151
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Hodel RGJ, Knowles LL, McDaniel SF, Payton AC, Dunaway JF, Soltis PS, Soltis DE. Terrestrial species adapted to sea dispersal: Differences in propagule dispersal of two Caribbean mangroves. Mol Ecol 2018; 27:4612-4626. [DOI: 10.1111/mec.14894] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 09/27/2018] [Accepted: 10/01/2018] [Indexed: 12/18/2022]
Affiliation(s)
- Richard G. J. Hodel
- Department of Biology; University of Florida; Gainesville Florida
- Florida Museum of Natural History; University of Florida; Gainesville Florida
- Department of Ecology and Evolutionary Biology; University of Michigan; Ann Arbor Michigan
| | - L. Lacey Knowles
- Department of Ecology and Evolutionary Biology; University of Michigan; Ann Arbor Michigan
| | - Stuart F. McDaniel
- Department of Biology; University of Florida; Gainesville Florida
- The Genetics Institute; University of Florida; Gainesville Florida
| | - Adam C. Payton
- Department of Biology; University of Florida; Gainesville Florida
| | | | - Pamela S. Soltis
- Florida Museum of Natural History; University of Florida; Gainesville Florida
- The Genetics Institute; University of Florida; Gainesville Florida
- The Biodiversity Institute; University of Florida; Gainesville Florida
| | - Douglas E. Soltis
- Department of Biology; University of Florida; Gainesville Florida
- Florida Museum of Natural History; University of Florida; Gainesville Florida
- The Genetics Institute; University of Florida; Gainesville Florida
- The Biodiversity Institute; University of Florida; Gainesville Florida
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152
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Austin JD, Greene DU, Honeycutt RL, McCleery RA. Genetic evidence indicates ecological divergence rather than geographic barriers structure Florida fox squirrels. J Mammal 2018. [DOI: 10.1093/jmammal/gyy128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- James D Austin
- Department of Wildlife Ecology and Conservation, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
| | - Daniel U Greene
- Department of Wildlife Ecology and Conservation, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
| | - Rodney L Honeycutt
- Natural Science Division, Pepperdine University, Pacific Coast Highway, Malibu, CA, USA
| | - Robert A McCleery
- Department of Wildlife Ecology and Conservation, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
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153
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Shaffer AA, Dowler RC, Perkins JC, Ferguson AW, McDonough MM, Ammerman LK. Genetic variation in the eastern spotted skunk (Spilogale putorius) with emphasis on the plains spotted skunk (S. p. interrupta). J Mammal 2018. [DOI: 10.1093/jmammal/gyy098] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
| | - Robert C Dowler
- Department of Biology, Angelo State University, San Angelo, TX, USA
| | - J Clint Perkins
- Department of Biology, Angelo State University, San Angelo, TX, USA
| | - Adam W Ferguson
- Gantz Family Collection Center, Field Museum of Natural History, Chicago, IL, USA
| | - Molly M McDonough
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoo, Washington, DC, USA
- Integrative Research Center, Field Museum of Natural History, Chicago, IL, USA
| | - Loren K Ammerman
- Department of Biology, Angelo State University, San Angelo, TX, USA
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154
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Katz AD, Taylor SJ, Davis MA. At the confluence of vicariance and dispersal: Phylogeography of cavernicolous springtails (Collembola: Arrhopalitidae, Tomoceridae) codistributed across a geologically complex karst landscape in Illinois and Missouri. Ecol Evol 2018; 8:10306-10325. [PMID: 30397468 PMCID: PMC6206200 DOI: 10.1002/ece3.4507] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 08/06/2018] [Accepted: 08/08/2018] [Indexed: 01/11/2023] Open
Abstract
The processes of vicariance and dispersal are central to our understanding of diversification, yet determining the factors that influence these processes remains a significant challenge in evolutionary biology. Caves offer ideal systems for examining the mechanisms underlying isolation, divergence, and speciation. Intrinsic ecological differences among cavernicolous organisms, such as the degree of cave dependence, are thought to be major factors influencing patterns of genetic isolation in caves. Using a comparative phylogeographic approach, we employed mitochondrial and nuclear markers to assess the evolutionary history of two ecologically distinct groups of terrestrial cave-dwelling springtails (Collembola) in the genera Pygmarrhopalites (Arrhopalitidae) and Pogonognathellus (Tomoceridae) that are codistributed in caves throughout the Salem Plateau-a once continuous karst region, now bisected by the Mississippi River Valley in Illinois and Missouri. Contrasting phylogeographic patterns recovered for troglobiotic Pygmarrhopalites sp. and eutroglophilic Pogonognathellus sp. suggests that obligate associations with cave habitats can restrict dispersal across major geographic barriers such as rivers and valleys, but may also facilitate subterranean dispersal between neighboring cave systems. Pygmarrhopalites sp. populations spanning the Mississippi River Valley were estimated to have diverged 2.9-4.8 Ma, which we attribute to vicariance resulting from climatic and geological processes involved in Mississippi River Valley formation beginning during the late Pliocene/early Pleistocene. Lastly, we conclude that the detection of many deeply divergent, morphologically cryptic, and microendemic lineages highlights our poor understanding of microarthropod diversity in caves and exposes potential conservation concerns.
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Affiliation(s)
- Aron D. Katz
- Department of EntomologyUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA
- Illinois Natural History SurveyPrairie Research InstituteUniversity of Illinois at Urbana‐ChampaignChampaignIllinoisUSA
| | - Steven J. Taylor
- Illinois Natural History SurveyPrairie Research InstituteUniversity of Illinois at Urbana‐ChampaignChampaignIllinoisUSA
- Present address:
Office of General StudiesColorado CollegeColorado SpringsColoradoUSA
| | - Mark A. Davis
- Illinois Natural History SurveyPrairie Research InstituteUniversity of Illinois at Urbana‐ChampaignChampaignIllinoisUSA
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155
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Bell KC, Demboski JR, Cook JA. Sympatric Parasites Have Similar Host-Associated, but Asynchronous, Patterns of Diversification. Am Nat 2018; 192:E106-E119. [DOI: 10.1086/698300] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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156
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Lower SE, Stanger-Hall KF, Hall DW. Molecular variation across populations of a widespread North American firefly, Photinus pyralis, reveals that coding changes do not underlie flash color variation or associated visual sensitivity. BMC Evol Biol 2018; 18:129. [PMID: 30170542 PMCID: PMC6119266 DOI: 10.1186/s12862-018-1251-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 08/20/2018] [Indexed: 01/22/2023] Open
Abstract
Background Genes underlying signal production and reception are expected to evolve to maximize signal detection in specific environments. Fireflies vary in their light signal color both within and between species, and thus provide an excellent system in which to study signal production and reception in the context of signaling environments. Differences in signal color have been hypothesized to be due to variation in the sequence of luciferase, the enzyme that catalyzes the light reaction. Similarly, differences in visual sensitivity, which are expected to match signal color, have been hypothesized to be due to variation in the sequence of opsins, the protein component of visual pigments. Here we investigated (1) whether sequence variation in luciferase correlates with variation in signal color and (2) whether sequence variation in opsins correlates with inferred matching visual sensitivity across populations of a widespread North American firefly species, Photinus pyralis. We further tested (3) whether selection has acted on these loci by examining their population-level differentiation relative to the distribution of differentiation derived from a genome-wide sample of loci generated by double-digest RADseq. Results We found virtually no coding variation in luciferase or opsins. However, there was extreme divergence in non-coding variation in luciferase across populations relative to a panel of random genomic loci. Conclusions The absence of protein variation at both loci challenges the paradigm that variation in signal color and visual sensitivity in fireflies is exclusively due to coding variation in luciferase and opsin genes. Instead, flash color variation within species must involve other mechanisms, such as abdominal pigmentation or regulation of light organ physiology. Evidence for selection at non-coding variation in luciferase suggests that selection is targeting luciferase regulation and may favor differ expression levels across populations. Electronic supplementary material The online version of this article (10.1186/s12862-018-1251-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sarah E Lower
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA. .,Present address: Department of Biology, Bucknell University, Lewisburg, PA, 17837, USA.
| | | | - David W Hall
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
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157
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Lait LA, Hebert PDN. A survey of molecular diversity and population genetic structure in North American clearwing moths (Lepidoptera: Sesiidae) using cytochrome c oxidase I. PLoS One 2018; 13:e0202281. [PMID: 30133486 PMCID: PMC6104984 DOI: 10.1371/journal.pone.0202281] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 07/31/2018] [Indexed: 12/04/2022] Open
Abstract
The phylogeographic structure of insect species in North America is poorly understood. The moth family Sesiidae (Lepidoptera) contains many economically important pests of agriculture and forestry, as well as beneficial species used in biological control. Despite their significance, this study constitutes the first broad-ranging population genetic study on North American sesiids. It probes the population structure of eight species of sesiid moths based on sequence variation in cytochrome c oxidase I (N = 191). Haplotype diversity levels were high in seven of the eight species, while nucleotide diversity varied considerably. Patterns ranged from limited structure and a starburst pattern in the raspberry crown borer Pennisetia marginata to highly geographically structured populations in the peachtree borer Synanthedon exitiosa and the maple callus borer Synanthedon acerni. These varied patterns suggest differing evolutionary histories and dispersal abilities. By elucidating population genetic structure and barriers to dispersal we can begin to devise conservation and management plans.
