201
|
|
202
|
Kowasupat C, Panijpan B, Laosinchai P, Ruenwongsa P, Phongdara A, Wanna W, Senapin S, Phiwsaiya K. Biodiversity of the Betta smaragdina (Teleostei: Perciformes) in the northeast region of Thailand as determined by mitochondrial COI and nuclear ITS1 gene sequences. Meta Gene 2014; 2:83-95. [PMID: 25606392 PMCID: PMC4287876 DOI: 10.1016/j.mgene.2013.12.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Revised: 12/07/2013] [Accepted: 12/12/2013] [Indexed: 11/25/2022] Open
Abstract
In Thailand, there are currently five recognized species members of the bubble-nesting Betta genus, namely Betta splendens, B. smaragdina, B. imbellis, B. mahachaiensis and B. siamorientalis. In 2010, we indicated the possibility, based on COI barcoding evidence, that there might be two additional species, albeit cryptic, related to the type-locality B. smaragdina in some provinces in the northeast of Thailand. In the present study, after a more extensive survey of the northeast, and phylogenetic analyses based on COI and ITS1 sequences, the B. smaragdina group may be composed of at least 3 cryptic species members. The phylogenetic positions of these B. smaragdina group members in the bubble-nesting bettas' tree together with those of their congeners have been consolidated by better DNA sequence quality and phylogenetic analyses. With a better supported tree, the species statuses of B. siamorientalis and the Cambodian B. smaragdina-like fish, B. stiktos, are also confirmed.
Collapse
Affiliation(s)
- Chanon Kowasupat
- Institute for Innovative Learning, Mahidol University, Salaya, Nakhon Pathom, Thailand
| | - Bhinyo Panijpan
- Multidisciplinary Unit, Faculty of Science, Mahidol University, Phayathai, Bangkok, Thailand
| | - Parames Laosinchai
- Institute for Innovative Learning, Mahidol University, Salaya, Nakhon Pathom, Thailand
| | - Pintip Ruenwongsa
- Multidisciplinary Unit, Faculty of Science, Mahidol University, Phayathai, Bangkok, Thailand
| | - Amornrat Phongdara
- Center for Genomics and Bioinformatics Research, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Warapond Wanna
- Center for Genomics and Bioinformatics Research, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Saengchan Senapin
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand ; Center of Excellence for Shrimp Molecular Biology and Biotechnology, Mahidol University, Bangkok, Thailand
| | - Kornsunee Phiwsaiya
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand ; Center of Excellence for Shrimp Molecular Biology and Biotechnology, Mahidol University, Bangkok, Thailand
| |
Collapse
|
203
|
Shahin A, Smulders MJM, van Tuyl JM, Arens P, Bakker FT. Using multi-locus allelic sequence data to estimate genetic divergence among four Lilium (Liliaceae) cultivars. FRONTIERS IN PLANT SCIENCE 2014; 5:567. [PMID: 25368628 PMCID: PMC4202788 DOI: 10.3389/fpls.2014.00567] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 10/01/2014] [Indexed: 05/19/2023]
Abstract
Next Generation Sequencing (NGS) may enable estimating relationships among genotypes using allelic variation of multiple nuclear genes simultaneously. We explored the potential and caveats of this strategy in four genetically distant Lilium cultivars to estimate their genetic divergence from transcriptome sequences using three approaches: POFAD (Phylogeny of Organisms from Allelic Data, uses allelic information of sequence data), RAxML (Randomized Accelerated Maximum Likelihood, tree building based on concatenated consensus sequences) and Consensus Network (constructing a network summarizing among gene tree conflicts). Twenty six gene contigs were chosen based on the presence of orthologous sequences in all cultivars, seven of which also had an orthologous sequence in Tulipa, used as out-group. The three approaches generated the same topology. Although the resolution offered by these approaches is high, in this case there was no extra benefit in using allelic information. We conclude that these 26 genes can be widely applied to construct a species tree for the genus Lilium.
Collapse
Affiliation(s)
- Arwa Shahin
- Wageningen UR Plant Breeding, Wageningen University and Research CentreWageningen, Netherlands
| | - Marinus J. M. Smulders
- Wageningen UR Plant Breeding, Wageningen University and Research CentreWageningen, Netherlands
| | - Jaap M. van Tuyl
- Wageningen UR Plant Breeding, Wageningen University and Research CentreWageningen, Netherlands
| | - Paul Arens
- Wageningen UR Plant Breeding, Wageningen University and Research CentreWageningen, Netherlands
| | - Freek T. Bakker
- Biosystematics Group, Wageningen UniversityWageningen, Netherlands
- *Correspondence: Freek T. Bakker, Biosystematics Group, Wageningen University, Droevendaalsesteeg 1, 6700 AP Wageningen, Netherlands e-mail:
| |
Collapse
|
204
|
Hearn J, Stone GN, Bunnefeld L, Nicholls JA, Barton NH, Lohse K. Likelihood-based inference of population history from low-coveragede novogenome assemblies. Mol Ecol 2013; 23:198-211. [DOI: 10.1111/mec.12578] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Revised: 09/16/2013] [Accepted: 09/20/2013] [Indexed: 01/15/2023]
Affiliation(s)
- Jack Hearn
- Institute of Evolutionary Biology; University of Edinburgh; Edinburgh EH9 3JT UK
| | - Graham N. Stone
- Institute of Evolutionary Biology; University of Edinburgh; Edinburgh EH9 3JT UK
| | - Lynsey Bunnefeld
- Institute of Evolutionary Biology; University of Edinburgh; Edinburgh EH9 3JT UK
| | - James A. Nicholls
- Institute of Evolutionary Biology; University of Edinburgh; Edinburgh EH9 3JT UK
| | - Nicholas H. Barton
- Institute of Science and Technology; Am Campus 1 A-3400 Klosterneuburg Austria
| | - Konrad Lohse
- Institute of Evolutionary Biology; University of Edinburgh; Edinburgh EH9 3JT UK
| |
Collapse
|
205
|
Seetharam AS, Stuart GW. Whole genome phylogeny for 21 Drosophila species using predicted 2b-RAD fragments. PeerJ 2013; 1:e226. [PMID: 24432193 PMCID: PMC3883493 DOI: 10.7717/peerj.226] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 11/28/2013] [Indexed: 01/16/2023] Open
Abstract
Type IIB restriction endonucleases are site-specific endonucleases that cut both strands of double-stranded DNA upstream and downstream of their recognition sequences. These restriction enzymes have recognition sequences that are generally interrupted and range from 5 to 7 bases long. They produce DNA fragments which are uniformly small, ranging from 21 to 33 base pairs in length (without cohesive ends). The fragments are generated from throughout the entire length of a genomic DNA providing an excellent fractional representation of the genome. In this study we simulated restriction enzyme digestions on 21 sequenced genomes of various Drosophila species using the predicted targets of 16 Type IIB restriction enzymes to effectively produce a large and arbitrary selection of loci from these genomes. The fragments were then used to compare organisms and to calculate the distance between genomes in pair-wise combination by counting the number of shared fragments between the two genomes. Phylogenetic trees were then generated for each enzyme using this distance measure and the consensus was calculated. The consensus tree obtained agrees well with the currently accepted tree for the Drosophila species. We conclude that multi-locus sub-genomic representation combined with next generation sequencing, especially for individuals and species without previous genome characterization, can accelerate studies of comparative genomics and the building of accurate phylogenetic trees.
Collapse
Affiliation(s)
- Arun S Seetharam
- Bioinformatics Core, Purdue University , West Lafayette, IN , USA
| | - Gary W Stuart
- Department of Biology, Indiana State University , Terre Haute, IN , USA
| |
Collapse
|
206
|
Abstract
The molecular signature of selection depends strongly on whether new mutations are immediately favorable and sweep to fixation (hard sweeps) as opposed to when selection acts on segregating variation (soft sweeps). The prediction of reduced sequence variation around selected polymorphisms is much stronger for hard than soft sweeps, particularly when considering quantitative traits where sweeps are likely to be incomplete. Here, we directly investigate the genomic signal of soft sweeps within an artificial selection experiment on Mimulus guttatus. We first develop a statistical method based on Fisher’s angular transformation of allele frequencies to identify selected loci. Application of this method identifies about 400 significant windows, but no fixed differences between phenotypically divergent populations. With two notable exceptions, we find a modest average effect of partial sweeps on the amount of molecular variation. The first exception is a polymorphic inversion on chromosome 6. The increase of the derived haplotype has a broad genomic effect due to recombination suppression coupled with substantial initial haplotype structure within the population. Second, we found significant increases in nucleotide variation around selected loci in the population evolving larger flowers. This suggests that “high” alleles for flower size were initially less frequent than “low” alleles. This result is consistent with prior studies of M. guttatus and illustrates how molecular evolution can depend on the allele frequency spectrum at quantitative trait loci.
