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Shastry V, Bell KL, Buerkle CA, Fordyce JA, Forister ML, Gompert Z, Lebeis SL, Lucas LK, Marion ZH, Nice CC. A continental-scale survey of Wolbachia infections in blue butterflies reveals evidence of interspecific transfer and invasion dynamics. G3 GENES|GENOMES|GENETICS 2022; 12:6670626. [PMID: 35976120 PMCID: PMC9526071 DOI: 10.1093/g3journal/jkac213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 08/10/2022] [Indexed: 11/23/2022]
Abstract
Infections by maternally inherited bacterial endosymbionts, especially Wolbachia, are common in insects and other invertebrates but infection dynamics across species ranges are largely under studied. Specifically, we lack a broad understanding of the origin of Wolbachia infections in novel hosts, and the historical and geographical dynamics of infections that are critical for identifying the factors governing their spread. We used Genotype-by-Sequencing data from previous population genomics studies for range-wide surveys of Wolbachia presence and genetic diversity in North American butterflies of the genus Lycaeides. As few as one sequence read identified by assembly to a Wolbachia reference genome provided high accuracy in detecting infections in host butterflies as determined by confirmatory PCR tests, and maximum accuracy was achieved with a threshold of only 5 sequence reads per host individual. Using this threshold, we detected Wolbachia in all but 2 of the 107 sampling localities spanning the continent, with infection frequencies within populations ranging from 0% to 100% of individuals, but with most localities having high infection frequencies (mean = 91% infection rate). Three major lineages of Wolbachia were identified as separate strains that appear to represent 3 separate invasions of Lycaeides butterflies by Wolbachia. Overall, we found extensive evidence for acquisition of Wolbachia through interspecific transfer between host lineages. Strain wLycC was confined to a single butterfly taxon, hybrid lineages derived from it, and closely adjacent populations in other taxa. While the other 2 strains were detected throughout the rest of the continent, strain wLycB almost always co-occurred with wLycA. Our demographic modeling suggests wLycB is a recent invasion. Within strain wLycA, the 2 most frequent haplotypes are confined almost exclusively to separate butterfly taxa with haplotype A1 observed largely in Lycaeides melissa and haplotype A2 observed most often in Lycaeides idas localities, consistent with either cladogenic mode of infection acquisition from a common ancestor or by hybridization and accompanying mutation. More than 1 major Wolbachia strain was observed in 15 localities. These results demonstrate the utility of using resequencing data from hosts to quantify Wolbachia genetic variation and infection frequency and provide evidence of multiple colonizations of novel hosts through hybridization between butterfly lineages and complex dynamics between Wolbachia strains.
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Affiliation(s)
- Vivaswat Shastry
- Committee on Genetics, Genomics and Systems Biology, University of Chicago , Chicago, IL 60637, USA
| | - Katherine L Bell
- Department of Biology, University of Nevada , Reno, NV 89557, USA
| | - C Alex Buerkle
- Department of Botany, University of Wyoming , Laramie, WY 82071, USA
| | - James A Fordyce
- Department of Ecology & Evolutionary Biology, University of Tennessee , Knoxville, TN 37996, USA
| | | | | | - Sarah L Lebeis
- Department of Microbiology & Molecular Genetics, Michigan State University , East Lansing, MI 48824, USA
| | - Lauren K Lucas
- Department of Biology, Utah State University , Logan, UT 84322, USA
| | - Zach H Marion
- Bio-Protection Research Centre, School of Biological Sciences, University of Canterbury , Christchurch, New Zealand
| | - Chris C Nice
- Department of Biology, Population and Conservation Biology, Texas State University , San Marcos, TX 78666, USA
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Bougie TC, Brelsford A, Hedin M. Evolutionary impacts of introgressive hybridization in a rapidly evolving group of jumping spiders (F. Salticidae, Habronattus americanus group). Mol Phylogenet Evol 2021; 161:107165. [PMID: 33798670 DOI: 10.1016/j.ympev.2021.107165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 03/11/2021] [Accepted: 03/25/2021] [Indexed: 10/21/2022]
Abstract
Introgressive hybridization can be a powerful force impacting patterns of evolution at multiple taxonomic levels. We aimed to understand how introgression has affected speciation and diversification within a species complex of jumping spiders. The Habronattus americanus subgroup is a recently radiating group of jumping spiders, with species now in contact after hypothesized periods of isolation during glaciation cycles of the Pleistocene. Effects of introgression on genomes and morphology were investigated using phylogenomic and clustering methods using RADseq, ultraconserved elements (UCEs), and morphological data. We characterized 14 unique species/morphs using non-metric multidimensional scaling of morphological data, a majority of which were not recovered as monophyletic in our phylogenomic analyses. Morphological clusters and genetic lineages are highly incongruent, such that geographic region was a greater predictor of phylogenetic relatedness and genomic similarity than species or morph identity. STRUCTURE analyses support this pattern, revealing clusters corresponding to larger geographic regions. A history of rapid radiation in combination with frequent introgression seems to have mostly homogenized the genomes of species in this system, while selective forces maintain distinct male morphologies. GEMMA analyses support this idea by identifying SNPs correlated with distinct male morphologies. Overall, we have uncovered a system at odds with a typical bifurcating evolutionary model, instead supporting one where closely related species evolve together connected through multiple introgression events, creating a reticulate evolutionary history.
