Can we stop transgenes from taking a walk on the wild side?

Whether the potential costs associated with broad‐scale use of genetically modified organisms (GMOs) outweigh possible benefits is highly contentious, including within the scientific community. Even among those generally in favour of commercialization of GM crops, there is nonetheless broad recognition that transgene escape into the wild should be minimized. But is it possible to achieve containment of engineered genetic elements in the context of large scale agricultural production? In a previous study, Warwick et al. (2003) documented transgene escape via gene flow from herbicide resistant (HR) canola (Brassica napus) into neighbouring weedy B. rapa populations ( Fig. 1 ) in two agricultural fields in Quebec, Canada. In a follow‐up study in this issue of Molecular Ecology, Warwick et al. (2008) show that the transgene has persisted and spread within the weedy population in the absence of selection for herbicide resistance. Certainly a trait like herbicide resistance is expected to spread when selected through the use of the herbicide, despite potentially negative epistatic effects on fitness. However, Warwick et al.'s findings suggest that direct selection favouring the transgene is not required for its persistence. So is there any hope of preventing transgene escape into the wild?

Figure 1 Open in figure viewer PowerPoint Weedy Brassica rapa (orange flags) growing in a B. napus field. (Photo: MJ Simard)     

Heritability not missing—genetic basis of sexual weaponry uncovered

The chase to uncover the genetic underpinnings of quantitative traits of ecological and evolutionary importance has been on for a good while. However, the potential power of genome‐wide association studies (GWAS) as an approach to identify genes of interest in wild animal populations has remained untapped. Setting technical and economic explanations aside, the sobering lack of success in human GWAS might have fed this restraint. Namely, while GWAS have successfully identified genetic variants associated with hundreds of complex traits (e.g. Ku et al. 2010 ), these variants have generally captured only a low percentage of variance in traits known to be highly heritable—an observation came to be known as the ‘missing heritability’ ( Maher 2008 ; Aulchenko et al. 2009 ). Hence, if the vastly resourced human studies have been unsuccessful (but see: Yang et al. 2010 ), why should we expect that less resourced studies of wild animal populations would be able do better? In this issue of Molecular Ecology, Johnston et al. (2011) prove this line of thinking wrong. In an impressive and what may well be the most advanced gene mapping study ever performed in a wild population, they identify a single locus (RXFP2) responsible for explaining horn phenotype in feral domestic sheep from St Kilda ( Fig. 1 ). This same locus is also shown to account for up to 76% of additive genetic variance in horn size in male sheep: this contrasts sharply with most human GWAS where mapped loci explain only a modest proportion of genetic variation in a given trait.

Figure 1 Open in figure viewer PowerPoint The Soay sheep of the St Kilda archipelago are a primitive feral breed of domestic sheep. Pictured are a male with vestigial horns (=‘scurred’; left) and two normal‐horned males (centre and right). Photograph courtesy of Peter Korsten.     

Triangulating the genetic basis of adaptation to multifarious selection

Understanding how natural populations adapt to their local environments is a major research theme for ecological genomics. This endeavour begins by sleuthing for shared genetic similarities among unrelated natural populations sharing adaptive traits to documented selective pressures. When the selective pressures have low dimensionality, and the genetic response is localized to a few genes of major effect, this detective work is relatively straightforward. However, in the real world, populations face a complex mixture of selective pressures and many adaptive responses are the result of changes in quantitative traits that have a polygenic genetic basis. This complex relationship between environment and adaptation presents a significant challenge. How can we begin to identify drivers of adaptation in natural settings? In this issue of Molecular Ecology, Orsini et al. (2012) take advantage of the biological attributes of the freshwater microcrustacean Daphnia ( Fig. 1 ) to disentangle multidimensional selection’s signature on the genome of populations that have repeatedly evolved adaptive responses to isolated selective pressures including predation, parasitism and anthropogenic changes in land use. Orsini et al. (2012) leverage a powerful combination of spatially structured populations in a geographic mosaic of environmental stressors, the historical archive of past genotypes preserved in lake‐bottom sediments and selection experiments to identify sets of candidate genomic regions associated with adaptation in response to these three environmental stressors. This study provides a template for future investigation in ecological genomics, combining multiple experimental approaches with the genomic investigation of a well‐studied ecological model species.

Figure 1 Open in figure viewer PowerPoint Adult Daphnia magna carrying a resting egg in the brood pouch. The water flea Daphnia is a renowned ecological model system and rapidly developing as an ecological and environmental genomics model species. Photo credit Joachim Mergeay.     