Collapse
Affiliation(s)
- John K Kelly
- Department of Ecology and Evolutionary Biology, University of Kansas.
| | | | | |
Collapse
|
207
|
Viricel A, Pante E, Dabin W, Simon-Bouhet B. Applicability of RAD-tag genotyping for interfamilial comparisons: empirical data from two cetaceans. Mol Ecol Resour 2013; 14:597-605. [DOI: 10.1111/1755-0998.12206] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Revised: 11/08/2013] [Accepted: 11/13/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Amélia Viricel
- Littoral, Environnement et Sociétés (LIENSs) UMR 7266 CNRS; Université de La Rochelle; 2 rue Olympe de Gouges La Rochelle 17000 France
| | - Eric Pante
- Littoral, Environnement et Sociétés (LIENSs) UMR 7266 CNRS; Université de La Rochelle; 2 rue Olympe de Gouges La Rochelle 17000 France
| | - Willy Dabin
- Observatoire PELAGIS, UMS 3462 CNRS; Université de La Rochelle; Pôle analytique 5 allées de l'océan La Rochelle 17000 France
| | - Benoit Simon-Bouhet
- Littoral, Environnement et Sociétés (LIENSs) UMR 7266 CNRS; Université de La Rochelle; 2 rue Olympe de Gouges La Rochelle 17000 France
| |
Collapse
|
208
|
Lemmon EM, Lemmon AR. High-Throughput Genomic Data in Systematics and Phylogenetics. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2013. [DOI: 10.1146/annurev-ecolsys-110512-135822] [Citation(s) in RCA: 355] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, Biomedical Research Facility, Tallahassee, Florida 32306;
| | - Alan R. Lemmon
- Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, Florida 32306;
| |
Collapse
|
209
|
Toonen RJ, Puritz JB, Forsman ZH, Whitney JL, Fernandez-Silva I, Andrews KR, Bird CE. ezRAD: a simplified method for genomic genotyping in non-model organisms. PeerJ 2013; 1:e203. [PMID: 24282669 PMCID: PMC3840413 DOI: 10.7717/peerj.203] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 10/13/2013] [Indexed: 12/17/2022] Open
Abstract
Here, we introduce ezRAD, a novel strategy for restriction site–associated DNA (RAD) that requires little technical expertise or investment in laboratory equipment, and demonstrate its utility for ten non-model organisms across a wide taxonomic range. ezRAD differs from other RAD methods primarily through its use of standard Illumina TruSeq library preparation kits, which makes it possible for any laboratory to send out to a commercial genomic core facility for library preparation and next-generation sequencing with virtually no additional investment beyond the cost of the service itself. This simplification opens RADseq to any lab with the ability to extract DNA and perform a restriction digest. ezRAD also differs from others in its flexibility to use any restriction enzyme (or combination of enzymes) that cuts frequently enough to generate fragments of the desired size range, without requiring the purchase of separate adapters for each enzyme or a sonication step, which can further decrease the cost involved in choosing optimal enzymes for particular species and research questions. We apply this method across a wide taxonomic diversity of non-model organisms to demonstrate the utility and flexibility of our approach. The simplicity of ezRAD makes it particularly useful for the discovery of single nucleotide polymorphisms and targeted amplicon sequencing in natural populations of non-model organisms that have been historically understudied because of lack of genomic information.
Collapse
Affiliation(s)
- Robert J Toonen
- Hawai'i Institute of Marine Biology, School of Ocean & Earth Sciences & Technology, University of Hawai'i at Mānoa , Coconut Island, Kāne'ohe, HI , United States
| | | | | | | | | | | | | |
Collapse
|
210
|
Ferretti L, Ramos-Onsins SE, Pérez-Enciso M. Population genomics from pool sequencing. Mol Ecol 2013; 22:5561-76. [DOI: 10.1111/mec.12522] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Revised: 08/03/2013] [Accepted: 09/06/2013] [Indexed: 11/30/2022]
Affiliation(s)
- Luca Ferretti
- Center for Research in Agricultural Genomics (CRAG); UAB 08193 Bellaterra Spain
| | | | - Miguel Pérez-Enciso
- Center for Research in Agricultural Genomics (CRAG); UAB 08193 Bellaterra Spain
- Department of Animal Science and Food; Faculty of Veterinary; Universitat Autonoma de Barcelona; 08193 Bellaterra Spain
- Institut Català de Recerca i Estudis Avancats (ICREA); Passeig Lluís Companys 23 08010 Barcelona Spain
| |
Collapse
|
211
|
Dufresnes C, Wassef J, Ghali K, Brelsford A, Stöck M, Lymberakis P, Crnobrnja-Isailovic J, Perrin N. Conservation phylogeography: does historical diversity contribute to regional vulnerability in European tree frogs (Hyla arborea)? Mol Ecol 2013; 22:5669-84. [PMID: 24102652 DOI: 10.1111/mec.12513] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Revised: 08/24/2013] [Accepted: 08/28/2013] [Indexed: 11/28/2022]
Abstract
Documenting and preserving the genetic diversity of populations, which conditions their long-term survival, have become a major issue in conservation biology. The loss of diversity often documented in declining populations is usually assumed to result from human disturbances; however, historical biogeographic events, otherwise known to strongly impact diversity, are rarely considered in this context. We apply a multilocus phylogeographic study to investigate the late-Quaternary history of a tree frog (Hyla arborea) with declining populations in the northern and western part of its distribution range. Mitochondrial and nuclear polymorphisms reveal high genetic diversity in the Balkan Peninsula, with a spatial structure moulded by the last glaciations. While two of the main refugial lineages remained limited to the Balkans (Adriatic coast, southern Balkans), a third one expanded to recolonize Northern and Western Europe, loosing much of its diversity in the process. Our findings show that mobile and a priori homogeneous taxa may also display substructure within glacial refugia ('refugia within refugia') and emphasize the importance of the Balkans as a major European biodiversity centre. Moreover, the distribution of diversity roughly coincides with regional conservation situations, consistent with the idea that historically impoverished genetic diversity may interact with anthropogenic disturbances, and increase the vulnerability of populations. Phylogeographic models seem important to fully appreciate the risks of local declines and inform conservation strategies.
Collapse
Affiliation(s)
- Christophe Dufresnes
- Department of Ecology & Evolution, University of Lausanne, Biophore Building, 1015, Lausanne, Switzerland
| | | | | | | | | | | | | | | |
Collapse
|
212
|
Smith BT, Harvey MG, Faircloth BC, Glenn TC, Brumfield RT. Target Capture and Massively Parallel Sequencing of Ultraconserved Elements for Comparative Studies at Shallow Evolutionary Time Scales. Syst Biol 2013; 63:83-95. [DOI: 10.1093/sysbio/syt061] [Citation(s) in RCA: 241] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Brian Tilston Smith
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA; 2Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA; 3Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA; and 4Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USA
| | - Michael G. Harvey
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA; 2Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA; 3Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA; and 4Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USA
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA; 2Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA; 3Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA; and 4Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USA
| | - Brant C. Faircloth
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA; 2Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA; 3Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA; and 4Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USA
| | - Travis C. Glenn
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA; 2Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA; 3Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA; and 4Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USA
| | - Robb T. Brumfield
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA; 2Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA; 3Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA; and 4Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USA
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA; 2Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA; 3Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA; and 4Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USA
| |
Collapse
|
213
|
Puritz JB, Toonen RJ. Next-generation sequencing for high-throughput molecular ecology: a step-by-step protocol for targeted multilocus genotyping by pyrosequencing. Methods Mol Biol 2013; 1006:89-99. [PMID: 23546785 DOI: 10.1007/978-1-62703-389-3_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Next-generation sequencing technology can now provide population biologists and phylogeographers with information at the genomic scale; however, many pertinent questions in population genetics and phylogeography can be answered effectively with modest levels of genomic information. For the past two decades, most population-level studies have lacked nuclear DNA (nDNA) sequence data due to the complications and cost of amplifying and sequencing diploid loci. However, pyrosequencing of emulsion PCR reactions, amplifying from only one molecule at a time, can generate megabases of clonally amplified loci at high coverage, thereby greatly simplifying allelic sequence determination. Here, we present a step-by-step methodology for utilizing the 454 GS FLX Titanium pyrosequencing platform to simultaneously sequence 16 populations (at 20 individuals per population) at 10 different nDNA loci (3,200 loci in total) in one plate of sequencing for less than the cost of traditional Sanger sequencing.
Collapse
Affiliation(s)
- Jonathan B Puritz
- Hawai'i Institute of Marine Biology, University of Hawai'I, Kāne'ohe, HI, USA
| | | |
Collapse
|
214
|
Merz C, Catchen JM, Hanson-Smith V, Emerson KJ, Bradshaw WE, Holzapfel CM. Replicate phylogenies and post-glacial range expansion of the pitcher-plant mosquito, Wyeomyia smithii, in North America. PLoS One 2013; 8:e72262. [PMID: 24039746 PMCID: PMC3765167 DOI: 10.1371/journal.pone.0072262] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Accepted: 07/12/2013] [Indexed: 11/28/2022] Open
Abstract
Herein we tested the repeatability of phylogenetic inference based on high throughput sequencing by increased taxon sampling using our previously published techniques in the pitcher-plant mosquito, Wyeomyia smithii in North America. We sampled 25 natural populations drawn from different localities nearby 21 previous collection localities and used these new data to construct a second, independent phylogeny, expressly to test the reproducibility of phylogenetic patterns. Comparison of trees between the two data sets based on both maximum parsimony and maximum likelihood with Bayesian posterior probabilities showed close correspondence in the grouping of the most southern populations into clear clades. However, discrepancies emerged, particularly in the middle of W. smithii's current range near the previous maximum extent of the Laurentide Ice Sheet, especially concerning the most recent common ancestor to mountain and northern populations. Combining all 46 populations from both studies into a single maximum parsimony tree and taking into account the post-glacial historical biogeography of associated flora provided an improved picture of W. smithii's range expansion in North America. In a more general sense, we propose that extensive taxon sampling, especially in areas of known geological disruption is key to a comprehensive approach to phylogenetics that leads to biologically meaningful phylogenetic inference.
