Molecular Ecology
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* Dữ liệu chỉ mang tính chất tham khảo
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Phát hiện số cụm cá thể bằng phần mềm <scp>structure</scp>: một nghiên cứu mô phỏng Tóm tắt Việc xác định các nhóm cá thể đồng nhất về di truyền là một vấn đề lâu dài trong di truyền học quần thể. Một thuật toán Bayesian gần đây được triển khai trong phần mềm structure cho phép phát hiện các nhóm như vậy. Tuy nhiên, khả năng của thuật toán này để xác định số lượng cụm thực sự (K ) trong một mẫu cá thể khi các mô hình phân tán giữa các quần thể không đồng nhất chưa được kiểm tra. Mục tiêu của nghiên cứu này là thực hiện các bài kiểm tra như vậy, sử dụng các kịch bản phân tán khác nhau từ dữ liệu được tạo ra với mô hình dựa trên cá thể. Chúng tôi nhận thấy rằng trong hầu hết các trường hợp, ‘xác suất đăng nhập của dữ liệu’ ước tính không cung cấp một ước tính chính xác về số cụm, K . Tuy nhiên, sử dụng thống kê phụ thuộc ΔK dựa trên tốc độ thay đổi trong xác suất đăng nhập của dữ liệu giữa các giá trị K liên tiếp, chúng tôi phát hiện ra rằng structure chính xác phát hiện cấp độ phân cấp cao nhất trong các kịch bản mà chúng tôi đã kiểm tra. Như mong đợi, kết quả rất nhạy cảm với loại dấu hiệu di truyền được sử dụng (AFLP vs. microsatellite), số lượng locus được đánh giá, số lượng quần thể được lấy mẫu, và số lượng cá thể được xác định trong mỗi mẫu.
Molecular Ecology - Tập 14 Số 8 - Trang 2611-2620 - 2005
#genetically homogeneous groups #Bayesian algorithm #population genetics #structure software #simulation study #dispersal scenarios #hierarchical structure #genetic markers #AFLP #microsatellite #population samples
Species boundaries, phylogeography and conservation genetics of the red‐legged frog (<i>Rana aurora/draytonii</i>) complex Abstract The red‐legged frog, Rana aurora , has been recognized as both a single, polytypic species and as two distinct species since its original description 150 years ago. It is currently recognized as one species with two geographically contiguous subspecies, aurora and draytonii ; the latter is protected under the US Endangered Species Act. We present the results of a survey of 50 populations of red‐legged frogs from across their range plus four outgroup species for variation in a phylogenetically informative, ∼400 base pairs (bp) fragment of the mitochondrial cytochrome b gene. Our mtDNA analysis points to several major results. (1) In accord with several other lines of independent evidence, aurora and draytonii are each diagnosably distinct, evolutionary lineages; the mtDNA data indicate that they do not constitute a monophyletic group, but rather that aurora and R. cascadae from the Pacific northwest are sister taxa; (2) the range of the draytonii mtDNA clade extends about 100 km further north in coastal California than was previously suspected, and corresponds closely with the range limits or phylogeographical breaks of several codistributed taxa; (3) a narrow zone of overlap exists in southern Mendocino County between aurora and draytonii haplotypes, rather than a broad intergradation zone; and (4) the critically endangered population of draytonii in Riverside County, CA forms a distinct clade with frogs from Baja California, Mexico. The currently available evidence favours recognition of aurora and draytonii as separate species with a narrow zone of overlap in northern California.
Molecular Ecology - Tập 13 Số 9 - Trang 2667-2677 - 2004
Population genetic structuring of the king weakfish, <i>Macrodon ancylodon</i> (Sciaenidae), in Atlantic coastal waters of South America: deep genetic divergence without morphological change Abstract Phylogeographic patterns in Macrodon ancylodon sampled from 12 locations across all its range were investigated using mitochondrial DNA cytochrome b sequences, and analysed together with patterns of morphometric differentiation. Populations of the North Brazil and the Brazil currents, with warmer waters, form a clade (tropical clade) separated by 23 fixed mutations from the populations that inhabit regions of colder waters influenced by the Brazil and Malvinas currents (subtropical clade). No gene flow exists between the tropical and subtropical clades, and most likely also between the two groups of the tropical clade. Distribution of these clades and groups is correlated with flow of currents and their temperatures, and is facilitated by larval retention and low adult migration. Despite differentiation at the molecular level, fishes analysed from all these current‐influenced regions are morphometrically homogeneous. Throughout its range M. ancylodon inhabits the same, or very similar niche; thus, stabilizing selection probably promotes the retention of highly conserved morphology despite deep genetic divergence at the mitochondrial DNA cytochrome b.