Evolutionary, behavioural and molecular ecology must meet to achieve long-term conservation goals

Founder populations in reintroduction programmes can experience a genetic bottleneck simply because of their small size. The influence of reproductive skew brought on by polygynous or polyandrous mating systems in these populations can exacerbate already difficult conservation genetic problems, such as inbreeding depression and loss of adaptive potential. Without an understanding of reproductive skew in a target species, and the effect it can have on genetic diversity retained over generations, long‐term conservation goals will be compromised. In this issue of Molecular Ecology, Miller et al. (2009a) test how founder group size and variance in male reproductive success influence the maintenance of genetic diversity following reintroduction on a long‐term scale. They evaluated genetic diversity in two wild populations of the iconic New Zealand tuatara ( Fig. 1 ), which differ greatly in population size and genetic diversity, and compared this to genetic diversity in multiple founder populations sourced from both populations. Population viability analysis on the maintenance of genetic diversity over 400 years (10 generations) demonstrated that while the loss of heterozygosity was low when compared with both source populations (1–14%), the greater the male reproductive skew, the greater the predicted losses of genetic diversity. Importantly however, the loss of genetic diversity was ameliorated after population size exceeded 250 animals, regardless of the level of reproductive skew. This study demonstrates that highly informed conservation decisions could be made when you build on a solid foundation of demographic, natural history and behavioural ecology data. These data, when informed by modern population and genetic analysis, mean that fundamental applied conservation questions (how many animals should make up a founder population?) can be answered accurately and with an eye to the long‐term consequences of management decisions.

Figure 1 Open in figure viewer PowerPoint Large adult male tuatara attacking a smaller male. Photo by Jeanine Refsnider.     

The memory remains: application of historical DNA for scaling biodiversity loss

Few species worldwide have attracted as much attention in relation to conservation and sustainable management as Pacific salmon. Most populations have suffered significant reductions, many have disappeared, and even entire evolutionary significant units (ESUs) are believed to have been lost. Until now, no ‘smoking gun’ in terms of direct genetic evidence of the loss of a salmon ESU has been produced. In this issue of Molecular Ecology, Iwamoto et al. (2012) use microsatellite analysis of historical scale samples of Columbia River sockeye salmon (Oncorhynchus nerka) from 1924 ( Fig. 1 ) to ask the pertinent question: Do the historical samples contain salmon from extirpated populations or ESUs? They identified four genetic groups in the historical samples of which two were almost genetically identical to contemporary ESUs in the river, one showed genetic relationship with a third ESU, but one group was not related to any of the contemporary populations. In association with ecological data, the genetic results suggest that an early migrating Columbia River headwater sockeye salmon ESU has been extirpated. The study has significant importance for conservation and reestablishment of sockeye populations in the Columbia River, but also underpins the general significance of shifting baselines in conservation biology, and how to assess loss of genetic biodiversity. The results clearly illustrate the huge and versatile potential of using historical DNA in population and conservation genetics. Because of the extraordinarily plentiful historical samples and rapid advances in fish genomics, fishes are likely to spearhead future studies of temporal ecological and population genomics in non‐model organisms.

Figure 1 Open in figure viewer PowerPoint (a) Kokanee sampling site between Columbia and Windermere lakes on the upper Columbia River at Fairmont Hot Springs, British Columbia, Canada. (b) Bureau of Fisheries scale books that contained sockeye salmon (locally called ‘blueback’ salmon) scales collected from commercial fisheries during the 1920s in the lower Columbia River. (c) Kokanee on spawning beds in Kuskanax Creek, a tributary to Upper Arrow Lake, British Columbia. Photo credit Rick Gustafson and Jim Myers.     