Collapse
Affiliation(s)
- Clayton Merz
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Julian M. Catchen
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Victor Hanson-Smith
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Kevin J. Emerson
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - William E. Bradshaw
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
- * E-mail: (WB); (CH)
| | - Christina M. Holzapfel
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
- * E-mail: (WB); (CH)
| |
Collapse
|
215
|
Ezawa K, Innan H. Theoretical framework of population genetics with somatic mutations taken into account: application to copy number variations in humans. Heredity (Edinb) 2013; 111:364-74. [PMID: 23981956 DOI: 10.1038/hdy.2013.59] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 01/05/2013] [Accepted: 05/10/2013] [Indexed: 11/09/2022] Open
Abstract
Traditionally, population genetics focuses on the dynamics of frequencies of alleles acquired by mutations on germ-lines, because only such mutations are heritable. Typical genotyping experiments, however, use DNA from some somatic tissues such as blood, which harbors somatic mutations at the current generation in addition to germ-line mutations accumulated since the most recent common ancestor of the sample. This common practice may sometimes cause erroneous interpretations of polymorphism data, unless we properly understand the role of somatic mutations in population genetics. We here introduce a very basic theoretical framework of population genetics with somatic mutations taken into account. It is easy to imagine that somatic mutations at the current generation simply add individual-specific variations, as errors in mutation detection do. Our theory quantifies this increment under various conditions. We find that the major contribution of somatic mutations plus errors is to very rare variants, particularly to singletons. The relative contribution is markedly large when mutations are deleterious. Because negative selection also increases rare variants, it is important to distinguish the roles of these mutually confounding factors when we interpret the data, even after correcting for demography. We apply this theory to human copy number variations (CNVs), for which the composite effect of somatic mutations and errors may not be negligible. Using genome-wide CNV data, we demonstrate how the joint action of the two factors, selection and somatic mutations plus errors, shapes the observed pattern of polymorphism.
Collapse
Affiliation(s)
- K Ezawa
- School of Advanced Sciences, The Graduate University for Advanced Studies, Hayama, Japan
| | | |
Collapse
|
216
|
Development and application of genomic tools to the restoration of green abalone in southern California. CONSERV GENET 2013. [DOI: 10.1007/s10592-013-0524-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
|
217
|
Sobel JM, Streisfeld MA. Flower color as a model system for studies of plant evo-devo. FRONTIERS IN PLANT SCIENCE 2013; 4:321. [PMID: 23970892 PMCID: PMC3748380 DOI: 10.3389/fpls.2013.00321] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2013] [Accepted: 07/30/2013] [Indexed: 05/20/2023]
Abstract
Even though pigmentation traits have had substantial impacts on the field of animal evolutionary developmental biology, they have played only relatively minor roles in plant evo-devo. This is surprising given the often direct connection between flower color and fitness variation mediated through the effects of pollinators. At the same time, ecological and evolutionary genetic studies have utilized the molecular resources available for the anthocyanin pathway to generate several examples of the molecular basis of putatively adaptive transitions in flower color. Despite this opportunity to synthesize experimental approaches in ecology, evolution, and developmental biology, the investigation of many fundamental questions in evo-devo using this powerful model is only at its earliest stages. For example, a long-standing question is whether predictable genetic changes accompany the repeated evolution of a trait. Due to the conserved nature of the biochemical and regulatory control of anthocyanin biosynthesis, it has become possible to determine whether, and under what circumstances, different types of mutations responsible for flower color variation are preferentially targeted by natural selection. In addition, because plants use anthocyanin and related compounds in vegetative tissue for other important physiological functions, the identification of naturally occurring transitions from unpigmented to pigmented flowers provides the opportunity to examine the mechanisms by which regulatory networks are co-opted into new developmental domains. Here, we review what is known about the ecological and molecular basis of anthocyanic flower color transitions in natural systems, focusing on the evolutionary and developmental features involved. In doing so, we provide suggestions for future work on this trait and suggest that there is still much to be learned from the evolutionary development of flower color transitions in nature.
Collapse
|
218
|
Pegadaraju V, Nipper R, Hulke B, Qi L, Schultz Q. De novo sequencing of sunflower genome for SNP discovery using RAD (Restriction site Associated DNA) approach. BMC Genomics 2013; 14:556. [PMID: 23947483 PMCID: PMC3765701 DOI: 10.1186/1471-2164-14-556] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 08/09/2013] [Indexed: 12/31/2022] Open
Abstract
Background Application of Single Nucleotide Polymorphism (SNP) marker technology as a tool in sunflower breeding programs offers enormous potential to improve sunflower genetics, and facilitate faster release of sunflower hybrids to the market place. Through a National Sunflower Association (NSA) funded initiative, we report on the process of SNP discovery through reductive genome sequencing and local assembly of six diverse sunflower inbred lines that represent oil as well as confection types. Results A combination of Restriction site Associated DNA Sequencing (RAD-Seq) protocols and Illumina paired-end sequencing chemistry generated high quality 89.4 M paired end reads from the six lines which represent 5.3 GB of the sequencing data. Raw reads from the sunflower line, RHA 464 were assembled de novo to serve as a framework reference genome. About 15.2 Mb of sunflower genome distributed over 42,267 contigs were obtained upon assembly of RHA 464 sequencing data, the contig lengths ranged from 200 to 950 bp with an N50 length of 393 bp. SNP calling was performed by aligning sequencing data from the six sunflower lines to the assembled reference RHA 464. On average, 1 SNP was located every 143 bp of the sunflower genome sequence. Based on several filtering criteria, a final set of 16,467 putative sequence variants with characteristics favorable for Illumina Infinium Genotyping Technology (IGT) were mined from the sequence data generated across six diverse sunflower lines. Conclusion Here we report the molecular and computational methodology involved in SNP development for a complex genome like sunflower lacking reference assembly, offering an attractive tool for molecular breeding purposes in sunflower.
Collapse
|
219
|
Gilabert A, Wasmuth JD. Unravelling parasitic nematode natural history using population genetics. Trends Parasitol 2013; 29:438-48. [PMID: 23948430 DOI: 10.1016/j.pt.2013.07.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 07/10/2013] [Accepted: 07/11/2013] [Indexed: 01/01/2023]
Abstract
The health and economic importance of parasitic nematodes cannot be overstated. Moreover, they offer a complex and diverse array of life strategies, raising a multitude of evolutionary questions. Researchers are applying population genetics to parasitic nematodes in order to disentangle some aspects of their life strategies, improve our knowledge about disease epidemiology, and design control strategies. However, population genetics studies of nematodes have been constrained due to the difficulty in sampling nematodes and developing molecular markers. In this context, new computational and sequencing technologies represent promising tools to investigate population genomics of parasitic, non-model, nematode species in an epidemiological context.
Collapse
Affiliation(s)
- Aude Gilabert
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, 3280 Hospital Drive NW, Calgary, Alberta, T2N 4Z6, Canada
| | | |
Collapse
|
220
|
Peijnenburg KTCA, Goetze E. High evolutionary potential of marine zooplankton. Ecol Evol 2013; 3:2765-81. [PMID: 24567838 PMCID: PMC3930040 DOI: 10.1002/ece3.644] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Revised: 04/30/2013] [Accepted: 05/06/2013] [Indexed: 11/17/2022] Open
Abstract
Open ocean zooplankton often have been viewed as slowly evolving species that have limited capacity to respond adaptively to changing ocean conditions. Hence, attention has focused on the ecological responses of zooplankton to current global change, including range shifts and changing phenology. Here, we argue that zooplankton also are well poised for evolutionary responses to global change. We present theoretical arguments that suggest plankton species may respond rapidly to selection on mildly beneficial mutations due to exceptionally large population size, and consider the circumstantial evidence that supports our inference that selection may be particularly important for these species. We also review all primary population genetic studies of open ocean zooplankton and show that genetic isolation can be achieved at the scale of gyre systems in open ocean habitats (100s to 1000s of km). Furthermore, population genetic structure often varies across planktonic taxa, and appears to be linked to the particular ecological requirements of the organism. In combination, these characteristics should facilitate adaptive evolution to distinct oceanographic habitats in the plankton. We conclude that marine zooplankton may be capable of rapid evolutionary as well as ecological responses to changing ocean conditions, and discuss the implications of this view. We further suggest two priority areas for future research to test our hypothesis of high evolutionary potential in open ocean zooplankton, which will require (1) assessing how pervasive selection is in driving population divergence and (2) rigorously quantifying the spatial and temporal scales of population differentiation in the open ocean. Recent attention has focused on the ecological responses of open ocean zooplankton to current global change, including range shifts and changing phenology. Here, we argue that marine zooplankton also are well poised for evolutionary responses to global change.
Collapse
Affiliation(s)
- Katja T C A Peijnenburg
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam P.O. Box 94248, 1090 GE, Amsterdam, The Netherlands ; Department Marine Zoology, Naturalis Biodiversity Center P.O. Box 9517, 2300 RA, Leiden, The Netherlands
| | - Erica Goetze
- Department of Oceanography School of Ocean and Earth Science and Technology, University of Hawaii at Manoa Honolulu, Hawaii, 96822
| |
Collapse
|
221
|
Kapralova KH, Gudbrandsson J, Reynisdottir S, Santos CB, Baltanás VC, Maier VH, Snorrason SS, Palsson A. Differentiation at the MHCIIα and Cath2 loci in sympatric Salvelinus alpinus resource morphs in Lake Thingvallavatn. PLoS One 2013; 8:e69402. [PMID: 23894470 PMCID: PMC3722248 DOI: 10.1371/journal.pone.0069402] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Accepted: 06/09/2013] [Indexed: 11/19/2022] Open
Abstract
Northern freshwater fish may be suitable for the genetic dissection of ecological traits because they invaded new habitats after the last ice age (∼10.000 years ago). Arctic charr (Salvelinus alpinus) colonizing streams and lakes in Iceland gave rise to multiple populations of small benthic morphotypes, often in sympatry with a pelagic morphotype. Earlier studies have revealed significant, but subtle, genetic differentiation between the three most common morphs in Lake Thingvallavatn. We conducted a population genetic screen on four immunological candidate genes Cathelicidin 2 (Cath2), Hepcidin (Hamp), Liver expressed antimicrobial peptide 2a (Leap-2a), and Major Histocompatibility Complex IIα (MHCIIα) and a mitochondrial marker (D-loop) among the three most common Lake Thingvallavatn charr morphs. Significant differences in allele frequencies were found between morphs at the Cath2 and MHCIIα loci. No such signal was detected in the D-loop nor in the other two immunological genes. In Cath2 the small benthic morph deviated from the other two (FST = 0.13), one of the substitutions detected constituting an amino acid replacement polymorphism in the antimicrobial peptide. A more striking difference was found in the MHCIIα. Two haplotypes were very common in the lake, and their frequency differed greatly between the morphotypes (from 22% to 93.5%, FST = 0.67). We then expanded our study by surveying the variation in Cath2 and MHCIIα in 9 Arctic charr populations from around Iceland. The populations varied greatly in terms of allele frequencies at Cath2, but the variation did not correlate with morphotype. At the MHCIIα locus, the variation was nearly identical to the variation in the two benthic morphs of Lake Thingvallavatn. The results are consistent with a scenario where parts of the immune systems have diverged substantially among Arctic charr populations in Iceland, after colonizing the island ∼10.000 years ago.
