301
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Molecular and morphometric data suggest the presence of a neglected species in the marine gastropod family Conidae. Mol Phylogenet Evol 2017; 109:421-429. [DOI: 10.1016/j.ympev.2017.02.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 02/12/2017] [Accepted: 02/15/2017] [Indexed: 11/15/2022]
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302
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Höllinger I, Hermisson J. Bounds to parapatric speciation: A Dobzhansky-Muller incompatibility model involving autosomes, X chromosomes, and mitochondria. Evolution 2017; 71:1366-1380. [PMID: 28272742 DOI: 10.1111/evo.13223] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 02/22/2017] [Indexed: 12/16/2022]
Abstract
We investigate the conditions for the origin and maintenance of postzygotic isolation barriers, so called (Bateson-)Dobzhansky-Muller incompatibilities or DMIs, among populations that are connected by gene flow. Specifically, we compare the relative stability of pairwise DMIs among autosomes, X chromosomes, and mitochondrial genes. In an analytical approach based on a continent-island framework, we determine how the maximum permissible migration rates depend on the genomic architecture of the DMI, on sex bias in migration rates, and on sex-dependence of allelic and epistatic effects, such as dosage compensation. Our results show that X-linkage of DMIs can enlarge the migration bounds relative to autosomal DMIs or autosome-mitochondrial DMIs, in particular in the presence of dosage compensation. The effect is further strengthened with male-biased migration. This mechanism might contribute to a higher density of DMIs on the X chromosome (large X-effect) that has been observed in several species clades. Furthermore, our results agree with empirical findings of higher introgression rates of autosomal compared to X-linked loci.
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Affiliation(s)
- Ilse Höllinger
- Mathematics and BioSciences Group, Faculty of Mathematics and Max F. Perutz Laboratories, University of Vienna, Vienna, Austria.,Vienna Graduate School of Population Genetics, Vienna, Austria
| | - Joachim Hermisson
- Mathematics and BioSciences Group, Faculty of Mathematics and Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
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303
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Exploring Evolutionary Relationships Across the Genome Using Topology Weighting. Genetics 2017; 206:429-438. [PMID: 28341652 PMCID: PMC5419486 DOI: 10.1534/genetics.116.194720] [Citation(s) in RCA: 135] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 03/14/2017] [Indexed: 12/30/2022] Open
Abstract
We introduce the concept of topology weighting, a method for quantifying relationships between taxa that are not necessarily monophyletic, and visualizing how these relationships change across the genome. A given set of taxa can be related in a limited number of ways, but if each taxon is represented by multiple sequences, the number of possible topologies becomes very large. Topology weighting reduces this complexity by quantifying the contribution of each taxon topology to the full tree. We describe our method for topology weighting by iterative sampling of subtrees (Twisst), and test it on both simulated and real genomic data. Overall, we show that this is an informative and versatile approach, suitable for exploring relationships in almost any genomic dataset. Scripts to implement the method described are available at http://github.com/simonhmartin/twisst.
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304
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Lu B, Zhang L, Leong HW. A program to compute the soft Robinson-Foulds distance between phylogenetic networks. BMC Genomics 2017; 18:111. [PMID: 28361712 PMCID: PMC5374702 DOI: 10.1186/s12864-017-3500-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Background Over the past two decades, phylogenetic networks have been studied to model reticulate evolutionary events. The relationships among phylogenetic networks, phylogenetic trees and clusters serve as the basis for reconstruction and comparison of phylogenetic networks. To understand these relationships, two problems are raised: the tree containment problem, which asks whether a phylogenetic tree is displayed in a phylogenetic network, and the cluster containment problem, which asks whether a cluster is represented at a node in a phylogenetic network. Both the problems are NP-complete. Results A fast exponential-time algorithm for the cluster containment problem on arbitrary networks is developed and implemented in C. The resulting program is further extended into a computer program for fast computation of the Soft Robinson–Foulds distance between phylogenetic networks. Conclusions Two computer programs are developed for facilitating reconstruction and validation of phylogenetic network models in evolutionary and comparative genomics. Our simulation tests indicated that they are fast enough for use in practice. Additionally, the distribution of the Soft Robinson–Foulds distance between phylogenetic networks is demonstrated to be unlikely normal by our simulation data. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3500-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bingxin Lu
- Department of Computer Science, National University of Singapore, 13 Computing Drive, Singapore, 117417, Singapore
| | - Louxin Zhang
- Department of Mathematics, National University of Singapore, 10 Lower Kent Ridge, Singapore, 119076, Singapore.
| | - Hon Wai Leong
- Department of Computer Science, National University of Singapore, 13 Computing Drive, Singapore, 117417, Singapore
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305
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Affiliation(s)
- B. Rosemary Grant
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Peter R. Grant
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
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306
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Fouet C, Kamdem C, Gamez S, White BJ. Extensive genetic diversity among populations of the malaria mosquito Anopheles moucheti revealed by population genomics. INFECTION GENETICS AND EVOLUTION 2017; 48:27-33. [DOI: 10.1016/j.meegid.2016.12.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 11/11/2016] [Accepted: 12/06/2016] [Indexed: 10/20/2022]
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307
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Ayala D, Acevedo P, Pombi M, Dia I, Boccolini D, Costantini C, Simard F, Fontenille D. Chromosome inversions and ecological plasticity in the main African malaria mosquitoes. Evolution 2017; 71:686-701. [PMID: 28071788 DOI: 10.1111/evo.13176] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 12/22/2016] [Indexed: 01/30/2023]
Abstract
Chromosome inversions have fascinated the scientific community, mainly because of their role in the rapid adaption of different taxa to changing environments. However, the ecological traits linked to chromosome inversions have been poorly studied. Here, we investigated the roles played by 23 chromosome inversions in the adaptation of the four major African malaria mosquitoes to local environments in Africa. We studied their distribution patterns by using spatially explicit modeling and characterized the ecogeographical determinants of each inversion range. We then performed hierarchical clustering and constrained ordination analyses to assess the spatial and ecological similarities among inversions. Our results show that most inversions are environmentally structured, suggesting that they are actively involved in processes of local adaptation. Some inversions exhibited similar geographical patterns and ecological requirements among the four mosquito species, providing evidence for parallel evolution. Conversely, common inversion polymorphisms between sibling species displayed divergent ecological patterns, suggesting that they might have a different adaptive role in each species. These results are in agreement with the finding that chromosomal inversions play a role in Anopheles ecotypic adaptation. This study establishes a strong ecological basis for future genome-based analyses to elucidate the genetic mechanisms of local adaptation in these four mosquitoes.
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Affiliation(s)
- Diego Ayala
- UMR 224 MIVEGEC/ESV, IRD, Montpellier, 34394, France.,CIRMF, BP 769, Franceville, Gabon
| | - Pelayo Acevedo
- SaBio, Instituto de Investigación en Recursos Cinegéticos (IREC), CSIC-UCLM-JCCM, Ciudad Real, 13005, Spain
| | - Marco Pombi
- Sezione di Parassitologia, Dipartimento di Scienze di Sanità Pubblica, Università di Roma "La Sapienza,", Rome, 00185, Italy
| | - Ibrahima Dia
- Medical Entomology Unit, Institut Pasteur de Dakar, BP 220, Dakar, Senegal
| | - Daniela Boccolini
- Department MIPI, Unit Vector-Borne Diseases and International Health, Istituto Superiore di Sanità, Rome, 00161, Italy
| | | | | | - Didier Fontenille
- UMR 224 MIVEGEC/ESV, IRD, Montpellier, 34394, France.,Current Address: Institut Pasteur du Cambodge, BP 983, Phnom Penh, Cambodia
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308
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Oppenheim SJ, Rosenfeld JA, DeSalle R. Genome content analysis yields new insights into the relationship between the human malaria parasite Plasmodium falciparum and its anopheline vectors. BMC Genomics 2017; 18:205. [PMID: 28241792 PMCID: PMC5327517 DOI: 10.1186/s12864-017-3590-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 02/13/2017] [Indexed: 11/24/2022] Open
Abstract
Background The persistent and growing gap between the availability of sequenced genomes and the ability to assign functions to sequenced genes led us to explore ways to maximize the information content of automated annotation for studies of anopheline mosquitos. Specifically, we use genome content analysis of a large number of previously sequenced anopheline mosquitos to follow the loss and gain of protein families over the evolutionary history of this group. The importance of this endeavor lies in the potential for comparative genomic studies between Anopheles and closely related non-vector species to reveal ancestral genome content dynamics involved in vector competence. In addition, comparisons within Anopheles could identify genome content changes responsible for variation in the vectorial capacity of this family of important parasite vectors. Results The competence and capacity of P. falciparum vectors do not appear to be phylogenetically constrained within the Anophelinae. Instead, using ancestral reconstruction methods, we suggest that a previously unexamined component of vector biology, anopheline nucleotide metabolism, may contribute to the unique status of anophelines as P. falciparum vectors. While the fitness effects of nucleotide co-option by P. falciparum parasites on their anopheline hosts are not yet known, our results suggest that anopheline genome content may be responding to selection pressure from P. falciparum. Whether this response is defensive, in an attempt to redress improper nucleotide balance resulting from P. falciparum infection, or perhaps symbiotic, resulting from an as-yet-unknown mutualism between anophelines and P. falciparum, is an open question that deserves further study. Conclusions Clearly, there is a wealth of functional information to be gained from detailed manual genome annotation, yet the rapid increase in the number of available sequences means that most researchers will not have the time or resources to manually annotate all the sequence data they generate. We believe that efforts to maximize the amount of information obtained from automated annotation can help address the functional annotation deficit that most evolutionary biologists now face, and here demonstrate the value of such an approach. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3590-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sara J Oppenheim
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, 10024, USA.
| | - Jeffrey A Rosenfeld
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, 10024, USA.,Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA
| | - Rob DeSalle
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, 10024, USA
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309
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Arcà B, Lombardo F, Struchiner CJ, Ribeiro JMC. Anopheline salivary protein genes and gene families: an evolutionary overview after the whole genome sequence of sixteen Anopheles species. BMC Genomics 2017; 18:153. [PMID: 28193177 PMCID: PMC5307786 DOI: 10.1186/s12864-017-3579-8] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 02/09/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mosquito saliva is a complex cocktail whose pharmacological properties play an essential role in blood feeding by counteracting host physiological response to tissue injury. Moreover, vector borne pathogens are transmitted to vertebrates and exposed to their immune system in the context of mosquito saliva which, in virtue of its immunomodulatory properties, can modify the local environment at the feeding site and eventually affect pathogen transmission. In addition, the host antibody response to salivary proteins may be used to assess human exposure to mosquito vectors. Even though the role of quite a few mosquito salivary proteins has been clarified in the last decade, we still completely ignore the physiological role of many of them as well as the extent of their involvement in the complex interactions taking place between the mosquito vectors, the pathogens they transmit and the vertebrate host. The recent release of the genomes of 16 Anopheles species offered the opportunity to get insights into function and evolution of salivary protein families in anopheline mosquitoes. RESULTS Orthologues of fifty three Anopheles gambiae salivary proteins were retrieved and annotated from 18 additional anopheline species belonging to the three subgenera Cellia, Anopheles, and Nyssorhynchus. Our analysis included 824 full-length salivary proteins from 24 different families and allowed the identification of 79 novel salivary genes and re-annotation of 379 wrong predictions. The comparative, structural and phylogenetic analyses yielded an unprecedented view of the anopheline salivary repertoires and of their evolution over 100 million years of anopheline radiation shedding light on mechanisms and evolutionary forces that contributed shaping the anopheline sialomes. CONCLUSIONS We provide here a comprehensive description, classification and evolutionary overview of the main anopheline salivary protein families and identify two novel candidate markers of human exposure to malaria vectors worldwide. This anopheline sialome catalogue, which is easily accessible as hyperlinked spreadsheet, is expected to be useful to the vector biology community and to improve the capacity to gain a deeper understanding of mosquito salivary proteins facilitating their possible exploitation for epidemiological and/or pathogen-vector-host interaction studies.