Assessing the impact of stocking northern-origin hatchery brook trout on the genetics of wild populations in North Carolina

The release of hatchery-origin fish into streams with endemics can degrade the genetics of wild populations if interbreeding occurs. Starting in the 1800s, brook trout descendent from wild populations in the northeastern United States were stocked from hatcheries into streams across broad areas of North America to create and enhance fishery resources. Across the southeastern United States, many millions of hatchery-origin brook trout have been released into hundreds of streams, but the extent of introgression with native populations is not well resolved despite large phylogeographic distances between these groups. We used three assessment approaches based on 12 microsatellite loci to examine the extent of hatchery introgression in 406 wild brook trout populations in North Carolina. We found high levels of differentiation among most collections (mean F′_ST = 0.718), and among most wild collections and hatchery strains (mean F′_ST = 0.732). Our assessment of hatchery introgression was consistent across the three metrics, and indicated that most wild populations have not been strongly influenced by supplemental stocking. However, a small proportion of wild populations in North Carolina appear to have been strongly influenced by stocked conspecifics, or in some cases, may have been founded entirely by hatchery lineages. In addition, we found significant differences in the apparent extent of hatchery introgression among major watersheds, with the Savannah River being the most strongly impacted. Conversely, populations in the Pee Dee River watershed showed little to no evidence of hatchery introgression. Our study represents the first large-scale effort to quantify the extent of hatchery introgression across brook trout populations in the southern Appalachians using highly polymorphic microsatellite markers.     

Revolution in food web analysis and trophic ecology: diet analysis by DNA and stable isotope analysis

Characterization of energy flow in ecosystems is one of the primary goals of ecology, and the analysis of trophic interactions and food web dynamics is key to quantifying energy flow. Predator‐prey interactions define the majority of trophic interactions and food web dynamics, and visual analysis of stomach, gut or fecal content composition is the technique traditionally used to quantify predator‐prey interactions. Unfortunately such techniques may be biased and inaccurate due to variation in digestion rates ( Sheppard & Hardwood 2005 ); however, those limitations can be largely overcome with new technology. In the last 20 years, the use of molecular genetic techniques in ecology has exploded ( King et al. 2008 ). The growing availability of molecular genetic methods and data has fostered the use of PCR‐based techniques to accurately distinguish and identify prey items in stomach, gut and fecal samples. In this month’s issue of Molecular Ecology Resources, Corse et al. (2010) describe and apply a new approach to quantifying predator‐prey relationships using an ecosystem‐level genetic characterization of available and consumed prey in European freshwater habitats ( Fig. 1a ). In this issue of Molecular Ecology, Hardy et al. (2010) marry the molecular genetic analysis of prey with a stable isotope (SI) analysis of trophic interactions in an Australian reservoir community ( Fig. 1b ). Both papers demonstrate novel and innovative approaches to an old problem – how do we effectively explore food webs and energy movement in ecosystems?

Figure 1 Open in figure viewer PowerPoint The aquatic habitats used for two studies of diet and trophic interactions that employed molecular genetic and stable isotope analyses. Panel a: Example of Rhone basin habitat (France) where fish diet was determined using PCR to classify prey to a series of ecological clades (photo by Emmanuel Corse). Panel b: A weir pool on the lower Murray River (Australia) where food web and prey use was evaluated using a combination of advanced molecular genetic and stable isotope analyses (photo credit: CSIRO).     

Introgression variability among Iberian brown trout Evolutionary Significant Units: the influence of local management and environmental features

1. A comprehensive analysis was carried out on the effects of stocking on the genetic structure of Iberian brown trout evolutionary lineages. Introgression and genetic diversity were estimated from allozyme results of 307 populations based on own data (180) and available literature (127). Stocking records, angling regulations and environmental features related to hatchery trout performance were also analysed to determine the underlying mechanisms of the introgression effects. 2. Fifty per cent of analysed populations showed introgression by genes of hatchery origin. The mean introgression estimated by the single locus approach was 0.134. An increment of both heterozygosity and polymorphism was observed when introgression increased in stream‐dwelling populations, which could finally produce a homogenisation of the genetic structure of populations and a decrease of the species’ genetic diversity. 3. Introgression rate varied among Iberian evolutionary lineages (Evolutionary Significant Units), and was correlated with the stocking effort, except for the North Atlantic basins. The lack of adaptations for migratory behaviour in hatchery trout could explain the low impact of stocking in North Atlantic rivers where anadromous populations occur. 4. Angling regulation did not seem to influence the survival of hatchery trout. Introgression tends to be higher in heavily stocked localities with fertile waters and stable discharge, which may favour the performance of hatchery trout. 5. Trout management must be based on increasing population size by means of habitat improvement and sustainability of naturally reproducing wild stocks through appropriate angling regulations.     

