51
|
A RAD-based phylogenetics for Orestias fishes from Lake Titicaca. Mol Phylogenet Evol 2015; 93:307-17. [DOI: 10.1016/j.ympev.2015.08.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 08/11/2015] [Accepted: 08/11/2015] [Indexed: 11/18/2022]
|
52
|
|
53
|
DaCosta JM, Sorenson MD. ddRAD-seq phylogenetics based on nucleotide, indel, and presence-absence polymorphisms: Analyses of two avian genera with contrasting histories. Mol Phylogenet Evol 2015; 94:122-35. [PMID: 26279345 DOI: 10.1016/j.ympev.2015.07.026] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 07/22/2015] [Accepted: 07/29/2015] [Indexed: 11/16/2022]
Abstract
Genotype-by-sequencing (GBS) methods have revolutionized the field of molecular ecology, but their application in molecular phylogenetics remains somewhat limited. In addition, most phylogenetic studies based on large GBS data sets have relied on analyses of concatenated data rather than species tree methods that explicitly account for genealogical stochasticity among loci. We explored the utility of "double-digest" restriction site-associated DNA sequencing (ddRAD-seq) for phylogenetic analyses of the Lagonosticta firefinches (family Estrildidae) and the Vidua brood parasitic finches (family Viduidae). As expected, the number of homologous loci shared among samples was negatively correlated with genetic distance due to the accumulation of restriction site polymorphisms. Nonetheless, for each genus, we obtained data sets of ∼3000 loci shared in common among all samples, including a more distantly related outgroup taxon. For all samples combined, we obtained >1000 homologous loci despite ∼20my divergence between estrildid and parasitic finches. In addition to nucleotide polymorphisms, the ddRAD-seq data yielded large sets of indel and locus presence-absence polymorphisms, all of which had higher consistency indices than mtDNA sequence data in the context of concatenated parsimony analyses. Species tree methods, using individual gene trees or single nucleotide polymorphisms as input, generated results broadly consistent with analyses of concatenated data, particularly for Lagonosticta, which appears to have a well resolved, bifurcating history. Results for Vidua were also generally consistent across methods and data sets, although nodal support and results from different species tree methods were more variable. Lower gene tree congruence in Vidua is likely the result of its unique evolutionary history, which includes rapid speciation by host shift and occasional hybridization and introgression due to incomplete reproductive isolation. We conclude that ddRAD-seq is a cost-effective method for generating robust phylogenetic data sets, particularly for analyses of closely related species and genera.
Collapse
|
54
|
Kottler VA, Künstner A, Koch I, Flötenmeyer M, Langenecker T, Hoffmann M, Sharma E, Weigel D, Dreyer C. Adenylate cyclase 5
is required for melanophore and male pattern development in the guppy (Poecilia reticulata
). Pigment Cell Melanoma Res 2015; 28:545-58. [DOI: 10.1111/pcmr.12386] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 05/27/2015] [Indexed: 11/30/2022]
Affiliation(s)
| | - Axel Künstner
- Max Planck Institute for Developmental Biology; Tübingen Germany
| | - Iris Koch
- Max Planck Institute for Developmental Biology; Tübingen Germany
| | | | | | | | - Eshita Sharma
- Max Planck Institute for Developmental Biology; Tübingen Germany
| | - Detlef Weigel
- Max Planck Institute for Developmental Biology; Tübingen Germany
| | - Christine Dreyer
- Max Planck Institute for Developmental Biology; Tübingen Germany
| |
Collapse
|
55
|
Gonen S, Bishop SC, Houston RD. Exploring the utility of cross-laboratory RAD-sequencing datasets for phylogenetic analysis. BMC Res Notes 2015; 8:299. [PMID: 26152111 PMCID: PMC4495686 DOI: 10.1186/s13104-015-1261-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 06/25/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Restriction site-Associated DNA sequencing (RAD-Seq) is widely applied to generate genome-wide sequence and genetic marker datasets. RAD-Seq has been extensively utilised, both at the population level and across species, for example in the construction of phylogenetic trees. However, the consistency of RAD-Seq data generated in different laboratories, and the potential use of cross-species orthologous RAD loci in the estimation of genetic relationships, have not been widely investigated. This study describes the use of SbfI RAD-Seq data for the estimation of evolutionary relationships amongst ten teleost fish species, using previously established phylogeny as a benchmark. RESULTS The number of orthologous SbfI RAD loci identified decreased with increasing evolutionary distance between the species, with several thousand loci conserved across five salmonid species (divergence ~50 MY), and several hundred conserved across the more distantly related teleost species (divergence ~100-360 MY). The majority (>70%) of loci identified between the more distantly related species were genic in origin, suggesting that the bias of SbfI towards genic regions is useful for identifying distant orthologs. Interspecific single nucleotide variants at each orthologous RAD locus were identified. Evolutionary relationships estimated using concatenated sequences of interspecific variants were congruent with previously published phylogenies, even for distantly (divergence up to ~360 MY) related species. CONCLUSION Overall, this study has demonstrated that orthologous SbfI RAD loci can be identified across closely and distantly related species. This has positive implications for the repeatability of SbfI RAD-Seq and its potential to address research questions beyond the scope of the original studies. Furthermore, the concordance in tree topologies and relationships estimated in this study with published teleost phylogenies suggests that similar meta-datasets could be utilised in the prediction of evolutionary relationships across populations and species with readily available RAD-Seq datasets, but for which relationships remain uncharacterised.
