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Wang X, Ma Z, Gao L, Yuan L, Ye Z, Cui F, Guo X, Liu W, Yan X. Genome-wide survey reveals the genetic background of Xinjiang Brown cattle in China. Front Genet 2024; 14:1348329. [PMID: 38283146 PMCID: PMC10811208 DOI: 10.3389/fgene.2023.1348329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 12/28/2023] [Indexed: 01/30/2024] Open
Abstract
Introduction: Xinjiang Brown cattle are a famous dual-purpose (dairy-beef) cultivated breed in China that occupy a pivotal position within the cattle breeding industry in Xinjiang, China. However, little information is available on the genetic background of this breed. To fill this research gap, we conducted a whole-genome screen using specific-locus amplified fragment sequencing to examine the genetic structure and diversity of 130 Xinjiang Brown cattle-grazing type (XBG, traditional type) cattle. Methods: A subsequent joint analysis incorporating two ancestral breeds, specifically 19 Brown Swiss (BS) foreign and nine Kazakh (KZ) Chinese cattle, as well as 20 Xinjiang Brown cattle-housing type (XBH) cattle, was used to explore the genetic background of the Xinjiang Brown cattle. Results: The results showed that, after nearly a century of crossbreeding, XBG cattle formed a single population with a stable genetic performance. The genetic structure, genetic diversity, and selection signature analysis of the two ancestral types showed highly different results compared to that of XBH cattle. Local ancestry inference showed that the average proportions of XGB cattle within the BS and KZ cattle lineages were 37.22% and 62.78%, respectively, whereas the average proportions of XBH cattle within the BS and KZ cattle lineages were 95.14% and 4.86%, respectively. Thus, XGB cattle are more representative of all Xinjiang Brown cattle, in line with their breeding history, which involves crossbreeding. Two complementary approaches, fixation index and mean nucleotide diversity, were used to detect selection signals in the four aforementioned cattle breeds. Finally, the analysis of 26 candidate genes in Xinjiang Brown cattle revealed significant enrichment in 19 Gene Ontology terms, and seven candidate genes were enriched in three pathways related to disease resistance (CDH4, SIRPB1, and SIRPα) and the endocrine system (ADCY5, ABCC8, KCNJ11, and KCNMA1). Finally, development of the core SNPs in XBG cattle yielded 8,379 loci. Conclusion: The results of this study detail the evolutionary process of crossbreeding in Xinjiang Brown cattle and provide guidance for selecting and breeding new strains of this species.
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Affiliation(s)
- Xiao Wang
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
- Yili Vocational and Technical College, Yili, China
| | - Zhen Ma
- Institute of Animal Science, Xinjiang Academy of Animal Science, Urumqi, China
| | - Liang Gao
- Yili Vocational and Technical College, Yili, China
| | - Lixin Yuan
- Institute of Animal Science, Xinjiang Academy of Animal Science, Urumqi, China
| | - Zhibing Ye
- Institute of Animal Science, Xinjiang Academy of Animal Science, Urumqi, China
| | - Fanrong Cui
- Institute of Animal Science, Xinjiang Academy of Animal Science, Urumqi, China
| | - Xiaoping Guo
- Yili Kazakh Autonomous Prefecture General Animal Husbandry Station, Yili, China
| | - Wujun Liu
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Xiangmin Yan
- Institute of Animal Science, Xinjiang Academy of Animal Science, Urumqi, China
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2
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Du K, Lu Y, Garcia-Olazabal M, Walter RB, Warren WC, Dodge T, Schumer M, Park H, Meyer A, Schartl M. Phylogenomics analyses of all species of Swordtails (Genus Xiphophorus ) highlights hybridization precedes speciation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.30.573732. [PMID: 38260540 PMCID: PMC10802237 DOI: 10.1101/2023.12.30.573732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Hybridization has been recognized as an important driving force for evolution, however studies of the genetic consequence and its cause are still lagging behind in vertebrates due to the lack of appropriate experimental systems. Fish of the central American genus Xiphophorus were proposed to have evolved with multiple ancient and ongoing hybridization events, and served as a valuable research model in evolutionary biology and in biomedical research on human disease for more than a century. Here, we provide the complete genome resource and its annotation of all 26 Xiphophorus species. On this dataset we resolved the so far conflicting phylogeny. Through comparative genomic analyses we investigated the molecular evolution of genes related to melanoma, for a main sexually selected trait and for the genetic control of puberty timing, which are predicted to be involved in pre-and postzygotic isolation and thus to influence the probability of interspecific hybridization in Xiphophorus . We demonstrate dramatic size-variation of some gene families across species, despite the reticulate evolution and short divergence time. Finally, we clarify the hybridization history in the genus Xiphophorus genus, settle the long dispute on the hybridization origin of two Southern swordtails, highlight hybridizations precedes speciation, and reveal the distribution of hybridization ancestry remaining in the fused genome.
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3
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Rahi ML, Mather PB, de Bello Cioffi M, Ezaz T, Hurwood DA. Genomic Basis of Freshwater Adaptation in the Palaemonid Prawn Genus Macrobrachium: Convergent Evolution Following Multiple Independent Colonization Events. J Mol Evol 2023; 91:976-989. [PMID: 38010517 DOI: 10.1007/s00239-023-10149-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 11/14/2023] [Indexed: 11/29/2023]
Abstract
Adaptation to different salinity environments can enhance morphological and genomic divergence between related aquatic taxa. Species of prawns in the genus Macrobrachium naturally inhabit different osmotic niches and possess distinctive lifecycle traits associated with salinity tolerance. This study was conducted to investigate the patterns of adaptive genomic divergence during freshwater colonization in 34 Macrobrachium species collected from four continents; Australia, Asia, North and South America. Genotyping-by-sequencing (GBS) technique identified 5018 loci containing 82,636 single nucleotide polymorphisms (SNPs) that were used to reconstruct a phylogenomic tree. An additional phylogeny was reconstructed based on 43 candidate genes, previously identified as being potentially associated with freshwater adaptation. Comparison of the two phylogenetic trees revealed contrasting topologies. The GBS tree indicated multiple independent continent-specific invasions into freshwater by Macrobrachium lineages following common marine ancestry, as species with abbreviated larval development (ALD), i.e., species having a full freshwater life history, appeared reciprocally monophyletic within each continent. In contrast, the candidate gene tree showed convergent evolution for all ALD species worldwide, forming a single, well-supported clade. This latter pattern is likely the result of common evolutionary pressures selecting key mutations favored in continental freshwater habitats Results suggest that following multiple independent invasions into continental freshwaters at different evolutionary timescales, Macrobrachium taxa experienced adaptive genomic divergence, and in particular, convergence in the same genomic regions with parallel shifts in specific conserved phenotypic traits, such as evolution of larger eggs with abbreviated larval developmental.
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Affiliation(s)
- Md Lifat Rahi
- Fisheries and Marine Resource Technology Discipline, Khulna University, Khulna, Bangladesh.
| | - Peter B Mather
- Faculty of Science, Queensland University of Technology (QUT), Brisbane, QLD, 4001, Australia
| | - Marcelo de Bello Cioffi
- Department of Genetics and Evolution, Federal University of Sao Carlos, São Carlos, SP, Brazil
| | - Tariq Ezaz
- Institute for Applied Ecology (IAE), University of Canberra (UC), Canberra, ACT, 2617, Australia
| | - David A Hurwood
- Faculty of Science, Queensland University of Technology (QUT), Brisbane, QLD, 4001, Australia
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4
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Martins AB, Valença-Montenegro MM, Lima MGM, Lynch JW, Svoboda WK, Silva-Júnior JDSE, Röhe F, Boubli JP, Fiore AD. A New Assessment of Robust Capuchin Monkey ( Sapajus) Evolutionary History Using Genome-Wide SNP Marker Data and a Bayesian Approach to Species Delimitation. Genes (Basel) 2023; 14:genes14050970. [PMID: 37239330 DOI: 10.3390/genes14050970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/11/2023] [Accepted: 04/12/2023] [Indexed: 05/28/2023] Open
Abstract
Robust capuchin monkeys, Sapajus genus, are among the most phenotypically diverse and widespread groups of primates in South America, with one of the most confusing and often shifting taxonomies. We used a ddRADseq approach to generate genome-wide SNP markers for 171 individuals from all putative extant species of Sapajus to access their evolutionary history. Using maximum likelihood, multispecies coalescent phylogenetic inference, and a Bayes Factor method to test for alternative hypotheses of species delimitation, we inferred the phylogenetic history of the Sapajus radiation, evaluating the number of discrete species supported. Our results support the recognition of three species from the Atlantic Forest south of the São Francisco River, with these species being the first splits in the robust capuchin radiation. Our results were congruent in recovering the Pantanal and Amazonian Sapajus as structured into three monophyletic clades, though new morphological assessments are necessary, as the Amazonian clades do not agree with previous morphology-based taxonomic distributions. Phylogenetic reconstructions for Sapajus occurring in the Cerrado, Caatinga, and northeastern Atlantic Forest were less congruent with morphology-based phylogenetic reconstructions, as the bearded capuchin was recovered as a paraphyletic clade, with samples from the Caatinga biome being either a monophyletic clade or nested with the blond capuchin monkey.
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Affiliation(s)
- Amely Branquinho Martins
- Centro Nacional de Pesquisa e Conservação de Primatas Brasileiros, Instituto Chico Mendes de Conservação da Biodiversidade, Cabedelo 58310-000, PB, Brazil
- Primate Molecular Ecology and Evolution Laboratory, Department of Anthropology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Mônica Mafra Valença-Montenegro
- Centro Nacional de Pesquisa e Conservação de Primatas Brasileiros, Instituto Chico Mendes de Conservação da Biodiversidade, Cabedelo 58310-000, PB, Brazil
| | - Marcela Guimarães Moreira Lima
- Laboratório de Biogeografia da Conservação e Macroecologia, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66077-530, PA, Brazil
| | - Jessica W Lynch
- Institute for Society and Genetics, Department of Anthropology, University of California-Los Angeles, Los Angeles, CA 90095, USA
| | - Walfrido Kühl Svoboda
- Instituto Latino-Americano de Ciências da Vida e da Natureza, Centro Interdisciplinar de Ciências da Vida, Universidade Federal da Integração Latino-Americana, Foz do Iguaçu 85870-650, PR, Brazil
| | - José de Sousa E Silva-Júnior
- Museu Paraense Emílio Goeldi, Ministério da Ciência, Tecnologia, Inovações e Comunicações, Coordenação de Zoologia, Campus de Pesquisa, Setor de Mastozoologia, Belém 66077-830, PA, Brazil
| | - Fábio Röhe
- Laboratório de Evolução e Genética Animal, Universidade Federal do Amazonas, Manaus 69067-005, AM, Brazil
| | - Jean Philippe Boubli
- School of Science, Engineering and the Environment, University of Salford, Salford M5 4WT, UK
| | - Anthony Di Fiore
- Primate Molecular Ecology and Evolution Laboratory, Department of Anthropology, The University of Texas at Austin, Austin, TX 78712, USA
- Tiputini Biodiversity Station, Universidad San Francisco de Quito, Quito 170901, Ecuador
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5
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Zeng Q, Sun Y, Zhong H, Yang C, Qin Q, Gu Q. Population Genomic Evidence for the Diversification of Bellamya aeruginosa in Different River Systems in China. BIOLOGY 2022; 12:biology12010029. [PMID: 36671722 PMCID: PMC9855799 DOI: 10.3390/biology12010029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 12/18/2022] [Accepted: 12/20/2022] [Indexed: 12/28/2022]
Abstract
Clarifying the genetic structure can facilitate the understanding of a species evolution history. It is crucial for the management of germplasm resources and providing useful guidance for effective selective breeding. Bellamya is an economically and ecologically important freshwater snail for fish, birds and even humans. Population genetic structures of the Bellamya species, however, were unknown in previous studies. Population genomics approaches with tens to hundreds of thousands of single nucleotide polymorphisms (SNPs) make it possible to detect previously unidentified structures. The population genomic study of seven populations of B. aeruginosa across three river systems (Yellow River, Yangtze River and Pearl River) in China was conducted by SLAF-seq. SLAF-seq obtained a total of 4737 polymorphisms SLAF-tags and 25,999 high-consistency genome-wide SNPs. The population genetic structure showed a clear division among populations from the Yellow River basin (YH and WL) and the Pearl River basin (QSH and LB), as well as population YC from the Yangtze River basin using the SNPs data. However, there existed no distinct population structure using the mitochondrial DNA (mtDNA). The anthropogenic translocation from the Yangtze River basin to the Pearl River basin and the passive dispersion from the Yangtze River basin to the Yellow River basin by flooding have weakened the phylogeographic pattern of B. aeruginosa. The divergence of B. aeruginosa in the three river systems suggests that the anthropogenic dispersal for aquaculture and breeding requires serious consideration of the population structure for the preservation of genetic diversity and effective utilization of germplasm resources.