Collapse
Affiliation(s)
- Kalina H. Kapralova
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavik, Iceland
| | - Johannes Gudbrandsson
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavik, Iceland
| | - Sigrun Reynisdottir
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavik, Iceland
| | - Cristina B. Santos
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavik, Iceland
| | - Vanessa C. Baltanás
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavik, Iceland
| | - Valerie H. Maier
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavik, Iceland
| | - Sigurdur S. Snorrason
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavik, Iceland
| | - Arnar Palsson
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavik, Iceland
| |
Collapse
|
222
|
Bourgeois YXC, Lhuillier E, Cézard T, Bertrand JAM, Delahaie B, Cornuault J, Duval T, Bouchez O, Milá B, Thébaud C. Mass production of
SNP
markers in a nonmodel passerine bird through
RAD
sequencing and contig mapping to the zebra finch genome. Mol Ecol Resour 2013; 13:899-907. [DOI: 10.1111/1755-0998.12137] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 05/24/2013] [Accepted: 06/04/2013] [Indexed: 01/01/2023]
Affiliation(s)
- Yann X. C. Bourgeois
- Laboratoire Évolution et Diversité Biologique UMR 5174 CNRS ‐ Université Paul Sabatier – ENFA 118 route de Narbonne, Bâtiment 4R1 F‐31062 Toulouse Cedex 9 France
| | - Emeline Lhuillier
- INRA UAR 1209 Département de Génétique Animale INRA Auzeville F‐31326 Castanet‐Tolosan France
- GeT‐PlaGe Genotoul INRA Auzeville F‐31326 Castanet‐Tolosan France
| | - Timothée Cézard
- The GenePool Ashworth Laboratories The University of Edinburgh The King's Building Edinburgh EH9 3JT UK
| | - Joris A. M. Bertrand
- Laboratoire Évolution et Diversité Biologique UMR 5174 CNRS ‐ Université Paul Sabatier – ENFA 118 route de Narbonne, Bâtiment 4R1 F‐31062 Toulouse Cedex 9 France
| | - Boris Delahaie
- Laboratoire Évolution et Diversité Biologique UMR 5174 CNRS ‐ Université Paul Sabatier – ENFA 118 route de Narbonne, Bâtiment 4R1 F‐31062 Toulouse Cedex 9 France
| | - Josselin Cornuault
- Laboratoire Évolution et Diversité Biologique UMR 5174 CNRS ‐ Université Paul Sabatier – ENFA 118 route de Narbonne, Bâtiment 4R1 F‐31062 Toulouse Cedex 9 France
| | - Thomas Duval
- Société Calédonienne d'Ornithologie Nord BP 236 F‐98822 Poindimié Nouvelle Calédonie France
| | - Olivier Bouchez
- GeT‐PlaGe Genotoul INRA Auzeville F‐31326 Castanet‐Tolosan France
- INRA UMR 444 Laboratoire de Génétique Cellulaire INRA Auzeville F‐31326 Castanet‐Tolosan France
| | - Borja Milá
- Museo Nacional de Ciencias Naturales CSIC José Gutiérrez Abascal 2 Madrid 28006 Spain
| | - Christophe Thébaud
- Laboratoire Évolution et Diversité Biologique UMR 5174 CNRS ‐ Université Paul Sabatier – ENFA 118 route de Narbonne, Bâtiment 4R1 F‐31062 Toulouse Cedex 9 France
| |
Collapse
|
223
|
Wang XQ, Zhao L, Eaton DAR, Li DZ, Guo ZH. Identification of
SNP
markers for inferring phylogeny in temperate bamboos (
P
oaceae:
B
ambusoideae) using
RAD
sequencing. Mol Ecol Resour 2013; 13:938-45. [DOI: 10.1111/1755-0998.12136] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Revised: 06/08/2013] [Accepted: 06/10/2013] [Indexed: 12/29/2022]
Affiliation(s)
- X. Q. Wang
- Plant Germplasm and Genomics Center Germplasm Bank of Wild Species Kunming Institute of Botany Chinese Academy of Sciences Kunming 650201 China
- College of Life Sciences University of Chinese Academy of Sciences Beijing 100049 China
| | - L. Zhao
- Plant Germplasm and Genomics Center Germplasm Bank of Wild Species Kunming Institute of Botany Chinese Academy of Sciences Kunming 650201 China
| | - D. A. R. Eaton
- Committee on Evolutionary Biology University of Chicago Chicago IL 60637 USA
| | - D. Z. Li
- Key Laboratory of Biodiversity and Biogeography Kunming Institute of Botany Chinese Academy of Sciences Kunming 650201 China
| | - Z. H. Guo
- Plant Germplasm and Genomics Center Germplasm Bank of Wild Species Kunming Institute of Botany Chinese Academy of Sciences Kunming 650201 China
| |
Collapse
|
224
|
Carstens BC, Brennan RS, Chua V, Duffie CV, Harvey MG, Koch RA, McMahan CD, Nelson BJ, Newman CE, Satler JD, Seeholzer G, Posbic K, Tank DC, Sullivan J. Model selection as a tool for phylogeographic inference: an example from the willow Salix melanopsis. Mol Ecol 2013; 22:4014-28. [PMID: 23848064 DOI: 10.1111/mec.12347] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 04/09/2013] [Accepted: 04/09/2013] [Indexed: 12/29/2022]
Abstract
Phylogeographic inference has typically relied on analyses of data from one or a few genes to provide estimates of demography and population histories. While much has been learned from these studies, all phylogeographic analysis is conditioned on the data, and thus, inferences derived from data that represent a small sample of the genome are unavoidably tenuous. Here, we demonstrate one approach for moving beyond classic phylogeographic research. We use sequence capture probes and Illumina sequencing to generate data from >400 loci in order to infer the phylogeographic history of Salix melanopsis, a riparian willow with a disjunct distribution in coastal and the inland Pacific Northwest. We evaluate a priori phylogeographic hypotheses using coalescent models for parameter estimation, and the results support earlier findings that identified post-Pleistocene dispersal as the cause of the disjunction in S. melanopsis. We also conduct a series of model selection exercises using IMa2, Migrate-n and ∂a∂i. The resulting ranking of models indicates that refugial dynamics were complex, with multiple regions in the inland regions serving as the source for postglacial colonization. Our results demonstrate that new sources of data and new approaches to data analysis can rejuvenate phylogeographic research by allowing for the identification of complex models that enable researchers to both identify and estimate the most relevant parameters for a given system.
Collapse
Affiliation(s)
- Bryan C Carstens
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH 43210, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
225
|
Catchen J, Bassham S, Wilson T, Currey M, O’Brien C, Yeates Q, Cresko WA. The population structure and recent colonization history of Oregon threespine stickleback determined using restriction-site associated DNA-sequencing. Mol Ecol 2013; 22:2864-83. [PMID: 23718143 PMCID: PMC3712868 DOI: 10.1111/mec.12330] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2012] [Revised: 02/11/2013] [Accepted: 02/27/2013] [Indexed: 12/16/2022]
Abstract
Understanding how genetic variation is partitioned across genomes within and among populations is a fundamental problem in ecological and evolutionary genetics. To address this problem, we studied the threespine stickleback fish, which has repeatedly undergone parallel phenotypic and genetic differentiation when oceanic fish have invaded freshwater habitats. While significant evolutionary genetic research has been performed using stickleback from geographic regions that have been deglaciated in the last 20 000 years, less research has focused on freshwater populations that predate the last glacial maximum. We performed restriction-site associated DNA-sequencing (RAD-seq) based population genomic analyses on stickleback from across Oregon, which was not glaciated during the last maximum. We sampled stickleback from coastal, Willamette Basin and central Oregon sites, analysed their genetic diversity using RAD-seq, performed structure analyses, reconstructed their phylogeographic history and tested the hypothesis of recent stickleback introduction into central Oregon, where incidence of this species was only recently documented. Our results showed a clear phylogeographic break between coastal and inland populations, with oceanic populations exhibiting the lowest levels of divergence from one another. Willamette Basin and central Oregon populations formed a clade of closely related populations, a finding consistent with a recent introduction of stickleback into central Oregon. Finally, genome-wide analysis of genetic diversity (π) and correlations of alleles within individuals in subpopulations (FIS) supported a role for introgressive hybridization in coastal populations and a recent expansion in central Oregon. Our results exhibit the power of next-generation sequencing genomic approaches such as RAD-seq to identify both historical population structure and recent colonization history.
