the genetic variance generated by trans acting loci remains unexplained. This implies a large reservoir of trans acting genes with subtle or diffuse effects. Mapped trans eQTLs show lower allelic diversity but much higher genetic dominance than cis eQTLs. Several analyses also indicate that trans eQTL make a substantial contribution to the genetic correlations in expression among different genes. They may thus be essential determinants of "gene expression modules", which has important implications for the evolution of gene expression and also how it is studied by geneticists.
Collapse
Affiliation(s)
- Paris Veltsos
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
- Current address: Ecology, Evolution and Genetics Research Group, Biology Department, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - John K. Kelly
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
| |
Collapse
|
8
|
James ME, Allsopp RN, Groh JS, Kaur A, Wilkinson MJ, Ortiz-Barrientos D. Uncovering the genetic architecture of parallel evolution. Mol Ecol 2023; 32:5575-5589. [PMID: 37740681 DOI: 10.1111/mec.17134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 07/31/2023] [Accepted: 08/07/2023] [Indexed: 09/25/2023]
Abstract
Identifying the genetic architecture underlying adaptive traits is exceptionally challenging in natural populations. This is because associations between traits not only mask the targets of selection but also create correlated patterns of genomic divergence that hinder our ability to isolate causal genetic effects. Here, we examine the repeated evolution of components of the auxin pathway that have contributed to the replicated loss of gravitropism (i.e. the ability of a plant to bend in response to gravity) in multiple populations of the Senecio lautus species complex in Australia. We use a powerful approach which combines parallel population genomics with association mapping in a Multiparent Advanced Generation Inter-Cross (MAGIC) population to break down genetic and trait correlations to reveal how adaptive traits evolve during replicated evolution. We sequenced auxin and shoot gravitropism-related gene regions in 80 individuals from six natural populations (three parallel divergence events) and 133 individuals from a MAGIC population derived from two of the recently diverged natural populations. We show that artificial tail selection on gravitropism in the MAGIC population recreates patterns of parallel divergence in the auxin pathway in the natural populations. We reveal a set of 55 auxin gene regions that have evolved repeatedly during the evolution of the species, of which 50 are directly associated with gravitropism divergence in the MAGIC population. Our work creates a strong link between patterns of genomic divergence and trait variation contributing to replicated evolution by natural selection, paving the way to understand the origin and maintenance of adaptations in natural populations.
Collapse
Affiliation(s)
- Maddie E James
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, St Lucia, Queensland, Australia
| | - Robin N Allsopp
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Jeffrey S Groh
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Avneet Kaur
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, St Lucia, Queensland, Australia
| | - Melanie J Wilkinson
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, St Lucia, Queensland, Australia
| | - Daniel Ortiz-Barrientos
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, St Lucia, Queensland, Australia
| |
Collapse
|
9
|
Farnitano MC, Sweigart AL. Strong postmating reproductive isolation in Mimulus section Eunanus. J Evol Biol 2023; 36:1393-1410. [PMID: 37691442 PMCID: PMC10592011 DOI: 10.1111/jeb.14219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 09/12/2023]
Abstract
Postmating reproductive isolation can help maintain species boundaries when premating barriers to reproduction are incomplete. The strength and identity of postmating reproductive barriers are highly variable among diverging species, leading to questions about their genetic basis and evolutionary drivers. These questions have been tackled in model systems but are less often addressed with broader phylogenetic resolution. In this study we analyse patterns of genetic divergence alongside direct measures of postmating reproductive barriers in an overlooked group of sympatric species within the model monkeyflower genus, Mimulus. Within this Mimulus brevipes species group, we find substantial divergence among species, including a cryptic genetic lineage. However, rampant gene discordance and ancient signals of introgression suggest a complex history of divergence. In addition, we find multiple strong postmating barriers, including postmating prezygotic isolation, hybrid seed inviability and hybrid male sterility. M. brevipes and M. fremontii have substantial but incomplete postmating isolation. For all other tested species pairs, we find essentially complete postmating isolation. Hybrid seed inviability appears linked to differences in seed size, providing a window into possible developmental mechanisms underlying this reproductive barrier. While geographic proximity and incomplete mating isolation may have allowed gene flow within this group in the distant past, strong postmating reproductive barriers today have likely played a key role in preventing ongoing introgression. By producing foundational information about reproductive isolation and genomic divergence in this understudied group, we add new diversity and phylogenetic resolution to our understanding of the mechanisms of plant speciation.
Collapse
|
10
|
Packard M, Gilbert MC, Tetrault E, Albertson RC. Zebrafish crocc2 mutants exhibit divergent craniofacial shape, misregulated variability, and aberrant cartilage morphogenesis. Dev Dyn 2023; 252:1026-1045. [PMID: 37032317 PMCID: PMC10524572 DOI: 10.1002/dvdy.591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 03/21/2023] [Accepted: 03/29/2023] [Indexed: 04/11/2023] Open
Abstract
BACKGROUND Phenotypic variation is of paramount importance in development, evolution, and human health; however, the molecular mechanisms that influence organ shape and shape variability are not well understood. During craniofacial development, the behavior of skeletal precursors is regulated by both biochemical and environmental inputs, and the primary cilia play critical roles in transducing both types of signals. Here, we examine a gene that encodes a key constituent of the ciliary rootlets, crocc2, and its role in cartilage morphogenesis in larval zebrafish. RESULTS Geometric morphometric analysis of crocc2 mutants revealed altered craniofacial shapes and expanded variation. At the cellular level, we observed altered chondrocyte shapes and planar cell polarity across multiple stages in crocc2 mutants. Notably, cellular defects were specific to areas that experience direct mechanical input. Cartilage cell number, apoptosis, and bone patterning were not affected in crocc2 mutants. CONCLUSIONS Whereas "regulatory" genes are widely implicated in patterning the craniofacial skeleton, genes that encode "structural" aspects of the cell are increasingly implicated in shaping the face. Our results add crocc2 to this list, and demonstrate that it affects craniofacial geometry and canalizes phenotypic variation. We propose that it does so via mechanosensing, possibly through the ciliary rootlet. If true, this would implicate a new organelle in skeletal development and evolution.
Collapse
Affiliation(s)
- Mary Packard
- Department of Biology, University of Massachusetts, Amherst, MA 01003, U.S.A
| | - Michelle C. Gilbert
- Organismic and Evolutionary Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, U.S.A
- Current address, Department of Biology, Penn State University, University Park, PA 16802, U.S.A
| | - Emily Tetrault
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, U.S.A
| | - R. Craig Albertson
- Department of Biology, University of Massachusetts, Amherst, MA 01003, U.S.A
| |
Collapse
|
11
|
Aubier TG, Bürger R, Servedio MR. The effectiveness of pseudomagic traits in promoting premating isolation. Proc Biol Sci 2023; 290:20222108. [PMID: 36883275 PMCID: PMC9993058 DOI: 10.1098/rspb.2022.2108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 02/10/2023] [Indexed: 03/09/2023] Open
Abstract
Upon the secondary contact of populations, speciation with gene flow is greatly facilitated when the same pleiotropic loci are both subject to divergent ecological selection and induce non-random mating, leading to loci with this fortuitous combination of functions being referred to as 'magic trait' loci. We use a population genetics model to examine whether 'pseudomagic trait' complexes, composed of physically linked loci fulfilling these two functions, are as efficient in promoting premating isolation as magic traits. We specifically measure the evolution of choosiness, which controls the strength of assortative mating. We show that, surprisingly, pseudomagic trait complexes, and to a lesser extent also physically unlinked loci, can lead to the evolution of considerably stronger assortative mating preferences than do magic traits, provided polymorphism at the involved loci is maintained. This is because assortative mating preferences are generally favoured when there is a risk of producing maladapted recombinants, as occurs with non-magic trait complexes but not with magic traits (since pleiotropy precludes recombination). Contrary to current belief, magic traits may not be the most effective genetic architecture for promoting strong premating isolation. Therefore, distinguishing between magic traits and pseudomagic trait complexes is important when inferring their role in premating isolation. This calls for further fine-scale genomic research on speciation genes.