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6
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Wright JJ, Bruce SA, Sinopoli DA, Palumbo JR, Stewart DJ. Phylogenomic analysis of the bowfin (Amia calva) reveals unrecognized species diversity in a living fossil lineage. Sci Rep 2022; 12:16514. [PMID: 36192509 PMCID: PMC9529906 DOI: 10.1038/s41598-022-20875-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 09/20/2022] [Indexed: 11/24/2022] Open
Abstract
The Bowfin (Amia calva), as currently recognized, represents the sole living member of the family Amiidae, which dates back to approximately 150 Ma. Prior to 1896, 13 species of extant Bowfins had been described, but these were all placed into a single species with no rationale or analysis given. This situation has persisted until the present day, with little attention given to re-evaluation of those previously described nominal forms. Here, we present a phylogenomic analysis based on over 21,000 single nucleotide polymorphisms (SNPs) from 94 individuals that unambiguously demonstrates the presence of at least two independent evolutionary lineages within extant Amia populations that merit species-level standing, as well as the possibility of two more. These findings not only expand the recognizable species diversity in an iconic, ancient lineage, but also demonstrate the utility of such methods in addressing previously intractable questions of molecular systematics and phylogeography in slowly evolving groups of ancient fishes.
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Affiliation(s)
- Jeremy J Wright
- Research & Collections, New York State Museum, 3140 Cultural Education Center, Albany, NY, USA.
| | - Spencer A Bruce
- Department of Information Technology Services, University at Albany-State University of New York, Albany, NY, USA
| | - Daniel A Sinopoli
- Department of Biological Sciences, Museum of Natural Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Jay R Palumbo
- Department of Environmental Science & Ecology, State University of New York at Brockport, Brockport, NY, USA
| | - Donald J Stewart
- Department of Environmental Biology, State University of New York College of Environmental Science and Forestry, Syracuse, NY, USA.
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7
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Chen Z, He Y, Iqbal Y, Shi Y, Huang H, Yi Z. Investigation of genetic relationships within three Miscanthus species using SNP markers identified with SLAF-seq. BMC Genomics 2022; 23:43. [PMID: 35012465 PMCID: PMC8751252 DOI: 10.1186/s12864-021-08277-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 12/22/2021] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Miscanthus, which is a leading dedicated-energy grass in Europe and in parts of Asia, is expected to play a key role in the development of the future bioeconomy. However, due to its complex genetic background, it is difficult to investigate phylogenetic relationships in this genus. Here, we investigated 50 Miscanthus germplasms: 1 female parent (M. lutarioriparius), 30 candidate male parents (M. lutarioriparius, M. sinensis, and M. sacchariflorus), and 19 offspring. We used high-throughput Specific-Locus Amplified Fragment sequencing (SLAF-seq) to identify informative single nucleotide polymorphisms (SNPs) in all germplasms. RESULTS We identified 257,889 SLAF tags, of which 87,162 were polymorphic. Each tag was 264-364 bp long. The obtained 724,773 population SNPs were used to investigate genetic relationships within three species of Miscanthus. We constructed a phylogenetic tree of the 50 germplasms using the obtained SNPs and grouped them into two clades: one clade comprised of M. sinensis alone and the other one included the offspring, M. lutarioriparius, and M. sacchariflorus. Genetic cluster analysis had revealed that M. lutarioriparius germplasm C3 was the most likely male parent of the offspring. CONCLUSIONS As a high-throughput sequencing method, SLAF-seq can be used to identify informative SNPs in Miscanthus germplasms and to rapidly characterize genetic relationships within this genus. Our results will support the development of breeding programs with the focus on utilizing Miscanthus cultivars with elite biomass- or fiber-production potential for the developing bioeconomy.
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Affiliation(s)
- Zhiyong Chen
- College of Bioscience & Biotechnology, Hunan Agricultural University, Changsha, 410128, PR China. .,Hunan Engineering Laboratory of Miscanthus Ecological Applications, Hunan Agricultural University, Changsha, 410128, PR China.
| | - Yancen He
- College of Bioscience & Biotechnology, Hunan Agricultural University, Changsha, 410128, PR China.,Hunan Engineering Laboratory of Miscanthus Ecological Applications, Hunan Agricultural University, Changsha, 410128, PR China
| | - Yasir Iqbal
- College of Bioscience & Biotechnology, Hunan Agricultural University, Changsha, 410128, PR China.,Hunan Engineering Laboratory of Miscanthus Ecological Applications, Hunan Agricultural University, Changsha, 410128, PR China
| | - Yanlan Shi
- College of Bioscience & Biotechnology, Hunan Agricultural University, Changsha, 410128, PR China.,Hunan Engineering Laboratory of Miscanthus Ecological Applications, Hunan Agricultural University, Changsha, 410128, PR China
| | - Hongmei Huang
- College of Bioscience & Biotechnology, Hunan Agricultural University, Changsha, 410128, PR China. .,Hunan Engineering Laboratory of Miscanthus Ecological Applications, Hunan Agricultural University, Changsha, 410128, PR China.
| | - Zili Yi
- College of Bioscience & Biotechnology, Hunan Agricultural University, Changsha, 410128, PR China. .,Hunan Engineering Laboratory of Miscanthus Ecological Applications, Hunan Agricultural University, Changsha, 410128, PR China.
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8
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Říčan O, Říčanová Š, Almirón A, Casciotta J, Piálek L. Parallel evolution of a new sympatric species pair of
Crenicichla
(Teleostei: Cichlidae) from Misiones, Argentina with a review of biogeography and mitonuclear discordance in the
C. mandelburgeri
species complex. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12566] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Oldřich Říčan
- Faculty of Science Department of Zoology University of South Bohemia České Budějovice Czech Republic
| | - Štěpánka Říčanová
- Faculty of Science Department of Zoology University of South Bohemia České Budějovice Czech Republic
| | - Adriana Almirón
- Facultad de Ciencias Naturales y Museo División Zoología Vertebrados UNLP La Plata Argentina
| | - Jorge Casciotta
- Facultad de Ciencias Naturales y Museo División Zoología Vertebrados UNLP La Plata Argentina
- CIC, Comisión de Investigaciones Científicas de la Provincia de Buenos Aires Buenos Aires Argentina
| | - Lubomír Piálek
- Faculty of Science Department of Zoology University of South Bohemia České Budějovice Czech Republic
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9
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Unravelling hybridization in Phytophthora using phylogenomics and genome size estimation. IMA Fungus 2021; 12:16. [PMID: 34193315 PMCID: PMC8246709 DOI: 10.1186/s43008-021-00068-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 05/23/2021] [Indexed: 02/06/2023] Open
Abstract
The genus Phytophthora comprises many economically and ecologically important plant pathogens. Hybrid species have previously been identified in at least six of the 12 phylogenetic clades. These hybrids can potentially infect a wider host range and display enhanced vigour compared to their progenitors. Phytophthora hybrids therefore pose a serious threat to agriculture as well as to natural ecosystems. Early and correct identification of hybrids is therefore essential for adequate plant protection but this is hampered by the limitations of morphological and traditional molecular methods. Identification of hybrids is also important in evolutionary studies as the positioning of hybrids in a phylogenetic tree can lead to suboptimal topologies. To improve the identification of hybrids we have combined genotyping-by-sequencing (GBS) and genome size estimation on a genus-wide collection of 614 Phytophthora isolates. Analyses based on locus- and allele counts and especially on the combination of species-specific loci and genome size estimations allowed us to confirm and characterize 27 previously described hybrid species and discover 16 new hybrid species. Our method was also valuable for species identification at an unprecedented resolution and further allowed correct naming of misidentified isolates. We used both a concatenation- and a coalescent-based phylogenomic method to construct a reliable phylogeny using the GBS data of 140 non-hybrid Phytophthora isolates. Hybrid species were subsequently connected to their progenitors in this phylogenetic tree. In this study we demonstrate the application of two validated techniques (GBS and flow cytometry) for relatively low cost but high resolution identification of hybrids and their phylogenetic relations.
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10
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Genome-wide SNPs redefines species boundaries and conservation units in the freshwater mussel genus Cyprogenia of North America. Sci Rep 2021; 11:10752. [PMID: 34031525 PMCID: PMC8144384 DOI: 10.1038/s41598-021-90325-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 05/10/2021] [Indexed: 11/08/2022] Open
Abstract
Detailed information on species delineation and population genetic structure is a prerequisite for designing effective restoration and conservation strategies for imperiled organisms. Phylogenomic and population genomic analyses based on genome-wide double digest restriction-site associated DNA sequencing (ddRAD-Seq) data has identified three allopatric lineages in the North American freshwater mussel genus Cyprogenia. Cyprogenia stegaria is restricted to the Eastern Highlands and displays little genetic structuring within this region. However, two allopatric lineages of C. aberti in the Ozark and Ouachita highlands exhibit substantial levels (mean uncorrected FST = 0.368) of genetic differentiation and each warrants recognition as a distinct evolutionary lineage. Lineages of Cyprogenia in the Ouachita and Ozark highlands are further subdivided reflecting structuring at the level of river systems. Species tree inference and species delimitation in a Bayesian framework using single nucleotide polymorphisms (SNP) data supported results from phylogenetic analyses, and supports three species of Cyprogenia over the currently recognized two species. A comparison of SNPs generated from both destructively and non-destructively collected samples revealed no significant difference in the SNP error rate, quality and amount of ddRAD sequence reads, indicating that nondestructive or trace samples can be effectively utilized to generate SNP data for organisms for which destructive sampling is not permitted.
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11
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Safian D, Wiegertjes GF, Pollux BJA. The Fish Family Poeciliidae as a Model to Study the Evolution and Diversification of Regenerative Capacity in Vertebrates. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.613157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The capacity of regenerating a new structure after losing an old one is a major challenge in the animal kingdom. Fish have emerged as an interesting model to study regeneration due to their high and diverse regenerative capacity. To date, most efforts have focused on revealing the mechanisms underlying fin regeneration, but information on why and how this capacity evolves remains incomplete. Here, we propose the livebearing fish family Poeciliidae as a promising new model system to study the evolution of fin regeneration. First, we review the current state of knowledge on the evolution of regeneration in the animal kingdom, with a special emphasis on fish fins. Second, we summarize recent advances in our understanding of the mechanisms behind fin regeneration in fish. Third, we discuss potential evolutionary pressures that may modulate the regenerative capacity of fish fins and propose three new theories for how natural and sexual selection can lead to the evolution of fin regeneration: (1) signaling-driven fin regeneration, (2) predation-driven fin regeneration, and (3) matrotrophy-suppressed fin regeneration. Finally, we argue that fish from the family Poeciliidae are an excellent model system to test these theories, because they comprise of a large variety of species in a well-defined phylogenetic framework that inhabit very different environments and display remarkable variation in reproductive traits, allowing for comparative studies of fin regeneration among closely related species, among populations within species or among individuals within populations. This new model system has the potential to shed new light on the underlying genetic and molecular mechanisms driving the evolution and diversification of regeneration in vertebrates.