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Affiliation(s)
- T C Bougie
- Dept. of Biology, San Diego State University, San Diego, CA 92182, United States; Evolution, Ecology, and Organismal Biology Department, University of California Riverside, Riverside, CA 92521, United States.
| | - A Brelsford
- Evolution, Ecology, and Organismal Biology Department, University of California Riverside, Riverside, CA 92521, United States
| | - M Hedin
- Dept. of Biology, San Diego State University, San Diego, CA 92182, United States
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Morozumi Y, Murakami T, Watanabe M, Ohta S, Ômura H. Oxygenated sesquiterpenoids characteristic of a male lycaenid butterfly Lycaeides argyrognomon praeterinsularis. BIOCHEM SYST ECOL 2018. [DOI: 10.1016/j.bse.2018.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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de la Harpe M, Paris M, Karger DN, Rolland J, Kessler M, Salamin N, Lexer C. Molecular ecology studies of species radiations: current research gaps, opportunities and challenges. Mol Ecol 2017; 26:2608-2622. [PMID: 28316112 DOI: 10.1111/mec.14110] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Revised: 02/11/2017] [Accepted: 03/06/2017] [Indexed: 12/28/2022]
Abstract
Understanding the drivers and limits of species radiations is a crucial goal of evolutionary genetics and molecular ecology, yet research on this topic has been hampered by the notorious difficulty of connecting micro- and macroevolutionary approaches to studying the drivers of diversification. To chart the current research gaps, opportunities and challenges of molecular ecology approaches to studying radiations, we examine the literature in the journal Molecular Ecology and revisit recent high-profile examples of evolutionary genomic research on radiations. We find that available studies of radiations are highly unevenly distributed among taxa, with many ecologically important and species-rich organismal groups remaining severely understudied, including arthropods, plants and fungi. Most studies employed molecular methods suitable over either short or long evolutionary time scales, such as microsatellites or restriction site-associated DNA sequencing (RAD-seq) in the former case and conventional amplicon sequencing of organellar DNA in the latter. The potential of molecular ecology studies to address and resolve patterns and processes around the species level in radiating groups of taxa is currently limited primarily by sample size and a dearth of information on radiating nuclear genomes as opposed to organellar ones. Based on our literature survey and personal experience, we suggest possible ways forward in the coming years. We touch on the potential and current limitations of whole-genome sequencing (WGS) in studies of radiations. We suggest that WGS and targeted ('capture') resequencing emerge as the methods of choice for scaling up the sampling of populations, species and genomes, including currently understudied organismal groups and the genes or regulatory elements expected to matter most to species radiations.