Collapse
Affiliation(s)
- Serap Gonen
- The Roslin Institute, University of Edinburgh, Midlothian, EH25 9RG, Scotland, UK.
| | - Stephen C Bishop
- The Roslin Institute, University of Edinburgh, Midlothian, EH25 9RG, Scotland, UK.
| | - Ross D Houston
- The Roslin Institute, University of Edinburgh, Midlothian, EH25 9RG, Scotland, UK.
| |
Collapse
|
56
|
Ebel ER, DaCosta JM, Sorenson MD, Hill RI, Briscoe AD, Willmott KR, Mullen SP. Rapid diversification associated with ecological specialization in NeotropicalAdelphabutterflies. Mol Ecol 2015; 24:2392-405. [DOI: 10.1111/mec.13168] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Revised: 03/17/2015] [Accepted: 03/18/2015] [Indexed: 01/15/2023]
Affiliation(s)
- Emily R. Ebel
- Department of Biology; Boston University; Boston MA 02215 USA
| | | | | | - Ryan I. Hill
- Department of Biological Sciences; University of the Pacific; Stockton CA 95211 USA
| | - Adriana D. Briscoe
- Department of Ecology and Evolutionary Biology; University of California; Irvine CA 92697 USA
| | - Keith R. Willmott
- McGuire Center for Lepidoptera and Biodiversity; Florida Museum of Natural History; University of Florida; Gainesville FL 32611 USA
| | - Sean P. Mullen
- Department of Biology; Boston University; Boston MA 02215 USA
| |
Collapse
|
57
|
Stervander M, Illera JC, Kvist L, Barbosa P, Keehnen NP, Pruisscher P, Bensch S, Hansson B. Disentangling the complex evolutionary history of the Western Palearctic blue tits (Cyanistes spp.) - phylogenomic analyses suggest radiation by multiple colonization events and subsequent isolation. Mol Ecol 2015; 24:2477-94. [PMID: 25753616 DOI: 10.1111/mec.13145] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 02/20/2015] [Accepted: 02/25/2015] [Indexed: 01/16/2023]
Abstract
Isolated islands and their often unique biota continue to play key roles for understanding the importance of drift, genetic variation and adaptation in the process of population differentiation and speciation. One island system that has inspired and intrigued evolutionary biologists is the blue tit complex (Cyanistes spp.) in Europe and Africa, in particular the complex evolutionary history of the multiple genetically distinct taxa of the Canary Islands. Understanding Afrocanarian colonization events is of particular importance because of recent unconventional suggestions that these island populations acted as source of the widespread population in mainland Africa. We investigated the relationship between mainland and island blue tits using a combination of Sanger sequencing at a population level (20 loci; 12 500 nucleotides) and next-generation sequencing of single population representatives (>3 200 000 nucleotides), analysed in coalescence and phylogenetic frameworks. We found (i) that Afrocanarian blue tits are monophyletic and represent four major clades, (ii) that the blue tit complex has a continental origin and that the Canary Islands were colonized three times, (iii) that all island populations have low genetic variation, indicating low long-term effective population sizes and (iv) that populations on La Palma and in Libya represent relicts of an ancestral North African population. Further, demographic reconstructions revealed (v) that the Canary Islands, conforming to traditional views, hold sink populations, which have not served as source for back colonization of the African mainland. Our study demonstrates the importance of complete taxon sampling and an extensive multimarker study design to obtain robust phylogeographical inferences.
