Do genetic drift and accumulation of deleterious mutations preclude adaptation? Empirical investigation using RADseq in a northern lacustrine fish

Understanding genomic signatures of divergent selection underlying long‐term adaptation in populations located in heterogeneous environments is a key goal in evolutionary biology. In this study, we investigated neutral, adaptive and deleterious genetic variation using 7,192 SNPs in 31 Lake Trout (Salvelinus namaycush) populations (n = 673) from Québec, Canada. Average genetic diversity was low, weakly shared among lakes, and positively correlated with lake size, indicating a major role for genetic drift subsequent to lake isolation. Putatively deleterious mutations were on average at lower frequencies than the other SNPs, and their abundance relative to the entire polymorphism in each population was positively correlated with inbreeding, suggesting that the effectiveness of purifying selection was negatively correlated with inbreeding, as predicted from theory. Despite evidence for pronounced genetic drift and inbreeding, several outlier loci were associated with temperature and found in or close to genes with biologically relevant functions notably related to heat stress and immune responses. Outcomes of gene–temperature associations were influenced by the inclusion of the most inbred populations, in which allele frequencies deviated the most from model predictions. This result illustrates challenge in identifying gene–environment associations in cases of high genetic drift and restricted gene flow and suggests limited adaptation in populations experiencing higher inbreeding. We discuss the relevance of these findings for the conservation and management, notably regarding stocking and genetic rescue, of Lake Trout populations and other species inhabiting highly fragmented habitats.     

Identifying units for conservation using molecular systematics: the cautionary tale of the Karner blue butterfly

The federally endangered North American Karner blue butterfly (Lycaeides melissa samuelis) and the closely related Melissa blue butterfly (L. m. melissa) can be distinguished based on life history and morphology. Western populations of L. m. samuelis share mitochondrial haplotypes with L. m. melissa populations, while eastern populations of L. m. samuelis have divergent haplotypes. Here we test two hypotheses concerning the presence of L. m. melissa mitochondrial haplotypes in western L. m. samuelis populations: (i) mitochondrial introgression has occurred from L. m. melissa populations into western L. m. samuelis populations, or (ii) western populations of the nominal L. m. samuelis are more closely related to L. m. melissa than to eastern L. m. samuelis populations, yet are phenotypically similar to the latter. A Bayesian algorithm was used to cluster 190 L. melissa individuals based on 143 informative amplified fragment length polymorphism (AFLP) loci. This method clearly differentiated L. m. samuelis and L. m. melissa. Thus, genomic divergence was greater between western L. m. samuelis populations and L. m. melissa populations than it was between western and eastern populations of L. m. samuelis. This supports the hypothesis that the presence of L. m. melissa mitochondrial haplotypes in western L. m. samuelis populations is the result of mitochondrial introgression. These data provide valuable information for conservation and management plans for the endangered L. m. samuelis, and illustrate the risks of using data from a single locus for diagnosing significant units of biodiversity for conservation.     

Principles for linking fish habitat to fisheries management and conservation

A set of eight simple ecological and social principles is proposed that could enhance the understanding of what constitutes fish 'habitat' and, if implemented, could contribute to improved management and conservation strategies. The habitat principles are a small, interrelated sub‐set that may be coupled with additional ones to formulate comprehensive guidelines for management and conservation strategies. It is proposed that: 1) habitat can be created by keystone species and interactions among species; 2) the productivity of aquatic and riparian habitat is interlinked by reciprocal exchanges of material; 3) the riparian zone is fish habitat; 4) fishless headwater streams are inseparable from fish‐bearing rivers downstream; 5) habitats can be coupled – in rivers, lakes, estuaries and oceans, and in time; 6) habitats change over hours to centuries; 7) fish production is dynamic due to biocomplexity, in species and in habitats; 8) management and conservation strategies must evolve in response to present conditions, but especially to the anticipated future. It is contended that the long‐term resilience of native fish communities in catchments shared by humans depends on incorporating these principles into management and conservation strategies. Further, traditional strategies poorly reflect the dynamic nature of habitat, the true extent of habitat, or the intrinsic complexity in societal perspectives. Forward‐thinking fish management and conservation plans view habitat as more than water. They are multilayered, ranging from pools to catchments to ecoregions, and from hours to seasons to centuries. They embrace, as a fundamental premise, that habitat evolves through both natural and anthropogenic processes, and that patterns of change may be as important as other habitat attributes.     

