1
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Rhoads DD, Williams DA. Background Color Matching in Texas Horned Lizards (Phrynosoma cornutum). J HERPETOL 2023. [DOI: 10.1670/22-008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
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2
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Scherz MD, Schmidt R, Brown JL, Glos J, Lattenkamp EZ, Rakotomalala Z, Rakotoarison A, Rakotonindrina RT, Randriamalala O, Raselimanana AP, Rasolonjatovo SM, Ratsoavina FM, Razafindraibe JH, Glaw F, Vences M. Repeated divergence of amphibians and reptiles across an elevational gradient in northern Madagascar. Ecol Evol 2023; 13:e9914. [PMID: 36937068 PMCID: PMC10019947 DOI: 10.1002/ece3.9914] [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: 09/12/2022] [Revised: 02/22/2023] [Accepted: 02/28/2023] [Indexed: 03/18/2023] Open
Abstract
How environmental factors shape patterns of biotic diversity in tropical ecosystems is an active field of research, but studies examining the possibility of ecological speciation in terrestrial tropical ecosystems are scarce. We use the isolated rainforest herpetofauna on the Montagne d'Ambre (Amber Mountain) massif in northern Madagascar as a model to explore elevational divergence at the level of populations and communities. Based on intensive sampling and DNA barcoding of amphibians and reptiles along a transect ranging from ca. 470-1470 m above sea level (a.s.l.), we assessed a main peak in species richness at an elevation of ca. 1000 m a.s.l. with 41 species. The proportion of local endemics was highest (about 1/3) at elevations >1100 m a.s.l. Two species of chameleons (Brookesia tuberculata, Calumma linotum) and two species of frogs (Mantidactylus bellyi, M. ambony) studied in depth by newly developed microsatellite markers showed genetic divergence up the slope of the mountain, some quite strong, others very weak, but in each case with genetic breaks between 1100 and 1270 m a.s.l. Genetic clusters were found in transect sections significantly differing in bioclimate and herpetological community composition. A decrease in body size was detected in several species with increasing elevation. The studied rainforest amphibians and reptiles show concordant population genetic differentiation across elevation along with morphological and niche differentiation. Whether this parapatric or microallopatric differentiation will suffice for the completion of speciation is, however, unclear, and available phylogeographic evidence rather suggests that a complex interplay between ecological and allopatric divergence processes is involved in generating the extraordinary species diversity of Madagascar's biota. Our study reveals concordant patterns of diversification among main elevational bands, but suggests that these adaptational processes are only part of the complex of processes leading to species formation, among which geographical isolation is probably also important.
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Affiliation(s)
- Mark D. Scherz
- Zoologisches InstitutTechnische Universität BraunschweigBraunschweigGermany
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagen ØDenmark
| | - Robin Schmidt
- Zoologisches InstitutTechnische Universität BraunschweigBraunschweigGermany
| | - Jason L. Brown
- School of Biological SciencesSouthern Illinois UniversityCarbondaleIllinoisUSA
| | - Julian Glos
- Institute of Cell and Systems BiologyUniversität HamburgHamburgGermany
| | - Ella Z. Lattenkamp
- Neurogenetics of Vocal Communication GroupMax Planck Institute for PsycholinguisticsNijmegenThe Netherlands
- Division of Neurobiology, Department of Biology IILudwig Maximilians University MunichMartinsriedGermany
| | | | - Andolalao Rakotoarison
- Mention Zoologie et Biodiversité AnimaleUniversité d'AntananarivoAntananarivoMadagascar
- School for International TrainingAntananarivoMadagascar
| | | | - Onja Randriamalala
- Mention Zoologie et Biodiversité AnimaleUniversité d'AntananarivoAntananarivoMadagascar
| | - Achille P. Raselimanana
- Mention Zoologie et Biodiversité AnimaleUniversité d'AntananarivoAntananarivoMadagascar
- Association VahatraAntananarivoMadagascar
| | - Safidy M. Rasolonjatovo
- Mention Zoologie et Biodiversité AnimaleUniversité d'AntananarivoAntananarivoMadagascar
- Association VahatraAntananarivoMadagascar
| | | | - Jary H. Razafindraibe
- Mention Zoologie et Biodiversité AnimaleUniversité d'AntananarivoAntananarivoMadagascar
| | - Frank Glaw
- Zoologische Staatssammlung München (ZSM‐SNSB)MunichGermany
| | - Miguel Vences
- Zoologisches InstitutTechnische Universität BraunschweigBraunschweigGermany
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3
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Clark JD, Benham PM, Maldonado JE, Luther DA, Lim HC. Maintenance of local adaptation despite gene flow in a coastal songbird. Evolution 2022; 76:1481-1494. [PMID: 35700208 PMCID: PMC9545442 DOI: 10.1111/evo.14538] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 03/09/2022] [Accepted: 03/19/2022] [Indexed: 01/22/2023]
Abstract
Adaptation to local environments is common in widespread species and the basis of ecological speciation. The song sparrow (Melospiza melodia) is a widespread, polytypic passerine that occurs in shrubland habitats throughout North America. We examined the population structure of two parapatric subspecies that inhabit different environments: the Atlantic song sparrow (M. m. atlantica), a coastal specialist, and the eastern song sparrow (M. m. melodia), a shrubland generalist. These populations lacked clear mitochondrial population structure, yet coastal birds formed a distinct nuclear genetic cluster. We found weak overall genomic differentiation between these subspecies, suggesting either recent divergence, extensive gene flow, or a combination thereof. There was a steep genetic cline at the transition to coastal habitats, consistent with isolation by environment, not isolation by distance. A phenotype under divergent selection, bill size, varied with the amount of coastal ancestry in transitional areas, but larger bill size was maintained in coastal habitats regardless of ancestry, further supporting a role for selection in the maintenance of these subspecies. Demographic modeling suggested a divergence history of limited gene flow followed by secondary contact, which has emerged as a common theme in adaptive divergence across taxa.
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Affiliation(s)
- Jonathan D. Clark
- Department of Environmental Science and PolicyGeorge Mason UniversityFairfaxVirginia22030,Current Address: Department of Natural Resources and the EnvironmentUniversity of New HampshireDurhamNew Hampshire03824
| | - Phred M. Benham
- Museum of Vertebrate ZoologyUniversity of California, BerkeleyBerkeleyCalifornia94720
| | - Jesus E. Maldonado
- Department of Environmental Science and PolicyGeorge Mason UniversityFairfaxVirginia22030,Center for Conservation GenomicsSmithsonian Conservation Biology InstituteWashingtonD.C.20013
| | - David A. Luther
- Department of BiologyGeorge Mason UniversityFairfaxVirginia22030
| | - Haw Chuan Lim
- Center for Conservation GenomicsSmithsonian Conservation Biology InstituteWashingtonD.C.20013,Department of BiologyGeorge Mason UniversityFairfaxVirginia22030
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4
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Gunderson AR, Riddell EA, Sears MW, Rosenblum EB. Thermal costs and benefits of replicated color evolution in the White Sands Desert lizard community. Am Nat 2022; 199:666-678. [DOI: 10.1086/719027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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5
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Sianta SA, Kay KM. Parallel evolution of phenological isolation across the speciation continuum in serpentine-adapted annual wildflowers. Proc Biol Sci 2021; 288:20203076. [PMID: 33849321 PMCID: PMC8059516 DOI: 10.1098/rspb.2020.3076] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 03/17/2021] [Indexed: 01/26/2023] Open
Abstract
Understanding the relative importance of reproductive isolating mechanisms across the speciation continuum remains an outstanding challenge in evolutionary biology. Here, we examine a common isolating mechanism, reproductive phenology, between plant sister taxa at different stages of adaptive divergence to gain insight into its relative importance during speciation. We study 17 plant taxa that have independently adapted to inhospitable serpentine soils, and contrast each with a nonserpentine sister taxon to form pairs at either ecotypic or species-level divergence. We use greenhouse-based reciprocal transplants in field soils to quantify how often flowering time (FT) shifts accompany serpentine adaptation, when FT shifts evolve during speciation, and the genetic versus plastic basis of these shifts. We find that genetically based shifts in FT in serpentine-adapted taxa are pervasive regardless of the stage of divergence. Although plasticity increases FT shifts in five of the pairs, the degree of plasticity does not differ when comparing ecotypic versus species-level divergence. FT shifts generally led to significant, but incomplete, reproductive isolation that did not vary in strength by stage of divergence. Our work shows that adaptation to a novel habitat may predictably drive phenological isolation early in the speciation process.