Collapse
Affiliation(s)
- Thomas G. Aubier
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Laboratoire Évolution & Diversité Biologique, Université Paul Sabatier Toulouse III, UMR 5174, CNRS/IRD, 31077 Toulouse, France
| | - Reinhard Bürger
- Department of Mathematics, University of Vienna, 1090 Vienna, Austria
| | - Maria R. Servedio
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| |
Collapse
|
12
|
Tataru D, Wheeler EC, Ferris KG. Spatially and temporally varying selection influence species boundaries in two sympatric Mimulus. Proc Biol Sci 2023; 290:20222279. [PMID: 36750191 PMCID: PMC9904950 DOI: 10.1098/rspb.2022.2279] [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] [Indexed: 02/09/2023] Open
Abstract
Spatially and temporally varying selection can maintain genetic variation within and between populations, but it is less well known how these forces influence divergence between closely related species. We identify the interaction of temporal and spatial variation in selection and their role in either reinforcing or eroding divergence between two closely related Mimulus species. Using repeated reciprocal transplant experiments with advanced generation hybrids, we compare the strength of selection on quantitative traits involved in adaptation and reproductive isolation in Mimulus guttatus and Mimulus laciniatus between two years with dramatically different water availability. We found strong divergent habitat-mediated selection on traits in the direction of species differences during a drought in 2013, suggesting that spatially varying selection maintains species divergence. However, a relaxation in divergent selection on most traits in an unusually wet year (2019), including flowering time, which is involved in pre-zygotic isolation, suggests that temporal variation in selection may weaken species differences. Therefore, we find evidence that temporally and spatially varying selection may have opposing roles in mediating species boundaries. Given our changing climate, future growing seasons are expected to be more similar to the dry year, suggesting that in this system climate change may actually increase species divergence.
Collapse
Affiliation(s)
- Diana Tataru
- Department of Ecology and Evolutionary Biology, Tulane University, 6823 St Charles Avenue, New Orleans, LA 70118, USA
| | - Emma C. Wheeler
- Department of Ecology and Evolutionary Biology, Tulane University, 6823 St Charles Avenue, New Orleans, LA 70118, USA
| | - Kathleen G. Ferris
- Department of Ecology and Evolutionary Biology, Tulane University, 6823 St Charles Avenue, New Orleans, LA 70118, USA
| |
Collapse
|
13
|
Feng C, Zou S, Zhang J. Genetic architecture of microhabitat adaptation traits in a pair of sympatric Primulina species. BIOTECHNOL BIOTEC EQ 2023. [DOI: 10.1080/13102818.2023.2176169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023] Open
Affiliation(s)
- Chen Feng
- Jiangxi Provincial Key Laboratory of ex situ Plant Conservation and Utilization, Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, Jiangxi, PR China
| | - Shuaiyu Zou
- Jiangxi Provincial Key Laboratory of ex situ Plant Conservation and Utilization, Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, Jiangxi, PR China
| | - Jie Zhang
- Jiangxi Provincial Key Laboratory of ex situ Plant Conservation and Utilization, Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, Jiangxi, PR China
| |
Collapse
|
14
|
Tremble K, Hoffman JI, Dentinger BTM. Contrasting continental patterns of adaptive population divergence in the holarctic ectomycorrhizal fungus Boletus edulis. THE NEW PHYTOLOGIST 2023; 237:295-309. [PMID: 36200167 DOI: 10.1111/nph.18521] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
In the hyperdiverse fungi, the process of speciation is virtually unknown, including for the > 20 000 species of ectomycorrhizal mutualists. To understand this process, we investigated patterns of genome-wide differentiation in the ectomycorrhizal porcini mushroom, Boletus edulis, a globally distributed species complex with broad ecological amplitude. By whole-genome sequencing 160 individuals from across the Northern Hemisphere, we genotyped 792 923 single nucleotide polymorphisms to characterize patterns of genome-wide differentiation and to identify the adaptive processes shaping global population structure. We show that B. edulis exhibits contrasting patterns of genomic divergence between continents, with multiple lineages present across North America, while a single lineage dominates Europe. These geographical lineages are inferred to have diverged 1.62-2.66 million years ago, during a period of climatic upheaval and the onset of glaciation in the Pliocene-Pleistocene boundary. High levels of genomic differentiation were observed among lineages despite evidence of substantial and ongoing introgression. Genome scans, demographic inference, and ecological niche models suggest that genomic differentiation is maintained by environmental adaptation, not physical isolation. Our study uncovers striking patterns of genome-wide differentiation on a global scale and emphasizes the importance of local adaptation and ecologically mediated divergence, rather than prezygotic barriers such as allopatry or genomic incompatibility, in fungal population differentiation.
Collapse
Affiliation(s)
- Keaton Tremble
- School of Biological Sciences, University of Utah, Salt Lake City, UT, 84112, USA
- Natural History Museum of Utah, Salt Lake City, UT, 84108, USA
| | - J I Hoffman
- Department of Animal Behaviour, Bielefeld University, Bielefeld, 33501, Germany
| | - Bryn T M Dentinger
- School of Biological Sciences, University of Utah, Salt Lake City, UT, 84112, USA
- Natural History Museum of Utah, Salt Lake City, UT, 84108, USA
| |
Collapse
|
15
|
Wong ELY, Nevado B, Hiscock SJ, Filatov DA. Rapid evolution of hybrid breakdown following recent divergence with gene flow in Senecio species on Mount Etna, Sicily. Heredity (Edinb) 2023; 130:40-52. [PMID: 36494489 PMCID: PMC9814926 DOI: 10.1038/s41437-022-00576-4] [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: 06/17/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 12/13/2022] Open
Abstract
How do nascent species evolve reproductive isolation during speciation with on-going gene flow? How do hybrid lineages become stabilised hybrid species? While commonly used genomic approaches provide an indirect way to identify species incompatibility factors, synthetic hybrids generated from interspecific crosses allow direct pinpointing of phenotypic traits involved in incompatibilities and the traits that are potentially adaptive in hybrid species. Here we report the analysis of phenotypic variation and hybrid breakdown in crosses between closely-related Senecio aethnensis and S. chrysanthemifolius, and their homoploid hybrid species, S. squalidus. The two former species represent a likely case of recent (<200 ky) speciation with gene flow driven by adaptation to contrasting conditions of high- and low-elevations on Mount Etna, Sicily. As these species form viable and fertile hybrids, it remains unclear whether they have started to evolve reproductive incompatibility. Our analysis represents the first study of phenotypic variation and hybrid breakdown involving multiple Senecio hybrid families. It revealed wide range of variation in multiple traits, including the traits previously unrecorded in synthetic hybrids. Leaf shape, highly distinct between S. aethnensis and S. chrysanthemifolius, was extremely variable in F2 hybrids, but more consistent in S. squalidus. Our study demonstrates that interspecific incompatibilities can evolve rapidly despite on-going gene flow between the species. Further work is necessary to understand the genetic bases of these incompatibilities and their role in speciation with gene flow.