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Affiliation(s)
- Marylaure de la Harpe
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg, CH-1700, Switzerland.,Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, A-1030, Austria
| | - Margot Paris
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg, CH-1700, Switzerland
| | - Dirk N Karger
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, Zürich, CH-8008, Switzerland
| | - Jonathan Rolland
- Department of Ecology and Evolution, Biophore, University of Lausanne, Lausanne, CH-1015, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge, Lausanne, CH-1015, Switzerland
| | - Michael Kessler
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, Zürich, CH-8008, Switzerland
| | - Nicolas Salamin
- Department of Ecology and Evolution, Biophore, University of Lausanne, Lausanne, CH-1015, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge, Lausanne, CH-1015, Switzerland
| | - Christian Lexer
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg, CH-1700, Switzerland.,Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, A-1030, Austria
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Moon KL, Banks SC, Fraser CI. Phylogeographic Structure in Penguin Ticks across an Ocean Basin Indicates Allopatric Divergence and Rare Trans-Oceanic Dispersal. PLoS One 2015; 10:e0128514. [PMID: 26083353 PMCID: PMC4471196 DOI: 10.1371/journal.pone.0128514] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 04/29/2015] [Indexed: 11/18/2022] Open
Abstract
The association of ticks (Acarina) and seabirds provides an intriguing system for assessing the influence of long-distance dispersal on the evolution of parasitic species. Recent research has focused on host-parasite evolutionary relationships and dispersal capacity of ticks parasitising flighted seabirds. Evolutionary research on the ticks of non-flighted seabirds is, in contrast, scarce. We conducted the first phylogeographic investigation of a hard tick species (Ixodes eudyptidis) that parasitises the Little Blue Penguin (Eudyptula minor). Using one nuclear (28S) and two mitochondrial (COI and 16S) markers, we assessed genetic diversity among several populations in Australia and a single population on the South Island of New Zealand. Our results reveal two deeply divergent lineages, possibly representing different species: one comprising all New Zealand samples and some from Australia, and the other representing all other samples from Australian sites. No significant population differentiation was observed among any Australian sites from within each major clade, even those separated by hundreds of kilometres of coastline. In contrast, the New Zealand population was significantly different to all samples from Australia. Our phylogenetic results suggest that the New Zealand and Australian populations are effectively isolated from each other; although rare long-distance dispersal events must occur, these are insufficient to maintain trans-Tasman gene flow. Despite the evidence for limited dispersal of penguin ticks between Australia and New Zealand, we found no evidence to suggest that ticks are unable to disperse shorter distances at sea with their hosts, with no pattern of population differentiation found among Australian sites. Our results suggest that terrestrial seabird parasites may be quite capable of short-distance movements, but only sporadic longer-distance (trans-oceanic) dispersal.
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Affiliation(s)
- Katherine L Moon
- Fenner School of Environment and Society, Australian National University, Acton, ACT 2601, Australia
| | - Sam C Banks
- Fenner School of Environment and Society, Australian National University, Acton, ACT 2601, Australia
| | - Ceridwen I Fraser
- Fenner School of Environment and Society, Australian National University, Acton, ACT 2601, Australia
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Jahner JP, Lucas LK, Wilson JS, Forister ML. Morphological outcomes of gynandromorphism in Lycaeides butterflies (Lepidoptera: Lycaenidae). JOURNAL OF INSECT SCIENCE (ONLINE) 2015; 15:iev020. [PMID: 25843591 PMCID: PMC7175718 DOI: 10.1093/jisesa/iev020] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Accepted: 02/02/2015] [Indexed: 06/04/2023]
Abstract
The genitalia of male insects have been widely used in taxonomic identification and systematics and are potentially involved in maintaining reproductive isolation between species. Although sexual selection has been invoked to explain patterns of morphological variation in genitalia among populations and species, developmental plasticity in genitalia likely contributes to observed variation but has been rarely examined, particularly in wild populations. Bilateral gynandromorphs are individuals that are genetically male on one side of the midline and genetically female on the other, while mosaic gynandromorphs have only a portion of their body developing as the opposite sex. Gynandromorphs might offer unique insights into developmental plasticity because individuals experience abnormal cellular interactions at the genitalic midline. In this study, we compare the genitalia and wing patterns of gynandromorphic Anna and Melissa blue butterflies, Lycaeides anna (Edwards) (formerly L. idas anna) and L. melissa (Edwards) (Lepidoptera: Lycaenidae), to the morphology of normal individuals from the same populations. Gynandromorph wing markings all fell within the range of variation of normal butterflies; however, a number of genitalic measurements were outliers when compared with normal individuals. From these results, we conclude that the gynandromorphs' genitalia, but not wing patterns, can be abnormal when compared with normal individuals and that the gynandromorphic genitalia do not deviate developmentally in a consistent pattern across individuals. Finally, genetic mechanisms are considered for the development of gynandromorphism in Lycaeides butterflies.