Population genetic structure and ancestry of steelhead/rainbow trout (<Emphasis Type="Italic">Oncorhynchus mykiss</Emphasis>) at the extreme southern edge of their range in North America

Steelhead (Oncorhynchus mykiss) populations have declined dramatically in many parts of their range in North America, most critically in Southern California, where these anadromous trout are now classified as ‘Endangered’ under the United States Endangered Species Act. The widespread introduction of hatchery rainbow trout, the domesticated freshwater resident form of the species O. mykiss, is one factor threatening the long-term persistence of native steelhead and other trout populations. To identify where native fish of coastal steelhead lineage remained, we performed a population genetic analysis of microsatellite and SNP genotypes from O. mykiss populations at the extreme southern end of their range in Southern California, USA and Baja California, Mexico. In the northern part of this region, nearly all populations appeared to be primarily descendants of native coastal steelhead. However, in the southern, more urbanized part of this region, the majority of the sampled populations were derived primarily from hatchery trout, indicating either complete replacement of native fish or a strong signal of introgression overlaying native ancestry. Nevertheless, these genetically introgressed populations represent potentially critical genetic resources for the continued persistence of viable networks of O. mykiss populations, given the limited native ancestry uncovered in this region and the importance of genetic variation in adaptation. This study elucidates the geographic distribution of native trout populations in this region, and serves as a baseline for evaluating the impacts of hatchery trout on native O. mykiss populations and the success of steelhead conservation and recovery efforts.     

Butterfly genomics sheds light on the process of hybrid speciation

How common is hybridization between species and what effect does it have on the evolutionary process? Can hybridization generate new species and what indeed is a species? In this issue, Gompert et al. (2014) show how massive, genome‐scale data sets can be used to shed light on these questions. They focus on the Lycaeides butterflies, and in particular, several populations from the western USA, which have characteristics suggesting that they may contain hybrids of two or more different species (Gompert et al. 2006). They demonstrate that these populations do contain mosaic genomes made up of components from different parental species. However, this appears to have been largely driven by historical admixture, with more recent processes appearing to be isolating the populations from each other. Therefore, these populations are on their way to becoming distinct species (if they are not already) but have arisen following extensive hybridization between other distinct populations or species (Fig.  1 ).

Figure 1 Open in figure viewer PowerPoint There has been extensive historical admixture between Lycaeides species with some new species arising from hybrid populations. (Photo credits: Lauren Lucas, Chris Nice, and James Fordyce).

Their data set must be one of the largest outside of humans, with over one and half thousand butterflies genotyped at over 45 thousand variable nucleotide positions. It is this sheer amount of data that has allowed the researchers to distinguish between historical and more recent evolutionary and demographic processes. This is because it has allowed them to partition the data into common and rare genetic variants and perform separate analyses on these. Common genetic variants are likely to be older while rare variants are more likely to be due to recent mutations. Therefore, by splitting the genetic variation into these components, the researchers were able to show more admixture among common variants, while rare variants showed less admixture and clear separation of the populations. The extensive geographic sampling of individuals, including overlapping distributions of several of the putative species, also allowed the authors to rule out the possibility that the separation of the populations was simply due to geographical distance. The authors have developed a new programme for detecting population structure and admixture, which does the same job as STRUCTURE (Pritchard et al. 2000 ), identifying genetically distinct populations and admixture between these populations, but is designed to be used with next generation sequence data. They use the output of this model for another promising new method to distinguish between contemporary and historical admixtures. They fixed the number of source populations in the model at two and estimated the proportion of each individual's genome coming from these two populations. Therefore, an individual can either be purely population 1, or population 2 or some mixture of the two (they call this value q, the same parameter exists in STRUCTURE). They then compared this to the level of heterozygosity coming from the two source populations in the individual's genome. If an individual is an F1 hybrid of two source populations, then it would have a q of 0.5 and also be heterozygous at all loci that distinguish the parental populations. On the other hand, if it is a member of a stable hybrid lineage, it might also have a q of 0.5 but would not be expected to be heterozygous at these loci, because over time the population would become fixed for one or other of the source population states either by drift or selection (Fig.  2 ). This is indeed what they find in the hybrid populations. They tend to have intermediate q values, but the level of heterozygosity coming from the source populations (which they call Q₁₂) was consistently lower than expected.

Figure 2 Open in figure viewer PowerPoint The Q‐matrix analysis used by Gompert et al. ( 2014 ) to distinguish between contemporary (hybrid swarm) and historical (stable hybrid lineage) admixture.