Collapse
Affiliation(s)
- Edgar L. Y. Wong
- grid.4991.50000 0004 1936 8948Department of Biology, University of Oxford, Oxford, UK ,grid.507705.0Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
| | - Bruno Nevado
- grid.4991.50000 0004 1936 8948Department of Biology, University of Oxford, Oxford, UK ,grid.9983.b0000 0001 2181 4263Centre for Ecology, Evolution and Environmental Changes, University of Lisbon, Lisbon, Portugal
| | - Simon J. Hiscock
- grid.4991.50000 0004 1936 8948Department of Biology, University of Oxford, Oxford, UK ,Oxford Botanic Garden and Arboretum, Oxford, UK
| | - Dmitry A. Filatov
- grid.4991.50000 0004 1936 8948Department of Biology, University of Oxford, Oxford, UK
| |
Collapse
|
16
|
Camelo-Júnior AE, Ferreira AWC, Andrade IM, Mayo SJ, Nollet F, Silva JL, Barros MC, Fraga E, Pessoa EM. Species delimitation in the Trichocentrum cepula (Oncidiinae, Orchidaceae) complex: a multidisciplinary approach. SYST BIODIVERS 2022. [DOI: 10.1080/14772000.2022.2099478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Antonio E. Camelo-Júnior
- Programa de Pós-Graduação em Biodiversidade, Ambiente e Saúde, Universidade Estadual do Maranhão, Campus Caxias, 65.604-380, Caxias, Maranhão, Brazil
| | | | - Ivanilza M. Andrade
- Núcleo de Pesquisa em Biodiversidade e Biotecnologia, Biotec, Campus de Parnaíba, Universidade Federal do Delta do Piauí, Parnaíba, Piauí, Brazil
| | - Simon J. Mayo
- Royal Botanic Gardens, Kew, Richmond TW9 3AE, Surrey, UK
| | - Felipe Nollet
- Departamento de Biologia, Programa de Pós-Graduação em Botânica, Universidade Federal Rural de Pernambuco, Dois Irmãos, Recife, 52171–900, Pernambuco, Brazil
| | - José L. Silva
- Departamento de Ciências Biológicas, Universidade Federal da Paraíba Centro de Ciências Agrárias, Campus II, Areia, 58397-000, Paraíba, Brazil
| | - Maria C. Barros
- Programa de Pós-Graduação em Biodiversidade, Ambiente e Saúde, Universidade Estadual do Maranhão, Campus Caxias, 65.604-380, Caxias, Maranhão, Brazil
| | - Elmary Fraga
- Programa de Pós-Graduação em Biodiversidade, Ambiente e Saúde, Universidade Estadual do Maranhão, Campus Caxias, 65.604-380, Caxias, Maranhão, Brazil
| | - Edlley M. Pessoa
- Programa de Pós-Graduação em Biodiversidade, Ambiente e Saúde, Universidade Estadual do Maranhão, Campus Caxias, 65.604-380, Caxias, Maranhão, Brazil
- Departamento de Botânica e Ecologia, Universidade Federal do Mato Grosso, Cuiabá, 78060-900, Mato Grosso, Brazil
| |
Collapse
|
17
|
Prapas D, Scalone R, Lee J, Nurkowski KA, Bou‐assi S, Rieseberg L, Battlay P, Hodgins KA. Quantitative trait loci mapping reveals an oligogenic architecture of a rapidly adapting trait during the European invasion of common ragweed. Evol Appl 2022; 15:1249-1263. [PMID: 36051461 PMCID: PMC9423086 DOI: 10.1111/eva.13453] [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: 03/19/2022] [Revised: 06/05/2022] [Accepted: 06/30/2022] [Indexed: 01/09/2023] Open
Abstract
Biological invasions offer a unique opportunity to investigate evolution over contemporary timescales. Rapid adaptation to local climates during range expansion can be a major determinant of invasion success, yet fundamental questions remain about its genetic basis. This study sought to investigate the genetic basis of climate adaptation in invasive common ragweed (Ambrosia artemisiifolia). Flowering time adaptation is key to this annual species' invasion success, so much so that it has evolved repeated latitudinal clines in size and phenology across its native and introduced ranges despite high gene flow among populations. Here, we produced a high-density linkage map (4493 SNPs) and paired this with phenotypic data from an F2 mapping population (n = 336) to identify one major and two minor quantitative trait loci (QTL) underlying flowering time and height differentiation in this species. Within each QTL interval, several candidate flowering time genes were also identified. Notably, the major flowering time QTL detected in this study was found to overlap with a previously identified haploblock (putative inversion). Multiple genetic maps of this region identified evidence of suppressed recombination in specific genotypes, consistent with inversions. These discoveries support the expectation that a concentrated genetic architecture with fewer, larger, and more tightly linked alleles should underlie rapid local adaptation during invasion, particularly when divergently adapting populations experience high levels of gene flow.
Collapse
Affiliation(s)
- Diana Prapas
- School of Biological SciencesMonash UniversityMelbourneVictoriaAustralia
| | - Romain Scalone
- Department of Crop Production Ecology, Uppsala Ecology CenterSwedish University of Agricultural SciencesUppsalaSweden
- Department of Grapevine BreedingHochschule Geisenheim UniversityGeisenheimGermany
| | - Jacqueline Lee
- School of Biological SciencesMonash UniversityMelbourneVictoriaAustralia
| | - Kristin A. Nurkowski
- School of Biological SciencesMonash UniversityMelbourneVictoriaAustralia
- Department of Botany and Biodiversity Research CentreUniversity of British ColumbiaVancouverCanada
| | - Sarah Bou‐assi
- School of Biological SciencesMonash UniversityMelbourneVictoriaAustralia
| | - Loren Rieseberg
- Department of Botany and Biodiversity Research CentreUniversity of British ColumbiaVancouverCanada
| | - Paul Battlay
- School of Biological SciencesMonash UniversityMelbourneVictoriaAustralia
| | - Kathryn A. Hodgins
- School of Biological SciencesMonash UniversityMelbourneVictoriaAustralia
| |
Collapse
|
18
|
Abstract
The rediscovery of Mendel’s work showing that the heredity of phenotypes is controlled by discrete genes was followed by the reconciliation of Mendelian genetics with evolution by natural selection in the middle of the last century with the Modern Synthesis. In the past two decades, dramatic advances in genomic methods have facilitated the identification of the loci, genes, and even individual mutations that underlie phenotypic variants that are the putative targets of natural selection. Moreover, these methods have also changed how we can study adaptation by flipping the problem around, allowing us to first examine what loci show evidence of having been under selection, and then connecting these genetic variants to phenotypic variation. As a result, we now have an expanding list of actual genetic changes that underlie potentially adaptive phenotypic variation. Here, we synthesize how considering the effects of these adaptive loci in the context of cellular environments, genomes, organisms, and populations has provided new insights to the genetic architecture of adaptation.
Collapse
|
19
|
Poulin V, Amesefe D, Gonzalez E, Alexandre H, Joly S. Testing candidate genes linked to corolla shape variation of a pollinator shift in Rhytidophyllum (Gesneriaceae). PLoS One 2022; 17:e0267540. [PMID: 35853078 PMCID: PMC9295946 DOI: 10.1371/journal.pone.0267540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 04/12/2022] [Indexed: 11/18/2022] Open
Abstract
Floral adaptations to specific pollinators like corolla shape variation often result in reproductive isolation and thus speciation. But despite their ecological importance, the genetic bases of corolla shape transitions are still poorly understood, especially outside model species. Hence, our goal was to identify candidate genes potentially involved in corolla shape variation between two closely related species of the Rhytidophyllum genus (Gesneriaceae family) from the Antilles with contrasting pollination strategies. Rhytidophyllum rupincola has a tubular corolla and is strictly pollinated by hummingbirds, whereas R. auriculatum has more open flowers and is pollinated by hummingbirds, bats, and insects. We surveyed the literature and used a comparative transcriptome sequence analysis of synonymous and non-synonymous nucleotide substitutions to obtain a list of genes that could explain floral variation between R. auriculatum and R. rupincola. We then tested their association with corolla shape variation using QTL mapping in a F2 hybrid population. Out of 28 genes tested, three were found to be good candidates because of a strong association with corolla shape: RADIALIS, GLOBOSA, and JAGGED. Although the role of these genes in Rhytidophyllum corolla shape variation remains to be confirmed, these findings are a first step towards identifying the genes that have been under selection by pollinators and thus involved in reproductive isolation and speciation in this genus.
Collapse
Affiliation(s)
- Valérie Poulin
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Canada
| | - Delase Amesefe
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Canada
| | - Emmanuel Gonzalez
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Canada
- Department of Human Genetics, Canadian Centre for Computational Genomics (C3G), McGill University, Montréal, QC, Canada
- Microbiome Research Platform, McGill Interdisciplinary Initiative in Infection and Immunity (MI4), Genome Centre, McGill University, Montréal, QC, Canada
| | - Hermine Alexandre
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Canada
| | - Simon Joly
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Canada
- Montreal Botanical Garden, Montréal, Canada
| |
Collapse
|
20
|
Evolutionary Divergence and Radula Diversification in Two Ecomorphs from an Adaptive Radiation of Freshwater Snails. Genes (Basel) 2022; 13:genes13061029. [PMID: 35741791 PMCID: PMC9222583 DOI: 10.3390/genes13061029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 05/27/2022] [Accepted: 05/31/2022] [Indexed: 12/13/2022] Open
Abstract
(1) Background: Adaptive diversification of complex traits plays a pivotal role in the evolution of organismal diversity. In the freshwater snail genus Tylomelania, adaptive radiations were likely promoted by trophic specialization via diversification of their key foraging organ, the radula. (2) Methods: To investigate the molecular basis of radula diversification and its contribution to lineage divergence, we used tissue-specific transcriptomes of two sympatric Tylomelania sarasinorum ecomorphs. (3) Results: We show that ecomorphs are genetically divergent lineages with habitat-correlated abundances. Sequence divergence and the proportion of highly differentially expressed genes are significantly higher between radula transcriptomes compared to the mantle and foot. However, the same is not true when all differentially expressed genes or only non-synonymous SNPs are considered. Finally, putative homologs of some candidate genes for radula diversification (hh, arx, gbb) were also found to contribute to trophic specialization in cichlids and Darwin’s finches. (4) Conclusions: Our results are in line with diversifying selection on the radula driving Tylomelania ecomorph divergence and indicate that some molecular pathways may be especially prone to adaptive diversification, even across phylogenetically distant animal groups.