Molecular Ecology - Tập 15 Số 14 - Trang 4361-4373 - 2006
Evolutionary genetics and biogeographic structure of <i>Rhizobium gallicum sensu lato</i>, a widely distributed bacterial symbiont of diverse legumes Abstract We used phylogenetic and population genetics approaches to evaluate the importance of the evolutionary forces on shaping the genetic structure of Rhizobium gallicum and related species. We analysed 54 strains from several populations distributed in the Northern Hemisphere, using nucleotide sequences of three ‘core’ chromosomal genes (rrs , glnII and atpD ) and two ‘auxiliary’ symbiotic genes (nifH and nodB ) to elucidate the biogeographic history of the species and symbiotic ecotypes (biovarieties) within species. The analyses revealed that strains classified as Rhizobium mongolense and Rhizobium yanglingense belong to the chromosomal evolutionary lineage of R. gallicum and harbour symbiotic genes corresponding to a new biovar; we propose their reclassification as R . gallicum bv. orientale . The comparison of the chromosomal and symbiotic genes revealed evidence of lateral transfer of symbiotic information within and across species. Genetic differentiation analyses based on the chromosomal protein‐coding genes revealed a biogeographic pattern with three main populations, whereas the 16S rDNA sequences did not resolve that biogeographic pattern. Both the phylogenetic and population genetic analyses showed evidence of recombination at the rrs locus. We discuss our results in the light of the contrasting views of bacterial species expressed by microbial taxonomist and evolutionary biologists.
Molecular Ecology - Tập 14 Số 13 - Trang 4033-4050 - 2005
Ecological specialization of the aphid <i>Aphis gossypii</i> Glover on cultivated host plants Abstract Many plant‐feeding insect species considered to be polyphagous are in fact composed of genetically differentiated sympatric populations that use different hosts and between which gene flow still exists. We studied the population genetic structure of the cotton‐melon aphid Aphis gossypii that is considered as one of the most polyphagous aphid species. We used eight microsatellites to analyse the genetic diversity of numerous samples of A. gossypii collected over several years at a large geographical scale on annual crops from different plant families. The number of multilocus genotypes detected was extremely low and the genotypes were found to be associated with host plants. Five host races were unambiguously identified (Cucurbitaceae, cotton, eggplant, potato and chili‐ or sweet pepper). These host races were dominated by asexual clones. Plant transfer experiments using several specialized clones further confirmed the existence of host‐associated trade‐offs. Finally, both genetic and experimental data suggested that plants of the genus Hibiscus may be used as refuge for the specialized clones. Resource abundance is discussed as a key factor involved in the process of ecological specialization in A. gossypii.
Molecular Ecology - Tập 18 Số 10 - Trang 2198-2212 - 2009
Variation in clonal diversity in glasshouse infestations of the aphid, <i>Aphis gossypii</i> Glover in southern France Abstract Aphis gossypii is an aphid species that is found throughout the world and is extremely polyphagous. It is considered a major pest of cotton and cucurbit species. In Europe, A. gossypii is assumed to reproduce exclusively by apomictic parthenogenesis. The present study investigates the genetic diversity of A. gossypii in a microgeographic, fragmented habitat consisting of eight glasshouses of cucurbit crops. This analysis, which was based on the results from seven microsatellite loci, has confirmed that A. gossypii populations in southern France are primarily asexual, as only 12 nonrecombinant genotypic classes (clones) were identified from 694 aphids. Moreover, a high proportion of the aphids (87%) had one of three common genotypes. No significant correlation was found between genotypic class and host plant species. Within a glasshouse population of A. gossypii , a significant reduction in clonal diversity was observed as the spring/summer season progressed. The final predominance of a clone could result from interclonal competition. At the microgeographic level (i.e. glasshouses within a 500‐m radius), significant genetic subdivision was detected and could be attributed to founder effects and the limitation of gene flow imposed by the enclosed nature of the glasshouse structure. Finally, the three common clones of A. gossypii detected in 1996 reappeared in spring 1997 following the winter extinction, together with rare clones that had not previously been seen. The probability that A. gossypii overwinters within refuges at a microgeographic scale from which populations are renewed each spring is discussed.
