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Moreno K, Rico DM, Middlebrooks M, Medrano S, Valdés ÁA, Krug PJ. A cryptic radiation of Caribbean sea slugs revealed by integrative analysis: Cyerce ' antillensis' (Sacoglossa: Caliphyllidae) is six distinct species. Zool J Linn Soc 2024; 200:940-979. [PMID: 38566915 PMCID: PMC10983082 DOI: 10.1093/zoolinnean/zlad111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 07/14/2023] [Accepted: 07/31/2023] [Indexed: 04/04/2024]
Abstract
Integrative studies have revealed cryptic radiations in several Caribbean lineages of heterobranch sea slugs, raising questions about the evolutionary mechanisms that promote speciation within the tropical Western Atlantic. Cyerce Bergh, 1871 is a genus comprising 12 named species in the family Caliphyllidae that lack the photosynthetic ability of other sacoglossans but are noted for vibrant colours on the large cerata (dorsal leaf-like appendages) that characterize many species. Two species are widely reported from the Caribbean: Cyerce cristallina (Trinchese, 1881) and Cyerce antillensis Engel, 1927. Here, we present an integrative assessment of diversity in Caribbean Cyerce. Four methods of molecular species delimitation supported seven species in samples from the Caribbean and adjacent subtropical Western Atlantic. Six delimited species formed a monophyletic lineage in phylogenetic analyses but were > 9% divergent at the barcoding COI locus and could be differentiated using ecological, reproductive and/or morphological traits. We redescribe C. antillensis, a senior synonym for the poorly known Cyerce habanensis Ortea & Templado, 1988, and describe five new species. Evolutionary shifts in algal host use, penial armature and larval life history might have acted synergistically to promote the rapid divergence of endemic species with restricted distributions in this radiation, substantially increasing global diversity of the genus.
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Affiliation(s)
- Karina Moreno
- Department of Biological Sciences, California State Polytechnic UniversityPomona, Pomona, CA 91768, USA
| | - Diane M Rico
- Department of Biological Sciences, California State University, Los Angeles, CA 90032-8201, USA
| | | | - Sabrina Medrano
- Department of Biological Sciences, California State Polytechnic UniversityPomona, Pomona, CA 91768, USA
| | - Ángel A Valdés
- Department of Biological Sciences, California State Polytechnic UniversityPomona, Pomona, CA 91768, USA
| | - Patrick J Krug
- Department of Biological Sciences, California State University, Los Angeles, CA 90032-8201, USA
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2
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Rodriguez AK, Krug PJ. Ecological speciation by sympatric host shifts in a clade of herbivorous sea slugs, with introgression and localized mitochondrial capture between species. Mol Phylogenet Evol 2022; 174:107523. [PMID: 35589054 DOI: 10.1016/j.ympev.2022.107523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 03/30/2022] [Accepted: 05/06/2022] [Indexed: 11/25/2022]
Abstract
Host shifting in insect-plant systems was historically important to the development of ecological speciation theory, yet surprisingly few studies have examined whether host shifting drives diversification of marine herbivores. When small-bodied consumers feed and also mate on a preferred host, disruptive selection can split a population into host races despite gene flow. Support for host shifts is notably lacking for invertebrates associated with macroalgae, where the scale of dispersal by planktonic larvae often far exceeds the grain of host patchiness, and adults are typically less specialized than terrestrial herbivores. Here, we present a candidate example of ecological speciation in a clade of sea slugs that primarily consume green algae in the genus Caulerpa, including highly invasive species. Ancestral character state reconstructions supported 'sea grapes' (C. racemosa, C. lentillifera) as the ancestral host for a tropical radiation of 12 Elysia spp., with one shift onto alternative Caulerpa spp. in the Indo-Pacific. A Caribbean radiation of three species included symaptric host shifts to Rhipocephalus brevicaulis in the ancestor of E. pratensis Ortea & Espinosa, 1996, and to C. prolifera in E. hamanni Krug, Vendetti & Valdes 2016, plus a niche expansion to a range of Caulerpa spp. in E. subornata Verrill, 1901. All three species are broadly sympatric across the Caribbean but are host-partitioned at a fine grain, and distinct by morphology and at nuclear loci. However, non-recombining mtDNA revealed a history of gene flow between E. pratensis and E. subornata: COI haplotypes from E. subornata were 10.4% divergent from E. pratensis haplotypes from four sites, but closely related to all E. pratensis haplotypes sampled from six Bahamian islands, indicating historical introgression and localized "mitochondrial capture." Disruptive selective likely fueled divergence and adaptation to distinct host environments, indicating ecological speciation may be an under-appreciated driver of diversification for marine herbivores as well as epibionts and other resource specialists.
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Affiliation(s)
- Albert K Rodriguez
- Department of Biological Sciences, California State University, Los Angeles, CA 90032-8201, U.S.A
| | - Patrick J Krug
- Department of Biological Sciences, California State University, Los Angeles, CA 90032-8201, U.S.A.
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3
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Trevisan B, Jacob Machado D, Lahr DJG, Marques FPL. Comparative Characterization of Mitogenomes From Five Orders of Cestodes (Eucestoda: Tapeworms). Front Genet 2022; 12:788871. [PMID: 35003223 PMCID: PMC8727539 DOI: 10.3389/fgene.2021.788871] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/23/2021] [Indexed: 12/26/2022] Open
Abstract
The recognized potential of using mitogenomics in phylogenetics and the more accessible use of high-throughput sequencing (HTS) offer an opportunity to investigate groups of neglected organisms. Here, we leveraged HTS to execute the most comprehensive documentation of mitogenomes for cestodes based on the number of terminals sequenced. We adopted modern approaches to obtain the complete mitogenome sequences of 86 specimens representing five orders of cestodes (three reported for the first time: Phyllobothriidea, “Tetraphyllidea” and Trypanorhyncha). These complete mitogenomes represent an increase of 41% of the mitogenomes available for cestodes (61–147) and an addition of 33% in the representativeness of the cestode orders. The complete mitochondrial genomes are conserved, circular, encoded in the same strand, and transcribed in the same direction, following the pattern observed previously for tapeworms. Their length varies from 13,369 to 13,795 bp, containing 36 genes in total. Except for the Trypanorhyncha specimen, the gene order of the other four cestode orders sequenced here suggests that it could be a synapomorphy for the acetabulate group (with a reversion for taenids). Our results also suggest that no single gene can tell all the evolutionary history contained in the mitogenome. Therefore, cestodes phylogenies based on a single mitochondrial marker may fail to capture their evolutionary history. We predict that such phylogenies would be improved if conducted under a total evidence framework. The characterization of the new mitochondrial genomes is the first step to provide a valuable resource for future studies on the evolutionary relationships of these groups of parasites.
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Affiliation(s)
- Bruna Trevisan
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Denis Jacob Machado
- Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina at Charlotte, Charlotte, NC, United States
| | - Daniel J G Lahr
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Fernando P L Marques
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
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Biswas MK, Bagchi M, Biswas D, Harikrishna JA, Liu Y, Li C, Sheng O, Mayer C, Yi G, Deng G. Genome-Wide Novel Genic Microsatellite Marker Resource Development and Validation for Genetic Diversity and Population Structure Analysis of Banana. Genes (Basel) 2020; 11:genes11121479. [PMID: 33317074 PMCID: PMC7763637 DOI: 10.3390/genes11121479] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/20/2020] [Accepted: 11/20/2020] [Indexed: 11/17/2022] Open
Abstract
Trait tagging through molecular markers is an important molecular breeding tool for crop improvement. SSR markers encoded by functionally relevant parts of a genome are well suited for this task because they may be directly related to traits. However, a limited number of these markers are known for Musa spp. Here, we report 35136 novel functionally relevant SSR markers (FRSMs). Among these, 17,561, 15,373 and 16,286 FRSMs were mapped in-silico to the genomes of Musa acuminata, M. balbisiana and M. schizocarpa, respectively. A set of 273 markers was validated using eight accessions of Musa spp., from which 259 markers (95%) produced a PCR product of the expected size and 203 (74%) were polymorphic. In-silico comparative mapping of FRSMs onto Musa and related species indicated sequence-based orthology and synteny relationships among the chromosomes of Musa and other plant species. Fifteen FRSMs were used to estimate the phylogenetic relationships among 50 banana accessions, and the results revealed that all banana accessions group into two major clusters according to their genomic background. Here, we report the first large-scale development and characterization of functionally relevant Musa SSR markers. We demonstrate their utility for germplasm characterization, genetic diversity studies, and comparative mapping in Musa spp. and other monocot species. The sequences for these novel markers are freely available via a searchable web interface called Musa Marker Database.
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Affiliation(s)
- Manosh Kumar Biswas
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Tianhe District, Guangzhou 510640, China; (Y.L.); (C.L.); (O.S.); (G.Y.)
- Department of Genetics, University of Leicester, Leicester LE1 7RH, UK; (M.B.); (J.A.H.)
- Correspondence: (M.K.B.); (G.D.)
| | - Mita Bagchi
- Department of Genetics, University of Leicester, Leicester LE1 7RH, UK; (M.B.); (J.A.H.)
- The College of Economics and Managements, South China Agricultural University, Guangzhou 510640, China
| | - Dhiman Biswas
- Department of Computer Science and Engineering, Maulana Abul Kalam Azad University of Technology, West Bengal 700064, India;
| | - Jennifer Ann Harikrishna
- Department of Genetics, University of Leicester, Leicester LE1 7RH, UK; (M.B.); (J.A.H.)
- University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Yuxuan Liu
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Tianhe District, Guangzhou 510640, China; (Y.L.); (C.L.); (O.S.); (G.Y.)
| | - Chunyu Li
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Tianhe District, Guangzhou 510640, China; (Y.L.); (C.L.); (O.S.); (G.Y.)
| | - Ou Sheng
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Tianhe District, Guangzhou 510640, China; (Y.L.); (C.L.); (O.S.); (G.Y.)
| | - Christoph Mayer
- Forschungsmuseum Alexander Koenig, Bonn, Adenauerallee 160, 53113 Bonn, Germany;
| | - Ganjun Yi
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Tianhe District, Guangzhou 510640, China; (Y.L.); (C.L.); (O.S.); (G.Y.)
| | - Guiming Deng
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Tianhe District, Guangzhou 510640, China; (Y.L.); (C.L.); (O.S.); (G.Y.)
- Correspondence: (M.K.B.); (G.D.)
