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Delmore K, Justen H, Kay KM, Kitano J, Moyle LC, Stelkens R, Streisfeld MA, Yamasaki YY, Ross J. Genomic Approaches Are Improving Taxonomic Representation in Genetic Studies of Speciation. Cold Spring Harb Perspect Biol 2024; 16:a041438. [PMID: 37848243 PMCID: PMC10835617 DOI: 10.1101/cshperspect.a041438] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2023]
Abstract
Until recently, our understanding of the genetics of speciation was limited to a narrow group of model species with a specific set of characteristics that made genetic analysis feasible. Rapidly advancing genomic technologies are eliminating many of the distinctions between laboratory and natural systems. In light of these genomic developments, we review the history of speciation genetics, advances that have been gleaned from model and non-model organisms, the current state of the field, and prospects for broadening the diversity of taxa included in future studies. Responses to a survey of speciation scientists across the world reveal the ongoing division between the types of questions that are addressed in model and non-model organisms. To bridge this gap, we suggest integrating genetic studies from model systems that can be reared in the laboratory or greenhouse with genomic studies in related non-models where extensive ecological knowledge exists.
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Affiliation(s)
- Kira 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
| | - Kathleen M Kay
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, California 95060, USA
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Leonie C Moyle
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
| | - Rike Stelkens
- Division of Population Genetics, Department of Zoology, Stockholm University, 106 91 Stockholm, Sweden
| | - Matthew A Streisfeld
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403, USA
| | - Yo Y Yamasaki
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Joseph Ross
- Department of Biology, California State University, Fresno, California 93740, USA
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Short AW, Streisfeld MA. Ancient hybridization leads to the repeated evolution of red flowers across a monkeyflower radiation. Evol Lett 2023; 7:293-304. [PMID: 37829500 PMCID: PMC10565894 DOI: 10.1093/evlett/qrad024] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/14/2023] [Accepted: 05/12/2023] [Indexed: 10/14/2023] Open
Abstract
The reuse of old genetic variation can promote rapid diversification in evolutionary radiations, but in most cases, the historical events underlying this divergence are not known. For example, ancient hybridization can generate new combinations of alleles that sort into descendant lineages, potentially providing the raw material to initiate divergence. In the Mimulus aurantiacus species complex, there is evidence for widespread gene flow among members of this radiation. In addition, allelic variation in the MaMyb2 gene is responsible for differences in flower color between the closely related ecotypes of subspecies puniceus, contributing to reproductive isolation by pollinators. Previous work suggested that MaMyb2 was introgressed into the red-flowered ecotype of puniceus. However, additional taxa within the radiation have independently evolved red flowers from their yellow-flowered ancestors, raising the possibility that this introgression had a more ancient origin. In this study, we used repeated tests of admixture from whole-genome sequence data across this diverse radiation to demonstrate that there has been both ancient and recurrent hybridization in this group. However, most of the signal of this ancient introgression has been removed due to selection, suggesting that widespread barriers to gene flow are in place between taxa. Yet, a roughly 30 kb region that contains the MaMyb2 gene is currently shared only among the red-flowered taxa. Patterns of admixture, sequence divergence, and extended haplotype homozygosity across this region confirm a history of ancient hybridization, where functional variants have been preserved due to positive selection in red-flowered taxa but lost in their yellow-flowered counterparts. The results of this study reveal that selection against gene flow can reduce genomic signatures of ancient hybridization, but that historical introgression can provide essential genetic variation that facilitates the repeated evolution of phenotypic traits between lineages.