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Affiliation(s)
- Bruno Arcà
- Department of Public Health and Infectious Diseases - Division of Parasitology, Sapienza University, Piazzale Aldo Moro 5, 00185, Rome, Italy.
| | - Fabrizio Lombardo
- Department of Public Health and Infectious Diseases - Division of Parasitology, Sapienza University, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Claudio J Struchiner
- Fundação Oswaldo Cruz, Avenida Brasil, 4365, Rio de Janeiro, Brazil.,Instituto de Medicina Social, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - José M C Ribeiro
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, 12735 Twinbrook Parkway, Rockville, MD, 20852, USA
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310
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Potter S, Bragg JG, Blom MPK, Deakin JE, Kirkpatrick M, Eldridge MDB, Moritz C. Chromosomal Speciation in the Genomics Era: Disentangling Phylogenetic Evolution of Rock-wallabies. Front Genet 2017; 8:10. [PMID: 28265284 PMCID: PMC5301020 DOI: 10.3389/fgene.2017.00010] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 01/18/2017] [Indexed: 12/24/2022] Open
Abstract
The association of chromosome rearrangements (CRs) with speciation is well established, and there is a long history of theory and evidence relating to "chromosomal speciation." Genomic sequencing has the potential to provide new insights into how reorganization of genome structure promotes divergence, and in model systems has demonstrated reduced gene flow in rearranged segments. However, there are limits to what we can understand from a small number of model systems, which each only tell us about one episode of chromosomal speciation. Progressing from patterns of association between chromosome (and genic) change, to understanding processes of speciation requires both comparative studies across diverse systems and integration of genome-scale sequence comparisons with other lines of evidence. Here, we showcase a promising example of chromosomal speciation in a non-model organism, the endemic Australian marsupial genus Petrogale. We present initial phylogenetic results from exon-capture that resolve a history of divergence associated with extensive and repeated CRs. Yet it remains challenging to disentangle gene tree heterogeneity caused by recent divergence and gene flow in this and other such recent radiations. We outline a way forward for better integration of comparative genomic sequence data with evidence from molecular cytogenetics, and analyses of shifts in the recombination landscape and potential disruption of meiotic segregation and epigenetic programming. In all likelihood, CRs impact multiple cellular processes and these effects need to be considered together, along with effects of genic divergence. Understanding the effects of CRs together with genic divergence will require development of more integrative theory and inference methods. Together, new data and analysis tools will combine to shed light on long standing questions of how chromosome and genic divergence promote speciation.
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Affiliation(s)
- Sally Potter
- Research School of Biology, Australian National University, ActonACT, Australia
- Australian Museum Research Institute, Australian Museum, SydneyNSW, Australia
| | - Jason G. Bragg
- National Herbarium of New South Wales, The Royal Botanic Gardens and Domain Trust, SydneyNSW, Australia
| | - Mozes P. K. Blom
- Department of Bioinformatics and Genetics, Swedish Museum of Natural HistoryStockholm, Sweden
| | - Janine E. Deakin
- Institute for Applied Ecology, University of Canberra, BruceACT, Australia
| | - Mark Kirkpatrick
- Department of Integrative Biology, University of Texas, AustinTX, USA
| | - Mark D. B. Eldridge
- Australian Museum Research Institute, Australian Museum, SydneyNSW, Australia
| | - Craig Moritz
- Research School of Biology, Australian National University, ActonACT, Australia
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311
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Cong Q, Shen J, Borek D, Robbins RK, Opler PA, Otwinowski Z, Grishin NV. When COI barcodes deceive: complete genomes reveal introgression in hairstreaks. Proc Biol Sci 2017; 284:20161735. [PMID: 28179510 PMCID: PMC5310595 DOI: 10.1098/rspb.2016.1735] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Accepted: 01/09/2017] [Indexed: 12/24/2022] Open
Abstract
Two species of hairstreak butterflies from the genus Calycopis are known in the United States: C. cecrops and C. isobeon Analysis of mitochondrial COI barcodes of Calycopis revealed cecrops-like specimens from the eastern US with atypical barcodes that were 2.6% different from either USA species, but similar to Central American Calycopis species. To address the possibility that the specimens with atypical barcodes represent an undescribed cryptic species, we sequenced complete genomes of 27 Calycopis specimens of four species: C. cecrops, C. isobeon, C. quintana and C. bactra Some of these specimens were collected up to 60 years ago and preserved dry in museum collections, but nonetheless produced genomes as complete as fresh samples. Phylogenetic trees reconstructed using the whole mitochondrial and nuclear genomes were incongruent. While USA Calycopis with atypical barcodes grouped with Central American species C. quintana by mitochondria, nuclear genome trees placed them within typical USA C. cecrops in agreement with morphology, suggesting mitochondrial introgression. Nuclear genomes also show introgression, especially between C. cecrops and C. isobeon About 2.3% of each C. cecrops genome has probably (p-value < 0.01, FDR < 0.1) introgressed from C. isobeon and about 3.4% of each C. isobeon genome may have come from C. cecrops. The introgressed regions are enriched in genes encoding transmembrane proteins, mitochondria-targeting proteins and components of the larval cuticle. This study provides the first example of mitochondrial introgression in Lepidoptera supported by complete genome sequencing. Our results caution about relying solely on COI barcodes and mitochondrial DNA for species identification or discovery.
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Affiliation(s)
- Qian Cong
- Department of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8816, USA
| | - Jinhui Shen
- Department of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8816, USA
| | - Dominika Borek
- Department of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8816, USA
| | - Robert K Robbins
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, PO Box 37012, NHB Stop 105, Washington, DC, USA
| | - Paul A Opler
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523-1177, USA
| | - Zbyszek Otwinowski
- Department of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8816, USA
| | - Nick V Grishin
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8816, USA
- Department of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8816, USA
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312
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Weber XA, Edgar GJ, Banks SC, Waters JM, Fraser CI. A morphological and phylogenetic investigation into divergence among sympatric Australian southern bull kelps (Durvillaea potatorum and D. amatheiae sp. nov.). Mol Phylogenet Evol 2017; 107:630-643. [PMID: 28017856 DOI: 10.1016/j.ympev.2016.12.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 12/11/2016] [Accepted: 12/20/2016] [Indexed: 11/19/2022]
Abstract
Genetic analyses can reveal a wealth of hitherto undiscovered cryptic biodiversity. For co-occurring and morphologically similar species, the combination of molecular, ecological and morphological analyses provides an excellent opportunity for understanding some of the processes that can lead to divergence and speciation. The Australian endemic brown macroalga Durvillaea potatorum (Phaeophyceae) was examined with a combination of genetic and morphological approaches to confirm the presence of two separate species and to infer the processes that led to their divergence. A total of 331 individuals from 11 sites around coastal Tasmania were collected and measured in situ for a range of morphological and ecological characteristics. Tissue samples were also collected for each individual to allow genetic analyses using mitochondrial (COI) and nuclear (28S) markers. Genetic analyses confirmed the presence of two deeply divergent clades. The significant morphological differentiation, despite high levels of intra-lineage variability, further supported their recognition as distinct species. We describe a new species, D. amatheiae sp. nov., which is characterised by a narrower and proportionately shorter stipe, shorter total length, and higher number of stipitate lateral blades and branches than D. potatorum (sensu stricto). The occurrence of both species in sympatry along Tasmania's eastern and western coasts, as well as their contrasting patterns of haplotype diversity, supports a hypothesis of geographical isolation, allopatric speciation and subsequent secondary contact in response to sea level and ocean current change throughout the Pleistocene glaciation cycles. This research contributes to resolving the phylogenetic relationships, taxonomy and evolution of the ecologically keystone kelp genus Durvillaea.
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Affiliation(s)
- Xénia A Weber
- Fenner School of Environment and Society, Australian National University, Building 141, Linnaeus Way, Acton ACT 2601, Australia.
| | - Graham J Edgar
- Institute for Marine and Antarctic Studies, University of Tasmania, GPO Box 252-49, Hobart, Tasmania 7001, Australia
| | - Sam C Banks
- Fenner School of Environment and Society, Australian National University, Building 141, Linnaeus Way, Acton ACT 2601, Australia
| | - Jonathan M Waters
- Department of Zoology, University of Otago, 340 Great King Street, Dunedin 9016, New Zealand
| | - Ceridwen I Fraser
- Fenner School of Environment and Society, Australian National University, Building 141, Linnaeus Way, Acton ACT 2601, Australia
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313
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Malmstrøm M, Matschiner M, Tørresen OK, Jakobsen KS, Jentoft S. Whole genome sequencing data and de novo draft assemblies for 66 teleost species. Sci Data 2017; 4:160132. [PMID: 28094797 PMCID: PMC5240625 DOI: 10.1038/sdata.2016.132] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 12/07/2016] [Indexed: 02/07/2023] Open
Abstract
Teleost fishes comprise more than half of all vertebrate species, yet genomic data are only available for 0.2% of their diversity. Here, we present whole genome sequencing data for 66 new species of teleosts, vastly expanding the availability of genomic data for this important vertebrate group. We report on de novo assemblies based on low-coverage (9-39×) sequencing and present detailed methodology for all analyses. To facilitate further utilization of this data set, we present statistical analyses of the gene space completeness and verify the expected phylogenetic position of the sequenced genomes in a large mitogenomic context. We further present a nuclear marker set used for phylogenetic inference and evaluate each gene tree in relation to the species tree to test for homogeneity in the phylogenetic signal. Collectively, these analyses illustrate the robustness of this highly diverse data set and enable extensive reuse of the selected phylogenetic markers and the genomic data in general. This data set covers all major teleost lineages and provides unprecedented opportunities for comparative studies of teleosts.
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Affiliation(s)
- Martin Malmstrøm
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, PO Box 1066, 0316 Oslo, Norway
| | - Michael Matschiner
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, PO Box 1066, 0316 Oslo, Norway
| | - Ole K. Tørresen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, PO Box 1066, 0316 Oslo, Norway
| | - Kjetill S. Jakobsen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, PO Box 1066, 0316 Oslo, Norway
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, PO Box 1066, 0316 Oslo, Norway
- Centre for Coastal Research, Department of Natural Sciences, University of Agder, PO Box 422, 4604 Kristiansand, Norway
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314
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Rosser NL, Thomas L, Stankowski S, Richards ZT, Kennington WJ, Johnson MS. Phylogenomics provides new insight into evolutionary relationships and genealogical discordance in the reef-building coral genus Acropora. Proc Biol Sci 2017; 284:20162182. [PMID: 28077772 PMCID: PMC5247495 DOI: 10.1098/rspb.2016.2182] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 12/12/2016] [Indexed: 01/08/2023] Open
Abstract
Understanding the genetic basis of reproductive isolation is a long-standing goal of speciation research. In recently diverged populations, genealogical discordance may reveal genes and genomic regions that contribute to the speciation process. Previous work has shown that conspecific colonies of Acropora that spawn in different seasons (spring and autumn) are associated with highly diverged lineages of the phylogenetic marker PaxC Here, we used 10 034 single-nucleotide polymorphisms to generate a genome-wide phylogeny and compared it with gene genealogies from the PaxC intron and the mtDNA Control Region in 20 species of Acropora, including three species with spring- and autumn-spawning cohorts. The PaxC phylogeny separated conspecific autumn and spring spawners into different genetic clusters in all three species; however, this pattern was not supported in two of the three species at the genome level, suggesting a selective connection between PaxC and reproductive timing in Acropora corals. This genome-wide phylogeny provides an improved foundation for resolving phylogenetic relationships in Acropora and, combined with PaxC, provides a fascinating platform for future research into regions of the genome that influence reproductive isolation and speciation in corals.