Collapse
Affiliation(s)
- Martin Stervander
- Molecular Ecology and Evolution Lab, Department of Biology, Lund University, Ecology Building, 223 62, Lund, Sweden
| | | | | | | | | | | | | | | |
Collapse
|
58
|
Mason NA, Taylor SA. Differentially expressed genes match bill morphology and plumage despite largely undifferentiated genomes in a Holarctic songbird. Mol Ecol 2015; 24:3009-25. [DOI: 10.1111/mec.13140] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 02/27/2015] [Indexed: 12/30/2022]
Affiliation(s)
- Nicholas A. Mason
- Department of Ecology and Evolutionary Biology; Cornell University; 215 Tower Rd. Ithaca NY 14853 USA
- Fuller Evolutionary Biology Program; Laboratory of Ornithology; Cornell University; 159 Sapsucker Woods Road Ithaca NY 14850 USA
| | - Scott A. Taylor
- Department of Ecology and Evolutionary Biology; Cornell University; 215 Tower Rd. Ithaca NY 14853 USA
- Fuller Evolutionary Biology Program; Laboratory of Ornithology; Cornell University; 159 Sapsucker Woods Road Ithaca NY 14850 USA
| |
Collapse
|
59
|
Macher JN, Rozenberg A, Pauls SU, Tollrian R, Wagner R, Leese F. Assessing the phylogeographic history of the montane caddisfly Thremma gallicum using mitochondrial and restriction-site-associated DNA (RAD) markers. Ecol Evol 2015; 5:648-62. [PMID: 25691988 PMCID: PMC4328769 DOI: 10.1002/ece3.1366] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 11/17/2014] [Indexed: 12/24/2022] Open
Abstract
Repeated Quaternary glaciations have significantly shaped the present distribution and diversity of several European species in aquatic and terrestrial habitats. To study the phylogeography of freshwater invertebrates, patterns of intraspecific variation have been examined primarily using mitochondrial DNA markers that may yield results unrepresentative of the true species history. Here, population genetic parameters were inferred for a montane aquatic caddisfly, Thremma gallicum, by sequencing a 658-bp fragment of the mitochondrial CO1 gene, and 12,514 nuclear RAD loci. T. gallicum has a highly disjunct distribution in southern and central Europe, with known populations in the Cantabrian Mountains, Pyrenees, Massif Central, and Black Forest. Both datasets represented rangewide sampling of T. gallicum. For the CO1 dataset, this included 352 specimens from 26 populations, and for the RAD dataset, 17 specimens from eight populations. We tested 20 competing phylogeographic scenarios using approximate Bayesian computation (ABC) and estimated genetic diversity patterns. Support for phylogeographic scenarios and diversity estimates differed between datasets with the RAD data favouring a southern origin of extant populations and indicating the Cantabrian Mountains and Massif Central populations to represent highly diverse populations as compared with the Pyrenees and Black Forest populations. The CO1 data supported a vicariance scenario (north-south) and yielded inconsistent diversity estimates. Permutation tests suggest that a few hundred polymorphic RAD SNPs are necessary for reliable parameter estimates. Our results highlight the potential of RAD and ABC-based hypothesis testing to complement phylogeographic studies on non-model species.
Collapse
Affiliation(s)
- Jan-Niklas Macher
- Department of Animal Ecology, Evolution and Biodiversity, Ruhr University BochumUniversitätsstraße 150, 44801, Bochum, Germany
| | - Andrey Rozenberg
- Department of Animal Ecology, Evolution and Biodiversity, Ruhr University BochumUniversitätsstraße 150, 44801, Bochum, Germany
| | - Steffen U Pauls
- Biodiversity and Climate Research Centre (BiK-F)Senckenberganlage 25, 60325, Frankfurt am Main, Germany
- Senckenberg Gesellschaft für NaturforschungSenckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Ralph Tollrian
- Department of Animal Ecology, Evolution and Biodiversity, Ruhr University BochumUniversitätsstraße 150, 44801, Bochum, Germany
| | - Rüdiger Wagner
- Working Group Limnology, University of KasselHeinrich-Plett-Straße 30, 34132, Kassel, Germany
- Max Planck Institute for Evolutionary BiologyAugust-Thienemann-Straße 2, 24306, Plön, Germany
| | - Florian Leese
- Department of Animal Ecology, Evolution and Biodiversity, Ruhr University BochumUniversitätsstraße 150, 44801, Bochum, Germany
| |
Collapse
|
60
|
Herrera S, Watanabe H, Shank TM. Evolutionary and biogeographical patterns of barnacles from deep-sea hydrothermal vents. Mol Ecol 2015; 24:673-89. [PMID: 25602032 PMCID: PMC5006861 DOI: 10.1111/mec.13054] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 12/14/2014] [Accepted: 12/20/2014] [Indexed: 01/16/2023]
Abstract
The characterization of evolutionary and biogeographical patterns is of fundamental importance to identify factors driving biodiversity. Due to their widespread but discontinuous distribution, deep-sea hydrothermal vent barnacles represent an excellent model for testing biogeographical hypotheses regarding the origin, dispersal and diversity of modern vent fauna. Here, we characterize the global genetic diversity of vent barnacles to infer their time of radiation, place of origin, mode of dispersal and diversification. Our approach was to target a suite of multiple loci in samples representing seven of the eight described genera. We also performed restriction-site associated DNA sequencing on individuals from each species. Phylogenetic inferences and topology hypothesis tests indicate that vent barnacles have colonized deep-sea hydrothermal vents at least twice in history. Consistent with preliminary estimates, we find a likely radiation of barnacles in vent ecosystems during the Cenozoic. Our analyses suggest that the western Pacific was the place of origin of the major vent barnacle lineage, followed by circumglobal colonization eastwards through the Southern Hemisphere during the Neogene. The inferred time of radiation rejects the classic hypotheses of antiquity of vent taxa. The timing and the mode of origin, radiation and dispersal are consistent with recent inferences made for other deep-sea taxa, including nonvent species, and are correlated with the occurrence of major geological events and mass extinctions. Thus, we suggest that the geological processes and dispersal mechanisms discussed here can explain the current distribution patterns of many other marine taxa and have played an important role shaping deep-sea faunal diversity. These results also constitute the critical baseline data with which to assess potential effects of anthropogenic disturbances on deep-sea ecosystems.