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Affiliation(s)
- Aidan W Short
- Institute of Ecology and Evolution, 5289 University of Oregon, Eugene, OR 97403-5289, United States
| | - Matthew A Streisfeld
- Institute of Ecology and Evolution, 5289 University of Oregon, Eugene, OR 97403-5289, United States
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Fetter KC, Keller SR. Admixture mapping and selection scans identify genomic regions associated with stomatal patterning and disease resistance in hybrid poplars. Ecol Evol 2023; 13:e10579. [PMID: 37881228 PMCID: PMC10597741 DOI: 10.1002/ece3.10579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 09/18/2023] [Accepted: 09/21/2023] [Indexed: 10/27/2023] Open
Abstract
Variation in fitness components can be linked in some cases to variation in key traits. Metric traits that lie at the intersection of development, defense, and ecological interactions may be expected to experience environmental selection, informing our understanding of evolutionary and ecological processes. Here, we use quantitative genetic and population genomic methods to investigate disease dynamics in hybrid and non-hybrid populations. We focus our investigation on morphological and ecophysiological traits which inform our understanding of physiology, growth, and defense against a pathogen. In particular, we investigate stomata, microscopic pores on the surface of a leaf that regulate gas exchange during photosynthesis and are sites of entry for various plant pathogens. Stomatal patterning traits were highly predictive of disease risk. Admixture mapping identified a polygenic basis of disease resistance. Candidate genes for stomatal and disease resistance map to the same genomic regions and experienced positive selection. Genes with functions to guard cell homeostasis, the plant immune system, components of constitutive defenses, and growth-related transcription factors were identified. Our results indicate positive selection acted on candidate genes for stomatal patterning and disease resistance, potentially acting in concert to structure their variation in naturally formed backcrossing hybrid populations.
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Affiliation(s)
- Karl C. Fetter
- Department of Plant BiologyUniversity of VermontBurlingtonVermontUSA
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticutUSA
| | - Stephen R. Keller
- Department of Plant BiologyUniversity of VermontBurlingtonVermontUSA
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Stankowski S, Chase MA, McIntosh H, Streisfeld MA. Integrating top-down and bottom-up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone. Mol Ecol 2023; 32:2041-2054. [PMID: 36651268 DOI: 10.1111/mec.16849] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 01/04/2023] [Accepted: 01/12/2023] [Indexed: 01/19/2023]
Abstract
Understanding the phenotypic and genetic architecture of reproductive isolation is a long-standing goal of speciation research. In several systems, large-effect loci contributing to barrier phenotypes have been characterized, but such causal connections are rarely known for more complex genetic architectures. In this study, we combine "top-down" and "bottom-up" approaches with demographic modelling toward an integrated understanding of speciation across a monkeyflower hybrid zone. Previous work suggests that pollinator visitation acts as a primary barrier to gene flow between two divergent red- and yellow-flowered ecotypes of Mimulus aurantiacus. Several candidate isolating traits and anonymous single nucleotide polymorphism loci under divergent selection have been identified, but their genomic positions remain unknown. Here, we report findings from demographic analyses that indicate this hybrid zone formed by secondary contact, but that subsequent gene flow was restricted by widespread barrier loci across the genome. Using a novel, geographic cline-based genome scan, we demonstrate that candidate barrier loci are broadly distributed across the genome, rather than mapping to one or a few "islands of speciation." Quantitative trait locus (QTL) mapping reveals that most floral traits are highly polygenic, with little evidence that QTL colocalize, indicating that most traits are genetically independent. Finally, we find little evidence that QTL and candidate barrier loci overlap, suggesting that some loci contribute to other forms of reproductive isolation. Our findings highlight the challenges of understanding the genetic architecture of reproductive isolation and reveal that barriers to gene flow other than pollinator isolation may play an important role in this system.