Collapse
|
21
|
Meng Q, Manghwar H, Hu W. Study on Supergenus Rubus L.: Edible, Medicinal, and Phylogenetic Characterization. PLANTS (BASEL, SWITZERLAND) 2022; 11:1211. [PMID: 35567211 PMCID: PMC9102695 DOI: 10.3390/plants11091211] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 06/15/2023]
Abstract
Rubus L. is one of the most diverse genera belonging to Rosaceae; it consists of more than 700 species with a worldwide distribution. It thus provides an ideal natural "supergenus" for studying the importance of its edible, medicinal, and phylogenetic characteristics for application in our daily lives and fundamental scientific studies. The Rubus genus includes many economically important species, such as blackberry (R. fruticosus L.), red raspberry (R. ideaus L.), black raspberry (R. occidentalis L.), and raspberry (R. chingii Hu), which are widely utilized in the fresh fruit market and the medicinal industry. Although Rubus species have existed in human civilization for hundreds of years, their utilization as fruit and in medicine is still largely inadequate, and many questions on their complex phylogenetic relationships need to be answered. In this review, we briefly summarize the history and progress of studies on Rubus, including its domestication as a source of fresh fruit, its medicinal uses in pharmacology, and its systematic position in the phylogenetic tree. Recent available evidence indicates that (1) thousands of Rubus cultivars were bred via time- and labor-consuming methods from only a few wild species, and new breeding strategies and germplasms were thus limited; (2) many kinds of species in Rubus have been used as medicinal herbs, though only a few species (R. ideaus L., R. chingii Hu, and R. occidentalis L.) have been well studied; (3) the phylogeny of Rubus is very complex, with the main reason for this possibly being the existence of multiple reproductive strategies (apomixis, hybridization, and polyploidization). Our review addresses the utilization of Rubus, summarizing major relevant achievements and proposing core prospects for future application, and thus could serve as a useful roadmap for future elite cultivar breeding and scientific studies.
Collapse
Affiliation(s)
- Qinglin Meng
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332900, China; (Q.M.); (H.M.)
| | - Hakim Manghwar
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332900, China; (Q.M.); (H.M.)
| | - Weiming Hu
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332900, China; (Q.M.); (H.M.)
| |
Collapse
|
22
|
Vest K, Sobel JM. Variation in seasonal timing traits and life history along a latitudinal transect in Mimulus ringens. J Evol Biol 2021; 34:1803-1816. [PMID: 34582606 DOI: 10.1111/jeb.13941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 09/13/2021] [Accepted: 09/14/2021] [Indexed: 11/28/2022]
Abstract
Seasonal timing traits are commonly under recurrent, spatially variable selection, and are therefore predicted to exhibit clinal variation. Temperate perennial plants often require vernalization to prompt growth and reproduction; however, little is known about whether vernalization requirements change across the range of a broadly distributed species. We performed a critical vernalization duration study in Mimulus ringens, coupled with population genomic analysis. Plants from eight populations spanning the latitudinal range were exposed to varying durations of 4°C vernalization between 0 and 56 days, and flowering response was assessed. RADSeq was also performed to generate 1179 polymorphic SNPs, which were used to examine population structure. We found unexpected life history variation, with some populations lacking vernalization requirement. Population genomic analyses show that these life history variants are highly divergent from perennials, potentially revealing a cryptic species. For perennial populations, minimum vernalization time was surprisingly consistent. However, once vernalized, northern populations flowered almost 3 weeks faster than southern. Furthermore, southern populations exhibited sensitivity to vernalization times beyond flowering competency, suggesting an ability to respond adaptively to different lengths of winter. Mimulus ringens, therefore, reveals evidence of clinal variation, and provides opportunities for future studies addressing mechanistic and ecological hypotheses both within and between incipient species.
Collapse
Affiliation(s)
- Kelly Vest
- Department of Biological Sciences, Binghamton University (SUNY), Binghamton, New York, USA
| | - James M Sobel
- Department of Biological Sciences, Binghamton University (SUNY), Binghamton, New York, USA
| |
Collapse
|
23
|
Kinser TJ, Smith RD, Lawrence AH, Cooley AM, Vallejo-Marín M, Conradi Smith GD, Puzey JR. Endosperm-based incompatibilities in hybrid monkeyflowers. THE PLANT CELL 2021; 33:2235-2257. [PMID: 33895820 PMCID: PMC8364248 DOI: 10.1093/plcell/koab117] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 04/15/2021] [Indexed: 05/31/2023]
Abstract
Endosperm is an angiosperm innovation central to their reproduction whose development, and thus seed viability, is controlled by genomic imprinting, where expression from certain genes is parent-specific. Unsuccessful imprinting has been linked to failed inter-specific and inter-ploidy hybridization. Despite their importance in plant speciation, the underlying mechanisms behind these endosperm-based barriers remain poorly understood. Here, we describe one such barrier between diploid Mimulus guttatus and tetraploid Mimulus luteus. The two parents differ in endosperm DNA methylation, expression dynamics, and imprinted genes. Hybrid seeds suffer from underdeveloped endosperm, reducing viability, or arrested endosperm and seed abortion when M. guttatus or M. luteus is seed parent, respectively, and transgressive methylation and expression patterns emerge. The two inherited M. luteus subgenomes, genetically distinct but epigenetically similar, are expressionally dominant over the M. guttatus genome in hybrid embryos and especially their endosperm, where paternal imprints are perturbed. In aborted seeds, de novo methylation is inhibited, potentially owing to incompatible paternal instructions of imbalanced dosage from M. guttatus imprints. We suggest that diverged epigenetic/regulatory landscapes between parental genomes induce epigenetic repatterning and global shifts in expression, which, in endosperm, may uniquely facilitate incompatible interactions between divergent imprinting schemes, potentially driving rapid barriers.
Collapse
Affiliation(s)
- Taliesin J. Kinser
- Biology Department, College of William and Mary, Williamsburg, Virginia 23185
| | - Ronald D. Smith
- Department of Applied Science, College of William and Mary, Williamsburg, Virginia 23185
| | - Amelia H. Lawrence
- Biology Department, College of William and Mary, Williamsburg, Virginia 23185
| | | | - Mario Vallejo-Marín
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, Scotland FK9 4LA, UK
| | | | - Joshua R. Puzey
- Biology Department, College of William and Mary, Williamsburg, Virginia 23185
| |
Collapse
|
24
|
Coughlan JM, Brown MW, Willis JH. The genetic architecture and evolution of life-history divergence among perennials in the Mimulus guttatus species complex. Proc Biol Sci 2021; 288:20210077. [PMID: 33823671 PMCID: PMC8059554 DOI: 10.1098/rspb.2021.0077] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 03/12/2021] [Indexed: 02/06/2023] Open
Abstract
Ecological divergence is a fundamental source of phenotypic diversity between closely related species, yet the genetic architecture of most ecologically relevant traits is poorly understood. Differences in elevation can impose substantial divergent selection on both complex, correlated suites of traits (such as life-history), as well as novel adaptations. We use the Mimulus guttatus species complex to assess if the divergence in elevation is accompanied by trait divergence in a group of closely related perennials and determine the genetic architecture of this divergence. We find that divergence in elevation is associated with differences in life-history, as well as a unique trait, the production of rhizomes. The divergence between two perennials is largely explained by few mid-to-large effect quantitative trait loci (QTLs). However, the presence of QTLs with correlated, but opposing effects on multiple traits leads to some hybrids with transgressive trait combinations. Lastly, we find that the genetic architecture of the ability to produce rhizomes changes through development, wherein most hybrids produce rhizomes, but only later in development. Our results suggest that elevational differences may shape life-history divergence between perennials, but aspects of the genetic architecture of divergence may have implications for hybrid fitness in nature.
Collapse
Affiliation(s)
- Jenn M. Coughlan
- Biology Department, Duke University, 125 Science Dr., Durham, NC 27708, USA
- Biology Department, University of North Carolina, 250 Bell Tower Dr., Chapel Hill, NC 27599, USA
| | - Maya Wilson Brown
- Biology Department, Duke University, 125 Science Dr., Durham, NC 27708, USA
- Department of Plant Biology, Michigan State University, 612 Wilson Rd, East Lansing, MI 48824, USA
| | - John H. Willis
- Biology Department, Duke University, 125 Science Dr., Durham, NC 27708, USA
| |
Collapse
|
25
|
Orsucci M, Sicard A. Flower evolution in the presence of heterospecific gene flow and its contribution to lineage divergence. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:971-989. [PMID: 33537708 DOI: 10.1093/jxb/eraa549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 11/16/2020] [Indexed: 06/12/2023]
Abstract
The success of species depends on their ability to exploit ecological resources in order to optimize their reproduction. However, species are not usually found within single-species ecosystems but in complex communities. Because of their genetic relatedness, closely related lineages tend to cluster within the same ecosystem, rely on the same resources, and be phenotypically similar. In sympatry, they will therefore compete for the same resources and, in the case of flowering plants, exchange their genes through heterospecific pollen transfer. These interactions, nevertheless, pose significant challenges to species co-existence because they can lead to resource limitation and reproductive interference. In such cases, divergent selective pressures on floral traits will favour genotypes that isolate or desynchronize the reproduction of sympatric lineages. The resulting displacement of reproductive characters will, in turn, lead to pre-mating isolation and promote intraspecific divergence, thus initiating or reinforcing the speciation process. In this review, we discuss the current theoretical and empirical knowledge on the influence of heterospecific pollen transfer on flower evolution, highlighting its potential to uncover the ecological and genomic constraints shaping the speciation process.