Collapse
Affiliation(s)
- Julian Catchen
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA 97403
| | - Susan Bassham
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA 97403
| | - Taylor Wilson
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA 97403
| | - Mark Currey
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA 97403
| | - Conor O’Brien
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA 97403
| | - Quick Yeates
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA 97403
| | - William A. Cresko
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA 97403
| |
Collapse
|
226
|
Roda F, Ambrose L, Walter GM, Liu HL, Schaul A, Lowe A, Pelser PB, Prentis P, Rieseberg LH, Ortiz-Barrientos D. Genomic evidence for the parallel evolution of coastal forms in theSenecio lautuscomplex. Mol Ecol 2013; 22:2941-52. [DOI: 10.1111/mec.12311] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Revised: 02/10/2013] [Accepted: 02/14/2013] [Indexed: 12/30/2022]
Affiliation(s)
- Federico Roda
- School of Biological Sciences; The University of Queensland; St. Lucia Qld 4072 Australia
| | - Luke Ambrose
- School of Biological Sciences; The University of Queensland; St. Lucia Qld 4072 Australia
| | - Gregory M. Walter
- School of Biological Sciences; The University of Queensland; St. Lucia Qld 4072 Australia
| | - Huanle L. Liu
- School of Biological Sciences; The University of Queensland; St. Lucia Qld 4072 Australia
| | - Andrea Schaul
- School of Biological Sciences; The University of Queensland; St. Lucia Qld 4072 Australia
| | - Andrew Lowe
- Australian Centre for Evolutionary Biology and Biodiversity; School of Earth and Environmental Science; University of Adelaide; Adelaide SA Australia
- Science Resource Centre; Department for Environment and Natural Resources; North Terrace Adelaide South Australia Australia
| | - Pieter B. Pelser
- School of Biological Sciences; University of Canterbury; Private Bag 4800 Christchurch 8140 New Zealand
| | - Peter Prentis
- School of Earth, Environmental and Biological Sciences; Queensland University of Technology; Brisbane Qld 4001 Australia
| | - Loren H. Rieseberg
- Department of Botany; University of British Columbia; 3529-6270 University Boulevard Vancouver BC V6T 1Z4 Canada
- Biology Department; Indiana University; 1001 E Third Street Bloomington IN 47405 USA
| | | |
Collapse
|
227
|
Catchen J, Hohenlohe PA, Bassham S, Amores A, Cresko WA. Stacks: an analysis tool set for population genomics. Mol Ecol 2013; 22:3124-40. [PMID: 23701397 DOI: 10.1111/mec.12354] [Citation(s) in RCA: 2109] [Impact Index Per Article: 191.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Revised: 04/16/2013] [Accepted: 04/16/2013] [Indexed: 02/06/2023]
Abstract
Massively parallel short-read sequencing technologies, coupled with powerful software platforms, are enabling investigators to analyse tens of thousands of genetic markers. This wealth of data is rapidly expanding and allowing biological questions to be addressed with unprecedented scope and precision. The sizes of the data sets are now posing significant data processing and analysis challenges. Here we describe an extension of the Stacks software package to efficiently use genotype-by-sequencing data for studies of populations of organisms. Stacks now produces core population genomic summary statistics and SNP-by-SNP statistical tests. These statistics can be analysed across a reference genome using a smoothed sliding window. Stacks also now provides several output formats for several commonly used downstream analysis packages. The expanded population genomics functions in Stacks will make it a useful tool to harness the newest generation of massively parallel genotyping data for ecological and evolutionary genetics.
Collapse
Affiliation(s)
- Julian Catchen
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403-5289, USA
| | | | | | | | | |
Collapse
|
228
|
Roda F, Liu H, Wilkinson MJ, Walter GM, James ME, Bernal DM, Melo MC, Lowe A, Rieseberg LH, Prentis P, Ortiz-Barrientos D. CONVERGENCE AND DIVERGENCE DURING THE ADAPTATION TO SIMILAR ENVIRONMENTS BY AN AUSTRALIAN GROUNDSEL. Evolution 2013; 67:2515-29. [DOI: 10.1111/evo.12136] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Accepted: 04/03/2013] [Indexed: 01/02/2023]
Affiliation(s)
- Federico Roda
- School of Biological Sciences; The University of Queensland; St. Lucia; QLD; 4072; Australia
| | - Huanle Liu
- School of Biological Sciences; The University of Queensland; St. Lucia; QLD; 4072; Australia
| | - Melanie J. Wilkinson
- School of Biological Sciences; The University of Queensland; St. Lucia; QLD; 4072; Australia
| | - Gregory M. Walter
- School of Biological Sciences; The University of Queensland; St. Lucia; QLD; 4072; Australia
| | - Maddie E. James
- School of Biological Sciences; The University of Queensland; St. Lucia; QLD; 4072; Australia
| | - Diana M. Bernal
- School of Biological Sciences; The University of Queensland; St. Lucia; QLD; 4072; Australia
| | - Maria C. Melo
- School of Biological Sciences; The University of Queensland; St. Lucia; QLD; 4072; Australia
| | | | | | - Peter Prentis
- Queensland Institute of Technology; Biogeosciences; Brisbane; QLD; 4001; Australia
| | - Daniel Ortiz-Barrientos
- School of Biological Sciences; The University of Queensland; St. Lucia; QLD; 4072; Australia
| |
Collapse
|
229
|
Pujolar JM, Jacobsen MW, Frydenberg J, Als TD, Larsen PF, Maes GE, Zane L, Jian JB, Cheng L, Hansen MM. A resource of genome-wide single-nucleotide polymorphisms generated by RAD tag sequencing in the critically endangered European eel. Mol Ecol Resour 2013; 13:706-14. [PMID: 23656721 DOI: 10.1111/1755-0998.12117] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 03/22/2013] [Accepted: 03/24/2013] [Indexed: 01/25/2023]
Abstract
Reduced representation genome sequencing such as restriction-site-associated DNA (RAD) sequencing is finding increased use to identify and genotype large numbers of single-nucleotide polymorphisms (SNPs) in model and nonmodel species. We generated a unique resource of novel SNP markers for the European eel using the RAD sequencing approach that was simultaneously identified and scored in a genome-wide scan of 30 individuals. Whereas genomic resources are increasingly becoming available for this species, including the recent release of a draft genome, no genome-wide set of SNP markers was available until now. The generated SNPs were widely distributed across the eel genome, aligning to 4779 different contigs and 19,703 different scaffolds. Significant variation was identified, with an average nucleotide diversity of 0.00529 across individuals. Results varied widely across the genome, ranging from 0.00048 to 0.00737 per locus. Based on the average nucleotide diversity across all loci, long-term effective population size was estimated to range between 132,000 and 1,320,000, which is much higher than previous estimates based on microsatellite loci. The generated SNP resource consisting of 82,425 loci and 376,918 associated SNPs provides a valuable tool for future population genetics and genomics studies and allows for targeting specific genes and particularly interesting regions of the eel genome.
Collapse
Affiliation(s)
- J M Pujolar
- Department of Bioscience, Aarhus University, Aarhus C, Denmark.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
230
|
Eaton DAR, Ree RH. Inferring phylogeny and introgression using RADseq data: an example from flowering plants (Pedicularis: Orobanchaceae). Syst Biol 2013; 62:689-706. [PMID: 23652346 PMCID: PMC3739883 DOI: 10.1093/sysbio/syt032] [Citation(s) in RCA: 326] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Phylogenetic relationships among recently diverged species are often difficult to resolve due to insufficient phylogenetic signal in available markers and/or conflict among gene trees. Here we explore the use of reduced-representation genome sequencing, specifically in the form of restriction-site associated DNA (RAD), for phylogenetic inference and the detection of ancestral hybridization in non-model organisms. As a case study, we investigate Pedicularis section Cyathophora, a systematically recalcitrant clade of flowering plants in the broomrape family (Orobanchaceae). Two methods of phylogenetic inference, maximum likelihood and Bayesian concordance, were applied to data sets that included as many as 40,000 RAD loci. Both methods yielded similar topologies that included two major clades: a "rex-thamnophila" clade, composed of two species and several subspecies with relatively low floral diversity, and geographically widespread distributions at lower elevations, and a "superba" clade, composed of three species characterized by relatively high floral diversity and isolated geographic distributions at higher elevations. Levels of molecular divergence between subspecies in the rex-thamnophila clade are similar to those between species in the superba clade. Using Patterson's D-statistic test, including a novel extension of the method that enables finer-grained resolution of introgression among multiple candidate taxa by removing the effect of their shared ancestry, we detect significant introgression among nearly all taxa in the rex-thamnophila clade, but not between clades or among taxa within the superba clade. These results suggest an important role for geographic isolation in the emergence of species barriers, by facilitating local adaptation and differentiation in the absence of homogenizing gene flow.
