Patterns Of Adaptive Variation Research Articles

Local adaptive variation in a highly migratory fish: The smooth hammerhead shark Sphyrna zygaena

Populations of highly mobile species that undertake long distance migrations are typically considered to be panmictic. Nonetheless, mechanisms related to behavior or local environmental conditions promote genetic isolation in the absence of physical barriers. Highly migratory shark species exhibit varying levels of fidelity to specific regions, shaping the genetic architecture of different populations and resulting in geographically based genetic variation with potential adaptive value. An understanding of the genetic variation of highly migratory species is needed to develop effective conservation strategies. This study aimed to assess the neutral and adaptive variation of the smooth hammerhead shark (Sphyrna zygaena) in the northern Mexican Pacific (NMP) via single nucleotide polymorphisms (SNPs). We analyzed 1480 SNPs in 92 individuals from four geographic regions in the NMP, of which 1469 SNPs were neutral loci (n-SNP), and 11 were putatively under selection (o-SNP) using four genoma scan methods. Genetic diversity was geographically similar among regions (Ho = 0.275). The neutral variation showed panmixia (n-SNPs; FST = 0.0012, p = 0.44), which may be associated with the high dispersal capacity of S. zygaena. A pattern of adaptive variation between individuals from the Gulf of California and Pacific coast was revealed using o-SNPs FST-based methods (24 oSNPs; FST = 0.061, p < 0.001), which may be promoted by individual preferences based on physiological limitations. The estimated effective population size (Ne) of S. zygaena was 1390 individuals, which is theoretically optimal for the population to persist over time.

275years of forestry meets genomics in Pinus sylvestris.

Pinus sylvestris has a long history of basic and applied research that is relevant for both forestry and evolutionary studies. Its patterns of adaptive variation and role in forest economic and ecological systems have been studied extensively for nearly 275 years, detailed demography for a 100 years and mating system more than 50 years. However, its reference genome sequence is not yet available and genomic studies have been lagging compared to, for example, Pinus taeda and Picea abies, two other economically important conifers. Despite the lack of reference genome, many modern genomic methods are applicable for a more detailed look at its biological characteristics. For example, RNA‐seq has revealed a complex transcriptional landscape and targeted DNA sequencing displays an excess of rare variants and geographically homogenously distributed molecular genetic diversity. Current DNA and RNA resources can be used as a reference for gene expression studies, SNP discovery, and further targeted sequencing. In the future, specific consequences of the large genome size, such as functional effects of regulatory open chromatin regions and transposable elements, should be investigated more carefully. For forest breeding and long‐term management purposes, genomic data can help in assessing the genetic basis of inbreeding depression and the application of genomic tools for genomic prediction and relatedness estimates. Given the challenges of breeding (long generation time, no easy vegetative propagation) and the economic importance, application of genomic tools has a potential to have a considerable impact. Here, we explore how genomic characteristics of P. sylvestris, such as rare alleles and the low extent of linkage disequilibrium, impact the applicability and power of the tools.

Consequences of seed origin and biological invasion for early establishment in restoration of a North American grass species.

Local, wild-collected seeds of native plants are recommended for use in ecological restoration to maintain patterns of adaptive variation. However, some environments are so drastically altered by exotic, invasive weeds that original environmental conditions may no longer exist. Under these circumstances, cultivated varieties selected for improved germination and vigor may have a competitive advantage at highly disturbed sites. This study investigated differences in early establishment and seedling performance between wild and cultivated seed sources of the native grass, Poa secunda, both with and without competition from the invasive exotic grass, Bromus tectorum. We measured seedling survival and above-ground biomass at two experimental sites in western Montana, and found that the source of seeds selected for restoration can influence establishment at the restoration site. Cultivars had an overall advantage when compared with local genotypes, supporting evidence of greater vigor among cultivated varieties of native species. This advantage, however, declined rapidly in the presence of B. tectorum and most accessions were not significantly different for growth and survival in competition plots. Only one cultivar had a consistent advantage despite a strong decline in its performance when competing with invasive plants. As a result, cultivated varieties did not meet expectations for greater establishment and persistence relative to local genotypes in the presence of invasive, exotic species. We recommend the use of representative local or regional wild seed sources in restoration to minimize commercial selection, and a mix of individual accessions (wild, or cultivated when necessary) in highly invaded settings to capture vigorous genotypes and increase the odds native plants will establish at restoration sites.