Molecular Ecology - Tập 8 Số 11 - Trang 1867-1877 - 1999
Genomic reaction norms: using integrative biology to understand molecular mechanisms of phenotypic plasticity Abstract Phenotypic plasticity is the development of different phenotypes from a single genotype, depending on the environment. Such plasticity is a pervasive feature of life, is observed for various traits and is often argued to be the result of natural selection. A thorough study of phenotypic plasticity should thus include an ecological and an evolutionary perspective. Recent advances in large‐scale gene expression technology make it possible to also study plasticity from a molecular perspective, and the addition of these data will help answer long‐standing questions about this widespread phenomenon. In this review, we present examples of integrative studies that illustrate the molecular and cellular mechanisms underlying plastic traits, and show how new techniques will grow in importance in the study of these plastic molecular processes. These techniques include: (i) heterologous hybridization to DNA microarrays; (ii) next generation sequencing technologies applied to transcriptomics; (iii) techniques for studying the function of noncoding small RNAs; and (iv) proteomic tools. We also present recent studies on genetic model systems that uncover how environmental cues triggering different plastic responses are sensed and integrated by the organism. Finally, we describe recent work on changes in gene expression in response to an environmental cue that persist after the cue is removed. Such long‐term responses are made possible by epigenetic molecular mechanisms, including DNA methylation. The results of these current studies help us outline future avenues for the study of plasticity.
Molecular Ecology - Tập 18 Số 18 - Trang 3763-3780 - 2009
Whole Transcriptome Analysis of the Coral <i>Acropora millepora</i> Reveals Complex Responses to CO<sub>2</sub>‐driven Acidification during the Initiation of Calcification Abstract The impact of ocean acidification (OA) on coral calcification, a subject of intense current interest, is poorly understood in part because of the presence of symbionts in adult corals. Early life history stages of Acropora spp. provide an opportunity to study the effects of elevated CO2 on coral calcification without the complication of symbiont metabolism. Therefore, we used the Illumina RNAseq approach to study the effects of acute exposure to elevated CO2 on gene expression in primary polyps of Acropora millepora , using as reference a novel comprehensive transcriptome assembly developed for this study. Gene ontology analysis of this whole transcriptome data set indicated that CO2 ‐driven acidification strongly suppressed metabolism but enhanced extracellular organic matrix synthesis, whereas targeted analyses revealed complex effects on genes implicated in calcification. Unexpectedly, expression of most ion transport proteins was unaffected, while many membrane‐associated or secreted carbonic anhydrases were expressed at lower levels. The most dramatic effect of CO2 ‐driven acidification, however, was on genes encoding candidate and known components of the skeletal organic matrix that controls CaCO3 deposition. The skeletal organic matrix effects included elevated expression of adult‐type galaxins and some secreted acidic proteins, but down‐regulation of other galaxins, secreted acidic proteins, SCRiPs and other coral‐specific genes, suggesting specialized roles for the members of these protein families and complex impacts of OA on mineral deposition. This study is the first exhaustive exploration of the transcriptomic response of a scleractinian coral to acidification and provides an unbiased perspective on its effects during the early stages of calcification.
Molecular Ecology - Tập 21 Số 10 - Trang 2440-2454 - 2012
Environmentally induced phenotypes and DNA methylation: how to deal with unpredictable conditions until the next generation and after Abstract Organisms often respond to environmental changes by producing alternative phenotypes. Epigenetic processes such as DNA methylation may contribute to environmentally induced phenotypic variation by modifying gene expression. Changes in DNA methylation, unlike DNA mutations, can be influenced by the environment; they are stable at the time scale of an individual and present different levels of heritability. These characteristics make DNA methylation a potentially important molecular process to respond to environmental change. The aim of this review is to present the implications of DNA methylation on phenotypic variations driven by environmental changes. More specifically, we explore epigenetic concepts concerning phenotypic change in response to the environment and heritability of DNA methylation, namely the Baldwin effect and genetic accommodation. Before addressing this point, we report major differences in DNA methylation across taxa and the role of this modification in producing and maintaining environmentally induced phenotypic variation. We also present the different methods allowing the detection of methylation polymorphism. We believe this review will be helpful to molecular ecologists, in that it highlights the importance of epigenetic processes in ecological and evolutionary studies.
Molecular Ecology - Tập 19 Số 7 - Trang 1283-1295 - 2010
Historical and contemporary factors shape the population genetic structure of the broadcast spawning coral, Acropora millepora, on the Great Barrier Reef
Molecular Ecology - Tập 20 Số 23 - Trang 4899-4914 - 2011
Tổng số: 187
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