Collapse
Affiliation(s)
- Marion Orsucci
- Department of Plant Biology, Swedish University of Agricultural, Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Adrien Sicard
- Department of Plant Biology, Swedish University of Agricultural, Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| |
Collapse
|
26
|
Thompson KA, Urquhart-Cronish M, Whitney KD, Rieseberg LH, Schluter D. Patterns, Predictors, and Consequences of Dominance in Hybrids. Am Nat 2021; 197:E72-E88. [PMID: 33625966 DOI: 10.1086/712603] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractCompared to those of their parents, are the traits of first-generation (F1) hybrids typically intermediate, biased toward one parent, or mismatched for alternative parental phenotypes? To address this empirical gap, we compiled data from 233 crosses in which traits were measured in a common environment for two parent taxa and their F1 hybrids. We find that individual traits in F1s are halfway between the parental midpoint and one parental value. Considering pairs of traits together, a hybrid's bivariate phenotype tends to resemble one parent (parent bias) about 50% more than the other, while also exhibiting a similar magnitude of mismatch due to different traits having dominance in conflicting directions. Using data from an experimental field planting of recombinant hybrid sunflowers, we illustrate that parent bias improves fitness, whereas mismatch reduces fitness. Our study has three major conclusions. First, hybrids are not phenotypically intermediate but rather exhibit substantial mismatch. Second, dominance is likely determined by the idiosyncratic evolutionary trajectories of individual traits and populations. Finally, selection against hybrids likely results from selection against both intermediate and mismatched phenotypes.
Collapse
|
27
|
Härer A, Bolnick DI, Rennison DJ. The genomic signature of ecological divergence along the benthic-limnetic axis in allopatric and sympatric threespine stickleback. Mol Ecol 2020; 30:451-463. [PMID: 33222348 DOI: 10.1111/mec.15746] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 10/21/2020] [Accepted: 11/09/2020] [Indexed: 12/23/2022]
Abstract
The repeated occurrence of similar phenotypes in independent lineages (i.e., parallel evolution) in response to similar ecological conditions can provide compelling insights into the process of adaptive evolution. An intriguing question is to what extent repeated phenotypic changes are underlain by repeated changes at the genomic level and whether patterns of genomic divergence differ with the geographic context in which populations evolve. Here, we combined genomic, morphological and ecological data sets to investigate the genomic signatures of divergence across populations of threespine stickleback (Gasterosteus aculeatus) that adapted to contrasting ecological niches (benthic or limnetic) in either sympatry or allopatry. We found that genome-wide differentiation (FST ) was an order of magnitude higher and substantially more repeatable for sympatric benthic and limnetic specialists compared to allopatric populations with similar levels of ecological divergence. We identified genomic regions consistently differentiated between sympatric ecotypes that were also differentiated between or associated with benthic vs. limnetic niche in allopatric populations. These candidate regions were enriched on three chromosomes known to be involved in the benthic-limnetic divergence of threespine stickleback. Some candidate regions overlapped with QTL for body shape and trophic traits such as gill raker number, traits that strongly differ between benthic and limnetic ecotypes. In summary, our study shows that magnitude and repeatability of genomic signatures of ecological divergence in threespine stickleback highly depend on the geographic context. The identified candidate regions provide starting points to identify functionally important genes for the adaptation to benthic and limnetic niches.
Collapse
Affiliation(s)
- Andreas Härer
- Division of Biological Sciences, Section of Ecology, Behavior, & Evolution, University of California San Diego, La Jolla, CA, USA
| | - Daniel I Bolnick
- Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Diana J Rennison
- Division of Biological Sciences, Section of Ecology, Behavior, & Evolution, University of California San Diego, La Jolla, CA, USA
| |
Collapse
|
28
|
Servedio MR, Bürger R. The effectiveness of pseudomagic traits in promoting divergence and enhancing local adaptation. Evolution 2020; 74:2438-2450. [PMID: 32652577 DOI: 10.1111/evo.14056] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 06/17/2020] [Accepted: 06/28/2020] [Indexed: 01/30/2023]
Abstract
"Magic traits," in which the same trait is both under divergent ecological selection and forms the basis of assortative mating, have been sought after due to their supposed unique ability to promote divergence with gene flow. Here, we ask how unique magic traits are, by exploring whether a tightly linked complex of a locus under divergent selection and a locus that acts as a mating cue can mimic a magic trait in its divergence. We find that these "pseudomagic traits" can be very effective in promoting divergence; with tight linkage they are essentially as effective as a magic trait and with loose linkage, and even no linkage, divergence can still be enhanced. Distinguishing between magic and pseudomagic traits in empirical cases may thus not be important when inferring their role in divergence. The ability of divergence in the mating trait to drive divergence in the ecological trait by lowering the effective migration rate, which occurs somewhat even without linkage, is particularly striking; magic traits are typically considered to have the other direction of causality. Our results thus suggest that divergence in a mating trait can at least modestly increase local adaption by allowing more ecological divergence, particularly with tighter linkage.
Collapse
Affiliation(s)
- Maria R Servedio
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, 27599
| | - Reinhard Bürger
- Department of Mathematics, University of Vienna, Vienna, 1090, Austria
| |
Collapse
|
29
|
Kooyers NJ, Donofrio A, Blackman BK, Holeski LM. The Genetic Architecture of Plant Defense Trade-offs in a Common Monkeyflower. J Hered 2020; 111:333-345. [DOI: 10.1093/jhered/esaa015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 05/25/2020] [Indexed: 12/11/2022] Open
Abstract
Abstract
Determining how adaptive combinations of traits arose requires understanding the prevalence and scope of genetic constraints. Frequently observed phenotypic correlations between plant growth, defenses, and/or reproductive timing have led researchers to suggest that pleiotropy or strong genetic linkage between variants affecting independent traits is pervasive. Alternatively, these correlations could arise via independent mutations in different genes for each trait and extensive correlational selection. Here we evaluate these alternatives by conducting a quantitative trait loci (QTL) mapping experiment involving a cross between 2 populations of common monkeyflower (Mimulus guttatus) that differ in growth rate as well as total concentration and arsenal composition of plant defense compounds, phenylpropanoid glycosides (PPGs). We find no evidence that pleiotropy underlies correlations between defense and growth rate. However, there is a strong genetic correlation between levels of total PPGs and flowering time that is largely attributable to a single shared QTL. While this result suggests a role for pleiotropy/close linkage, several other QTLs also contribute to variation in total PPGs. Additionally, divergent PPG arsenals are influenced by a number of smaller-effect QTLs that each underlie variation in 1 or 2 PPGs. This result indicates that chemical defense arsenals can be finely adapted to biotic environments despite sharing a common biochemical precursor. Together, our results show correlations between defense and life-history traits are influenced by pleiotropy or genetic linkage, but genetic constraints may have limited impact on future evolutionary responses, as a substantial proportion of variation in each trait is controlled by independent loci.