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12
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Powell DL, Payne C, Banerjee SM, Keegan M, Bashkirova E, Cui R, Andolfatto P, Rosenthal GG, Schumer M. The Genetic Architecture of Variation in the Sexually Selected Sword Ornament and Its Evolution in Hybrid Populations. Curr Biol 2021; 31:923-935.e11. [PMID: 33513352 DOI: 10.1016/j.cub.2020.12.049] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 10/27/2020] [Accepted: 12/25/2020] [Indexed: 10/22/2022]
Abstract
Biologists since Darwin have been fascinated by the evolution of sexually selected ornaments, particularly those that reduce viability. Uncovering the genetic architecture of these traits is key to understanding how they evolve and are maintained. Here, we investigate the genetic architecture and evolutionary loss of a sexually selected ornament, the "sword" fin extension that characterizes many species of swordtail fish (Xiphophorus). Using sworded and swordless sister species of Xiphophorus, we generated a mapping population and show that the sword ornament is polygenic-with ancestry across the genome explaining substantial variation in the trait. After accounting for the impacts of genome-wide ancestry, we identify one major-effect quantitative trait locus (QTL) that explains ~5% of the overall variation in the trait. Using a series of approaches, we narrow this large QTL interval to several likely candidate genes, including genes involved in fin regeneration and growth. Furthermore, we find evidence of selection on ancestry at one of these candidates in four natural hybrid populations, consistent with selection against the sword in these populations.
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Affiliation(s)
- Daniel L Powell
- Department of Biology, Stanford University, 327 Campus Drive, Stanford, CA 94305, USA; Centro de Investigaciones Científicas de las Huastecas "Aguazarca," A.C., 16 de Septiembre, 392 Barrio Aguazarca, Calnali, Hidalgo 43240, México; Department of Biology, Texas A&M University, 3258 TAMU, College Station, TX 77843, USA.
| | - Cheyenne Payne
- Department of Biology, Stanford University, 327 Campus Drive, Stanford, CA 94305, USA; Centro de Investigaciones Científicas de las Huastecas "Aguazarca," A.C., 16 de Septiembre, 392 Barrio Aguazarca, Calnali, Hidalgo 43240, México
| | - Shreya M Banerjee
- Department of Biology, Stanford University, 327 Campus Drive, Stanford, CA 94305, USA; Centro de Investigaciones Científicas de las Huastecas "Aguazarca," A.C., 16 de Septiembre, 392 Barrio Aguazarca, Calnali, Hidalgo 43240, México
| | - Mackenzie Keegan
- Department of Biology, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA
| | - Elizaveta Bashkirova
- Department of Biochemistry and Molecular Biophysics, Columbia University, 701 West 168th Street, New York, NY 10032, USA; Integrated Program in Cellular, Molecular and Biomedical Studies, Columbia University Irving Medical Center, 622 West 168th Street, New York, NY 10032, USA
| | - Rongfeng Cui
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca," A.C., 16 de Septiembre, 392 Barrio Aguazarca, Calnali, Hidalgo 43240, México; Department of Biology, Texas A&M University, 3258 TAMU, College Station, TX 77843, USA; Max Planck Institute for the Biology of Aging, Postfach 41 06 23, 50931 Cologne, Germany; School of Ecology, Sun Yat-sen University, 135 Xingang West Road, Binjiang Road, Haizhu District, Guangdong Province, China
| | - Peter Andolfatto
- Department of Biological Sciences, Columbia University, 1212 Amsterdam Avenue, New York, NY 10027, USA
| | - Gil G Rosenthal
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca," A.C., 16 de Septiembre, 392 Barrio Aguazarca, Calnali, Hidalgo 43240, México; Department of Biology, Texas A&M University, 3258 TAMU, College Station, TX 77843, USA
| | - Molly Schumer
- Department of Biology, Stanford University, 327 Campus Drive, Stanford, CA 94305, USA; Centro de Investigaciones Científicas de las Huastecas "Aguazarca," A.C., 16 de Septiembre, 392 Barrio Aguazarca, Calnali, Hidalgo 43240, México; Howard Hughes Medical Institute, 327 Campus Drive, Stanford, CA 94305, USA.
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13
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Schartl M, Kneitz S, Ormanns J, Schmidt C, Anderson JL, Amores A, Catchen J, Wilson C, Geiger D, Du K, Garcia-Olazábal M, Sudaram S, Winkler C, Hedrich R, Warren WC, Walter R, Meyer A, Postlethwait JH. The Developmental and Genetic Architecture of the Sexually Selected Male Ornament of Swordtails. Curr Biol 2021; 31:911-922.e4. [PMID: 33275891 PMCID: PMC8580132 DOI: 10.1016/j.cub.2020.11.028] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/12/2020] [Accepted: 11/11/2020] [Indexed: 12/21/2022]
Abstract
Sexual selection results in sex-specific characters like the conspicuously pigmented extension of the ventral tip of the caudal fin-the "sword"-in males of several species of Xiphophorus fishes. To uncover the genetic architecture underlying sword formation and to identify genes that are associated with its development, we characterized the sword transcriptional profile and combined it with genetic mapping approaches. Results showed that the male ornament of swordtails develops from a sexually non-dimorphic prepattern of transcription factors in the caudal fin. Among genes that constitute the exclusive sword transcriptome and are located in the genomic region associated with this trait we identify the potassium channel, Kcnh8, as a sword development gene. In addition to its neural function kcnh8 performs a known role in fin growth. These findings indicate that during evolution of swordtails a brain gene has been co-opted for an additional novel function in establishing a male ornament.
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Affiliation(s)
- Manfred Schartl
- Developmental Biochemistry, Biocenter, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany; The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA.
| | - Susanne Kneitz
- Biochemistry and Cell Biology, Biocenter, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany
| | - Jenny Ormanns
- Biochemistry and Cell Biology, Biocenter, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany
| | - Cornelia Schmidt
- Biochemistry and Cell Biology, Biocenter, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany
| | - Jennifer L Anderson
- Systematic Biology, Department of Organismal Biology, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden
| | - Angel Amores
- Institute of Neuroscience, University of Oregon, Eugene, OR 97401, USA
| | - Julian Catchen
- Department of Animal Biology, University of Illinois, Urbana, IL 6812, USA
| | - Catherine Wilson
- Institute of Neuroscience, University of Oregon, Eugene, OR 97401, USA
| | - Dietmar Geiger
- Julius-von-Sachs-Institute for Biosciences, Molecular Plant Physiology and Biophysics, Biocenter, University Würzburg, Julius-von-Sachs-Platz 2, 97082 Würzburg, Germany
| | - Kang Du
- Developmental Biochemistry, Biocenter, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany; The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
| | | | - Sudha Sudaram
- Department of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Christoph Winkler
- Department of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Rainer Hedrich
- Julius-von-Sachs-Institute for Biosciences, Molecular Plant Physiology and Biophysics, Biocenter, University Würzburg, Julius-von-Sachs-Platz 2, 97082 Würzburg, Germany
| | - Wesley C Warren
- 440G Bond Life Sciences Center, 1201 Rollins Street, University of Missouri, Columbia, MO 65211, USA
| | - Ronald Walter
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
| | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany.
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14
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Conservation in the face of hybridisation: genome-wide study to evaluate taxonomic delimitation and conservation status of a threatened orchid species. CONSERV GENET 2021. [DOI: 10.1007/s10592-020-01325-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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15
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Jaiswal SK, Gupta A, Shafer ABA, P. K. VP, Vijay N, Sharma VK. Genomic Insights Into the Molecular Basis of Sexual Selection in Birds. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.538498] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Sexual selection is a well-known biological process, yet the genomic basis and patterns of sexual selection are not fully understood. The extravagant ornamental plumage of peacock (Pavo cristatus) was instrumental in shaping Charles Darwin's theory of sexual selection and is considered to be an honest signal of its immunocompetence. Here, we used the recently generated draft genome sequence of peafowl (Pavo cristatus) and carried out a comparative analysis across 11 bird genomes that encompass a range of sexual selection and also had high-quality genomic and phenotypic data publically available to study the genomic basis of sexual selection. We found that varying degree of purifying selection was the predominant mechanism of action for sexual selection at the genome-wide scale and observed that sexual selection mostly influences genes regulating gene expression and protein processing. Specifically, the genome-wide phylogenetically corrected regression analysis supported the continuous or ongoing model of sexual selection. Genes involved in nucleic acid binding and gene expression regulation, including a specific regulator of sex-determination known as TRA2A to be under positive selection in the species with high post-copulatory sexual selection manifested as high sperm competition. We also detected specific feather-related and immune-related gene-pairs evolving under similar selection pressures across the 11 species, including peacock (Pavo cristatus), which is consistent with the Hamilton-Zuk hypothesis. The comparative genomics analysis of 11 avian taxa has provided new insights on the molecular underpinnings of sexual selection and identifies specific genomic regions for future in-depth analysis.
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16
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Lu Y, Olivas TJ, Boswell M, Boswell W, Warren WC, Schartl M, Walter RB. Intra-Strain Genetic Variation of Platyfish ( Xiphophorus maculatus) Strains Determines Tumorigenic Trajectory. Front Genet 2020; 11:562594. [PMID: 33133148 PMCID: PMC7573281 DOI: 10.3389/fgene.2020.562594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 09/09/2020] [Indexed: 11/16/2022] Open
Abstract
Xiphophorus interspecies hybrids represent a valuable model system to study heritable tumorigenesis, and the only model system that exhibits both spontaneous and inducible tumors. Types of tumorigenesis depend on the specific pedigree of the parental species, X. maculatus, utilized to produce interspecies hybrids. Although the ancestors of the two currently used X. maculatus parental lines, Jp163 A and Jp163 B, were originally siblings produced by the same mother, backcross interspecies hybrid progeny between X. hellerii and X. maculatus Jp163 A develop spontaneous melanoma initiating at the dorsal fin due to segregation of an oncogene and a regulator encoded by the X. maculatus genome, while the backcross hybrid progeny with X. hellerii or X. couchianus and Jp163 B exhibit melanoma on the flanks of their bodies, especially after treatment with ultraviolet light. Therefore, dissecting the genetic differences between these two closely related lines may lead to better understanding of functional molecular differences associated with tumorigenic mechanisms. For this purpose, comparative genomic analyses were undertaken to establish genetic variants between these two X. maculatus lines. Surprisingly, given the heritage of these two fish lines, we found genetic variants are clustered together in select chromosomal regions. Among these variants are non-synonymous mutations located in 381 genes. The non-random distribution of genetic variants between these two may highlight ancestral chromosomal recombination patterns that became fixed during subsequent inbreeding. Employing comparative transcriptomics, we also determined differences in the skin transcriptional landscape between the two lines. The genetic differences observed are associated with pathways highlighting fundamental cellular functions including inter-cellular and microenvironment-cellular interactions, and DNA repair. These results collectively lead to the conclusion that diverged functional genetic baselines are present between Jp163 A and B strains. Further, disruption of these fixed genetic baselines in the hybrids may give rise to spontaneous or inducible mechanisms of tumorigenesis.