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Affiliation(s)
- Shelley A. Sianta
- Department of Ecology and Evolutionary Biology, University of California, 130 McAllister Way, Santa Cruz, CA 95060, USA
| | - Kathleen M. Kay
- Department of Ecology and Evolutionary Biology, University of California, 130 McAllister Way, Santa Cruz, CA 95060, USA
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6
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Rich C, Reilly SB, Sinervo B. Relaxed predation selection on rare morphs of Ensatina salamanders (Caudata: Plethodontidae) promotes a polymorphic population in a novel dune sand habitat. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blaa211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
The ring species Ensatina represents a classic example of locally adapted lineages. The Monterey ensatina (Ensatina eschscholtzii eschscholtzii) is a cryptic subspecies with brown coloration, although a recently discovered polymorphic population within a wind-blown sand region also contains leucistic (pink) and xanthistic (orange) morphs. In the present study, the frequency of leucism/xanthism was mapped across the subspecies’ range, revealing that these morphs are generally rare or absent except within regions containing light-coloured substrate. Attack rates were estimated using clay models of the three morphs, deployed only at the crepuscular period and during the night, on both light and dark substrates at a site within the dune sand region. Model selection found that the interaction between morph and substrate colour best predicted attack rates. Typical morphs had equal attack rates on both substrates while xanthistic and leucistic morphs incurred significantly fewer attacks on light vs. dark substrate, and there was no significant difference in attack rates among morphs on light substrates. These results support the idea that xanthistic and leucistic morphs are poorly adapted for dark substrates compared to typical morphs, but they are more or less equally adapted for light substrates. We suggest that this microgeographic island of relaxed selection on light-coloured morphs helps to explain the existence of this polymorphic population.
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Affiliation(s)
- Caitlyn Rich
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA
| | - Sean B Reilly
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA
| | - Barry Sinervo
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA
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7
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Prates I, Singhal S. Predicting speciation probability from replicated population histories. Mol Ecol 2020; 29:2954-2956. [PMID: 32745299 DOI: 10.1111/mec.15577] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 07/27/2020] [Indexed: 11/30/2022]
Abstract
In this issue of Molecular Ecology, Yamasaki et al. (2020) use genetic data from extensive sampling of Rhinogobius goby fish across the Ryukyu Archipelago in Japan to demonstrate the parallel speciation of a freshwater form from an ancestral amphidromous form. They then show that ecosystem size strongly predicts the probability of speciation between the two forms across islands. In doing so, this study connects population-level processes (microevolution) to broad-scale biodiversity patterns (macroevolution), an important but understudied link in evolutionary biology. Moving forward, we can build on this research to (a) more directly determine how geographic, ecological and historical factors influence the different stages of the speciation process, and (b) understand whether mechanisms inferred from insular radiations extend to those on continents, where both demographic histories and environmental regimes are likely more complex.
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Affiliation(s)
- Ivan Prates
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Sonal Singhal
- Department of Biology, California State University Dominguez Hills, Carson, CA, USA
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8
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Curran EV, Stankowski S, Pardo‐Diaz C, Salazar C, Linares M, Nadeau NJ. Müllerian mimicry of a quantitative trait despite contrasting levels of genomic divergence and selection. Mol Ecol 2020; 29:2016-2030. [DOI: 10.1111/mec.15460] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 03/24/2020] [Accepted: 04/24/2020] [Indexed: 11/26/2022]
Affiliation(s)
- Emma V. Curran
- Department of Animal and Plant Sciences University of Sheffield Sheffield UK
| | - Sean Stankowski
- Department of Animal and Plant Sciences University of Sheffield Sheffield UK
| | - Carolina Pardo‐Diaz
- Biology Program Faculty of Natural Sciences and Mathematics Universidad del Rosario Bogota Colombia
| | - Camilo Salazar
- Biology Program Faculty of Natural Sciences and Mathematics Universidad del Rosario Bogota Colombia
| | - Mauricio Linares
- Biology Program Faculty of Natural Sciences and Mathematics Universidad del Rosario Bogota Colombia
| | - Nicola J. Nadeau
- Department of Animal and Plant Sciences University of Sheffield Sheffield UK
- The Smithsonian Tropical Research Institute Panama City Republic of Panama
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9
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Weinstein SY, Thrower FP, Nichols KM, Hale MC. A large-scale chromosomal inversion is not associated with life history development in rainbow trout from Southeast Alaska. PLoS One 2019; 14:e0223018. [PMID: 31539414 PMCID: PMC6754156 DOI: 10.1371/journal.pone.0223018] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 09/11/2019] [Indexed: 01/12/2023] Open
Abstract
In studying the causative mechanisms behind migration and life history, the salmonids-salmon, trout, and charr-are an exemplary taxonomic group, as life history development is known to have a strong genetic component. A double inversion located on chromosome 5 in rainbow trout (Oncorhynchus mykiss) is associated with life history development in multiple populations, but the importance of this inversion has not been thoroughly tested in conjunction with other polymorphisms in the genome. To that end, we used a high-density SNP chip to genotype 192 F1 migratory and resident rainbow trout and focused our analyses to determine whether this inversion is important in life history development in a well-studied population of rainbow trout from Southeast Alaska. We identified 4,994 and 436 SNPs-predominantly outside of the inversion region-associated with life history development in the migrant and resident familial lines, respectively. Although F1 samples showed genomic patterns consistent with the double inversion on chromosome 5 (reduced observed and expected heterozygosity and an increase in linkage disequilibrium), we found no statistical association between the inversion and life history development. Progeny produced by crossing resident trout and progeny produced by crossing migrant trout both consisted of a mix of migrant and resident individuals, irrespective of the individuals' inversion haplotype on chromosome 5. This suggests that although the inversion is present at a low frequency, it is not strongly associated with migration as it is in populations of Oncorhynchus mykiss from lower latitudes.
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Affiliation(s)
- Spencer Y. Weinstein
- Department of Biology, Texas Christian University, Fort Worth, United States of America
| | - Frank P. Thrower
- Ted Stevens Marine Research Institute, Alaska Fisheries Center, NOAA, Juneau, AK, United States of America
| | - Krista M. Nichols
- Conservation Biology Division, Northwest Fisheries Science Center, Seattle, WA, United States of America
| | - Matthew C. Hale
- Department of Biology, Texas Christian University, Fort Worth, United States of America
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10
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Oke KB, Cunningham CJ, Quinn TP, Hendry AP. Independent lineages in a common environment: the roles of determinism and contingency in shaping the migration timing of even- versus odd-year pink salmon over broad spatial and temporal scales. Ecol Lett 2019; 22:1547-1556. [PMID: 31290586 DOI: 10.1111/ele.13337] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 03/30/2019] [Accepted: 06/13/2019] [Indexed: 01/02/2023]
Abstract
Studies of parallel evolution are seldom able to disentangle the influence of cryptic environmental variation from that of evolutionary history; whereas the unique life history of pink salmon (Oncorhynchus gorbuscha) presents an opportunity to do so. All pink salmon mature at age two and die after breeding. Hence, pink salmon bred in even years are completely reproductively isolated from those bred in odd years, even if the two lineages bred in same location. We used time series (mean = 7 years, maximum = 74 years) of paired even- and odd-year populations from 36 rivers spanning over 2000 km to explore parallelism in migration timing, a trait with a strong genetic basis. Migration timing was highly parallel, being determined almost entirely by local environmental differences among rivers. Interestingly, interannual changes in migration timing different somewhat between lineages. Overall, our findings indicate very strong determinism, with only a minor contribution of contingency.
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Affiliation(s)
- Krista B Oke
- Department of Biology and Redpath Museum, McGill University, Montreal, QC, H3A 2K6, Canada
| | - Curry J Cunningham
- Fisheries, Aquatic Science & Technology Laboratory, Alaska Pacific University, 4101 University Dr, Anchorage, AK, 99508, USA
| | - Thomas P Quinn
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Andrew P Hendry
- Department of Biology and Redpath Museum, McGill University, Montreal, QC, H3A 2K6, Canada
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11
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Hu CC, Wu YQ, Ma L, Chen YJ, Ji X. Genetic and morphological divergence among three closely related Phrynocephalus species (Agamidae). BMC Evol Biol 2019; 19:114. [PMID: 31170905 PMCID: PMC6551896 DOI: 10.1186/s12862-019-1443-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Accepted: 05/27/2019] [Indexed: 11/25/2022] Open
Abstract
Background The Qinghai-Tibetan Plateau (QTP) is the world’s highest and largest plateau, but the role of its uplift in the evolution of species or biotas still remains poorly known. Toad-headed lizards of the reproductively bimodal genus Phrynocephalus are a clade of agamids, with all viviparous species restricted to the QTP and adjacent regions. The eastern part of the range of the viviparous taxa is occupied by three closely related but taxonomically controversial species, P. guinanensis, P. putjatia and P. vlangalii. Here, we combined genetic (mitochondrial ND4 gene and nine microsatellite loci), morphological (11 mensural and 11 meristic variables), and ecological (nine climatic variables) data to explore possible scenarios that may explain the discordance between genetic and morphological patterns, and to test whether morphological divergence is associated with local adaptation. Results We found weak genetic differentiation but pronounced morphological divergence, especially between P. guinanensis and P. vlangalii. Genetically, the species boundary was not so clear between any species pair. Morphologically, the species boundary was clear between P. guinanensis and P. vlangalii but not between other two species pairs. Body size and scale characters accounted best for morphological divergence between species. Morphological divergence was related to habitat types that differ climatically. Conclusions Our study provides evidence for genetic and morphological divergence among the three closely related viviparous species of Phrynocephalus lizards, and supports the idea that natural selection in spatially heterogeneous environments can lead to population divergence even in the presence of gene flow. Our study supports the hypothesis that the evolutionary divergence between viviparous Phrynocephalus species was a consequence of environmental change after the uplift of the QTP. Electronic supplementary material The online version of this article (10.1186/s12862-019-1443-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chao-Chao Hu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China.,Analysis and Testing Center, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
| | - Yan-Qing Wu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China.,Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, 210000, Jiangsu, China
| | - Li Ma
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
| | - Yi-Jing Chen
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
| | - Xiang Ji
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China.