Collapse
Affiliation(s)
- Santiago Herrera
- Massachusetts Institute of Technology77 Massachusetts AvenueCambridgeMA02139USA
- Biology DepartmentWoods Hole Oceanographic Institution266 Woods Hole RoadWoods HoleMA02543USA
| | - Hiromi Watanabe
- Institute of BiogeosciencesJapan Agency for Marine‐Earth Science and TechnologyYokosukaKanagawaJapan
| | - Timothy M. Shank
- Biology DepartmentWoods Hole Oceanographic Institution266 Woods Hole RoadWoods HoleMA02543USA
| |
Collapse
|
61
|
Kang JH, Manousaki T, Franchini P, Kneitz S, Schartl M, Meyer A. Transcriptomics of two evolutionary novelties: how to make a sperm-transfer organ out of an anal fin and a sexually selected "sword" out of a caudal fin. Ecol Evol 2015; 5:848-64. [PMID: 25750712 PMCID: PMC4338968 DOI: 10.1002/ece3.1390] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 12/10/2014] [Accepted: 12/12/2014] [Indexed: 01/09/2023] Open
Abstract
Swords are exaggerated male ornaments of swordtail fishes that have been of great interest to evolutionary biologists ever since Darwin described them in the Descent of Man (1871). They are a novel sexually selected trait derived from modified ventral caudal fin rays and are only found in the genus Xiphophorus. Another phylogenetically more widespread and older male trait is the gonopodium, an intromittent organ found in all poeciliid fishes, that is derived from a modified anal fin. Despite many evolutionary and behavioral studies on both traits, little is known so far about the molecular mechanisms underlying their development. By investigating transcriptomic changes (utilizing a RNA-Seq approach) in response to testosterone treatment in the swordtail fish, Xiphophorus hellerii, we aimed to better understand the architecture of the gene regulatory networks underpinning the development of these two evolutionary novelties. Large numbers of genes with tissue-specific expression patterns were identified. Among the "sword genes" those involved in embryonic organ development, sexual character development and coloration were highly expressed, while in the gonopodium rather more morphogenesis-related genes were found. Interestingly, many genes and genetic pathways are shared between both developing novel traits derived from median fins: the sword and the gonopodium. Our analyses show that a larger set of gene networks was co-opted during the development and evolution of the "older" gonopodium than in the "younger," and morphologically less complex trait, the sword. We provide a catalog of candidate genes for future efforts to dissect the development of those sexually selected exaggerated male traits in swordtails.
Collapse
Affiliation(s)
- Ji Hyoun Kang
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of KonstanzUniversitätsstraβe 10, 78457, Konstanz, Germany
- Konstanz Research School Chemical Biology, University of KonstanzKonstanz, Germany
| | - Tereza Manousaki
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of KonstanzUniversitätsstraβe 10, 78457, Konstanz, Germany
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine ResearchHeraklion, Greece
| | - Paolo Franchini
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of KonstanzUniversitätsstraβe 10, 78457, Konstanz, Germany
| | - Susanne Kneitz
- Physiological Chemistry, Biozentrum, University of WürzburgAm Hubland, Würzburg, Germany
| | - Manfred Schartl
- Physiological Chemistry, Biozentrum, University of WürzburgAm Hubland, Würzburg, Germany
- Comprehensive Cancer Center, University Clinic WürzburgJosef Schneider Straβe 6, 97074, Würzburg, Germany
| | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of KonstanzUniversitätsstraβe 10, 78457, Konstanz, Germany
- Konstanz Research School Chemical Biology, University of KonstanzKonstanz, Germany
| |
Collapse
|
62
|
|
63
|
McCluskey BM, Postlethwait JH. Phylogeny of zebrafish, a "model species," within Danio, a "model genus". Mol Biol Evol 2014; 32:635-52. [PMID: 25415969 DOI: 10.1093/molbev/msu325] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Zebrafish (Danio rerio) is an important model for vertebrate development, genomics, physiology, behavior, toxicology, and disease. Additionally, work on numerous Danio species is elucidating evolutionary mechanisms for morphological development. Yet, the relationships of zebrafish and its closest relatives remain unclear possibly due to incomplete lineage sorting, speciation with gene flow, and interspecies hybridization. To clarify these relationships, we first constructed phylogenomic data sets from 30,801 restriction-associated DNA (RAD)-tag loci (483,026 variable positions) with clear orthology to a single location in the sequenced zebrafish genome. We then inferred a well-supported species tree for Danio and tested for gene flow during the diversification of the genus. An approach independent of the sequenced zebrafish genome verified all inferred relationships. Although identification of the sister taxon to zebrafish has been contentious, multiple RAD-tag data sets and several analytical methods provided strong evidence for Danio aesculapii as the most closely related extant zebrafish relative studied to date. Data also displayed patterns consistent with gene flow during speciation and postspeciation introgression in the lineage leading to zebrafish. The incorporation of biogeographic data with phylogenomic analyses put these relationships in a phylogeographic context and supplied additional support for D. aesculapii as the sister species to D. rerio. The clear resolution of this study establishes a framework for investigating the evolutionary biology of Danio and the heterogeneity of genome evolution in the recent history of a model organism within an emerging model genus for genetics, development, and evolution.