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Affiliation(s)
- Joshua P Jahner
- Program in Ecology, Evolution, and Conservation Biology, Department of Biology, University of Nevada, Reno, NV 89557, USA
| | - Lauren K Lucas
- Department of Biology, Texas State University, San Marcos, TX 78666, USA
| | - Joseph S Wilson
- Department of Biology, Utah State University, Tooele, UT 84074, USA
| | - Matthew L Forister
- Program in Ecology, Evolution, and Conservation Biology, Department of Biology, University of Nevada, Reno, NV 89557, USA
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Nice CC, Gompert Z, Fordyce JA, Forister ML, Lucas LK, Buerkle CA. Hybrid speciation and independent evolution in lineages of alpine butterflies. Evolution 2013; 67:1055-68. [PMID: 23550755 DOI: 10.1111/evo.12019] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The power of hybridization between species to generate variation and fuel adaptation is poorly understood despite long-standing interest. There is, however, increasing evidence that hybridization often generates biodiversity, including via hybrid speciation. We tested the hypothesis of hybrid speciation in butterflies occupying extreme, high-altitude habitats in four mountain ranges in western North America with an explicit, probabilistic model, and genome-wide DNA sequence data. Using this approach, in concert with ecological experiments and observations and morphological data, we document three lineages of hybrid origin. These lineages have different genome admixture proportions and distinctive trait combinations that suggest unique and independent evolutionary histories.
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Affiliation(s)
- Chris C Nice
- Department of Biology, Population and Conservation Biology Program, Texas State University, San Marcos, Texas 78666, USA.
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Talavera G, Lukhtanov VA, Pierce NE, Vila R. Establishing criteria for higher-level classification using molecular data: the systematics ofPolyommatusblue butterflies (Lepidoptera, Lycaenidae). Cladistics 2012; 29:166-192. [DOI: 10.1111/j.1096-0031.2012.00421.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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9
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Forister ML, Scholl CF. Use of an exotic host plant affects mate choice in an insect herbivore. Am Nat 2012; 179:805-10. [PMID: 22617267 DOI: 10.1086/665647] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
The colonization of exotic plants by herbivorous insects has provided opportunities for investigating causes and consequences of the evolution of niche breadth. The butterfly Lycaeides melissa utilizes exotic alfalfa, Medicago sativa, which is a relatively poor larval resource, and previous studies have found that caterpillars that consume M. sativa develop into smaller and less fecund adults. Here we investigate the effect of smaller female body size on male mate preference, a previously unexplored consequence of novel host use. Smaller females, which developed on the exotic host, were less likely to be visited by males. This result was confirmed with a second set of choice tests involving females reared on a single plant species, thus ruling out host-specific confounding factors. We suggest that an effect on mate choice be considered part of the complex suite of factors determining persistence of herbivorous insects following colonization of new habitats or resources.
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Affiliation(s)
- Matthew L Forister
- Program in Ecology, Evolution, and Conservation Biology, Department of Biology, University of Nevada, Reno, Nevada 89557, USA.
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10
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Wilson JS, Pitts JP. Identifying Pleistocene refugia in North American cold deserts using phylogeographic analyses and ecological niche modelling. DIVERS DISTRIB 2012. [DOI: 10.1111/j.1472-4642.2012.00902.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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11
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Placyk JS, Fitzpatrick BM, Casper GS, Small RL, Reynolds RG, Noble DWA, Brooks RJ, Burghardt GM. Hybridization between two gartersnake species (Thamnophis) of conservation concern: a threat or an important natural interaction? CONSERV GENET 2012. [DOI: 10.1007/s10592-012-0315-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Abstract
The selection and development of a study system for evolutionary and ecological functional genomics (EEFG) depend on a variety of factors. Here, we present the genus Boechera as an exemplary system with which to address ecological and evolutionary questions. Our focus on Boechera is based on several characteristics as follows: (i) native populations in undisturbed habitats where current environments reflect historical conditions over several thousand years; (ii) functional genomics benefitting from its close relationship to Arabidopsis thaliana; (iii) inbreeding tolerance enabling development of recombinant inbred lines, near-isogenic lines and positional cloning; (iv) interspecific crosses permitting mapping for genetic analysis of speciation; (v) apomixis (asexual reproduction by seeds) in a genetically tractable diploid; and (vi) broad geographic distribution in North America, permitting ecological genetics for a large research community. These characteristics, along with the current sequencing of three Boechera species by the Joint Genome Institute, position Boechera as a rapidly advancing system for EEFG studies.