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Ben Slimen H, Awadi A, Tolesa ZG, Knauer F, Alves PC, Makni M, Suchentrunk F. Positive selection on the mitochondrial ATP synthase 6and the NADH dehydrogenase 2genes across 22 hare species (genus Lepus). J ZOOL SYST EVOL RES 2018. [DOI: 10.1111/jzs.12204] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hichem Ben Slimen
- Unité de recherche Génomique des Insectes ravageurs des Cultures d'intérêt agronomique; Faculty of Sciences of Tunis; University of Tunis El Manar; Tunis Tunisia
- Institut Supérieur de Biotechnologie de Béja; University of Jendouba; Béja Tunisia
| | - Asma Awadi
- Unité de recherche Génomique des Insectes ravageurs des Cultures d'intérêt agronomique; Faculty of Sciences of Tunis; University of Tunis El Manar; Tunis Tunisia
| | | | - Felix Knauer
- Research Institute of Wildlife Ecology; University of Veterinary Medicine Vienna; Vienna Austria
| | - Paulo Célio Alves
- CIBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos; Universidade do Porto; Vairão Portugal
| | - Mohamed Makni
- Unité de recherche Génomique des Insectes ravageurs des Cultures d'intérêt agronomique; Faculty of Sciences of Tunis; University of Tunis El Manar; Tunis Tunisia
| | - Franz Suchentrunk
- Research Institute of Wildlife Ecology; University of Veterinary Medicine Vienna; Vienna Austria
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Abstract
Summary Metagenomics revolutionized the field of microbial ecology, giving access to Gb-sized datasets of microbial communities under natural conditions. This enables fine-grained analyses of the functions of community members, studies of their association with phenotypes and environments, as well as of their microevolution and adaptation to changing environmental conditions. However, phylogenetic methods for studying adaptation and evolutionary dynamics are not able to cope with big data. EDEN is the first software for the rapid detection of protein families and regions under positive selection, as well as their associated biological processes, from meta- and pangenome data. It provides an interactive result visualization for detailed comparative analyses. Availability and implementation EDEN is available as a Docker installation under the GPL 3.0 license, allowing its use on common operating systems, at http://www.github.com/hzi-bifo/eden. Contact alice.mchardy@helmholtz-hzi.de. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Philipp C Münch
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, 38124 Brunswick, Germany.,Max von Pettenkofer-Institute for Hygiene and Clinical Microbiology, Ludwig-Maximilian University of Munich, 80336 Munich, Germany.,German Centre for Infection Research (DZIF), Partner Site Hanover-Brunswick, 38124 Brunswick, Germany
| | - Bärbel Stecher
- Max von Pettenkofer-Institute for Hygiene and Clinical Microbiology, Ludwig-Maximilian University of Munich, 80336 Munich, Germany.,DZIF, Partner Site LMU Munich, 80336 Munich, Germany
| | - Alice C McHardy
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, 38124 Brunswick, Germany.,German Centre for Infection Research (DZIF), Partner Site Hanover-Brunswick, 38124 Brunswick, Germany.,Department of Algorithmic Bioinformatics.,Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University Dusseldorf, 40225 Dusseldorf, Germany
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7
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Gilroy DL, Phillips KP, Richardson DS, van Oosterhout C. Toll-like receptor variation in the bottlenecked population of the Seychelles warbler: computer simulations see the 'ghost of selection past' and quantify the 'drift debt'. J Evol Biol 2017; 30:1276-1287. [PMID: 28370771 DOI: 10.1111/jeb.13077] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Accepted: 03/21/2017] [Indexed: 01/09/2023]
Abstract
Balancing selection can maintain immunogenetic variation within host populations, but detecting its signal in a postbottlenecked population is challenging due to the potentially overriding effects of drift. Toll-like receptor genes (TLRs) play a fundamental role in vertebrate immune defence and are predicted to be under balancing selection. We previously characterized variation at TLR loci in the Seychelles warbler (Acrocephalus sechellensis), an endemic passerine that has undergone a historical bottleneck. Five of seven TLR loci were polymorphic, which is in sharp contrast to the low genomewide variation observed. However, standard population genetic statistical methods failed to detect a contemporary signature of selection at any TLR locus. We examined whether the observed TLR polymorphism could be explained by neutral evolution, simulating the population's demography in the software DIYABC. This showed that the posterior distributions of mutation rates had to be unrealistically high to explain the observed genetic variation. We then conducted simulations with an agent-based model using typical values for the mutation rate, which indicated that weak balancing selection has acted on the three TLR genes. The model was able to detect evidence of past selection elevating TLR polymorphism in the prebottleneck populations, but was unable to discern any effects of balancing selection in the contemporary population. Our results show drift is the overriding evolutionary force that has shaped TLR variation in the contemporary Seychelles warbler population, and the observed TLR polymorphisms might be merely the 'ghost of selection past'. Forecast models predict immunogenetic variation in this species will continue to be eroded in the absence of contemporary balancing selection. Such 'drift debt' occurs when a gene pool has not yet reached its new equilibrium level of polymorphism, and this loss could be an important threat to many recently bottlenecked populations.
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Affiliation(s)
- D L Gilroy
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - K P Phillips
- School of Biological Sciences, University of East Anglia, Norwich, UK.,Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - D S Richardson
- School of Biological Sciences, University of East Anglia, Norwich, UK.,Nature Seychelles, Mahe, Republic of Seychelles
| | - C van Oosterhout
- School of Environmental Sciences, University of East Anglia, Norwich, UK
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8
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Veličković N, Ferreira E, Djan M, Ernst M, Obreht Vidaković D, Monaco A, Fonseca C. Demographic history, current expansion and future management challenges of wild boar populations in the Balkans and Europe. Heredity (Edinb) 2016; 117:348-357. [PMID: 27436523 PMCID: PMC5061920 DOI: 10.1038/hdy.2016.53] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 05/31/2016] [Accepted: 06/08/2016] [Indexed: 02/01/2023] Open
Abstract
Wild boar (Sus scrofa), one of the most widespread wildlife species, has entered a stage of continuous growth in Europe, and could even be considered a pest species. We analysed microsatellite variability in 723 wild boars from across Europe, including the northern Dinaric Balkans. Our aims were: (1) to define the population structure of wild boars in the Balkans and its relation with other European populations; (2) to estimate effective populations sizes, levels of intra- and inter-population diversity, inbreeding migration and gene flow patterns; (3) to test subpopulations for bottlenecks; (4) to interpret these results in light of current knowledge about the demographic history of wild boars in Europe; and (5) to discuss the relevance of these findings for management and conservation. Strong population structuring was observed and 14 subpopulations were revealed. High genetic diversity was found, and besides the well-known identity of the Italian populations of Sardinia and Castelporziano, we bring new insights into other potential relevant, refugial populations such as Littoral Slovenia, South Portugal, North-western Iberia and an entire cluster in the Balkans. There was evidence of gene flow going from these refugial subpopulations towards less peripheral and more admixed subpopulations. Recent population bottlenecks and expansions were detected, mostly in the peninsular refuge subpopulations. The results are consistent with the fluctuations of wild boar numbers in Europe since the beginning of the twentieth century. These results should be taken into account in future conservation and management plans for wild boar populations in Europe.
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Affiliation(s)
- N Veličković
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia
| | - E Ferreira
- Department of Biology & CESAM, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
| | - M Djan
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia
| | - M Ernst
- Department of Forest Protection and Wildlife Management, Mendel University in Brno, Brno, Czech Republic
| | - D Obreht Vidaković
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia
| | - A Monaco
- Regional Parks Agency–Lazio Region, Rome, Italy
| | - C Fonseca
- Department of Biology & CESAM, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
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9
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Salgueiro P, Lopes AS, Mendes C, Charlwood JD, Arez AP, Pinto J, Silveira H. Molecular evolution and population genetics of a Gram-negative binding protein gene in the malaria vector Anopheles gambiae (sensu lato). Parasit Vectors 2016; 9:515. [PMID: 27658383 PMCID: PMC5034674 DOI: 10.1186/s13071-016-1800-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 09/14/2016] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Clarifying the role of the innate immune system of the malaria vector Anopheles gambiae is a potential way to block the development of the Plasmodium parasites. Pathogen recognition is the first step of innate immune response, where pattern recognition proteins like GNBPs play a central role. RESULTS We analysed 70 sequences of the protein coding gene GNBPB2 from two species, Anopheles gambiae (s.s.) and An. coluzzii, collected in six African countries. We detected 135 segregating sites defining 63 distinct haplotypes and 30 proteins. Mean nucleotide diversity (π) was 0.014 for both species. We found no significant genetic differentiation between species, but a significant positive correlation between genetic differentiation and geographical distance among populations. CONCLUSIONS Species status seems to contribute less for the molecular differentiation in GNBPB2 than geographical region in the African continent (West and East). Purifying selection was found to be the most common form of selection, as in many other immunity-related genes. Diversifying selection may be also operating in the GNBPB2 gene.
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Affiliation(s)
- Patrícia Salgueiro
- Global Health and Tropical Medicine Centre (GHTM), Unidade de Parasitologia Médica, Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa, Lisboa, Portugal
| | - Ana Sofia Lopes
- Global Health and Tropical Medicine Centre (GHTM), Unidade de Parasitologia Médica, Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa, Lisboa, Portugal
| | - Cristina Mendes
- Global Health and Tropical Medicine Centre (GHTM), Unidade de Parasitologia Médica, Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa, Lisboa, Portugal
| | - Jacques Derek Charlwood
- Global Health and Tropical Medicine Centre (GHTM), Unidade de Parasitologia Médica, Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa, Lisboa, Portugal
- London School of Hygiene and Tropical Medicine, London, UK
| | - Ana Paula Arez
- Global Health and Tropical Medicine Centre (GHTM), Unidade de Parasitologia Médica, Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa, Lisboa, Portugal
| | - João Pinto
- Global Health and Tropical Medicine Centre (GHTM), Unidade de Parasitologia Médica, Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa, Lisboa, Portugal
| | - Henrique Silveira
- Global Health and Tropical Medicine Centre (GHTM), Unidade de Parasitologia Médica, Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa, Lisboa, Portugal
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10
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Kamau LM, Skilton RA, Githaka N, Kiara H, Kabiru E, Shah T, Musoke AJ, Bishop RP. Extensive polymorphism of Ra86 genes in field populations of Rhipicephalus appendiculatus from Kenya. Ticks Tick Borne Dis 2016; 7:772-781. [PMID: 27051976 DOI: 10.1016/j.ttbdis.2016.03.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 03/15/2016] [Accepted: 03/16/2016] [Indexed: 10/22/2022]
Abstract
Commercial vaccines based on recombinant forms of the Bm86 tick gut antigen are used to control the southern cattle tick, Rhipicephalus microplus, a 1-host species, in Australia and Latin America. We describe herein sequence polymorphism in genes encoding Ra86 homologues of Bm86 in the brown ear tick, Rhipicephalus appendiculatus, isolated from four Kenyan field populations and one laboratory colony. Sequencing of 19 Ra86 sequences defined two alleles differentiated by indels, encoding 693 amino acids (aa) and 654 aa respectively, from the Muguga laboratory reference strain. Ra86 sequences were also determined from gut cDNA from four field populations of R. appendiculatus collected in different livestock production systems in Kenya. Analysis of approximately 20 Ra86 sequences from each of the four field sites in central and Western Kenya; Makuyu, Kiambu, Kakamega and Uasin Gishu, revealed three additional size types differentiated by 39-49 amino acid indels resulting in a total of 5 indel-defined genotypes. The 693 aa type 5 was isolated only from the laboratory tick stock; genotypes 1, 2 and 3 were identified in ticks from the four Kenyan field sites and appeared to be derivatives of the shorter RA86 genotype found in Muguga laboratory stock genotype 4. By contrast no large indels have yet been observed between R. microplus sequences from Australia, South America or Africa. Evidence that selection contributes to the observed sequence variation was provided by analysis of ratio of synonymous and non-synonymous substitutions and application of the selective neutrality and neutral evolution tests to the primary data. Phylogenetic analysis clustered sequences from all Ra86 size types and Bm86, into four major clades based on amino acid substitutions, but there was no evidence that these groupings correlated with geographical separation of R. appendiculatus populations.