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Affiliation(s)
- Natalie L Rosser
- School of Animal Biology, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Luke Thomas
- School of Plant Biology, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Sean Stankowski
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Zoe T Richards
- Department of Aquatic Zoology, Western Australian Museum, 49 Kew Street, Welshpool, Western Australia 6106, Australia
| | - W Jason Kennington
- School of Animal Biology, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Michael S Johnson
- School of Animal Biology, University of Western Australia, Crawley, Western Australia 6009, Australia
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315
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Ranford-Cartwright LC, McGeechan S, Inch D, Smart G, Richterová L, Mwangi JM. Characterisation of Species and Diversity of Anopheles gambiae Keele Colony. PLoS One 2016; 11:e0168999. [PMID: 28033418 PMCID: PMC5199079 DOI: 10.1371/journal.pone.0168999] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 12/09/2016] [Indexed: 11/18/2022] Open
Abstract
Anopheles gambiae sensu stricto was recently reclassified as two species, An. coluzzii and An. gambiae s.s., in wild-caught mosquitoes, on the basis of the molecular form, denoted M or S, of a marker on the X chromosome. The An. gambiae Keele line is an outbred laboratory colony strain that was developed around 12 years ago by crosses between mosquitoes from 4 existing An. gambiae colonies. Laboratory colonies of mosquitoes often have limited genetic diversity because of small starting populations (founder effect) and subsequent fluctuations in colony size. Here we describe the characterisation of the chromosomal form(s) present in the Keele line, and investigate the diversity present in the colony using microsatellite markers on chromosome 3. We also characterise the large 2La inversion on chromosome 2. The results indicate that only the M-form of the chromosome X marker is present in the Keele colony, which was unexpected given that 3 of the 4 parent colonies were probably S-form. Levels of diversity were relatively high, as indicated by a mean number of microsatellite alleles of 6.25 across 4 microsatellites, in at least 25 mosquitoes. Both karyotypes of the inversion on chromosome 2 (2La/2L+a) were found to be present at approximately equal proportions. The Keele colony has a mixed M- and S-form origin, and in common with the PEST strain, we propose continuing to denote it as an An. gambiae s.s. line.
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Affiliation(s)
- Lisa C Ranford-Cartwright
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Sion McGeechan
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Donald Inch
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Graeme Smart
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Lenka Richterová
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Jonathan M Mwangi
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
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316
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Worley KC, Richards S, Rogers J. The value of new genome references. Exp Cell Res 2016; 358:433-438. [PMID: 28017728 DOI: 10.1016/j.yexcr.2016.12.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 12/22/2016] [Indexed: 12/24/2022]
Abstract
Genomic information has become a ubiquitous and almost essential aspect of biological research. Over the last 10-15 years, the cost of generating sequence data from DNA or RNA samples has dramatically declined and our ability to interpret those data increased just as remarkably. Although it is still possible for biologists to conduct interesting and valuable research on species for which genomic data are not available, the impact of having access to a high quality whole genome reference assembly for a given species is nothing short of transformational. Research on a species for which we have no DNA or RNA sequence data is restricted in fundamental ways. In contrast, even access to an initial draft quality genome (see below for definitions) opens a wide range of opportunities that are simply not available without that reference genome assembly. Although a complete discussion of the impact of genome sequencing and assembly is beyond the scope of this short paper, the goal of this review is to summarize the most common and highest impact contributions that whole genome sequencing and assembly has had on comparative and evolutionary biology.
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Affiliation(s)
- Kim C Worley
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.
| | - Stephen Richards
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
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317
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Kjer K, Borowiec ML, Frandsen PB, Ware J, Wiegmann BM. Advances using molecular data in insect systematics. CURRENT OPINION IN INSECT SCIENCE 2016; 18:40-47. [PMID: 27939709 DOI: 10.1016/j.cois.2016.09.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 09/26/2016] [Indexed: 06/06/2023]
Abstract
The size of molecular datasets has been growing exponentially since the mid 1980s, and new technologies have now dramatically increased the slope of this increase. New datasets include genomes, transcriptomes, and hybrid capture data, producing hundreds or thousands of loci. With these datasets, we are approaching a consensus on the higher level insect phylogeny. Huge datasets can produce new challenges in interpreting branch support, and new opportunities in developing better models and more sophisticated partitioning schemes. Dating analyses are improving as we recognize the importance of careful fossil calibration selection. With thousands of genes now available, coalescent methods have come of age. Barcode libraries continue to expand, and new methods are being developed for incorporating them into phylogenies with tens of thousands of individuals.
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Affiliation(s)
- Karl Kjer
- Rutgers University, Department of Biological Sciences, 415 Boyden Hall, Newark, NJ 07012, USA
| | - Marek L Borowiec
- University of Rochester, 226 Hutchison Hall, Rochester, NY 14627, USA
| | - Paul B Frandsen
- Smithsonian Institution, Office of Research Information Services, Office of the Chief Information Officer, Washington, D.C. 20024, USA
| | - Jessica Ware
- Rutgers University, Department of Biological Sciences, 415 Boyden Hall, Newark, NJ 07012, USA
| | - Brian M Wiegmann
- Department of Entomology & Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA.
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318
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Distribution of coalescent histories under the coalescent model with gene flow. Mol Phylogenet Evol 2016; 105:177-192. [DOI: 10.1016/j.ympev.2016.08.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Revised: 08/16/2016] [Accepted: 08/31/2016] [Indexed: 12/19/2022]
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319
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A whole genome gene content phylogenetic analysis of anopheline mosquitoes. Mol Phylogenet Evol 2016; 107:266-269. [PMID: 27866013 DOI: 10.1016/j.ympev.2016.11.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 10/25/2016] [Accepted: 11/09/2016] [Indexed: 11/21/2022]
Abstract
Construction of stringent gene content matrices was accomplished for 21 Anopheline mosquito species and strains and four outgroups species. The presence absence matrix using e-75 as a cutoff in single linkage clustering had over 17,000 ortholog groups. We used the gene content matrix to generate a phylogenetic hypothesis that is in general agreement with gene sequence based phylogenies. In addition to establishing a congruent gene content phylogeny we examined the consistency of three methods for analyzing presence absence data - unweighted parsimony, dollo parsimonly and maximum likelihood using a BINGAMMA model. An examination of the chromosomal location of the gains and losses in the presence absence matrix revealed a low frequency of gains and losses at centromeres and tips of chromosomes.
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320
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Abstract
BACKGROUND Phylogenetic networks model reticulate evolutionary histories. The last two decades have seen an increased interest in establishing mathematical results and developing computational methods for inferring and analyzing these networks. A salient concept underlying a great majority of these developments has been the notion that a network displays a set of trees and those trees can be used to infer, analyze, and study the network. RESULTS In this paper, we show that in the presence of coalescence effects, the set of displayed trees is not sufficient to capture the network. We formally define the set of parental trees of a network and make three contributions based on this definition. First, we extend the notion of anomaly zone to phylogenetic networks and report on anomaly results for different networks. Second, we demonstrate how coalescence events could negatively affect the ability to infer a species tree that could be augmented into the correct network. Third, we demonstrate how a phylogenetic network can be viewed as a mixture model that lends itself to a novel inference approach via gene tree clustering. CONCLUSIONS Our results demonstrate the limitations of focusing on the set of trees displayed by a network when analyzing and inferring the network. Our findings can form the basis for achieving higher accuracy when inferring phylogenetic networks and open up new venues for research in this area, including new problem formulations based on the notion of a network's parental trees.
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Affiliation(s)
- Jiafan Zhu
- Department of Computer Science, Rice University, Houston, 77005 Texas USA
| | - Yun Yu
- Department of Computer Science, Rice University, Houston, 77005 Texas USA
| | - Luay Nakhleh
- Department of Computer Science, Rice University, Houston, 77005 Texas USA
- Department of BioSciences, Rice University, Houston, 77005 Texas USA
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321
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Yu Y, Jermaine C, Nakhleh L. Exploring phylogenetic hypotheses via Gibbs sampling on evolutionary networks. BMC Genomics 2016; 17:784. [PMID: 28185563 PMCID: PMC5123299 DOI: 10.1186/s12864-016-3099-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background Phylogenetic networks are leaf-labeled graphs used to model and display complex evolutionary relationships that do not fit a single tree. There are two classes of phylogenetic networks: Data-display networks and evolutionary networks. While data-display networks are very commonly used to explore data, they are not amenable to incorporating probabilistic models of gene and genome evolution. Evolutionary networks, on the other hand, can accommodate such probabilistic models, but they are not commonly used for exploration. Results In this work, we show how to turn evolutionary networks into a tool for statistical exploration of phylogenetic hypotheses via a novel application of Gibbs sampling. We demonstrate the utility of our work on two recently available genomic data sets, one from a group of mosquitos and the other from a group of modern birds. We demonstrate that our method allows the use of evolutionary networks not only for explicit modeling of reticulate evolutionary histories, but also for exploring conflicting treelike hypotheses. We further demonstrate the performance of the method on simulated data sets, where the true evolutionary histories are known. Conclusion We introduce an approach to explore phylogenetic hypotheses over evolutionary phylogenetic networks using Gibbs sampling. The hypotheses could involve reticulate and non-reticulate evolutionary processes simultaneously as we illustrate on mosquito and modern bird genomic data sets.
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Affiliation(s)
- Yun Yu
- Department of Computer Science, Rice University, Houston, Texas, 77005, USA
| | | | - Luay Nakhleh
- Department of Computer Science, Rice University, Houston, Texas, 77005, USA. .,Department of BioSciences, Rice University, Houston, Texas, 77005, USA.
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322
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Love RR, Steele AM, Coulibaly MB, Traore SF, Emrich SJ, Fontaine MC, Besansky NJ. Chromosomal inversions and ecotypic differentiation in Anopheles gambiae: the perspective from whole-genome sequencing. Mol Ecol 2016; 25:5889-5906. [PMID: 27759895 DOI: 10.1111/mec.13888] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 09/13/2016] [Accepted: 10/03/2016] [Indexed: 12/30/2022]
Abstract
The molecular mechanisms and genetic architecture that facilitate adaptive radiation of lineages remain elusive. Polymorphic chromosomal inversions, due to their recombination-reducing effect, are proposed instruments of ecotypic differentiation. Here, we study an ecologically diversifying lineage of Anopheles gambiae, known as the Bamako chromosomal form based on its unique complement of three chromosomal inversions, to explore the impact of these inversions on ecotypic differentiation. We used pooled and individual genome sequencing of Bamako, typical (non-Bamako) An. gambiae and the sister species Anopheles coluzzii to investigate evolutionary relationships and genomewide patterns of nucleotide diversity and differentiation among lineages. Despite extensive shared polymorphism and limited differentiation from the other taxa, Bamako clusters apart from the other taxa, and forms a maximally supported clade in neighbour-joining trees based on whole-genome data (including inversions) or solely on collinear regions. Nevertheless, FST outlier analysis reveals that the majority of differentiated regions between Bamako and typical An. gambiae are located inside chromosomal inversions, consistent with their role in the ecological isolation of Bamako. Exceptionally differentiated genomic regions were enriched for genes implicated in nervous system development and signalling. Candidate genes associated with a selective sweep unique to Bamako contain substitutions not observed in sympatric samples of the other taxa, and several insecticide resistance gene alleles shared between Bamako and other taxa segregate at sharply different frequencies in these samples. Bamako represents a useful window into the initial stages of ecological and genomic differentiation from sympatric populations in this important group of malaria vectors.