Genome-wide scans detect adaptation to aridity in a widespread forest tree species.

Patterns of adaptive variation within plant species are best studied through common garden experiments, but these are costly and time-consuming, especially for trees that have long generation times. We explored whether genome-wide scanning technology combined with outlier marker detection could be used to detect adaptation to climate and provide an alternative to common garden experiments. As a case study, we sampled nine provenances of the widespread forest tree species, Eucalyptus tricarpa, across an aridity gradient in southeastern Australia. Using a Bayesian analysis, we identified a suite of 94 putatively adaptive (outlying) sequence-tagged markers across the genome. Population-level allele frequencies of these outlier markers were strongly correlated with temperature and moisture availability at the site of origin, and with population differences in functional traits measured in two common gardens. Using the output from a canonical analysis of principal coordinates, we devised a metric that provides a holistic measure of genomic adaptation to aridity that could be used to guide assisted migration or genetic augmentation.

Spring phenology shows genetic variation among and within populations in seedlings of Scots pine (Pinus sylvestris L.) in the Scottish Highlands

Background: Genetic differentiation in phenotypic traits is often observed among forest tree populations, but less is known about patterns of adaptive variation within populations. Such variation is expected to enhance the survival likelihood of extant populations under climate change. Aims: Scots pine (Pinus sylvestris) occurs over a spatially and temporally heterogeneous landscape in Scotland. Our goal was to examine whether populations had differentiated genetically in timing of bud flush in response to spatial heterogeneity and whether variation was also maintained within populations. Methods: Two common-garden studies, involving maternal families of seedlings from 21 native pinewoods, were established and variation in the trait was measured at the beginning of the second growing season. Results: Populations showed genetic differences in the trait correlated with the length of growing season at their site of origin, but the majority of variation was observed within populations. Populations also differed in their levels of variation in the trait; a pattern that may be influenced by spatial variation in the extent of temporal climate variability. Conclusions: Our findings suggest that populations have adapted to their home environments and that they also have substantial ability to adapt in situ to changes in growing season length.

Widespread phenotypic and genetic divergence along altitudinal gradients in animals

Altitudinal gradients offer valuable study systems to investigate how adaptive genetic diversity is distributed within and between natural populations and which factors promote or prevent adaptive differentiation. The environmental clines along altitudinal gradients tend to be steep relative to the dispersal distance of many organisms, providing an opportunity to study the joint effects of divergent natural selection and gene flow. Temperature is one variable showing consistent altitudinal changes, and altitudinal gradients can therefore provide spatial surrogates for some of the changes anticipated under climate change. Here, we investigate the extent and patterns of adaptive divergence in animal populations along altitudinal gradients by surveying the literature for (i) studies on phenotypic variation assessed under common garden or reciprocal transplant designs and (ii) studies looking for signatures of divergent selection at the molecular level. Phenotypic data show that significant between-population differences are common and taxonomically widespread, involving traits such as mass, wing size, tolerance to thermal extremes and melanization. Several lines of evidence suggest that some of the observed differences are adaptively relevant, but rigorous tests of local adaptation or the link between specific phenotypes and fitness are sorely lacking. Evidence for a role of altitudinal adaptation also exists for a number of candidate genes, most prominently haemoglobin, and for anonymous molecular markers. Novel genomic approaches may provide valuable tools for studying adaptive diversity, also in species that are not amenable to experimentation.