Collapse
Affiliation(s)
- Nicholas J Kooyers
- Department of Biology, University of Louisiana, Lafayette, LA
- Department of Integrative Biology, University of South Florida, Tampa, FL
| | - Abigail Donofrio
- Department of Integrative Biology, University of South Florida, Tampa, FL
| | - Benjamin K Blackman
- Department of Plant and Microbial Biology, University of California, Berkeley, CA
| | - Liza M Holeski
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ
| |
Collapse
|
30
|
Tian X, Ye J, Wang T, Bao L, Wang H. Different processes shape the patterns of divergence in the nuclear and chloroplast genomes of a relict tree species in East Asia. Ecol Evol 2020; 10:4331-4342. [PMID: 32489600 PMCID: PMC7246201 DOI: 10.1002/ece3.6200] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 02/25/2020] [Accepted: 02/26/2020] [Indexed: 02/05/2023] Open
Abstract
Isolation by spatial distance (IBD), environment (IBE), and historical climatic instability (IBI) are three common processes assessed in phylogeographic and/or landscape genetic studies. However, the relative contributions of these three processes with respect to spatial genetic patterns have seldom been compared. Moreover, whether the relative contribution differs in different regions or when assessed using different genetic markers has rarely been reported. Lindera obtusiloba has been found to have two sister genetic clades of chloroplast (cpDNA) and nuclear microsatellite (nSSR), both of which show discontinuous distribution in northern and southern East Asia. In this study, we used the Mantel test and multiple matrix regression with randomization (MMRR) to determine the relative contributions of IBD, IBE, and IBI with respect to L. obtusiloba populations. Independent Mantel tests and MMRR calculations were conducted for two genetic data sets (cpDNA and nSSR) and for different regions (the overall species range, and northern and southern subregions of the range). We found a significant IBI pattern in nSSR divergence for all assessed regions, whereas no clear IBI pattern was detected with respect to cpDNA. In contrast, significant (or marginal) divergent IBD patterns were detected for cpDNA in all regions, whereas although a significant IBE was apparent with respect to the overall range, the effect was not detected in the two subregions. The differences identified in nSSR and cpDNA population divergence may be related to differences in the heredity and ploidy of the markers. Compared with the southern region, the northern region showed less significant correlation patterns, which may be related to the shorter population history and restricted population range. The findings of this study serve to illustrate that comparing between markers or regions can contribute to gaining a better understanding the population histories of different genomes or within different regions of a species' range.
Collapse
Affiliation(s)
- Xiang‐Yu Tian
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological EngineeringCollege of Life SciencesBeijing Normal UniversityBeijingChina
| | - Jun‐Wei Ye
- Germplasm Bank of Wild Species in Southwest ChinaKunming Institute of BotanyChinese Academy of SciencesKunmingChina
| | - Tian‐Ming Wang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological EngineeringCollege of Life SciencesBeijing Normal UniversityBeijingChina
| | - Lei Bao
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological EngineeringCollege of Life SciencesBeijing Normal UniversityBeijingChina
| | - Hong‐Fang Wang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological EngineeringCollege of Life SciencesBeijing Normal UniversityBeijingChina
| |
Collapse
|
31
|
Feng C, Yi H, Yang L, Kang M. The genetic basis of hybrid male sterility in sympatric Primulina species. BMC Evol Biol 2020; 20:49. [PMID: 32349663 PMCID: PMC7191819 DOI: 10.1186/s12862-020-01617-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 04/21/2020] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Sympatric sister species provide an opportunity to investigate the genetic mechanisms and evolutionary forces that maintain species boundaries. The persistence of morphologically and genetically distinct populations in sympatry can only occur if some degree of reproductive isolation exists. A pair of sympatric sister species of Primulina (P. depressa and P. danxiaensis) was used to explore the genetic architecture of hybrid male sterility. RESULTS We mapped one major- and seven minor-effect quantitative trait loci (QTLs) that underlie pollen fertility rate (PFR). These loci jointly explained 55.4% of the phenotypic variation in the F2 population. A Bateson-Dobzhansky-Muller (BDM) model involving three loci was observed in this system. We found genotypic correlations between hybrid male sterility and flower morphology, consistent with the weak but significant phenotypic correlations between PFR and floral traits. CONCLUSIONS Hybrid male sterility in Primulina is controlled by a polygenic genetic basis with a complex pattern. The genetic incompatibility involves a three-locus BDM model. Hybrid male sterility is genetically correlated with floral morphology and divergence hitchhiking may occur between them.
Collapse
Affiliation(s)
- Chen Feng
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650 China
| | - Huiqin Yi
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Lihua Yang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650 China
| | - Ming Kang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650 China
| |
Collapse
|
32
|
Feller AF, Haesler MP, Peichel CL, Seehausen O. Genetic architecture of a key reproductive isolation trait differs between sympatric and non-sympatric sister species of Lake Victoria cichlids. Proc Biol Sci 2020; 287:20200270. [PMID: 32259470 PMCID: PMC7209058 DOI: 10.1098/rspb.2020.0270] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
One hallmark of the East African cichlid radiations is the rapid evolution of reproductive isolation that is robust to full sympatry of many closely related species. Theory predicts that species persistence and speciation in sympatry with gene flow are facilitated if loci of large effect or physical linkage (or pleiotropy) underlie traits involved in reproductive isolation. Here, we investigate the genetic architecture of a key trait involved in behavioural isolation, male nuptial coloration, by crossing two sister species pairs of Lake Victoria cichlids of the genus Pundamilia and mapping nuptial coloration in the F2 hybrids. One is a young sympatric species pair, representative of an axis of colour motif differentiation, red-dorsum versus blue, that is highly recurrent in closely related sympatric species. The other is a species pair representative of colour motifs, red-chest versus blue, that are common in allopatric but uncommon in sympatric closely related species. We find significant quantitative trait loci (QTLs) with moderate to large effects (some overlapping) for red and yellow in the sympatric red-dorsum × blue cross, whereas we find no significant QTLs in the non-sympatric red-chest × blue cross. These findings are consistent with theory predicting that large effect loci or linkage/pleiotropy underlying mating trait differentiation could facilitate speciation and species persistence with gene flow in sympatry.
Collapse
Affiliation(s)
- Anna F Feller
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.,Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum, Switzerland
| | - Marcel P Haesler
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.,Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum, Switzerland
| | - Catherine L Peichel
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Ole Seehausen
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.,Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum, Switzerland
| |
Collapse
|
33
|
Hämälä T, Gorton AJ, Moeller DA, Tiffin P. Pleiotropy facilitates local adaptation to distant optima in common ragweed (Ambrosia artemisiifolia). PLoS Genet 2020; 16:e1008707. [PMID: 32210431 PMCID: PMC7135370 DOI: 10.1371/journal.pgen.1008707] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 04/06/2020] [Accepted: 03/05/2020] [Indexed: 12/23/2022] Open
Abstract
Pleiotropy, the control of multiple phenotypes by a single locus, is expected to slow the rate of adaptation by increasing the chance that beneficial alleles also have deleterious effects. However, a prediction arising from classical theory of quantitative trait evolution states that pleiotropic alleles may have a selective advantage when phenotypes are distant from their selective optima. We examine the role of pleiotropy in regulating adaptive differentiation among populations of common ragweed (Ambrosia artemisiifolia); a species that has recently expanded its North American range due to human-mediated habitat change. We employ a phenotype-free approach by using connectivity in gene networks as a proxy for pleiotropy. First, we identify loci bearing footprints of local adaptation, and then use genotype-expression mapping and co-expression networks to infer the connectivity of the genes. Our results indicate that the putatively adaptive loci are highly pleiotropic, as they are more likely than expected to affect the expression of other genes, and they reside in central positions within the gene networks. We propose that the conditionally advantageous alleles at these loci avoid the cost of pleiotropy by having large phenotypic effects that are beneficial when populations are far from their selective optima. We further use evolutionary simulations to show that these patterns are in agreement with a model where populations face novel selective pressures, as expected during a range expansion. Overall, our results suggest that highly connected genes may be targets of positive selection during environmental change, even though they likely experience strong purifying selection in stable selective environments.
Collapse
Affiliation(s)
- Tuomas Hämälä
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Amanda J. Gorton
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, United States of America
| | - David A. Moeller
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Peter Tiffin
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, United States of America
| |
Collapse
|
34
|
Gaudinier A, Blackman BK. Evolutionary processes from the perspective of flowering time diversity. THE NEW PHYTOLOGIST 2020; 225:1883-1898. [PMID: 31536639 DOI: 10.1111/nph.16205] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 08/30/2019] [Indexed: 05/18/2023]
Abstract
Although it is well appreciated that genetic studies of flowering time regulation have led to fundamental advances in the fields of molecular and developmental biology, the ways in which genetic studies of flowering time diversity have enriched the field of evolutionary biology have received less attention despite often being equally profound. Because flowering time is a complex, environmentally responsive trait that has critical impacts on plant fitness, crop yield, and reproductive isolation, research into the genetic architecture and molecular basis of its evolution continues to yield novel insights into our understanding of domestication, adaptation, and speciation. For instance, recent studies of flowering time variation have reconstructed how, when, and where polygenic evolution of phenotypic plasticity proceeded from standing variation and de novo mutations; shown how antagonistic pleiotropy and temporally varying selection maintain polymorphisms in natural populations; and provided important case studies of how assortative mating can evolve and facilitate speciation with gene flow. In addition, functional studies have built detailed regulatory networks for this trait in diverse taxa, leading to new knowledge about how and why developmental pathways are rewired and elaborated through evolutionary time.