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Affiliation(s)
- R Rebecca Love
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA.,Department of Biological Sciences, University of Notre Dame, Galvin Life Sciences Center, Notre Dame, IN, 46556, USA
| | - Aaron M Steele
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA.,Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Mamadou B Coulibaly
- Malaria Research and Training Centre, Faculty of Medicine Pharmacy and Dentistry, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Sékou F Traore
- Malaria Research and Training Centre, Faculty of Medicine Pharmacy and Dentistry, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Scott J Emrich
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA.,Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Michael C Fontaine
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA.,Department of Biological Sciences, University of Notre Dame, Galvin Life Sciences Center, Notre Dame, IN, 46556, USA.,Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Nora J Besansky
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA.,Department of Biological Sciences, University of Notre Dame, Galvin Life Sciences Center, Notre Dame, IN, 46556, USA
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323
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Caputo B, Pichler V, Mancini E, Pombi M, Vicente JL, Dinis J, Steen K, Petrarca V, Rodrigues A, Pinto J, Della Torre A, Weetman D. The last bastion? X chromosome genotyping of Anopheles gambiae species pair males from a hybrid zone reveals complex recombination within the major candidate 'genomic island of speciation'. Mol Ecol 2016; 25:5719-5731. [PMID: 27661465 DOI: 10.1111/mec.13840] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 07/19/2016] [Accepted: 09/01/2016] [Indexed: 01/19/2023]
Abstract
Speciation with gene flow may be aided by reduced recombination helping to build linkage between genes involved in the early stages of reproductive isolation. Reduced recombination on chromosome X has been implicated in speciation within the Anopheles gambiae complex, species of which represent the major Afrotropical malaria vectors. The most recently diverged, morphologically indistinguishable, species pair, A. gambiae and Anopheles coluzzii, ubiquitously displays a 'genomic island of divergence' spanning over 4 Mb from chromosome X centromere, which represents a particularly promising candidate region for reproductive isolation genes, in addition to containing the diagnostic markers used to distinguish the species. Very low recombination makes the island intractable for experimental recombination studies, but an extreme hybrid zone in Guinea Bissau offers the opportunity for natural investigation of X-island recombination. SNP analysis of chromosome X hemizygous males revealed: (i) strong divergence in the X-island despite a lack of autosomal divergence; (ii) individuals with multiple-recombinant genotypes, including likely double crossovers and localized gene conversion; (iii) recombination-driven discontinuity both within and between the molecular species markers, suggesting that the utility of the diagnostics is undermined under high hybridization. The largely, but incompletely protected nature of the X centromeric genomic island is consistent with a primary candidate area for accumulation of adaptive variants driving speciation with gene flow, while permitting some selective shuffling and removal of genetic variation.
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Affiliation(s)
- Beniamino Caputo
- Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Dipartimento di Sanità Pubblica e Malattie Infettive, Università 'Sapienza', Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Verena Pichler
- Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Dipartimento di Sanità Pubblica e Malattie Infettive, Università 'Sapienza', Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Emiliano Mancini
- Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Dipartimento di Sanità Pubblica e Malattie Infettive, Università 'Sapienza', Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Marco Pombi
- Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Dipartimento di Sanità Pubblica e Malattie Infettive, Università 'Sapienza', Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - José L Vicente
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Rua daJunqueira, 100, 1349-008, Lisboa, Portugal
| | - Joao Dinis
- Instituto Nacional de Saúde Pública, Ministério da Saúde Pública, Avenida Combatentes da Liberdade da Pátria, Apartado 861, 1004, Bissau Codex, Guinea Bissau
| | - Keith Steen
- Vector Biology Department, Liverpool School of Tropical Medicine, Pembroke Pl, Liverpool, Merseyside, L3 5QA, UK
| | - Vincenzo Petrarca
- Istituto Pasteur-Fondazione Cenci-Bolognetti, Dipartimento di Biologia e Biotecnologie Charles Darwin, Università 'Sapienza', Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Amabelia Rodrigues
- Instituto Nacional de Saúde Pública, Ministério da Saúde Pública, Avenida Combatentes da Liberdade da Pátria, Apartado 861, 1004, Bissau Codex, Guinea Bissau
| | - Joao Pinto
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Rua daJunqueira, 100, 1349-008, Lisboa, Portugal
| | - Alessandra Della Torre
- Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Dipartimento di Sanità Pubblica e Malattie Infettive, Università 'Sapienza', Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - David Weetman
- Vector Biology Department, Liverpool School of Tropical Medicine, Pembroke Pl, Liverpool, Merseyside, L3 5QA, UK
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324
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Bouchemousse S, Liautard-Haag C, Bierne N, Viard F. Distinguishing contemporary hybridization from past introgression with postgenomic ancestry-informative SNPs in strongly differentiated Ciona species. Mol Ecol 2016; 25:5527-5542. [PMID: 27662427 DOI: 10.1111/mec.13854] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 09/09/2016] [Accepted: 09/16/2016] [Indexed: 12/13/2022]
Abstract
Biological introductions bring into contact species that can still hybridize. The evolutionary outcomes of such secondary contacts may be diverse (e.g. adaptive introgression from or into the introduced species) but are not yet well examined in the wild. The recent secondary contact between the non-native sea squirt Ciona robusta (formerly known as C. intestinalis type A) and its native congener C. intestinalis (formerly known as C. intestinalis type B), in the Western English Channel, provides an excellent case study to examine. To examine contemporary hybridization between the two species, we developed a panel of 310 ancestry-informative SNPs from a population transcriptomic study. Hybridization rates were examined on 449 individuals sampled in eight sites from the sympatric range and five sites from allopatric ranges. The results clearly showed an almost complete absence of contemporary hybridization between the two species in syntopic localities, with only one-first-generation hybrid and no other genotype compatible with recent backcrosses. Despite the almost lack of contemporary hybridization, shared polymorphisms were observed in sympatric and allopatric populations of both species. Furthermore, one allopatric population from SE Pacific exhibited a higher rate of shared polymorphisms compared to all other C. robusta populations. Altogether, these results indicate that the observed level of shared polymorphism is more probably the outcome of ancient gene flow spread afterwards at a worldwide scale. They also emphasize efficient reproductive barriers preventing hybridization between introduced and native species, which suggests hybridization should not impede too much the expansion and the establishment of the non-native species in its introduction range.
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Affiliation(s)
- Sarah Bouchemousse
- UPMC Univ Paris 6, UMR 7144, Equipe DIVCO, Sorbonne Universités, Station Biologique de Roscoff, Place Georges Teissier, 29680, Roscoff, France.,CNRS, UMR 7144, Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Place Georges Teissier, 29680, Roscoff, France
| | - Cathy Liautard-Haag
- Station Marine - OSU OREME, Université de Montpellier, 2 Rue des Chantiers, 34200, Sète, France.,CNRS-UM-IRD-EPHE, UMR 5554, Institut des Sciences de l'Evolution, Place Eugène Bataillon, 34095, Montpellier, France
| | - Nicolas Bierne
- Station Marine - OSU OREME, Université de Montpellier, 2 Rue des Chantiers, 34200, Sète, France.,CNRS-UM-IRD-EPHE, UMR 5554, Institut des Sciences de l'Evolution, Place Eugène Bataillon, 34095, Montpellier, France
| | - Frédérique Viard
- UPMC Univ Paris 6, UMR 7144, Equipe DIVCO, Sorbonne Universités, Station Biologique de Roscoff, Place Georges Teissier, 29680, Roscoff, France. .,CNRS, UMR 7144, Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Place Georges Teissier, 29680, Roscoff, France.
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325
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Molina-Cruz A, Zilversmit MM, Neafsey DE, Hartl DL, Barillas-Mury C. Mosquito Vectors and the Globalization of Plasmodium falciparum Malaria. Annu Rev Genet 2016; 50:447-465. [PMID: 27732796 DOI: 10.1146/annurev-genet-120215-035211] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Plasmodium falciparum malaria remains a devastating public health problem. Recent discoveries have shed light on the origin and evolution of Plasmodium parasites and their interactions with their vertebrate and mosquito hosts. P. falciparum malaria originated in Africa from a single horizontal transfer between an infected gorilla and a human, and became global as the result of human migration. Today, P. falciparum malaria is transmitted worldwide by more than 70 different anopheline mosquito species. Recent studies indicate that the mosquito immune system can be a barrier to malaria transmission and that the P. falciparum Pfs47 gene allows the parasite to evade mosquito immune detection. Here, we review the origin and globalization of P. falciparum and integrate this history with analysis of the biology, evolution, and dispersal of the main mosquito vectors. This new perspective broadens our understanding of P. falciparum population structure and the dispersal of important parasite genetic traits.
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Affiliation(s)
- Alvaro Molina-Cruz
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland 20852;
| | - Martine M Zilversmit
- Richard Guilder Graduate School and Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024
| | - Daniel E Neafsey
- Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
| | - Daniel L Hartl
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Carolina Barillas-Mury
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland 20852;
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326
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Main BJ, Lee Y, Ferguson HM, Kreppel KS, Kihonda A, Govella NJ, Collier TC, Cornel AJ, Eskin E, Kang EY, Nieman CC, Weakley AM, Lanzaro GC. The Genetic Basis of Host Preference and Resting Behavior in the Major African Malaria Vector, Anopheles arabiensis. PLoS Genet 2016; 12:e1006303. [PMID: 27631375 PMCID: PMC5025075 DOI: 10.1371/journal.pgen.1006303] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Accepted: 08/16/2016] [Indexed: 11/19/2022] Open
Abstract
Malaria transmission is dependent on the propensity of Anopheles mosquitoes to bite humans (anthropophily) instead of other dead end hosts. Recent increases in the usage of Long Lasting Insecticide Treated Nets (LLINs) in Africa have been associated with reductions in highly anthropophilic and endophilic vectors such as Anopheles gambiae s.s., leaving species with a broader host range, such as Anopheles arabiensis, as the most prominent remaining source of transmission in many settings. An. arabiensis appears to be more of a generalist in terms of its host choice and resting behavior, which may be due to phenotypic plasticity and/or segregating allelic variation. To investigate the genetic basis of host choice and resting behavior in An. arabiensis we sequenced the genomes of 23 human-fed and 25 cattle-fed mosquitoes collected both in-doors and out-doors in the Kilombero Valley, Tanzania. We identified a total of 4,820,851 SNPs, which were used to conduct the first genome-wide estimates of "SNP heritability" for host choice and resting behavior in this species. A genetic component was detected for host choice (human vs cow fed; permuted P = 0.002), but there was no evidence of a genetic component for resting behavior (indoors versus outside; permuted P = 0.465). A principal component analysis (PCA) segregated individuals based on genomic variation into three groups which were characterized by differences at the 2Rb and/or 3Ra paracentromeric chromosome inversions. There was a non-random distribution of cattle-fed mosquitoes between the PCA clusters, suggesting that alleles linked to the 2Rb and/or 3Ra inversions may influence host choice. Using a novel inversion genotyping assay, we detected a significant enrichment of the standard arrangement (non-inverted) of 3Ra among cattle-fed mosquitoes (N = 129) versus all non-cattle-fed individuals (N = 234; χ2, p = 0.007). Thus, tracking the frequency of the 3Ra in An. arabiensis populations may be of use to infer selection on host choice behavior within these vector populations; possibly in response to vector control. Controlled host-choice assays are needed to discern whether the observed genetic component has a direct relationship with innate host preference. A better understanding of the genetic basis for host feeding behavior in An. arabiensis may also open avenues for novel vector control strategies based on driving genes for zoophily into wild mosquito populations.
