Evolutionary consequences of autopolyploidy Parisod, Christian; Holderegger, Rolf; Brochmann, Christian
The New phytologist,
April 2010, Volume:
186, Issue:
1
Journal Article
Peer reviewed
Open access
Autopolyploidy is more common in plants than traditionally assumed, but has received little attention compared with allopolyploidy. Hence, the advantages and disadvantages of genome doubling per se ...compared with genome doubling coupled with hybridizations in allopolyploids remain unclear. Autopolyploids are characterized by genomic redundancy and polysomic inheritance, increasing effective population size. To shed light on the evolutionary consequences of autopolyploidy, we review a broad range of studies focusing on both synthetic and natural autopolyploids encompassing levels of biological organization from genes to evolutionary lineages. The limited evidence currently available suggests that autopolyploids neither experience strong genome restructuring nor wide reorganization of gene expression during the first generations following genome doubling, but that these processes may become more important in the longer term. Biogeographic and ecological surveys point to an association between the formation of autopolyploid lineages and environmental change. We thus hypothesize that polysomic inheritance may provide a short-term evolutionary advantage for autopolyploids compared to diploid relatives when environmental change enforces range shifts. In addition, autopolyploids should possess increased genome flexibility, allowing them to adapt and persist across heterogeneous landscapes in the long run.
Roads exert various effects of conservation concern. They cause road mortality of wildlife, change the behaviour of animals and lead to habitat fragmentation. Roads also have genetic effects, as they ...restrict animal movement and increase the functional isolation of populations. We first formulate theoretical expectations on the genetic effects of roads with respect to a decrease in genetic diversity and an increase in genetic differentiation or distance of populations or individuals. We then review the empirical evidence on the genetic effects of roads based on the available literature. We found that roads often, but not always, decrease the genetic diversity of affected populations due to reduced population size and genetic drift. Whether the reduction in genetic diversity influences the long-term fitness of affected populations is, however, not yet clear. Roads, especially fenced highways, also act as barriers to movement, migration and gene flow. Roads therefore often decrease functional connectivity and increase the genetic differentiation of populations or the genetic distance among individuals. Nevertheless, roads and highways rarely act as complete barriers as shown by genetic studies assessing contemporary migration across roads (by using assignment tests). Some studies also showed that road verges act as dispersal corridors for native and exotic plants and animals. Genetic methods are well suited to retrospectively trace such migration pathways. Most roads and highways have only recently been built. Although only few generations might thus have passed since road construction, our literature survey showed that many studies found negative effects of roads on genetic diversity and genetic differentiation in animal species, especially for larger mammals and amphibians. Roads may thus rapidly cause genetic effects. This result stresses the importance of defragmentation measures such as over- and underpasses or wildlife bridges across roads.
Straßen üben verschiedene Effekte aus, die für den Naturschutz von Bedeutung sind. Straßen verursachen den Straßentod von Tieren, verändern deren Verhalten und führen zu Habitatfragmentierung. Da Straßen die Bewegung von Tieren einschränken und die funktionale Zerschneidung von Populationen hervorrufen, verursachen Straßen auch genetische Effekte. Wir formulieren zuerst theoretische Erwartungen zu den genetischen Effekten von Straßen in Bezug auf eine Verminderung der genetischen Diversität und eine Erhöhung der genetischen Differenzierung oder Distanz zwischen Populationen oder Individuen. Wir geben dann einen Überblick über die empirische Literatur zu den genetischen Effekten von Straßen. Wir zeigen, dass Straßen oft, aber nicht immer, die genetische Diversität von Populationen infolge kleinerer Populationsgröße und erhöhter genetischer Drift vermindern. Ob diese Reduktion der genetischen Diversität längerfristig die Fitness der betroffenen Populationen beeinträchtigt ist allerdings unklar. Straßen, und insbesondere eingezäunte Autobahnen, sind auch Barrieren für Tierbewegungen, Wanderung und Genfluss. Straßen reduzieren oft die funktionale Vernetztheit und erhöhen die genetische Differenzierung von Populationen oder die genetischen Distanz zwischen Individuen. Allerdings wirken Straßen und Autobahnen nur selten als vollständige Barrieren, wie dies genetische Studien zeigen, die die aktuelle Wanderung über Straßen hinweg nachweisen (mittels assignment tests). Einige Studien zeigen zudem, dass Straßenränder als Ausbreitungskorridore für einheimische und exotische Tiere und Pflanzen dienen. Genetische Methoden sind gut geeignet, entsprechende Ausbreitungswege retrospektiv zu erfassen. Die meisten Straßen wurden erst vor kurzer Zeit gebaut. Obwohl deshalb meist nur wenige Generationen seit der Erstellung der Straßen verflossen sind, zeigt unsere Literaturübersicht, dass viele Studien negative Auswirkungen von Straßen auf die genetische Diversität und Differenzierung von Tierarten fanden, insbesondere bei größeren Säugetieren und Amphibien. Straßen führen somit schnell zu genetischen Effekten. Dieses Resultat unterstreicht die Bedeutung von Defragmentierungsmaßnahmen an Straßen wie etwa Durchlässen, Überführungen oder Grünbrücken.