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Affiliation(s)
- L M Kamau
- Department of Zoological Sciences, Kenyatta University, P.O. Box 43844, Nairobi, Kenya; International Livestock Research Institute (ILRI), P.O. Box 30709, Nairobi, Kenya
| | - R A Skilton
- International Livestock Research Institute (ILRI), P.O. Box 30709, Nairobi, Kenya
| | - N Githaka
- International Livestock Research Institute (ILRI), P.O. Box 30709, Nairobi, Kenya.
| | - H Kiara
- International Livestock Research Institute (ILRI), P.O. Box 30709, Nairobi, Kenya
| | - E Kabiru
- Department of Zoological Sciences, Kenyatta University, P.O. Box 43844, Nairobi, Kenya
| | - T Shah
- International Livestock Research Institute (ILRI), P.O. Box 30709, Nairobi, Kenya
| | - A J Musoke
- International Livestock Research Institute (ILRI), P.O. Box 30709, Nairobi, Kenya
| | - R P Bishop
- International Livestock Research Institute (ILRI), P.O. Box 30709, Nairobi, Kenya
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11
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Ashoff M, Schmitt T. Are Different Allozyme Genotypes of the ButterflyPolyommatus coridonAdapted to Resist Cold and Heat Shocks? ANN ZOOL FENN 2014. [DOI: 10.5735/086.051.0502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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12
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Marra NJ, Romero A, DeWoody JA. Natural selection and the genetic basis of osmoregulation in heteromyid rodents as revealed by RNA-seq. Mol Ecol 2014; 23:2699-711. [PMID: 24754676 DOI: 10.1111/mec.12764] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 04/12/2014] [Accepted: 04/17/2014] [Indexed: 12/23/2022]
Abstract
One adaptation of ecological and evolutionary interest is the extraordinary ability of desert rodents to retain water during waste production. Much is known regarding the unique kidney physiology of kangaroo rats (Dipodomys spp.) and their ability to retain water during waste production, yet the genetic basis of these physiological adaptations is relatively unknown. Herein, we utilized RNA-seq data to conduct a comparative study to identify osmoregulatory genes expressed in heteromyid rodents. We sequenced kidney tissue from two temperate desert species (Dipodomys spectabilis and Chaetodipus baileyi) from two separate subfamilies of the Heteromyidae and compared these transcriptomes to a tropical mesic species (Heteromys desmarestianus) from a third subfamily. The evolutionary history of these subfamilies provided a robust phylogenetic control that allowed us to separate shared evolutionary history from convergence. Using two methods to detect differential expression (DE), we identified 1890 genes that showed consistent patterns of DE between the arid and mesic species. A three-species reciprocal BLAST analysis revealed 3511 sets of putative orthologues that, upon comparison to known Mus musculus sequences, revealed 323 annotated and full-length genic regions. Selection tests displayed evidence of positive selection (dn/ds > 1) on six genes in the two desert species and remained significant for one of these genes after correction for multiple testing. Thus, our data suggest that both the coding sequence and expression of genes have been shaped by natural selection to provide the genetic architecture for efficient osmoregulation in desert-adapted heteromyid rodents.
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Affiliation(s)
- Nicholas J Marra
- Department of Forestry & Natural Resources, Purdue University, West Lafayette, IN, 47907, USA
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Olsen MT, Pampoulie C, Daníelsdóttir AK, Lidh E, Bérubé M, Víkingsson GA, Palsbøll PJ. Fin whale MDH-1 and MPI allozyme variation is not reflected in the corresponding DNA sequences. Ecol Evol 2014; 4:1787-803. [PMID: 24963377 PMCID: PMC4063476 DOI: 10.1002/ece3.1046] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 02/07/2014] [Indexed: 11/07/2022] Open
Abstract
The appeal of genetic inference methods to assess population genetic structure and guide management efforts is grounded in the correlation between the genetic similarity and gene flow among populations. Effects of such gene flow are typically genomewide; however, some loci may appear as outliers, displaying above or below average genetic divergence relative to the genomewide level. Above average population, genetic divergence may be due to divergent selection as a result of local adaptation. Consequently, substantial efforts have been directed toward such outlying loci in order to identify traits subject to local adaptation. Here, we report the results of an investigation into the molecular basis of the substantial degree of genetic divergence previously reported at allozyme loci among North Atlantic fin whale (Balaenoptera physalus) populations. We sequenced the exons encoding for the two most divergent allozyme loci (MDH-1 and MPI) and failed to detect any nonsynonymous substitutions. Following extensive error checking and analysis of additional bioinformatic and morphological data, we hypothesize that the observed allozyme polymorphisms may reflect phenotypic plasticity at the cellular level, perhaps as a response to nutritional stress. While such plasticity is intriguing in itself, and of fundamental evolutionary interest, our key finding is that the observed allozyme variation does not appear to be a result of genetic drift, migration, or selection on the MDH-1 and MPI exons themselves, stressing the importance of interpreting allozyme data with caution. As for North Atlantic fin whale population structure, our findings support the low levels of differentiation found in previous analyses of DNA nucleotide loci.
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Affiliation(s)
- Morten Tange Olsen
- Evolutionary Genetics Group, Department of Genetics, Microbiology, and Toxicology, Stockholm University Svante Arrhenius Väg 20C, S-106 91 Stockholm, Sweden
| | | | | | - Emmelie Lidh
- Evolutionary Genetics Group, Department of Genetics, Microbiology, and Toxicology, Stockholm University Svante Arrhenius Väg 20C, S-106 91 Stockholm, Sweden
| | - Martine Bérubé
- Evolutionary Genetics Group, Department of Genetics, Microbiology, and Toxicology, Stockholm University Svante Arrhenius Väg 20C, S-106 91 Stockholm, Sweden ; Marine Evolution and Conservation, Centre for Ecological and Evolutionary Studies, University of Groningen PO Box 11103, 9700 CC, Groningen, The Netherlands
| | | | - Per J Palsbøll
- Evolutionary Genetics Group, Department of Genetics, Microbiology, and Toxicology, Stockholm University Svante Arrhenius Väg 20C, S-106 91 Stockholm, Sweden ; Marine Evolution and Conservation, Centre for Ecological and Evolutionary Studies, University of Groningen PO Box 11103, 9700 CC, Groningen, The Netherlands
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Anderson JD, Karel WJ, Mace CE, Bartram BL, Hare MP. Spatial genetic features of eastern oysters (Crassostrea virginica Gmelin) in the Gulf of Mexico: northward movement of a secondary contact zone. Ecol Evol 2014; 4:1671-85. [PMID: 24967084 PMCID: PMC4063467 DOI: 10.1002/ece3.1064] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 03/18/2014] [Accepted: 03/19/2014] [Indexed: 11/07/2022] Open
Abstract
The eastern oyster (Crassostrea virginica Gmelin) is an economically and ecologically valuable marine bivalve occurring in the Gulf of Mexico. This study builds upon previous research that identified two divergent populations of eastern oysters in the western Gulf of Mexico. Allelic and genotypic patterns from 11 microsatellite markers were used to assess genetic structure and migration between the previously described oyster populations in Texas. The main findings are as follows: (1) there are two distinct populations (F ST = 0.392, P < 0.001) of oysters that overlap in the Corpus Christi/Aransas Bay estuarine complex in Texas, (2) the distribution of genotypes among individuals in the contact zone suggests limited hybridization between populations, (3) the variables of salinity, temperature, dissolved oxygen, turbidity and depth are not correlated with allele frequencies on reefs in the contact zone or when analyzed across Texas, and (4) there is little evidence of directional selection acting on the loci assayed here, although patterns at four markers suggested the influence of balancing selection based on outlier analyses. These results are consistent with long-term historical isolation between populations, followed by secondary contact. Recent hydrological changes in the area of secondary contact may be promoting migration in areas that were previously inhospitable to eastern oysters, and observed differences in the timing of spawning may limit hybridization between populations. Comparison of these findings with the results of an earlier study of oysters in Texas suggests that the secondary contact zone has shifted approximately 27 km north, in as little as a 23-year span.
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Affiliation(s)
- Joel D Anderson
- Perry R. Bass Marine Fisheries Research Station, Texas Parks and Wildlife 3864 FM 3280, Palacios, Texas, 77465
| | - William J Karel
- Perry R. Bass Marine Fisheries Research Station, Texas Parks and Wildlife 3864 FM 3280, Palacios, Texas, 77465
| | - Christopher E Mace
- Rockport Marine Lab, Texas Parks and Wildlife 824 S. Fuqua St., Rockport, TX, 78382
| | - Brian L Bartram
- Rockport Marine Lab, Texas Parks and Wildlife 824 S. Fuqua St., Rockport, TX, 78382
| | - Matthew P Hare
- Department of Natural Resources, Cornell University 213 Bruckner Hall, Ithaca, NY, 14853
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15
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Manoharan SS, Miao VPW, Andrésson ÓS. LEC-2, a highly variable lectin in the lichen Peltigera membranacea.. Symbiosis 2012; 58:91-98. [PMID: 23482294 PMCID: PMC3589653 DOI: 10.1007/s13199-012-0206-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Accepted: 11/26/2012] [Indexed: 12/31/2022]
Abstract
Lectins are a diverse group of carbohydrate binding proteins often involved in cellular interactions. A lectin gene, lec-2, was identified in the mycobiont of the lichen Peltigera membranacea. Sequencing of lec-2 open reading frames from 21 individual samples showed an unexpectedly high level of polymorphism in the deduced protein (LEC-2), which was sorted into nine haplotypes based on amino acid sequence. Calculations showed that the rates of nonsynonymous versus synonymous nucleotide substitutions deviated significantly from the null hypothesis of neutrality, indicating strong positive selection. Molecular modeling revealed that most amino acid replacements were around the putative carbohydrate-binding pocket, indicating changes in ligand binding. Lectins have been thought to be involved in the recognition of photobiont partners in lichen symbioses, and the hypothesis that positive selection of LEC-2 is driven by variation in the Nostoc photobiont partner was tested by comparing mycobiont LEC-2 haplotypes and photobiont genotypes, as represented by the rbcLX region. It was not possible to pair up the two types of marker sequences without conflicts, suggesting that positive selection of LEC-2 was not due to variation in photobiont partners.