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Affiliation(s)
- Bradley J Main
- Vector Genetics Laboratory, Department of Pathology, Microbiology and Immunology/University of California, Davis, Davis, California, United States of America
- * E-mail:
| | - Yoosook Lee
- Vector Genetics Laboratory, Department of Pathology, Microbiology and Immunology/University of California, Davis, Davis, California, United States of America
| | - Heather M. Ferguson
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Katharina S. Kreppel
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
- Environmental Health and Ecological Sciences Group, Ifakara Health Institute, Ifakara, United Republic of Tanzania
| | - Anicet Kihonda
- Environmental Health and Ecological Sciences Group, Ifakara Health Institute, Ifakara, United Republic of Tanzania
| | - Nicodem J. Govella
- Environmental Health and Ecological Sciences Group, Ifakara Health Institute, Ifakara, United Republic of Tanzania
| | - Travis C. Collier
- Vector Genetics Laboratory, Department of Pathology, Microbiology and Immunology/University of California, Davis, Davis, California, United States of America
| | - Anthony J. Cornel
- Department of Entomology and Nematology, University of California, Davis, Davis, California, United States of America
| | - Eleazar Eskin
- Department of Computer Science, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Eun Yong Kang
- Department of Computer Science, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Catelyn C. Nieman
- Vector Genetics Laboratory, Department of Pathology, Microbiology and Immunology/University of California, Davis, Davis, California, United States of America
| | - Allison M. Weakley
- Vector Genetics Laboratory, Department of Pathology, Microbiology and Immunology/University of California, Davis, Davis, California, United States of America
| | - Gregory C. Lanzaro
- Vector Genetics Laboratory, Department of Pathology, Microbiology and Immunology/University of California, Davis, Davis, California, United States of America
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327
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Mendes FK, Hahn Y, Hahn MW. Gene Tree Discordance Can Generate Patterns of Diminishing Convergence over Time. Mol Biol Evol 2016; 33:3299-3307. [PMID: 27634870 DOI: 10.1093/molbev/msw197] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Phenotypic convergence is an exciting outcome of adaptive evolution, occurring when different species find similar solutions to the same problem. Unraveling the molecular basis of convergence provides a way to link genotype to adaptive phenotypes, but can also shed light on the extent to which molecular evolution is repeatable and predictable. Many recent genome-wide studies have uncovered a striking pattern of diminishing convergence over time, ascribing this pattern to the presence of intramolecular epistatic interactions. Here, we consider gene tree discordance as an alternative cause of changes in convergence levels over time in a primate dataset. We demonstrate that gene tree discordance can produce patterns of diminishing convergence by itself, and that controlling for discordance as a cause of apparent convergence makes the pattern disappear. We also show that synonymous substitutions, where neither selection nor epistasis should be prevalent, have the same diminishing pattern of molecular convergence in primates. Finally, we demonstrate that even in situations where biological discordance is not possible, discordance due to errors in species tree inference can drive similar patterns. Though intramolecular epistasis could in principle create a pattern of declining convergence over time, our results suggest a possible alternative explanation for this widespread pattern. These results contribute to a growing appreciation not just of the presence of gene tree discordance, but of the unpredictable effects this discordance can have on analyses of molecular evolution.
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Affiliation(s)
- Fábio K Mendes
- Department of Biology, Indiana University, Bloomington, IN
| | - Yoonsoo Hahn
- Department of Life Science, Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul, Republic of Korea
| | - Matthew W Hahn
- Department of Biology, Indiana University, Bloomington, IN.,School of Informatics and Computing, Indiana University, Bloomington, IN
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328
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Zarza E, Faircloth BC, Tsai WL, Bryson RW, Klicka J, McCormack JE. Hidden histories of gene flow in highland birds revealed with genomic markers. Mol Ecol 2016; 25:5144-5157. [DOI: 10.1111/mec.13813] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 08/10/2016] [Accepted: 08/12/2016] [Indexed: 01/03/2023]
Affiliation(s)
- Eugenia Zarza
- Moore Laboratory of Zoology Occidental College Los Angeles CA 90041 USA
| | - Brant C. Faircloth
- Department of Biological Sciences and Museum of Natural Science Louisiana State University Baton Rouge LA 70803 USA
| | - Whitney L.E. Tsai
- Moore Laboratory of Zoology Occidental College Los Angeles CA 90041 USA
| | - Robert W. Bryson
- Moore Laboratory of Zoology Occidental College Los Angeles CA 90041 USA
- Burke Museum of Natural History and Culture and Department of Biology University of Washington Seattle WA 98195 USA
| | - John Klicka
- Burke Museum of Natural History and Culture and Department of Biology University of Washington Seattle WA 98195 USA
| | - John E. McCormack
- Moore Laboratory of Zoology Occidental College Los Angeles CA 90041 USA
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329
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Abstract
Anopheles melas is a member of the recently diverged An. gambiae species complex, a model for speciation studies, and is a locally important malaria vector along the West-African coast where it breeds in brackish water. A recent population genetic study of An. melas revealed species-level genetic differentiation between three population clusters. An. melas West extends from The Gambia to the village of Tiko, Cameroon. The other mainland cluster, An. melas South, extends from the southern Cameroonian village of Ipono to Angola. Bioko Island, Equatorial Guinea An. melas populations are genetically isolated from mainland populations. To examine how genetic differentiation between these An. melas forms is distributed across their genomes, we conducted a genome-wide analysis of genetic differentiation and selection using whole genome sequencing data of pooled individuals (Pool-seq) from a representative population of each cluster. The An. melas forms exhibit high levels of genetic differentiation throughout their genomes, including the presence of numerous fixed differences between clusters. Although the level of divergence between the clusters is on a par with that of other species within the An. gambiae complex, patterns of genome-wide divergence and diversity do not provide evidence for the presence of pre- and/or postmating isolating mechanisms in the form of speciation islands. These results are consistent with an allopatric divergence process with little or no introgression.
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330
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Abstract
Malaria continues to impose a significant disease burden on low- and middle-income countries in the tropics. However, revolutionary progress over the last 3 years in nucleic acid sequencing, reverse genetics, and post-genome analyses has generated step changes in our understanding of malaria parasite (Plasmodium spp.) biology and its interactions with its host and vector. Driven by the availability of vast amounts of genome sequence data from Plasmodium species strains, relevant human populations of different ethnicities, and mosquito vectors, researchers can consider any biological component of the malarial process in isolation or in the interactive setting that is infection. In particular, considerable progress has been made in the area of population genomics, with Plasmodium falciparum serving as a highly relevant model. Such studies have demonstrated that genome evolution under strong selective pressure can be detected. These data, combined with reverse genetics, have enabled the identification of the region of the P. falciparum genome that is under selective pressure and the confirmation of the functionality of the mutations in the kelch13 gene that accompany resistance to the major frontline antimalarial, artemisinin. Furthermore, the central role of epigenetic regulation of gene expression and antigenic variation and developmental fate in P. falciparum is becoming ever clearer. This review summarizes recent exciting discoveries that genome technologies have enabled in malaria research and highlights some of their applications to healthcare. The knowledge gained will help to develop surveillance approaches for the emergence or spread of drug resistance and to identify new targets for the development of antimalarial drugs and perhaps vaccines.
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Affiliation(s)
- Sebastian Kirchner
- Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical Veterinary & Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK
| | - B Joanne Power
- Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical Veterinary & Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK
| | - Andrew P Waters
- Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical Veterinary & Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK.
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331
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Sougoufara S, Harry M, Doucouré S, Sembène PM, Sokhna C. Shift in species composition in the Anopheles gambiae complex after implementation of long-lasting insecticidal nets in Dielmo, Senegal. MEDICAL AND VETERINARY ENTOMOLOGY 2016; 30:365-368. [PMID: 27058993 DOI: 10.1111/mve.12171] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 12/03/2015] [Accepted: 01/15/2016] [Indexed: 06/05/2023]
Abstract
Long-lasting insecticidal nets (LLINs) and indoor residual spraying (IRS) are the cornerstones of malaria vector control. However, the effectiveness of these control tools depends on vector ecology and behaviour, which also largely determine the efficacy of certain Anopheles mosquitoes (Diptera: Culicidae) as vectors. Malaria vectors in sub-Saharan Africa are primarily species of the Anopheles gambiae complex, which present intraspecific differences in behaviour that affect how they respond to vector control tools. The focus of this study is the change in species composition in the An. gambiae complex after the implementation of LLINs in Dielmo, Senegal. The main findings referred to dramatic decreases in the proportions of Anopheles coluzzii and An. gambiae after the introduction of LLINs, and an increase in the proportion of Anopheles arabiensis. Two years after LLINs were first introduced, An. arabiensis remained the most prevalent species and An. gambiae had begun to rebound. This indicated a need to develop additional vector control tools that can target the full range of malaria vectors.
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Affiliation(s)
- S Sougoufara
- Unité de Recherche sur les Maladies Infectieuses Tropicales Emergentes (URMITE), Unité Mixte de Recherche (UMR), Centre National de la Recherche Scientifique (CNRS) 6236, Institut de Recherche pour le Développement (IRD) 198, Aix Marseille Université, Campus Universitaire IRD de Hann, Dakar, Senegal
- Département de Biologie Animale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop de Dakar, Dakar Fann, Senegal
| | - M Harry
- Unité de Formation et de Recherche (UFR) Sciences, Université Paris-Sud, Orsay, France
- UMR Évolution, Génomes, Comportement, Écologie (EGCE), CNRS-IRD Université Paris Sud, Institut Diversité, Écologie et Évolution du Vivant (IDEEV), Université Paris-Saclay, Gif-sur-Yvette, France
| | - S Doucouré
- Unité de Recherche sur les Maladies Infectieuses Tropicales Emergentes (URMITE), Unité Mixte de Recherche (UMR), Centre National de la Recherche Scientifique (CNRS) 6236, Institut de Recherche pour le Développement (IRD) 198, Aix Marseille Université, Campus Universitaire IRD de Hann, Dakar, Senegal
| | - P M Sembène
- Département de Biologie Animale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop de Dakar, Dakar Fann, Senegal
| | - C Sokhna
- Unité de Recherche sur les Maladies Infectieuses Tropicales Emergentes (URMITE), Unité Mixte de Recherche (UMR), Centre National de la Recherche Scientifique (CNRS) 6236, Institut de Recherche pour le Développement (IRD) 198, Aix Marseille Université, Campus Universitaire IRD de Hann, Dakar, Senegal
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332
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Gante HF, Matschiner M, Malmstrøm M, Jakobsen KS, Jentoft S, Salzburger W. Genomics of speciation and introgression in Princess cichlid fishes from Lake Tanganyika. Mol Ecol 2016; 25:6143-6161. [DOI: 10.1111/mec.13767] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 05/30/2016] [Accepted: 07/11/2016] [Indexed: 01/02/2023]
Affiliation(s)
- Hugo F. Gante
- Zoological Institute University of Basel Vesalgasse 1 4051 Basel Switzerland
| | - Michael Matschiner
- Department of Biosciences CEES (Centre for Ecological and Evolutionary Synthesis) University of Oslo 0316 Oslo Norway
| | - Martin Malmstrøm
- Department of Biosciences CEES (Centre for Ecological and Evolutionary Synthesis) University of Oslo 0316 Oslo Norway
| | - Kjetill S. Jakobsen
- Department of Biosciences CEES (Centre for Ecological and Evolutionary Synthesis) University of Oslo 0316 Oslo Norway
| | - Sissel Jentoft
- Department of Biosciences CEES (Centre for Ecological and Evolutionary Synthesis) University of Oslo 0316 Oslo Norway
- Department of Natural Sciences University of Agder 4604 Kristiansand Norway
| | - Walter Salzburger
- Zoological Institute University of Basel Vesalgasse 1 4051 Basel Switzerland
- Department of Biosciences CEES (Centre for Ecological and Evolutionary Synthesis) University of Oslo 0316 Oslo Norway
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333
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Novikova PY, Hohmann N, Nizhynska V, Tsuchimatsu T, Ali J, Muir G, Guggisberg A, Paape T, Schmid K, Fedorenko OM, Holm S, Säll T, Schlötterer C, Marhold K, Widmer A, Sese J, Shimizu KK, Weigel D, Krämer U, Koch MA, Nordborg M. Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism. Nat Genet 2016; 48:1077-82. [PMID: 27428747 DOI: 10.1038/ng.3617] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 06/14/2016] [Indexed: 12/17/2022]
Abstract
The notion of species as reproductively isolated units related through a bifurcating tree implies that gene trees should generally agree with the species tree and that sister taxa should not share polymorphisms unless they diverged recently and should be equally closely related to outgroups. It is now possible to evaluate this model systematically. We sequenced multiple individuals from 27 described taxa representing the entire Arabidopsis genus. Cluster analysis identified seven groups, corresponding to described species that capture the structure of the genus. However, at the level of gene trees, only the separation of Arabidopsis thaliana from the remaining species was universally supported, and, overall, the amount of shared polymorphism demonstrated that reproductive isolation was considerably more recent than the estimated divergence times. We uncovered multiple cases of past gene flow that contradict a bifurcating species tree. Finally, we showed that the pattern of divergence differs between gene ontologies, suggesting a role for selection.