Overall, the results support several of the populations as being stable hybrid lineages. Nevertheless, the strictest definitions of hybrid species specify that the process of hybridization between the parental species must be instrumental in driving the reproductive isolation of the new species from both parental populations (Abbott et al. 2013 ). This is extremely hard to demonstrate conclusively because it requires us to first of all identify the isolating mechanisms that operated in the early evolution of the species and then to show that these were caused by the hybridization event itself. One advantage of the Lycaeides system is that the species appear to be in the early stages of divergence, so barriers to gene flow that are operating currently are likely to be those that are driving the species divergence. While there is some evidence that hybridization gave rise to traits that allowed the new populations to colonize new environments (Gompert et al. 2006 ; Lucas et al. 2008 ), there is clearly further work to be carried out in this direction. One of the rare examples of homoploid hybrid speciation (hybrid speciation without a change in chromosome number) where the reproductive isolation criterion has been demonstrated, comes from the Heliconius butterflies. In this case, hybridization of two species has been shown to give rise to a new colour pattern that instantly becomes reproductively isolated from the parental species due to mate preference for that pattern (Mavárez et al. 2006 ). However, while this has become a widely accepted example (Abbott et al. 2013 ), the naturally occurring ‘hybrid species’ in fact has derived most of its genome from one of the parental species, with largely just the colour pattern controlling locus coming from the other parent, a process that has been termed ‘hybrid trait speciation’ (Salazar et al. 2010 ). This distinction is an important one in terms of our understanding of the organization of biological diversity. While hybrid trait speciation will still largely fit the model of a neatly branching evolutionary tree, with perhaps only the region surrounding the single introgressed gene deviating from this model, hybrid species that end up with mosaic genomes, like Lycaeides, will not fit this model when considering the genome as a whole. This distinction also more broadly applies when comparing the patterns of divergence between Heliconius and Lycaeides. These two butterfly genera have been driving forward our understanding of the prevalence and importance of hybridization at the genomic level, but they reveal different ways in which hybridization can influence the organization of biological diversity. Recent work in Heliconius has shown that admixture is extensive and has been ongoing over a large portion of the evolutionary history of species (Martin et al. 2013 ; Nadeau et al. 2013 ). Nevertheless, this has not obscured the clear and robust pattern of a bifurcating evolutionary tree when considering the genome as a whole (Nadeau et al. 2013 ). In contrast in Lycaeides, the genome‐wide phylogeny clearly does not fit a bifurcating tree, resembling more of a messy shrub, with hybrid taxa falling at intermediate positions on the phylogeny (Gompert et al. 2014 ). The extent to which we need to rethink the way we describe and organize biological diversity will depend on the relative prevalence of these different outcomes of hybridization. We are likely to see many more of these types of large sequence data sets for ecologically interesting organisms. Gompert et al. ( 2014 ) show that these data need not only be a quantitative advance, but can also qualitatively change our understanding of the evolutionary history of these organisms. In particular, analysing common and rare genetic variants separately may provide information that would otherwise be missed. The emerging field of ‘speciation genomics’ (Seehausen et al. 2014 ) should follow this lead in developing new ways of making the most of the flood of genomic data that is being generated, but also improve methods for integrating this with field observations and experiments to identify the sources and targets of selection and divergence.

References

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This article was written and figures prepared by N.N. except as specified in the text (photo credits).

Citing Literature

Number of times cited according to CrossRef: 4

• V. Alex Sotola, David S. Ruppel, Timothy H. Bonner, Chris C. Nice, Noland H. Martin, Asymmetric introgression between fishes in the Red River basin of Texas is associated with variation in water quality, Ecology and Evolution, 10.1002/ece3.4901, 9 , 4, (2083-2095), (2019). Wiley Online Library
• Matej Bocek, Dominik Kusy, Michal Motyka, Ladislav Bocak, Persistence of multiple patterns and intraspecific polymorphism in multi-species Müllerian communities of net-winged beetles, Frontiers in Zoology, 10.1186/s12983-019-0335-8, 16 , 1, (2019). Crossref
• Nicola J. Nadeau, Takeshi Kawakami, Population Genomics of Speciation and Admixture, , 10.1007/13836_2018_24, (2018). Crossref
• Amanda Roe, Julian Dupuis, Felix Sperling, Molecular Dimensions of Insect Taxonomy in the Genomics Era, Insect Biodiversity, 10.1002/9781118945568, (547-573), (2017). Wiley Online Library