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Affiliation(s)
- Sean Stankowski
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - Madeline A Chase
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - Hanna McIntosh
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
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Morales‐Briones DF, Lin N, Huang EY, Grossenbacher DL, Sobel JM, Gilmore CD, Tank DC, Yang Y. Phylogenomic analyses in Phrymaceae reveal extensive gene tree discordance in relationships among major clades. AMERICAN JOURNAL OF BOTANY 2022; 109:1035-1046. [PMID: 35462411 PMCID: PMC9328367 DOI: 10.1002/ajb2.1860] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 04/13/2022] [Accepted: 04/14/2022] [Indexed: 06/14/2023]
Abstract
PREMISE Phylogenomic datasets using genomes and transcriptomes provide rich opportunities beyond resolving bifurcating phylogenetic relationships. Monkeyflower (Phrymaceae) is a model system for evolutionary ecology. However, it lacks a well-supported phylogeny as a basis for a stable taxonomy and for macroevolutionary comparisons. METHODS We sampled 24 genomes and transcriptomes in Phrymaceae and closely related families, including eight newly sequenced transcriptomes. We reconstructed the phylogeny using IQ-TREE and ASTRAL, evaluated gene tree discordance using PhyParts, Quartet Sampling, and a cloudogram, and carried out reticulation analyses using PhyloNet and HyDe. We searched for whole genome duplication (WGD) events using chromosome numbers, synonymous distances, and gene duplication events as evidence. RESULTS Most gene trees support the monophyly of Phrymaceae and each of its tribes. Most gene trees also support tribe Mimuleae being sister to Phrymeae + Diplaceae + Leucocarpeae, with extensive gene tree discordance among the latter three. Despite the discordance, the monophyly of Mimulus s.l. is rejected, and no individual reticulation event among the Phrymaceae tribes is well-supported. Reticulation likely occurred among Erythranthe bicolor and closely related species. No ancient WGD was detected in Phrymaceae. Instead, small-scale duplications are among potential drivers of macroevolutionary diversification of Phrymaceae. CONCLUSIONS We show that analysis of reticulate evolution is sensitive to taxon sampling and methods used. We also demonstrate that phylogenomic datasets using genomes and transcriptomes present rich opportunities to investigate gene family evolution and genome duplication events involved in lineage diversification and adaptation.
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Affiliation(s)
- Diego F. Morales‐Briones
- Department of Plant and Microbial BiologyUniversity of Minnesota‐Twin Cities1445 Gortner AvenueSt. PaulMinnesota55108‐1095USA
- Systematics, Biodiversity and Evolution of Plants, Department of Biology I, Ludwig‐Maximilians‐Universität MünchenMenzinger Strasse 6780638MunichGermany
| | - Nan Lin
- Department of Plant and Microbial BiologyUniversity of Minnesota‐Twin Cities1445 Gortner AvenueSt. PaulMinnesota55108‐1095USA
- College of Life ScienceHenan Agricultural University63 Nongye RoadZhengzhouHenan450002China
| | - Eileen Y. Huang
- Department of Plant and Microbial BiologyUniversity of Minnesota‐Twin Cities1445 Gortner AvenueSt. PaulMinnesota55108‐1095USA
| | - Dena L. Grossenbacher
- Biological Sciences DepartmentCalifornia Polytechnic State University, 1 Grand Avenue, San Luis ObispoCalifornia93407USA
| | - James M. Sobel
- Department of Biological SciencesBinghamton University (State University of New York), 4400 Vestal Parkway E, BinghamtonNew York13902USA
| | - Caroline D. Gilmore
- Department of Biological SciencesBinghamton University (State University of New York), 4400 Vestal Parkway E, BinghamtonNew York13902USA
| | - David C. Tank
- Department of Botany & Rocky Mountain HerbariumUniversity of Wyoming, 1000 E. University Avenue, LaramieWyoming82071USA
| | - Ya Yang
- Department of Plant and Microbial BiologyUniversity of Minnesota‐Twin Cities1445 Gortner AvenueSt. PaulMinnesota55108‐1095USA
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Holeski LM, Keefover-Ring K, Sobel JM, Kooyers NJ. Evolutionary history and ecology shape the diversity and abundance of phytochemical arsenals across monkeyflowers. J Evol Biol 2021; 34:571-583. [PMID: 33484000 DOI: 10.1111/jeb.13760] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 12/30/2020] [Indexed: 11/29/2022]
Abstract
We examine the extent to which phylogenetic effects and ecology are associated with macroevolutionary patterns of phytochemical defence production across the Mimulus phylogeny. We grew plants from 21 species representing the five major sections of the Mimulus phylogeny in a common garden to assess how the arsenals (NMDS groupings) and abundances (concentrations) of a phytochemical defence, phenylpropanoid glycosides (PPGs), vary across the phylogeny. Very few PPGs are widespread across the genus, but many are common to multiple sections of the genus. Phytochemical arsenals cluster among sections in an NMDS and are not associated with total concentration of PPGs. There is a strong phylogenetic signal for phytochemical arsenal composition across the Mimulus genus, whereas ecological variables such as growing season length, latitude, and elevation do not significantly influence arsenal. In contrast, there is little phylogenetic signal for total PPG concentration, and this trait is significantly influenced by several ecological factors. Phytochemical arsenals and abundances are influenced by plant life history form. Both phylogenetic effects and ecology are related to phytochemical patterns across species, albeit in different ways. The independence of phytochemical defence concentrations from arsenal compositions indicates that these aspects of defence may continue to evolve independently of one another.