Landscape genomics is an emerging research field that aims to identify the environmental factors that shape adaptive genetic variation and the gene variants that drive local adaptation. Its ...development has been facilitated by next‐generation sequencing, which allows for screening thousands to millions of single nucleotide polymorphisms in many individuals and populations at reasonable costs. In parallel, data sets describing environmental factors have greatly improved and increasingly become publicly accessible. Accordingly, numerous analytical methods for environmental association studies have been developed. Environmental association analysis identifies genetic variants associated with particular environmental factors and has the potential to uncover adaptive patterns that are not discovered by traditional tests for the detection of outlier loci based on population genetic differentiation. We review methods for conducting environmental association analysis including categorical tests, logistic regressions, matrix correlations, general linear models and mixed effects models. We discuss the advantages and disadvantages of different approaches, provide a list of dedicated software packages and their specific properties, and stress the importance of incorporating neutral genetic structure in the analysis. We also touch on additional important aspects such as sampling design, environmental data preparation, pooled and reduced‐representation sequencing, candidate‐gene approaches, linearity of allele–environment associations and the combination of environmental association analyses with traditional outlier detection tests. We conclude by summarizing expected future directions in the field, such as the extension of statistical approaches, environmental association analysis for ecological gene annotation, and the need for replication and post hoc validation studies.
Landscape genetics: where are we now Storfer, Andrew; Murphy, Melanie A; Spear, Stephen F ...
Molecular ecology,
September 2010, Volume:
19, Issue:
17
Journal Article
Peer reviewed
Open access
Landscape genetics has seen rapid growth in number of publications since the term was coined in 2003. An extensive literature search from 1998 to 2008 using keywords associated with landscape ...genetics yielded 655 articles encompassing a vast array of study organisms, study designs and methodology. These publications were screened to identify 174 studies that explicitly incorporated at least one landscape variable with genetic data. We systematically reviewed this set of papers to assess taxonomic and temporal trends in: (i) geographic regions studied; (ii) types of questions addressed; (iii) molecular markers used; (iv) statistical analyses used; and (v) types and nature of spatial data used. Overall, studies have occurred in geographic regions proximal to developed countries and more commonly in terrestrial vs. aquatic habitats. Questions most often focused on effects of barriers and/or landscape variables on gene flow. The most commonly used molecular markers were microsatellites and amplified fragment length polymorphism (AFLPs), with AFLPs used more frequently in plants than animals. Analysis methods were dominated by Mantel and assignment tests. We also assessed differences among journals to evaluate the uniformity of reporting and publication standards. Few studies presented an explicit study design or explicit descriptions of spatial extent. While some landscape variables such as topographic relief affected most species studied, effects were not universal, and some species appeared unaffected by the landscape. Effects of habitat fragmentation were mixed, with some species altering movement paths and others unaffected. Taken together, although some generalities emerged regarding effects of specific landscape variables, results varied, thereby reinforcing the need for species-specific work. We conclude by: highlighting gaps in knowledge and methodology, providing guidelines to authors and reviewers of landscape genetics studies, and suggesting promising future directions of inquiry.