Volume 23 , Issue 18 September 2014

Pages 4441-4443     

The flickering genes of the last mammoths

Woolly mammoths, Mammuthus primigenius, are arguably the most iconic of the extinct Pleistocene megafauna, and an abundance of large permafrost‐embedded bone and ivory material ( Fig. 1 ) means they were also among the first to yield credible DNA sequences ( Hagelberg et al. 1994 ; Hoss et al. 1994 ). Despite mammoth remains being numerous throughout northern Eurasia and North America, both the earliest and most recent fossils are found in northeast Siberia, with the last known population being confined to Wrangel Island in the Arctic Ocean from around 10,000 years ago until their extinction around 4,000 years ago. The extent to which these Holocene mammoths were descended from the Pleistocene populations of Wrangel Island and the demographic nature of their terminal decline have, until now, remained something of a mystery. In this issue of Molecular Ecology, Nyström et al. (2012) report the first use of autosomal variation to track the decline of the last mammoths and, in doing so, take a significant step towards resolving these questions. The authors genotyped four microsatellite loci in 59 Pleistocene and Holocene mammoths from Wrangel Island and Chukotka in mainland northeastern Siberia and showed that while the Pleistocene‐to‐Holocene transition is associated with a significant reduction in genetic diversity, subsequent levels of variation remain constant until extinction. Such a pattern is somewhat surprising as it indicates that while the last mammoths were confined to only a few Arctic islands, their final extinction on Wrangel Island was not a gradual process resulting from loss of genetic diversity/inbreeding. Instead, it seems they maintained a viable effective population size of around 500 until near their presumably rapid extinction. While the ultimate agent of mammoth extinction remains unknown, the work of Nyström et al. (2012) . suggests that we should be looking for something sudden, like a rapid change in climate/ecology or perhaps the arrival of humans.

Figure 1 Open in figure viewer PowerPoint Sergey Vartanyan during field collection, holding a woolly mammoth tusk found along a river embankment in northeast Siberia (photographer: Diana Solovyeva).     

The nearness of you: the effect of population structure on siring success in a gynodioecious species

Theoretically, both balancing selection and genetic drift can contribute to the maintenance of gender polymorphism within and/or among populations. However, if strong differences exist among genotypes in the quantity of viable gametes they produce, then it is expected that these differences will play an important role in determining the relative frequency of the genotypes and contribute to whether or not such polymorphism is maintained. In this issue, De Cauwer et al. (2010) describe an investigation of gynodioecious wild sea beet, which in addition to containing females, contain two types of hermaphrodites: restored hermaphrodites carrying a cytoplasm that causes pollen sterility and a nuclear gene that restores pollen fertility, and hermaphrodites without the sterilizing cytoplasm. The results show that restored hermaphrodites, who have relatively low pollen viability, achieve disproportionately high siring success simply because of where they are located in a patchy population ( Fig. 1 ). Notably, these individuals tend to be close to females because of the genetics of sex determination. These results indicate that population structure caused by drift processes can have an unexpectedly large effect on the fitness of these low quality hermaphrodites, thereby contributing in the short term to the maintenance of gynodioecy in this population. While these results indicate that population structure caused by drift processes can have a large effect on the relative fitness of genetic variants, whether these effects promote or discourage the maintenance of polymorphism in the long term is still up for debate.

Figure 1 Open in figure viewer PowerPoint A stretch of beach along which wild sea beet can be seen to be growing among the rocks above the splash zone. This linear arrangement enhances the potential for mating success to depend on proximity to other plants (Photo: J.‐F. Arnaud).     

Opening Pandora's box: comparative studies of genetic mating systems reveal reproductive complexity

Genetic analyses of realized reproductive success have fundamentally changed our understanding of mating behaviour in natural systems. While behavioural ecologists have long been interested in what factors influence mating behaviour, early studies were limited to direct observations of matings and thus provided an incomplete picture of reproductive activity. Genetic assessments of parentage have revolutionized the study of reproductive behaviour, revealing that many individuals engage in extra‐pair copulations ( Griffith et al. 2002 ) and that social mating partners frequently invest substantial resources into raising offspring that are unrelated to one or both of them ( Avise et al. 2002 ). While these findings have changed the way we think about reproductive behaviour, most investigations of genetic parentage have been restricted to single populations at a single point in time, obscuring spatial and/or temporal variation in mating behaviour and limiting our ability to determine how environmental changes can lead to shifts in mating strategies. In this issue of Molecular Ecology, Mobley & Jones (2009) compare genetic mating behaviour across five populations of Syngnathus floridae ( Fig. 1 ), a widespread species of pipefish distributed along the Gulf‐ and Atlantic Coasts of North America. The authors document how genetic mating behaviour varies across space in S. floridae and identify correlations between reproductive variation and particular ecological characteristics. Mobley & Jones’ paper is one of an increasing number of studies which address the question of how ecological variables influence mating behaviour, and highlights how our understanding of mating system variation and evolution is likely to expand through the wider application of high‐throughput parentage assessment in a comparative context.