Collapse
Affiliation(s)
- Deren A R Eaton
- Committee on Evolutionary Biology, University of Chicago, Chicago, IL 60637, USA; and Botany Department, Field Museum of Natural History, Chicago, IL 60605, USA
| | | |
Collapse
|
231
|
DeWoody JA, Abts KC, Fahey AL, Ji Y, Kimble SJA, Marra NJ, Wijayawardena BK, Willoughby JR. Of contigs and quagmires: next‐generation sequencing pitfalls associated with transcriptomic studies. Mol Ecol Resour 2013; 13:551-8. [PMID: 23615313 DOI: 10.1111/1755-0998.12107] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 03/13/2013] [Accepted: 03/14/2013] [Indexed: 12/15/2022]
Affiliation(s)
- J. Andrew DeWoody
- Department of Biological Sciences Purdue University West Lafayette IN 47907 USA
- Department of Forestry & Natural Resources Purdue University West Lafayette IN 47907 USA
| | - Kendra C. Abts
- Department of Forestry & Natural Resources Purdue University West Lafayette IN 47907 USA
| | - Anna L. Fahey
- Department of Forestry & Natural Resources Purdue University West Lafayette IN 47907 USA
| | - Yanzhu Ji
- Department of Forestry & Natural Resources Purdue University West Lafayette IN 47907 USA
| | - Steven J. A. Kimble
- Department of Forestry & Natural Resources Purdue University West Lafayette IN 47907 USA
| | - Nicholas J. Marra
- Department of Forestry & Natural Resources Purdue University West Lafayette IN 47907 USA
| | | | - Janna R. Willoughby
- Department of Forestry & Natural Resources Purdue University West Lafayette IN 47907 USA
| |
Collapse
|
232
|
Andrew RL, Bernatchez L, Bonin A, Buerkle CA, Carstens BC, Emerson BC, Garant D, Giraud T, Kane NC, Rogers SM, Slate J, Smith H, Sork VL, Stone GN, Vines TH, Waits L, Widmer A, Rieseberg LH. A road map for molecular ecology. Mol Ecol 2013; 22:2605-26. [DOI: 10.1111/mec.12319] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 03/16/2013] [Indexed: 12/18/2022]
Affiliation(s)
- Rose L. Andrew
- Department of Botany; University of British Columbia; 3529-6270 University Blvd Vancouver BC V6T 1Z4 Canada
| | - Louis Bernatchez
- DInstitut de Biologie Intégrative et des Systémes; Département de Biologie; 1030, Avenue de la Médecine Université Laval; Québec QC G1V 0A6 Canada
| | - Aurélie Bonin
- Laboratoire d'Ecologie Alpine; CNRS UMR 5553 Université Joseph Fourier; BP 53, 38041 Grenoble Cedex 9 France
| | - C. Alex. Buerkle
- Department of Botany; University of Wyoming; 1000 E. University Ave. Laramie WY 82071 USA
| | - Bryan C. Carstens
- Department of Evolution, Ecology and Organismal Biology; 318 W. 12th Ave. The Ohio State University; Columbus OH 43210 USA
| | - Brent C. Emerson
- Island Ecology and Evolution Research Group; Instituto de Productos Naturales y Agrobiología (IPNA-CSIC) C/Astrofísico Francisco Sánchez 3 La Laguna Tenerife; Canary Islands 38206 Spain
| | - Dany Garant
- Département de Biologie; Université de Sherbrooke; Sherbrooke QC J1K 2R1 Canada
| | - Tatiana Giraud
- Laboratoire Ecologie, Systématique et Evolution; UMR 8079 CNRS-UPS-AgroParisTech, Bâtiment 360 Univ. Paris Sud; 91405 Orsay cedex France
| | - Nolan C. Kane
- Department of Botany; University of British Columbia; 3529-6270 University Blvd Vancouver BC V6T 1Z4 Canada
| | - Sean M. Rogers
- Department of Biological Sciences; University of Calgary; 2500 University Drive N.W., Calgary AB T2N 1N4 Canada
| | - Jon Slate
- Department of Animal and Plant Sciences; University of Sheffield; Sheffield S10 2TN UK
| | - Harry Smith
- 79 Melton Road Burton-on-the-Wolds Loughborough LE12 5TQ UK
| | - Victoria L. Sork
- Department of Ecology and Evolutionary Biology; University of California Los Angeles; 4139 Terasaki Life Sciences Building, 610 Charles E. Young Drive East Los Angeles CA 90095 USA
| | - Graham N. Stone
- Institute of Evolutionary Biology; University of Edinburgh; The King's Buildings, West Mains Road, Edinburgh EH9 3JT UK
| | - Timothy H. Vines
- Molecular Ecology Editorial Office; 6270 University Blvd Vancouver BC V6T 1Z4 Canada
| | - Lisette Waits
- Department of Fish and Wildlife Sciences; University of Idaho; 875 Perimeter Drive MS 1136 Moscow ID 83844 USA
| | - Alex Widmer
- ETH Zurich; Institute of Integrative Biology; Universitätstrasse 16 Zurich 8092 Switzerland
| | - Loren H. Rieseberg
- Department of Botany; University of British Columbia; 3529-6270 University Blvd Vancouver BC V6T 1Z4 Canada
- Department of Biology; Indiana University; 1001 E. 3 St., Bloomington IN 47405 USA
| |
Collapse
|
233
|
Arnold B, Corbett-Detig RB, Hartl D, Bomblies K. RADseq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling. Mol Ecol 2013; 22:3179-90. [DOI: 10.1111/mec.12276] [Citation(s) in RCA: 297] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 01/24/2013] [Accepted: 01/25/2013] [Indexed: 12/16/2022]
Affiliation(s)
- B. Arnold
- Department of Organismic and Evolutionary Biology; Harvard University; Cambridge MA 02138 USA
| | - R. B. Corbett-Detig
- Department of Organismic and Evolutionary Biology; Harvard University; Cambridge MA 02138 USA
| | - D. Hartl
- Department of Organismic and Evolutionary Biology; Harvard University; Cambridge MA 02138 USA
| | - K. Bomblies
- Department of Organismic and Evolutionary Biology; Harvard University; Cambridge MA 02138 USA
| |
Collapse
|
234
|
Jones JC, Fan S, Franchini P, Schartl M, Meyer A. The evolutionary history of Xiphophorus fish and their sexually selected sword: a genome-wide approach using restriction site-associated DNA sequencing. Mol Ecol 2013; 22:2986-3001. [PMID: 23551333 DOI: 10.1111/mec.12269] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2012] [Revised: 01/10/2013] [Accepted: 01/15/2013] [Indexed: 11/27/2022]
Abstract
Next-generation sequencing (NGS) techniques are now key tools in the detection of population genomic and gene expression differences in a large array of organisms. However, so far few studies have utilized such data for phylogenetic estimations. Here, we use NGS data obtained from genome-wide restriction site-associated DNA (RAD) (∼66000 SNPs) to estimate the phylogenetic relationships among all 26 species of swordtail and platyfish (genus Xiphophorus) from Central America. Past studies, both sequence and morphology-based, have differed in their inferences of the evolutionary relationships within this genus, particularly at the species-level and among monophyletic groupings. We show that using a large number of markers throughout the genome, we are able to infer the phylogenetic relationships with unparalleled resolution for this genus. The relationships among all three major clades and species within each of them are highly resolved and consistent under maximum likelihood, Bayesian inference and maximum parsimony. However, we also highlight the current cautions with this data type and analyses. This genus exhibits a particularly interesting evolutionary history where at least two species may have arisen through hybridization events. Here, we are able to infer the paternal lineages of these putative hybrid species. Using the RAD-marker-based tree we reconstruct the evolutionary history of the sexually selected sword trait and show that it may have been present in the common ancestor of the genus. Together our results highlight the outstanding capacity that RAD sequencing data has for resolving previously problematic phylogenetic relationships, particularly among relatively closely related species.
Collapse
Affiliation(s)
- Julia C Jones
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstrasße 10, 78457, Konstanz, Germany
| | | | | | | | | |
Collapse
|
235
|
Cariou M, Duret L, Charlat S. Is RAD-seq suitable for phylogenetic inference? An in silico assessment and optimization. Ecol Evol 2013; 3:846-52. [PMID: 23610629 PMCID: PMC3631399 DOI: 10.1002/ece3.512] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Revised: 01/10/2013] [Accepted: 01/17/2013] [Indexed: 02/03/2023] Open
Abstract
INFERRING PHYLOGENETIC RELATIONSHIPS BETWEEN CLOSELY RELATED TAXA CAN BE HINDERED BY THREE FACTORS: (1) the lack of informative molecular variation at short evolutionary timescale; (2) the lack of established markers in poorly studied taxa; and (3) the potential phylogenetic conflicts among different genomic regions due to incomplete lineage sorting or introgression. In this context, Restriction site Associated DNA sequencing (RAD-seq) seems promising as this technique can generate sequence data from numerous DNA fragments scattered throughout the genome, from a large number of samples, and without preliminary knowledge on the taxa under study. However, divergence beyond the within-species level will necessarily reduce the number of conserved and non-duplicated restriction sites, and therefore the number of loci usable for phylogenetic inference. Here, we assess the suitability of RAD-seq for phylogeny using a simulated experiment on the 12 Drosophila genomes, with divergence times ranging from 5 to 63 million years. These simulations show that RAD-seq allows the recovery of the known Drosophila phylogeny with strong statistical support, even for relatively ancient nodes. Notably, this conclusion is robust to the potentially confounding effects of sequencing errors, heterozygosity, and low coverage. We further show that clustering RAD-seq data using the BLASTN and SiLiX programs significantly improves the recovery of orthologous RAD loci compared with previously proposed approaches, especially for distantly related species. This study therefore validates the view that RAD sequencing is a powerful tool for phylogenetic inference.
Collapse
Affiliation(s)
- Marie Cariou
- Université de Lyon, Université Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive 43 boulevard du 11 novembre 1918, Villeurbanne, F-69622, France
| | | | | |
Collapse
|
236
|
Richards PM, Liu MM, Lowe N, Davey JW, Blaxter ML, Davison A. RAD-Seq derived markers flank the shell colour and banding loci of the Cepaea nemoralis supergene. Mol Ecol 2013; 22:3077-89. [PMID: 23496771 PMCID: PMC3712483 DOI: 10.1111/mec.12262] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Revised: 01/11/2013] [Accepted: 01/15/2013] [Indexed: 01/24/2023]
Abstract
Studies on the classic shell colour and banding polymorphism of the land snail Cepaea played a crucial role in establishing the importance of natural selection in maintaining morphological variation. Cepaea is also a pre-eminent model for ecological genetics because the outward colour and banding phenotype is entirely genetically determined, primarily by a 'supergene' of at least five loci. Unfortunately, progress in understanding the evolution and maintenance of the Cepaea polymorphism stalled, partly because of a lack of genetic markers. With a view to re-establish Cepaea as a prominent model of molecular ecology, we made six laboratory crosses of Cepaea nemoralis, five of which segregated for shell ground colour (C) and the presence or absence of bands (B). First, scoring of colour and banding in 323 individuals found no recombination between the C and B loci of the supergene. Second, using restriction site-associated DNA sequencing (RAD-Seq) of two parents and 22 offspring, we identified 44 anonymous markers putatively linked to the colour (C) and banding (B) loci. The genotype of eleven of the most promising RAD-Seq markers was independently validated in the same 22 offspring, then up to a further 146 offspring were genotyped. The closest RAD-Seq markers scored are within ~0.6 centimorgan (cM) of the C-B supergene linkage group, with the combined loci together forming a 35.8 cM linkage map of markers that flank both sides of the Cepaea C-B supergene.