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Affiliation(s)
- Catherine A Rushworth
- Department of Biology, Institute for Genome Sciences and Policy, Duke University, PO Box 90338, Durham, NC 27708, USA
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13
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Forister ML, Gompert Z, Fordyce JA, Nice CC. After 60 years, an answer to the question: what is the Karner blue butterfly? Biol Lett 2010; 7:399-402. [PMID: 21177692 DOI: 10.1098/rsbl.2010.1077] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Karner blue butterfly (KBB), Lycaeides melissa samuelis, is a federally protected taxon whose relationship to the Melissa blue, Lycaeides melissa, has been a point of contention during the 66 years since the KBB was first described. Using a large population-genomic dataset and a model of population divergence with migration, we investigated the relationship between the KBB and L. melissa, as well as the relationship between L. melissa and a third taxon, Lycaeides idas. We report that gene flow between the KBB and L. melissa is low, and comparable to gene flow between L. melissa and L. idas. Considering this population-genetic evidence, we conclude that the KBB is a unique evolutionary lineage that should be recognized as Lycaeides samuelis.
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Gompert Z, Lucas LK, Fordyce JA, Forister ML, Nice CC. Secondary contact between Lycaeides idas and L. melissa in the Rocky Mountains: extensive admixture and a patchy hybrid zone. Mol Ecol 2010; 19:3171-92. [DOI: 10.1111/j.1365-294x.2010.04727.x] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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16
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Koch MA, Karl R, Kiefer C, Al-Shehbaz IA. Colonizing the American continent: Systematics of the genus Arabis in North America (Brassicaceae). AMERICAN JOURNAL OF BOTANY 2010; 97:1040-57. [PMID: 21622474 DOI: 10.3732/ajb.0900366] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The circumscription of the genus Arabis underwent many and drastic changes within the past. Using DNA sequence information from the nuclear ribosomal RNA and parts of the plastid genome (trnL-trnLF), as well as a critical evaluation of herbarium material from East Asia and North America, we circumscribe the various Arabis taxa of North America. The American and East Asian Arabis species are closely related and, contrary to what was previously believed, they are not closely related to the Eurasian A. hirsuta. Using cpDNA, we found five North American lineages of Arabis with distinct distribution patterns, of which only the purple/red-flowered lineage consists of proven diploids that evolved directly from East Asian progenitors. All other four lineages evolved via ancient hybridization either on the Asian continent prior to migration to North America or showed significant evidence for hybridization and reticulation while diversifying on the American continent. We also provide the first evidence for the systematic circumscription of East Asian Arabis taxa, which together with the North American taxa, form one clade distantly related to European A. ciliata and Eurasian A. hirsuta. The findings also represent the first record of A. pycnocarpa for the floras of China, Japan, and Russian Far East.
