Abstract：
:Experimental evolution (EE) combined with whole-genome sequencing (WGS) has become a compelling approach to study the fundamental mechanisms and processes that drive evolution. Most EE-WGS studies published to date have used microbes, owing to their ease of propagation and manipulation in the laboratory and relatively small genome sizes. These experiments are particularly suited to answer long-standing questions such as: How many mutations underlie adaptive evolution, and how are they distributed across the genome and through time? Are there general rules or principles governing which genes contribute to adaptation, and are certain kinds of genes more likely to be targets than others? How common is epistasis among adaptive mutations, and what does this reveal about the variety of genetic routes to adaptation? How common is parallel evolution, where the same mutations evolve repeatedly and independently in response to similar selective pressures? Here, we summarize the significant findings of this body of work, identify important emerging trends and propose promising directions for future research. We also outline an example of a computational pipeline for use in EE-WGS studies, based on freely available bioinformatics tools.
journal_name
Mol Ecoljournal_title
Molecular ecologyauthors
Dettman JR,Rodrigue N,Melnyk AH,Wong A,Bailey SF,Kassen Rdoi
10.1111/j.1365-294X.2012.05484.xsubject
Has Abstractpub_date
2012-05-01 00:00:00pages
2058-77issue
9eissn
0962-1083issn
1365-294Xjournal_volume
21pub_type
杂志文章,评审abstract：:Photosynthetic tissues, the major food source of many invertebrates and vertebrates, are well defended. Many defence traits in leaves are controlled via the jasmonate signalling pathway in which jasmonate acts as a hormone by binding to a receptor to activate responses that lead to increased resistance to invertebrate...
journal_title：Molecular ecology
pub_type： 杂志文章
doi：10.1111/j.1365-294X.2012.05533.x
更新日期：2012-05-01 00:00:00
abstract：:The extent to which the gut microbiota may play a role in latitudinal clines of body mass variation (i.e., Bergmann's rule) remains largely unexplored. Here, we collected wild house mice from three latitudinal transects across North and South America and investigated the relationship between variation in the gut micro...
journal_title：Molecular ecology
pub_type： 杂志文章
doi：10.1111/mec.15476
更新日期：2020-06-01 00:00:00
abstract：:Recombination rate is a heritable trait that varies among individuals. Despite the major impact of recombination rate on patterns of genetic diversity and the efficacy of selection, natural variation in this phenotype remains poorly characterized. We present a comparison of genetic maps, sampling 1212 meioses, from a ...
journal_title：Molecular ecology
pub_type： 杂志文章
doi：10.1111/mec.13932
更新日期：2017-01-01 00:00:00
abstract：:Both models and case studies suggest that chromosomal inversions can facilitate adaptation and speciation in the presence of gene flow by suppressing recombination between locally adapted alleles. Until recently, however, it has been laborious and time-consuming to identify and genotype inversions in natural populatio...
journal_title：Molecular ecology
pub_type： 杂志文章
doi：10.1111/mec.15428
更新日期：2020-07-01 00:00:00
abstract：:We evaluate the relative effectiveness of four methods for preserving faecal samples for DNA analysis. PCR assays of fresh faecal samples collected from free-ranging baboons showed that amplification success was dependent on preservation method, PCR-product size, and whether nuclear or mitochondrial DNA was assayed. S...
journal_title：Molecular ecology
pub_type： 杂志文章
doi：10.1046/j.1365-294x.1998.00449.x
更新日期：1998-10-01 00:00:00
abstract：:Island ecosystems provide an opportunity to examine a range of evolutionary and ecological processes. The Chatham Islands are an isolated archipelago situated approximately 800 km east of New Zealand. Geological evidence indicates that the Chatham Islands re-emerged within the last 1-4 million years, following a prolo...
journal_title：Molecular ecology
pub_type： 杂志文章
doi：10.1111/j.1365-294X.2008.03832.x
更新日期：2008-07-01 00:00:00
abstract：:The evolution of reproductive isolation in the presence of gene flow is supported by theoretical models but rarely by data. Empirical support might be gained from studies of parallel hybrid zones between interbreeding taxa. We analysed gene flow over two hybrid zones separating ecotypes of Littorina saxatilis to test ...
journal_title：Molecular ecology
pub_type： 杂志文章
doi：10.1111/j.1365-294X.2006.03067.x
更新日期：2006-11-01 00:00:00
abstract：:The spatial genetic structure of the neotropical, clustered tree species Vouacapoua americana (Aublet) was studied in two natural forest stands (Paracou and Nouragues) in French Guiana. Using eight microsatellite loci, V. americana is characterized by a marked genetic structure at small spatial distances (under 30-60 ...