Collapse
Affiliation(s)
- Paul M Richards
- Centre for Genetics and Genomics, School of Biology, University of Nottingham, Nottingham, NG7 2RD, UK
| | | | | | | | | | | |
Collapse
|
237
|
Reitzel AM, Herrera S, Layden MJ, Martindale MQ, Shank TM. Going where traditional markers have not gone before: utility of and promise for RAD sequencing in marine invertebrate phylogeography and population genomics. Mol Ecol 2013; 22:2953-70. [PMID: 23473066 DOI: 10.1111/mec.12228] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2012] [Accepted: 12/11/2012] [Indexed: 12/20/2022]
Abstract
Characterization of large numbers of single-nucleotide polymorphisms (SNPs) throughout a genome has the power to refine the understanding of population demographic history and to identify genomic regions under selection in natural populations. To this end, population genomic approaches that harness the power of next-generation sequencing to understand the ecology and evolution of marine invertebrates represent a boon to test long-standing questions in marine biology and conservation. We employed restriction-site-associated DNA sequencing (RAD-seq) to identify SNPs in natural populations of the sea anemone Nematostella vectensis, an emerging cnidarian model with a broad geographic range in estuarine habitats in North and South America, and portions of England. We identified hundreds of SNP-containing tags in thousands of RAD loci from 30 barcoded individuals inhabiting four locations from Nova Scotia to South Carolina. Population genomic analyses using high-confidence SNPs resulted in a highly-resolved phylogeography, a result not achieved in previous studies using traditional markers. Plots of locus-specific FST against heterozygosity suggest that a majority of polymorphic sites are neutral, with a smaller proportion suggesting evidence for balancing selection. Loci inferred to be under balancing selection were mapped to the genome, where 90% were located in gene bodies, indicating potential targets of selection. The results from analyses with and without a reference genome supported similar conclusions, further highlighting RAD-seq as a method that can be efficiently applied to species lacking existing genomic resources. We discuss the utility of RAD-seq approaches in burgeoning Nematostella research as well as in other cnidarian species, particularly corals and jellyfishes, to determine phylogeographic relationships of populations and identify regions of the genome undergoing selection.
Collapse
Affiliation(s)
- A M Reitzel
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA.
| | | | | | | | | |
Collapse
|
238
|
A New Method for Genome-wide Marker Development and Genotyping Holds Great Promise for Molecular Primatology. INT J PRIMATOL 2013. [DOI: 10.1007/s10764-013-9663-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
|
239
|
Yoder JB, Briskine R, Mudge J, Farmer A, Paape T, Steele K, Weiblen GD, Bharti AK, Zhou P, May GD, Young ND, Tiffin P. Phylogenetic signal variation in the genomes of Medicago (Fabaceae). Syst Biol 2013; 62:424-38. [PMID: 23417680 DOI: 10.1093/sysbio/syt009] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Genome-scale data offer the opportunity to clarify phylogenetic relationships that are difficult to resolve with few loci, but they can also identify genomic regions with evolutionary history distinct from that of the species history. We collected whole-genome sequence data from 29 taxa in the legume genus Medicago, then aligned these sequences to the Medicago truncatula reference genome to confidently identify 87 596 variable homologous sites. We used this data set to estimate phylogenetic relationships among Medicago species, to investigate the number of sites needed to provide robust phylogenetic estimates and to identify specific genomic regions supporting topologies in conflict with the genome-wide phylogeny. Our full genomic data set resolves relationships within the genus that were previously intractable. Subsampling the data reveals considerable variation in phylogenetic signal and power in smaller subsets of the data. Even when sampling 5000 sites, no random sample of the data supports a topology identical to that of the genome-wide phylogeny. Phylogenetic relationships estimated from 500-site sliding windows revealed genome regions supporting several alternative species relationships among recently diverged taxa, consistent with the expected effects of deep coalescence or introgression in the recent history of Medicago.
Collapse
Affiliation(s)
- Jeremy B Yoder
- Department of Plant Biology, University of Minnesota, Saint Paul MN 55108, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
240
|
McCormack JE, Hird SM, Zellmer AJ, Carstens BC, Brumfield RT. Applications of next-generation sequencing to phylogeography and phylogenetics. Mol Phylogenet Evol 2013; 66:526-38. [DOI: 10.1016/j.ympev.2011.12.007] [Citation(s) in RCA: 445] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Revised: 12/02/2011] [Accepted: 12/05/2011] [Indexed: 01/09/2023]
|
241
|
Allele identification for transcriptome-based population genomics in the invasive plant Centaurea solstitialis. G3-GENES GENOMES GENETICS 2013; 3:359-67. [PMID: 23390612 PMCID: PMC3564996 DOI: 10.1534/g3.112.003871] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Accepted: 12/19/2012] [Indexed: 01/09/2023]
Abstract
Transcriptome sequences are becoming more broadly available for multiple individuals of the same species, providing opportunities to derive population genomic information from these datasets. Using the 454 Life Science Genome Sequencer FLX and FLX-Titanium next-generation platforms, we generated 11−430 Mbp of sequence for normalized cDNA for 40 wild genotypes of the invasive plant Centaurea solstitialis, yellow starthistle, from across its worldwide distribution. We examined the impact of sequencing effort on transcriptome recovery and overlap among individuals. To do this, we developed two novel publicly available software pipelines: SnoWhite for read cleaning before assembly, and AllelePipe for clustering of loci and allele identification in assembled datasets with or without a reference genome. AllelePipe is designed specifically for cases in which read depth information is not appropriate or available to assist with disentangling closely related paralogs from allelic variation, as in transcriptome or previously assembled libraries. We find that modest applications of sequencing effort recover most of the novel sequences present in the transcriptome of this species, including single-copy loci and a representative distribution of functional groups. In contrast, the coverage of variable sites, observation of heterozygosity, and overlap among different libraries are all highly dependent on sequencing effort. Nevertheless, the information gained from overlapping regions was informative regarding coarse population structure and variation across our small number of population samples, providing the first genetic evidence in support of hypothesized invasion scenarios.
Collapse
|
242
|
Switchgrass genomic diversity, ploidy, and evolution: novel insights from a network-based SNP discovery protocol. PLoS Genet 2013; 9:e1003215. [PMID: 23349638 PMCID: PMC3547862 DOI: 10.1371/journal.pgen.1003215] [Citation(s) in RCA: 401] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Accepted: 11/19/2012] [Indexed: 01/01/2023] Open
Abstract
Switchgrass (Panicum virgatum L.) is a perennial grass that has been designated as an herbaceous model biofuel crop for the United States of America. To facilitate accelerated breeding programs of switchgrass, we developed both an association panel and linkage populations for genome-wide association study (GWAS) and genomic selection (GS). All of the 840 individuals were then genotyped using genotyping by sequencing (GBS), generating 350 GB of sequence in total. As a highly heterozygous polyploid (tetraploid and octoploid) species lacking a reference genome, switchgrass is highly intractable with earlier methodologies of single nucleotide polymorphism (SNP) discovery. To access the genetic diversity of species like switchgrass, we developed a SNP discovery pipeline based on a network approach called the Universal Network-Enabled Analysis Kit (UNEAK). Complexities that hinder single nucleotide polymorphism discovery, such as repeats, paralogs, and sequencing errors, are easily resolved with UNEAK. Here, 1.2 million putative SNPs were discovered in a diverse collection of primarily upland, northern-adapted switchgrass populations. Further analysis of this data set revealed the fundamentally diploid nature of tetraploid switchgrass. Taking advantage of the high conservation of genome structure between switchgrass and foxtail millet (Setaria italica (L.) P. Beauv.), two parent-specific, synteny-based, ultra high-density linkage maps containing a total of 88,217 SNPs were constructed. Also, our results showed clear patterns of isolation-by-distance and isolation-by-ploidy in natural populations of switchgrass. Phylogenetic analysis supported a general south-to-north migration path of switchgrass. In addition, this analysis suggested that upland tetraploid arose from upland octoploid. All together, this study provides unparalleled insights into the diversity, genomic complexity, population structure, phylogeny, phylogeography, ploidy, and evolutionary dynamics of switchgrass. Recent advances in sequencing technologies have enabled large-scale surveys of genetic diversity in model species with a wholly or partly sequenced reference genome. However, thousands of key species, which are essential for food, health, energy, and ecology, do not have reference genomes. To accelerate their breeding cycle via marker assisted selection, high-throughput genotyping is required for these valuable species, in spite of the absence of reference genomes. Based on genotyping by sequencing (GBS) technology, we developed a new single nucleotide polymorphism (SNP) discovery protocol, the Universal Network-Enabled Analysis Kit (UNEAK), which can be widely used in any species, regardless of genome complexity or the availability of a reference genome. Here we test this protocol on switchgrass, currently the prime energy crop species in the United States of America. In addition to the discovery of over a million SNPs and construction of high-density linkage maps, we provide novel insights into the genome complexity, ploidy, phylogeny, and evolution of switchgrass. This is only the beginning: we believe UNEAK offers the key to the exploration and exploitation of the genetic diversity of thousands of non-model species.