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Affiliation(s)
- Sheeba S. Manoharan
- Department of Life and Environmental Sciences, University of Iceland, 101 Reykjavík, Iceland
| | - Vivian P. W. Miao
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
| | - Ólafur S. Andrésson
- Department of Life and Environmental Sciences, University of Iceland, 101 Reykjavík, Iceland
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16
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Chaoui L, Gagnaire PA, Guinand B, Quignard JP, Tsigenopoulos C, Kara MH, Bonhomme F. Microsatellite length variation in candidate genes correlates with habitat in the gilthead sea bream Sparus aurata. Mol Ecol 2012; 21:5497-511. [PMID: 23061421 DOI: 10.1111/mec.12062] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Revised: 08/31/2012] [Accepted: 09/04/2012] [Indexed: 11/30/2022]
Abstract
The genetic basis and evolutionary implications of local adaptation in high gene flow marine organisms are still poorly understood. In several Mediterranean fish species, alternative migration patterns exist between individuals entering coastal lagoons that offer favourable conditions for growth and those staying in the sea where environmental conditions are less subject to rapid and stressful change. Whether these coexisting strategies are phenotypically plastic or include a role for local adaptation through differential survival needs to be determined. Here, we explore the genetic basis of alternate habitat use in western Mediterranean populations of the gilthead sea bream (Sparus aurata). Samples from lagoonal and open-sea habitats were typed for three candidate gene microsatellite loci, seven anonymous microsatellites and 44 amplified fragment length polymorphism markers to test for genotype-environment associations. While anonymous markers globally indicated high levels of gene flow across geographic locations and habitats, non-neutral differentiation patterns correlated with habitat type were found at two candidate microsatellite loci located in the promoter region of the growth hormone and prolactin genes. Further analysis of these two genes revealed that a mechanism based on habitat choice alone could not explain the distribution of genotype frequencies at a regional scale, thus implying a role for differential survival between habitats. We also found an association between allele size and habitat type, which, in the light of previous studies, suggests that polymorphisms in the proximal promoter region could influence gene expression by modulating transcription factor binding, thus providing a potential explanatory link between genotype and growth phenotype in nature.
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Affiliation(s)
- Lamya Chaoui
- Institut des Sciences de l'Evolution, Université Montpellier II, SMEL, 2 rue des chantiers, 34200 Sète, France
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17
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O'Farrell B, Dennis C, Benzie JA, McGinnity P, Carlsson J, de Eyto E, Coughlan JP, Igoe F, Meehan R, Cross TF. Balancing selection on MHC class I in wild brown trout Salmo trutta. JOURNAL OF FISH BIOLOGY 2012; 81:1357-1374. [PMID: 22957875 DOI: 10.1111/j.1095-8649.2012.03421.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Evidence is reported for balancing selection acting on variation at major histocompatibility complex (MHC) in wild populations of brown trout Salmo trutta. First, variation at an MHC class I (satr-uba)-linked microsatellite locus (mhc1) is retained in small S. trutta populations isolated above waterfalls although variation is lost at neutral microsatellite markers. Second, populations across several catchments are less differentiated at mhc1 than at neutral markers, as predicted by theory. The population structure of these fish was also elucidated.
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Affiliation(s)
- B O'Farrell
- Environmental Research Institute, University College Cork, Cork, Ireland.
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18
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McMullan M, van Oosterhout C. Inference of selection based on temporal genetic differentiation in the study of highly polymorphic multigene families. PLoS One 2012; 7:e42119. [PMID: 22900006 PMCID: PMC3416836 DOI: 10.1371/journal.pone.0042119] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Accepted: 07/02/2012] [Indexed: 01/12/2023] Open
Abstract
The co-evolutionary arms race between host immune genes and parasite virulence genes is known as Red Queen dynamics. Temporal fluctuations in allele frequencies, or the ‘turnover’ of alleles at immune genes, are concordant with predictions of the Red Queen hypothesis. Such observations are often taken as evidence of host-parasite co-evolution. Here, we use computer simulations of the Major Histocompatibility Complex (MHC) of guppies (Poecilia reticulata) to study the turnover rate of alleles (temporal genetic differentiation, G'ST). Temporal fluctuations in MHC allele frequencies can be ≥≤order of magnitude larger than changes observed at neutral loci. Although such large fluctuations in the MHC are consistent with Red Queen dynamics, simulations show that other demographic and population genetic processes can account for this observation, these include: (1) overdominant selection, (2) fluctuating population size within a metapopulation, and (3) the number of novel MHC alleles introduced by immigrants when there are multiple duplicated genes. Synergy between these forces combined with migration rate and the effective population size can drive the rapid turnover in MHC alleles. We posit that rapid allelic turnover is an inherent property of highly polymorphic multigene families and that it cannot be taken as evidence of Red Queen dynamics. Furthermore, combining temporal samples in spatial FST outlier analysis may obscure the signal of selection.
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Affiliation(s)
- Mark McMullan
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom.
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Xu T, Sun Y, Shi G, Wang R. Miiuy croaker hepcidin gene and comparative analyses reveal evidence for positive selection. PLoS One 2012; 7:e35449. [PMID: 22511989 PMCID: PMC3325200 DOI: 10.1371/journal.pone.0035449] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Accepted: 03/17/2012] [Indexed: 12/03/2022] Open
Abstract
Hepcidin antimicrobial peptide (HAMP) is a small cysteine-rich peptide and a key molecule of the innate immune system against bacterial infections. Molecular cloning and genomic characterization of HAMP gene in the miiuy croaker (Miichthys miiuy) were reported in this study. The miiuy croaker HAMP was predicted to encode a prepropeptide of 99 amino acids, a tentative RX(K/R)R cleavage motif and eight characteristic cysteine residues were also identified. The gene organization is also similar to corresponding genes in mammals and fish consisting of three exons and two introns. Sequence polymorphism analysis showed that only two different sequences were identified and encoded two proteins in six individuals. As reported for most other species, the expression level was highest in liver and an up-regulation of transcription was seen in spleen, intestine and kidney examined at 24 h after injection of pathogenic bacteria, Vibrio anguillarum, the expression pattern implied that miiuy croaker HAMP is an important component of the first line defense against invading pathogens. In addition, we report on the underlying mechanism that maintains sequences diversity among fish and mammalian species, respectively. A series of site-model tests implemented in the CODEML program revealed that moderate positive Darwinian selection is likely to cause the molecular evolution in the fish HAMP2 genes and it also showed that the fish HAMP1 genes and HAMP2 genes under different selection pressures.
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Affiliation(s)
- Tianjun Xu
- Laboratory for Marine Living Resources and Molecular Engineering, College of Marine Science, Zhejiang Ocean University, Zhoushan, People's Republic of China
| | - Yuena Sun
- Laboratory for Marine Living Resources and Molecular Engineering, College of Marine Science, Zhejiang Ocean University, Zhoushan, People's Republic of China
| | - Ge Shi
- Laboratory for Marine Living Resources and Molecular Engineering, College of Marine Science, Zhejiang Ocean University, Zhoushan, People's Republic of China
| | - Rixin Wang
- Laboratory for Marine Living Resources and Molecular Engineering, College of Marine Science, Zhejiang Ocean University, Zhoushan, People's Republic of China
- * E-mail:
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Chen D, Li P, Guo W, Ye F, Wu J, Wei D, Guo Z, Ye C. Molecular evolution of candidate sour taste receptor gene PKD1L3 in mammals. Genome 2011; 54:890-7. [PMID: 22011139 DOI: 10.1139/g11-057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The PKD1L3 gene encodes an ion channel protein that can interact with the PKD2L1 protein to form a candidate sour taste receptor. In the present study, we have analyzed the evolutionary patterns of PKD1L3 genes from 10 mammalian species. The results showed that PKD1L3 genes have evolved under a dominant purifying selection force. However, for some branches and sites, PKD1L3 genes were detected to have been operated by positive selection. Moreover, some of these positive evolutionary sites are likely to participate in acid stimulus recognition. In rodents, PKD1L3 genes evolved more rapidly than other mammalian lineages. Combined with other functional research reports, our results suggest that rodents may not be the most appropriate model for functional research on the PKD1L3 gene.
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Affiliation(s)
- Dazhi Chen
- School of Life Sciences and Bioengineering, Southwest Jiaotong University, Chengdu, Sichuan 610031, PR China
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21
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Xu T, Sun Y, Shi G, Cheng Y, Wang R. Characterization of the major histocompatibility complex class II genes in miiuy croaker. PLoS One 2011; 6:e23823. [PMID: 21901139 PMCID: PMC3162010 DOI: 10.1371/journal.pone.0023823] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2011] [Accepted: 07/27/2011] [Indexed: 11/18/2022] Open
Abstract
Major histocompatibility complex (MHC) has a central role in the adaptive immune system by presenting foreign peptide to the T-cell receptor. In order to study the molecular function and genomic characteristic of class II genes in teleost, the full lengths of MHC class IIA and IIB cDNA and genomic sequence were cloned from miiuy croaker (Miichthys miiuy). As in other teleost, four exons and three introns were identified in miiuy croaker class IIA gene; but the difference is that six exons and five introns were identified in the miiuy croaker class IIB gene. The deduced amino acid sequence of class IIA and class IIB had 26.3–85.7% and 11.0–88.8% identity with those of mammal and teleost, respectively. Real-time quantitative RT-PCR demonstrated that the MHC class IIA and IIB were ubiquitously expressed in ten normal tissues; expression levels of MHC genes were found first upregulated and then downregulated, and finally by a recovery to normal level throughout the pathogenic bacteria infection process. In addition, we report on the underlying mechanism that maintains sequences diversity among many fish species. A series of site-model tests implemented in the CODEML program revealed that positive Darwinian selection is likely the cause of the molecular evolution in the fish MHC class II genes.
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Affiliation(s)
- Tianjun Xu
- Laboratory for Marine Living Resources and Molecular Engineering, College of Marine Science, Zhejiang Ocean University, Zhoushan, People's Republic of China.