Collapse
|
64
|
Pante E, Abdelkrim J, Viricel A, Gey D, France SC, Boisselier MC, Samadi S. Use of RAD sequencing for delimiting species. Heredity (Edinb) 2014; 114:450-9. [PMID: 25407078 DOI: 10.1038/hdy.2014.105] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2014] [Revised: 09/12/2014] [Accepted: 09/16/2014] [Indexed: 11/10/2022] Open
Abstract
RAD-tag sequencing is a promising method for conducting genome-wide evolutionary studies. However, to date, only a handful of studies empirically tested its applicability above the species level. In this communication, we use RAD tags to contribute to the delimitation of species within a diverse genus of deep-sea octocorals, Chrysogorgia, for which few classical genetic markers have proved informative. Previous studies have hypothesized that single mitochondrial haplotypes can be used to delimit Chrysogorgia species. On the basis of two lanes of Illumina sequencing, we inferred phylogenetic relationships among 12 putative species that were delimited using mitochondrial data, comparing two RAD analysis pipelines (Stacks and PyRAD). The number of homologous RAD loci decreased dramatically with increasing divergence, as >70% of loci are lost when comparing specimens separated by two mutations on the 700-nt long mitochondrial phylogeny. Species delimitation hypotheses based on the mitochondrial mtMutS gene are largely supported, as six out of nine putative species represented by more than one colony were recovered as discrete, well-supported clades. Significant genetic structure (correlating with geography) was detected within one putative species, suggesting that individuals characterized by the same mtMutS haplotype may belong to distinct species. Conversely, three mtMutS haplotypes formed one well-supported clade within which no population structure was detected, also suggesting that intraspecific variation exists at mtMutS in Chrysogorgia. Despite an impressive decrease in the number of homologous loci across clades, RAD data helped us to fine-tune our interpretations of classical mitochondrial markers used in octocoral species delimitation, and discover previously undetected diversity.
Collapse
Affiliation(s)
- E Pante
- Laboratoire LIENSs, UMR 7266 CNRS-Université de La Rochelle, La Rochelle, France
| | - J Abdelkrim
- 1] Département Systématique et Evolution, UMS 2700 MNHN-CNRS, SSM, Muséum national d'Histoire naturelle, Paris, France [2] ISYEB-UMR 7205-CNRS, MNHN, UPMC, EPHE, Muséum national d'Histoire naturelle, Sorbonne Universités, Paris, France
| | - A Viricel
- Laboratoire LIENSs, UMR 7266 CNRS-Université de La Rochelle, La Rochelle, France
| | - D Gey
- Département Systématique et Evolution, UMS 2700 MNHN-CNRS, SSM, Muséum national d'Histoire naturelle, Paris, France
| | - S C France
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA, USA
| | - M C Boisselier
- 1] Département Systématique et Evolution, UMS 2700 MNHN-CNRS, SSM, Muséum national d'Histoire naturelle, Paris, France [2] ISYEB-UMR 7205-CNRS, MNHN, UPMC, EPHE, Muséum national d'Histoire naturelle, Sorbonne Universités, Paris, France
| | - S Samadi
- ISYEB-UMR 7205-CNRS, MNHN, UPMC, EPHE, Muséum national d'Histoire naturelle, Sorbonne Universités, Paris, France
| |
Collapse
|
65
|
Takahashi T, Nagata N, Sota T. Application of RAD-based phylogenetics to complex relationships among variously related taxa in a species flock. Mol Phylogenet Evol 2014; 80:137-44. [DOI: 10.1016/j.ympev.2014.07.016] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 06/30/2014] [Accepted: 07/24/2014] [Indexed: 11/17/2022]
|
66
|
Braasch I, Peterson SM, Desvignes T, McCluskey BM, Batzel P, Postlethwait JH. A new model army: Emerging fish models to study the genomics of vertebrate Evo-Devo. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2014; 324:316-41. [PMID: 25111899 DOI: 10.1002/jez.b.22589] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Revised: 06/19/2014] [Accepted: 06/25/2014] [Indexed: 01/08/2023]
Abstract
Many fields of biology--including vertebrate Evo-Devo research--are facing an explosion of genomic and transcriptomic sequence information and a multitude of fish species are now swimming in this "genomic tsunami." Here, we first give an overview of recent developments in sequencing fish genomes and transcriptomes that identify properties of fish genomes requiring particular attention and propose strategies to overcome common challenges in fish genomics. We suggest that the generation of chromosome-level genome assemblies--for which we introduce the term "chromonome"--should be a key component of genomic investigations in fish because they enable large-scale conserved synteny analyses that inform orthology detection, a process critical for connectivity of genomes. Orthology calls in vertebrates, especially in teleost fish, are complicated by divergent evolution of gene repertoires and functions following two rounds of genome duplication in the ancestor of vertebrates and a third round at the base of teleost fish. Second, using examples of spotted gar, basal teleosts, zebrafish-related cyprinids, cavefish, livebearers, icefish, and lobefin fish, we illustrate how next generation sequencing technologies liberate emerging fish systems from genomic ignorance and transform them into a new model army to answer longstanding questions on the genomic and developmental basis of their biodiversity. Finally, we discuss recent progress in the genetic toolbox for the major fish models for functional analysis, zebrafish, and medaka, that can be transferred to many other fish species to study in vivo the functional effect of evolutionary genomic change as Evo-Devo research enters the postgenomic era.