Microsatellite markers are widely used for estimating genetic diversity within and differentiation among populations. However, it has rarely been tested whether such estimates are useful proxies for ...genome-wide patterns of variation and differentiation. Here, we compared microsatellite variation with genome-wide single nucleotide polymorphisms (SNPs) to assess and quantify potential marker-specific biases and derive recommendations for future studies. Overall, we genotyped 180 Arabidopsis halleri individuals from nine populations using 20 microsatellite markers. Twelve of these markers were originally developed for Arabidopsis thaliana (cross-species markers) and eight for A. halleri (species-specific markers). We further characterized 2 million SNPs across the genome with a pooled whole-genome re-sequencing approach (Pool-Seq).
Our analyses revealed that estimates of genetic diversity and differentiation derived from cross-species and species-specific microsatellites differed substantially and that expected microsatellite heterozygosity (SSR-H
) was not significantly correlated with genome-wide SNP diversity estimates (SNP-H
and θ
) in A. halleri. Instead, microsatellite allelic richness (A
) was a better proxy for genome-wide SNP diversity. Estimates of genetic differentiation among populations (F
) based on both marker types were correlated, but microsatellite-based estimates were significantly larger than those from SNPs. Possible causes include the limited number of microsatellite markers used, marker ascertainment bias, as well as the high variance in microsatellite-derived estimates. In contrast, genome-wide SNP data provided unbiased estimates of genetic diversity independent of whether genome- or only exome-wide SNPs were used. Further, we inferred that a few thousand random SNPs are sufficient to reliably estimate genome-wide diversity and to distinguish among populations differing in genetic variation.
We recommend that future analyses of genetic diversity within and differentiation among populations use randomly selected high-throughput sequencing-based SNP data to draw conclusions on genome-wide diversity patterns. In species comparable to A. halleri, a few thousand SNPs are sufficient to achieve this goal.
Studies of genetic adaptation in plant populations along elevation gradients in mountains have a long history, but there has until now been neither a synthesis of how frequently plant populations ...exhibit adaptation to elevation nor an evaluation of how consistent underlying trait differences across species are. We reviewed studies of adaptation along elevation gradients (i) from a meta‐analysis of phenotypic differentiation of three traits (height, biomass and phenology) from plants growing in 70 common garden experiments; (ii) by testing elevation adaptation using three fitness proxies (survival, reproductive output and biomass) from 14 reciprocal transplant experiments; (iii) by qualitatively assessing information at the molecular level, from 10 genomewide surveys and candidate gene approaches. We found that plants originating from high elevations were generally shorter and produced less biomass, but phenology did not vary consistently. We found significant evidence for elevation adaptation in terms of survival and biomass, but not for reproductive output. Variation in phenotypic and fitness responses to elevation across species was not related to life history traits or to environmental conditions. Molecular studies, which have focussed mainly on loci related to plant physiology and phenology, also provide evidence for adaptation along elevation gradients. Together, these studies indicate that genetically based trait differentiation and adaptation to elevation are widespread in plants. We conclude that a better understanding of the mechanisms underlying adaptation, not only to elevation but also to environmental change, will require more studies combining the ecological and molecular approaches.