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Girard P, Angers B. The functional gene diversity in natural populations over postglacial areas: the shaping mechanisms behind genetic composition of longnose dace (Rhinichthys cataractae) in northeastern North America. J Mol Evol 2011; 73:45-57. [PMID: 21861120 DOI: 10.1007/s00239-011-9456-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Accepted: 08/09/2011] [Indexed: 10/17/2022]
Abstract
The diversity of functional genes and the related processes are important issues for conservation biology. This is especially relevant for populations that have suffered from demographic reduction as a consequence of the processes of postglacial colonization. In this perspective, the aims of the present study are (1) to quantify the genetic diversity of functional genes and (2) to disentangle the long- and short-term effects of natural selection that shapes genetic diversity from those of drift, mutation, and allopatric fragmentation. This research was conducted using an extensive genetic polymorphism analysis of populations of longnose dace (Rhinichthys cataractae) living over an area once covered by Pleistocene glaciations. The sequence and diversity of one exon of three genes (MHC IIβ, growth hormone, and trypsin) were jointly analyzed with non-coding nuclear loci from 27 populations; these populations were sampled over four major basins of northeastern North America. The survey revealed a surprisingly low allelic richness, especially for the MHC gene, considering the number of individuals and populations sampled. The results suggest that there is a complex mixture of different evolutionary processes shaping the level of polymorphism among longnose dace. While our study underlines the importance of the short-term effects of neutral processes and the major impact of post-glacial colonization on gene diversity, locally dependent balancing selection was detected on MHC. From this perspective, our results support an understanding of the importance of drift on functional gene diversity but also highlight the transient effects of natural selection on allelic composition, even in populations that show drastic reduction of genetic diversity.
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Affiliation(s)
- Philippe Girard
- Département de Géographie, Université de Montréal, C.P. 6128, Succ. Centre-Ville, Montréal, QC H3C 3J7, Canada.
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Jang-Liaw NH, Chou WH. Phylogeography of the fanged dicroglossine frog, Limnonectes fujianensis (Anura, Ranidae), in Taiwan. Zoolog Sci 2011; 28:254-63. [PMID: 21466342 DOI: 10.2108/zsj.28.254] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A phylogenetic analysis of Taiwanese fanged dicroglossine frog, Limnonectes fujianensis (Anura, Ranidae), was conducted to examine its genetic diversification using sequence data from a portion of the mitochondrial DNA (mtDNA) cytochrome b sequences. We collected genetic data from 200 individuals at 23 localities in Taiwan and three localities in China. A neighbor-joining tree of 39 haplotypes revealed two clades in Taiwan and a clade in China, each showing restricted geographical distribution. The pattern of geographical divergence suggests a single invasion into Taiwan. Divergence times between clades were inferred using molecular clock tests. The population relationship of L. fujianensis between Taiwan and mainland China, and the phylogenetic relationships with its congeners, e.g., L. bannaensis, L. fragilis and L. kuhlii, were obtained and discussed.
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Affiliation(s)
- Nian-Hong Jang-Liaw
- Department of Zoology, National Museum of Natural Science, 1st Kuang-Chien Rd., Taichung 404, Taiwan
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Bajgain P, Richardson BA, Price JC, Cronn RC, Udall JA. Transcriptome characterization and polymorphism detection between subspecies of big sagebrush (Artemisia tridentata). BMC Genomics 2011; 12:370. [PMID: 21767398 PMCID: PMC3150299 DOI: 10.1186/1471-2164-12-370] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Accepted: 07/18/2011] [Indexed: 12/14/2022] Open
Abstract
Background Big sagebrush (Artemisia tridentata) is one of the most widely distributed and ecologically important shrub species in western North America. This species serves as a critical habitat and food resource for many animals and invertebrates. Habitat loss due to a combination of disturbances followed by establishment of invasive plant species is a serious threat to big sagebrush ecosystem sustainability. Lack of genomic data has limited our understanding of the evolutionary history and ecological adaptation in this species. Here, we report on the sequencing of expressed sequence tags (ESTs) and detection of single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers in subspecies of big sagebrush. Results cDNA of A. tridentata sspp. tridentata and vaseyana were normalized and sequenced using the 454 GS FLX Titanium pyrosequencing technology. Assembly of the reads resulted in 20,357 contig consensus sequences in ssp. tridentata and 20,250 contigs in ssp. vaseyana. A BLASTx search against the non-redundant (NR) protein database using 29,541 consensus sequences obtained from a combined assembly resulted in 21,436 sequences with significant blast alignments (≤ 1e-15). A total of 20,952 SNPs and 119 polymorphic SSRs were detected between the two subspecies. SNPs were validated through various methods including sequence capture. Validation of SNPs in different individuals uncovered a high level of nucleotide variation in EST sequences. EST sequences of a third, tetraploid subspecies (ssp. wyomingensis) obtained by Illumina sequencing were mapped to the consensus sequences of the combined 454 EST assembly. Approximately one-third of the SNPs between sspp. tridentata and vaseyana identified in the combined assembly were also polymorphic within the two geographically distant ssp. wyomingensis samples. Conclusion We have produced a large EST dataset for Artemisia tridentata, which contains a large sample of the big sagebrush leaf transcriptome. SNP mapping among the three subspecies suggest the origin of ssp. wyomingensis via mixed ancestry. A large number of SNP and SSR markers provide the foundation for future research to address questions in big sagebrush evolution, ecological genetics, and conservation using genomic approaches.
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Affiliation(s)
- Prabin Bajgain
- Plant and Wildlife Science Department, Brigham Young University, Provo, UT 84602, USA
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Brieuc MSO, Naish KA. Detecting signatures of positive selection in partial sequences generated on a large scale: pitfalls, procedures and resources. Mol Ecol Resour 2011; 11 Suppl 1:172-83. [PMID: 21429173 DOI: 10.1111/j.1755-0998.2010.02948.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Studying the actions of selection provides insight into adaptation, population divergence and gene function. Next-generation sequencing produces large amounts of partial sequences, potentially facilitating efforts to detect signatures of selection based on comparisons between synonymous (d(S)) and nonsynonymous (d(N)) substitutions, and single nucleotide polymorphism assays placed in selected genes would improve the ability to study adaptation in population surveys. However, sequences generated by these technologies are typically short. In nonmodel organisms that are a focus of evolutionary studies, the lack of a reference genome that facilitates the assembly of short sequences has limited surveys of positive selection in large numbers of genes. Here, we describe a series of steps to facilitate these surveys. We provide PERL scripts to assist data analysis, and describe the use of commonly available programs. We demonstrate these approaches in six salmon species, which have partially duplicated genomes. We recommend using multiway blast to optimize the number of alignments between partial coding sequences. Reading frames should be manually detected after alignment with sequences in Genbank using the BLASTX program. We encourage the use of a phylogenetic approach to separate orthologs from paralogs in duplicated genomes. Simple simulations on a gene known to have undergone selection in salmon species, transferrin, showed that the ability to detect selection in short sequences (<600 bp) depended on the proportion of codons under selection (1-2%) within that sequence. This relationship was less relevant in longer sequences. In this exploratory study, we detected 11 genes showing evidence of positive selection.
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Affiliation(s)
- Marine S O Brieuc
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, 98195, USA.
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Kuchma O, Finkeldey R. Evidence for selection in response to radiation exposure: Pinus sylvestris in the Chernobyl exclusion zone. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2011; 159:1606-1612. [PMID: 21429640 DOI: 10.1016/j.envpol.2011.02.049] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2010] [Revised: 02/17/2011] [Accepted: 02/26/2011] [Indexed: 05/30/2023]
Abstract
Changes of genetic structures due to viability selection are likely to occur in populations exposed to rapidly and extremely changing environmental conditions after catastrophic events. However, very little is known about the extent of selective responses and in particular the proportion of the genome involved in putatively adaptive reactions for non-model plants. We used amplified fragment length polymorphisms (AFLPs) in order to investigate genetic differences between pine (Pinus sylvestris) trees which were partially exposed to extreme environmental conditions. Genetic variation patterns of pines exposed to high radiation in the Chernobyl exclusion zone with or without phenotypic stress symptoms were compared to control trees with a similar origin. Six percent of the investigated loci (15 of 222 loci) were identified as candidates for selective responses. Moderate differentiation was observed between groups of trees showing either weak or strong phenotypic responses to high radiation levels.
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Affiliation(s)
- Oleksandra Kuchma
- Forest Genetics and Forest Tree Breeding, Büsgen Institute, Georg-August University Göttingen, Büsgenweg 2, Göttingen 37077, Germany
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Contrasting responses to selection in class I and class IIα major histocompatibility-linked markers in salmon. Heredity (Edinb) 2011; 107:143-54. [PMID: 21266985 DOI: 10.1038/hdy.2010.177] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Comparison of levels and patterns of genetic variation in natural populations either across loci or against neutral expectation can yield insight into locus-specific differences in the strength and direction of evolutionary forces. We used both approaches to test the hypotheses on patterns of selection on major histocompatibility (MH)-linked markers. We performed temporal analyses of class I and class IIα MH-linked markers and eight microsatellite loci in two Atlantic salmon populations in Ireland on two temporal scales: over six decades and 9 years in the rivers Burrishoole and Delphi, respectively. We also compared contemporary Burrishoole and Delphi samples with nearby populations for the same loci. On comparing patterns of temporal and spatial differentiation among classes of loci, the class IIα MH-linked marker was consistently identified as an outlier compared with patterns at the other microsatellite loci or neutral expectation. We found higher levels of temporal and spatial heterogeneity in heterozygosity (but not in allelic richness) for the class IIα MH-linked marker compared with microsatellites. Tests on both within- and among-population differentiation are consistent with directional selection acting on the class IIα-linked marker in both temporal and spatial comparisons, but only in temporal comparisons for the class I-linked marker. Our results indicate a complex pattern of selection on MH-linked markers in natural populations of Atlantic salmon. These findings highlight the importance of considering selection on MH-linked markers when using these markers for management and conservation purposes.
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Hayes ML, Eytan RI, Hellberg ME. High amino acid diversity and positive selection at a putative coral immunity gene (tachylectin-2). BMC Evol Biol 2010; 10:150. [PMID: 20482872 PMCID: PMC2880987 DOI: 10.1186/1471-2148-10-150] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2009] [Accepted: 05/19/2010] [Indexed: 12/22/2022] Open
Abstract
Background Genes involved in immune functions, including pathogen recognition and the activation of innate defense pathways, are among the most genetically variable known, and the proteins that they encode are often characterized by high rates of amino acid substitutions, a hallmark of positive selection. The high levels of variation characteristic of immunity genes make them useful tools for conservation genetics. To date, highly variable immunity genes have yet to be found in corals, keystone organisms of the world's most diverse marine ecosystem, the coral reef. Here, we examine variation in and selection on a putative innate immunity gene from Oculina, a coral genus previously used as a model for studies of coral disease and bleaching. Results In a survey of 244 Oculina alleles, we find high nonsynonymous variation and a signature of positive selection, consistent with a putative role in immunity. Using computational protein structure prediction, we generate a structural model of the Oculina protein that closely matches the known structure of tachylectin-2 from the Japanese horseshoe crab (Tachypleus tridentatus), a protein with demonstrated function in microbial recognition and agglutination. We also demonstrate that at least three other genera of anthozoan cnidarians (Acropora, Montastrea and Nematostella) possess proteins structurally similar to tachylectin-2. Conclusions Taken together, the evidence of high amino acid diversity, positive selection and structural correspondence to the horseshoe crab tachylectin-2 suggests that this protein is 1) part of Oculina's innate immunity repertoire, and 2) evolving adaptively, possibly under selective pressure from coral-associated microorganisms. Tachylectin-2 may serve as a candidate locus to screen coral populations for their capacity to respond adaptively to future environmental change.