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12
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Scale-dependent patterns of intraspecific trait variations in two globally invasive species. Oecologia 2019; 189:1083-1094. [DOI: 10.1007/s00442-019-04374-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 02/26/2019] [Indexed: 10/27/2022]
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13
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Klonoski K, Bi K, Rosenblum EB. Phenotypic and genetic diversity in aposematic Malagasy poison frogs (genus Mantella). Ecol Evol 2019; 9:2725-2742. [PMID: 30891212 PMCID: PMC6406014 DOI: 10.1002/ece3.4943] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 12/07/2018] [Accepted: 01/02/2019] [Indexed: 12/17/2022] Open
Abstract
Intraspecific color variation has long fascinated evolutionary biologists. In species with bright warning coloration, phenotypic diversity is particularly compelling because many factors, including natural and sexual selection, contribute to intraspecific variation. To better understand the causes of dramatic phenotypic variation in Malagasy poison frogs, we quantified genetic structure and color and pattern variation across three closely related species, Mantella aurantiaca, Mantella crocea, and Mantella milotympanum. Although our restriction site-associated DNA (RAD) sequencing approach identified clear genetic clusters, they do not align with current species designations, which has important conservation implications for these imperiled frogs. Moreover, our results suggest that levels of intraspecific color variation within this group have been overestimated, while species diversity has been underestimated. Within major genetic clusters, we observed distinct patterns of variation including: populations that are phenotypically similar yet genetically distinct, populations where phenotypic and genetic breaks coincide, and populations that are genetically similar but have high levels of within-population phenotypic variation. We also detected admixture between two of the major genetic clusters. Our study suggests that several mechanisms-including hybridization, selection, and drift-are contributing to phenotypic diversity. Ultimately, our work underscores the need for a reevaluation of how polymorphic and polytypic populations and species are classified, especially in aposematic organisms.
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Affiliation(s)
- Karina Klonoski
- Department of Environmental Science, Policy, and ManagementUniversity of California, BerkeleyBerkeleyCalifornia
- Museum of Vertebrate ZoologyUniversity of California, BerkeleyBerkeleyCalifornia
| | - Ke Bi
- Museum of Vertebrate ZoologyUniversity of California, BerkeleyBerkeleyCalifornia
- Computational Genomics Resource Laboratory (CGRL), California Institute for Quantitative Biosciences (QB3)University of California, BerkeleyBerkeleyCalifornia
| | - Erica Bree Rosenblum
- Department of Environmental Science, Policy, and ManagementUniversity of California, BerkeleyBerkeleyCalifornia
- Museum of Vertebrate ZoologyUniversity of California, BerkeleyBerkeleyCalifornia
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14
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Bolnick DI, Barrett RD, Oke KB, Rennison DJ, Stuart YE. (Non)Parallel Evolution. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2018. [DOI: 10.1146/annurev-ecolsys-110617-062240] [Citation(s) in RCA: 155] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Parallel evolution across replicate populations has provided evolutionary biologists with iconic examples of adaptation. When multiple populations colonize seemingly similar habitats, they may evolve similar genes, traits, or functions. Yet, replicated evolution in nature or in the laboratory often yields inconsistent outcomes: Some replicate populations evolve along highly similar trajectories, whereas other replicate populations evolve to different extents or in distinct directions. To understand these heterogeneous outcomes, biologists are increasingly treating parallel evolution not as a binary phenomenon but rather as a quantitative continuum ranging from parallel to nonparallel. By measuring replicate populations’ positions along this (non)parallel continuum, we can test hypotheses about evolutionary and ecological factors that influence the extent of repeatable evolution. We review evidence regarding the manifestation of (non)parallel evolution in the laboratory, in natural populations, and in applied contexts such as cancer. We enumerate the many genetic, ecological, and evolutionary processes that contribute to variation in the extent of parallel evolution.
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Affiliation(s)
- Daniel I. Bolnick
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712, USA
- Current affiliation: Department of Ecology and Evolution, University of Connecticut, Storrs, Connecticut 06268, USA
| | | | - Krista B. Oke
- Redpath Museum, McGill University, Montreal, Quebec H3A 2K6, Canada
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, California 95060, USA
| | - Diana J. Rennison
- Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Yoel E. Stuart
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712, USA
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15
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Dick C, Hinh J, Hayashi CY, Reznick DN. Convergent evolution of coloration in experimental introductions of the guppy ( Poecilia reticulata). Ecol Evol 2018; 8:8999-9006. [PMID: 30271561 PMCID: PMC6157698 DOI: 10.1002/ece3.4418] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 06/30/2018] [Accepted: 07/04/2018] [Indexed: 01/01/2023] Open
Abstract
Despite the multitude of examples of evolution in action, relatively fewer studies have taken a replicated approach to understand the repeatability of evolution. Here, we examine the convergent evolution of adaptive coloration in experimental introductions of guppies from a high-predation (HP) environment into four low-predation (LP) environments. LP introductions were replicated across 2 years and in two different forest canopy cover types. We take a complementary approach by examining both phenotypes and genetics. For phenotypes, we categorize the whole color pattern on the tail fin of male guppies and analyze evolution using a correspondence analysis. We find that coloration in the introduction sites diverged from the founding Guanapo HP site. Sites group together based on canopy cover, indicating convergence in response to light environment. However, the axis that explains the most variation indicates a lack of convergence. Therefore, evolution may proceed along similar phenotypic trajectories, but still maintain unique variation within sites. For the genetics underlying the divergent phenotypes, we examine expression levels of color genes. We find no evidence for differential expression, indicating that the genetic basis for the color changes remains undetermined.
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Affiliation(s)
- Cynthia Dick
- Department of Evolution, Ecology and Organismal BiologyUniversity of California‐RiversideRiversideCalifornia
| | - Jasmine Hinh
- Department of Evolution, Ecology and Organismal BiologyUniversity of California‐RiversideRiversideCalifornia
| | - Cheryl Y. Hayashi
- Division of Invertebrate Zoology and Sackler Institute for Comparative GenomicsAmerican Museum of Natural HistoryNew YorkNew York
| | - David N. Reznick
- Department of Evolution, Ecology and Organismal BiologyUniversity of California‐RiversideRiversideCalifornia
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16
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Tobler M, Kelley JL, Plath M, Riesch R. Extreme environments and the origins of biodiversity: Adaptation and speciation in sulphide spring fishes. Mol Ecol 2018; 27:843-859. [DOI: 10.1111/mec.14497] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 01/08/2018] [Accepted: 01/10/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Michael Tobler
- Division of Biology Kansas State University Manhattan KS USA
| | - Joanna L. Kelley
- School of Biological Sciences Washington State University Pullman WA USA
| | - Martin Plath
- Shaanxi Key Laboratory of Molecular Biology for Agriculture College of Animal Science and Technology Northwest A&F University Yangling Shaanxi China
| | - Rüdiger Riesch
- School of Biological Sciences Centre for Ecology, Evolution and Behaviour Royal Holloway University of London Egham Surrey UK
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17
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Walter GM, Aguirre JD, Blows MW, Ortiz-Barrientos D. Evolution of Genetic Variance during Adaptive Radiation. Am Nat 2018; 191:E108-E128. [PMID: 29570402 DOI: 10.1086/696123] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Genetic correlations between traits can concentrate genetic variance into fewer phenotypic dimensions that can bias evolutionary trajectories along the axis of greatest genetic variance and away from optimal phenotypes, constraining the rate of evolution. If genetic correlations limit adaptation, rapid adaptive divergence between multiple contrasting environments may be difficult. However, if natural selection increases the frequency of rare alleles after colonization of new environments, an increase in genetic variance in the direction of selection can accelerate adaptive divergence. Here, we explored adaptive divergence of an Australian native wildflower by examining the alignment between divergence in phenotype mean and divergence in genetic variance among four contrasting ecotypes. We found divergence in mean multivariate phenotype along two major axes represented by different combinations of plant architecture and leaf traits. Ecotypes also showed divergence in the level of genetic variance in individual traits and the multivariate distribution of genetic variance among traits. Divergence in multivariate phenotypic mean aligned with divergence in genetic variance, with much of the divergence in phenotype among ecotypes associated with changes in trait combinations containing substantial levels of genetic variance. Overall, our results suggest that natural selection can alter the distribution of genetic variance underlying phenotypic traits, increasing the amount of genetic variance in the direction of natural selection and potentially facilitating rapid adaptive divergence during an adaptive radiation.