Figure 1 Open in figure viewer PowerPoint A pregnant male dusky pipefish (Syngnathus floridae) in its natural habitat. Photo credit: Joe O’Hop.     

Connecting genetic variation to phenotypic clines

From early allozyme work to recent genome‐wide scans, many studies have reported associations between molecular markers and latitude. These geographic patterns are tantalizing because they hint at the possibility of identifying specific mutations responsible for climatic adaptation. Unfortunately, few studies have done so because these exciting first glances often prove extremely challenging to follow up. Many difficulties can hinder connecting genetic and phenotypic variation in this context, and without such links, distinguishing the action of spatially varying selection from the other evolutionary processes capable of generating these patterns can be quite thorny. Nevertheless, two papers in this issue report excellent progress in overcoming these obstacles and provide persuasive evidence supporting the involvement of specific natural variants in clinal adaptation of Drosophila melanogaster populations ( Fig. 1 ). In the first paper, Paaby et al. (2010) describe replicated allele frequency clines for a coding polymorphism in the Insulin‐like Receptor (InR) gene on two continents, findings that strongly point to selection acting at this locus and that likely reflect life history adaptation. McKechnie et al. (2010) report compelling functional evidence that cis‐regulatory variation in the Dca (drosophila cold acclimation) gene contributes to an adaptive cline in wing size. Notably, these papers employ largely alternative and complementary approaches, and together they exemplify how diverse strategies may be interwoven to draw convincing connections between genotype, phenotype, and evolutionary process.

Figure 1 Open in figure viewer PowerPoint Drosophila melanogaster mating in the field. Credit: Annalise Paaby.     

The relative role of relatives in conspecific brood parasitism

Conspecific brood parasites lay their eggs in the nests of other females in the same population, leading to a fascinating array of possible ‘games’ among parasites and their hosts ( Davies 2000 ; Lyon & Eadie 2008 ). Almost 30 years ago, Andersson & Eriksson (1982) first suggested that perhaps this form of parasitism was not what it seemed—indeed, perhaps it was not parasitism at all! Andersson & Eriksson (1982) observed that conspecific brood parasitism (CBP) was disproportionally common in waterfowl (Anatidae), a group of birds for which natal philopatry is female‐biased rather than the more usual avian pattern of male‐biased natal philopatry. Accordingly, Andersson (1984) reasoned (and demonstrated in an elegantly simple model) that relatedness among females might facilitate the evolution of CBP—prodding us to reconsider it as a kin‐selected and possibly cooperative breeding system rather than a parasitic interaction. The idea was much cited but rarely tested empirically until recently—a number of new studies, empowered with a battery of molecular techniques, have now put Andersson’s hypothesis to the test ( Table 1 ). The results are tantalizing, but also somewhat conflicting. Several studies, focusing on waterfowl, have found clear evidence that hosts and parasites are often related ( Andersson & Åhlund 2000 ; Roy Nielsen et al. 2006 ; Andersson & Waldeck 2007 ; Waldeck et al. 2008 ; Jaatinen et al. 2009 ; Tiedemann et al. 2011 ). However, this is not always the case ( Semel & Sherman 2001 ; Anderholm et al. 2009 ; and see Pöysa 2004 ). In a new study reported in this issue of Molecular Ecology, Jaatinen et al. (2011a) provide yet another twist to this story that might explain not only why such variable results have been obtained, but also suggests that the games between parasites and their hosts—and the role of kinship in these games—may be even more complex than Andersson (1984) imagined. Indeed, the role of kinship in CBP may be very much one of relative degree!