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Affiliation(s)
- Linda A. Lait
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
- * E-mail:
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
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158
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Camps GA, Martínez-Meyer E, Verga AR, Sérsic AN, Cosacov A. Genetic and climatic approaches reveal effects of Pleistocene refugia and climatic stability in an old giant of the Neotropical Dry Forest. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly115] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Gonzalo A Camps
- Instituto de Fisiología y Recursos Genéticos Vegetales (IFRGV), CIAP, INTA, Córdoba, Argentina
- Laboratorio de Ecología Evolutiva—Biología Floral, Instituto Multidisciplinario de Biología Vegetal (IMBIV), CONICET-Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Enrique Martínez-Meyer
- Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, México
- Centro del Cambio Global y la Sustentabilidad en el Sureste, AC, Villahermosa, México
| | - Anibal R Verga
- Instituto de Fisiología y Recursos Genéticos Vegetales (IFRGV), CIAP, INTA, Córdoba, Argentina
| | - Alicia N Sérsic
- Laboratorio de Ecología Evolutiva—Biología Floral, Instituto Multidisciplinario de Biología Vegetal (IMBIV), CONICET-Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Andrea Cosacov
- Laboratorio de Ecología Evolutiva—Biología Floral, Instituto Multidisciplinario de Biología Vegetal (IMBIV), CONICET-Universidad Nacional de Córdoba, Córdoba, Argentina
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159
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Approximate Bayesian computation analysis of EST-associated microsatellites indicates that the broadleaved evergreen tree Castanopsis sieboldii survived the Last Glacial Maximum in multiple refugia in Japan. Heredity (Edinb) 2018; 122:326-340. [PMID: 30072800 DOI: 10.1038/s41437-018-0123-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 06/10/2018] [Accepted: 06/19/2018] [Indexed: 11/09/2022] Open
Abstract
Climatic changes have played major roles in plants' evolutionary history. Glacial oscillations have been particularly important, but some of their effects on plants' populations are poorly understood, including the numbers and locations of refugia in Asian warm temperate zones. In the present study, we investigated the demographic history of the broadleaved evergreen tree species Castanopsis sieboldii (Fagaceae) during the last glacial period in Japan. We used approximate Bayesian computation (ABC) for model comparison and parameter estimation for the demographic modeling using 27 EST-associated microsatellites. We also performed the species distribution modeling (SDM). The results strongly support a demographic scenario that the Ryukyu Islands and the western parts in the main islands (Kyushu and western Shikoku) were derived from separate refugia and the eastern parts in the main islands and the Japan Sea groups were diverged from the western parts prior to the coldest stage of the Last Glacial Maximum (LGM). Our data indicate that multiple refugia survived at least one in the Ryukyu Islands, and the other three regions of the western and eastern parts and around the Japan Sea of the main islands of Japan during the LGM. The SDM analysis also suggests the potential habitats under LGM climate conditions were mainly located along the Pacific Ocean side of the coastal region. Our ABC-based study helps efforts resolve the demographic history of a dominant species in warm temperate broadleaved forests during and after the last glacial period, which provides a basic model for future phylogeographical studies using this approach.
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160
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Folk RA, Visger CJ, Soltis PS, Soltis DE, Guralnick RP. Geographic Range Dynamics Drove Ancient Hybridization in a Lineage of Angiosperms. Am Nat 2018; 192:171-187. [DOI: 10.1086/698120] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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161
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Chabarria RE, Murray CM, Moler PE, Bart HL, Crother BI, Guyer C. Evolutionary insights into the North American Necturus beyericomplex (Amphibia: Caudata) based on molecular genetic and morphological analyses. J ZOOL SYST EVOL RES 2018. [DOI: 10.1111/jzs.12203] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | - Paul E. Moler
- Florida Fish and Wildlife Conservation Commission; Gainesville FL USA
| | - Henry L. Bart
- Department of Ecology and Evolutionary Biology; Tulane University; New Orleans LA USA
| | - Brian I. Crother
- Department of Biological Sciences; Southeastern Louisiana University; Hammond LA USA
| | - Craig Guyer
- Department of Biological Sciences; Auburn University; Auburn AL USA
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162
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Phylogeny of the egg-loving green alga Oophila amblystomatis (Chlamydomonadales) and its response to the herbicides atrazine and 2,4-D. Symbiosis 2018. [DOI: 10.1007/s13199-018-0564-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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163
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Stubbs RL, Folk RA, Xiang CL, Soltis DE, Cellinese N. Pseudo-parallel patterns of disjunctions in an Arctic-alpine plant lineage. Mol Phylogenet Evol 2018; 123:88-100. [DOI: 10.1016/j.ympev.2018.02.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 02/10/2018] [Accepted: 02/15/2018] [Indexed: 12/22/2022]
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164
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Lamb T, Justice TC, Brewer MS, Moler PE, Hopkins H, Bond JE. A biogeographical profile of the sand cockroach Arenivaga floridensis and its bearing on origin hypotheses for Florida scrub biota. Ecol Evol 2018; 8:5254-5266. [PMID: 29938050 PMCID: PMC6010915 DOI: 10.1002/ece3.3885] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 11/02/2017] [Accepted: 12/11/2017] [Indexed: 11/12/2022] Open
Abstract
Florida scrub is a xeric ecosystem associated with the peninsula's sand ridges, whose intermittent Pliocene-Pleistocene isolation is considered key to scrub endemism. One scrub origin hypothesis posits endemics were sourced by the Pliocene dispersal of arid-adapted taxa from southwestern North America; a second invokes Pleistocene migration within eastern North America. Only one study to date has explicitly tested these competing hypotheses, supporting an eastern origin for certain scrub angiosperms. For further perspective, we conducted a genetic analysis of an endemic arthropod, the Florida sand cockroach (Arenivaga floridensis), with two aims: (1) to reconstruct the peninsular colonization and residence history of A. floridensis and (2) determine whether its biogeographic profile favors either origin hypothesis. We sequenced the cox2 mitochondrial gene for 237 specimens (65 populations) as well as additional loci (cox1, nuclear H3) for a subset of Florida roaches and congeners. Using Network and Bayesian inference methods, we identified three major lineages whose genetic differentiation and phylogeographical structure correspond with late Pliocene peninsula insularization, indicating Arenivaga was present and broadly distributed in Florida at that time. Stem and crown divergence estimates (6.36 Ma; 2.78 Ma) between A. floridensis and western sister taxa span a period of extensive dispersal by western biota along an arid Gulf Coast corridor. These phylogeographical and phylogenetic results yield a biogeographic profile consistent with the western origin hypothesis. Moreover, age estimates for the roach's peninsular residence complement those of several other endemics, favoring a Pliocene (or earlier) inception of the scrub ecosystem. We argue that eastern versus western hypotheses are not mutually exclusive; rather, a composite history of colonization involving disparate biotas better explains the diverse endemism of Florida scrub.
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Affiliation(s)
- Trip Lamb
- Department of BiologyEast Carolina UniversityGreenvilleNCUSA
| | - Teresa C. Justice
- Department of BiologyEast Carolina UniversityGreenvilleNCUSA
- LynchburgVAUSA
| | | | - Paul E. Moler
- Florida Fish & Wildlife Conservation CommissionGainesvilleFLUSA
| | | | - Jason E. Bond
- Department of Biological Sciences and Auburn University Museum of Natural HistoryAuburn UniversityAuburnALUSA
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165
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Kim SH, Cho MS, Li P, Kim SC. Phylogeography and Ecological Niche Modeling Reveal Reduced Genetic Diversity and Colonization Patterns of Skunk Cabbage ( Symplocarpus foetidus; Araceae) From Glacial Refugia in Eastern North America. FRONTIERS IN PLANT SCIENCE 2018; 9:648. [PMID: 29872442 PMCID: PMC5972301 DOI: 10.3389/fpls.2018.00648] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 04/27/2018] [Indexed: 06/08/2023]
Abstract
Alternating glacial and interglacial periods during the Quaternary have dramatically affected the distribution and population genetic structure of plant and animal species throughout the northern hemisphere. Surprisingly, little is known about the post-glacial recolonization history of wetland herbaceous perennials that are widely distributed in the understory of deciduous or mixed deciduous-evergreen forests in eastern North America. In this study, we investigated infraspecific variation among 32 populations of skunk cabbage, Symplocarpus foetidus, to test the hypothesis that the extant species diversity of skunk cabbage is the result of a post-glacial range expansion from southern refugia during the Quaternary Ice Age. A total of 4041 base pairs (bp) of the chloroplast intergenic spacer region (cpDNA) was sequenced from 485 individuals sampled from glaciated (18 populations, 275 individuals) and unglaciated (14 populations, 210 individuals) regions east and west of the Appalachian Mountains. Haplotype number, haplotype diversity, and nucleotide diversity were calculated, and genetic variation within and among populations was assessed by analysis of molecular variance (AMOVA). The geographic pattern of genetic differentiation was further investigated with a spatial analysis of molecular variance (SAMOVA). A total of eight haplotypes and three genetic groups (SAMOVA) were recovered and a much higher haplotype number (eight haplotypes) and haplotype diversity (0.7425) was observed in unglaciated compared to glaciated populations (five haplotypes, haplotype diversity = 0.6099). All haplotypes found in glaciated regions represented a subset of haplotypes found in unglaciated regions. Haplotypes of S. foetidus likely diverged during the Tertiary (mid-Miocene and late Pliocene), predating the last glacial maximum (LGM). Predictions based on ecological niche modeling (ENM) suggested that there was considerably less suitable habitat for skunk cabbage during the LGM, and the habitat range was further south compared to the current distribution. Reduced variation and a subset of haplotypes in glaciated regions suggest a founder effect associated with range expansion via long-distance seed dispersal. Our results do not support the "Driftless Area" scenario for the northern refugium, rather the data suggest a "Northeastern" refugium near the southernmost extent of the LGM.