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Affiliation(s)
- Yuan Lu
- Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, United States
| | - Taryn J Olivas
- Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, United States.,Department of Cell Biology, Yale University School of Medicine, New Haven, CT, United States
| | - Mikki Boswell
- Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, United States
| | - William Boswell
- Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, United States
| | - Wes C Warren
- Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Manfred Schartl
- Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, United States.,Developmental Biochemistry, Theodor-Boveri-Institute, Biozentrum, University of Würzburg, Würzburg, Germany
| | - Ronald B Walter
- Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, United States
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17
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Jones JC, Du ZG, Bernstein R, Meyer M, Hoppe A, Schilling E, Ableitner M, Juling K, Dick R, Strauss AS, Bienefeld K. Tool for genomic selection and breeding to evolutionary adaptation: Development of a 100K single nucleotide polymorphism array for the honey bee. Ecol Evol 2020; 10:6246-6256. [PMID: 32724511 PMCID: PMC7381592 DOI: 10.1002/ece3.6357] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 04/19/2020] [Accepted: 04/20/2020] [Indexed: 01/03/2023] Open
Abstract
High-throughput high-density genotyping arrays continue to be a fast, accurate, and cost-effective method for genotyping thousands of polymorphisms in high numbers of individuals. Here, we have developed a new high-density SNP genotyping array (103,270 SNPs) for honey bees, one of the most ecologically and economically important pollinators worldwide. SNPs were detected by conducting whole-genome resequencing of 61 honey bee drones (haploid males) from throughout Europe. Selection of SNPs for the chip was done in multiple steps using several criteria. The majority of SNPs were selected based on their location within known candidate regions or genes underlying a range of honey bee traits, including hygienic behavior against pathogens, foraging, and subspecies. Additionally, markers from a GWAS of hygienic behavior against the major honey bee parasite Varroa destructor were brought over. The chip also includes SNPs associated with each of three major breeding objectives-honey yield, gentleness, and Varroa resistance. We validated the chip and make recommendations for its use by determining error rates in repeat genotypings, examining the genotyping performance of different tissues, and by testing how well different sample types represent the queen's genotype. The latter is a key test because it is highly beneficial to be able to determine the queen's genotype by nonlethal means. The array is now publicly available and we suggest it will be a useful tool in genomic selection and honey bee breeding, as well as for GWAS of different traits, and for population genomic, adaptation, and conservation questions.
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Affiliation(s)
- Julia C. Jones
- Institute for Bee ResearchHohen NeuendorfGermany
- School of Biology and Environmental ScienceUniversity College DublinDublinIreland
| | - Zhipei G. Du
- Institute for Bee ResearchHohen NeuendorfGermany
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18
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Cagnano G, Lenk I, Roulund N, Jensen CS, Cox MP, Asp T. Mycelial biomass and concentration of loline alkaloids driven by complex population structure in Epichloë uncinata and meadow fescue ( Schedonorus pratensis). Mycologia 2020; 112:474-490. [PMID: 32412888 DOI: 10.1080/00275514.2020.1746607] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Many efforts have been made to select and isolate naturally occurring animal-friendly Epichloë strains for later reinfection into elite cultivars. Often this process involves large-scale screening of Epichloë-infected wild grass populations where strains are characterized and alkaloids measured. Here, we describe for the first time the use of genotyping-by-sequencing (GBS) on a collection of 217 Epichloë-infected grasses (7 S. arundinaceum, 4 L. perenne, and 206 S. pratensis). This genotyping strategy is cheaper than complete genome sequencing, is suitable for a large number of individuals, and, when applied to endophyte-infected grasses, conveniently genotypes both organisms. In total, 6273 single nucleotide polymorphisms (SNPs) in the endophyte data set and 38 323 SNPs in the host data set were obtained. Our findings reveal a composite structure with three distinct endophyte clusters unrelated to the three main S. pratensis gene pools that have most likely spread from different glacial refugia in Eurasia. All three gene pools can establish symbiosis with E. uncinata. A comparison of the endophyte clusters with microsatellite-based fingerprinting of the same samples allows a quick test to discriminate between these clusters using two simple sequence repeats (SSRs). Concentrations of loline alkaloids and mycelial biomass are correlated and differ significantly among the plant and endophyte subpopulations; one endophyte strain has higher levels of lolines than others, and one specific host genotype is particularly suitable to host E. uncinata. These findings pave the way for targeted artificial inoculations of specific host-endophyte combinations to boost loline production in the symbiota and for genome association studies with the aim of isolating genes involved in the compatibility between meadow fescue and E. uncinata.
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Affiliation(s)
- G Cagnano
- DLF Seeds A/S, Højerupvej 31, 4660 Store Heddinge , Denmark
| | - I Lenk
- DLF Seeds A/S, Højerupvej 31, 4660 Store Heddinge , Denmark
| | - N Roulund
- DLF Seeds A/S, Højerupvej 31, 4660 Store Heddinge , Denmark
| | - C S Jensen
- DLF Seeds A/S, Højerupvej 31, 4660 Store Heddinge , Denmark
| | - M P Cox
- Statistics and Bioinformatics Group, School of Fundamental Sciences, Massey University , Palmerston North 4442, New Zealand
| | - T Asp
- Department of Molecular Biology and Genetics, Faculty of Science and Technology, Aarhus University , Aarhus, Denmark
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19
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White SJ, Pascall DJ, Wilson AJ. Towards a comparative approach to the structure of animal personality variation. Behav Ecol 2020; 31:340-351. [PMID: 32210524 PMCID: PMC7083098 DOI: 10.1093/beheco/arz198] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 10/25/2019] [Accepted: 11/07/2019] [Indexed: 01/26/2023] Open
Abstract
Latent personality traits underpinning observed behavioral variation have been studied in a great many species. However, a lack of standardized behavioral assays, coupled to a common reliance on inferring personality from a single, observed, behavioral trait makes it difficult to determine if, when, and how conclusions can be directly compared across taxa. Here, we estimate the among-individual (co)variance structure (ID) for a set of four behaviors expressed in an open field trial, putatively indicative of boldness, in seven species of small freshwater fish. We show that the ID matrices differ in terms of the total amount of variation present, and crucially the orientation, and as a consequence, biological interpretation of the first eigenvector. Specifically, loading of observed traits on the main axis of variation in ID matched a priori expectations for a shy-bold continuum in only three of the seven cases. Nonetheless, when the "shape" of the matrices was compared in higher dimensions, there was a high level of similarity among species, and weak evidence of phylogenetic signal. Our study highlights the present difficulty of trying to compare empirical inferences about specific personality traits across studies. However, it also shows how multivariate data collection and analysis allows the structure of behavioral variation to be quantitatively compared across populations or species without reliance on ambiguous verbal labels. This suggests that the field may have much to gain from greater uptake of phylogenetically informed comparative approaches when seeking to test evolutionary hypotheses about the origin and maintenance of personality variation.
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Affiliation(s)
- Stephen John White
- Animal Ecology, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - David John Pascall
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Alastair James Wilson
- Centre for Ecology and Conservation, University of Exeter (Penryn Campus), Cornwall, UK
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20
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Halbritter DA, Storer CG, Kawahara AY, Daniels JC. Phylogeography and population genetics of pine butterflies: Sky islands increase genetic divergence. Ecol Evol 2019; 9:13389-13401. [PMID: 31871652 PMCID: PMC6912906 DOI: 10.1002/ece3.5793] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 10/04/2019] [Accepted: 10/07/2019] [Indexed: 12/05/2022] Open
Abstract
The sky islands of southeastern Arizona (AZ) mark a major transition zone between tropical and temperate biota and are considered a neglected biodiversity hotspot. Dispersal ability and host plant specificity are thought to impact the history and diversity of insect populations across the sky islands. We aimed to investigate the population structure and phylogeography of two pine-feeding pierid butterflies, the pine white (Neophasia menapia) and the Mexican pine white (Neophasia terlooii), restricted to these "islands" at this transition zone. Given their dependence on pines as the larval hosts, we hypothesized that habitat connectivity affects population structure and is at least in part responsible for their allopatry. We sampled DNA from freshly collected butterflies from 17 sites in the sky islands and adjacent high-elevation habitats and sequenced these samples using ddRADSeq. Up to 15,399 SNPs were discovered and analyzed in population genetic and phylogenetic contexts with Stacks and pyRAD pipelines. Low genetic differentiation in N. menapia suggests that it is panmictic. Conversely, there is strong evidence for population structure within N. terlooii. Each sky island likely contains a population of N. terlooii, and clustering is hierarchical, with populations on proximal mountains being more related to each other. The N. menapia habitat, which is largely contiguous, facilitates panmixia, while the N. terlooii habitat, restricted to the higher elevations on each sky island, creates distinct population structure. Phylogenetic results corroborate those from population genetic analyses. The historical climate-driven fluxes in forest habitat connectivity have implications for understanding the biodiversity of fragmented habitats.
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Affiliation(s)
- Dale A. Halbritter
- Entomology and Nematology DepartmentUniversity of FloridaGainesvilleFLUSA
- Present address:
USDA‐ARS Invasive Plant Research Laboratory3225 College AveFort LauderdaleFL33314USA
| | - Caroline G. Storer
- McGuire Center for Lepidoptera and BiodiversityFlorida Museum of Natural HistoryUniversity of FloridaGainesvilleFLUSA
| | - Akito Y. Kawahara
- McGuire Center for Lepidoptera and BiodiversityFlorida Museum of Natural HistoryUniversity of FloridaGainesvilleFLUSA
| | - Jaret C. Daniels
- Entomology and Nematology DepartmentUniversity of FloridaGainesvilleFLUSA
- McGuire Center for Lepidoptera and BiodiversityFlorida Museum of Natural HistoryUniversity of FloridaGainesvilleFLUSA
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21
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Martín-Hernanz S, Aparicio A, Fernández-Mazuecos M, Rubio E, Reyes-Betancort JA, Santos-Guerra A, Olangua-Corral M, Albaladejo RG. Maximize Resolution or Minimize Error? Using Genotyping-By-Sequencing to Investigate the Recent Diversification of Helianthemum (Cistaceae). FRONTIERS IN PLANT SCIENCE 2019; 10:1416. [PMID: 31781140 PMCID: PMC6859804 DOI: 10.3389/fpls.2019.01416] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 10/11/2019] [Indexed: 05/27/2023]
Abstract
A robust phylogenetic framework, in terms of extensive geographical and taxonomic sampling, well-resolved species relationships and high certainty of tree topologies and branch length estimations, is critical in the study of macroevolutionary patterns. Whereas Sanger sequencing-based methods usually recover insufficient phylogenetic signal, especially in recently diversified lineages, reduced-representation sequencing methods tend to provide well-supported phylogenetic relationships, but usually entail remarkable bioinformatic challenges due to the inherent trade-off between the number of SNPs and the magnitude of associated error rates. The genus Helianthemum (Cistaceae) is a species-rich and taxonomically complex Palearctic group of plants that diversified mainly since the Upper Miocene. It is a challenging case study since previous attempts using Sanger sequencing were unable to resolve the intrageneric phylogenetic relationships. Aiming to obtain a robust phylogenetic reconstruction based on genotyping-by-sequencing (GBS), we established a rigorous methodological workflow in which we i) explored how variable settings during dataset assembly have an impact on error rates and on the degree of resolution under concatenation and coalescent approaches, ii) assessed the effect of two extreme parameter configurations (minimizing error rates vs. maximizing phylogenetic resolution) on tree topology and branch lengths, and iii) evaluated the effects of these two configurations on estimates of divergence times and diversification rates. Our analyses produced highly supported topologically congruent phylogenetic trees for both configurations. However, minimizing error rates did produce more reliable branch lengths, critically affecting the accuracy of downstream analyses (i.e. divergence times and diversification rates). In addition to recommending a revision of intrageneric systematics, our results enabled us to identify three highly diversified lineages in Helianthemum in contrasting geographical areas and ecological conditions, which started radiating in the Upper Miocene.