Table 1. A summary of recent studies that have tested for evidence of relatedness between hosts and parasites in avian conspecific brood parasites

Role of environmental factors in the spread of domestic trout in Mediterranean streams

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Massive parallel MHC genotyping: titanium that shines

The power of population genetic analyses is often limited by sample size resulting from constraints in financial resources and time to genotype large numbers of individuals. This particularly applies to nonmodel species where detailed genomic knowledge is lacking. Next‐generation sequencing technology using primers ‘tagged’ with an individual barcode of a few nucleotides offers the opportunity to genotype hundreds of individuals at several loci in parallel ( Binladen et al. 2007 ; Meyer et al. 2008 ). The large number of sequence reads can also be used to identify artefacts by frequency distribution thresholds intrinsically determined for each run and data set. In Babik et al. (2009 ), next‐generation deep sequencing was used to genotype several major histocompatibility complex (MHC) class IIB loci of the European bank vole ( Fig. 1 ). Their approach can be useful for many researchers working with complex multiallelic templates and large sample sizes.

Figure 1 Open in figure viewer PowerPoint Hypothetical example of parallel genotyping of two individuals using individually bar‐coded primers. Polymerase chain reactions (PCRs) are performed separately for each individual using a forward primer with a unique Tag‐sequence of four nucleotides. After sequencing of pooled PCR products, sequences can be sorted by their forward primer Tag (Tag‐sorting error rate was estimated < 0.1%). Rare sequences most likely represent artefacts and due to the large amount of sequences obtained (up to 10⁶) the artefact threshold can be determined intrinsically for each data set and was estimated to be around 3% in the case of bank vole MHC class IIB genes ( Babik et al. 2009 ). Photos by Gabriela Bydlon.     

Incipient ring speciation revealed by a migratory divide

Ever since Ernst Mayr (1942) called ring species the ‘perfect demonstration of speciation’, they have attracted much interest from researchers examining how two species evolve from one. In a ring species, two sympatric and reproductively isolated forms are connected by a long chain of intermediate populations that encircle a geographic barrier. Ring species have the potential to demonstrate that speciation can occur without complete geographic isolation, in contrast to the classic model of allopatric speciation. They also allow researchers to examine the causes of reproductive isolation in the contact zone and to use spatial variation to infer the steps by which speciation occurs. According to the classical definition, a ring species must have (i) gradual variation through a chain of populations connecting two divergent and sympatric forms, and (ii) complete or nearly complete reproductive isolation between the terminal forms. But evolutionary biologists now recognize that the process of speciation might often occur with some periods of geographic contact and hybridization between diverging forms; during these phases, even partial reproductive isolation can limit gene flow and permit further divergence to occur. In this issue Bensch et al. (2009) make an exciting and important contribution by extending the ring species concept to a case in which the divergence is much younger and not yet advanced to full reproductive isolation. Their study of geographic variation in willow warblers (Phylloscopus trochilus; Fig. 1 ) provides a beautiful example of gradual variation through a ring of populations connecting two forms that are partially reproductively isolated where they meet, possibly due to divergent migratory behaviours of the terminal forms.

Figure 1 Open in figure viewer PowerPoint A male willow warbler resembling the southeastern‐migrating form (Phylloscopus trochilus acredula), on its breeding territory in central Sweden. (Photo: Anders Hedenström).     

Fungal defences against animal antagonists – lectins &; more

Unlike in the laboratory, in nature fungi are exposed to antagonists including competitors, pathogens, parasites and predators. In this issue of Molecular Ecology, an exciting paper by Bleuler‐Martínez et al. (2011) has unearthed on one of the processes used by fungi to protect themselves against animal antagonists. The authors from Markus Künzler′s group at the ETH Zürich, Switzerland present direct evidence that filamentous fungi possess an inducible resistance mechanism against predators and parasites. This is based on cytoplasmic lectins, which specifically bind to glycans of these predators and parasites, and thus provide toxicity against them. These lectins are expressed at high levels in fruiting bodies and sclerotia of these fungi ( Fig. 1 ). While there have been previous suggestions and efforts to implicate mycotoxins such as sterigmatocystin into fungal defence mechanisms and as an evolutionary force (see Kempken & Rohlfs 2010 ), the data presented by Markus Künzler′s group highlight the ecological relevance of lectins in defending fungi from parasites and fungivorous animals. As such this paper provides important ecological clues and suggests that secondary metabolites are not the sole player in fungal–animal competition. It rather appears that fungi have evolved several lines of defence against antagonistic organisms.

Figure 1 Open in figure viewer PowerPoint Fungi protect their fruiting bodies by the use of lectin (picture of Aleuria aurantia provided by Taylor F. Lockwood).