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Affiliation(s)
- Seon-Hee Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
| | - Myong-Suk Cho
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
| | - Pan Li
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, Laboratory of Systematic and Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Seung-Chul Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
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166
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Hayes MM, Piller KR. Patterns of diversification in a North American endemic fish, the Blackbanded Darter (Perciformes, Percidae). ZOOL SCR 2018. [DOI: 10.1111/zsc.12288] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Malorie M. Hayes
- Department of Biological Sciences; Southeastern Louisiana University; Hammond Louisiana
- Auburn University; Auburn Alabama
| | - Kyle R. Piller
- Department of Biological Sciences; Southeastern Louisiana University; Hammond Louisiana
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167
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Padilla-Jacobo G, Cano-Camacho H, López-Zavala R, Cornejo-Pérez ME, Zavala-Páramo MG. Evolutionary history of Mexican domesticated and wild Meleagris gallopavo. Genet Sel Evol 2018; 50:19. [PMID: 29665772 PMCID: PMC5905111 DOI: 10.1186/s12711-018-0388-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 04/02/2018] [Indexed: 02/08/2023] Open
Abstract
Background The distribution of the wild turkey (Meleagris gallopavo) extends from Mexico to southeastern Canada and to the eastern and southern regions of the USA. Six subspecies have been described based on morphological characteristics and/or geographical variations in wild and domesticated populations. In this paper, based on DNA sequence data from the mitochondrial D-loop, we investigated the genetic diversity and structure, genealogical relationships, divergence time and demographic history of M. gallopavo populations including domesticated individuals. Results Analyses of 612 wild and domesticated turkey mitochondrial D-loop sequences, including 187 that were collected for this study and 425 from databases, revealed 64 haplotypes with few mutations, some of which are shared between domesticated and wild turkeys. We found a high level of haplotype and nucleotide diversity, which suggests that the total population of this species is large and stable with an old evolutionary history. The results of genetic differentiation, haplotype network, and genealogical relationships analyses revealed three main genetic groups within the species: mexicana as a population relict (C1), merriami (C2), and mexicana/intermedia/silvestris/osceola (C3). Haplotypes detected in domesticated turkeys belong to group C3. Estimates of divergence times agree with range expansion and diversification events of the relict population of M. gallopavo in northwestern Mexico during the Pliocene–Pleistocene and Pleistocene–Holocene boundaries. Demographic reconstruction showed that an expansion of the population occurred 110,000 to 130,000 years ago (Kya), followed by a stable period 100 Kya and finally a decline ~ 10 Kya (Pleistocene–Holocene boundary). In Mexico, the Trans-Mexican Volcanic Belt may be responsible for the range expansion of the C3 group. Two haplotypes with different divergence times, MGMDgoB/MICH1 and MICH2, are dominant in domesticated and commercial turkeys. Conclusions During the Pleistocene, a large and stable population of M. gallopavo covered a wide geographic distribution from the north to the center of America (USA and Mexico). The mexicana, merriami, and mexicana/intermedia/silvestris/osceola genetic groups originated after divergence and range expansion from northwestern Mexico during the Pliocene–Pleistocene and Pleistocene–Holocene boundaries. Old and new maternal lines of the mexicana/intermedia/silvestris/osceola genetic group were distributed within the Trans-Mexican Volcanic Belt where individuals were captured for domestication. Two haplotypes are the main founder maternal lines of domesticated turkeys. Electronic supplementary material The online version of this article (10.1186/s12711-018-0388-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gabriela Padilla-Jacobo
- Centro Multidisciplinario de Estudios en Biotecnología, FMVZ, Universidad Michoacana de San Nicolás de Hidalgo, Km. 9.5 Carretera Morelia-Zinapécuaro, Posta Veterinaria, C.P. 58000, Tarímbaro, Michoacán, Mexico
| | - Horacio Cano-Camacho
- Centro Multidisciplinario de Estudios en Biotecnología, FMVZ, Universidad Michoacana de San Nicolás de Hidalgo, Km. 9.5 Carretera Morelia-Zinapécuaro, Posta Veterinaria, C.P. 58000, Tarímbaro, Michoacán, Mexico
| | - Rigoberto López-Zavala
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Autónoma de Tamaulipas, Km. 5, Carretera a Cd. Mante S/S, C.P. 87276, Ciudad Victoria, Tamaulipas, Mexico
| | - María E Cornejo-Pérez
- Centro Multidisciplinario de Estudios en Biotecnología, FMVZ, Universidad Michoacana de San Nicolás de Hidalgo, Km. 9.5 Carretera Morelia-Zinapécuaro, Posta Veterinaria, C.P. 58000, Tarímbaro, Michoacán, Mexico
| | - María G Zavala-Páramo
- Centro Multidisciplinario de Estudios en Biotecnología, FMVZ, Universidad Michoacana de San Nicolás de Hidalgo, Km. 9.5 Carretera Morelia-Zinapécuaro, Posta Veterinaria, C.P. 58000, Tarímbaro, Michoacán, Mexico.
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168
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Kuchta SR, Brown AD, Highton R. Disintegrating over space and time: Paraphyly and species delimitation in the Wehrle's Salamander complex. ZOOL SCR 2018. [DOI: 10.1111/zsc.12281] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Shawn R. Kuchta
- Department of Biological Sciences; Ohio Center for Ecology and Evolutionary Studies; Ohio University; Athens OH USA
| | - Ashley D. Brown
- Department of Biological Sciences; Ohio Center for Ecology and Evolutionary Studies; Ohio University; Athens OH USA
| | - Richard Highton
- Department of Biology; University of Maryland; College Park MD USA
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169
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Zhou W, Ji X, Obata S, Pais A, Dong Y, Peet R, Xiang QYJ. Resolving relationships and phylogeographic history of the Nyssa sylvatica complex using data from RAD-seq and species distribution modeling. Mol Phylogenet Evol 2018; 126:1-16. [PMID: 29631052 DOI: 10.1016/j.ympev.2018.04.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Revised: 03/30/2018] [Accepted: 04/01/2018] [Indexed: 01/08/2023]
Abstract
Nyssa sylvatica complex consists of several woody taxa occurring in eastern North America. These taxa were recognized as two or three species including three or four varieties by different authors. Due to high morphological similarities and complexity of morphological variation, classification and delineation of taxa in the group have been difficult and controversial. Here we employ data from RAD-seq to elucidate the genetic structure and phylogenetic relationships within the group. Using the genetic evidence, we evaluate previous classifications and delineate species. We also employ Species Distribution Modeling (SDM) to evaluate impacts of climatic changes on the ranges of the taxa and to gain insights into the relevant refugia in eastern North America. Results from Molecular Variance Analysis (AMOVA), STRUCTURE, phylogenetic analyses using Maximum likelihood, Bayesian Inference, and Splittree methods of RAD-seq data strongly support a two-clade pattern, largely separating samples of N. sylvatica from those of N. biflora-N. ursina mix. Divergence time analysis with BEAST suggests the two clades diverged in the mid Miocene. The ancestor of the present trees of N. sylvatica was suggested to be in the Pliocene and that of N. biflora-N. ursina mix in the end of the Miocene. Results from SDM predicted a smaller range in the southern part of the species present range of each clade during the Last Glacial Maximum (LGM). A northward expansion of the ranges during interglacial period and a northward shift of the ranges in the future under a model of global warming were also predicted. Our results support the recognition of two species in the complex, N. sylvatica and N. biflora, following the phylogenetic species concept. We found no genetic evidence supporting recognitions of intraspecific taxa. However, we propose subsp. ursina and subsp. biflora within N. biflora due to their distinction in habits, distributions, and habitats. Our results further support movements of trees in eastern North America in response to climatic changes. Finally, our study demonstrates that RAD-seq data and a combination of population genomics and SDM are valuable in resolving relationship and biogeographic history of closely related species that are taxonomically difficult.
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Affiliation(s)
- Wenbin Zhou
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695-7612, USA
| | - Xiang Ji
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695-7566, USA; Department of Statistics, North Carolina State University, Raleigh, NC 27695-8203, USA
| | - Shihori Obata
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695-7612, USA
| | - Andrew Pais
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695-7612, USA
| | - Yibo Dong
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695-7612, USA
| | - Robert Peet
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA.
| | - Qiu-Yun Jenny Xiang
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695-7612, USA.