journal_title：Molecular ecology
pub_type： 杂志文章
doi：10.1046/j.1365-294x.2002.01475.x
更新日期：2002-04-01 00:00:00
abstract：:Conservation programmes aim at maximizing the survival probability of populations, by minimizing the loss of genetic diversity, which allows populations to adapt to changes, and controlling inbreeding increases. The best known strategy to achieve these goals is optimizing the contributions of the parents to minimize g...
journal_title：Molecular ecology
pub_type： 杂志文章
doi：10.1111/mec.12560
更新日期：2013-12-01 00:00:00
abstract：:Most landscape genetic studies assess the impact of landscape elements on species' dispersal and gene flow. Many of these studies perform their analysis on all possible population pairs in a study area and do not explicitly consider the effects of spatial scale and population network topology on their results. Here, w...
journal_title：Molecular ecology
pub_type： 杂志文章
doi：10.1111/mec.12265
更新日期：2013-05-01 00:00:00
abstract：:Mate-choice theory predicts different optimal mating systems depending on resource availability and habitat stability. Regions with limited resources are thought to promote monogamy. We tested predictions of monogamy in a social rodent, the hoary marmot (Marmota caligata), at the northern climatic extreme of its distr...
journal_title：Molecular ecology
pub_type： 杂志文章
doi：10.1111/j.1365-294X.2006.03211.x
更新日期：2007-03-01 00:00:00
abstract：:Crater lakes provide a natural laboratory to study speciation of cichlid fishes by ecological divergence. Up to now, there has been a dearth of transcriptomic and genomic information that would aid in understanding the molecular basis of the phenotypic differentiation between young species. We used next-generation seq...
journal_title：Molecular ecology
pub_type： 杂志文章
doi：10.1111/j.1365-294X.2009.04488.x
更新日期：2010-03-01 00:00:00
abstract：:Parallel evolution and the extent to which it involves gene reuse have attracted much interest. Whereas it has theoretically been predicted under which circumstances gene reuse is expected, empirical studies that directly compare systems showing high and low parallelism are rare. Three-spined stickleback (Gasterosteus...
journal_title：Molecular ecology
pub_type： 杂志文章
doi：10.1111/mec.14782
更新日期：2018-12-01 00:00:00
abstract：:Differential gene flow, reductions in diversity following linked selection and/or features of the genome can structure patterns of genomic differentiation during the process of speciation. Possible sources of reproductive isolation are well studied between coastal and inland subspecies groups of Swainson's thrushes, w...
journal_title：Molecular ecology
pub_type： 杂志文章
doi：10.1111/mec.13150
更新日期：2015-04-01 00:00:00
abstract：:What makes a species able to colonize novel environments? This question is key to understand the dynamics of adaptive radiations and ecological niche shifts, but the mechanisms that underlie expansion into novel habitats remain poorly understood at a genomic scale. Lizards from the genus Anolis are typically tropical,...
journal_title：Molecular ecology
pub_type： 杂志文章
doi：10.1111/mec.15162
更新日期：2019-08-01 00:00:00
abstract：:Many salmonid fish populations have anadromous (i.e. migratory) and nonanadromous individuals co-existing in sympatry. The nonanadromous individuals, frequently males, mature at a much smaller size in freshwater without undergoing marine migrations and often successfully fertilize many eggs laid by anadromous females....
journal_title：Molecular ecology
pub_type： 评论,杂志文章
doi：10.1111/mec.12222
更新日期：2013-05-01 00:00:00
abstract：:Swordtails (Xiphophorus; Poeciliidae) have figured prominently in research on fish mating behaviours, sexual selection, and carcinogenesis, but their population structures and dispersal patterns have been relatively neglected. Using nine microsatellite loci, we estimated genetic differentiation in Xiphophorus helleri ...
journal_title：Molecular ecology
pub_type： 杂志文章
doi：10.1111/j.1365-294X.2009.04464.x
更新日期：2010-01-01 00:00:00
abstract：:Mutation rates at microsatellites tend to increase with the number of repeats of the motif, leading to higher levels of polymorphism at long microsatellites. To standardize levels of diversity when microsatellites differ in size, we investigate the relationship between tract length and variation and provide a formula ...
journal_title：Molecular ecology
pub_type： 杂志文章
doi：10.1111/j.1365-294X.2005.02446.x
更新日期：2005-03-01 00:00:00
abstract：:Adaptive radiations provide unique opportunities to test whether and how recent ecological and evolutionary diversification of host species structures the composition of entire bacterial communities. We used 16S rRNA gene sequencing of faecal samples to test for differences in the gut microbiota of six species of Puer...