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Affiliation(s)
- Polina Yu Novikova
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria.,Vienna Graduate School of Population Genetics, Institut für Populationsgenetik, Vetmeduni, Vienna, Austria
| | - Nora Hohmann
- Centre for Organismal Studies Heidelberg, University of Heidelberg, Heidelberg, Germany
| | - Viktoria Nizhynska
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Takashi Tsuchimatsu
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Jamshaid Ali
- Department of Plant Physiology, Ruhr-Universität Bochum, Bochum, Germany
| | - Graham Muir
- Vienna Graduate School of Population Genetics, Institut für Populationsgenetik, Vetmeduni, Vienna, Austria
| | | | - Tim Paape
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Karl Schmid
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, Germany
| | - Olga M Fedorenko
- Institute of Biology, Karelian Research Center of the Russian Academy of Sciences, Petrozavodsk, Russia
| | - Svante Holm
- Faculty of Science, Technology and Media, Department of Natural Sciences, Mid Sweden University, Sundsvall, Sweden
| | - Torbjörn Säll
- Department of Biology, Lund University, Lund, Sweden
| | | | - Karol Marhold
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic.,Institute of Botany, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Alex Widmer
- Department of Plant Physiology, Ruhr-Universität Bochum, Bochum, Germany
| | - Jun Sese
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Kentaro K Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Detlef Weigel
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Ute Krämer
- Department of Plant Physiology, Ruhr-Universität Bochum, Bochum, Germany
| | - Marcus A Koch
- Centre for Organismal Studies Heidelberg, University of Heidelberg, Heidelberg, Germany
| | - Magnus Nordborg
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
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334
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Kirkpatrick M. The Evolution of Genome Structure by Natural and Sexual Selection. J Hered 2016; 108:3-11. [PMID: 27388336 DOI: 10.1093/jhered/esw041] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 06/28/2016] [Indexed: 11/13/2022] Open
Abstract
Progress on understanding how genome structure evolves is accelerating with the arrival of new genomic, comparative, and theoretical approaches. This article reviews progress in understanding how chromosome inversions and sex chromosomes evolve, and how their evolution affects species' ecology. Analyses of clines in inversion frequencies in flies and mosquitoes imply strong local adaptation, and roles for both over- and under dominant selection. Those results are consistent with the hypothesis that inversions become established when they capture locally adapted alleles. Inversions can carry alleles that are beneficial to closely related species, causing them to introgress following hybridization. Models show that this "adaptive cassette" scenario can trigger large range expansions, as recently happened in malaria mosquitoes. Sex chromosomes are the most rapidly evolving genome regions of some taxa. Sexually antagonistic selection may be the key force driving transitions of sex determination between different pairs of chromosomes and between XY and ZW systems. Fusions between sex-chromosomes and autosomes most often involve the Y chromosome, a pattern that can be explained if fusions are mildly deleterious and fix by drift. Sexually antagonistic selection is one of several hypotheses to explain the recent discovery that the sex determination system has strong effects on the adult sex ratios of tetrapods. The emerging view of how genome structure evolves invokes a much richer constellation of forces than was envisioned during the Golden Age of research on Drosophila karyotypes.
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Affiliation(s)
- Mark Kirkpatrick
- From the Department of Integrative Biology C-0990, University of Texas, Austin, TX 78712 USA (Kirkpatrick).
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335
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Affiliation(s)
- Louxin Zhang
- Department of Mathematics, National University of Singapore, Singapore
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336
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Stuglik MT, Babik W. Genomic heterogeneity of historical gene flow between two species of newts inferred from transcriptome data. Ecol Evol 2016; 6:4513-25. [PMID: 27386093 PMCID: PMC4930998 DOI: 10.1002/ece3.2152] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 04/02/2016] [Accepted: 04/04/2016] [Indexed: 01/31/2023] Open
Abstract
The role of gene flow in species formation is a major unresolved issue in speciation biology. Progress in this area requires information on the long-term patterns of gene flow between diverging species. Here, we used thousands of single-nucleotide polymorphisms derived from transcriptome resequencing and a method modeling the joint frequency spectrum of these polymorphisms to reconstruct patterns of historical gene flow between two Lissotriton newts: L. vulgaris (Lv) and L. montandoni (Lm). We tested several models of divergence including complete isolation and various scenarios of historical gene flow. The model of secondary contact received the highest support. According to this model, the species split from their common ancestor ca. 5.5 million years (MY) ago, evolved in isolation for ca. 2 MY, and have been exchanging genes for the last 3.5 MY Demographic changes have been inferred in both species, with the current effective population size of ca. 0.7 million in Lv and 0.2 million in Lm. The postdivergence gene flow resulted in two-directional introgression which affected the genomes of both species, but was more pronounced from Lv to Lm. Interestingly, we found evidence for genomic heterogeneity of interspecific gene flow. This study demonstrates the complexity of long-term gene flow between distinct but incompletely reproductively isolated taxa which divergence was initiated millions of years ago.
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Affiliation(s)
- Michał T. Stuglik
- Institute of Environmental SciencesJagiellonian UniversityGronostajowa 730387KrakowPoland
| | - Wiesław Babik
- Institute of Environmental SciencesJagiellonian UniversityGronostajowa 730387KrakowPoland
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337
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Payseur BA, Rieseberg LH. A genomic perspective on hybridization and speciation. Mol Ecol 2016; 25:2337-60. [PMID: 26836441 PMCID: PMC4915564 DOI: 10.1111/mec.13557] [Citation(s) in RCA: 292] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 01/18/2016] [Accepted: 01/25/2016] [Indexed: 12/13/2022]
Abstract
Hybridization among diverging lineages is common in nature. Genomic data provide a special opportunity to characterize the history of hybridization and the genetic basis of speciation. We review existing methods and empirical studies to identify recent advances in the genomics of hybridization, as well as issues that need to be addressed. Notable progress has been made in the development of methods for detecting hybridization and inferring individual ancestries. However, few approaches reconstruct the magnitude and timing of gene flow, estimate the fitness of hybrids or incorporate knowledge of recombination rate. Empirical studies indicate that the genomic consequences of hybridization are complex, including a highly heterogeneous landscape of differentiation. Inferred characteristics of hybridization differ substantially among species groups. Loci showing unusual patterns - which may contribute to reproductive barriers - are usually scattered throughout the genome, with potential enrichment in sex chromosomes and regions of reduced recombination. We caution against the growing trend of interpreting genomic variation in summary statistics across genomes as evidence of differential gene flow. We argue that converting genomic patterns into useful inferences about hybridization will ultimately require models and methods that directly incorporate key ingredients of speciation, including the dynamic nature of gene flow, selection acting in hybrid populations and recombination rate variation.
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Affiliation(s)
- Bret A. Payseur
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Loren H. Rieseberg
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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338
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Abstract
Almost 20 % of all infectious human diseases are vector borne and, together, are responsible for over one million deaths per annum. Over the past decade, the decreasing costs of massively parallel sequencing technologies have facilitated the agnostic interrogation of insect vector genomes, giving medical entomologists access to an ever-expanding volume of high-quality genomic and transcriptomic data. In this review, we highlight how genomics resources have provided new insights into the physiology, behavior, and evolution of human disease vectors within the context of the global health landscape.
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Affiliation(s)
- David C Rinker
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - R Jason Pitts
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Laurence J Zwiebel
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA. .,Department of Pharmacology, Vanderbilt Brain Institute, Program in Developmental Biology, and Institutes of Chemical Biology and Global Health, Vanderbilt University Medical Center, Nashville, Tennessee, USA.
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339
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Bayesian Inference of Reticulate Phylogenies under the Multispecies Network Coalescent. PLoS Genet 2016; 12:e1006006. [PMID: 27144273 PMCID: PMC4856265 DOI: 10.1371/journal.pgen.1006006] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Accepted: 04/04/2016] [Indexed: 11/19/2022] Open
Abstract
The multispecies coalescent (MSC) is a statistical framework that models how gene genealogies grow within the branches of a species tree. The field of computational phylogenetics has witnessed an explosion in the development of methods for species tree inference under MSC, owing mainly to the accumulating evidence of incomplete lineage sorting in phylogenomic analyses. However, the evolutionary history of a set of genomes, or species, could be reticulate due to the occurrence of evolutionary processes such as hybridization or horizontal gene transfer. We report on a novel method for Bayesian inference of genome and species phylogenies under the multispecies network coalescent (MSNC). This framework models gene evolution within the branches of a phylogenetic network, thus incorporating reticulate evolutionary processes, such as hybridization, in addition to incomplete lineage sorting. As phylogenetic networks with different numbers of reticulation events correspond to points of different dimensions in the space of models, we devise a reversible-jump Markov chain Monte Carlo (RJMCMC) technique for sampling the posterior distribution of phylogenetic networks under MSNC. We implemented the methods in the publicly available, open-source software package PhyloNet and studied their performance on simulated and biological data. The work extends the reach of Bayesian inference to phylogenetic networks and enables new evolutionary analyses that account for reticulation. Trees have long formed in biology the basic structure with which to represent and understand evolutionary relationships. Mathematical models, computational methods, and software tools for inferring phylogenetic trees and studying their mathematical properties are currently the norm in biology. The availability of genomic data from closely related species, as well as from multiple individuals within species, have brought the two fields of phylogenetics and population genetics closer than ever. In particular, the last two decades have witnessed a great flourish in the development and implementation of phylogenetic methods based on the multispecies coalescent model to capture the intricate relationship between gene and genome evolution. However, when reticulation processes such as hybridization occur, the phylogenetic history is best represented by a network. In this work, we demonstrate how the multispecies coalescent model can be adapted to reticulate evolutionary histories and report on a Bayesian method for inference of such histories under this extended model. As networks subsume trees, the model and method provide a principled and unified statistical framework for inferring treelike and non-treelike evolutionary relationships.