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170
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Barrow LN, Lemmon AR, Lemmon EM. Targeted Sampling and Target Capture: Assessing Phylogeographic Concordance with Genome-wide Data. Syst Biol 2018; 67:979-996. [DOI: 10.1093/sysbio/syy021] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 03/15/2018] [Indexed: 01/09/2023] Open
Affiliation(s)
- Lisa N Barrow
- Department of Biology, Museum of Southwestern Biology, MSC03 2020, 1 University of New Mexico, Albuquerque, NM 87131-0001, USA
- Department of Biological Science, Florida State University, 319 Stadium Drive, PO Box 3064295, Tallahassee, FL 32306-4295, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL 32306-4120, USA
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, 319 Stadium Drive, PO Box 3064295, Tallahassee, FL 32306-4295, USA
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171
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Lait LA, Hebert PDN. Phylogeographic structure in three North American tent caterpillar species (Lepidoptera: Lasiocampidae): Malacosoma americana, M. californica, and M. disstria. PeerJ 2018; 6:e4479. [PMID: 29576956 PMCID: PMC5863710 DOI: 10.7717/peerj.4479] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Accepted: 02/19/2018] [Indexed: 11/23/2022] Open
Abstract
While phylogeographic structure has been examined in many North American vertebrate species, insects have received much less attention despite their central ecological roles. The moth genus Malacosoma (Hübner, 1820), is an important group of forestry pests responsible for large-scale defoliation across much of the Nearctic and Palearctic. The present study uses sequence variation in the mitochondrial cytochrome c oxidase 1 (COI) gene to examine the population genetic structure of the three widespread Malacosoma species (M. americana, M. californica, and M. disstria). Populations of all three species showed highest diversity in the south, suggesting that modern populations derived from southern refugia with loss of variation as these lineages dispersed northwards. However, despite similar life histories and dispersal abilities, the extent of regional variation varied among the taxa. M. americana, a species restricted to eastern North America, showed much less genetic structure than the western M. californica or the widespread M. disstria. The regional differentiation in the latter reflects the likely derivation of modern lineages from several refugia, as well as taxonomic uncertainty in M. californica. In these respects, the three species of Malacosoma share phylogeographic patterns similar to those detected in vertebrates which are characterised by greater phylogeographic breaks in the western half of the continent and limited structure in the east.
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Affiliation(s)
- Linda A Lait
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
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172
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Cavender-Bares J, Kothari S, Meireles JE, Kaproth MA, Manos PS, Hipp AL. The role of diversification in community assembly of the oaks (Quercus L.) across the continental U.S. AMERICAN JOURNAL OF BOTANY 2018; 105:565-586. [PMID: 29689630 DOI: 10.1002/ajb2.1049] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 12/20/2017] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY Evolutionary and biogeographic history, including past environmental change and diversification processes, are likely to have influenced the expansion, migration, and extinction of populations, creating evolutionary legacy effects that influence regional species pools and the composition of communities. We consider the consequences of the diversification process in shaping trait evolution and assembly of oak-dominated communities throughout the continental United States (U.S.). METHODS Within the U.S. oaks, we tested for phylogenetic and functional trait patterns at different spatial scales, taking advantage of a dated phylogenomic analysis of American oaks and the U.S. Forest Service (USFS) Forest Inventory and Analysis (FIA). KEY RESULTS We find (1) phylogenetic overdispersion at small grain sizes throughout the U.S. across all spatial extents and (2) a shift from overdispersion to clustering with increasing grain sizes. Leaf traits have evolved in a convergent manner, and these traits are clustered in communities at all spatial scales, except in the far west, where species with contrasting leaf types co-occur. CONCLUSIONS Our results support the hypotheses that (1) interspecific interactions were important in parallel adaptive radiation of the genus into a range of habitats across the continent and (2) that the diversification process is a critical driver of community assembly. Functional convergence of complementary species from distinct clades adapted to the same local habitats is a likely mechanism that allows distantly related species to coexist. Our findings contribute to an explanation of the long-term maintenance of high oak diversity and the dominance of the oak genus in North America.
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Affiliation(s)
- Jeannine Cavender-Bares
- Department of Ecology, Evolution and Behavior, University of Minnesota, 1479 Gortner Avenue, St. Paul, MN, 55108, USA
| | - Shan Kothari
- Department of Plant Biology, University of Minnesota, 1479 Gortner Ave, St. Paul, MN, 55108, USA
| | - José Eduardo Meireles
- Department of Ecology, Evolution and Behavior, University of Minnesota, 1479 Gortner Avenue, St. Paul, MN, 55108, USA
| | - Matthew A Kaproth
- Department of Ecology, Evolution and Behavior, University of Minnesota, 1479 Gortner Avenue, St. Paul, MN, 55108, USA
- Department of Biological Sciences, Minnesota State University, Mankato, MN, 56001, USA
| | - Paul S Manos
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Andrew L Hipp
- The Morton Arboretum, 4100 Illinois Route 53, Lisle, IL, 60532, USA
- The Field Museum, 1400 S Lake Shore Drive, Chicago, IL, 60605, USA
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173
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Meireles JE, Manos PS. Pervasive migration across rainforest and sandy coastal plain Aechmea nudicaulis (Bromeliaceae) populations despite contrasting environmental conditions. Mol Ecol 2018; 27:1261-1272. [PMID: 29417698 DOI: 10.1111/mec.14512] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 01/12/2018] [Accepted: 01/22/2018] [Indexed: 01/18/2023]
Abstract
Understanding the colonization of extreme marginal habitats and the relative roles of space and environment in maintaining peripheral populations remains challenging. Here, we leverage a system of pairs of rainforest and sandy coastal plain communities that allow us to decouple spatial and environmental effects in the population structure and migration rates of the bromeliad Aechmea nudicaulis. Structure and gene flow between populations were estimated from Bayesian clustering and coalescent-based migration models applied to chloroplast sequence and nuclear microsatellite data. Contrary to our initial expectation, the sharp environmental gradient between rainforest and sandy plains does not seem to have affected the colonization and migration dynamics in A. nudicaulis. Our analyses uncover pervasive gene flow between neighbouring habitats in both chloroplast and nuclear data despite the striking differences in environmental conditions. This result is consistent with a scenario of repeated colonization of the sandy coastal plains from forest populations through seed dispersal, as well as the maintenance of gene flow between habitats through pollination. We also recovered a broad north/south population structure that has been found in other Atlantic rainforest groups and possibly reflects older phylogeographic dynamics.
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Affiliation(s)
| | - Paul S Manos
- Department of Biology, Duke University, Durham, NC, USA
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174
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Folk RA, Sun M, Soltis PS, Smith SA, Soltis DE, Guralnick RP. Challenges of comprehensive taxon sampling in comparative biology: Wrestling with rosids. AMERICAN JOURNAL OF BOTANY 2018; 105:433-445. [PMID: 29665035 DOI: 10.1002/ajb2.1059] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 12/19/2017] [Indexed: 06/08/2023]
Abstract
Using phylogenetic approaches to test hypotheses on a large scale, in terms of both species sampling and associated species traits and occurrence data-and doing this with rigor despite all the attendant challenges-is critical for addressing many broad questions in evolution and ecology. However, application of such approaches to empirical systems is hampered by a lingering series of theoretical and practical bottlenecks. The community is still wrestling with the challenges of how to develop species-level, comprehensively sampled phylogenies and associated geographic and phenotypic resources that enable global-scale analyses. We illustrate difficulties and opportunities using the rosids as a case study, arguing that assembly of biodiversity data that is scale-appropriate-and therefore comprehensive and global in scope-is required to test global-scale hypotheses. Synthesizing comprehensive biodiversity data sets in clades such as the rosids will be key to understanding the origin and present-day evolutionary and ecological dynamics of the angiosperms.
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Affiliation(s)
- Ryan A Folk
- Florida Museum of Natural History, Gainesville, FL, 32611, USA
| | - Miao Sun
- Florida Museum of Natural History, Gainesville, FL, 32611, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, Gainesville, FL, 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
| | - Stephen A Smith
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Douglas E Soltis
- Florida Museum of Natural History, Gainesville, FL, 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
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175
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Resolving taxonomic turbulence and uncovering cryptic diversity in the musk turtles (Sternotherus) using robust demographic modeling. Mol Phylogenet Evol 2018; 120:1-15. [DOI: 10.1016/j.ympev.2017.11.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 11/09/2017] [Accepted: 11/16/2017] [Indexed: 01/25/2023]
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176
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Sampson J, Tapper S, Coates D, Hankinson M, Mcarthur S, Byrne M. Persistence with episodic range expansion from the early Pleistocene: the distribution of genetic variation in the forest tree Corymbia calophylla (Myrtaceae) in south-western Australia. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/blx168] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Jane Sampson
- Science and Conservation Division, Department of Biodiversity, Conservation and Attractions, Bentley Delivery Centre, WA, Australia
| | - Sarah Tapper
- Science and Conservation Division, Department of Biodiversity, Conservation and Attractions, Bentley Delivery Centre, WA, Australia
| | - David Coates
- Science and Conservation Division, Department of Biodiversity, Conservation and Attractions, Bentley Delivery Centre, WA, Australia
| | - Maggie Hankinson
- Science and Conservation Division, Department of Biodiversity, Conservation and Attractions, Bentley Delivery Centre, WA, Australia
| | - Shelley Mcarthur
- Science and Conservation Division, Department of Biodiversity, Conservation and Attractions, Bentley Delivery Centre, WA, Australia
| | - Margaret Byrne
- Science and Conservation Division, Department of Biodiversity, Conservation and Attractions, Bentley Delivery Centre, WA, Australia
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177
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Schmid S, Neuenschwander S, Pitteloud C, Heckel G, Pajkovic M, Arlettaz R, Alvarez N. Spatial and temporal genetic dynamics of the grasshopper Oedaleus decorus revealed by museum genomics. Ecol Evol 2018; 8:1480-1495. [PMID: 29435226 PMCID: PMC5792620 DOI: 10.1002/ece3.3699] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 11/06/2017] [Accepted: 11/10/2017] [Indexed: 12/14/2022] Open
Abstract
Analyzing genetic variation through time and space is important to identify key evolutionary and ecological processes in populations. However, using contemporary genetic data to infer the dynamics of genetic diversity may be at risk of a bias, as inferences are performed from a set of extant populations, setting aside unavailable, rare, or now extinct lineages. Here, we took advantage of new developments in next-generation sequencing to analyze the spatial and temporal genetic dynamics of the grasshopper Oedaleus decorus, a steppic Southwestern-Palearctic species. We applied a recently developed hybridization capture (hyRAD) protocol that allows retrieving orthologous sequences even from degraded DNA characteristic of museum specimens. We identified single nucleotide polymorphisms in 68 historical and 51 modern samples in order to (i) unravel the spatial genetic structure across part of the species distribution and (ii) assess the loss of genetic diversity over the past century in Swiss populations. Our results revealed (i) the presence of three potential glacial refugia spread across the European continent and converging spatially in the Alpine area. In addition, and despite a limited population sample size, our results indicate (ii) a loss of allelic richness in contemporary Swiss populations compared to historical populations, whereas levels of expected heterozygosities were not significantly different. This observation is compatible with an increase in the bottleneck magnitude experienced by central European populations of O. decorus following human-mediated land-use change impacting steppic habitats. Our results confirm that application of hyRAD to museum samples produces valuable information to study genetic processes across time and space.