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Affiliation(s)
- Marcus A Koch
- Heidelberg Institute of Plant Sciences, Department of Biodiversity and Plant Systematics, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany
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Gompert Z, Forister ML, Fordyce JA, Nice CC, Williamson RJ, Buerkle CA. Bayesian analysis of molecular variance in pyrosequences quantifies population genetic structure across the genome of Lycaeides butterflies. Mol Ecol 2010; 19:2455-73. [PMID: 20497324 DOI: 10.1111/j.1365-294x.2010.04666.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The distribution of genetic variation within and among populations is commonly used to infer their demographic and evolutionary histories. This endeavour has the potential to benefit substantially from high-throughput next-generation sequencing technologies through a rapid increase in the amount of data available and a corresponding increase in the precision of parameter estimation. Here we report the results of a phylogeographic study of the North American butterfly genus Lycaeides using 454 sequence data. This study serves the dual purpose of demonstrating novel molecular and analytical methods for population genetic analyses with 454 sequence data and expanding our knowledge of the phylogeographic history of Lycaeides. We obtained 341,045 sequence reads from 12 populations that we were able to assemble into 15,262 contigs (most of which were variable), representing one of the largest population genetic data sets for a non-model organism to date. We examined patterns of genetic variation using a hierarchical Bayesian analysis of molecular variance model, which provides precise estimates of genome-level phi(ST) while appropriately modelling uncertainty in locus-specific phi(ST). We found that approximately 36% of sequence variation was partitioned among populations, suggesting historical or current isolation among the sampled populations. Estimates of pairwise genome-level phi(ST) were largely consistent with a previous phylogeographic model for Lycaeides, suggesting fragmentation into two to three refugia during Pleistocene glacial cycles followed by post-Pleistocene range expansion and secondary contact leading to introgressive hybridization. This study demonstrates the potential of using genome-level data to better understand the phylogeographic history of populations.
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Affiliation(s)
- Zachariah Gompert
- Department of Botany, Program in Ecology, University of Wyoming, Laramie, WY 82071, USA.
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18
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Kiefer C, Dobes C, Sharbel TF, Koch MA. Phylogeographic structure of the chloroplast DNA gene pool in North American Boechera – A genus and continental-wide perspective. Mol Phylogenet Evol 2009; 52:303-11. [PMID: 19328239 DOI: 10.1016/j.ympev.2009.03.016] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2008] [Revised: 03/10/2009] [Accepted: 03/11/2009] [Indexed: 11/19/2022]
Affiliation(s)
- Christiane Kiefer
- Heidelberg Institute of Plant Sciences, Department Biodiversity and Plant Systematics, University of Heidelberg, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany
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RIVERA JULIO, CURRIE DOUGLASC. Identification of Nearctic black flies using DNA barcodes (Diptera: Simuliidae). Mol Ecol Resour 2009; 9 Suppl s1:224-36. [DOI: 10.1111/j.1755-0998.2009.02648.x] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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20
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Gompert Z, Fordyce JA, Forister ML, Nice CC. Recent colonization and radiation of North American Lycaeides (Plebejus) inferred from mtDNA. Mol Phylogenet Evol 2008; 48:481-90. [DOI: 10.1016/j.ympev.2008.04.035] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2007] [Revised: 04/24/2008] [Accepted: 04/24/2008] [Indexed: 10/22/2022]
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Bailey NW, Gwynne DT, Ritchie MG. Dispersal differences predict population genetic structure in Mormon crickets. Mol Ecol 2008; 16:2079-89. [PMID: 17498233 DOI: 10.1111/j.1365-294x.2007.03265.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Research investigating the geographical context of speciation has primarily focused on abiotic factors such as the role of Pleistocene glacial cycles, or geotectonic events. Few study systems allow a direct comparison of how biological differences, such as dispersal behaviour, affect population genetic structure of organisms that were subdivided during the Pleistocene. Mormon crickets exist in solitary and gregarious 'phases', which broadly correspond with an east-west mtDNA division across the Rocky Mountains. Gregarious individuals form bands that can move up to 2 km daily. This study assessed whether population genetic structure results mainly from deep Pleistocene vicariance or if we can also detect more recent genetic patterns due to phase and dispersal differences superimposed on the older, deeper divisions. We found that separation in refugia was a more important influence on genetic divergence than phase, with the Rockies acting as a barrier that separated Mormon cricket populations into eastern and western refugia during Pleistocene glacial cycles. However, patterns of isolation by distance differ between eastern and western clades for both mitochondrial and nuclear DNA, with greater divergence within the eastern, solitary clade. An mtDNA haplotype mismatch distribution is compatible with historical population expansion in the western clade but not in the eastern clade. A persistent (and possibly sex-biased) difference in dispersal ability has most likely influenced the greater population genetic structure seen in the eastern clade, emphasizing the importance of the interaction of Quaternary climate fluctuations and geography with biotic factors in producing the patterns of genetic subdivision observed today.
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Affiliation(s)
- Nathan W Bailey
- Department of Biology, 3357 Spieth Hall, University of California, Riverside, CA 92521, USA.