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Affiliation(s)
- Marshall L Hayes
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
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Spurgin LG, Richardson DS. How pathogens drive genetic diversity: MHC, mechanisms and misunderstandings. Proc Biol Sci 2010; 277:979-88. [PMID: 20071384 DOI: 10.1098/rspb.2009.2084] [Citation(s) in RCA: 514] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Major histocompatibility complex (MHC) genes have been put forward as a model for studying how genetic diversity is maintained in wild populations. Pathogen-mediated selection (PMS) is believed to generate the extraordinary levels of MHC diversity observed. However, establishing the relative importance of the three proposed mechanisms of PMS (heterozygote advantage, rare-allele advantage and fluctuating selection) has proved extremely difficult. Studies have attempted to differentiate between mechanisms of PMS using two approaches: (i) comparing MHC diversity with that expected under neutrality and (ii) relating MHC diversity to pathogen regime. Here, we show that in many cases the same predictions arise from the different mechanisms under these approaches, and that most studies that have inferred one mechanism of selection have not fully considered the alternative explanations. We argue that, while it may be possible to demonstrate that particular mechanisms of PMS are occurring, resolving their relative importance within a system is probably impossible. A more realistic target is to continue to demonstrate when and where the different mechanisms of PMS occur, with the aim of determining their relative importance across systems. We put forward what we believe to be the most promising approaches that will allow us to progress towards achieving this.
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Affiliation(s)
- Lewis G Spurgin
- Centre for Ecology, Evolution and Conservation, School of Biological Sciences, University of East Anglia, Norwich, UK
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Bonin A, Paris M, Tetreau G, David JP, Després L. Candidate genes revealed by a genome scan for mosquito resistance to a bacterial insecticide: sequence and gene expression variations. BMC Genomics 2009; 10:551. [PMID: 19930593 PMCID: PMC2799440 DOI: 10.1186/1471-2164-10-551] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2009] [Accepted: 11/21/2009] [Indexed: 12/12/2022] Open
Abstract
Background Genome scans are becoming an increasingly popular approach to study the genetic basis of adaptation and speciation, but on their own, they are often helpless at identifying the specific gene(s) or mutation(s) targeted by selection. This shortcoming is hopefully bound to disappear in the near future, thanks to the wealth of new genomic resources that are currently being developed for many species. In this article, we provide a foretaste of this exciting new era by conducting a genome scan in the mosquito Aedes aegypti with the aim to look for candidate genes involved in resistance to Bacillus thuringiensis subsp. israelensis (Bti) insecticidal toxins. Results The genome of a Bti-resistant and a Bti-susceptible strains was surveyed using about 500 MITE-based molecular markers, and the loci showing the highest inter-strain genetic differentiation were sequenced and mapped on the Aedes aegypti genome sequence. Several good candidate genes for Bti-resistance were identified in the vicinity of these highly differentiated markers. Two of them, coding for a cadherin and a leucine aminopeptidase, were further examined at the sequence and gene expression levels. In the resistant strain, the cadherin gene displayed patterns of nucleotide polymorphisms consistent with the action of positive selection (e.g. an excess of high compared to intermediate frequency mutations), as well as a significant under-expression compared to the susceptible strain. Conclusion Both sequence and gene expression analyses agree to suggest a role for positive selection in the evolution of this cadherin gene in the resistant strain. However, it is unlikely that resistance to Bti is conferred by this gene alone, and further investigation will be needed to characterize other genes significantly associated with Bti resistance in Ae. aegypti. Beyond these results, this article illustrates how genome scans can build on the body of new genomic information (here, full genome sequence and MITE characterization) to finally hold their promises and help pinpoint candidate genes for adaptation and speciation.
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Affiliation(s)
- Aurélie Bonin
- Laboratoire d'Ecologie Alpine, CNRS-UMR 5553, Université Joseph Fourier, BP 53, 38041 Grenoble cedex 09, France.
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Shubina EA, Ponomareva EV, Glubokov AI. Population genetic structure of walleye pollock Theragra chalcogramma (Gadidae, Pisces) from the Bering Sea and Sea of Okhotsk. Mol Biol 2009. [DOI: 10.1134/s0026893309050161] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Mason RAB, Browning TL, Eldridge MDB. Reduced MHC class II diversity in island compared to mainland populations of the black-footed rock-wallaby (Petrogale lateralis lateralis). CONSERV GENET 2009. [DOI: 10.1007/s10592-009-9993-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Kerdelhué C, Zane L, Simonato M, Salvato P, Rousselet J, Roques A, Battisti A. Quaternary history and contemporary patterns in a currently expanding species. BMC Evol Biol 2009; 9:220. [PMID: 19732434 PMCID: PMC2753568 DOI: 10.1186/1471-2148-9-220] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2009] [Accepted: 09/04/2009] [Indexed: 11/13/2022] Open
Abstract
Background Quaternary climatic oscillations had dramatic effects on species evolution. In northern latitudes, populations had to survive the coldest periods in refugial areas and recurrently colonized northern regions during interglacials. Such a history usually results in a loss of genetic diversity. Populations that did not experience glaciations, in contrast, probably maintained most of their ancestral genetic diversity. These characteristics dramatically affected the present-day distribution of genetic diversity and may influence the ability of species to cope with the current global changes. We conducted a range-wide study of mitochondrial genetic diversity in the pine processionary moth (Thaumetopoea pityocampa/T. wilkinsoni complex, Notodontidae), a forest pest occurring around the Mediterranean Basin and in southern Europe. This species is responding to the current climate change by rapid natural range expansion and can also be accidentally transported by humans. Our aim was to assess if Quaternary climatic oscillations had a different effect across the species' range and to determine if genetic footprints of contemporary processes can be identified in areas of recent introduction. Results We identified three main clades that were spatially structured. In most of Europe, the genetic diversity pattern was typical for species that experienced marked glaciation cycles. Except in refugia, European populations were characterized by the occurrence of one main haplotype and by a strong reduction in genetic diversity, which is expected in regions that were rapidly re-colonized when climatic conditions improved. In contrast, all other sub-clades around the Mediterranean Basin occurred in limited parts of the range and were strongly structured in space, as is expected in regions in which the impact of glaciations was limited. In such places, genetic diversity was retained in most populations, and almost all haplotypes were endemic. This pattern was extreme on remote Mediterranean islands (Crete, Cyprus, Corsica) where highly differentiated, endemic haplotypes were found. Recent introductions were typified by the existence of closely-related haplotypes in geographically distant populations, which is difficult to detect in most of Europe because of a lack of overall genetic structure. Conclusion In regions that were not prone to marked glaciations, recent moth introductions/expansions could be detected due to the existence of a strong spatial genetic structure. In contrast, in regions that experienced the most intense Quaternary climatic oscillations, the natural populations are not genetically structured, and contemporary patterns of population expansion remain undetected.
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NIELSEN EINARE, HEMMER-HANSEN JAKOB, LARSEN PETERFOGED, BEKKEVOLD DORTE. Population genomics of marine fishes: identifying adaptive variation in space and time. Mol Ecol 2009; 18:3128-50. [DOI: 10.1111/j.1365-294x.2009.04272.x] [Citation(s) in RCA: 236] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Neiman M, Olson MS, Tiffin P. Selective histories of poplar protease inhibitors: elevated polymorphism, purifying selection, and positive selection driving divergence of recent duplicates. THE NEW PHYTOLOGIST 2009; 183:740-750. [PMID: 19566812 DOI: 10.1111/j.1469-8137.2009.02936.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
To further our understanding of plant defense evolution and the consistency of selection at the nucleotide level we analysed polymorphism data from five protease inhibitor (PI) genes in Populus balsamifera. We compared diversity at the five PI genes to diversity at nondefense loci in both range-wide samples as well as in two subpopulations, one from the northern edge of the species range and one from the southern edge of the range. We also compared our data with previously reported diversity in Populus tremula, a European species with similar ecology to North American P. balsamifera. The PIs show diverse histories, including repeated bouts of positive selection and excess diversity. These genes also exhibit diverse histories in P. tremula but the signatures of selection acting at the specific loci differed between the species. One locus, KTI3, segregates several recent duplicates that show evidence of either positive selection or relaxed selective constraints. The patterns of diversity at the PIs varied within P. balsamifera and between two closely related species. The lack of consistent patterns suggests that evolution of host defense genes, including adaptations to enemy-imposed selection, may often be lineage- and gene-specific.
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Affiliation(s)
- Maurine Neiman
- Department of Plant Biology, 250 Biosciences, University of Minnesota, Saint Paul, MN 55105, USA
| | - Matthew S Olson
- Institute of Arctic Biology, 311 Irving 1, University of Alaska Fairbanks, Fairbanks, AK 99775, USA
| | - Peter Tiffin
- Department of Plant Biology, 250 Biosciences, University of Minnesota, Saint Paul, MN 55105, USA
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Barrett LG, Thrall PH, Dodds PN, van der Merwe M, Linde CC, Lawrence GJ, Burdon JJ. Diversity and evolution of effector loci in natural populations of the plant pathogen Melampsora lini. Mol Biol Evol 2009; 26:2499-513. [PMID: 19633228 DOI: 10.1093/molbev/msp166] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Genetic variation for pathogen infectivity is an important driver of disease incidence and prevalence in both natural and managed systems. Here, we use the interaction between the rust pathogen, Melampsora lini, and two host plants, Linum marginale and Linum usitatissimum, to examine how host-pathogen interactions influence the maintenance of polymorphism in genes underlying pathogen virulence. Extensive sequence variation at two effector loci (AvrP123, AvrP4) was found in M. lini isolates collected from across the native range of L. marginale in Australia, as well as in isolates collected from a second host, the cultivated species L. usitatissimum. A highly significant excess of nonsynonymous compared with synonymous polymorphism was found at both loci, suggesting that diversifying selection is important for the maintenance of the observed sequence diversity. Agrobacterium-mediated transient transformation assays were used to demonstrate that variants of both the AvrP123 and AvrP4 genes are differentially recognized by resistance genes in L. marginale. We further characterized patterns of nucleotide variation at AvrP123 and AvrP4 in 10 local populations of M. lini infecting the wild host L. marginale. Populations were significantly differentiated with respect to allelic representation at the Avr loci, suggesting the possibility of local selection maintaining distinct genetic structures between pathogen populations, whereas limited diversity may be explained via selective sweeps and demographic bottlenecks. Together, these results imply that interacting selective and nonselective factors, acting across a broad range of scales, are important for the generation and maintenance of adaptively significant variation in populations of M. lini.
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Affiliation(s)
- Luke G Barrett
- CSIRO Plant Industry, GPO Box 1600, Canberra, ACT Australia.