Evolutionary potential in the wild: more than meets the eye

The genus Aquilegia consists of 60–70 perennial plant species widely distributed throughout the northern hemisphere. Its flowers have a delicate and ornamental appearance that makes them a favourite of gardeners. In this genus, adaptive radiations for both floral and vegetative traits have occurred. These adaptive radiations, and the key phylogenetic placement of Aquilegia between Arabidopsis and rice, make this genus a ‘model system’ for plant evolution ( Kramer 2009 ). In this issue, Castellanos et al. (2011) use a marker‐based method to infer heritability for floral and vegetative traits in two Aquilegia species. Layered on top of this are estimates of the strength of natural selection. This novel joint estimation of heritability and selection in the wild showed that vegetative traits, compared to floral traits, have the highest evolutionarily potential. Evolutionary potential is the most important quantity to measure in wild populations. It combines inheritance and strength of selection and predicts the potential for populations to adapt to changing environments. The combination of molecular techniques with species in natural environments makes this work a model for molecular ecological investigations.     

Birdsong and anthropogenic noise: implications and applications for conservation

The dramatic increase in human activities all over the world has caused, on an evolutionary time scale, a sudden rise in especially low-pitched noise levels. Ambient noise may be detrimental to birds through direct stress, masking of predator arrival or associated alarm calls, and by interference of acoustic signals in general. Two of the most important functions of avian acoustic signals are territory defence and mate attraction. Both of these functions are hampered when signal efficiency is reduced through rising noise levels, resulting in direct negative fitness consequences. Many bird species are less abundant near highways and studies are becoming available on reduced reproductive success in noisy territories. Urbanization typically leads to homogenization of bird communities over large geographical ranges. We review current evidence for whether and how anthropogenic noise plays a role in these patterns of decline in diversity and density. We also provide details of a case study on great tits (Parus major), a successful urban species. Great tits show features that other species may lack and make them unsuitable for city life. We hypothesize that behavioural plasticity in singing behaviour may allow species more time to adapt to human-altered environments and we address the potential for microevolutionary changes and urban speciation in European blackbirds (Turdus merula). We conclude by providing an overview of mitigating measures available to abate noise levels that are degrading bird breeding areas. Bird conservationists probably gain most by realizing that birds and humans often benefit from the same or only slightly modified measures.     

Adaptive landscape genetics: pitfalls and benefits

Landscape genetics offers a promising framework for assessing the interactions between the environment and adaptive genetic variation in natural populations. A recent workshop held at the University of Neuchatel brought together leading experts in this field to address current insights and future research directions in adaptive landscape genetics. Considerable amounts of genetic and/or environmental data can now be collected, but the forthcoming challenge is to do more with such manna. This requires a markedly better understanding of the genetic variation that is adaptive and prompts for advances in information management together with the development of a balance between theory and data. Moreover, showing the links between landscapes and adaptive genetic variation will ultimately move the field beyond association studies.     

Integrating population genetics and conservation biology in the era of genomics

As one of the final activities of the ESF-CONGEN Networking programme, a conference entitled ‘Integrating Population Genetics and Conservation Biology’ was held at Trondheim, Norway, from 23 to 26 May 2009. Conference speakers and poster presenters gave a display of the state-of-the-art developments in the field of conservation genetics. Over the five-year running period of the successful ESF-CONGEN Networking programme, much progress has been made in theoretical approaches, basic research on inbreeding depression and other genetic processes associated with habitat fragmentation and conservation issues, and with applying principles of conservation genetics in the conservation of many species. Future perspectives were also discussed in the conference, and it was concluded that conservation genetics is evolving into conservation genomics, while at the same time basic and applied research on threatened species and populations from a population genetic point of view continues to be emphasized.     

Ant genomics: strength and diversity in numbers

A recent workshop held at the Arizona State University Center for Social Dynamics and Complexity gathered over 50 prominent researchers from around the globe to discuss the development of genomic resources for several ant species. Ants play crucial roles in many ecological niches and the sequencing of several ant genomes promises to elucidate topics ranging from the genetic basis for social complexity, longevity and behaviour to systems biology and the identification of novel antimicrobial compounds. Unlike other species, most ant genomes are being generated by individual labs and small collaborations without the annotation and computational resources that support prominent model organism genome databases such those for the fruitfly and roundworm. Attendees summarized their current progress and future plans for several ant genomes and discussed how best to coordinate the analysis and annotation of ant sequences to benefit the broad research interests of the social insect community.