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Affiliation(s)
- Sara Martín-Hernanz
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Sevilla, Spain
| | - Abelardo Aparicio
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Sevilla, Spain
| | | | - Encarnación Rubio
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Sevilla, Spain
| | - J. Alfredo Reyes-Betancort
- Jardín de Aclimatación de la Orotava, Instituto Canario de Investigaciones Agrarias (ICIA), Santa Cruz de Tenerife, Spain
| | - Arnoldo Santos-Guerra
- Jardín de Aclimatación de la Orotava, Instituto Canario de Investigaciones Agrarias (ICIA), Santa Cruz de Tenerife, Spain
| | - María Olangua-Corral
- Departamento de Biología Reproductiva y Micro-morfología, Jardín Botánico Canario ‘Viera y Clavijo’—Unidad Asociada CSIC (Cabildo de Gran Canaria), Las Palmas de Gran Canaria, Spain
| | - Rafael G. Albaladejo
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Sevilla, Spain
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22
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Liu C, Chen H, Ren Z, Zhang C, Yang X. Population genetic analysis of the domestic Bactrian camel in China by RAD-seq. Ecol Evol 2019; 9:11232-11242. [PMID: 31641468 PMCID: PMC6802064 DOI: 10.1002/ece3.5624] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 07/31/2019] [Accepted: 08/01/2019] [Indexed: 12/30/2022] Open
Abstract
Restriction site-associated DNA sequencing (RAD-seq) is one of the most effective high-throughput sequencing technologies for SNP development and utilization and has been applied to studying the origin and evolution of various species. The domestic Bactrian camels play an important role in economic trade and cultural construction. They are precious species resources and indispensable animals in China's agricultural production. Recently, the rapid development of modern transportation and agriculture, and the deterioration of the environment have led to a sharp decline in the number of camels. Although there have been some reports on the evolution history of the domestic Bactrian camel in China, the origin, evolutionary relationship, and genetic diversity of the camels are unclear due to the limitations of sample size and sequencing technology. Therefore, 47 samples of seven domestic Bactrian camel species from four regions (Inner Mongolia, Gansu, Qinghai, and Xinjiang) were prepared for RAD-seq analysis to study the evolutionary relationship and genetic diversity. In addition, seven domestic Bactrian camel species are located in different ecological zones, forming different characteristics and having potential development value. A total of 6,487,849 SNPs were genotyped. On the one hand, the filtered SNP information was used to conduct polymorphism mapping construction, LD attenuation analysis, and nucleotide diversity analysis. The results showed that the number of SNPs in Dongjiang camel was the highest, the LD coefficient decayed the fastest, and the nucleotide diversity was the highest. It indicates that Dongjiang camel has the highest genetic diversity. On the other hand, the filtered SNPs information was used to construct the phylogenetic tree, and F ST analysis, inbreeding coefficient analysis, principal component analysis, and population structure analysis were carried out. The results showed that Nanjiang camel and Beijiang camels grouped together, and the other five Bactrian camel populations gathered into another branch. It may be because the mountains in the northern part of Xinjiang and the desert in the middle isolate the two groups from the other five groups.
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Affiliation(s)
- Chenmiao Liu
- College of Animal Science and TechnologyNorthwest A&F UniversityYanglingChina
| | - Huiling Chen
- College of Animal Science and TechnologyNorthwest A&F UniversityYanglingChina
| | - Zhanjun Ren
- College of Animal Science and TechnologyNorthwest A&F UniversityYanglingChina
| | - Chengdong Zhang
- College of Animal Science and TechnologyNorthwest A&F UniversityYanglingChina
| | - Xuejiao Yang
- College of Animal Science and TechnologyNorthwest A&F UniversityYanglingChina
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23
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Godefroid M, Meseguer AS, Sauné L, Genson G, Streito JC, Rossi JP, Zaldívar Riverón A, Mayer F, Cruaud A, Rasplus JY. Restriction-site associated DNA markers provide new insights into the evolutionary history of the bark beetle genus Dendroctonus. Mol Phylogenet Evol 2019; 139:106528. [PMID: 31176966 DOI: 10.1016/j.ympev.2019.106528] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/02/2019] [Accepted: 06/05/2019] [Indexed: 10/26/2022]
Abstract
The bark beetle genus Dendroctonus contains some of the most economically important pests of conifers worldwide. Despite many attempts, there is no agreement today on the phylogenetic relationships within the genus, which limits our understanding of its evolutionary history. Here, using restriction-site associated DNA (RAD) markers from 70 specimens representing 17 species (85% of the known diversity) we inferred the phylogeny of the genus, its time of origin and biogeographic history, as well as the evolution of key ecological traits (host plants, larval behavior and adults' attack strategies). For all combinations of tested parameters (from 6444 to 23,570 RAD tags analyzed), the same, fully resolved topology was inferred. Our analyses suggest that the most recent common ancestor (mrca) of all extant Dendroctonus species was widely distributed across eastern Palearctic and western Nearctic during the early Miocene, from where species dispersed to other Holarctic regions. A first main inter-continental vicariance event occurred during early Miocene isolating the ancestors of D. armandi in the Palearctic, which was followed by the radiation of the main Dendroctonus lineages in North America. During the Late Miocene, the ancestor of the 'rufipennis' species group colonized north-east Palearctic regions from western North America, which was followed by a second main inter-continental vicariance event isolating Pleistocene populations in Asia (D. micans) and western North America (D. murrayanae and D. punctatus). The present study supports previous hypotheses explaining intercontinental range disjunctions across the Northern Hemisphere by the fragmentation of a continuous distribution due to climatic cooling, host range fragmentation and geological changes during the late Cenozoic. The reconstruction of ancestral ecological traits indicates that the mrca bored individual galleries and mass attacked the boles of pines. The gregarious feeding behavior of the larvae as well as the individual attack of the base of trees have apparently independently evolved twice in North America (in the 'rufipennis' and the 'valens' species groups), which suggests a higher adaptive potential than previously thought and may be of interest for plant protection and biodiversity conservation in a rapidly changing world.
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Affiliation(s)
- Martin Godefroid
- CBGP, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France; Consejo Superior de Investigaciones Cientificas - Instituto de Ciencias Agrarias (ICA - CSIC), Madrid, Spain.
| | - Andrea S Meseguer
- CNRS, UMR 5554 Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier
- CNRS
- IRD
- EPHE), Montpellier, France
| | - Laure Sauné
- CBGP, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
| | - Guenaëlle Genson
- CBGP, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
| | - Jean-Claude Streito
- CBGP, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
| | - Jean-Pierre Rossi
- CBGP, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
| | - Alejandro Zaldívar Riverón
- Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de Mexico, Mexico, D.F., Mexico
| | - François Mayer
- Biological Control and Spatial Ecology Laboratory (LUBIES), University of Brussels, Belgium
| | - Astrid Cruaud
- CBGP, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
| | - Jean-Yves Rasplus
- CBGP, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
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24
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Pfaller JB, Payton AC, Bjorndal KA, Bolten AB, McDaniel SF. Hitchhiking the high seas: Global genomics of rafting crabs. Ecol Evol 2019; 9:957-974. [PMID: 30805133 PMCID: PMC6374717 DOI: 10.1002/ece3.4694] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 10/04/2018] [Accepted: 10/05/2018] [Indexed: 12/04/2022] Open
Abstract
Population differentiation and diversification depend in large part on the ability and propensity of organisms to successfully disperse. However, our understanding of these processes in organisms with high dispersal ability is biased by the limited genetic resolution offered by traditional genotypic markers. Many neustonic animals disperse not only as pelagic larvae, but also as juveniles and adults while drifting or rafting at the surface of the open ocean. In theory, the heightened dispersal ability of these animals should limit opportunities for species diversification and population differentiation. To test these predictions, we used next-generation sequencing of genomewide restriction-site-associated DNA tags (RADseq) and traditional mitochondrial DNA sequencing, to investigate the species-level relationships and global population structure of Planes crabs collected from oceanic flotsam and sea turtles. Our results indicate that species diversity in this clade is low-likely three closely related species-with no evidence of cryptic or undescribed species. Moreover, our results indicate weak population differentiation among widely separated aggregations with genetic indices showing only subtle genetic discontinuities across all oceans of the world (RADseq F ST = 0.08-0.16). The results of this study provide unprecedented resolution of the systematics and global biogeography of this group and contribute valuable information to our understanding of how theoretical dispersal potential relates to actual population differentiation and diversification among marine organisms. Moreover, these results demonstrate the limitations of single gene analyses and the value of genomic-level resolution for estimating contemporary population structure in organisms with large, highly connected populations.
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Affiliation(s)
- Joseph B. Pfaller
- Department of Biology, Archie Carr Center for Sea Turtle ResearchUniversity of FloridaGainesvilleFlorida
- Caretta Research ProjectSavannahGeorgia
| | - Adam C. Payton
- Department of BiologyUniversity of FloridaGainesvilleFlorida
| | - Karen A. Bjorndal
- Department of Biology, Archie Carr Center for Sea Turtle ResearchUniversity of FloridaGainesvilleFlorida
| | - Alan B. Bolten
- Department of Biology, Archie Carr Center for Sea Turtle ResearchUniversity of FloridaGainesvilleFlorida
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25
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Crotti M, Barratt CD, Loader SP, Gower DJ, Streicher JW. Causes and analytical impacts of missing data in RADseq phylogenetics: Insights from an African frog (Afrixalus
). ZOOL SCR 2019. [DOI: 10.1111/zsc.12335] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Marco Crotti
- Department of Life Sciences; The Natural History Museum; London UK
- Department of Life Sciences; Imperial College London; London UK
- Institute of Biodiversity, Animal Health and Comparative Medicine; University of Glasgow; Glasgow UK
| | - Christopher D. Barratt
- Department of Environmental Sciences; University of Basel; Basel Switzerland
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig; Leipzig Germany
| | - Simon P. Loader
- Department of Life Sciences; The Natural History Museum; London UK
- Department of Environmental Sciences; University of Basel; Basel Switzerland
| | - David J. Gower
- Department of Life Sciences; The Natural History Museum; London UK
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26
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Nadukkalam Ravindran P, Bentzen P, Bradbury IR, Beiko RG. RADProc: A computationally efficient de novo locus assembler for population studies using RADseq data. Mol Ecol Resour 2018; 19:272-282. [PMID: 30312001 DOI: 10.1111/1755-0998.12954] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 09/09/2018] [Accepted: 09/26/2018] [Indexed: 11/30/2022]
Abstract
Restriction site-associated DNA sequencing (RADseq) is a powerful tool for genotyping of individuals, but the identification of loci and assignment of sequence reads is a crucial and often challenging step. The optimal parameter settings for a given de novo RADseq assembly vary between data sets and can be difficult and computationally expensive to determine. Here, we introduce RADProc, a software package that uses a graph data structure to represent all sequence reads and their similarity relationships. Storing sequence-comparison results in a graph eliminates unnecessary and redundant sequence similarity calculations. De novo locus formation for a given parameter set can be performed on the precomputed graph, making parameter sweeps far more efficient. RADProc also uses a clustering approach for faster nucleotide-distance calculation. The performance of RADProc compares favourably with that of the widely used Stacks software. The run-time comparisons between RADProc and Stacks for 32 different parameter settings using 20 green-crab (Carcinus maenas) samples showed that RADProc took as little as 2 hr 40 min compared to 78 hr by Stacks, while 16 brown trout (Salmo trutta L.) samples were processed by RADProc and Stacks in 23 and 263 hr, respectively. Comparisons of the de novo loci formed, and catalog built using both the methods demonstrate that the improvement in processing speeds achieved by RADProc does not affect much the actual loci formed and the results of downstream analyses based on those loci.