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Affiliation(s)
- Sarah Schmid
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
| | | | - Camille Pitteloud
- Department of Environmental Systems ScienceEidgenössische Technische Hochschule ZürichZürichSwitzerland
| | - Gerald Heckel
- Institute of Ecology and EvolutionUniversity of BernBernSwitzerland
| | - Mila Pajkovic
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
| | - Raphaël Arlettaz
- Institute of Ecology and EvolutionUniversity of BernBernSwitzerland
| | - Nadir Alvarez
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
- Natural History Museum of GenevaGenevaSwitzerland
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178
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Fontanella FM, Victoriano PF, Sites JW. Secondary contact, gene flow and clinal variation between two mtDNA lineages of the Northeastern ringneck snake Diadophis punctatus edwardsii (Colubroidea: Dipsadidae). Zool J Linn Soc 2018. [DOI: 10.1093/zoolinnean/zlx036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
| | - Pedro F Victoriano
- Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Chile
| | - Jack W Sites
- Department of Biology and Bean Life Science Museum, Brigham Young University, USA
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179
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Giencke LM, Carol Denhof R, Katherine Kirkman L, Stribling Stuber O, Brantley ST. Seed sourcing for longleaf pine ground cover restoration: using plant performance to assess seed transfer zones and home-site advantage. Restor Ecol 2018. [DOI: 10.1111/rec.12673] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Lisa M. Giencke
- Joseph W. Jones Ecological Research Center; Newton GA 39870 U.S.A
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180
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Comparison of genetic variation between northern and southern populations of Lilium cernuum (Liliaceae): Implications for Pleistocene refugia. PLoS One 2018; 13:e0190520. [PMID: 29300767 PMCID: PMC5754063 DOI: 10.1371/journal.pone.0190520] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Accepted: 12/15/2017] [Indexed: 11/19/2022] Open
Abstract
The so-called "Baekdudaegan" (BDDG), a mountain range that stretches along the Korean Peninsula, has been recently proposed as a major "southern" glacial refugium for boreal or temperate plant species based on palaeoecological and, especially, genetic data. Genetic studies comparing genetic variation between population occurring on the BDDG and more northern ones (i.e. in NE China and/or in Russian Far East) are, however, still too few to draw firm conclusions on the role of the BDDG as a refugium and a source for possible northward post-glacial recolonizations. In order to fill this gap, we selected a boreal/temperate herb, Lilium cernuum, and compared levels of allozyme-based genetic diversity of five populations from NE China with five populations from South Korea (home of its hypothesized refuge areas). As a complementary tool, we used the maximum entropy algorithm implemented in MaxEnt to infer the species' potential distribution for the present time, which was projected to different past climate scenarios for the Last Glacial Maximum (LGM). Permutation tests revealed that Korean populations harbored significantly higher levels of within-population genetic variation than those from NE China (expected heterozygosity = 0.173 vs. 0.095, respectively). Our results suggest that the lowered levels of genetic diversity in NE Chinese populations might be due to founder effects associated with post-glacial migration from southern regions. Congruent with genetic data, past distribution models showed higher probability of occurrence in southern ranges than in northern ones during the LGM. In addition, a positive correlation was detected between the expected heterozygosity and environmental LGM suitability. From a conservation perspective, our results further suggest that the southern populations in South Korea may be particularly worthy of protection.
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181
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Advancing Understanding of Amphibian Evolution, Ecology, Behavior, and Conservation with Massively Parallel Sequencing. POPULATION GENOMICS 2018. [DOI: 10.1007/13836_2018_61] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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182
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Oliveira EF, Martinez PA, São-Pedro VA, Gehara M, Burbrink FT, Mesquita DO, Garda AA, Colli GR, Costa GC. Climatic suitability, isolation by distance and river resistance explain genetic variation in a Brazilian whiptail lizard. Heredity (Edinb) 2017; 120:251-265. [PMID: 29238076 DOI: 10.1038/s41437-017-0017-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 06/30/2017] [Accepted: 10/03/2017] [Indexed: 11/09/2022] Open
Abstract
Spatial patterns of genetic variation can help understand how environmental factors either permit or restrict gene flow and create opportunities for regional adaptations. Organisms from harsh environments such as the Brazilian semiarid Caatinga biome may reveal how severe climate conditions may affect patterns of genetic variation. Herein we combine information from mitochondrial DNA with physical and environmental features to study the association between different aspects of the Caatinga landscape and spatial genetic variation in the whiptail lizard Ameivula ocellifera. We investigated which of the climatic, environmental, geographical and/or historical components best predict: (1) the spatial distribution of genetic diversity, and (2) the genetic differentiation among populations. We found that genetic variation in A. ocellifera has been influenced mainly by temperature variability, which modulates connectivity among populations. Past climate conditions were important for shaping current genetic diversity, suggesting a time lag in genetic responses. Population structure in A. ocellifera was best explained by both isolation by distance and isolation by resistance (main rivers). Our findings indicate that both physical and climatic features are important for explaining the observed patterns of genetic variation across the xeric Caatinga biome.
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Affiliation(s)
- Eliana Faria Oliveira
- Pós-Graduação em Ecologia, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil. .,Universidade Federal de Mato Grosso do Sul, Centro de Ciências Biológicas e da Saúde, Laboratório de Zoologia, Campo Grande, MS, Brazil.
| | - Pablo Ariel Martinez
- Universidade Federal de Sergipe, Laboratório de Pesquisas Integrativas em Biodiversidade (PIBi Lab), Pós-Graduação em Ecologia e Conservação, São Cristovão, SE, Brazil
| | - Vinícius Avelar São-Pedro
- Universidade Federal de São Carlos, Campus Lagoa do Sino, Centro de Ciências da Natureza, Buri, SP, Brazil
| | - Marcelo Gehara
- Department of Herpetology, American Museum of Natural History, New York, NY, USA
| | | | - Daniel Oliveira Mesquita
- Departamento de Sistemática e Ecologia, Universidade Federal da Paraíba, João Pessoa, PB, Brazil
| | - Adrian Antonio Garda
- Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Centro de Biociências, Natal, RN, Brazil
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183
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Adding loci improves phylogeographic resolution in red mangroves despite increased missing data: comparing microsatellites and RAD-Seq and investigating loci filtering. Sci Rep 2017; 7:17598. [PMID: 29242627 PMCID: PMC5730610 DOI: 10.1038/s41598-017-16810-7] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 11/15/2017] [Indexed: 12/17/2022] Open
Abstract
The widespread adoption of RAD-Seq data in phylogeography means genealogical relationships previously evaluated using relatively few genetic markers can now be addressed with thousands of loci. One challenge, however, is that RAD-Seq generates complete genotypes for only a small subset of loci or individuals. Simulations indicate that loci with missing data can produce biased estimates of key population genetic parameters, although the influence of such biases in empirical studies is not well understood. Here we compare microsatellite data (8 loci) and RAD-Seq data (six datasets ranging from 239 to 25,198 loci) from red mangroves (Rhizophora mangle) in Florida to evaluate how different levels of data filtering influence phylogeographic inferences. For all datasets, we calculated population genetic statistics and evaluated population structure, and for RAD-Seq datasets, we additionally examined population structure using coalescence. We found higher FST using microsatellites, but that RAD-Seq-based estimates approached those based on microsatellites as more loci with more missing data were included. Analyses of RAD-Seq datasets resolved the classic Gulf-Atlantic coastal phylogeographic break, which was not significant in the microsatellite analyses. Applying multiple levels of filtering to RAD-Seq datasets can provide a more complete picture of potential biases in the data and elucidate subtle phylogeographic patterns.