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340
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He Q, Knowles LL. Identifying targets of selection in mosaic genomes with machine learning: applications inAnopheles gambiaefor detecting sites within locally adapted chromosomal inversions. Mol Ecol 2016; 25:2226-43. [DOI: 10.1111/mec.13619] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 03/01/2016] [Accepted: 03/08/2016] [Indexed: 01/25/2023]
Affiliation(s)
- Qixin He
- Department of Ecology & Evolutionary Biology, Museum of Zoology; University of Michigan; 1109 Geddes Ave. Ann Arbor MI 48109-1079 USA
| | - L. Lacey Knowles
- Department of Ecology & Evolutionary Biology, Museum of Zoology; University of Michigan; 1109 Geddes Ave. Ann Arbor MI 48109-1079 USA
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341
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Osborne OG, Chapman MA, Nevado B, Filatov DA. Maintenance of Species Boundaries Despite Ongoing Gene Flow in Ragworts. Genome Biol Evol 2016; 8:1038-47. [PMID: 26979797 PMCID: PMC4860686 DOI: 10.1093/gbe/evw053] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/07/2016] [Indexed: 12/22/2022] Open
Abstract
The role of hybridization between diversifying species has been the focus of a huge amount of recent evolutionary research. While gene flow can prevent speciation or initiate species collapse, it can also generate new hybrid species. Similarly, while adaptive divergence can be wiped out by gene flow, new adaptive variation can be introduced via introgression. The relative frequency of these outcomes, and indeed the frequency of hybridization and introgression in general are largely unknown. One group of closely-related species with several documented cases of hybridization is the Mediterranean ragwort (genus: Senecio) species-complex. Examples of both polyploid and homoploid hybrid speciation are known in the clade, although their evolutionary relationships and the general frequency of introgressive hybridization among them remain unknown. Using a whole genome gene-space dataset comprising eight Senecio species we fully resolve the phylogeny of these species for the first time despite phylogenetic incongruence across the genome. Using a D-statistic approach, we demonstrate previously unknown cases of introgressive hybridization between multiple pairs of taxa across the species tree. This is an important step in establishing these species as a study system for diversification with gene flow, and suggests that introgressive hybridization may be a widespread and important process in plant evolution.
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Affiliation(s)
- Owen G Osborne
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom Department of Life Sciences, Imperial College London - Silwood Park Campus, Berkshire, United Kingdom
| | - Mark A Chapman
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom Department of Life Sciences, Imperial College London - Silwood Park Campus, Berkshire, United Kingdom Centre for Biological Sciences, Faculty of Natural & Environmental Sciences, University of Southampton, Southampton, United Kingdom
| | - Bruno Nevado
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Dmitry A Filatov
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
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342
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Hall AB, Papathanos PA, Sharma A, Cheng C, Akbari OS, Assour L, Bergman NH, Cagnetti A, Crisanti A, Dottorini T, Fiorentini E, Galizi R, Hnath J, Jiang X, Koren S, Nolan T, Radune D, Sharakhova MV, Steele A, Timoshevskiy VA, Windbichler N, Zhang S, Hahn MW, Phillippy AM, Emrich SJ, Sharakhov IV, Tu ZJ, Besansky NJ. Radical remodeling of the Y chromosome in a recent radiation of malaria mosquitoes. Proc Natl Acad Sci U S A 2016; 113:E2114-23. [PMID: 27035980 PMCID: PMC4839409 DOI: 10.1073/pnas.1525164113] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Y chromosomes control essential male functions in many species, including sex determination and fertility. However, because of obstacles posed by repeat-rich heterochromatin, knowledge of Y chromosome sequences is limited to a handful of model organisms, constraining our understanding of Y biology across the tree of life. Here, we leverage long single-molecule sequencing to determine the content and structure of the nonrecombining Y chromosome of the primary African malaria mosquito, Anopheles gambiae We find that the An. gambiae Y consists almost entirely of a few massively amplified, tandemly arrayed repeats, some of which can recombine with similar repeats on the X chromosome. Sex-specific genome resequencing in a recent species radiation, the An. gambiae complex, revealed rapid sequence turnover within An. gambiae and among species. Exploiting 52 sex-specific An. gambiae RNA-Seq datasets representing all developmental stages, we identified a small repertoire of Y-linked genes that lack X gametologs and are not Y-linked in any other species except An. gambiae, with the notable exception of YG2, a candidate male-determining gene. YG2 is the only gene conserved and exclusive to the Y in all species examined, yet sequence similarity to YG2 is not detectable in the genome of a more distant mosquito relative, suggesting rapid evolution of Y chromosome genes in this highly dynamic genus of malaria vectors. The extensive characterization of the An. gambiae Y provides a long-awaited foundation for studying male mosquito biology, and will inform novel mosquito control strategies based on the manipulation of Y chromosomes.
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Affiliation(s)
- Andrew Brantley Hall
- The Interdisciplinary PhD Program in Genetics, Bioinformatics, and Computational Biology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
| | - Philippos-Aris Papathanos
- Section of Genomics and Genetics, Department of Experimental Medicine, University of Perugia, 06132 Perugia, Italy; Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Atashi Sharma
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
| | - Changde Cheng
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556; Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556
| | - Omar S Akbari
- Department of Entomology, Riverside Center for Disease Vector Research, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521
| | - Lauren Assour
- Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556
| | - Nicholas H Bergman
- National Biodefense Analysis and Countermeasures Center, Frederick, MD 21702
| | - Alessia Cagnetti
- Section of Genomics and Genetics, Department of Experimental Medicine, University of Perugia, 06132 Perugia, Italy
| | - Andrea Crisanti
- Section of Genomics and Genetics, Department of Experimental Medicine, University of Perugia, 06132 Perugia, Italy; Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Tania Dottorini
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Elisa Fiorentini
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Roberto Galizi
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Jonathan Hnath
- National Biodefense Analysis and Countermeasures Center, Frederick, MD 21702
| | - Xiaofang Jiang
- The Interdisciplinary PhD Program in Genetics, Bioinformatics, and Computational Biology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892
| | - Tony Nolan
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Diane Radune
- National Biodefense Analysis and Countermeasures Center, Frederick, MD 21702
| | - Maria V Sharakhova
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061; Laboratory of Evolutionary Cytogenetics, Tomsk State University, Tomsk 634050, Russia
| | - Aaron Steele
- Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556
| | - Vladimir A Timoshevskiy
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
| | - Nikolai Windbichler
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Simo Zhang
- School of Informatics and Computing, Indiana University, Bloomington, IN 47405
| | - Matthew W Hahn
- School of Informatics and Computing, Indiana University, Bloomington, IN 47405; Department of Biology, Indiana University, Bloomington, IN 47405
| | - Adam M Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892
| | - Scott J Emrich
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556; Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556
| | - Igor V Sharakhov
- The Interdisciplinary PhD Program in Genetics, Bioinformatics, and Computational Biology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061; Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061; Laboratory of Evolutionary Cytogenetics, Tomsk State University, Tomsk 634050, Russia;
| | - Zhijian Jake Tu
- The Interdisciplinary PhD Program in Genetics, Bioinformatics, and Computational Biology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061; Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
| | - Nora J Besansky
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556; Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556;
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343
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Rosenzweig BK, Pease JB, Besansky NJ, Hahn MW. Powerful methods for detecting introgressed regions from population genomic data. Mol Ecol 2016; 25:2387-97. [PMID: 26945783 DOI: 10.1111/mec.13610] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 02/22/2016] [Indexed: 12/31/2022]
Abstract
Understanding the types and functions of genes that are able to cross species boundaries-and those that are not-is an important step in understanding the forces maintaining species as largely independent lineages across the remainder of the genome. With large next-generation sequencing data sets we are now able to ask whether introgression has occurred across the genome, and multiple methods have been proposed to detect the signature of such events. Here, we introduce a new summary statistic that can be used to test for introgression, RNDmin , that makes use of the minimum pairwise sequence distance between two population samples relative to divergence to an outgroup. We find that our method offers a modest increase in power over other, related tests, but that all such tests have high power to detect introgressed loci when migration is recent and strong. RNDmin is robust to variation in the mutation rate, and remains reliable even when estimates of the divergence time between sister species are inaccurate. We apply RNDmin to population genomic data from the African mosquitoes Anopheles quadriannulatus and A. arabiensis, identifying three novel candidate regions for introgression. Interestingly, one of the introgressed loci is on the X chromosome, but outside of an inversion separating these two species. Our results suggest that significant, but rare, sharing of alleles is occurring between species that diverged more than 1 million years ago, and that application of these methods to additional systems are likely to reveal similar results.
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Affiliation(s)
- Benjamin K Rosenzweig
- School of Informatics and Computing, Indiana University, Bloomington, IN, 47405, USA
| | - James B Pease
- School of Informatics and Computing, Indiana University, Bloomington, IN, 47405, USA.,Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Nora J Besansky
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA.,Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Matthew W Hahn
- School of Informatics and Computing, Indiana University, Bloomington, IN, 47405, USA.,Department of Biology, Indiana University, Bloomington, IN, 47405, USA
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344
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Uyhelji HA, Cheng C, Besansky NJ. Transcriptomic differences between euryhaline and stenohaline malaria vector sibling species in response to salinity stress. Mol Ecol 2016; 25:2210-25. [PMID: 26945667 DOI: 10.1111/mec.13609] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 01/09/2016] [Accepted: 02/22/2016] [Indexed: 01/04/2023]
Abstract
Evolution of osmoregulatory systems is a key factor in the transition of species between fresh- and saltwater habitats. Anopheles coluzzii and Anopheles merus are stenohaline and euryhaline malaria vector mosquitoes belonging to a larger group of sibling species, the Anopheles gambiae complex, which radiated in Africa within the last 2 million years. Comparative ecological genomics of these vector species can provide insight into the mechanisms that permitted the rapid radiation of this species complex into habitats of contrasting salinity. Here, we use RNA-Seq to investigate gene expression differences between An. coluzzii and An. merus after briefly exposing both young and old larval instars of each species to either saltwater (SW) or freshwater (FW). Our study aims to identify candidate genes and pathways responsible for the greater SW tolerance of An. merus. Our results are congruent with the ability of gene induction to mediate salinity tolerance, with both species showing increasing amounts of differential gene expression between SW and FW as salt concentrations increase. Besides ion transporters such as AgAE2 that may serve as effectors for osmoregulation, we also find mitogen-activated protein kinases that may serve in a phosphorylation signalling pathway responding to salinity, and report potential cross-talk between the mosquito immune response and osmoregulation. This study provides a key step towards applying the growing molecular knowledge of these malaria vectors to improve understanding of their ecological tolerances and habitat occupancy.
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Affiliation(s)
- Hilary A Uyhelji
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA.,Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA.,Functional Genomics Team, Civil Aerospace Medical Institute, Federal Aviation Administration, Oklahoma City, OK, 73169, USA
| | - Changde Cheng
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA.,Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Nora J Besansky
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA.,Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA
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345
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Crawford JE, Riehle MM, Markianos K, Bischoff E, Guelbeogo WM, Gneme A, Sagnon N, Vernick KD, Nielsen R, Lazzaro BP. Evolution of GOUNDRY, a cryptic subgroup of Anopheles gambiae s.l., and its impact on susceptibility to Plasmodium infection. Mol Ecol 2016; 25:1494-510. [PMID: 26846876 DOI: 10.1111/mec.13572] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 01/02/2016] [Accepted: 01/18/2016] [Indexed: 01/12/2023]
Abstract
The recent discovery of a previously unknown genetic subgroup of Anopheles gambiae sensu lato underscores our incomplete understanding of complexities of vector population demographics in Anopheles. This subgroup, named GOUNDRY, does not rest indoors as adults and is highly susceptible to Plasmodium infection in the laboratory. Initial description of GOUNDRY suggested it differed from other known Anopheles taxa in surprising and sometimes contradictory ways, raising a number of questions about its age, population size and relationship to known subgroups. To address these questions, we sequenced the complete genomes of 12 wild-caught GOUNDRY specimens and compared these genomes to a panel of Anopheles genomes. We show that GOUNDRY is most closely related to Anopheles coluzzii, and the timing of cladogenesis is not recent, substantially predating the advent of agriculture. We find a large region of the X chromosome that has swept to fixation in GOUNDRY within the last 100 years, which may be an inversion that serves as a partial barrier to contemporary gene flow. Interestingly, we show that GOUNDRY has a history of inbreeding that is significantly associated with susceptibility to Plasmodium infection in the laboratory. Our results illuminate the genomic evolution of one of probably several cryptic, ecologically specialized subgroups of Anopheles and provide a potent example of how vector population dynamics may complicate efforts to control or eradicate malaria.