Collapse
Affiliation(s)
- Allison Gaudinier
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Benjamin K Blackman
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| |
Collapse
|
35
|
Popovic D, Lowry DB. Contrasting environmental factors drive local adaptation at opposite ends of an environmental gradient in the yellow monkeyflower (Mimulus guttatus). AMERICAN JOURNAL OF BOTANY 2020; 107:298-307. [PMID: 31989586 DOI: 10.1002/ajb2.1419] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 09/13/2019] [Indexed: 05/22/2023]
Abstract
PREMISE Identifying the environmental factors responsible for natural selection across different habitats is crucial for understanding the process of local adaptation in plants. Despite its importance, few studies have successfully isolated the environmental factors driving local adaptation in nature. In this study, we evaluated the agents of selection responsible for local adaptation of the monkeyflower Mimulus guttatus to California's coastal and inland habitats. METHODS We implemented a manipulative reciprocal transplant experiment at coastal and inland sites, where we excluded aboveground stressors in an effort to elucidate their role in the evolution of local adaptation. RESULTS Excluding aboveground stressors, most likely a combination of salt spray and herbivory, completely rescued inland annual plant fitness when transplanted to coastal habitat. The exclosures in inland habitat provided a benefit to the performance of coastal perennial plants. However, the exclosures are unlikely to provide much fitness benefit to the coastal plants at the inland site because of their general inability to flower in time to escape from the summer drought. CONCLUSIONS Our study demonstrates that a distinct set of selective agents (aboveground vs. belowground) are responsible for local adaptation at opposite ends of an environmental gradient.
Collapse
Affiliation(s)
- Damian Popovic
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
- Program in Ecology, Evolutionary Biology, and Behavior, Michigan State University, East Lansing, MI, 48824, USA
| | - David B Lowry
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
- Program in Ecology, Evolutionary Biology, and Behavior, Michigan State University, East Lansing, MI, 48824, USA
- Plant Resilience Institute, Michigan State University, East Lansing, MI, 48824, USA
| |
Collapse
|
36
|
Cai Z, Zhou L, Ren NN, Xu X, Liu R, Huang L, Zheng XM, Meng QL, Du YS, Wang MX, Geng MF, Chen WL, Jing CY, Zou XH, Guo J, Chen CB, Zeng HZ, Liang YT, Wei XH, Guo YL, Zhou HF, Zhang FM, Ge S. Parallel Speciation of Wild Rice Associated with Habitat Shifts. Mol Biol Evol 2019; 36:875-889. [PMID: 30861529 PMCID: PMC6501882 DOI: 10.1093/molbev/msz029] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The occurrence of parallel speciation strongly implies the action of natural selection. However, it is unclear how general a phenomena parallel speciation is since it was only shown in a small number of animal species. In particular, the adaptive process and mechanisms underlying the process of parallel speciation remain elusive. Here, we used an integrative approach incorporating population genomics, common garden, and crossing experiments to investigate parallel speciation of the wild rice species Oryza nivara from O. rufipogon. We demonstrated that O. nivara originated multiple times from different O. rufipogon populations and revealed that different O. nivara populations have evolved similar phenotypes under divergent selection, a reflection of recurrent local adaptation of ancient O. rufipogon populations to dry habitats. Almost completed premating isolation was detected between O. nivara and O. rufipogon in the absence of any postmating barriers between and within these species. These results suggest that flowering time is a “magic” trait that contributes to both local adaptation and reproductive isolation in the origin of wild rice species. Our study thus demonstrates a convincing case of parallel ecological speciation as a consequence of adaptation to new environments.
Collapse
Affiliation(s)
- Zhe Cai
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Lian Zhou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ning-Ning Ren
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xun Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Rong Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Lei Huang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xiao-Ming Zheng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Qing-Lin Meng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yu-Su Du
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Mei-Xia Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Mu-Fan Geng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wen-Li Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Chun-Yan Jing
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xin-Hui Zou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jie Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Cheng-Bin Chen
- Guangxi Academy Agricultural Sciences, Nanning, Guangxi, China
| | - Hua-Zhong Zeng
- Guangxi Academy Agricultural Sciences, Nanning, Guangxi, China
| | - Yun-Tao Liang
- Guangxi Academy Agricultural Sciences, Nanning, Guangxi, China
| | - Xing-Hua Wei
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Ya-Long Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Hai-Fei Zhou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Fu-Min Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
37
|
Christie K, Strauss SY. Reproductive isolation and the maintenance of species boundaries in two serpentine endemic Jewelflowers. Evolution 2019; 73:1375-1391. [PMID: 31152435 DOI: 10.1111/evo.13767] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 04/28/2019] [Accepted: 05/03/2019] [Indexed: 12/30/2022]
Abstract
Speciation occurs when reproductive barriers substantially reduce gene flow between lineages. Understanding how specific barriers contribute to reproductive isolation offers insight into the initial forces driving divergence and the evolutionary and ecological processes responsible for maintaining diversity. Here, we quantified multiple pre- and post-pollination isolating barriers in a pair of closely related California Jewelflowers (Streptanthus, Brassicaceae) living in an area of sympatry. S. breweri and S. hesperidis are restricted to similar serpentine habitats; however, populations are spatially isolated at fine-scales and rarely co-occur in intermixed stands. Several intrinsic postzygotic barriers were among the strongest we quantified, yet, postzygotic barriers currently contribute little to overall reproductive isolation due to the cumulative strength of earlier-acting extrinsic barriers, including spatial isolation, and flowering time and pollinator differences. Data from multiple years suggest that pre-pollination barriers may have different strengths depending on annual environmental conditions. Similarly, crossing data suggest that the strength of intrinsic isolation may vary among different population pairs. Estimates of total reproductive isolation in S. breweri and S. hesperidis are robust to uncertainty and variability in individual barrier strength estimates, demonstrating how multiple barriers can act redundantly to prevent gene flow between close relatives living in sympatry.
Collapse
Affiliation(s)
- Kyle Christie
- UC Davis Department of Evolution and Ecology, and Center for Population Biology, University of California, One Shields Avenue, Davis, California, 95616
| | - Sharon Y Strauss
- UC Davis Department of Evolution and Ecology, and Center for Population Biology, University of California, One Shields Avenue, Davis, California, 95616
| |
Collapse
|
38
|
Lowry DB, Popovic D, Brennan DJ, Holeski LM. Mechanisms of a locally adaptive shift in allocation among growth, reproduction, and herbivore resistance in
Mimulus guttatus
*. Evolution 2019; 73:1168-1181. [DOI: 10.1111/evo.13699] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 01/21/2019] [Accepted: 01/31/2019] [Indexed: 12/24/2022]
Affiliation(s)
- David B. Lowry
- Department of Plant BiologyMichigan State University East Lansing Michigan 48824
- Program in Ecology, Evolutionary Biology, and BehaviorMichigan State University East Lansing Michigan 48824
- Plant Resilience Institute,Michigan State University East Lansing Michigan 48824
| | - Damian Popovic
- Department of Plant BiologyMichigan State University East Lansing Michigan 48824
- Program in Ecology, Evolutionary Biology, and BehaviorMichigan State University East Lansing Michigan 48824
| | - Darlene J. Brennan
- Department of Plant BiologyMichigan State University East Lansing Michigan 48824
| | - Liza M. Holeski
- Department of Biological SciencesNorthern Arizona University Flagstaff Arizona 86011
| |
Collapse
|
39
|
Plus ça change, plus c'est la même chose: The developmental evolution of flowers. Curr Top Dev Biol 2019; 131:211-238. [DOI: 10.1016/bs.ctdb.2018.11.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
40
|
Genetic architecture of quantitative flower and leaf traits in a pair of sympatric sister species of Primulina. Heredity (Edinb) 2018; 122:864-876. [PMID: 30518967 DOI: 10.1038/s41437-018-0170-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 11/19/2018] [Accepted: 11/19/2018] [Indexed: 01/10/2023] Open
Abstract
Flowers and leaves each represent suites of functionally interrelated traits that are often involved in species divergence and local adaptation. However, a major unresolved issue is how the individual component traits that make up a complex trait such as a flower evolve in a coordinated fashion to retain a high degree of functionality. We use a quantitative trait loci (QTL) approach to elucidate the genetic architecture of divergence in flower and leaf traits between the sister species Primulina depressa and Primulina danxiaensis, which grow sympatrically but in contrasting microhabitats. We found that flower traits were controlled by multiple QTL of small effect, while leaf physiological and morphological traits tended to be controlled by QTL of larger effect. The observed floral integration, manifested by a high degree overlap in both individual trait QTL and QTL for principal component scores (PCA QTL), may have been critical for evolutionary divergence of floral morphology in relation to their pollinators. This overlap suggests that direct selection on only one or a few of the component traits could have caused substantial divergence in other floral traits due to genetic correlations, while the low QTL overlap between floral and vegetative traits suggests that these trait suites are genetically unlinked and can evolve independently in response to different selective pressures corresponding to their distinct functions.