Collapse
Affiliation(s)
- Ingo Braasch
- Institute of Neuroscience, University of Oregon, Eugene, Oregon
| | | | | | | | - Peter Batzel
- Institute of Neuroscience, University of Oregon, Eugene, Oregon
| | | |
Collapse
|
67
|
Mastretta-Yanes A, Arrigo N, Alvarez N, Jorgensen TH, Piñero D, Emerson BC. Restriction site-associated DNA sequencing, genotyping error estimation andde novoassembly optimization for population genetic inference. Mol Ecol Resour 2014; 15:28-41. [DOI: 10.1111/1755-0998.12291] [Citation(s) in RCA: 281] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Revised: 05/27/2014] [Accepted: 06/04/2014] [Indexed: 11/28/2022]
Affiliation(s)
- A. Mastretta-Yanes
- Centre for Ecology, Evolution and Conservation; School of Biological Sciences; University of East Anglia; 14 Norwich NR4 7TJ UK
| | - N. Arrigo
- Department of Ecology and Evolution; Biophore Building; University of Lausanne; 1015 Lausanne Switzerland
| | - N. Alvarez
- Department of Ecology and Evolution; Biophore Building; University of Lausanne; 1015 Lausanne Switzerland
| | - T. H. Jorgensen
- Department of Bioscience; Aarhus University; Universitets Parken; 8000 Aarhus C Aarhus Denmark
| | - D. Piñero
- Departamento de Ecología Evolutiva; Instituto de Ecología; Universidad Nacional Autónoma de México; Apartado postal 70-275 Mexico DF 04510 Mexico
| | - B. C. Emerson
- Centre for Ecology, Evolution and Conservation; School of Biological Sciences; University of East Anglia; 14 Norwich NR4 7TJ UK
- Island Ecology and Evolution Research Group; Instituto de Productos Naturales y Agrobiología (IPNA-CSIC); C/Astrofísico Francisco Sánchez 3 La Laguna Tenerife Canary Islands 38206 Spain
| |
Collapse
|
68
|
Streicher JW, Devitt TJ, Goldberg CS, Malone JH, Blackmon H, Fujita MK. Diversification and asymmetrical gene flow across time and space: lineage sorting and hybridization in polytypic barking frogs. Mol Ecol 2014; 23:3273-91. [DOI: 10.1111/mec.12814] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 05/20/2014] [Accepted: 05/23/2014] [Indexed: 12/20/2022]
Affiliation(s)
- Jeffrey W. Streicher
- Department of Biology; The University of Texas at Arlington; Arlington TX 76010 USA
| | - Thomas J. Devitt
- Department of Integrative Biology; The University of Texas at Austin; Austin TX 78712 USA
| | - Caren S. Goldberg
- Fish and Wildlife Sciences; University of Idaho; Moscow ID 83844 USA
| | - John H. Malone
- Department of Molecular and Cell Biology; University of Connecticut; Storrs CT 06269 USA
| | - Heath Blackmon
- Department of Biology; The University of Texas at Arlington; Arlington TX 76010 USA
| | - Matthew K. Fujita
- Department of Biology; The University of Texas at Arlington; Arlington TX 76010 USA
| |
Collapse
|
69
|
Henning F, Meyer A. The evolutionary genomics of cichlid fishes: explosive speciation and adaptation in the postgenomic era. Annu Rev Genomics Hum Genet 2014; 15:417-41. [PMID: 24898042 DOI: 10.1146/annurev-genom-090413-025412] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
With more than 1,500 species, cichlid fishes provide textbook examples of recent and diverse adaptive radiations, rapid rates of speciation, and the parallel evolution of adaptive phenotypes among both recently and distantly related lineages. This extraordinary diversity has attracted considerable interest from researchers across several biological disciplines. Their broad phenotypic variation coupled with recent divergence makes cichlids an ideal model system for understanding speciation, adaptation, and phenotypic diversification. Genetic mapping, genome-wide analyses, and genome projects have flourished in the past decade and have added new insights on the question of why there are so many cichlids. These recent findings also show that the sharing of older DNA polymorphisms is extensive and suggest that linage sorting is incomplete and that adaptive introgression played a role in the African radiation. Here, we review the results of genetic and genomic research on cichlids in the past decade and suggest some potential avenues to further exploit the potential of the cichlid model system to provide a better understanding of the genomics of adaptation and speciation.