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Affiliation(s)
- Jacob E Crawford
- Department of Entomology, Cornell University, Ithaca, NY, USA.,Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Michelle M Riehle
- Department of Microbiology, University of Minnesota, St. Paul, MN, USA
| | - Kyriacos Markianos
- Program in Genomics, Harvard Medical School, Children's Hospital Boston, Boston, MA, USA
| | - Emmanuel Bischoff
- Unit for Genetics and Genomics of Insect Vectors, Institut Pasteur, Paris, France
| | - Wamdaogo M Guelbeogo
- Centre National de Recherche et de Formation sur le Paludisme, 1487 Avenue de l'Oubritenga, 01 BP 2208, Ouagadougou, Burkina Faso
| | - Awa Gneme
- Centre National de Recherche et de Formation sur le Paludisme, 1487 Avenue de l'Oubritenga, 01 BP 2208, Ouagadougou, Burkina Faso
| | - N'Fale Sagnon
- Centre National de Recherche et de Formation sur le Paludisme, 1487 Avenue de l'Oubritenga, 01 BP 2208, Ouagadougou, Burkina Faso
| | - Kenneth D Vernick
- Unit for Genetics and Genomics of Insect Vectors, Institut Pasteur, Paris, France
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Brian P Lazzaro
- Department of Entomology, Cornell University, Ithaca, NY, USA
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346
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Wen D, Yu Y, Hahn MW, Nakhleh L. Reticulate evolutionary history and extensive introgression in mosquito species revealed by phylogenetic network analysis. Mol Ecol 2016; 25:2361-72. [PMID: 26808290 DOI: 10.1111/mec.13544] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2015] [Revised: 12/15/2015] [Accepted: 01/06/2016] [Indexed: 12/27/2022]
Abstract
The role of hybridization and subsequent introgression has been demonstrated in an increasing number of species. Recently, Fontaine et al. (Science, 347, 2015, 1258524) conducted a phylogenomic analysis of six members of the Anopheles gambiae species complex. Their analysis revealed a reticulate evolutionary history and pointed to extensive introgression on all four autosomal arms. The study further highlighted the complex evolutionary signals that the co-occurrence of incomplete lineage sorting (ILS) and introgression can give rise to in phylogenomic analyses. While tree-based methodologies were used in the study, phylogenetic networks provide a more natural model to capture reticulate evolutionary histories. In this work, we reanalyse the Anopheles data using a recently devised framework that combines the multispecies coalescent with phylogenetic networks. This framework allows us to capture ILS and introgression simultaneously, and forms the basis for statistical methods for inferring reticulate evolutionary histories. The new analysis reveals a phylogenetic network with multiple hybridization events, some of which differ from those reported in the original study. To elucidate the extent and patterns of introgression across the genome, we devise a new method that quantifies the use of reticulation branches in the phylogenetic network by each genomic region. Applying the method to the mosquito data set reveals the evolutionary history of all the chromosomes. This study highlights the utility of 'network thinking' and the new insights it can uncover, in particular in phylogenomic analyses of large data sets with extensive gene tree incongruence.
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Affiliation(s)
- Dingqiao Wen
- Department of Computer Science, Rice University, Houston, TX, 77005, USA
| | - Yun Yu
- Department of Computer Science, Rice University, Houston, TX, 77005, USA
| | - Matthew W Hahn
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA.,School of Informatics and Computing, Indiana University, Bloomington, IN, 47405, USA
| | - Luay Nakhleh
- Department of Computer Science, Rice University, Houston, TX, 77005, USA.,Department of BioSciences, Rice University, Houston, TX, 77005, USA
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347
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Solís-Lemus C, Ané C. Inferring Phylogenetic Networks with Maximum Pseudolikelihood under Incomplete Lineage Sorting. PLoS Genet 2016; 12:e1005896. [PMID: 26950302 PMCID: PMC4780787 DOI: 10.1371/journal.pgen.1005896] [Citation(s) in RCA: 244] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 02/03/2016] [Indexed: 11/23/2022] Open
Abstract
Phylogenetic networks are necessary to represent the tree of life expanded by edges to represent events such as horizontal gene transfers, hybridizations or gene flow. Not all species follow the paradigm of vertical inheritance of their genetic material. While a great deal of research has flourished into the inference of phylogenetic trees, statistical methods to infer phylogenetic networks are still limited and under development. The main disadvantage of existing methods is a lack of scalability. Here, we present a statistical method to infer phylogenetic networks from multi-locus genetic data in a pseudolikelihood framework. Our model accounts for incomplete lineage sorting through the coalescent model, and for horizontal inheritance of genes through reticulation nodes in the network. Computation of the pseudolikelihood is fast and simple, and it avoids the burdensome calculation of the full likelihood which can be intractable with many species. Moreover, estimation at the quartet-level has the added computational benefit that it is easily parallelizable. Simulation studies comparing our method to a full likelihood approach show that our pseudolikelihood approach is much faster without compromising accuracy. We applied our method to reconstruct the evolutionary relationships among swordtails and platyfishes (Xiphophorus: Poeciliidae), which is characterized by widespread hybridizations. Phylogenetic networks display the evolutionary history of groups of individuals (species or populations) including reticulation events such as hybridization, horizontal gene transfer or migration. Here, we present a likelihood method to learn networks from molecular sequences at multiple genes. Our model accounts for several biological processes: mutations, incomplete lineage sorting of alleles in ancestral populations, and reticulations in the network. The likelihood is decomposed into 4-taxon subsets to make the analyses scale to many species and many genes. Our work makes it possible to learn large phylogenetic networks from large data sets, with a statistical approach and a biologically relevant model.
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Affiliation(s)
- Claudia Solís-Lemus
- Department of Statistics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- * E-mail:
| | - Cécile Ané
- Department of Statistics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
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348
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Love RR, Weisenfeld NI, Jaffe DB, Besansky NJ, Neafsey DE. Evaluation of DISCOVAR de novo using a mosquito sample for cost-effective short-read genome assembly. BMC Genomics 2016; 17:187. [PMID: 26944054 PMCID: PMC4779211 DOI: 10.1186/s12864-016-2531-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 02/24/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND De novo reference assemblies that are affordable, practical to produce, and of sufficient quality for most downstream applications, remain an unattained goal for many taxa. Insects, which may yield too little DNA from individual specimens for long-read sequencing library construction and often have highly heterozygous genomes, can be particularly hard to assemble using inexpensive short-read sequencing data. The large number of insect species with medical or economic importance makes this a critical problem to address. RESULTS Using the assembler DISCOVAR de novo, we assembled the genome of the African malaria mosquito Anopheles arabiensis using 250 bp reads from a single library. The resulting assembly had a contig N50 of 22,433 bp, and recovered the gene set nearly as well as the ALLPATHS-LG AaraD1 An. arabiensis assembly produced with reads from three sequencing libraries and much greater resources. DISCOVAR de novo appeared to perform better than ALLPATHS-LG in regions of low complexity. CONCLUSIONS DISCOVAR de novo performed well assembling the genome of an insect of medical importance, using simpler sequencing input than previous anopheline assemblies. We have shown that this program is a viable tool for cost-effective assembly of a modestly-sized insect genome.
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Affiliation(s)
- R Rebecca Love
- Eck Institute for Global Health, University of Notre Dame, South Bend, IN, 46556, USA. .,Department of Biological Sciences, University of Notre Dame, South Bend, IN, 46556, USA.
| | - Neil I Weisenfeld
- Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA.
| | - David B Jaffe
- Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA.
| | - Nora J Besansky
- Eck Institute for Global Health, University of Notre Dame, South Bend, IN, 46556, USA. .,Department of Biological Sciences, University of Notre Dame, South Bend, IN, 46556, USA.
| | - Daniel E Neafsey
- Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA.
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349
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Abstract
Concepts and definitions of species have been debated by generations of biologists and remain controversial. Microbes pose a particular challenge because of their genetic diversity, asexual reproduction, and often promiscuous horizontal gene transfer (HGT). However, microbes also present an opportunity to study and understand speciation because of their rapid evolution, both in nature and in the lab, and small, easily sequenced genomes. Here, we review how microbial population genomics has enabled us to catch speciation "in the act" and how the results have challenged and enriched our concepts of species, with implications for all domains of life. We describe how recombination (including HGT and introgression) has shaped the genomes of nascent microbial, animal, and plant species and argue for a prominent role of natural selection in initiating and maintaining speciation. We ask how universal is the process of speciation across the tree of life, and what lessons can be drawn from microbes? Comparative genomics showing the extent of HGT in natural populations certainly jeopardizes the relevance of vertical descent (i.e., the species tree) in speciation. Nevertheless, we conclude that species do indeed exist as clusters of genetic and ecological similarity and that speciation is driven primarily by natural selection, regardless of the balance between horizontal and vertical descent.
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Affiliation(s)
- B. Jesse Shapiro
- Département de sciences biologiques, Université de Montréal, Montréal, Quebec, Canada
| | - Jean-Baptiste Leducq
- Département de sciences biologiques, Université de Montréal, Montréal, Quebec, Canada
| | - James Mallet
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
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350
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Zhang W, Dasmahapatra KK, Mallet J, Moreira GRP, Kronforst MR. Genome-wide introgression among distantly related Heliconius butterfly species. Genome Biol 2016; 17:25. [PMID: 26921238 PMCID: PMC4769579 DOI: 10.1186/s13059-016-0889-0] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Accepted: 01/28/2016] [Indexed: 12/30/2022] Open
Abstract
Background Although hybridization is thought to be relatively rare in animals, the raw genetic material introduced via introgression may play an important role in fueling adaptation and adaptive radiation. The butterfly genus Heliconius is an excellent system to study hybridization and introgression but most studies have focused on closely related species such as H. cydno and H. melpomene. Here we characterize genome-wide patterns of introgression between H. besckei, the only species with a red and yellow banded ‘postman’ wing pattern in the tiger-striped silvaniform clade, and co-mimetic H. melpomene nanna. Results We find a pronounced signature of putative introgression from H. melpomene into H. besckei in the genomic region upstream of the gene optix, known to control red wing patterning, suggesting adaptive introgression of wing pattern mimicry between these two distantly related species. At least 39 additional genomic regions show signals of introgression as strong or stronger than this mimicry locus. Gene flow has been on-going, with evidence of gene exchange at multiple time points, and bidirectional, moving from the melpomene to the silvaniform clade and vice versa. The history of gene exchange has also been complex, with contributions from multiple silvaniform species in addition to H. besckei. We also detect a signature of ancient introgression of the entire Z chromosome between the silvaniform and melpomene/cydno clades. Conclusions Our study provides a genome-wide portrait of introgression between distantly related butterfly species. We further propose a comprehensive and efficient workflow for gene flow identification in genomic data sets. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-0889-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wei Zhang
- Department of Ecology & Evolution, University of Chicago, Chicago, IL, 60637, USA.
| | | | - James Mallet
- Department of Organismic & Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Gilson R P Moreira
- Departamento de Zoologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, 91501-970, Brazil
| | - Marcus R Kronforst
- Department of Ecology & Evolution, University of Chicago, Chicago, IL, 60637, USA.
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