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Huang Y, Tan F, Su G, Deng S, He H, Shi S. Population genetic structure of three tree species in the mangrove genus Ceriops (Rhizophoraceae) from the Indo West Pacific. Genetica 2007; 133:47-56. [PMID: 17690989 DOI: 10.1007/s10709-007-9182-1] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2006] [Accepted: 07/18/2007] [Indexed: 11/24/2022]
Abstract
Ceriops is a viviparous mangrove with widespread species Ceriops decandra and C. tagal, and an endemic species C. australis. Genetic diversity of the three species was screened in 30 populations collected from 23 locations in the Indo West Pacific (IWP) using Inter-simple sequence repeats (ISSR) and sequences of partial nuclear gene (G3pdh) and chloroplast DNA (trnV-trnM). At the species level, the total gene diversity (Ht) revealed by ISSRs was 0.270, 0.118, and 0.089 in C. decandra, C. tagal, and C. australis, respectively. A total of six haplotypes of G3pdh and five haplotypes of trnV-trnM were recognized among the three species. Only C. decandra was detected containing more than one haplotype from each sequence data set (four G3pdh haplotypes and three trnV-trnM haplotypes). At the population level, genetic diversity of Ceriops was relatively low inferred from ISSRs (He = 0.028, 0.023, and 0.053 in C. decandra, C. tagal, and C. australis, respectively). No haplotype diversity within population was detected from any of the three species. Cluster analysis based on ISSRs identified three major geographical groups in correspond to the East Indian Ocean (EIO), South China Sea (SCS), and North Australia (NA) in both C. decandra and C. tagal. The cladogram from DNA sequences also detected the same three geographical groups in C. decandra. Analysis of molecular variance (AMOVA) revealed that most of the total variation was accounted for by differentiation between the three major geographical regions of both C. decandra and C. tagal. The significant genetic structure may result from the geological events in these regions during the recent Pleistocene glaciations. This study also provided insights into the phylogenetics of Ceriops.
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Affiliation(s)
- Yelin Huang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
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Sei M, Porter AH. Delimiting species boundaries and the conservation genetics of the endangered maritime ringlet butterfly (Coenonympha nipisiquit McDunnough). Mol Ecol 2007; 16:3313-25. [PMID: 17688535 DOI: 10.1111/j.1365-294x.2007.03384.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Species delimitation is a difficult problem that has implications across organismal biology, yet no single method has proved wholly satisfactory. We tested the utility of combining species-delimitation methods based on phylogeny and gene flow statistics using two parapatric members of the Coenonympha tullia group as an example: the endangered maritime ringlet butterfly (Coenonympha nipisiquit McDunnough) and the common inornate ringlet butterfly (Coenonympha inornata Edwards). We reconstructed the phylogeny of the nearctic C. tullia-group taxa from mitochondrial DNA (mtDNA) sequences (cytochrome oxidase I and mitochondrial control region) to explore the ancestry of the C. nipisiquit lineage within the group. We investigated the extent of gene flow between the two taxa with F-statistics using 587 nuclear amplified fragment length polymorphism markers, accounting for the effect of potential scoring 'collisions' where a marker may represent more than one DNA fragment. Combining species-delimitation methods was especially effective because it uncovered both historical and recent evolutionary patterns. Phylogenetic analysis of mtDNA revealed the early divergence of C. nipisiquit from other C. tullia-group taxa, including the morphologically similar C. inornata. F-statistics and gene-by-gene introgression profiles demonstrated clear isolation between the two taxa and revealed strong population structure within C. nipisiquit. C. nipisiquit is the first taxon in the nearctic C. tullia group showing strong evidence of genetic isolation. The methods we used are relatively inexpensive and can be widely used to delimit taxonomic boundaries near the species level, both generally and in particular for taxa that may be targets of conservation efforts.
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Affiliation(s)
- Makiri Sei
- The Graduate Program in Organismic and Evolutionary Biology, Department of Plant, Soil, and Insect Sciences, University of Massachusetts, Amherst, MA 01003-9297, USA.