Collapse
Affiliation(s)
- Frederico Henning
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany;
| | | |
Collapse
|
70
|
|
71
|
Martin CH, Feinstein LC. Novel trophic niches drive variable progress towards ecological speciation within an adaptive radiation of pupfishes. Mol Ecol 2014; 23:1846-62. [PMID: 24393262 DOI: 10.1111/mec.12658] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 12/09/2013] [Accepted: 12/20/2013] [Indexed: 01/15/2023]
Abstract
Adaptive radiation is recognized by a rapid burst of phenotypic, ecological and species diversification. However, it is unknown whether different species within an adaptive radiation evolve reproductive isolation at different rates. We compared patterns of genetic differentiation between nascent species within an adaptive radiation of Cyprinodon pupfishes using genotyping by sequencing. Similar to classic adaptive radiations, this clade exhibits rapid morphological diversification rates and two species are novel trophic specialists, a scale-eater and hard-shelled prey specialist (durophage), yet the radiation is <10 000 years old. Both specialists and an abundant generalist species all coexist in the benthic zone of lakes on San Salvador Island, Bahamas. Based on 13 912 single-nucleotide polymorphisms (SNPs), we found consistent differences in genetic differentiation between each specialist species and the generalist across seven lakes. The scale-eater showed the greatest genetic differentiation and clustered by species across lakes, whereas durophage populations often clustered with sympatric generalist populations, consistent with parallel speciation across lakes. However, we found strong evidence of admixture between durophage populations in different lakes, supporting a single origin of this species and genome-wide introgression with sympatric generalist populations. We conclude that the scale-eater is further along the speciation-with-gene-flow continuum than the durophage and suggest that different adaptive landscapes underlying these two niche environments drive variable progress towards speciation within the same habitat. Our previous measurements of fitness surfaces in these lakes support this conclusion: the scale-eating fitness peak may be more distant than the durophage peak on the complex adaptive landscape driving adaptive radiation.
Collapse
Affiliation(s)
- Christopher H Martin
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, 94720, USA; Department of Evolution & Ecology, University of California, Davis, CA, 94616, USA
| | | |
Collapse
|
72
|
Cruaud A, Gautier M, Galan M, Foucaud J, Sauné L, Genson G, Dubois E, Nidelet S, Deuve T, Rasplus JY. Empirical Assessment of RAD Sequencing for Interspecific Phylogeny. Mol Biol Evol 2014; 31:1272-4. [DOI: 10.1093/molbev/msu063] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
73
|
Rieseberg L, Vines T, Gow J, Kane N. Molecular Ecology continues to perform well according to the major publication metrics. Introduction. Mol Ecol 2014; 23:1-15. [PMID: 24372750 DOI: 10.1111/mec.12586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 11/06/2013] [Indexed: 11/28/2022]
|
74
|
Franchini P, Fruciano C, Spreitzer ML, Jones JC, Elmer KR, Henning F, Meyer A. Genomic architecture of ecologically divergent body shape in a pair of sympatric crater lake cichlid fishes. Mol Ecol 2013; 23:1828-45. [PMID: 24237636 DOI: 10.1111/mec.12590] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Revised: 10/18/2013] [Accepted: 10/28/2013] [Indexed: 12/26/2022]
Abstract
Determining the genetic bases of adaptations and their roles in speciation is a prominent issue in evolutionary biology. Cichlid fish species flocks are a prime example of recent rapid radiations, often associated with adaptive phenotypic divergence from a common ancestor within a short period of time. In several radiations of freshwater fishes, divergence in ecomorphological traits - including body shape, colour, lips and jaws - is thought to underlie their ecological differentiation, specialization and, ultimately, speciation. The Midas cichlid species complex (Amphilophus spp.) of Nicaragua provides one of the few known examples of sympatric speciation where species have rapidly evolved different but parallel morphologies in young crater lakes. This study identified significant QTL for body shape using SNPs generated via ddRAD sequencing and geometric morphometric analyses of a cross between two ecologically and morphologically divergent, sympatric cichlid species endemic to crater Lake Apoyo: an elongated limnetic species (Amphilophus zaliosus) and a high-bodied benthic species (Amphilophus astorquii). A total of 453 genome-wide informative SNPs were identified in 240 F2 hybrids. These markers were used to construct a genetic map in which 25 linkage groups were resolved. Seventy-two segregating SNPs were linked to 11 QTL. By annotating the two most highly supported QTL-linked genomic regions, genes that might contribute to divergence in body shape along the benthic-limnetic axis in Midas cichlid sympatric adaptive radiations were identified. These results suggest that few genomic regions of large effect contribute to early stage divergence in Midas cichlids.