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Jorgensen TH, Emerson BC. RPW8 and resistance to powdery mildew pathogens in natural populations of Arabidopsis lyrata. THE NEW PHYTOLOGIST 2009; 182:984-993. [PMID: 19383106 DOI: 10.1111/j.1469-8137.2009.02787.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
It is not clear to what extent the orthologues of genes that are adaptively important in one species also contribute to adaptive variation in others. Here, we examine Arabidopsis lyrata to assess the functional and evolutionary significance of natural variation in an orthologue of the gene RPW8 known to be a major determinant of powdery mildew resistance in Arabidopsis thaliana. We assessed the sequence variation at RPW8 and the associated resistance reaction in populations of A. lyrata ssp. petraea. Neutrality tests were performed to understand the importance of local adaptation in maintaining variation at the locus. Highly truncated RPW8 proteins were frequent in all populations and were associated with an increased risk of susceptibility. Haplotypes encoding full-length proteins were highly significantly associated with resistance. There were no signatures of selection at the species-wide level, but some evidence for positive selection in two populations. RPW8 in A. lyrata appears to have a role in powdery mildew resistance, similar to its orthologue in A. thaliana. Unlike A. thaliana, A. lyrata contains a genetic component that can act independently of RPW8 to confer resistance to powdery mildew pathogens. Infrequent local selective sweeps may favour different alleles in different populations, and thereby contribute to the maintenance of species-wide variation at the locus.
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Affiliation(s)
- T H Jorgensen
- Centre for Ecology, Evolution and Conservation, School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - B C Emerson
- Centre for Ecology, Evolution and Conservation, School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
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Garamszegi LZ, de Groot NG, Bontrop RE. Correlated evolution of nucleotide substitution rates and allelic variation in Mhc-DRB lineages of primates. BMC Evol Biol 2009; 9:73. [PMID: 19361342 PMCID: PMC2674423 DOI: 10.1186/1471-2148-9-73] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2008] [Accepted: 04/12/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The major histocompatibility complex (MHC) is a key model of genetic polymorphism. Selection pressure by pathogens or other microevolutionary forces may result in a high rate of non-synonymous substitutions at the codons specifying the contact residues of the antigen binding sites (ABS), and the maintenance of extreme MHC allelic variation at the population/species level. Therefore, selection forces favouring MHC variability for any reason should cause a correlated evolution between substitution rates and allelic polymorphism. To investigate this prediction, we characterised nucleotide substitution rates and allelic polymorphism (i.e. the number of alleles detected in relation to the number of animals screened) of several Mhc class II DRB lineages in 46 primate species, and tested for a correlation between them. RESULTS First, we demonstrate that species-specific and lineage-specific evolutionary constraints favour species- and lineage-dependent substitution rate at the codons specifying the ABS contact residues (i.e. certain species and lineages can be characterised by high substitution rate, while others have low rate). Second, we show that although the degree of the non-synonymous substitution rate at the ABS contact residues was systematically higher than the degree of the synonymous substitution rate, these estimates were strongly correlated when we controlled for species-specific and lineage-specific effects, and also for the fact that different studies relied on different sample size. Such relationships between substitution rates of different types could even be extended to the non-contact residues of the molecule. Third, we provide statistical evidence that increased substitution rate along a MHC gene may lead to allelic variation, as a high substitution rate can be observed in those lineages in which many alleles are maintained. Fourth, we show that the detected patterns were independent of phylogenetic constraints. When we used phylogenetic models that control for similarity between species, due to common descent, and focused on variations within a single lineage (DRB1*03), the positive relationship between different substitution rates and allelic polymorphisms was still robust. Finally, we found the same effects to emerge in the analyses that eliminated within-species variation in MHC traits by using strictly single population-level studies. However, in a set of contrasting analyses, in which we focused on the non-functional DRB6 locus, the correlation between substitution rates and allelic variation was not prevalent. CONCLUSION Our results indicate that positive selection for the generation of allelic polymorphism acting on the functional part of the protein has consequences for the nucleotide substitution rate along the whole exon 2 sequence of the Mhc-DRB gene. Additionally, we proved that an increased substitution rate can promote allelic variation within lineages. Consequently, the evolution of different characteristics of genetic polymorphism is not independent.
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Affiliation(s)
- László Z Garamszegi
- Department of Biology, University of Antwerp, Campus Drie Eiken Universiteitsplein 1, B-2610 Wilrijk, Belgium
- Department of Evolutionary Ecology, Estación Biológica de Doñana-CSIC, c/Americo Vespucio, s/n, 41092, Sevilla, Spain
| | - Natasja G de Groot
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, PO Box 3306, 2280 GH Rijswijk, the Netherlands
| | - Ronald E Bontrop
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, PO Box 3306, 2280 GH Rijswijk, the Netherlands
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Pariset L, Joost S, Marsan PA, Valentini A. Landscape genomics and biased FST approaches reveal single nucleotide polymorphisms under selection in goat breeds of North-East Mediterranean. BMC Genet 2009; 10:7. [PMID: 19228375 PMCID: PMC2663570 DOI: 10.1186/1471-2156-10-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2008] [Accepted: 02/19/2009] [Indexed: 01/18/2023] Open
Abstract
Background In this study we compare outlier loci detected using a FST based method with those identified by a recently described method based on spatial analysis (SAM). We tested a panel of single nucleotide polymorphisms (SNPs) previously genotyped in individuals of goat breeds of southern areas of the Mediterranean basin (Italy, Greece and Albania). We evaluate how the SAM method performs with SNPs, which are increasingly employed due to their high number, low cost and easy of scoring. Results The combined use of the two outlier detection approaches, never tested before using SNP polymorphisms, resulted in the identification of the same three loci involved in milk and meat quality data by using the two methods, while the FST based method identified 3 more loci as under selection sweep in the breeds examined. Conclusion Data appear congruent by using the two methods for FST values exceeding the 99% confidence limits. The methods of FST and SAM can independently detect signatures of selection and therefore can reduce the probability of finding false positives if employed together. The outlier loci identified in this study could indicate adaptive variation in the analysed species, characterized by a large range of climatic conditions in the rearing areas and by a history of intense trade, that implies plasticity in adapting to new environments.
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Affiliation(s)
- Lorraine Pariset
- Dipartimento di Produzioni Animali, Università della Tuscia, Viterbo, Italy.
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Zaffarano PL, McDonald BA, Linde CC. Phylogeographical analyses reveal global migration patterns of the barley scald pathogen Rhynchosporium secalis. Mol Ecol 2008; 18:279-93. [PMID: 19076278 DOI: 10.1111/j.1365-294x.2008.04013.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
A phylogeographical analysis of the scald pathogen Rhynchosporium secalis was conducted using nuclear DNA sequences from two neutral restriction fragment length polymorphism loci and the mating-type idiomorphs. Approximately 500 isolates sampled from more than 60 field populations from five continents were analysed to infer migration patterns and the demographic history of the fungus. Migration rates among continents were generally low, consistent with earlier reports of significant population subdivision among continents. Northern Europe was mainly a source population for global migration. We hypothesize that the pathogen only recently moved out of its centre of origin, resulting in founder populations that are reproductively isolated due to the contemporary absence of long-distance gene flow.
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Affiliation(s)
- Pascal L Zaffarano
- Forest Pathology and Dendrology, Institute of Integrative Biology, ETH-Zurich, CHN, CH-8092 Zürich, Switzerland.
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Cavatorta JR, Savage AE, Yeam I, Gray SM, Jahn MM. Positive Darwinian selection at single amino acid sites conferring plant virus resistance. J Mol Evol 2008; 67:551-9. [PMID: 18953590 DOI: 10.1007/s00239-008-9172-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2007] [Revised: 09/08/2008] [Accepted: 09/29/2008] [Indexed: 01/26/2023]
Abstract
Explicit evaluation of the accuracy and power of maximum likelihood and Bayesian methods for detecting site-specific positive Darwinian selection presents a challenge because selective consequences of single amino acid changes are generally unknown. We exploited extensive molecular and functional characterization of amino acid substitutions in the plant gene eIF4E to evaluate the performance of these methods in detecting site-specific positive selection. We documented for the first time a molecular signature of positive selection within a recessive resistance gene in plants. We then used two statistical platforms, Phylogenetic Analysis Using Maximum Likelihood and Hypothesis Testing Using Phylogenies (HyPhy), to look for site-specific positive selection. Their relative power and accuracy are assessed by comparing the sites they identify as being positively selected with those of resistance-determining amino acids. Our results indicate that although both methods are surprisingly accurate in their identification of resistance sites, HyPhy appears to more accurately identify biologically significant amino acids using our data set.
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Affiliation(s)
- J R Cavatorta
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, USA.
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Obbard DJ, Callister DM, Jiggins FM, Soares DC, Yan G, Little TJ. The evolution of TEP1, an exceptionally polymorphic immunity gene in Anopheles gambiae. BMC Evol Biol 2008; 8:274. [PMID: 18840262 PMCID: PMC2576239 DOI: 10.1186/1471-2148-8-274] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2008] [Accepted: 10/07/2008] [Indexed: 01/20/2023] Open
Abstract
Background Host-parasite coevolution can result in balancing selection, which maintains genetic variation in the susceptibility of hosts to parasites. It has been suggested that variation in a thioester-containing protein called TEP1 (AGAP010815) may alter the ability of Anopheles mosquitoes to transmit Plasmodium parasites, and high divergence between alleles of this gene suggests the possible action of long-term balancing selection. We studied whether TEP1 is a case of an ancient balanced polymorphism in an animal immune system. Results We found evidence that the high divergence between TEP1 alleles is the product of genetic exchange between TEP1 and other TEP loci, i.e. gene conversion. Additionally, some TEP1 alleles showed unexpectedly low variability. Conclusion The TEP1 gene appears to be a chimera produced from at least two other TEP loci, and the divergence between TEP1 alleles is probably not caused by long-term balancing selection, but is instead due to two independent gene conversion events from one of these other genes. Nevertheless, TEP1 still shows evidence of natural selection, in particular there appears to have been recent changes in the frequency of alleles that has diminished polymorphism within each allelic class. Although the selective force driving this dynamic was not identified, given that susceptibility to Plasmodium parasites is known to be associated with allelic variation in TEP1, these changes in allele frequencies could alter the vectoring capacity of populations.
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Affiliation(s)
- Darren J Obbard
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, West Mains Rd, Edinburgh EH9 3JT, UK.
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Padhi A, Verghese B. Detecting positively selected codons in the glycoprotein of spring viraemia of carp virus (SVCV) isolates from the USA and China. JOURNAL OF FISH DISEASES 2008; 31:785-791. [PMID: 18801064 DOI: 10.1111/j.1365-2761.2008.00938.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Affiliation(s)
- A Padhi
- Department of Biological Science, University of Tulsa, Tulsa, OK, USA.