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184
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López-Uribe MM, Cane JH, Minckley RL, Danforth BN. Crop domestication facilitated rapid geographical expansion of a specialist pollinator, the squash bee Peponapis pruinosa. Proc Biol Sci 2017; 283:rspb.2016.0443. [PMID: 27335417 DOI: 10.1098/rspb.2016.0443] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Accepted: 05/24/2016] [Indexed: 11/12/2022] Open
Abstract
Squash was first domesticated in Mexico and is now found throughout North America (NA) along with Peponapis pruinosa, a pollen specialist bee species of the squash genus Cucurbita The origin and spread of squash cultivation is well-studied archaeologically and phylogenetically; however, no study has documented how cultivation of this or any other crop has influenced species in mutualistic interactions. We used molecular markers to reconstruct the demographic range expansion and colonization routes of P. pruinosa from its native range into temperate NA. Populations east of the Rocky Mountains expanded from the wild host plant's range in Mexico and were established by a series of founder events. Eastern North America was most likely colonized from squash bee populations in the present-day continental Midwest USA and not from routes that followed the Gulf and Atlantic coasts from Mexico. Populations of P. pruinosa west of the Rockies spread north from the warm deserts much more recently, showing two genetically differentiated populations with no admixture: one in California and the other one in eastern Great Basin. These bees have repeatedly endured severe bottlenecks as they colonized NA, following human spread of their Cucurbita pollen hosts during the Holocene.
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Affiliation(s)
- Margarita M López-Uribe
- Department of Entomology, Cornell University, Ithaca, NY 14850, USA Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA Department of Applied Ecology, North Carolina State University, Raleigh, NC 27695, USA
| | - James H Cane
- USDA-ARS Bee Biology and Systematics Laboratory, Utah State University, Logan, UT 84322, USA
| | - Robert L Minckley
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Bryan N Danforth
- Department of Entomology, Cornell University, Ithaca, NY 14850, USA
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185
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Abstract
Phylogeography documents the spatial distribution of genetic lineages that result from demographic processes, such as population expansion, population contraction, and gene movement, shaped by climate fluctuations and the physical landscape. Because most phylogeographic studies have used neutral markers, the role of selection may have been undervalued. In this paper, we contend that plants provide a useful evolutionary lesson about the impact of selection on spatial patterns of neutral genetic variation, when the environment affects which individuals can colonize new sites, and on adaptive genetic variation, when environmental heterogeneity creates divergence at specific loci underlying local adaptation. Specifically, we discuss five characteristics found in plants that intensify the impact of selection: sessile growth form, high reproductive output, leptokurtic dispersal, isolation by environment, and the potential to evolve longevity. Collectively, these traits exacerbate the impact of environment on movement between populations and local selection pressures-both of which influence phylogeographic structure. We illustrate how these unique traits shape these processes with case studies of the California endemic oak, Quercus lobata, and the western North American lichen, Ramalina menziesii Obviously, the lessons we learn from plant traits are not unique to plants, but they highlight the need for future animal, plant, and microbe studies to incorporate its impact. Modern tools that generate genome-wide sequence data are now allowing us to decipher how evolutionary processes affect the spatial distribution of different kinds of genes and also to better model future spatial distribution of species in response to climate change.
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186
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Comparative phylogeography clarifies the complexity and problems of continental distribution that drove A. R. Wallace to favor islands. Proc Natl Acad Sci U S A 2017; 113:7970-7. [PMID: 27432953 DOI: 10.1073/pnas.1601072113] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Deciphering the geographic context of diversification and distributional dynamics in continental biotas has long been an interest of biogeographers, ecologists, and evolutionary biologists. Thirty years ago, the approach now known as comparative phylogeography was introduced in a landmark study of a continental biota. Here, I use a set of 455 studies to explore the current scope of continental comparative phylogeography, including geographic, conceptual, temporal, ecological, and genomic attributes. Geographically, studies are more frequent in the northern hemisphere, but the south is catching up. Most studies focus on a Quaternary timeframe, but the Neogene is well represented. As such, explanations for geographic structure and history include geological and climatic events in Earth history, and responses include vicariance, dispersal, and range contraction-expansion into and out of refugia. Focal taxa are biased toward terrestrial or semiterrestrial vertebrates, although plants and invertebrates are well represented in some regions. The use of various kinds of nuclear DNA markers is increasing, as are multiple locus studies, but use of organelle DNA is not decreasing. Species distribution models are not yet widely incorporated into studies. In the future, continental comparative phylogeographers will continue to contribute to erosion of the simple vicariance vs. dispersal paradigm, including exposure of the widespread nature of temporal pseudocongruence and its implications for models of diversification; provide new templates for addressing a variety of ecological and evolutionary traits; and develop closer working relationships with earth scientists and biologists in a variety of disciplines.
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187
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Shahzad K, Jia Y, Chen FL, Zeb U, Li ZH. Effects of Mountain Uplift and Climatic Oscillations on Phylogeography and Species Divergence in Four Endangered Notopterygium Herbs. FRONTIERS IN PLANT SCIENCE 2017; 8:1929. [PMID: 29167679 PMCID: PMC5682393 DOI: 10.3389/fpls.2017.01929] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 10/25/2017] [Indexed: 05/26/2023]
Abstract
Mountain uplift and climatic fluctuations are important driving forces that have affected the geographic distribution and population dynamics history of organisms. However, it is unclear how geological and climatic events might have affected the phylogeographic history and species divergence in high-alpine herbal plants. In this study, we analyzed the population demographic history and species differentiation of four endangered Notopterygium herbs on the high-altitude Qinghai-Tibetan Plateau (QTP) and adjacent areas. We combined phylogeographic analysis with species distribution modeling to detect the genetic variations in four Notopterygium species (N. incisum, N. franchetii, N. oviforme, and N. forrestii). In total, 559 individuals from 74 populations of the four species were analyzed based on three maternally inherited chloroplast fragments (matK, rbcL, and trnS-trnG) and one nuclear DNA region (internal transcribed spacer, ITS). Fifty-five chloroplast DNA (cpDNA) and 48 ITS haplotypes were identified in the four species. All of the cpDNA and ITS haplotypes were species-specific, except N. franchetii and N. oviforme shared one cpDNA haplotype, H32. Phylogenetic analysis suggested that all four species formed a monophyletic clade with high bootstrap support, where N. franchetii and N. oviforme were sisters. In addition, each Notopterygium species generated an individual clade that corresponded to their respective species in the ITS tree. Population dynamics analyses and species distribution modeling showed that the two widely distributed herbs N. incisum and N. franchetii exhibited obvious demographic expansions during the Pleistocene ice ages. Molecular dating suggested that the divergence of the four Notopterygium species occurred approximately between 3.6 and 1.2 Mya, and it was significantly associated with recent extensive uplifts of the QTP. Our results support the hypothesis that mountain uplift and Quaternary climatic oscillations profoundly shaped the population genetic divergence and demographic dynamics of Notopterygium species. The findings of this and previous studies provide important insights into the effects of QTP uplifts and climatic changes on phylogeography and species differentiation in high altitude mountainous areas. Our results may also facilitate the conservation of endangered herbaceous medicinal plants in the genus Notopterygium.
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Affiliation(s)
| | | | | | | | - Zhong-Hu Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, China
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188
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Shepard DB, Kuhns AR. Shifting rivers and stationary ground: biogeographic history of slimy salamanders on an isolated bluff in the Mississippi River floodplain. J Zool (1987) 2017. [DOI: 10.1111/jzo.12514] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- D. B. Shepard
- School of Biological Sciences Louisiana Tech University Ruston LA USA
| | - A. R. Kuhns
- Illinois Natural History Survey Prairie Research Institute University of Illinois at Urbana‐Champaign Champaign IL USA
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189
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Myers EA, Burgoon JL, Ray JM, Martínez-Gómez JE, Matías-Ferrer N, Mulcahy DG, Burbrink FT. Coalescent Species Tree Inference of Coluber and Masticophis. COPEIA 2017. [DOI: 10.1643/ch-16-552] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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190
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Koski MH, Grossenbacher DL, Busch JW, Galloway LF. A geographic cline in the ability to self-fertilize is unrelated to the pollination environment. Ecology 2017; 98:2930-2939. [PMID: 28869778 DOI: 10.1002/ecy.2001] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 06/22/2017] [Accepted: 08/18/2017] [Indexed: 01/14/2023]
Abstract
The reproductive assurance (RA) hypothesis predicts that the ability to autonomously self-fertilize should be favored in environments where a lack of mates or pollinators limits outcross reproduction. Because such limits to outcrossing are predicted to be most severe at range edges, elevated autonomy in peripheral populations is often attributed to RA. We test this hypothesis in 24 populations spanning the range of Campanula americana, including sampling at the range interior and three geographic range edges. We scored autonomous fruit set in a pollinator-free environment and detected clinal variation-autonomy increased linearly from the southern to the northern edge, and from the eastern to the western edge. We then address whether the cline reflects the contemporary pollination environment. We measured population size, plant density, pollinator visitation, outcross pollen limitation and RA in natural populations over two years. Most populations were pollen limited, and those that experienced higher visitation rates by bumblebees had reduced pollen limitation. Reproductive assurance, however, was generally low across populations and was unrelated to pollen limitation or autonomy. Neither pollen limitation nor RA displayed geographic clines. Finally, autonomy was not associated with pollinator visitation rates or mate availability. Thus, the data do not support the RA hypothesis; clinal variation in autonomy is unrelated to the current pollination environment. Therefore, geographic patterns of autonomy are likely the result of historical processes rather than contemporary natural selection for RA.