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Affiliation(s)
- Liza M Holeski
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Ken Keefover-Ring
- Departments of Botany and Geography, University of Wisconsin-Madison, Madison, WI, USA
| | - James M Sobel
- Department of Biological Sciences, Binghamton University (SUNY), Binghamton, NY, USA
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Nelson TC, Stathos AM, Vanderpool DD, Finseth FR, Yuan YW, Fishman L. Ancient and recent introgression shape the evolutionary history of pollinator adaptation and speciation in a model monkeyflower radiation (Mimulus section Erythranthe). PLoS Genet 2021; 17:e1009095. [PMID: 33617525 PMCID: PMC7951852 DOI: 10.1371/journal.pgen.1009095] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 03/11/2021] [Accepted: 01/22/2021] [Indexed: 12/20/2022] Open
Abstract
Inferences about past processes of adaptation and speciation require a gene-scale and genome-wide understanding of the evolutionary history of diverging taxa. In this study, we use genome-wide capture of nuclear gene sequences, plus skimming of organellar sequences, to investigate the phylogenomics of monkeyflowers in Mimulus section Erythranthe (27 accessions from seven species). Taxa within Erythranthe, particularly the parapatric and putatively sister species M. lewisii (bee-pollinated) and M. cardinalis (hummingbird-pollinated), have been a model system for investigating the ecological genetics of speciation and adaptation for over five decades. Across >8000 nuclear loci, multiple methods resolve a predominant species tree in which M. cardinalis groups with other hummingbird-pollinated taxa (37% of gene trees), rather than being sister to M. lewisii (32% of gene trees). We independently corroborate a single evolution of hummingbird pollination syndrome in Erythranthe by demonstrating functional redundancy in genetic complementation tests of floral traits in hybrids; together, these analyses overturn a textbook case of pollination-syndrome convergence. Strong asymmetries in allele sharing (Patterson's D-statistic and related tests) indicate that gene tree discordance reflects ancient and recent introgression rather than incomplete lineage sorting. Consistent with abundant introgression blurring the history of divergence, low-recombination and adaptation-associated regions support the new species tree, while high-recombination regions generate phylogenetic evidence for sister status for M. lewisii and M. cardinalis. Population-level sampling of core taxa also revealed two instances of chloroplast capture, with Sierran M. lewisii and Southern Californian M. parishii each carrying organelle genomes nested within respective sympatric M. cardinalis clades. A recent organellar transfer from M. cardinalis, an outcrosser where selfish cytonuclear dynamics are more likely, may account for the unexpected cytoplasmic male sterility effects of selfer M. parishii organelles in hybrids with M. lewisii. Overall, our phylogenomic results reveal extensive reticulation throughout the evolutionary history of a classic monkeyflower radiation, suggesting that natural selection (re-)assembles and maintains species-diagnostic traits and barriers in the face of gene flow. Our findings further underline the challenges, even in reproductively isolated species, in distinguishing re-use of adaptive alleles from true convergence and emphasize the value of a phylogenomic framework for reconstructing the evolutionary genetics of adaptation and speciation.