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Affiliation(s)
| | - Paul Bentzen
- Marine Gene Probe Laboratory, Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Ian R Bradbury
- Salmonids Section, Science Branch, Department of Fisheries and Oceans Canada, St. John's, Newfoundland, Canada
| | - Robert G Beiko
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada
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27
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Franchini P, Jones JC, Xiong P, Kneitz S, Gompert Z, Warren WC, Walter RB, Meyer A, Schartl M. Long-term experimental hybridisation results in the evolution of a new sex chromosome in swordtail fish. Nat Commun 2018; 9:5136. [PMID: 30510159 PMCID: PMC6277394 DOI: 10.1038/s41467-018-07648-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 11/13/2018] [Indexed: 01/13/2023] Open
Abstract
The remarkable diversity of sex determination mechanisms known in fish may be fuelled by exceptionally high rates of sex chromosome turnovers or transitions. However, the evolutionary causes and genomic mechanisms underlying this variation and instability are yet to be understood. Here we report on an over 30-year evolutionary experiment in which we tested the genomic consequences of hybridisation and selection between two Xiphophorus fish species with different sex chromosome systems. We find that introgression and imposing selection for pigmentation phenotypes results in the retention of an unexpectedly large maternally derived genomic region. During the hybridisation process, the sex-determining region of the X chromosome from one parental species was translocated to an autosome in the hybrids leading to the evolution of a new sex chromosome. Our results highlight the complexity of factors contributing to patterns observed in hybrid genomes, and we experimentally demonstrate that hybridisation can catalyze rapid evolution of a new sex chromosome. Fish have a high diversity of sex-determining systems, but the mechanisms responsible for this are not well understood. Here, Franchini et al. show how hybridization and backcrossing have led to the evolution of a new sex chromosome in swordtail fish during 30 years of experimental evolution.
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Affiliation(s)
- Paolo Franchini
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Julia C Jones
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany.,Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, 75123, Sweden
| | - Peiwen Xiong
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Susanne Kneitz
- Physiological Chemistry, Biozentrum, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
| | | | - Wesley C Warren
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, 63108, MO, USA
| | - Ronald B Walter
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, 78666-4616, TX, USA
| | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany. .,Radcliffe Institute for Advanced Study, Harvard University, 9 Garden Street, Cambridge, MA, 02139, USA.
| | - Manfred Schartl
- Physiological Chemistry, Biozentrum, University of Würzburg, Am Hubland, 97074, Würzburg, Germany. .,Comprehensive Cancer Centre, University Clinic Würzburg, Josef Schneider Straße 6, 97074, Würzburg, Germany. .,Hagler Institute for Advanced Study and Department of Biology, Texas A&M University, College Station, TX, 77843, USA.
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28
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Tekle YI, Wood FC. A practical implementation of large transcriptomic data analysis to resolve cryptic species diversity problems in microbial eukaryotes. BMC Evol Biol 2018; 18:170. [PMID: 30445905 PMCID: PMC6240226 DOI: 10.1186/s12862-018-1283-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 10/30/2018] [Indexed: 01/09/2023] Open
Abstract
Background Transcriptome sequencing has become a method of choice for evolutionary studies in microbial eukaryotes due to low cost and minimal sample requirements. Transcriptome data has been extensively used in phylogenomic studies to infer ancient evolutionary histories. However, its utility in studying cryptic species diversity is not well explored. An empirical investigation was conducted to test the applicability of transcriptome data in resolving two major types of discordances at lower taxonomic levels. These include cases where species have the same morphology but different genetics (cryptic species) and species of different morphologies but have the same genetics. We built a species comparison bioinformatic pipeline that takes into account the nature of transcriptome data in amoeboid microbes exemplifying such discordances. Result Our analyses of known or suspected cryptic species yielded consistent results regardless of the methods of culturing, RNA collection or sequencing. Over 95% of the single copy genes analyzed in samples of the same species sequenced using different methods and cryptic species had intra- and interspecific divergences below 2%. Only a minority of groups (2.91–4.87%) had high distances exceeding 2% in these taxa, which was likely caused by low data quality. This pattern was also observed in suspected genetically similar species with different morphologies. Transcriptome data consistently delineated all taxa above species level, including cryptically diverse species. Using our approach we were able to resolve cryptic species problems, uncover misidentification and discover new species. We also identified several potential barcode markers with varying evolutionary rates that can be used in lineages with different evolutionary histories. Conclusion Our findings demonstrate that transcriptome data is appropriate for understanding cryptic species diversity in microbial eukaryotes. Electronic supplementary material The online version of this article (10.1186/s12862-018-1283-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yonas I Tekle
- Spelman College, 350 Spelman Lane Southwest, Atlanta, GA, 30314, USA.
| | - Fiona C Wood
- Spelman College, 350 Spelman Lane Southwest, Atlanta, GA, 30314, USA
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29
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Cruaud A, Groussier G, Genson G, Sauné L, Polaszek A, Rasplus JY. Pushing the limits of whole genome amplification: successful sequencing of RADseq library from a single microhymenopteran (Chalcidoidea, Trichogramma). PeerJ 2018; 6:e5640. [PMID: 30356952 PMCID: PMC6195110 DOI: 10.7717/peerj.5640] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 08/27/2018] [Indexed: 11/20/2022] Open
Abstract
A major obstacle to high-throughput genotyping of microhymenoptera is their small size. As species are difficult to discriminate, and because complexes may exist, the sequencing of a pool of specimens is hazardous. Thus, one should be able to sequence pangenomic markers (e.g., RADtags) from a single specimen. To date, whole genome amplification (WGA) prior to library construction is still a necessity as at most 10 ng of DNA can be obtained from single specimens (sometimes less). However, this amount of DNA is not compatible with manufacturer's requirements for commercial kits. Here we test the accuracy of the GenomiPhi kit V2 on Trichogramma wasps by comparing RAD libraries obtained from the WGA of single specimens (F0 and F1 generation, about1 ng input DNA for the WGA (0.17-2.9 ng)) and a biological amplification of genomic material (the pool of the progeny of the F1 generation). Globally, we found that 99% of the examined loci (up to 48,189 for one of the crosses, 109 bp each) were compatible with the mode of reproduction of the studied model (haplodiploidy) and Mendelian inheritance of alleles. The remaining 1% (0.01% of the analysed nucleotides) could represent WGA bias or other experimental/analytical bias. This study shows that the multiple displacement amplification method on which the GenomiPhi kit relies, could also be of great help for the high-throughput genotyping of microhymenoptera used for biological control, or other organisms from which only a very small amount of DNA can be extracted, such as human disease vectors (e.g., sandflies, fleas, ticks etc.).
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Affiliation(s)
- Astrid Cruaud
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Géraldine Groussier
- Institut Sophia Agrobiotech, INRA, CNRS, Université Côte d’Azur, Sophia Antipolis, France
| | - Guenaëlle Genson
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Laure Sauné
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Andrew Polaszek
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Jean-Yves Rasplus
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
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30
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Wagner ND, Gramlich S, Hörandl E. RAD sequencing resolved phylogenetic relationships in European shrub willows ( Salix L. subg. Chamaetia and subg. Vetrix) and revealed multiple evolution of dwarf shrubs. Ecol Evol 2018; 8:8243-8255. [PMID: 30250699 PMCID: PMC6145212 DOI: 10.1002/ece3.4360] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 06/15/2018] [Accepted: 06/22/2018] [Indexed: 01/03/2023] Open
Abstract
The large and diverse genus Salix L. is of particular interest for decades of biological research. However, despite the morphological plasticity, the reconstruction of phylogenetic relationships was so far hampered by the lack of informative molecular markers. Infrageneric classification based on morphology separates dwarf shrubs (subg. Chamaetia) and taller shrubs (subg. Vetrix), while previous phylogenetic studies placed species of these two subgenera just in one largely unresolved clade. Here we want to test the utility of genomic RAD sequencing markers for resolving relationships at different levels of divergence in Salix. Based on a sampling of 15 European species representing 13 sections of the two subgenera, we used five different RAD sequencing datasets generated by ipyrad to conduct phylogenetic analyses. Additionally we reconstructed the evolution of growth form and analyzed the genetic composition of the whole clade. The results showed fully resolved trees in both ML and BI analysis with high statistical support. The two subgenera Chamaetia and Vetrix were recognized as nonmonophyletic, which suggests that they should be merged. Within the Vetrix/Chamaetia clade, a division into three major subclades could be observed. All species were confirmed to be monophyletic. Based on our data, arctic-alpine dwarf shrubs evolved four times independently. The structure analysis showed five mainly uniform genetic clusters which are congruent in sister relationships observed in the phylogenies. Our study confirmed RAD sequencing as a useful genomic tool for the reconstruction of relationships on different taxonomic levels in the genus Salix.
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Affiliation(s)
- Natascha Dorothea Wagner
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium)University of GoettingenGöttingenGermany
| | - Susanne Gramlich
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium)University of GoettingenGöttingenGermany
| | - Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium)University of GoettingenGöttingenGermany
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31
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Bell CD, Gonzalez LA. Exploring the utility of “next-generation” sequence data on inferring the phylogeny of the South American Valeriana (Valerianaceae). Mol Phylogenet Evol 2018; 123:44-49. [DOI: 10.1016/j.ympev.2018.02.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 02/14/2018] [Accepted: 02/14/2018] [Indexed: 10/18/2022]
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32
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Culumber ZW, Tobler M. Correlated evolution of thermal niches and functional physiology in tropical freshwater fishes. J Evol Biol 2018; 31:722-734. [DOI: 10.1111/jeb.13260] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 01/13/2018] [Accepted: 02/23/2018] [Indexed: 11/30/2022]
Affiliation(s)
| | - Michael Tobler
- Division of Biology Kansas State University Manhattan KS USA
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33
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Dupuis JR, Mcdonald CM, Acorn JH, Sperling FAH. Genomics-informed species delimitation to support morphological identification of anglewing butterflies (Lepidoptera: Nymphalidae: Polygonia). Zool J Linn Soc 2017. [DOI: 10.1093/zoolinnean/zlx081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Julian R Dupuis
- Department of Plant and Environmental Protection Sciences, University of Hawai’i at Mānoa, Honolulu, HI, USA
- Department of Biological Sciences, CW 405 Biosciences Centre, University of Alberta, Edmonton, AB, Canada
| | - Christianne M Mcdonald
- Department of Biological Sciences, CW 405 Biosciences Centre, University of Alberta, Edmonton, AB, Canada
| | - John H Acorn
- Department of Renewable Resources, University of Alberta, Edmonton, AB, Canada
| | - Felix A H Sperling
- Department of Biological Sciences, CW 405 Biosciences Centre, University of Alberta, Edmonton, AB, Canada
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34
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Suchan T, Espíndola A, Rutschmann S, Emerson BC, Gori K, Dessimoz C, Arrigo N, Ronikier M, Alvarez N. Assessing the potential of RAD-sequencing to resolve phylogenetic relationships within species radiations: The fly genus Chiastocheta (Diptera: Anthomyiidae) as a case study. Mol Phylogenet Evol 2017. [DOI: 10.1016/j.ympev.2017.06.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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35
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Baker Z, Schumer M, Haba Y, Bashkirova L, Holland C, Rosenthal GG, Przeworski M. Repeated losses of PRDM9-directed recombination despite the conservation of PRDM9 across vertebrates. eLife 2017; 6:e24133. [PMID: 28590247 PMCID: PMC5519329 DOI: 10.7554/elife.24133] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Accepted: 06/03/2017] [Indexed: 01/01/2023] Open
Abstract
Studies of highly diverged species have revealed two mechanisms by which meiotic recombination is directed to the genome-through PRDM9 binding or by targeting promoter-like features-that lead to dramatically different evolutionary dynamics of hotspots. Here, we identify PRDM9 orthologs from genome and transcriptome data in 225 species. We find the complete PRDM9 ortholog across distantly related vertebrates but, despite this broad conservation, infer a minimum of six partial and three complete losses. Strikingly, taxa carrying the complete ortholog of PRDM9 are precisely those with rapid evolution of its predicted binding affinity, suggesting that all domains are necessary for directing recombination. Indeed, as we show, swordtail fish carrying only a partial but conserved ortholog share recombination properties with PRDM9 knock-outs.