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18
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19
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Landscape Genomics: Understanding Relationships Between Environmental Heterogeneity and Genomic Characteristics of Populations. ACTA ACUST UNITED AC 2017. [DOI: 10.1007/13836_2017_2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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20
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Worsham MLD, Julius EP, Nice CC, Diaz PH, Huffman DG. Geographic isolation facilitates the evolution of reproductive isolation and morphological divergence. Ecol Evol 2017; 7:10278-10288. [PMID: 29238554 PMCID: PMC5723600 DOI: 10.1002/ece3.3474] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Revised: 07/17/2017] [Accepted: 08/31/2017] [Indexed: 11/07/2022] Open
Abstract
Geographic isolation is known to contribute to divergent evolution, resulting in unique phenotypes. Oftentimes morphologically distinct populations are found to be interfertile while reproductive isolation is found to exist within nominal morphological species revealing the existence of cryptic species. These disparities can be difficult to predict or explain especially when they do not reflect an inferred history of common ancestry which suggests that environmental factors affect the nature of ecological divergence. A series of laboratory experiments and observational studies were used to address what role biogeographic factors may play in the ecological divergence of Hyalella amphipods. It was found that geographic isolation plays a key role in the evolution of reproductive isolation and divergent morphology and that divergence cannot be explained by molecular genetic variation.
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Affiliation(s)
- McLean L. D. Worsham
- Department of BiologyTexas State UniversitySan MarcosTXUSA
- Department of ZoologyUniversity of HawaiiHonoluluHIUSA
| | - Eric P. Julius
- Department of BiologyTexas State UniversitySan MarcosTXUSA
| | - Chris C. Nice
- Department of BiologyTexas State UniversitySan MarcosTXUSA
| | - Peter H. Diaz
- U.S. Fish and Wildlife ServiceTexas Fish and Wildlife Conservation OfficeSan MarcosTXUSA
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21
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Rosenblum EB, Parent CE, Diepeveen ET, Noss C, Bi K. Convergent Phenotypic Evolution despite Contrasting Demographic Histories in the Fauna of White Sands. Am Nat 2017; 190:S44-S56. [DOI: 10.1086/692138] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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22
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Oke KB, Rolshausen G, LeBlond C, Hendry AP. How Parallel Is Parallel Evolution? A Comparative Analysis in Fishes. Am Nat 2017; 190:1-16. [DOI: 10.1086/691989] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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23
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Neuroanatomical Changes Related to a Changing Environment in Lesser Earless Lizards. J HERPETOL 2017. [DOI: 10.1670/16-056] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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24
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de Fraga R, Lima AP, Magnusson WE, Ferrão M, Stow AJ. Contrasting Patterns of Gene Flow for Amazonian Snakes That Actively Forage and Those That Wait in Ambush. J Hered 2017; 108:524-534. [DOI: 10.1093/jhered/esx051] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 05/18/2017] [Indexed: 02/05/2023] Open
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25
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Veale AJ, Russello MA. An ancient selective sweep linked to reproductive life history evolution in sockeye salmon. Sci Rep 2017; 7:1747. [PMID: 28496186 PMCID: PMC5431894 DOI: 10.1038/s41598-017-01890-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 04/05/2017] [Indexed: 11/09/2022] Open
Abstract
Study of parallel (or convergent) phenotypic evolution can provide important insights into processes driving sympatric, ecologically-mediated divergence and speciation, as ecotype pairs may provide a biological replicate of the underlying signals and mechanisms. Here, we provide evidence for a selective sweep creating an island of divergence associated with reproductive behavior in sockeye salmon (Oncorhynchus nerka), identifying a series of linked single nucleotide polymorphisms across a ~22,733 basepair region spanning the leucine-rich repeat-containing protein 9 gene exhibiting signatures of divergent selection associated with stream- and shore-spawning in both anadromous and resident forms across their pan-Pacific distribution. This divergence likely occurred ~3.8 Mya (95% HPD = 2.1–6.03 Mya), after sockeye separated from pink (O. gorbuscha) and chum (O. keta) salmon, but prior to the Pleistocene glaciations. Our results suggest recurrent evolution of reproductive ecotypes across the native range of O. nerka is at least partially associated with divergent selection of pre-existing genetic variation within or linked to this region. As sockeye salmon are unique among Pacific salmonids in their flexibility to spawn in lake-shore benthic environments, this region provides great promise for continued investigation of the genomic basis of O. nerka life history evolution, and, more broadly, for increasing our understanding of the heritable basis of adaptation of complex traits in novel environments.
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Affiliation(s)
- Andrew J Veale
- Department of Biology, The University of British Columbia, Okanagan Campus, 3247 University Way, Kelowna, British Columbia, V1V 1V7, Canada.,Department of Zoology, University of Otago, 340 Great King Street, Dunedin, 9016, New Zealand
| | - Michael A Russello
- Department of Biology, The University of British Columbia, Okanagan Campus, 3247 University Way, Kelowna, British Columbia, V1V 1V7, Canada.
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26
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Kaufmann J, Lenz TL, Kalbe M, Milinski M, Eizaguirre C. A field reciprocal transplant experiment reveals asymmetric costs of migration between lake and river ecotypes of three-spined sticklebacks (Gasterosteus aculeatus
). J Evol Biol 2017; 30:938-950. [DOI: 10.1111/jeb.13057] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 12/15/2016] [Accepted: 02/06/2017] [Indexed: 12/18/2022]
Affiliation(s)
- J. Kaufmann
- Department of Evolutionary Ecology; Max Planck Institute for Evolutionary Biology; Plön Germany
- DEE; University of Lausanne; Lausanne Switzerland
| | - T. L. Lenz
- Department of Evolutionary Ecology; Max Planck Institute for Evolutionary Biology; Plön Germany
| | - M. Kalbe
- Department of Evolutionary Ecology; Max Planck Institute for Evolutionary Biology; Plön Germany
| | - M. Milinski
- Department of Evolutionary Ecology; Max Planck Institute for Evolutionary Biology; Plön Germany
| | - C. Eizaguirre
- GEOMAR Helmholtz Centre for Ocean Research; Kiel Germany
- School of Biological and Chemical Sciences; Queen Mary University of London; London UK
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27
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Des Roches S, Sollmann R, Calhoun K, Rothstein AP, Rosenblum EB. Survival by genotype: patterns at Mc1r are not black and white at the White Sands ecotone. Mol Ecol 2016; 26:320-329. [PMID: 27775197 DOI: 10.1111/mec.13894] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 10/06/2016] [Accepted: 10/12/2016] [Indexed: 12/30/2022]
Abstract
Measuring links among genotype, phenotype and survival in the wild has long been a focus of studies of adaptation. We conducted a 4-year capture-recapture study to measure survival by genotype and phenotype in the Southwestern Fence Lizard (Sceloporus cowlesi) at the White Sands ecotone (transition area between white sands and dark soil habitats). We report several unanticipated findings. First, in contrast with previous work showing that cryptic blanched coloration in S. cowlesi from the heart of the dunes is associated with mutations in the melanocortin-1 receptor gene (Mc1r), ecotonal S. cowlesi showed minimal association between colour phenotype and Mc1r genotype. Second, the frequency of the derived Mc1r allele in ecotonal S. cowlesi appeared to decrease over time. Third, our capture-recapture data revealed a lower survival rate for S. cowlesi individuals with the derived Mc1r allele. Thus, our results suggest that selection at the ecotone may have favoured the wild-type allele in recent years. Even in a system where a genotype-phenotype association appeared to be black and white, our study suggests that additional factors - including phenotypic plasticity, epistasis, pleiotropy and gene flow - may play important roles at the White Sands ecotone. Our study highlights the importance of linking molecular, genomic and organismal approaches for understanding adaptation in the wild. Furthermore, our findings indicate that dynamics of natural selection can be particularly complex in transitional habitats like ecotones and emphasize the need for future research that examines the patterns of ongoing selection in other ecological 'grey' zones.
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Affiliation(s)
- S Des Roches
- Department of Environmental Science, Policy, & Management, University of California, Berkeley, 54 Mulford Hall, Berkeley, CA, 94720, USA
| | - R Sollmann
- Department of Wildlife, Fish, & Conservation Biology, University of California, Davis, Davis, CA, 95616, USA
| | - K Calhoun
- Department of Environmental Science, Policy, & Management, University of California, Berkeley, 54 Mulford Hall, Berkeley, CA, 94720, USA
| | - A P Rothstein
- Department of Environmental Science, Policy, & Management, University of California, Berkeley, 54 Mulford Hall, Berkeley, CA, 94720, USA
| | - E B Rosenblum
- Department of Environmental Science, Policy, & Management, University of California, Berkeley, 54 Mulford Hall, Berkeley, CA, 94720, USA
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28
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Greenway R, Drexler S, Arias‐Rodriguez L, Tobler M. Adaptive, but not condition‐dependent, body shape differences contribute to assortative mating preferences during ecological speciation. Evolution 2016; 70:2809-2822. [DOI: 10.1111/evo.13087] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 09/26/2016] [Accepted: 09/27/2016] [Indexed: 02/05/2023]
Affiliation(s)
- Ryan Greenway
- Division of Biology Kansas State University Manhattan Kansas 66506
| | - Shannon Drexler
- Department of Biology University of Wisconsin‐Platteville 1 University Plaza Platteville Wisconsin 53818
| | - Lenin Arias‐Rodriguez
- División Académica de Ciencias Biológicas Universidad Juárez Autónoma de Tabasco Villahermosa Tabasco México
| | - Michael Tobler
- Division of Biology Kansas State University Manhattan Kansas 66506
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29
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Ng J, Ossip-Klein AG, Glor RE. Adaptive signal coloration maintained in the face of gene flow in a Hispaniolan Anolis Lizard. BMC Evol Biol 2016; 16:193. [PMID: 27650469 PMCID: PMC5029017 DOI: 10.1186/s12862-016-0763-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 09/07/2016] [Indexed: 11/17/2022] Open
Abstract
Background Studies of geographic variation can provide insight into the evolutionary processes involved in the early stages of biological diversification. In particular, multiple, replicated cases of geographic trait divergence present a powerful approach to study how patterns of introgression and adaptive divergence can vary with geographic space and time. In this study, we conduct replicated, fine-scaled molecular genetic analyses of striking geographic dewlap color variation of a Hispaniolan Anolis lizard, Anolis distichus, to investigate whether adaptive trait divergence is consistently associated with speciation, whereby genetic divergence is observed with neutral markers, or whether locally adapted traits are maintained in the face of continued gene flow. Results We find instances where shifts in adaptive dewlap coloration across short geographic distances are associated with reproductive isolation as well as maintained in the face of gene flow, suggesting the importance of both processes in maintaining geographic dewlap variation. Conclusion Our study suggests that adaptive dewlap color differences are maintained under strong divergent natural selection, but this divergence does not necessarily lead to anole speciation. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0763-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Julienne Ng
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA.