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Affiliation(s)
- Thomas C. Nelson
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - Angela M. Stathos
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - Daniel D. Vanderpool
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - Findley R. Finseth
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - Yao-wu Yuan
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut, United States of America
| | - Lila Fishman
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
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Rivera-Colón AG, Rochette NC, Catchen JM. Simulation with RADinitio improves RADseq experimental design and sheds light on sources of missing data. Mol Ecol Resour 2020; 21:363-378. [PMID: 32275349 DOI: 10.1111/1755-0998.13163] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 03/25/2020] [Indexed: 12/20/2022]
Abstract
Restriction-site associated DNA sequencing (RADseq) has become a powerful and versatile tool in modern population genomics, enabling large-scale evolutionary and genomic analyses in otherwise inaccessible biological systems. With its widespread use, different variants on the protocol have been developed to suit specific experimental needs. Researchers face the challenge of choosing the optimal molecular and sequencing protocols for their reduced representation experimental design, an often-complicated process. Strategic errors can lead to biased data generation that has reduced power to answer biological questions. Here, we present RADinitio, simulation software for the selection and optimization of RADseq experiments via the generation of sequencing data that behave similarly to empirical sources. RADinitio provides an evolutionary simulation of populations, implementation of various RADseq protocols with customizable parameters, and thorough assessment of missing data. We test the efficacy of the software using different RAD protocols across several organisms, highlighting the importance of protocol selection on the magnitude and quality of data acquired. Additionally, we test the effects of RAD library preparation and sequencing on allelic dropout, observing that library preparation and sequencing often contributes more to missing alleles than population-level variation.
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Affiliation(s)
- Angel G Rivera-Colón
- Department of Evolution, Ecology and Behavior, University of Illinois, Urbana, Illinois, USA
| | - Nicolas C Rochette
- Department of Evolution, Ecology and Behavior, University of Illinois, Urbana, Illinois, USA
| | - Julian M Catchen
- Department of Evolution, Ecology and Behavior, University of Illinois, Urbana, Illinois, USA
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Stankowski S, Chase MA, Fuiten AM, Rodrigues MF, Ralph PL, Streisfeld MA. Widespread selection and gene flow shape the genomic landscape during a radiation of monkeyflowers. PLoS Biol 2019; 17:e3000391. [PMID: 31339877 PMCID: PMC6660095 DOI: 10.1371/journal.pbio.3000391] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 07/26/2019] [Accepted: 07/03/2019] [Indexed: 12/12/2022] Open
Abstract
Speciation genomic studies aim to interpret patterns of genome-wide variation in light of the processes that give rise to new species. However, interpreting the genomic "landscape" of speciation is difficult, because many evolutionary processes can impact levels of variation. Facilitated by the first chromosome-level assembly for the group, we use whole-genome sequencing and simulations to shed light on the processes that have shaped the genomic landscape during a radiation of monkeyflowers. After inferring the phylogenetic relationships among the 9 taxa in this radiation, we show that highly similar diversity (π) and differentiation (FST) landscapes have emerged across the group. Variation in these landscapes was strongly predicted by the local density of functional elements and the recombination rate, suggesting that the landscapes have been shaped by widespread natural selection. Using the varying divergence times between pairs of taxa, we show that the correlations between FST and genome features arose almost immediately after a population split and have become stronger over time. Simulations of genomic landscape evolution suggest that background selection (BGS; i.e., selection against deleterious mutations) alone is too subtle to generate the observed patterns, but scenarios that involve positive selection and genetic incompatibilities are plausible alternative explanations. Finally, tests for introgression among these taxa reveal widespread evidence of heterogeneous selection against gene flow during this radiation. Combined with previous evidence for adaptation in this system, we conclude that the correlation in FST among these taxa informs us about the processes contributing to adaptation and speciation during a rapid radiation.
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Affiliation(s)
- Sean Stankowski
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Madeline A. Chase
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Allison M. Fuiten
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Murillo F. Rodrigues
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Peter L. Ralph
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Matthew A. Streisfeld
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
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Sobel JM, Stankowski S, Streisfeld MA. Variation in ecophysiological traits might contribute to ecogeographic isolation and divergence between parapatric ecotypes of
Mimulus aurantiacus. J Evol Biol 2019; 32:604-618. [DOI: 10.1111/jeb.13442] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 03/06/2019] [Accepted: 03/11/2019] [Indexed: 12/11/2022]
Affiliation(s)
- James M. Sobel
- Department of Biological Sciences Binghamton University (SUNY) Binghamton New York
| | - Sean Stankowski
- Institute of Ecology and Evolution University of Oregon Eugene Oregon
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