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44
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Piertney SB, Webster LMI. Characterising functionally important and ecologically meaningful genetic diversity using a candidate gene approach. Genetica 2008; 138:419-32. [PMID: 18803023 DOI: 10.1007/s10709-008-9322-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2008] [Accepted: 08/20/2008] [Indexed: 01/13/2023]
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Nelson L, Anderson S, Archibald AL, Rhind S, Lu ZH, Condie A, McIntyre N, Thompson J, Nenutil R, Vojtesek B, Whitelaw CBA, Little TJ, Hupp T. An animal model to evaluate the function and regulation of the adaptively evolving stress protein SEP53 in oesophageal bile damage responses. Cell Stress Chaperones 2008; 13:375-85. [PMID: 18465210 PMCID: PMC2673944 DOI: 10.1007/s12192-008-0037-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2007] [Revised: 03/04/2008] [Accepted: 03/12/2008] [Indexed: 01/19/2023] Open
Abstract
Squamous epithelium in mammals has evolved an atypical stress response involving down-regulation of the classic HSP70 protein and induction of sets of proteins including one named SEP53. This atypical stress response might be due to the unusual environmental pressures placed on squamous tissue. In fact, SEP53 plays a role as an anti-apoptotic factor in response to DNA damage induced by deoxycholic acid stresses implicated in oesophageal reflux disease. SEP53 also has a genetic signature characteristic of an adaptively and rapidly evolving gene, and this observation has been used to imply a role for SEP53 in immunity. Physiological models of squamous tissue are required to further define the regulation and function of SEP53. We examined whether porcine squamous epithelium would be a good model to study SEP53, since this animal suffers from a bile-reflux disease in squamous oesophageal tissue. We have (1) cloned and sequenced the porcine SEP53 locus from porcine bacterial artificial chromosome genomic DNA, (2) confirmed the strikingly divergent nature of the C-terminal portion of the SEP53 gene amongst mammals, (3) discovered that a function of the conserved N-terminal domain of the gene is to maintain cytoplasmic localisation, and (4) examined SEP53 expression in normal and diseased porcine pars oesophagea. SEP53 expression in porcine tissue was relatively confined to gastric squamous epithelium, consistent with its expression in normal human squamous epithelium. Immunohistochemical staining for SEP53 protein in normal and damaged pars oesophagea demonstrated significant stabilisation of SEP53 protein in the injured tissue. These results suggest that porcine squamous epithelium would be a robust physiological model to examine the evolution and function of the SEP53 stress pathway in modulating stress-induced responses in squamous tissue.
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Affiliation(s)
- Lenny Nelson
- CRUK p53 Signal Transduction Group, University of Edinburgh, South Crewe Road, Edinburgh, EH4 2XR UK
| | - Susan Anderson
- Division of Genomics and Genetics, Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin, Midlothian, EH25 9PS UK
| | - Alan L. Archibald
- Division of Genomics and Genetics, Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin, Midlothian, EH25 9PS UK
| | - Susan Rhind
- Division of Animal Health and Welfare, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Roslin, Midlothian, EH25 9RG UK
| | - Zen H. Lu
- Division of Genomics and Genetics, Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin, Midlothian, EH25 9PS UK
| | - Alison Condie
- Wellcome Trust Clinical Research Facility, South Crewe Road, Edinburgh, EH4 2XU UK
| | - Neal McIntyre
- Division of Animal Health and Welfare, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Roslin, Midlothian, EH25 9RG UK
| | - Jill Thompson
- SAC Veterinary Services (Edinburgh), Bush Estate, Penicuik, Midlothian, EH26 0QE UK
| | | | | | - C. Bruce A. Whitelaw
- Division of Genomics and Genetics, Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin, Midlothian, EH25 9PS UK
| | - Tom J. Little
- Institute of Evolutionary Biology, University of Edinburgh, School of Biology, Kings Buildings, EH9 3JT Edinburgh, UK
| | - Ted Hupp
- CRUK p53 Signal Transduction Group, University of Edinburgh, South Crewe Road, Edinburgh, EH4 2XR UK
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Jang-Liaw NH, Lee TH, Chou WH. Phylogeography of Sylvirana latouchii (Anura, Ranidae) in Taiwan. Zoolog Sci 2008; 25:68-79. [PMID: 18275248 DOI: 10.2108/zsj.25.68] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2007] [Accepted: 09/24/2007] [Indexed: 11/17/2022]
Abstract
Biogeographic studies are important for understanding the natural history of faunas. To comprehend the geographical patterns of genetic variation in anurans in Taiwan, we investigated the genetic structure of Sylvirana latouchii (Anura, Ranidae) from 31 populations by using mitochondrial DNA (mtDNA) cytochrome b sequences. A neighbor-joining tree of 38 haplotypes revealed three major divergences in Taiwanese S. latouchii: the northern, western, and eastern-and-southern clades. Each clade was restricted to a single geographical district and showed obvious differentiation. The patterns of geographical divergence in this species reflect common historical events experienced by other native animals distributed in Taiwan. The order of divergence times between clades was inferred using a molecular clock test. The population relationship of S. latouchii between Taiwan and mainland China is discussed. Further study employing more populations of S. latouchii from mainland China is necessary to clarify the original geographical patterns and migratory history of this species.
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Affiliation(s)
- Nian-Hong Jang-Liaw
- Department of Life Sciences, National Chung Hsing University, 250 Kuo-Kuang Rd., Taichung 402, Taiwan.
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Simões P, Santos J, Fragata I, Mueller LD, Rose MR, Matos M. HOW REPEATABLE IS ADAPTIVE EVOLUTION? THE ROLE OF GEOGRAPHICAL ORIGIN AND FOUNDER EFFECTS IN LABORATORY ADAPTATION. Evolution 2008; 62:1817-29. [DOI: 10.1111/j.1558-5646.2008.00423.x] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Namroud MC, Beaulieu J, Juge N, Laroche J, Bousquet J. Scanning the genome for gene single nucleotide polymorphisms involved in adaptive population differentiation in white spruce. Mol Ecol 2008; 17:3599-613. [PMID: 18662225 PMCID: PMC2613251 DOI: 10.1111/j.1365-294x.2008.03840.x] [Citation(s) in RCA: 158] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Conifers are characterized by a large genome size and a rapid decay of linkage disequilibrium, most often within gene limits. Genome scans based on noncoding markers are less likely to detect molecular adaptation linked to genes in these species. In this study, we assessed the effectiveness of a genome-wide single nucleotide polymorphism (SNP) scan focused on expressed genes in detecting local adaptation in a conifer species. Samples were collected from six natural populations of white spruce (Picea glauca) moderately differentiated for several quantitative characters. A total of 534 SNPs representing 345 expressed genes were analysed. Genes potentially under natural selection were identified by estimating the differentiation in SNP frequencies among populations (F(ST)) and identifying outliers, and by estimating local differentiation using a Bayesian approach. Both average expected heterozygosity and population differentiation estimates (H(E) = 0.270 and F(ST) = 0.006) were comparable to those obtained with other genetic markers. Of all genes, 5.5% were identified as outliers with F(ST) at the 95% confidence level, while 14% were identified as candidates for local adaptation with the Bayesian method. There was some overlap between the two gene sets. More than half of the candidate genes for local adaptation were specific to the warmest population, about 20% to the most arid population, and 15% to the coldest and most humid higher altitude population. These adaptive trends were consistent with the genes' putative functions and the divergence in quantitative traits noted among the populations. The results suggest that an approach separating the locus and population effects is useful to identify genes potentially under selection. These candidates are worth exploring in more details at the physiological and ecological levels.
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Affiliation(s)
- Marie-Claire Namroud
- Canada Research Chair in Forest and Environmental Genomics and Arborea, Forest Research Centre, Pavillon Charles-Eugène-Marchand, Université Laval, Québec, Québec, CanadaP4
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Cohuet A, Krishnakumar S, Simard F, Morlais I, Koutsos A, Fontenille D, Mindrinos M, Kafatos FC. SNP discovery and molecular evolution in Anopheles gambiae, with special emphasis on innate immune system. BMC Genomics 2008; 9:227. [PMID: 18489733 PMCID: PMC2405807 DOI: 10.1186/1471-2164-9-227] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2007] [Accepted: 05/19/2008] [Indexed: 01/10/2023] Open
Abstract
Background Anopheles innate immunity affects Plasmodium development and is a potential target of innovative malaria control strategies. The extent and distribution of nucleotide diversity in immunity genes might provide insights into the evolutionary forces that condition pathogen-vector interactions. The discovery of polymorphisms is an essential step towards association studies of susceptibility to infection. Results We sequenced coding fragments of 72 immune related genes in natural populations of Anopheles gambiae and of 37 randomly chosen genes to provide a background measure of genetic diversity across the genome. Mean nucleotide diversity (π) was 0.0092 in the A. gambiae S form, 0.0076 in the M form and 0.0064 in A. arabiensis. Within each species, no statistically significant differences in mean nucleotide diversity were detected between immune related and non immune related genes. Strong purifying selection was detected in genes of both categories, presumably reflecting strong functional constraints. Conclusion Our results suggest similar patterns and rates of molecular evolution in immune and non-immune genes in A. gambiae. The 3,214 Single Nucleotide Polymorphisms (SNPs) that we identified are the first large set of Anopheles SNPs from fresh, field-collected material and are relevant markers for future phenotype-association studies.
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Affiliation(s)
- Anna Cohuet
- Institut de Recherche pour le Développement, UR 016, BP 64501, 911 Avenue Agropolis, 34394 Montpellier Cedex 5, France.
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Liu X, Fu YX. Summary statistics of neutral mutations in longitudinal DNA samples. Theor Popul Biol 2008; 74:56-67. [PMID: 18547598 DOI: 10.1016/j.tpb.2008.04.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2006] [Revised: 02/07/2008] [Accepted: 04/21/2008] [Indexed: 10/22/2022]
Abstract
Longitudinal samples of DNA sequences are the DNA sequences sampled from the same population at different time points. For fast evolving organisms, e.g. RNA virus, these kind of samples have increasingly been used to study the evolutionary process in action. Longitudinal samples provide some interesting new summary statistics of genetic variation, such as the frequency of mutation of size i in one sample and size j in another, the average number of mutations accumulated since the common ancestor of two sequences each from a different sample, and number of private, shared and fixed mutations within samples. To make the results more applicable, we used in this study a general two-sample model, which assumes two longitudinal samples were taken from the same measurably evolving population. Inspired by the HIV study, we also studied a two-sample-two-stage model, which is a special case of two-sample model and assumes a treatment after the first sampling instantaneously changes the population size. We derived the formulas for calculating statistical properties, e.g. expectations, variances and covariances, of these new summary statistics under the two models. Potential applications of these results were discussed.
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Affiliation(s)
- Xiaoming Liu
- Human Genetics Center, School of Public Health, University of Texas at Houston, 1200 Herman Pressler, Houston, TX 77030, USA
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