Collapse
|
41
|
Schlüter PM. The magic of flowers or: speciation genes and where to find them. AMERICAN JOURNAL OF BOTANY 2018; 105:1957-1961. [PMID: 30462832 DOI: 10.1002/ajb2.1193] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 08/02/2018] [Indexed: 05/03/2023]
Affiliation(s)
- Philipp M Schlüter
- Institute of Botany, University of Hohenheim, Garbenstraße 30, D-70599, Stuttgart, Germany
| |
Collapse
|
42
|
Coughlan JM, Willis JH. Dissecting the role of a large chromosomal inversion in life history divergence throughout the Mimulus guttatus species complex. Mol Ecol 2018; 28:1343-1357. [PMID: 30028906 DOI: 10.1111/mec.14804] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 07/03/2018] [Accepted: 07/06/2018] [Indexed: 01/01/2023]
Abstract
Chromosomal inversions can play an important role in adaptation, but the mechanism of their action in many natural populations remains unclear. An inversion could suppress recombination between locally beneficial alleles, thereby preventing maladaptive reshuffling with less-fit, migrant alleles. The recombination suppression hypothesis has gained much theoretical support but empirical tests are lacking. Here, we evaluated the evolutionary history and phenotypic effects of a chromosomal inversion which differentiates annual and perennial forms of Mimulus guttatus. We found that perennials likely possess the derived orientation of the inversion. In addition, this perennial orientation occurs in a second perennial species, M. decorus, where it is strongly associated with life history differences between co-occurring M. decorus and annual M. guttatus. One prediction of the recombination suppression hypothesis is that loci contributing to local adaptation will predate the inversion. To test whether the loci influencing perenniality pre-date this inversion, we mapped QTLs for life history traits that differ between annual M. guttatus and a more distantly related, collinear perennial species, M. tilingii. Consistent with the recombination suppression hypothesis, we found that this region is associated with life history in the absence of the inversion, and this association can be broken into at least two QTLs. However, the absolute phenotypic effect of the LG8 inversion region on life history is weaker in M. tilingii than in perennials which possess the inversion. Thus, while we find support for the recombination suppression hypothesis, the contribution of this inversion to life history divergence in this group is likely complex.
Collapse
Affiliation(s)
| | - John H Willis
- Biology Department, Duke University, Durham, North Carolina
| |
Collapse
|
43
|
Ferris KG, Willis JH. Differential adaptation to a harsh granite outcrop habitat between sympatric
Mimulus
species. Evolution 2018; 72:1225-1241. [DOI: 10.1111/evo.13476] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 02/20/2018] [Accepted: 02/28/2018] [Indexed: 12/11/2022]
Affiliation(s)
- Kathleen G. Ferris
- Department of Biology Duke University 125 Science Drive Durham North Carolina 27705
- Current Address: Center for Population Biology, 2320 Storer Hall University of California Davis One Shields Avenue Davis California 95616
| | - John H. Willis
- Department of Biology Duke University 125 Science Drive Durham North Carolina 27705
| |
Collapse
|
44
|
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
|
45
|
Christie K, Strauss SY. Along the speciation continuum: Quantifying intrinsic and extrinsic isolating barriers across five million years of evolutionary divergence in California jewelflowers. Evolution 2018; 72:1063-1079. [DOI: 10.1111/evo.13477] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Accepted: 02/27/2018] [Indexed: 12/11/2022]
Affiliation(s)
- Kyle Christie
- Department of Evolution and Ecology and Center for Population Biology University of California One Shields Avenue Davis California 95616
| | - Sharon Y. Strauss
- Department of Evolution and Ecology and Center for Population Biology University of California One Shields Avenue Davis California 95616
| |
Collapse
|
46
|
Affiliation(s)
- Yaniv Brandvain
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Daniel R. Matute
- Biology Department, University of North Carolina, Chapel Hill, North Carolina, United States of America
| |
Collapse
|
47
|
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
|
48
|
Yu WB, Randle CP, Lu L, Wang H, Yang JB, dePamphilis CW, Corlett RT, Li DZ. The Hemiparasitic Plant Phtheirospermum (Orobanchaceae) Is Polyphyletic and Contains Cryptic Species in the Hengduan Mountains of Southwest China. FRONTIERS IN PLANT SCIENCE 2018; 9:142. [PMID: 29479366 PMCID: PMC5812252 DOI: 10.3389/fpls.2018.00142] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 01/25/2018] [Indexed: 05/04/2023]
Abstract
Phtheirospermum (Orobanchaceae), a hemiparasitic genus of Eastern Asia, is characterized by having long and viscous glandular hairs on stems and leaves. Despite this unifying character, previous phylogenetic analyses indicate that Phtheirospermum is polyphyletic, with Phtheirospermum japonicum allied with tribe Pedicularideae and members of the Ph. tenuisectum complex allied with members of tribe Rhinantheae. However, no analyses to date have included broad phylogenetic sampling necessary to test the monophyly of Phtheirospermum species, and to place these species into the existing subfamiliar taxonomic organization of Orobanchaceae. Two other genera of uncertain phylogenetic placement are Brandisia and Pterygiella, also both of Eastern Asia. In this study, broadly sampled phylogenetic analyses of nrITS and plastid DNA revealed hard incongruence between these datasets in the placement of Brandisia. However, both nrITS and the plastid datasets supported the placement of Ph. japonicum within tribe Pedicularideae, and a separate clade consisting of the Ph. tenuisectum complex and a monophyletic Pterygiella. Analyses were largely in agreement that Pterygiella, the Ptheirospermum complex, and Xizangia form a clade not nested within any of the monophyletic tribes of Orobanchaceae recognized to date. Ph. japonicum, a model species for parasitic plant research, is widely distributed in Eastern Asia. Despite this broad distribution, both nrITS and plastid DNA regions from a wide sampling of this species showed high genetic identity, suggesting that the wide species range is likely due to a recent population expansion. The Ph. tenuisectum complex is mainly distributed in the Hengduan Mountains region. Two cryptic species were identified by both phylogenetic analyses and morphological characters. Relationships among species of the Ph. tenuisectum complex and Pterygiella remain uncertain. Estimated divergence ages of the Ph. tenuisectum complex corresponding to the last two uplifts of the Qinghai-Tibet Plateau at around 8.0-7.0 Mya and 3.6-1.5 Mya indicated that the development of a hot-dry valley climate during these uplifts may have driven species diversification in the Ph. tenuisectum complex.
Collapse
Affiliation(s)
- Wen-Bin Yu
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden (CAS), Mengla, China
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Myanmar
| | - Christopher P. Randle
- Department of Biological Sciences, Sam Houston State University, Huntsville, TX, United States
| | - Lu Lu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Hong Wang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jun-Bo Yang
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Claude W. dePamphilis
- Department of Biology, Graduate Program in Plant Biology, The Pennsylvania State University, State College, PA, United States
| | - Richard T. Corlett
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden (CAS), Mengla, China
| | - De-Zhu Li
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| |
Collapse
|
49
|
|
50
|
Foote AD. Sympatric Speciation in the Genomic Era. Trends Ecol Evol 2017; 33:85-95. [PMID: 29198471 DOI: 10.1016/j.tree.2017.11.003] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 11/03/2017] [Accepted: 11/07/2017] [Indexed: 10/18/2022]
Abstract
Sympatric speciation has been of key interest to biologists investigating how natural and sexual selection drive speciation without the confounding variable of geographic isolation. The advent of the genomic era has provided a more nuanced and quantitative understanding of the different and often complex modes of speciation by which sympatric sister taxa arose, and a reassessment of some of the most compelling empirical case studies of sympatric speciation. However, I argue that genomic studies based on contemporary populations may never be able to provide unequivocal evidence of true primary sympatric speciation, and there is a need to incorporate palaeogenomic studies into this field. This inability to robustly distinguish cases of primary and secondary 'divergence with gene flow' may be inconsequential, as both are useful for understanding the role of large effect barrier loci in the progression from localised genic isolation to genome-wide reproductive isolation. I argue that they can be of equivalent interest due to shared underlying mechanisms driving divergence and potentially leaving similar patterns of coalescence.
Collapse
Affiliation(s)
- Andrew D Foote
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK.
| |
Collapse
|