| | | | - Richard E Glor
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, 66045, USA
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30
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Laport RG, Minckley RL, Ramsey J. Ecological distributions, phenological isolation, and genetic structure in sympatric and parapatric populations of the Larrea tridentata polyploid complex. AMERICAN JOURNAL OF BOTANY 2016; 103:1358-1374. [PMID: 27440793 DOI: 10.3732/ajb.1600105] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Accepted: 05/20/2016] [Indexed: 06/06/2023]
Abstract
PREMISE OF THE STUDY Polyploidy is widely recognized as a mechanism of diversification. Contributions of polyploidy to specific pre- and postzygotic barriers-and classifications of polyploid speciation as "ecological" vs. "non-ecological"-are more contentious. Evaluation of these issues requires comprehensive studies that test ecological characteristics of cytotypes as well as the coincidence of genetic structure with cytotype distributions. METHODS We investigated a classical example of autopolyploid speciation, Larrea tridentata, at multiple areas of cytotype co-occurrence. Habitat and phenological differences were compared between diploid, tetraploid, and hexaploid populations on the basis of edaphic, community composition, and flowering time surveys. Frequency of hybridization between diploids and tetraploids was investigated using a diploid-specific chloroplast DNA (cpDNA) marker; genetic structure for all cytotypes was assessed using amplified fragment length polymorphisms (AFLPs). KEY RESULTS Across contact zones, we found cytotypes in habitats distinguished by soil and vegetation. We observed modest differences in timing and production of flowers, indicating a degree of assortative mating that was asymmetric between cytotypes. Nonetheless, cpDNA analyses in diploid-tetraploid contact zones suggested that ∼5% of tetraploid plants had hybrid origins involving unilateral sexual polyploidization. Genetic structure of AFLPs largely coincided with cytotype distributions in diploid-tetraploid contact zones. In contrast, there was little structure in areas of contact between tetraploids and hexaploids, suggesting intercytotype gene flow or recurrent hexaploid formation. CONCLUSIONS Diploid, tetraploid, and hexaploid cytotypes of L. tridentata are segregated by environmental distributions and flowering phenology in contact zones, with diploid and tetraploid populations having corresponding differences in genetic structure.
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Affiliation(s)
- Robert G Laport
- University of Nebraska-Lincoln, School of Biological Sciences, Lincoln, Nebraska 68588 USA
| | - Robert L Minckley
- University of Rochester, Department of Biology, River Campus, Rochester, New York 14627 USA
| | - Justin Ramsey
- Black Hills State University, School of Natural Sciences, Spearfish, South Dakota 57799 USA
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31
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Rice AM, McQuillan MA, Seears HA, Warren JA. Population differentiation at a regional scale in spadefoot toads: contributions of distance and divergent selective environments. Curr Zool 2016; 62:193-206. [PMID: 29491906 PMCID: PMC5804232 DOI: 10.1093/cz/zow010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 01/16/2016] [Indexed: 11/12/2022] Open
Abstract
The causes of population differentiation can provide insight into the origins of early barriers to gene flow. Two key drivers of population differentiation are geographic distance and local adaptation to divergent selective environments. When reproductive isolation arises because some populations of a species are under selection to avoid hybridization while others are not, population differentiation and even speciation can result. Spadefoot toad populations Spea multiplicata that are sympatric with a congener have undergone reinforcement. This reinforcement has resulted not only in increased reproductive isolation from the congener, but also in the evolution of reproductive isolation from nearby and distant conspecific allopatric populations. We used multiple approaches to evaluate the contributions of geographic distance and divergent selective environments to population structure across this regional scale in S. multiplicata, based on genotypes from six nuclear microsatellite markers. We compared groups of populations varying in both geographic location and in the presence of a congener. Hierarchical F-statistics and results from cluster analyses and discriminant analyses of principal components all indicate that geographic distance is the stronger contributor to genetic differentiation among S. multiplicata populations at a regional scale. However, we found evidence that adaptation to divergent selective environments also contributes to population structure. Our findings highlight how variation in the balance of evolutionary forces acting across a species' range can lead to variation in the relative contributions of geographic distance and local adaptation to population differentiation across different spatial scales.
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Affiliation(s)
- Amber M Rice
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA
| | - Michael A McQuillan
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA
| | - Heidi A Seears
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA
| | - Joanna A Warren
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA
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32
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Twomey E, Vestergaard JS, Venegas PJ, Summers K. Mimetic Divergence and the Speciation Continuum in the Mimic Poison Frog Ranitomeya imitator. Am Nat 2015; 187:205-24. [PMID: 26807748 DOI: 10.1086/684439] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
While divergent ecological adaptation can drive speciation, understanding the factors that facilitate or constrain this process remains a major goal in speciation research. Here, we study two mimetic transition zones in the poison frog Ranitomeya imitator, a species that has undergone a Müllerian mimetic radiation to establish four morphs in Peru. We find that mimetic morphs are strongly phenotypically differentiated, producing geographic clines with varying widths. However, distinct morphs show little neutral genetic divergence, and landscape genetic analyses implicate isolation by distance as the primary determinant of among-population genetic differentiation. Mate choice experiments suggest random mating at the transition zones, although certain allopatric populations show a preference for their own morph. We present evidence that this preference may be mediated by color pattern specifically. These results contrast with an earlier study of a third transition zone, in which a mimetic shift was associated with reproductive isolation. Overall, our results suggest that the three known mimetic transition zones in R. imitator reflect a speciation continuum, which we have characterized at the geographic, phenotypic, behavioral, and genetic levels. We discuss possible explanations for variable progress toward speciation, suggesting that multifarious selection on both mimetic color pattern and body size may be responsible for generating reproductive isolation.
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33
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Laurent S, Pfeifer SP, Settles ML, Hunter SS, Hardwick KM, Ormond L, Sousa VC, Jensen JD, Rosenblum EB. The population genomics of rapid adaptation: disentangling signatures of selection and demography in white sands lizards. Mol Ecol 2015; 25:306-23. [PMID: 26363411 DOI: 10.1111/mec.13385] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Revised: 08/31/2015] [Accepted: 09/04/2015] [Indexed: 02/03/2023]
Abstract
Understanding the process of adaptation during rapid environmental change remains one of the central focal points of evolutionary biology. The recently formed White Sands system of southern New Mexico offers an outstanding example of rapid adaptation, with a variety of species having rapidly evolved blanched forms on the dunes that contrast with their close relatives in the surrounding dark soil habitat. In this study, we focus on two of the White Sands lizard species, Sceloporus cowlesi and Aspidoscelis inornata, for which previous research has linked mutations in the melanocortin-1 receptor gene (Mc1r) to blanched coloration. We sampled populations both on and off the dunes and used a custom sequence capture assay based on probed fosmid libraries to obtain >50 kb of sequence around Mc1r and hundreds of other random genomic locations. We then used model-based statistical inference methods to describe the demographic and adaptive history characterizing the colonization of White Sands. We identified a number of similarities between the two focal species, including strong evidence of selection in the blanched populations in the Mc1r region. We also found important differences between the species, suggesting different colonization times, different genetic architecture underlying the blanched phenotype and different ages of the beneficial alleles. Finally, the beneficial allele is dominant in S. cowlesi and recessive in A. inornata, allowing for a rare empirical test of theoretically expected patterns of selective sweeps under these differing models.