journal_title：Molecular ecology
pub_type： 杂志文章
doi：10.1111/mec.13796
更新日期：2016-10-01 00:00:00
abstract：:Reproducibility is the benchmark for results and conclusions drawn from scientific studies, but systematic studies on the reproducibility of scientific results are surprisingly rare. Moreover, many modern statistical methods make use of 'random walk' model fitting procedures, and these are inherently stochastic in the...
journal_title：Molecular ecology
pub_type： 杂志文章
doi：10.1111/j.1365-294X.2012.05754.x
更新日期：2012-10-01 00:00:00
abstract：:Genome reduction is a general process that has been studied in numerous symbiotic bacteria associated with insects. We investigated the last stages of genome degradation in Blochmannia floridanus, a mutualistic bacterial endosymbiont of the ant Camponotus floridanus. We determined the tempo (rates of insertion and del...
journal_title：Molecular ecology
pub_type： 杂志文章
doi：10.1111/j.1365-294x.2008.03912.x
更新日期：2008-10-01 00:00:00
abstract：:The seemingly eternal cycles of clonal growth in many tree species, with members of Populus (aspen, poplars, cottonwoods and the like) featuring most prominently, provoke a number of questions on the interface between ecology, genetics and forestry. In this issue, two groups present their approaches to clonal dynamics...
journal_title：Molecular ecology
pub_type： 杂志文章
doi：10.1111/j.1365-294X.2008.03964.x
更新日期：2008-11-01 00:00:00
abstract：:Threespine stickleback populations are model systems for studying adaptive evolution and the underlying genetics. In lakes on the Haida Gwaii archipelago (off western Canada), stickleback have undergone a remarkable local radiation and show phenotypic diversity matching that seen throughout the species distribution. T...
journal_title：Molecular ecology
pub_type： 杂志文章
doi：10.1111/mec.12215
更新日期：2013-04-01 00:00:00
abstract：:Episodes of trans-Arctic faunal exchange and isolation between the north Pacific and Atlantic ocean basins have been implicated as important historic geological events contributing to extant patterns of genetic diversity and structure in Holarctic faunas. We made a further test of the significance of such biogeographi...
journal_title：Molecular ecology
pub_type： 杂志文章
doi：10.1111/j.1365-294x.1994.tb00057.x
更新日期：1994-06-01 00:00:00
abstract：:Reproductive skew - the extent to which reproduction is unevenly shared between individuals in a social group - varies greatly between and within animal species. In this study, we investigated how queens share parentage in polygynous (multiple queen) colonies of the Mediterranean ant Pheidole pallidula. We used highly...
journal_title：Molecular ecology
pub_type： 杂志文章
doi：10.1046/j.1365-294x.2003.02036.x
更新日期：2004-01-01 00:00:00
abstract：:Population studies have revealed that the fungal ectomycorrhizal morphospecies Tricholoma scalpturatum consists of at least two genetically distinct groups that occur sympatrically in several geographical areas. This discovery prompted us to examine species boundaries and relationships between members formerly assigne...
journal_title：Molecular ecology
pub_type： 杂志文章
doi：10.1111/j.1365-294X.2010.04863.x
更新日期：2010-12-01 00:00:00
abstract：:Homologous recombination between bacterial strains is theoretically capable of preventing the separation of daughter clusters, and producing cohesive clouds of genotypes in sequence space. However, numerous barriers to recombination are known. Barriers may be essential such as adaptive incompatibility, or ecological, ...
journal_title：Molecular ecology
pub_type： 杂志文章
doi：10.1111/mec.12742
更新日期：2014-05-01 00:00:00
abstract：:Black rats are major invasive vertebrate pests with severe ecological, economic and health impacts. Remarkably, their evolutionary history has received little attention, and there is no firm agreement on how many species should be recognized within the black rat complex. This species complex is native to India and Sou...
journal_title：Molecular ecology
pub_type： 杂志文章
doi：10.1111/mec.12149
更新日期：2013-02-01 00:00:00
abstract：:Chloroplast DNA (cpDNA) restriction site and isozyme data were combined to explore the spatial-temporal influence of the Messinian desiccation in the Mediterranean on the disjunct distribution of Androcymbium gramineum in Almería and Morocco (north and south of the straits of Gibraltar, respectively). Lack of evidence...
journal_title：Molecular ecology
pub_type： 杂志文章
doi：10.1046/j.1365-294x.2003.01839.x
更新日期：2003-06-01 00:00:00
abstract：:MtDNA sequencing was used to investigate the genetic population structure of Litoria pearsoniana, a wet forest-restricted hylid frog, endemic to southeast Queensland and northeast New South Wales, Australia. L. pearsoniana is regarded as endangered under Queensland legislation. Significant genetic divergence among pop...
journal_title：Molecular ecology
pub_type： 杂志文章
doi：10.1046/j.1365-294x.1998.00329.x
更新日期：1998-02-01 00:00:00