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Affiliation(s)
- Zachary Baker
- Department of Systems Biology, Columbia University, New York City, United States
| | - Molly Schumer
- Department of Biological Sciences, Columbia University, New York City, United States
- Harvard Society of Fellows, Harvard University, Cambridge, United States
- Centro de Investigaciones Científicas de las Huastecas 'Aguazarca', Hidalgo, Mexico
| | - Yuki Haba
- Department of Evolution, Ecology and Environmental Biology, Columbia University, New York City, United States
| | - Lisa Bashkirova
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York City, United States
| | - Chris Holland
- Centro de Investigaciones Científicas de las Huastecas 'Aguazarca', Hidalgo, Mexico
- Department of Biology, Texas A&M University, College Station, United States
| | - Gil G Rosenthal
- Centro de Investigaciones Científicas de las Huastecas 'Aguazarca', Hidalgo, Mexico
- Department of Biology, Texas A&M University, College Station, United States
| | - Molly Przeworski
- Department of Systems Biology, Columbia University, New York City, United States
- Department of Biological Sciences, Columbia University, New York City, United States
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36
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Dupuis J, Brunet B, Bird H, Lumley L, Fagua G, Boyle B, Levesque R, Cusson M, Powell J, Sperling F. Genome-wide SNPs resolve phylogenetic relationships in the North American spruce budworm (Choristoneura fumiferana) species complex. Mol Phylogenet Evol 2017; 111:158-168. [DOI: 10.1016/j.ympev.2017.04.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 02/27/2017] [Accepted: 04/03/2017] [Indexed: 01/02/2023]
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37
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Affiliation(s)
- Josephine R. Paris
- Biosciences College of Life and Environmental Sciences University of Exeter Exeter UK
| | - Jamie R. Stevens
- Biosciences College of Life and Environmental Sciences University of Exeter Exeter UK
| | - Julian M. Catchen
- Department of Animal Biology University of Illinois at Urbana–Champaign Urbana IL 61801 USA
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38
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Franchini P, Monné Parera D, Kautt AF, Meyer A. quaddRAD: a new high-multiplexing and PCR duplicate removal ddRAD protocol produces novel evolutionary insights in a nonradiating cichlid lineage. Mol Ecol 2017; 26:2783-2795. [PMID: 28247584 DOI: 10.1111/mec.14077] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 02/20/2017] [Accepted: 02/21/2017] [Indexed: 12/14/2022]
Affiliation(s)
- Paolo Franchini
- Zoology and Evolutionary Biology; Department of Biology; University of Konstanz; Universitätsstraße 10 78457 Konstanz Germany
| | - Daniel Monné Parera
- Zoology and Evolutionary Biology; Department of Biology; University of Konstanz; Universitätsstraße 10 78457 Konstanz Germany
| | - Andreas F. Kautt
- Zoology and Evolutionary Biology; Department of Biology; University of Konstanz; Universitätsstraße 10 78457 Konstanz Germany
| | - Axel Meyer
- Zoology and Evolutionary Biology; Department of Biology; University of Konstanz; Universitätsstraße 10 78457 Konstanz Germany
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39
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Jones JC, Fruciano C, Keller A, Schartl M, Meyer A. Evolution of the elaborate male intromittent organ of Xiphophorus fishes. Ecol Evol 2016; 6:7207-7220. [PMID: 27891216 PMCID: PMC5114703 DOI: 10.1002/ece3.2396] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 07/26/2016] [Accepted: 08/01/2016] [Indexed: 11/08/2022] Open
Abstract
Internally fertilizing animals show a remarkable diversity in male genital morphology that is associated with sexual selection, and these traits are thought to be evolving particularly rapidly. Male fish in some internally fertilizing species have "gonopodia," highly modified anal fins that are putatively important for sexual selection. However, our understanding of the evolution of genital diversity remains incomplete. Contrary to the prediction that male genital traits evolve more rapidly than other traits, here we show that gonopodial traits and other nongonopodial traits exhibit similar evolutionary rates of trait change and also follow similar evolutionary models in an iconic genus of poeciliid fish (Xiphophorus spp.). Furthermore, we find that both mating and nonmating natural selection mechanisms are unlikely to be driving the diverse Xiphophorus gonopodial morphology. Putative holdfast features of the male genital organ do not appear to be influenced by water flow, a candidate selective force in aquatic habitats. Additionally, interspecific divergence in gonopodial morphology is not significantly higher between sympatric species, than between allopatric species, suggesting that male genitals have not undergone reproductive character displacement. Slower rates of evolution in gonopodial traits compared with a subset of putatively sexually selected nongenital traits suggest that different selection mechanisms may be acting on the different trait types. Further investigations of this elaborate trait are imperative to determine whether it is ultimately an important driver of speciation.
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Affiliation(s)
- Julia C Jones
- Lehrstuhl für Zoologie und Evolutionsbiologie Department of Biology University of Konstanz Universitätstraße 10 78457 Konstanz Germany; Zukunftskolleg University of Konstanz Konstanz Germany; Present address: Evolution, Behaviour and Environment School of Life Sciences University of Sussex Brighton UK
| | - Carmelo Fruciano
- Lehrstuhl für Zoologie und Evolutionsbiologie Department of Biology University of Konstanz Universitätstraße 10 78457 Konstanz Germany; School of Earth, Environmental & Biological Sciences Queensland University of Technology Brisbane Qld 4000 Australia
| | - Anja Keller
- Lehrstuhl für Zoologie und Evolutionsbiologie Department of Biology University of Konstanz Universitätstraße 10 78457 Konstanz Germany
| | - Manfred Schartl
- Physiological Chemistry, Biozentrum University of Würzburg Am Hubland 97074 Würzburg Germany; Comprehensive Cancer Centre University Clinic Würzburg Josef Schneider Straße 697074 Würzburg Germany
| | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie Department of Biology University of Konstanz Universitätstraße 10 78457 Konstanz Germany
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40
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Díaz-Arce N, Arrizabalaga H, Murua H, Irigoien X, Rodríguez-Ezpeleta N. RAD-seq derived genome-wide nuclear markers resolve the phylogeny of tunas. Mol Phylogenet Evol 2016; 102:202-7. [DOI: 10.1016/j.ympev.2016.06.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 06/02/2016] [Indexed: 10/21/2022]
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41
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Burns M, Starrett J, Derkarabetian S, Richart CH, Cabrero A, Hedin M. Comparative performance of double‐digest
RAD
sequencing across divergent arachnid lineages. Mol Ecol Resour 2016; 17:418-430. [DOI: 10.1111/1755-0998.12575] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 06/23/2016] [Indexed: 11/28/2022]
Affiliation(s)
- Mercedes Burns
- Department of Biology San Diego State University 5500 Campanile Drive San Diego CA 92182 USA
| | - James Starrett
- Department of Biology San Diego State University 5500 Campanile Drive San Diego CA 92182 USA
| | - Shahan Derkarabetian
- Department of Biology San Diego State University 5500 Campanile Drive San Diego CA 92182 USA
- Department of Biology University of California 900 University Avenue Riverside CA 92521 USA
| | - Casey H. Richart
- Department of Biology San Diego State University 5500 Campanile Drive San Diego CA 92182 USA
- Department of Biology University of California 900 University Avenue Riverside CA 92521 USA
| | - Allan Cabrero
- Department of Biology San Diego State University 5500 Campanile Drive San Diego CA 92182 USA
| | - Marshal Hedin
- Department of Biology San Diego State University 5500 Campanile Drive San Diego CA 92182 USA
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42
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Burns M, Tsurusaki N. Male Reproductive Morphology Across Latitudinal Clines and Under Long-Term Female Sex-Ratio Bias. Integr Comp Biol 2016; 56:715-27. [DOI: 10.1093/icb/icw017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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43
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Burford Reiskind MO, Coyle K, Daniels HV, Labadie P, Reiskind MH, Roberts NB, Roberts RB, Schaff J, Vargo EL. Development of a universal double-digest RAD sequencing approach for a group of nonmodel, ecologically and economically important insect and fish taxa. Mol Ecol Resour 2016; 16:1303-1314. [PMID: 27739656 DOI: 10.1111/1755-0998.12527] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 03/03/2016] [Accepted: 03/09/2016] [Indexed: 11/28/2022]
Abstract
The generation of genome-scale data is critical for a wide range of questions in basic biology using model organisms, but also in questions of applied biology in nonmodel organisms (agriculture, natural resources, conservation and public health biology). Using a genome-scale approach on a diverse group of nonmodel organisms and with the goal of lowering costs of the method, we modified a multiplexed, high-throughput genomic scan technique utilizing two restriction enzymes. We analysed several pairs of restriction enzymes and completed double-digestion RAD sequencing libraries for nine different species and five genera of insects and fish. We found one particular enzyme pair produced consistently higher number of sequence-able fragments across all nine species. Building libraries off this enzyme pair, we found a range of usable SNPs between 4000 and 37 000 SNPS per species and we found a greater number of usable SNPs using reference genomes than de novo pipelines in STACKS. We also found fewer reads in the Read 2 fragments from the paired-end Illumina Hiseq run. Overall, the results of this study provide empirical evidence of the utility of this method for producing consistent data for diverse nonmodel species and suggest specific considerations for sequencing analysis strategies.
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Affiliation(s)
- M O Burford Reiskind
- Department of Applied Ecology, North Carolina State University, Campus Box 7617, Raleigh, NC, 27695, USA.
| | - K Coyle
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, 27695, USA
| | - H V Daniels
- Department of Applied Ecology, North Carolina State University, Campus Box 7617, Raleigh, NC, 27695, USA
| | - P Labadie
- Department of Entomology, North Carolina State University, Raleigh, NC, 27695, USA
| | - M H Reiskind
- Department of Entomology, North Carolina State University, Raleigh, NC, 27695, USA
| | - N B Roberts
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, 27695, USA
| | - R B Roberts
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, 27695, USA
| | - J Schaff
- Genomic Sciences Laboratory, North Carolina State University, Raleigh, NC, 27695, USA
| | - E L Vargo
- Department of Entomology, Texas A&M University, College Station, TX, 77843, USA
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44
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Wessinger CA, Freeman CC, Mort ME, Rausher MD, Hileman LC. Multiplexed shotgun genotyping resolves species relationships within the North American genus Penstemon. AMERICAN JOURNAL OF BOTANY 2016; 103:912-22. [PMID: 27208359 PMCID: PMC10874106 DOI: 10.3732/ajb.1500519] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 03/16/2016] [Indexed: 06/05/2023]
Abstract
PREMISE OF THE STUDY Evolutionary radiations provide opportunities to examine large-scale patterns in diversification and character evolution, yet are often recalcitrant to phylogenetic resolution due to rapid speciation events. The plant genus Penstemon has been difficult to resolve using Sanger sequence-based markers, leading to the hypothesis that it represents a recent North American radiation. The current study demonstrates the utility of multiplexed shotgun genotyping (MSG), a style of restriction site-associated DNA sequencing (RADseq), to infer phylogenetic relationships within a subset of species in this genus and provide insight into evolutionary patterns. METHODS We sampled genomic DNA, primarily from herbarium material, and subjected it to MSG library preparation and Illumina sequencing. The resultant sequencing reads were clustered into homologous loci, aligned, and concatenated into data matrices that differed according to clustering similarity and amount of missing data. We performed phylogenetic analyses on these matrices using maximum likelihood (RAxML) and a species tree approach (SVDquartets). KEY RESULTS MSG data provide a highly resolved estimate of species relationships within Penstemon. While most species relationships were highly supported, the position of certain taxa remains ambiguous, suggesting that increased taxonomic sampling or additional methodologies may be required. The data confirm that evolutionary shifts from hymenopteran- to hummingbird-adapted flowers have occurred independently many times. CONCLUSIONS This study demonstrates that phylogenomic approaches yielding thousands of variable sites can greatly improve species-level resolution of recent and rapid radiations. Similar to other studies, we found that less conservative similarity and missing data thresholds resulted in more highly supported topologies.