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Affiliation(s)
- Matthew H Koski
- Department of Biology, University of Virginia, PO Box 400328, Charlottesville, Virginia, 22904, USA
| | - Dena L Grossenbacher
- School of Biological Sciences, Washington State University, PO Box 644236, Pullman, Washington, 99164-4236, USA.,Department of Biology, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California, 93407, USA
| | - Jeremiah W Busch
- School of Biological Sciences, Washington State University, PO Box 644236, Pullman, Washington, 99164-4236, USA
| | - Laura F Galloway
- Department of Biology, University of Virginia, PO Box 400328, Charlottesville, Virginia, 22904, USA
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191
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Fahrenkrog AM, Neves LG, Resende MFR, Dervinis C, Davenport R, Barbazuk WB, Kirst M. Population genomics of the eastern cottonwood ( Populus deltoides). Ecol Evol 2017; 7:9426-9440. [PMID: 29187979 PMCID: PMC5696417 DOI: 10.1002/ece3.3466] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 08/14/2017] [Accepted: 08/16/2017] [Indexed: 12/30/2022] Open
Abstract
Despite its economic importance as a bioenergy crop and key role in riparian ecosystems, little is known about genetic diversity and adaptation of the eastern cottonwood (Populus deltoides). Here, we report the first population genomics study for this species, conducted on a sample of 425 unrelated individuals collected in 13 states of the southeastern United States. The trees were genotyped by targeted resequencing of 18,153 genes and 23,835 intergenic regions, followed by the identification of single nucleotide polymorphisms (SNPs). This natural P. deltoides population showed low levels of subpopulation differentiation (FST = 0.022–0.106), high genetic diversity (θW = 0.00100, π = 0.00170), a large effective population size (Ne ≈ 32,900), and low to moderate levels of linkage disequilibrium. Additionally, genomewide scans for selection (Tajima's D), subpopulation differentiation (XTX), and environmental association analyses with eleven climate variables carried out with two different methods (LFMM and BAYENV2) identified genes putatively involved in local adaptation. Interestingly, many of these genes were also identified as adaptation candidates in another poplar species, Populus trichocarpa, indicating possible convergent evolution. This study constitutes the first assessment of genetic diversity and local adaptation in P. deltoides throughout the southern part of its range, information we expect to be of use to guide management and breeding strategies for this species in future, especially in the face of climate change.
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Affiliation(s)
- Annette M Fahrenkrog
- School of Forest Resources and Conservation University of Florida Gainesville FL USA.,Plant Molecular and Cellular Biology Graduate Program University of Florida Gainesville FL USA
| | - Leandro G Neves
- School of Forest Resources and Conservation University of Florida Gainesville FL USA.,Plant Molecular and Cellular Biology Graduate Program University of Florida Gainesville FL USA.,Present address: RAPiD Genomics LLC756 2nd Avenue Gainesville FL 32601 USA
| | - Márcio F R Resende
- Horticultural Sciences Department University of Florida Gainesville FL USA
| | - Christopher Dervinis
- School of Forest Resources and Conservation University of Florida Gainesville FL USA
| | - Ruth Davenport
- Biology Department University of Florida Gainesville FL USA
| | - W Brad Barbazuk
- Biology Department University of Florida Gainesville FL USA.,University of Florida Genetics Institute University of Florida Gainesville FL USA
| | - Matias Kirst
- School of Forest Resources and Conservation University of Florida Gainesville FL USA.,University of Florida Genetics Institute University of Florida Gainesville FL USA
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192
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Baeza JA, Behringer DC. Integrative taxonomy of the ornamental 'peppermint' shrimp public market and population genetics of Lysmata boggessi, the most heavily traded species worldwide. PeerJ 2017; 5:e3786. [PMID: 28948100 PMCID: PMC5607919 DOI: 10.7717/peerj.3786] [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: 03/10/2017] [Accepted: 08/18/2017] [Indexed: 11/20/2022] Open
Abstract
The ornamental trade is a worldwide industry worth >15 billion USD with a problem of rampant product misidentification. Minimizing misidentification is critical in the face of overexploitation of species in the trade. We surveyed the peppermint shrimp ornamental marketplace in the southeastern USA, the most intense market for peppermint shrimps worldwide, to characterize the composition of species in the trade, reveal the extent of misidentification, and describe the population genetics of the true target species. Shrimps were bought from aquarium shops in FL, GA, SC, and NC. We demonstrated, contrary to popular belief (information from dealers), that the most heavily traded species in the market was Lysmata boggessi, an endemic species to the eastern Gulf of Mexico, and not Lysmata wurdemanni. Importantly, only when color pattern or genetic markers in conjunction with morphological traits were employed, was it was possible to unequivocally identify L. boggessi as the only species in the trade. The intensity of the market for peppermint shrimps in the USA has led to L. boggessi being the most traded species worldwide. Misidentification in the shrimp aquarium trade is accidental and involuntary, and is explained by remarkable similarity among congeneric species. Using sequences of the 16S-mt-DNA marker, we found no indication of population genetic structure in the endemic L. boggessi across 550 km of linear coast. Therefore, this species can be considered genetically homogeneous and a single fished stock. Still, we argue in favor of additional studies using more powerful markers (e.g., SNPs) capable of revealing genetic structure at a finer spatial-scale. Our results will help advance management and conservation policies in this lucrative yet understudied fishery. Future studies of other ornamental fisheries will benefit from using an integrative taxonomic approach, as we demonstrate here.
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Affiliation(s)
- J Antonio Baeza
- Department of Biological Sciences, Clemson University, Clemson, SC, United States of America.,Smithsonian Marine Station at Fort Pierce, Fort Pierce, FL, United States of America.,Departamento de Biologia Marina, Universidad Catolica del Norte, Coquimbo, IV Region, Chile
| | - Donald C Behringer
- Program in Fisheries and Aquatic Sciences, University of Florida, Gainesville, FL, United States of America.,Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States of America
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193
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Lumibao CY, Hoban SM, McLachlan J. Ice ages leave genetic diversity 'hotspots' in Europe but not in Eastern North America. Ecol Lett 2017; 20:1459-1468. [PMID: 28942617 DOI: 10.1111/ele.12853] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 06/01/2017] [Accepted: 08/27/2017] [Indexed: 12/01/2022]
Abstract
After the last glacial cycle, temperate European trees migrated northward, experiencing genetic bottlenecks and founder effects, which left high haplotype endemism in southern populations and clines in genetic diversity northward. These patterns are thought to be ubiquitous across temperate forests, and are therefore used to anticipate the potential genetic consequences of future warming. We compared existing and new phylogeographic data sets (chloroplast DNA) from 14 woody taxa in Eastern North America (ENA) to data sets from 21 ecologically similar European species to test for common impacts of Quaternary climate swings on genetic diversity across diverse taxa and between continents. Unlike their European counterparts, ENA taxa do not share common southern centres of haplotype endemism and they generally maintain high genetic diversity even at their northern range limits. Differences between the genetic impacts of Quaternary climate cycles across continents suggest refined lessons for managing genetic diversity in today's warming world.
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Affiliation(s)
- Candice Y Lumibao
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Sean M Hoban
- The Morton Arboretum, Lisle, IL, USA.,National Institute for Mathematical and Biological Synthesis (NIMBioS), Knoxville, TN, USA
| | - Jason McLachlan
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
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194
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Conservation genetics of redside dace (Clinostomus elongatus): phylogeography and contemporary spatial structure. CONSERV GENET 2017. [DOI: 10.1007/s10592-017-1012-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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195
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O'Connell KA, Streicher JW, Smith EN, Fujita MK. Geographical features are the predominant driver of molecular diversification in widely distributed North American whipsnakes. Mol Ecol 2017; 26:5729-5751. [PMID: 28802078 DOI: 10.1111/mec.14295] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 07/17/2017] [Accepted: 07/24/2017] [Indexed: 01/08/2023]
Abstract
Allopatric divergence following the formation of geographical features has been implicated as a major driver of evolutionary diversification. Widespread species complexes provide opportunities to examine allopatric divergence across varying degrees of isolation in both time and space. In North America, several geographical features may play such a role in diversification, including the Mississippi River, Pecos River, Rocky Mountains, Cochise Filter Barrier, Gulf of California and Isthmus of Tehuantepec. We used thousands of nuclear single nucleotide polymorphisms (SNPs) and mitochondrial DNA from several species of whipsnakes (genera Masticophis and Coluber) distributed across North and Central America to investigate the role that these geographical features have played on lineage divergence. We hypothesize that these features restrict gene flow and separate whipsnakes into diagnosable genomic clusters. We performed genomic clustering and phylogenetic reconstructions at the species and population levels using Bayesian and likelihood analyses and quantified migration levels across geographical features to assess the degree of genetic isolation due to allopatry. Our analyses suggest that (i) major genetic divisions are often consistent with isolation by geographical features, (ii) migration rates between clusters are asymmetrical across major geographical features, and (iii) areas that receive proportionally more migrants possess higher levels of genetic diversity. Collectively, our findings suggest that multiple features of the North American landscape contributed to allopatric divergence in this widely distributed snake group.