Issue Title: Special issue on Landscape Genetics Genetic diversity is important for the maintenance of the viability and the evolutionary or adaptive potential of populations and species. However, ...there are two principal types of genetic diversity: adaptive and neutral - a fact widely neglected by non-specialists. We introduce these two types of genetic diversity and critically point to their potential uses and misuses in population or landscape genetic studies. First, most molecular-genetic laboratory techniques analyse neutral genetic variation. This means that the gene variants detected do not have any direct effect on fitness. This type of genetic variation is thus selectively neutral and tells us nothing about the adaptive or evolutionary potential of a population or a species. Nevertheless, neutral genetic markers have great potential for investigating processes such as gene flow, migration or dispersal. Hence, they allow us to empirically test the functional relevance of spatial indices such as connectivity used in landscape ecology. Second, adaptive genetic variation, i.e. genetic variation under natural selection, is analysed in quantitative genetic experiments under controlled and uniform environmental conditions. Unfortunately, the genetic variation (i.e. heritability) and population differentiation at quantitative, adaptive traits is not directly linked with neutral genetic diversity or differentiation. Thus, neutral genetic data cannot serve as a surrogate of adaptive genetic data. In summary, neutral genetic diversity is well suited for the study of processes within landscapes such as gene flow, while the evolutionary or adaptive potential of populations or species has to be assessed in quantitative genetic experiments. Landscape ecologists have to mind these differences between neutral and adaptive genetic variation when interpreting the results of landscape genetic studies.PUBLICATION ABSTRACT
Erratic boulders provide habitat for rock-dwelling species and contribute to the biodiversity of landscapes. In the calcareous Swiss lowlands, siliceous erratic boulders are exclusive habitat islands ...for the regionally critically endangered fern
Asplenium septentrionale
, about 20 bryophyte species and numerous lichens. Focusing on island biogeographical processes, we analysed the conservation genomics of
A. septentrionale
and the moss
Hedwigia ciliata
on insular erratic boulders in the Swiss lowlands and the adjacent “mainland” in siliceous mountains. We genotyped both species using double digest restriction associated DNA sequencing (ddRAD). For the tetraploid
A. septentrionale
, abundant identical multilocus genotypes within populations suggested prevalent intragametophytic selfing, and six out of eight boulder populations consisting of a single multilocus genotype each indicated single spore founder events. The genetic structure of
A. septentrionale
mainland populations coincided with Pleistocene glacial refugia. Four genetic lineages of
H. ciliata
were identified, and populations consisting of a single multilocus genotype were less common than in
A. septentrionale
. For both taxa, multilocus genotype diversity on boulders was lower than in mainland populations. The absence of common genetic groups among boulder populations, and the absence of isolation by distance patterns, suggested colonisation of boulders through independent long-distance dispersal events. Successful boulder colonisation of
A. septentrionale
seems to be rare, while colonisation by
H. ciliata
appears to be more frequent. We conclude that pivotal principles of conservation biology, such as connectivity and genetic diversity, are of less importance for the studied cryptogams on insular erratic boulders because of long-distance dispersal, intragametophytic selfing and polyploidy.
Revisitation studies use historical information from literature or museum collections to assess rates of local extinction. However, revisitation studies suffer from the bias that they can only detect ...decline or stasis relative to the number of historical sites, as newly colonized sites are not detected. This drawback can be avoided with complete resurveys of study areas. We used 100‐year‐old historical information on 99 mountain plants from a 174 km2 area in Switzerland and performed a revisitation study and a complete resurvey. The resurvey was used to determine the magnitude of the bias of revisitation. In the revisitation study, we found an average loss of historical sites of plant species of 51.1% (SE = 3.4%). When sites newly observed in the resurvey were also considered and assumed to represent new colonizations, the average loss in sites declined to 26.8% (SE = 5.7%). However, if newly observed sites were treated as historically overlooked sites the loss of sites was only 45.7% (SE = 3.4%). Our results thus show that revisitation studies can overestimate local extinction, but that the corresponding bias depends on whether newly observed sites are considered as historically overlooked sites or as new colonizations.
Revisitation studies using historical information from literature or museums to assess the rate of local extinction of species suffer from the bias that they can only find decline or stasis in the number of historical sites, while newly colonized sites are not detected. In a study also considering newly colonized sites we show that the bias of revisitation studies can be substantial.
Landscape features exist at multiple spatial and temporal scales, and these naturally affect spatial genetic structure and our ability to make inferences about gene flow. This article discusses how ...decisions about sampling of genotypes (including choices about analytical methods and genetic markers) should be driven by the scale of spatial genetic structure, the time frame that landscape features have existed in their current state, and all aspects of a species' life history. Researchers should use caution when making inferences about gene flow, especially when the spatial extent of the study area is limited. The scale of sampling of the landscape introduces different features that may affect gene flow. Sampling grain should be smaller than the average home-range size or dispersal distance of the study organism and, for raster data, existing research suggests that simplifying the thematic resolution into discrete classes may result in low power to detect effects on gene flow. Therefore, the methods used to characterize the landscape between sampling sites may be a primary determinant for the spatial scale at which analytical results are applicable, and the use of only one sampling scale for a particular statistical method may lead researchers to overlook important factors affecting gene flow. The particular analytical technique used to correlate landscape data and genetic data may also influence results; common landscape-genetic methods may not be suitable for all study systems, particularly when the rate of landscape change is faster than can be resolved by common molecular markers.
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