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Affiliation(s)
- Carolyn A Wessinger
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas 66045 USA
| | - Craig C Freeman
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas 66045 USA R.L. McGregor Herbarium and Kansas Biological Survey, University of Kansas, Lawrence, Kansas 66047 USA
| | - Mark E Mort
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas 66045 USA
| | - Mark D Rausher
- Department of Biology, Duke University, Box 90338 Durham, North Carolina 27708 USA
| | - Lena C Hileman
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas 66045 USA
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45
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Schumer M, Cui R, Powell DL, Rosenthal GG, Andolfatto P. Ancient hybridization and genomic stabilization in a swordtail fish. Mol Ecol 2016; 25:2661-79. [DOI: 10.1111/mec.13602] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 01/06/2016] [Accepted: 01/06/2016] [Indexed: 01/13/2023]
Affiliation(s)
- Molly Schumer
- Department of Ecology and Evolutionary Biology Princeton University Princeton NJ 08544 USA
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca” 16 de Septiembre 392 Calnali Hidalgo 43230 Mexico
| | - Rongfeng Cui
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca” 16 de Septiembre 392 Calnali Hidalgo 43230 Mexico
- Department of Biology Texas A&M University TAMU College Station TX 77843 USA
- Max Planck Institute for the Biology of Aging D‐50931 Cologne Germany
| | - Daniel L. Powell
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca” 16 de Septiembre 392 Calnali Hidalgo 43230 Mexico
- Department of Biology Texas A&M University TAMU College Station TX 77843 USA
| | - Gil G. Rosenthal
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca” 16 de Septiembre 392 Calnali Hidalgo 43230 Mexico
- Department of Biology Texas A&M University TAMU College Station TX 77843 USA
| | - Peter Andolfatto
- Department of Ecology and Evolutionary Biology Princeton University Princeton NJ 08544 USA
- Lewis‐Sigler Institute for Integrative Genomics Princeton University Princeton NJ 08544 USA
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46
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Takahashi T, Sota T. A robust phylogeny among major lineages of the East African cichlids. Mol Phylogenet Evol 2016; 100:234-242. [PMID: 27068840 DOI: 10.1016/j.ympev.2016.04.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 03/16/2016] [Accepted: 04/07/2016] [Indexed: 11/30/2022]
Abstract
The huge monophyletic group of the East African cichlid radiations (EAR) consists of thousands of species belonging to 12-14 tribes; the number of tribes differs among studies. Many studies have inferred phylogenies of EAR tribes using various genetic markers. However, these phylogenies partly contradict one another and can have weak statistic support. In this study, we conducted maximum-likelihood (ML) phylogenetic analyses using restriction site-associated DNA (RAD) sequences and propose a new robust phylogenetic hypothesis among Lake Tanganyika cichlid fishes, which cover most EAR tribes. Data matrices can vary in size and contents depending on the strategies used to process RAD sequences. Therefore, we prepared 23 data matrices with various processing strategies. The ML phylogenies inferred from 15 large matrices (2.0×10(6) to 1.1×10(7) base pairs) resolved every tribe as a monophyletic group with 100% bootstrap support and shared the same topology regarding relationships among the tribes. Most nodes among the tribes were supported by 100% bootstrap values, and the bootstrap support for the other node varied among the 15 ML trees from 70% to 100%. These robust ML trees differ partly in topology from those in earlier studies, and these phylogenetic relationships have important implications for the tribal classification of EAR.
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Affiliation(s)
- Tetsumi Takahashi
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan; National Institute of Genetics, Yata, Mishima, Shizuoka 411-8540, Japan.
| | - Teiji Sota
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
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47
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Fountain ED, Pauli JN, Reid BN, Palsbøll PJ, Peery MZ. Finding the right coverage: the impact of coverage and sequence quality on single nucleotide polymorphism genotyping error rates. Mol Ecol Resour 2016; 16:966-78. [DOI: 10.1111/1755-0998.12519] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 02/10/2016] [Accepted: 02/11/2016] [Indexed: 12/13/2022]
Affiliation(s)
- Emily D. Fountain
- Department of Forest and Wildlife Ecology University of Wisconsin‐Madison Madison WI 53706 USA
| | - Jonathan N. Pauli
- Department of Forest and Wildlife Ecology University of Wisconsin‐Madison Madison WI 53706 USA
| | - Brendan N. Reid
- Department of Forest and Wildlife Ecology University of Wisconsin‐Madison Madison WI 53706 USA
| | - Per J. Palsbøll
- Marine Evolution and Conservation Groningen Institute of Evolutionary Life Sciences University of Groningen Groningen9747 AG The Netherlands
| | - M. Zachariah Peery
- Department of Forest and Wildlife Ecology University of Wisconsin‐Madison Madison WI 53706 USA
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48
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Suchan T, Pitteloud C, Gerasimova NS, Kostikova A, Schmid S, Arrigo N, Pajkovic M, Ronikier M, Alvarez N. Hybridization Capture Using RAD Probes (hyRAD), a New Tool for Performing Genomic Analyses on Collection Specimens. PLoS One 2016; 11:e0151651. [PMID: 26999359 PMCID: PMC4801390 DOI: 10.1371/journal.pone.0151651] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 03/02/2016] [Indexed: 11/19/2022] Open
Abstract
In the recent years, many protocols aimed at reproducibly sequencing reduced-genome subsets in non-model organisms have been published. Among them, RAD-sequencing is one of the most widely used. It relies on digesting DNA with specific restriction enzymes and performing size selection on the resulting fragments. Despite its acknowledged utility, this method is of limited use with degraded DNA samples, such as those isolated from museum specimens, as these samples are less likely to harbor fragments long enough to comprise two restriction sites making possible ligation of the adapter sequences (in the case of double-digest RAD) or performing size selection of the resulting fragments (in the case of single-digest RAD). Here, we address these limitations by presenting a novel method called hybridization RAD (hyRAD). In this approach, biotinylated RAD fragments, covering a random fraction of the genome, are used as baits for capturing homologous fragments from genomic shotgun sequencing libraries. This simple and cost-effective approach allows sequencing of orthologous loci even from highly degraded DNA samples, opening new avenues of research in the field of museum genomics. Not relying on the restriction site presence, it improves among-sample loci coverage. In a trial study, hyRAD allowed us to obtain a large set of orthologous loci from fresh and museum samples from a non-model butterfly species, with a high proportion of single nucleotide polymorphisms present in all eight analyzed specimens, including 58-year-old museum samples. The utility of the method was further validated using 49 museum and fresh samples of a Palearctic grasshopper species for which the spatial genetic structure was previously assessed using mtDNA amplicons. The application of the method is eventually discussed in a wider context. As it does not rely on the restriction site presence, it is therefore not sensitive to among-sample loci polymorphisms in the restriction sites that usually causes loci dropout. This should enable the application of hyRAD to analyses at broader evolutionary scales.
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Affiliation(s)
- Tomasz Suchan
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- * E-mail: (TS); (N. Alvarez)
| | - Camille Pitteloud
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Nadezhda S. Gerasimova
- Biology Faculty, Lomonosov Moscow State University, Moscow, Russia
- InsideDNA Ltd., London, United Kingdom
| | | | - Sarah Schmid
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Nils Arrigo
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Mila Pajkovic
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Michał Ronikier
- Institute of Botany, Polish Academy of Sciences, Kraków, Poland
| | - Nadir Alvarez
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- * E-mail: (TS); (N. Alvarez)
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49
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Culumber ZW, Tobler M. Ecological divergence and conservatism: spatiotemporal patterns of niche evolution in a genus of livebearing fishes (Poeciliidae: Xiphophorus). BMC Evol Biol 2016; 16:44. [PMID: 26895994 PMCID: PMC4761163 DOI: 10.1186/s12862-016-0593-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 01/13/2016] [Indexed: 01/23/2023] Open
Abstract
Background Ecological factors often have a strong impact on spatiotemporal patterns of biodiversity. The integration of spatial ecology and phylogenetics allows for rigorous tests of whether speciation is associated with niche conservatism (constraints on ecological divergence) or niche divergence. We address this question in a genus of livebearing fishes for which the role of sexual selection in speciation has long been studied, but in which the potential role of ecological divergence during speciation has not been tested. Results By combining reconstruction of ancestral climate tolerances and disparity indices, we show that the earliest evolutionary split in Xiphophorus was associated with significant divergence for temperature variables. Niche evolution and present day niches were most closely associated with each species’ geographic distribution relative to a biogeographic barrier, the Trans-Mexican Volcanic Belt. Tests for similarity of the environmental backgrounds of closely related species suggested that the relative importance of niche conservatism and divergence during speciation varied among the primary clades of Xiphophorus. Closely related species in the two swordtail clades exhibited higher levels of niche overlap than expected given environmental background similarity indicative of niche conservatism. In contrast, almost all species of platyfish had significantly divergent niches compared to environmental backgrounds, which is indicative of niche divergence. Conclusion The results suggest that the relative importance of niche conservatism and divergence differed among the clades of Xiphophorus and that traits associated with niche evolution may be more evolutionarily labile in the platyfishes. Our results ultimately suggest that the taxonomic scale of tests for conservatism and divergence could greatly influence inferences of their relative importance in the speciation process. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0593-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zachary W Culumber
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA.
| | - Michael Tobler
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
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50
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Uribe-Convers S, Settles ML, Tank DC. A Phylogenomic Approach Based on PCR Target Enrichment and High Throughput Sequencing: Resolving the Diversity within the South American Species of Bartsia L. (Orobanchaceae). PLoS One 2016; 11:e0148203. [PMID: 26828929 PMCID: PMC4734709 DOI: 10.1371/journal.pone.0148203] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 01/14/2016] [Indexed: 11/30/2022] Open
Abstract
Advances in high-throughput sequencing (HTS) have allowed researchers to obtain large amounts of biological sequence information at speeds and costs unimaginable only a decade ago. Phylogenetics, and the study of evolution in general, is quickly migrating towards using HTS to generate larger and more complex molecular datasets. In this paper, we present a method that utilizes microfluidic PCR and HTS to generate large amounts of sequence data suitable for phylogenetic analyses. The approach uses the Fluidigm Access Array System (Fluidigm, San Francisco, CA, USA) and two sets of PCR primers to simultaneously amplify 48 target regions across 48 samples, incorporating sample-specific barcodes and HTS adapters (2,304 unique amplicons per Access Array). The final product is a pooled set of amplicons ready to be sequenced, and thus, there is no need to construct separate, costly genomic libraries for each sample. Further, we present a bioinformatics pipeline to process the raw HTS reads to either generate consensus sequences (with or without ambiguities) for every locus in every sample or—more importantly—recover the separate alleles from heterozygous target regions in each sample. This is important because it adds allelic information that is well suited for coalescent-based phylogenetic analyses that are becoming very common in conservation and evolutionary biology. To test our approach and bioinformatics pipeline, we sequenced 576 samples across 96 target regions belonging to the South American clade of the genus Bartsia L. in the plant family Orobanchaceae. After sequencing cleanup and alignment, the experiment resulted in ~25,300bp across 486 samples for a set of 48 primer pairs targeting the plastome, and ~13,500bp for 363 samples for a set of primers targeting regions in the nuclear genome. Finally, we constructed a combined concatenated matrix from all 96 primer combinations, resulting in a combined aligned length of ~40,500bp for 349 samples.
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Affiliation(s)
- Simon Uribe-Convers
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, United States of America
- Stillinger Herbarium, University of Idaho, Moscow, Idaho, United States of America
- * E-mail:
| | - Matthew L. Settles
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, United States of America
| | - David C. Tank
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, United States of America
- Stillinger Herbarium, University of Idaho, Moscow, Idaho, United States of America
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