Characterization of MHC class II B polymorphism in bottlenecked New Zealand saddlebacks reveals low levels of genetic diversity

The major histocompatibility complex (MHC) is integral to the vertebrate adaptive immune system. Characterizing diversity at functional MHC genes is invaluable for elucidating patterns of adaptive variation in wild populations, and is particularly interesting in species of conservation concern, which may suffer from reduced genetic diversity and compromised disease resilience. Here, we use next generation sequencing to investigate MHC class II B (MHCIIB) diversity in two sister taxa of New Zealand birds: South Island saddleback (SIS), Philesturnus carunculatus, and North Island saddleback (NIS), Philesturnus rufusater. These two species represent a passerine family outside the more extensively studied Passerida infraorder, and both have experienced historic bottlenecks. We examined exon 2 sequence data from populations that represent the majority of genetic diversity remaining in each species. A high level of locus co-amplification was detected, with from 1 to 4 and 3 to 12 putative alleles per individual for South and North Island birds, respectively. We found strong evidence for historic balancing selection in peptide-binding regions of putative alleles, and we identified a cluster combining non-classical loci and pseudogene sequences from both species, although no sequences were shared between the species. Fewer total alleles and fewer alleles per bird in SIS may be a consequence of their more severe bottleneck history; however, overall nucleotide diversity was similar between the species. Our characterization of MHCIIB diversity in two closely related species of New Zealand saddlebacks provides an important step in understanding the mechanisms shaping MHC diversity in wild, bottlenecked populations.

ODoSE: A Webserver for Genome-Wide Calculation of Adaptive Divergence in Prokaryotes

Quantifying patterns of adaptive divergence between taxa is a major goal in the comparative and evolutionary study of prokaryote genomes. When applied appropriately, the McDonald-Kreitman (MK) test is a powerful test of selection based on the relative frequency of non-synonymous and synonymous substitutions between species compared to non-synonymous and synonymous polymorphisms within species. The webserver ODoSE (Ortholog Direction of Selection Engine) allows the calculation of a novel extension of the MK test, the Direction of Selection (DoS) statistic, as well as the calculation of a weighted-average Neutrality Index (NI) statistic for the entire core genome, allowing for systematic analysis of the evolutionary forces shaping core genome divergence in prokaryotes. ODoSE is hosted in a Galaxy environment, which makes it easy to use and amenable to customization and is freely available at www.odose.nl.

Spatial and temporal patterns of neutral and adaptive genetic variation in the endangered African wild dog (Lycaon pictus)

Deciphering patterns of genetic variation within a species is essential for understanding population structure, local adaptation and differences in diversity between populations. Whilst neutrally evolving genetic markers can be used to elucidate demographic processes and genetic structure, they are not subject to selection and therefore are not informative about patterns of adaptive variation. As such, assessments of pertinent adaptive loci, such as the immunity genes of the major histocompatibility complex (MHC), are increasingly being incorporated into genetic studies. In this study, we combined neutral (microsatellite, mtDNA) and adaptive (MHC class II DLA-DRB1 locus) markers to elucidate the factors influencing patterns of genetic variation in the African wild dog (Lycaon pictus); an endangered canid that has suffered extensive declines in distribution and abundance. Our genetic analyses found all extant wild dog populations to be relatively small (N(e) < 30). Furthermore, through coalescent modelling, we detected a genetic signature of a recent and substantial demographic decline, which correlates with human expansion, but contrasts with findings in some other African mammals. We found strong structuring of wild dog populations, indicating the negative influence of extensive habitat fragmentation and loss of gene flow between habitat patches. Across populations, we found that the spatial and temporal structure of microsatellite diversity and MHC diversity were correlated and strongly influenced by demographic stability and population size, indicating the effects of genetic drift in these small populations. Despite this correlation, we detected signatures of selection at the MHC, implying that selection has not been completely overwhelmed by genetic drift.

Comparison of FST outlier tests for SNP loci under selection

Genome scans with many genetic markers provide the opportunity to investigate local adaptation in natural populations and identify candidate genes under selection. In particular, SNPs are dense throughout the genome of most organisms and are commonly observed in functional genes making them ideal markers to study adaptive molecular variation. This approach has become commonly employed in ecological and population genetics studies to detect outlier loci that are putatively under selection. However, there are several challenges to address with outlier approaches including genotyping errors, underlying population structure and false positives, variation in mutation rate and limited sensitivity (false negatives). In this study, we evaluated multiple outlier tests and their type I (false positive) and type II (false negative) error rates in a series of simulated data sets. Comparisons included simulation procedures (FDIST2, ARLEQUIN v.3.5 and BAYESCAN) as well as more conventional tools such as global F(ST) histograms. Of the three simulation methods, FDIST2 and BAYESCAN typically had the lowest type II error, BAYESCAN had the least type I error and Arlequin had highest type I and II error. High error rates in Arlequin with a hierarchical approach were partially because of confounding scenarios where patterns of adaptive variation were contrary to neutral structure; however, Arlequin consistently had highest type I and type II error in all four simulation scenarios tested in this study. Given the results provided here, it is important that outlier loci are interpreted cautiously and error rates of various methods are taken into consideration in studies of adaptive molecular variation, especially when hierarchical structure is included.