Collapse
Affiliation(s)
- Paolo Franchini
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätstraße 10, 78457, Konstanz, Germany
| | | | | | | | | | | | | |
Collapse
|
75
|
Viricel A, Pante E, Dabin W, Simon-Bouhet B. Applicability of RAD-tag genotyping for interfamilial comparisons: empirical data from two cetaceans. Mol Ecol Resour 2013; 14:597-605. [DOI: 10.1111/1755-0998.12206] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Revised: 11/08/2013] [Accepted: 11/13/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Amélia Viricel
- Littoral, Environnement et Sociétés (LIENSs) UMR 7266 CNRS; Université de La Rochelle; 2 rue Olympe de Gouges La Rochelle 17000 France
| | - Eric Pante
- Littoral, Environnement et Sociétés (LIENSs) UMR 7266 CNRS; Université de La Rochelle; 2 rue Olympe de Gouges La Rochelle 17000 France
| | - Willy Dabin
- Observatoire PELAGIS, UMS 3462 CNRS; Université de La Rochelle; Pôle analytique 5 allées de l'océan La Rochelle 17000 France
| | - Benoit Simon-Bouhet
- Littoral, Environnement et Sociétés (LIENSs) UMR 7266 CNRS; Université de La Rochelle; 2 rue Olympe de Gouges La Rochelle 17000 France
| |
Collapse
|
76
|
Culumber ZW. Pigmentation in Xiphophorus: an emerging system in ecological and evolutionary genetics. Zebrafish 2013; 11:57-70. [PMID: 24320948 DOI: 10.1089/zeb.2013.0939] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The genus Xiphophorus has great potential to contribute to the study of vertebrate pigmentation and elucidating the relative influence of ecology, physiology, and behavior on evolution at the molecular level. More importantly, the association between pigmentation and a functional oncogene offers the potential to understand the evolution and maintenance of cancer-causing genetic elements. Using criteria laid out recently in the literature, I demonstrate the power of the Xiphophorus system for studying pigment evolution through integrative organismal biology. Using the most recent phylogeny, the phylogenetic distribution of several important pigmentation loci are reevaluated. I then review support for existing hypotheses of the functional importance of pigmentation. Finally, new observations and hypotheses regarding some of the characteristics of pigment patterns in natural populations and open questions and future directions in the study of the evolution of these traits are discussed.
Collapse
Affiliation(s)
- Zachary W Culumber
- 1 Centro de Investigaciones Cientificas de las Huastecas "Aguazarca" , Calnali, Mexico
| |
Collapse
|
77
|
De novo SNP discovery in the Scandinavian brown bear (Ursus arctos). PLoS One 2013; 8:e81012. [PMID: 24260529 PMCID: PMC3832409 DOI: 10.1371/journal.pone.0081012] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 10/08/2013] [Indexed: 01/22/2023] Open
Abstract
Information about relatedness between individuals in wild populations is advantageous when studying evolutionary, behavioural and ecological processes. Genomic data can be used to determine relatedness between individuals either when no prior knowledge exists or to confirm suspected relatedness. Here we present a set of 96 SNPs suitable for inferring relatedness for brown bears (Ursus arctos) within Scandinavia. We sequenced reduced representation libraries from nine individuals throughout the geographic range. With consensus reads containing putative SNPs, we applied strict filtering criteria with the aim of finding only high-quality, highly-informative SNPs. We tested 150 putative SNPs of which 96% were validated on a panel of 68 individuals. Ninety-six of the validated SNPs with the highest minor allele frequency were selected. The final SNP panel includes four mitochondrial markers, two monomorphic Y-chromosome sex-determination markers, three X-chromosome SNPs and 87 autosomal SNPs. From our validation sample panel, we identified two previously known parent-offspring dyads with reasonable accuracy. This panel of SNPs is a promising tool for inferring relatedness in the brown bear population in Scandinavia.
Collapse
|
78
|
Retinoic acid is involved in the metamorphosis of the anal fin into an intromittent organ, the gonopodium, in the green swordtail (Xiphophorus hellerii). PLoS One 2013; 8:e77580. [PMID: 24204880 PMCID: PMC3808415 DOI: 10.1371/journal.pone.0077580] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2013] [Accepted: 09/03/2013] [Indexed: 01/10/2023] Open
Abstract
In poeciliid fish the male anal fin has been transformed into a gonopodium, an intromittent organ required for internal fertilization. Elevated testosterone levels induce metamorphosis of a subset of anal fin rays to grow and form the specialized terminal structures of the gonopodium. The molecular mechanisms underlying these processes are largely unknown. Here, we investigated whether retinoic acid (RA) signaling is involved in gonopodium development in the swordtail Xiphophorus hellerii. We showed that aldh1a2, a RA synthesizing enzyme, and the RA receptors, rar-ga and rar-gb, are expressed in anal fins during metamorphosis. aldh1a2 expression is regulated by testosterone in a concentration-dependent manner and is up-regulated in both hormone-induced and naturally developing gonopodia. Androgen receptor (ar), a putative regulator of gonopodial development, is co-expressed with aldh1a2 and the RA receptors in gonopodial rays. Importantly, experimental increase of RA signaling promoted growth of the gonopodium and increased the number of new segments. Based on gene expression analyses and pharmacological manipulation of gonopodium development, we show that the RA signaling pathway is activated in response to androgen signaling and promotes fin ray growth and development during the metamorphosis of the anal fin into the gonopodium.
Collapse
|
79
|
Narum SR, Buerkle CA, Davey JW, Miller MR, Hohenlohe PA. Genotyping-by-sequencing in ecological and conservation genomics. Mol Ecol 2013; 22:2841-7. [PMID: 23711105 DOI: 10.1111/mec.12350] [Citation(s) in RCA: 343] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Revised: 04/09/2013] [Accepted: 04/10/2013] [Indexed: 12/12/2022]
|