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Affiliation(s)
- Stefan Laurent
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), EPFL SV IBI-SV UPJENSEN, Station 15, CH-1015, Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Susanne P Pfeifer
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), EPFL SV IBI-SV UPJENSEN, Station 15, CH-1015, Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Matthew L Settles
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, 83844, USA
| | - Samuel S Hunter
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, 83844, USA
| | - Kayla M Hardwick
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, 83844, USA
| | - Louise Ormond
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), EPFL SV IBI-SV UPJENSEN, Station 15, CH-1015, Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Vitor C Sousa
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.,Institute of Ecology and Evolution, University of Berne, Baltzerstrasse 6, CH-3012, Berne, Switzerland
| | - Jeffrey D Jensen
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), EPFL SV IBI-SV UPJENSEN, Station 15, CH-1015, Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Erica Bree Rosenblum
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, 83844, USA.,Department of Environmental Sciences, Policy & Management, Berkeley, CA, 94720, USA
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34
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Bourguet D, Ponsard S, Streiff R, Meusnier S, Audiot P, Li J, Wang ZY. 'Becoming a species by becoming a pest' or how two maize pests of the genus Ostrinia possibly evolved through parallel ecological speciation events. Mol Ecol 2015; 23:325-42. [PMID: 24289254 DOI: 10.1111/mec.12608] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Revised: 11/15/2013] [Accepted: 11/19/2013] [Indexed: 11/26/2022]
Abstract
New agricultural pest species attacking introduced crops may evolve from pre-existing local herbivores by ecological speciation, thereby becoming a species by becoming a pest. We compare the evolutionary pathways by which two maize pests (the Asian and the European corn borers, ACB and ECB) in the genus Ostrinia (Lepidoptera, Crambidae) probably diverged from an ancestral species close to the current Adzuki bean borer (ABB). We typed larval Ostrinia populations collected on maize and dicotyledons across China and eastern Siberia, at microsatellite and mitochondrial loci. We found only two clusters: one on maize (as expected) and a single one on dicotyledons despite differences in male mid-tibia morphology, suggesting that all individuals from dicotyledons belonged to the ABB. We found evidence for migrants and hybrids on both host plant types. Hybrids suggest that field reproductive isolation is incomplete between ACB and ABB. Interestingly, a few individuals with an 'ABB-like' microsatellite profile collected on dicotyledons had 'ACB' mtDNA rather than 'ABB-like' mtDNA, whereas the reverse was never found on maize. This suggests asymmetrical gene flow directed from the ACB towards the ABB. Hybrids and backcrosses in all directions were obtained in no-choice tests. In laboratory conditions, they survived as well as parental strain individuals. In Xinjiang, we found ACB and ECB in sympatry, but no hybrids. Altogether, our results suggest that reproductive isolation between ACB and ABB is incomplete and mostly prezygotic. This points to ecological speciation as a possible evolutionary scenario, as previously found for ECB and ABB in Europe.
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Affiliation(s)
- Denis Bourguet
- Centre de Biologie pour la Gestion des Populations (CBGP), UMR INRA-IRD-CIRAD-Montpellier SupAgro, Campus International de Baillarguet, 34988, Montferrier-sur-Lez Cedex, France
| | - Sergine Ponsard
- UMR 5174 EDB (Laboratoire Evolution & Diversité Biologique), Université de Toulouse, ENFA, 118 route de Narbonne, F-31062, Toulouse, France.,UMR 5174 EDB, CNRS, Université Paul Sabatier, F-31062, Toulouse, France.,State Key Laboratory for the Biology of the Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No.2 West Yuanmingyuan Road, Beijing, 100193, China.,UMR 5175, CNRS, Centre d'Ecologie Fonctionnelle et Evolutive (CEFE), 1919 route de Mende, Montpellier Cedex 05, 34293, Montpellier, France
| | - Rejane Streiff
- Centre de Biologie pour la Gestion des Populations (CBGP), UMR INRA-IRD-CIRAD-Montpellier SupAgro, Campus International de Baillarguet, 34988, Montferrier-sur-Lez Cedex, France
| | - Serge Meusnier
- Centre de Biologie pour la Gestion des Populations (CBGP), UMR INRA-IRD-CIRAD-Montpellier SupAgro, Campus International de Baillarguet, 34988, Montferrier-sur-Lez Cedex, France
| | - Philippe Audiot
- Centre de Biologie pour la Gestion des Populations (CBGP), UMR INRA-IRD-CIRAD-Montpellier SupAgro, Campus International de Baillarguet, 34988, Montferrier-sur-Lez Cedex, France
| | - Jing Li
- UMR 5174 EDB (Laboratoire Evolution & Diversité Biologique), Université de Toulouse, ENFA, 118 route de Narbonne, F-31062, Toulouse, France.,UMR 5174 EDB, CNRS, Université Paul Sabatier, F-31062, Toulouse, France.,State Key Laboratory for the Biology of the Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No.2 West Yuanmingyuan Road, Beijing, 100193, China.,School of biological technology, Xi'an University of Arts and Science, No.168 South Taibai Road, Xi'an, Shaanxi Province, 710065, China
| | - Zhen-Ying Wang
- State Key Laboratory for the Biology of the Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No.2 West Yuanmingyuan Road, Beijing, 100193, China
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Giery ST, Layman CA, Langerhans RB. Anthropogenic ecosystem fragmentation drives shared and unique patterns of sexual signal divergence among three species of Bahamian mosquitofish. Evol Appl 2015; 8:679-91. [PMID: 26240605 PMCID: PMC4516420 DOI: 10.1111/eva.12275] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 04/13/2015] [Indexed: 12/13/2022] Open
Abstract
When confronted with similar environmental challenges, different organisms can exhibit dissimilar phenotypic responses. Therefore, understanding patterns of phenotypic divergence for closely related species requires considering distinct evolutionary histories. Here, we investigated how a common form of human-induced environmental alteration, habitat fragmentation, may drive phenotypic divergence among three closely related species of Bahamian mosquitofish (Gambusia spp.). Focusing on one phenotypic trait (male coloration), having a priori predictions of divergence, we tested whether populations persisting in fragmented habitats differed from those inhabiting unfragmented habitats and examined the consistency of the pattern across species. Species exhibited both shared and unique patterns of phenotypic divergence between the two types of habitats, with shared patterns representing the stronger effect. For all species, populations in fragmented habitats had fewer dorsal-fin spots. In contrast, the magnitude and trajectory of divergence in dorsal-fin color, a sexually selected trait, differed among species. We identified fragmentation-mediated increased turbidity as a possible driver of these trait shifts. These results suggest that even closely related species can exhibit diverse phenotypic responses when encountering similar human-mediated selection regimes. This element of unpredictability complicates forecasting the phenotypic responses of wild organisms faced with anthropogenic change – an important component of biological conservation and ecosystem management.
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Affiliation(s)
- Sean T Giery
- Marine Sciences Program, Department of Biological Sciences, Florida International University North Miami, FL, USA
| | - Craig A Layman
- Marine Sciences Program, Department of Biological Sciences, Florida International University North Miami, FL, USA ; Department of Applied Ecology, David Clark Labs, North Carolina State University Raleigh, NC, 27695, USA
| | - R Brian Langerhans
- Department of Biological Sciences and W.M. Keck Center for Behavioral Biology, North Carolina State University Raleigh, NC, USA
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Des Roches S, Harmon LJ, Rosenblum EB. Colonization of a novel depauperate habitat leads to trophic niche shifts in three desert lizard species. OIKOS 2015. [DOI: 10.1111/oik.02493] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Simone Des Roches
- Dept of Environmental Science; Policy and Management, Univ. of California; Berkeley CA 94720 USA
| | - Luke J. Harmon
- Dept of Biological Sciences; Univ. of Idaho; Moscow ID 83844-3051 USA
| | - Erica B. Rosenblum
- Dept of Environmental Science; Policy and Management, Univ. of California; Berkeley CA 94720 USA
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Refsnider JM, Des Roches S, Rosenblum EB. Evidence for ecological release over a fine spatial scale in a lizard from the White Sands formation. OIKOS 2015. [DOI: 10.1111/oik.02406] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Jeanine M. Refsnider
- Dept of Environmental Science, Policy and Management; Univ. of California at Berkeley; 130 Mulford Hall Berkeley CA 94720-3114 USA
| | - Simone Des Roches
- Dept of Environmental Science, Policy and Management; Univ. of California at Berkeley; 130 Mulford Hall Berkeley CA 94720-3114 USA
| | - Erica Bree Rosenblum
- Dept of Environmental Science, Policy and Management; Univ. of California at Berkeley; 130 Mulford Hall Berkeley CA 94720-3114 USA
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Hardwick KM, Harmon LJ, Hardwick SD, Rosenblum EB. When field experiments yield unexpected results: lessons learned from measuring selection in White Sands lizards. PLoS One 2015; 10:e0118560. [PMID: 25714838 PMCID: PMC4340912 DOI: 10.1371/journal.pone.0118560] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 01/20/2015] [Indexed: 12/03/2022] Open
Abstract
Determining the adaptive significance of phenotypic traits is key for understanding evolution and diversification in natural populations. However, evolutionary biologists have an incomplete understanding of how specific traits affect fitness in most populations. The White Sands system provides an opportunity to study the adaptive significance of traits in an experimental context. Blanched color evolved recently in three species of lizards inhabiting the gypsum dunes of White Sands and is likely an adaptation to avoid predation. To determine whether there is a relationship between color and susceptibility to predation in White Sands lizards, we conducted enclosure experiments, quantifying survivorship of Holbrookia maculate exhibiting substrate-matched and substrate-mismatched phenotypes. Lizards in our study experienced strong predation. Color did not have a significant effect on survival, but we found several unexpected relationships including variation in predation over small spatial and temporal scales. In addition, we detected a marginally significant interaction between sex and color, suggesting selection for substrate matching may be stronger for males than females. We use our results as a case study to examine six major challenges frequently encountered in field-based studies of natural selection, and suggest that insight into the complexities of selection often results when experiments turn out differently than expected.