Collapse
|
243
|
Wall JD, Kim SK, Luca F, Carbone L, Mootnick AR, de Jong PJ, Di Rienzo A. Incomplete lineage sorting is common in extant gibbon genera. PLoS One 2013; 8:e53682. [PMID: 23341974 PMCID: PMC3544895 DOI: 10.1371/journal.pone.0053682] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Accepted: 12/04/2012] [Indexed: 11/25/2022] Open
Abstract
We sequenced reduced representation libraries by means of Illumina technology to generate over 1.5 Mb of orthologous sequence from a representative of each of the four extant gibbon genera (Nomascus, Hylobates, Symphalangus, and Hoolock). We used these data to assess the evolutionary relationships between the genera by evaluating the likelihoods of all possible bifurcating trees involving the four taxa. Our analyses provide weak support for a tree with Nomascus and Hylobates as sister taxa and with Hoolock and Symphalangus as sister taxa, though bootstrap resampling suggests that other phylogenetic scenarios are also possible. This uncertainty is due to short internal branch lengths and extensive incomplete lineage sorting across taxa. The true phylogenetic relationships among gibbon genera will likely require a more extensive whole-genome sequence analysis.
Collapse
Affiliation(s)
- Jeffrey D Wall
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America.
| | | | | | | | | | | | | |
Collapse
|
244
|
Corander J, Majander KK, Cheng L, Merilä J. High degree of cryptic population differentiation in the Baltic Sea herring Clupea harengus. Mol Ecol 2013; 22:2931-40. [PMID: 23294045 DOI: 10.1111/mec.12174] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Revised: 11/01/2012] [Accepted: 11/06/2012] [Indexed: 12/27/2022]
Abstract
Marine fish species are characterized by a low degree of population differentiation at putatively neutral marker genes. This has been traditionally attributed to ecological homogeneity and a lack of obvious dispersal barriers in marine habitats, as well as to the large (effective) population sizes of most marine fish species. The herring (Clupea harengus) is a case in point - the levels of population differentiation at neutral markers, even across vast geographic areas, are typically very low (FST ≈ 0.005). We used a RAD-sequencing approach to identify 5985 novel single-nucleotide polymorphism markers (SNPs) in herring and estimated genome-wide levels of divergence using pooled DNA samples between two Baltic Sea populations separated by 387 km. We found a total of 4756 divergent SNPs (79% of all SNPs) between the populations, of which 117 showed evidence of substantial divergence, corresponding to F(ST) = 0.128 (0.125, 0.131) after accounting for possible biases due to minor alleles and uneven DNA amplification over the pooled samples. This estimate - based on screening many genomic polymorphisms - suggests the existence of hitherto unrecognized levels of genetic differentiation in this commercially important species, challenging the view of genetic homogeneity in marine fish species, and in that of the Baltic Sea herring in particular.
Collapse
Affiliation(s)
- Jukka Corander
- Department of Mathematics and Statistics, University Helsinki, FI-00014, Helsinki, Finland
| | | | | | | |
Collapse
|
245
|
Abstract
The genomics era has opened up exciting possibilities in the field of conservation biology by enabling genomic analyses of threatened species that previously were limited to model organisms. Next-generation sequencing (NGS) and the collection of genome-wide data allow for more robust studies of the demographic history of populations and adaptive variation associated with fitness and local adaptation. Genomic analyses can also advance management efforts for threatened wild and captive populations by identifying loci contributing to inbreeding depression and disease susceptibility, and predicting fitness consequences of introgression. However, the development of genomic tools in wild species still carries multiple challenges, particularly those associated with computational and sampling constraints. This review provides an overview of the most significant applications of NGS and the implications and limitations of genomic studies in conservation.
Collapse
Affiliation(s)
- Cynthia C Steiner
- Institute for Conservation Research, San Diego Zoo Global, Escondido, California 92027; ; ;
| | | | | | | |
Collapse
|
246
|
Lu F, Lipka AE, Glaubitz J, Elshire R, Cherney JH, Casler MD, Buckler ES, Costich DE. Switchgrass genomic diversity, ploidy, and evolution: novel insights from a network-based SNP discovery protocol. PLoS Genet 2013. [PMID: 23349638 DOI: 10.1371/journalpgen1003215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2023] Open
Abstract
Switchgrass (Panicum virgatum L.) is a perennial grass that has been designated as an herbaceous model biofuel crop for the United States of America. To facilitate accelerated breeding programs of switchgrass, we developed both an association panel and linkage populations for genome-wide association study (GWAS) and genomic selection (GS). All of the 840 individuals were then genotyped using genotyping by sequencing (GBS), generating 350 GB of sequence in total. As a highly heterozygous polyploid (tetraploid and octoploid) species lacking a reference genome, switchgrass is highly intractable with earlier methodologies of single nucleotide polymorphism (SNP) discovery. To access the genetic diversity of species like switchgrass, we developed a SNP discovery pipeline based on a network approach called the Universal Network-Enabled Analysis Kit (UNEAK). Complexities that hinder single nucleotide polymorphism discovery, such as repeats, paralogs, and sequencing errors, are easily resolved with UNEAK. Here, 1.2 million putative SNPs were discovered in a diverse collection of primarily upland, northern-adapted switchgrass populations. Further analysis of this data set revealed the fundamentally diploid nature of tetraploid switchgrass. Taking advantage of the high conservation of genome structure between switchgrass and foxtail millet (Setaria italica (L.) P. Beauv.), two parent-specific, synteny-based, ultra high-density linkage maps containing a total of 88,217 SNPs were constructed. Also, our results showed clear patterns of isolation-by-distance and isolation-by-ploidy in natural populations of switchgrass. Phylogenetic analysis supported a general south-to-north migration path of switchgrass. In addition, this analysis suggested that upland tetraploid arose from upland octoploid. All together, this study provides unparalleled insights into the diversity, genomic complexity, population structure, phylogeny, phylogeography, ploidy, and evolutionary dynamics of switchgrass.
Collapse
Affiliation(s)
- Fei Lu
- Institute for Genomic Diversity, Cornell University, Ithaca, New York, USA
| | | | | | | | | | | | | | | |
Collapse
|
247
|
Effects of species biology on the historical demography of sharks and their implications for likely consequences of contemporary climate change. CONSERV GENET 2012. [DOI: 10.1007/s10592-012-0437-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
248
|
Schoville SD, Bonin A, François O, Lobreaux S, Melodelima C, Manel S. Adaptive Genetic Variation on the Landscape: Methods and Cases. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2012. [DOI: 10.1146/annurev-ecolsys-110411-160248] [Citation(s) in RCA: 217] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Sean D. Schoville
- Laboratoire TIMC-IMAG, UMR-CNRS 5525, Université Joseph Fourier, 38041 Grenoble, France; ,
- Laboratoire d'Ecologie Alpine, UMR-CNRS 5553, Université Joseph Fourier, 38041 Grenoble, France; , , ,
| | - Aurélie Bonin
- Laboratoire d'Ecologie Alpine, UMR-CNRS 5553, Université Joseph Fourier, 38041 Grenoble, France; , , ,
| | - Olivier François
- Laboratoire TIMC-IMAG, UMR-CNRS 5525, Université Joseph Fourier, 38041 Grenoble, France; ,
| | - Stéphane Lobreaux
- Laboratoire d'Ecologie Alpine, UMR-CNRS 5553, Université Joseph Fourier, 38041 Grenoble, France; , , ,
| | - Christelle Melodelima
- Laboratoire d'Ecologie Alpine, UMR-CNRS 5553, Université Joseph Fourier, 38041 Grenoble, France; , , ,
| | - Stéphanie Manel
- Laboratoire d'Ecologie Alpine, UMR-CNRS 5553, Université Joseph Fourier, 38041 Grenoble, France; , , ,
- Laboratoire Population Environnement et Développement, UMR-IRD 151, Université Aix-Marseille, 13331 Marseille, France
| |
Collapse
|
249
|
Takahashi T, Sota T, Hori M. Genetic basis of male colour dimorphism in a Lake Tanganyika cichlid fish. Mol Ecol 2012; 22:3049-60. [PMID: 23176589 DOI: 10.1111/mec.12120] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Revised: 10/06/2012] [Accepted: 10/10/2012] [Indexed: 12/24/2022]
Abstract
Phenotypic polymorphisms can be applied to study the micro-evolutionary forces that maintain genetic variation and can mediate speciation, but it can be difficult to determine the genetic basis of polymorphisms. Recently, restriction-site-associated DNA (RAD) sequencing has become popular, which can easily produce multiple single nucleotide polymorphisms from whole genomes. Here, we combined RAD sequencing, allele-specific PCR and Sanger sequencing to determine the genetic basis underlying male colour dimorphism of a Lake Tanganyika cichlid fish, Cyprichromis leptosoma. Our analyses using both a cross-family (two parents and 12 F2 males) and 64 wild individuals do not contradict a hypothesis that two alleles of one-locus control male colour dimorphism. Also, the locus may be located on a genome region that experiences reduced levels of recombination. Although more analyses will be needed to conclude these findings, this study is the first to suggest the genetic basis of a colour polymorphism using RAD sequencing.
Collapse
Affiliation(s)
- T Takahashi
- Laboratory of Animal Ecology, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake, Sakyo, Kyoto, 606-8502, Japan.
| | | | | |
Collapse
|
250
|
Genome sequence of dwarf birch (Betula nana) and cross-species RAD markers. Mol Ecol 2012; 22:3098-111. [DOI: 10.1111/mec.12131] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2012] [Revised: 10/12/2012] [Accepted: 10/17/2012] [Indexed: 12/17/2022]
|