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Affiliation(s)
- Kyle A O'Connell
- Department of Biology, The University of Texas at Arlington, Arlington, TX, USA.,The Amphibian and Reptile Diversity Research Center, University of Texas at Arlington, Arlington, TX, USA
| | | | - Eric N Smith
- Department of Biology, The University of Texas at Arlington, Arlington, TX, USA.,The Amphibian and Reptile Diversity Research Center, University of Texas at Arlington, Arlington, TX, USA
| | - Matthew K Fujita
- Department of Biology, The University of Texas at Arlington, Arlington, TX, USA.,The Amphibian and Reptile Diversity Research Center, University of Texas at Arlington, Arlington, TX, USA
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196
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Chen W, Zhong Z, Dai W, Fan Q, He S. Phylogeographic structure, cryptic speciation and demographic history of the sharpbelly (Hemiculter leucisculus), a freshwater habitat generalist from southern China. BMC Evol Biol 2017; 17:216. [PMID: 28899345 PMCID: PMC5596851 DOI: 10.1186/s12862-017-1058-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 08/30/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Species with broad distributions frequently divide into multiple genetic forms and may therefore be viewed as "cryptic species". Here, we used the mitochondrial cytochrome b (Cytb) and 12 nuclear DNA loci to investigate phylogeographic structures of the sharpbelly (Hemiculter leucisculus) in rivers in southern China and explored how the geological and climatic factors have shaped the genetic diversity and evolutionary history of this species. RESULTS Our mitochondrial phylogenetic analysis identified three major lineages (lineages A, B, and C). Lineages B and C showed a relatively narrower geographic distribution, whereas lineage A was widely distributed in numerous drainages. Divergence dates suggested that H. leucisculus populations diverged between 1.61-2.38 Ma. Bayesian species delimitation analysis using 12 nuclear DNA loci indicated the three lineages probably represented three valid taxa. Isolation-with-migration (IM) analysis found substantial gene flow has occurred among the three lineages. Demographic analyses showed that lineages B and C have experienced rapid demographic expansion at 0.03 Ma and 0.08 Ma, respectively. CONCLUSIONS Hemiculter leucisculus populations in drainages in southern China comprise three mtDNA lineages, and each of which may represent a separate species. Intense uplift of the Qinghai-Tibetan Plateau, evolution of Asian monsoons, changes in paleo-drainages, and poor dispersal ability may have driven the divergence of the three putative species. However, gene flow occurs among the three lineages. Climatic fluctuations have a prominent impact on the populations from the lineages B and C, but exerted little influence on the lineage A.
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Affiliation(s)
- Weitao Chen
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Zaixuan Zhong
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Wei Dai
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Qi Fan
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China
| | - Shunping He
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China.
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197
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Harvey MG, Aleixo A, Ribas CC, Brumfield RT. Habitat Association Predicts Genetic Diversity and Population Divergence in Amazonian Birds. Am Nat 2017; 190:631-648. [PMID: 29053360 DOI: 10.1086/693856] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The ecological traits of organisms may predict their genetic diversity and population genetic structure and mediate the action of evolutionary processes important for speciation and adaptation. Making these ecological-evolutionary links is difficult because it requires comparable genetic estimates from many species with differing ecologies. In Amazonian birds, habitat association is an important component of ecological diversity. Here, we examine the link between habitat association and genetic parameters using 20 pairs of closely related Amazonian bird species in which one member of the pair occurs primarily in forest edge and floodplains and the other occurs in upland forest interior. We use standardized geographic sampling and data from 2,416 genomic markers to estimate genetic diversity, population genetic structure, and statistics reflecting demographic and evolutionary processes. We find that species of upland forest have greater genetic diversity and divergence across the landscape as well as signatures of older histories and less gene flow than floodplain species. Our results reveal that species ecology in the form of habitat association is an important predictor of genetic diversity and population divergence and suggest that differences in diversity between floodplain and upland avifaunas in the Amazon may be driven by differences in the demographic and evolutionary processes at work in the two habitats.
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198
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Pham KK, Hipp AL, Manos PS, Cronn RC. A time and a place for everything: phylogenetic history and geography as joint predictors of oak plastome phylogeny. Genome 2017; 60:720-732. [DOI: 10.1139/gen-2016-0191] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Owing to high rates of introgressive hybridization, the plastid genome is poorly suited to fine-scale DNA barcoding and phylogenetic studies of the oak genus (Quercus, Fagaceae). At the tips of the oak plastome phylogeny, recent gene migration and reticulation generally cause topology to reflect geographic structure, while deeper branches reflect lineage divergence. In this study, we quantify the simple and partial effects of geographic proximity and nucleome-inferred phylogenetic history on oak plastome phylogeny at different evolutionary scales. Our study compares pairwise phylogenetic distances based on complete plastome sequences, pairwise phylogenetic distances from nuclear restriction site-associated DNA sequences (RADseq), and pairwise geographic distances for 34 individuals of the white oak clade representing 24 North American and Eurasian species. Within the North American white oak clade alone, phylogenetic history has essentially no effect on plastome variation, while geography explains 11%–21% of plastome phylogenetic variance. However, across multiple continents and clades, phylogeny predicts 30%–41% of plastome variation, geography 3%–41%. Tipwise attenuation of phylogenetic informativeness in the plastome means that in practical terms, plastome data has little use in solving phylogenetic questions, but can still be a useful barcoding or phylogenetic marker for resolving questions among major clades.
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Affiliation(s)
- Kasey K. Pham
- The Morton Arboretum, 4100 Illinois Route 53, Lisle, IL 60532-1293, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824-1312, USA
| | - Andrew L. Hipp
- The Morton Arboretum, 4100 Illinois Route 53, Lisle, IL 60532-1293, USA
- The Field Museum, 1400 S Lake Shore Drive, Chicago, IL 60605, USA
| | - Paul S. Manos
- Department of Biology, Duke University, Durham, NC 27708-0338, USA
| | - Richard C. Cronn
- Pacific Northwest Research Station, 3200 SW Jefferson Way, Corvallis, OR 97331-4401, USA
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199
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Turtle soup, Prohibition, and the population genetic structure of Diamondback Terrapins (Malaclemys terrapin). PLoS One 2017; 12:e0181898. [PMID: 28792964 PMCID: PMC5549917 DOI: 10.1371/journal.pone.0181898] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 07/10/2017] [Indexed: 11/29/2022] Open
Abstract
Diamondback terrapins (Malaclemys terrapin) were a popular food item in early twentieth century America, and were consumed in soup with sherry. Intense market demand for terrapin meat resulted in population declines, notably along the Atlantic seaboard. Efforts to supply terrapins to markets resulted in translocation events, as individuals were moved about to stock terrapin farms. However, in 1920 the market for turtle soup buckled with the enactment of the eighteenth amendment to the United States’ Constitution—which initiated the prohibition of alcoholic drinks—and many terrapin fisheries dumped their stocks into local waters. We used microsatellite data to show that patterns of genetic diversity along the terrapin’s coastal range are consistent with historical accounts of translocation and cultivation activities. We identified possible instances of human-mediated dispersal by estimating gene flow over historical and contemporary timescales, Bayesian model testing, and bottleneck tests. We recovered six genotypic clusters along the Gulf and Atlantic coasts with varying degrees of admixture, including increased contemporary gene flow from Texas to South Carolina, from North Carolina to Maryland, and from North Carolina to New York. In addition, Bayesian models incorporating translocation events outperformed stepping-stone models. Finally, we were unable to detect population bottlenecks, possibly due to translocation reintroducing genetic diversity into bottlenecked populations. Our data suggest that current patterns of genetic diversity in the terrapin were altered by the demand for turtle soup followed by the enactment of alcohol prohibition. In addition, our study shows that population genetic tools can elucidate metapopulation dynamics in taxa with complex genetic histories impacted by anthropogenic activities.
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200
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Krysko KL, Nuñez LP, Newman CE, Bowen BW. Phylogenetics of Kingsnakes, Lampropeltis getula Complex (Serpentes: Colubridae), in Eastern North America. J Hered 2017; 108:226-238. [PMID: 28119446 DOI: 10.1093/jhered/esw086] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 12/08/2016] [Indexed: 01/25/2023] Open
Abstract
Kingsnakes of the Lampropeltis getula complex range throughout much of temperate and subtropical North America. Studies over the last century have used morphology and color pattern to describe numerous subspecies. More recently, DNA analyses have made invaluable contributions to our understanding of their evolution and taxonomy. We use genetic and ecological methods to test previous hypotheses of distinct evolutionary lineages by examining 66 total snakes and 1) analyzing phylogeographic structure using 2 mtDNA loci and 1 nuclear locus, 2) estimating divergence dates and historical demography among lineages in a Bayesian coalescent framework, and 3) applying ecological niche modeling (ENM). Our molecular data and ENMs illustrate that 3 previously recognized subspecies in the eastern United States comprise well-supported monophyletic lineages that diverged during the Pleistocene. The geographic boundaries of these 3 lineages correspond closely to known biogeographic barriers (Florida peninsula, Appalachian Mountains, and Apalachicola River) previously identified for other plants and animals, indicating shared geographic influences on evolutionary history. We conclude that genetic, ecological, and morphological data support recognition of these 3 lineages as distinct species (Lampropeltis floridana, Lampropeltis getula, and Lampropeltis meansi).
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Affiliation(s)
- Kenneth L Krysko
- Division of Herpetology, Florida Museum of Natural History, University of Florida, 1659 Museum Road, Gainesville, FL, USA
| | - Leroy P Nuñez
- Division of Herpetology, Florida Museum of Natural History, University of Florida, 1659 Museum Road, Gainesville, FL, USA.,School of Natural Resources and Environment, University of Florida, Gainesville, FL, USA
| | - Catherine E Newman
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA, USA.,Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Brian W Bowen
- Hawaii Institute of Marine Biology, University of Hawaii, Kaneohe, Hawaii, USA
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