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Affiliation(s)
- Kayla M. Hardwick
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
- * E-mail:
| | - Luke J. Harmon
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Scott D. Hardwick
- Department of Mechanical Engineering, University of Idaho, Moscow, Idaho, United States of America
| | - Erica Bree Rosenblum
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, United States of America
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Beheregaray LB, Cooke GM, Chao NL, Landguth EL. Ecological speciation in the tropics: insights from comparative genetic studies in Amazonia. Front Genet 2015; 5:477. [PMID: 25653668 PMCID: PMC4301025 DOI: 10.3389/fgene.2014.00477] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 12/29/2014] [Indexed: 11/26/2022] Open
Abstract
Evolution creates and sustains biodiversity via adaptive changes in ecologically relevant traits. Ecologically mediated selection contributes to genetic divergence both in the presence or absence of geographic isolation between populations, and is considered an important driver of speciation. Indeed, the genetics of ecological speciation is becoming increasingly studied across a variety of taxa and environments. In this paper we review the literature of ecological speciation in the tropics. We report on low research productivity in tropical ecosystems and discuss reasons accounting for the rarity of studies. We argue for research programs that simultaneously address biogeographical and taxonomic questions in the tropics, while effectively assessing relationships between reproductive isolation and ecological divergence. To contribute toward this goal, we propose a new framework for ecological speciation that integrates information from phylogenetics, phylogeography, population genomics, and simulations in evolutionary landscape genetics (ELG). We introduce components of the framework, describe ELG simulations (a largely unexplored approach in ecological speciation), and discuss design and experimental feasibility within the context of tropical research. We then use published genetic datasets from populations of five codistributed Amazonian fish species to assess the performance of the framework in studies of tropical speciation. We suggest that these approaches can assist in distinguishing the relative contribution of natural selection from biogeographic history in the origin of biodiversity, even in complex ecosystems such as Amazonia. We also discuss on how to assess ecological speciation using ELG simulations that include selection. These integrative frameworks have considerable potential to enhance conservation management in biodiversity rich ecosystems and to complement historical biogeographic and evolutionary studies of tropical biotas.
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Affiliation(s)
- Luciano B Beheregaray
- Molecular Ecology Lab, School of Biological Sciences, Flinders University Adelaide, SA, Australia
| | - Georgina M Cooke
- The Australian Museum, The Australian Museum Research Institute Sydney, NSW, Australia
| | - Ning L Chao
- Departamento de Ciências Pesqueiras, Universidade Federal do Amazonas Manaus, Brazil ; National Museum of Marine Biology and Aquarium Pintung, Taiwan
| | - Erin L Landguth
- Division of Biological Sciences, University of Montana Missoula, MT, USA
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Shaffer HB, Gidiş M, McCartney-Melstad E, Neal KM, Oyamaguchi HM, Tellez M, Toffelmier EM. Conservation genetics and genomics of amphibians and reptiles. Annu Rev Anim Biosci 2015; 3:113-38. [PMID: 25580719 DOI: 10.1146/annurev-animal-022114-110920] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Amphibians and reptiles as a group are often secretive, reach their greatest diversity often in remote tropical regions, and contain some of the most endangered groups of organisms on earth. Particularly in the past decade, genetics and genomics have been instrumental in the conservation biology of these cryptic vertebrates, enabling work ranging from the identification of populations subject to trade and exploitation, to the identification of cryptic lineages harboring critical genetic variation, to the analysis of genes controlling key life history traits. In this review, we highlight some of the most important ways that genetic analyses have brought new insights to the conservation of amphibians and reptiles. Although genomics has only recently emerged as part of this conservation tool kit, several large-scale data sources, including full genomes, expressed sequence tags, and transcriptomes, are providing new opportunities to identify key genes, quantify landscape effects, and manage captive breeding stocks of at-risk species.
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Sullivan BK, Douglas MR, Walker JM, Cordes JE, Davis MA, Anthonysamy WJB, Sullivan KO, Douglas ME. Conservation and Management of Polytypic Species: The Little Striped Whiptail Complex (Aspidoscelis inornata) as a Case Study. COPEIA 2014. [DOI: 10.1643/cg-13-140] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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42
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Des Roches S, Brinkmeyer MS, Harmon LJ, Rosenblum EB. Ecological release and directional change in White Sands lizard trophic ecomorphology. Evol Ecol 2014. [DOI: 10.1007/s10682-014-9740-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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43
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Wang IJ, Bradburd GS. Isolation by environment. Mol Ecol 2014; 23:5649-62. [DOI: 10.1111/mec.12938] [Citation(s) in RCA: 505] [Impact Index Per Article: 50.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 09/07/2014] [Accepted: 09/21/2014] [Indexed: 12/15/2022]
Affiliation(s)
- Ian J. Wang
- Department of Environmental Science, Policy, and Management; University of California; 130 Mulford Hall #3114 Berkeley CA 94705 USA
| | - Gideon S. Bradburd
- Center for Population Biology; Department of Evolution and Ecology; University of California; 2320 Storer Hall 1 Shields Ave Davis CA 95616 USA
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Dowle EJ, Morgan-Richards M, Trewick SA. Morphological differentiation despite gene flow in an endangered grasshopper. BMC Evol Biol 2014; 14:216. [PMID: 25318347 PMCID: PMC4219001 DOI: 10.1186/s12862-014-0216-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 09/29/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Gene flow is traditionally considered a limitation to speciation because selection is required to counter the homogenising effect of allele exchange. Here we report on two sympatric short-horned grasshoppers species in the South Island of New Zealand; one (Sigaus australis) widespread and the other (Sigaus childi) a narrow endemic. RESULTS Of the 79 putatively neutral markers (mtDNA, microsatellite loci, ITS sequences and RAD-seq SNPs) all but one marker we examined showed extensive allele sharing, and similar or identical allele frequencies in the two species where they co-occur. We found no genetic evidence of deviation from random mating in the region of sympatry. However, analysis of morphological and geometric traits revealed no evidence of morphological introgression. CONCLUSIONS Based on phenotype the two species are clearly distinct, but their genotypes thus far reveal no divergence. The best explanation for this is that some loci associated with the distinguishing morphological characters are under strong selection, but exchange of neutral loci is occurring freely between the two species. Although it is easier to define species as requiring a barrier between them, a dynamic model that accommodates gene flow is a biologically more reasonable explanation for these grasshoppers.
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Affiliation(s)
- Eddy J Dowle
- Ecology Group, IAE, Massey University, Private Bag 11222, Palmerston North, 4442, New Zealand.
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand.
| | - Mary Morgan-Richards
- Ecology Group, IAE, Massey University, Private Bag 11222, Palmerston North, 4442, New Zealand.
| | - Steven A Trewick
- Ecology Group, IAE, Massey University, Private Bag 11222, Palmerston North, 4442, New Zealand.
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Cooke GM, Landguth EL, Beheregaray LB. Riverscape genetics identifies replicated ecological divergence across an Amazonian ecotone. Evolution 2014; 68:1947-60. [PMID: 24641091 DOI: 10.1111/evo.12410] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 03/04/2014] [Indexed: 01/22/2023]
Abstract
Ecological speciation involves the evolution of reproductive isolation and niche divergence in the absence of a physical barrier to gene flow. The process is one of the most controversial topics of the speciation debate, particularly in tropical regions. Here, we investigate ecologically based divergence across an Amazonian ecotone in the electric fish, Steatogenys elegans. We combine phylogenetics, genome scans, and population genetics with a recently developed individual-based evolutionary landscape genetics approach that incorporates selection. This framework is used to assess the relative contributions of geography and divergent natural selection between environments as biodiversity drivers. We report on two closely related and sympatric lineages that exemplify how divergent selection across a major Amazonian aquatic ecotone (i.e., between rivers with markedly different hydrochemical properties) may result in replicated ecologically mediated speciation. The results link selection across an ecological gradient with reproductive isolation and we propose that assortative mating based on water color may be driving the divergence. Divergence resulting from ecologically driven selection highlights the importance of considering environmental heterogeneity in studies of speciation in tropical regions. Furthermore, we show that framing ecological speciation in a spatially explicit evolutionary landscape genetics framework provides an important first step in exploring a wide range of the potential effects of spatial dependence in natural selection.