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Gompert Z, Fordyce JA, Forister ML, Shapiro AM, Nice CC. Homoploid Hybrid Speciation in an Extreme Habitat. Science 2006; 314:1923-5. [PMID: 17138866 DOI: 10.1126/science.1135875] [Citation(s) in RCA: 238] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
According to theory, homoploid hybrid speciation, which is hybrid speciation without a change in chromosome number, is facilitated by adaptation to a novel or extreme habitat. Using molecular and ecological data, we found that the alpine-adapted butterflies in the genus Lycaeides are the product of hybrid speciation. The alpine populations possess a mosaic genome derived from both L. melissa and L. idas and are differentiated from and younger than their putative parental species. As predicted, adaptive traits may allow for persistence in the environmentally extreme alpine habitat and reproductively isolate these populations from their parental species.
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Affiliation(s)
- Zachariah Gompert
- Department of Biology, Population and Conservation Biology Program, Texas State University, San Marcos, TX 78666, USA
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Hickerson MJ, Meyer CP, Moritz C. DNA Barcoding Will Often Fail to Discover New Animal Species over Broad Parameter Space. Syst Biol 2006; 55:729-39. [PMID: 17060195 DOI: 10.1080/10635150600969898] [Citation(s) in RCA: 241] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
With increasing force, genetic divergence of mitochondrial DNA (mtDNA) is being argued as the primary tool for discovery of animal species. Two thresholds of single-gene divergence have been proposed: reciprocal monophyly, and 10 times greater genetic divergence between than within species (the "10x rule"). To explore quantitatively the utility of each approach, we couple neutral coalescent theory and the classical Bateson-Dobzhansky-Muller (BDM) model of speciation. The joint stochastic dynamics of these two processes demonstrate that both thresholds fail to "discover" many reproductively isolated lineages under a single incompatibility BDM model, especially when BDM loci have been subject to divergent selection. Only when populations have been isolated for > 4 million generations did these thresholds achieve error rates of < 10% under our model that incorporates variable population sizes. The high error rate evident in simulations is corroborated with six empirical data sets. These properties suggest that single-gene, high-throughput approaches to discovering new animal species will bias large-scale biodiversity surveys, particularly toward missing reproductively isolated lineages that have emerged by divergent selection or other mechanisms that accelerate reproductive isolation. Because single-gene thresholds for species discovery can result in substantial error at recent divergence times, they will misrepresent the correspondence between recently isolated populations and reproductively isolated lineages (= species).
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Affiliation(s)
- Michael J Hickerson
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720-3160, USA.
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Gompert Z, Nice CC, Fordyce JA, Forister ML, Shapiro AM. Identifying units for conservation using molecular systematics: the cautionary tale of the Karner blue butterfly. Mol Ecol 2006; 15:1759-68. [PMID: 16689896 DOI: 10.1111/j.1365-294x.2006.02905.x] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The federally endangered North American Karner blue butterfly (Lycaeides melissa samuelis) and the closely related Melissa blue butterfly (L. m. melissa) can be distinguished based on life history and morphology. Western populations of L. m. samuelis share mitochondrial haplotypes with L. m. melissa populations, while eastern populations of L. m. samuelis have divergent haplotypes. Here we test two hypotheses concerning the presence of L. m. melissa mitochondrial haplotypes in western L. m. samuelis populations: (i) mitochondrial introgression has occurred from L. m. melissa populations into western L. m. samuelis populations, or (ii) western populations of the nominal L. m. samuelis are more closely related to L. m. melissa than to eastern L. m. samuelis populations, yet are phenotypically similar to the latter. A Bayesian algorithm was used to cluster 190 L. melissa individuals based on 143 informative amplified fragment length polymorphism (AFLP) loci. This method clearly differentiated L. m. samuelis and L. m. melissa. Thus, genomic divergence was greater between western L. m. samuelis populations and L. m. melissa populations than it was between western and eastern populations of L. m. samuelis. This supports the hypothesis that the presence of L. m. melissa mitochondrial haplotypes in western L. m. samuelis populations is the result of mitochondrial introgression. These data provide valuable information for conservation and management plans for the endangered L. m. samuelis, and illustrate the risks of using data from a single locus for diagnosing significant units of biodiversity for conservation.
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Affiliation(s)
- Zachariah Gompert
- Department of Biology, Population and Conservation Biology Program, Texas State University, San Marcos, TX 78666, USA.
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