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Affiliation(s)
- Georgina M Cooke
- Molecular Ecology Lab, Department of Biological Sciences, Macquarie University, Sydney, New South Wales, 2109, Australia; The Australian Museum, The Australian Museum Research Institute, Sydney, New South Wales, 2010, Australia
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Pearse DE, Miller MR, Abadía-Cardoso A, Garza JC. Rapid parallel evolution of standing variation in a single, complex, genomic region is associated with life history in steelhead/rainbow trout. Proc Biol Sci 2014; 281:20140012. [PMID: 24671976 DOI: 10.1098/rspb.2014.0012] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Rapid adaptation to novel environments may drive changes in genomic regions through natural selection. Such changes may be population-specific or, alternatively, may involve parallel evolution of the same genomic region in multiple populations, if that region contains genes or co-adapted gene complexes affecting the selected trait(s). Both quantitative and population genetic approaches have identified associations between specific genomic regions and the anadromous (steelhead) and resident (rainbow trout) life-history strategies of Oncorhynchus mykiss. Here, we use genotype data from 95 single nucleotide polymorphisms and show that the distribution of variation in a large region of one chromosome, Omy5, is strongly associated with life-history differentiation in multiple above-barrier populations of rainbow trout and their anadromous steelhead ancestors. The associated loci are in strong linkage disequilibrium, suggesting the presence of a chromosomal inversion or other rearrangement limiting recombination. These results provide the first evidence of a common genomic basis for life-history variation in O. mykiss in a geographically diverse set of populations and extend our knowledge of the heritable basis of rapid adaptation of complex traits in novel habitats.
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Affiliation(s)
- Devon E Pearse
- Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, , 110 Shaffer Road, Santa Cruz, CA 95060, USA, Institute of Marine Sciences, University of California, , Santa Cruz, CA 95060, USA, Institute of Molecular Biology, University of Oregon, , Eugene, OR 97403, USA, Department of Animal Science, University of California, , One Shields Avenue, Davis, CA 95616, USA
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Gutiérrez-Pinto N, McCracken KG, Alza L, Tubaro P, Kopuchian C, Astie A, Cadena CD. The validity of ecogeographical rules is context-dependent: testing for Bergmann's and Allen's rules by latitude and elevation in a widespread Andean duck. Biol J Linn Soc Lond 2014. [DOI: 10.1111/bij.12249] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Natalia Gutiérrez-Pinto
- Laboratorio de Biología Evolutiva de Vertebrados; Departamento de Ciencias Biológicas; Universidad de los Andes; Apartado 4976 Bogotá Colombia
| | - Kevin G. McCracken
- Department of Biology; 1301 Memorial Dr.; University of Miami; Coral Gables FL 33146 USA
- Division of Marine Biology and Fisheries; 4600 Rickenbacker Causeway; Rosenstiel School of Marine and Atmospheric Sciences; Miami FL 33149 USA
- Institute of Arctic Biology; University of Alaska Museum; Department of Biology and Wildlife; 902 N. Koyukuk Drive Fairbanks AK 99775 USA
| | - Luis Alza
- Institute of Arctic Biology; University of Alaska Museum; Department of Biology and Wildlife; 902 N. Koyukuk Drive Fairbanks AK 99775 USA
- Centro de Ornitología y Biodiversidad (CORBIDI); Calle Santa Rita 105, Surco Lima Perú
| | - Pablo Tubaro
- División Ornitología; Museo Argentino de Ciencias Naturales ‘Bernardino Rivadavia’ (MACN-CONICET); Av. Angel Gallardo 470 Buenos Aires Argentina
| | - Cecilia Kopuchian
- División Ornitología; Museo Argentino de Ciencias Naturales ‘Bernardino Rivadavia’ (MACN-CONICET); Av. Angel Gallardo 470 Buenos Aires Argentina
- Centro de Ecología Aplicada del Litoral (CECOAL-CONICET); Ruta 5 Km 2.5 Corrientes Argentina
| | - Andrea Astie
- Instituto Argentino de Investigaciones de las Zonas Áridas (CCT Mendoza-CONICET); Av. Ruiz Leal s/n Parque General San Martín Mendoza Argentina
| | - Carlos Daniel Cadena
- Laboratorio de Biología Evolutiva de Vertebrados; Departamento de Ciencias Biológicas; Universidad de los Andes; Apartado 4976 Bogotá Colombia
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48
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Grant PR, Grant BR. Synergism of natural selection and introgression in the origin of a new species. Am Nat 2014; 183:671-81. [PMID: 24739199 DOI: 10.1086/675496] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
This article explores how introgressive hybridization enhances the evolutionary effects of natural selection and how, reciprocally, natural selection can enhance the evolutionary effects of introgression. Both types of interaction were observed during a 40-year study of Darwin's finches (Geospiza) on the small Galápagos island of Daphne Major. Hybrids, produced rarely by Geospiza fortis (medium ground finch) breeding with Geospiza scandens (cactus finch) and Geospiza fuliginosa (small ground finch), survived and bred as well as the parental species in the past 3 decades. By backcrossing, they increased the standing genetic variation and thereby the evolutionary responsiveness of the populations to natural selection. Natural selection occurred in droughts and oscillated in direction as a result of climatically induced fluctuations in food composition. Introgressive hybridization has led to the formation of a new lineage. It was initiated by a large, introgressed, hybrid male with a unique song and genetic marker that immigrated from the nearby island of Santa Cruz and bred with local hybrids and with G. fortis. All members of the lineage died in the 2003-2005 drought except a brother and a sister, who then bred with each other. Subsequent increase in the lineage was facilitated by selective mortality of the largest G. fortis. Breeding endogamously, the lineage is behaving as a biological species.
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Affiliation(s)
- Peter R Grant
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey 08544
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Martin CH, Feinstein LC. Novel trophic niches drive variable progress towards ecological speciation within an adaptive radiation of pupfishes. Mol Ecol 2014; 23:1846-62. [PMID: 24393262 DOI: 10.1111/mec.12658] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 12/09/2013] [Accepted: 12/20/2013] [Indexed: 01/15/2023]
Abstract
Adaptive radiation is recognized by a rapid burst of phenotypic, ecological and species diversification. However, it is unknown whether different species within an adaptive radiation evolve reproductive isolation at different rates. We compared patterns of genetic differentiation between nascent species within an adaptive radiation of Cyprinodon pupfishes using genotyping by sequencing. Similar to classic adaptive radiations, this clade exhibits rapid morphological diversification rates and two species are novel trophic specialists, a scale-eater and hard-shelled prey specialist (durophage), yet the radiation is <10 000 years old. Both specialists and an abundant generalist species all coexist in the benthic zone of lakes on San Salvador Island, Bahamas. Based on 13 912 single-nucleotide polymorphisms (SNPs), we found consistent differences in genetic differentiation between each specialist species and the generalist across seven lakes. The scale-eater showed the greatest genetic differentiation and clustered by species across lakes, whereas durophage populations often clustered with sympatric generalist populations, consistent with parallel speciation across lakes. However, we found strong evidence of admixture between durophage populations in different lakes, supporting a single origin of this species and genome-wide introgression with sympatric generalist populations. We conclude that the scale-eater is further along the speciation-with-gene-flow continuum than the durophage and suggest that different adaptive landscapes underlying these two niche environments drive variable progress towards speciation within the same habitat. Our previous measurements of fitness surfaces in these lakes support this conclusion: the scale-eating fitness peak may be more distant than the durophage peak on the complex adaptive landscape driving adaptive radiation.
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Affiliation(s)
- Christopher H Martin
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, 94720, USA; Department of Evolution & Ecology, University of California, Davis, CA, 94616, USA
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Peakall R, Whitehead MR. Floral odour chemistry defines species boundaries and underpins strong reproductive isolation in sexually deceptive orchids. ANNALS OF BOTANY 2014; 113:341-55. [PMID: 24052555 PMCID: PMC3890385 DOI: 10.1093/aob/mct199] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
BACKGROUND AND AIMS The events leading to speciation are best investigated in systems where speciation is ongoing or incomplete, such as incipient species. By examining reproductive barriers among incipient sister taxa and their congeners we can gain valuable insights into the relative timing and importance of the various barriers involved in the speciation process. The aim of this study was to identify the reproductive barriers among sexually deceptive orchid taxa in the genus Chiloglottis. METHODS The study targeted four closely related taxa with varying degrees of geographic overlap. Chemical, morphological and genetic evidence was combined to explore the basis of reproductive isolation. Of primary interest was the degree of genetic differentiation among taxa at both nuclear and chloroplast DNA markers. To objectively test whether or not species boundaries are defined by the chemistry that controls pollinator specificity, genetic analysis was restricted to samples of known odour chemistry. KEY RESULTS Floral odour chemical analysis was performed for 600+ flowers. The three sympatric taxa were defined by their specific chiloglottones, the semiochemicals responsible for pollinator attraction, and were found to be fully cross-compatible. Multivariate morphometric analysis could not reliably distinguish among the four taxa. Although varying from very low to moderate, significant levels of genetic differentiation were detected among all pairwise combinations of taxa at both nuclear and chloroplast loci. However, the levels of genetic differentiation were lower than expected for mature species. Critically, a lack of chloroplast DNA haplotype sharing among the morphologically indistinguishable and most closely related taxon pair confirmed that chemistry alone can define taxon boundaries. CONCLUSIONS The results confirmed that pollinator isolation, mediated by specific pollinator attraction, underpins strong reproductive isolation in these taxa. A combination of large effective population sizes, initial neutral mutations in the genes controlling floral scent, and a pool of available pollinators likely drives diversity in this system.
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