Genetic Variation in Picea glauca for Growth and Phenological Traits From Provenance Tests in Ontario

Abstract Ecologically based management of white spruce (Picea glauca [Moench] Voss.) requires an understanding of its patterns of adaptive variation. This understanding will become increasingly important under changing climate conditions. Five common garden tests and a greenhouse trial established in 2002 across Ontario were used to assess levels of genetic variation and relate this variation to local climate. Growth and phenological variables, including height, root collar diameter, survival, timing of spring budflush, and timing of fall budset were measured. Intraclass correlation coefficients were calculated for all traits to determine levels of genetic variation. Simple linear regressions were used to relate these differences to local climate conditions. After two growing season’s levels of between-provenance genetic variation ranged from 0 percent for several of the budflush variables to 22 percent for 2003 survival at the Englehart field trial. Overall, growth variables showed higher levels of between-provenance variation than phenological variables. Variation was predominately explained by longitude, a surrogate for precipitation patterns in Ontario, and temperature variables related to the growing season with r2 values ranging from 0.03 to 0.55. Generally, patterns of adaptive variation followed a southeast to northwest trend across Ontario. Northern sources flushed earlier and set bud earlier, while southern sources demonstrated superior growth. Results support previous white spruce genecology studies showing superior growth of sources from the Ottawa valley region of Ontario and Quebec.

Notice to Contributors

Changes in forestry policy have increased the importance and extended the scope of genetic management of native species. Recent debate on genetic management prescriptions has been conducted with insufficient access to sound scientific information. This paper attempts to remedy this by: (1) presenting an overview of genetic variation and the processes which control it; (2) reviewing current measures; and (3) proposing a range of improvements to policy and practice. Genetic variation in Scottish tree and shrub populations is a neglected field of research, except for Scots pine ( Pinus sylvestris ). Some useful information can be provided by considering the history, ecology and biology of species together with genetic theory. Current patterns of variation reflect both the historical origins (as demonstrated by biochemical markers) and adaptation through natural selection (as indicated by provenance research). Existing populations probably still retain significant elements of adaptive variation; though this will vary according to species, with some showing close correlation between patterns of adaptive variation and environmental factors and others being more plastic. Indigenous genepools have been modified by fragmentation, changes in the forest environment, and introduction of foreign material, much of which is maladapted to upland sites. With some exceptions, the levels of genetic variation in existing indigenous populations comprise an adequate basis for restoring and expanding native woodland. The current undiscriminating use of continental provenances needs to be strongly discouraged; but equally restricting choice of seed sources to the most local provenances can also be inappropriate. Use of Scottish material from the same region and similar site type as the planting site needs to be encouraged. Current genetic management measures are rudimentary and fail to address adequately key issues of provenance choice, genetic conservation, seed supply or provision of selected or improved materials especially in broadleaves. Changes in legislation, regulation, seed supply, advice and research are proposed to address these shortcomings. The need for more provenance research is highlighted.

The genetic management of native species in Scotland

Summary Changes in forestry policy have increased the importance and extended the scope of genetic management of native species. Recent debate on genetic management prescriptions has been conducted with insufficient access to sound scientific information. This paper attempts to remedy this by: (1) presenting an overview of genetic variation and the processes which control it; (2) reviewing current measures; and (3) proposing a range of improvements to policy and practice. Genetic variation in Scottish tree and shrub populations is a neglected field of research, except for Scots pine (Pinus sylvestris). Some useful information can be provided by considering the history, ecology and biology of species together with genetic theory. Current patterns of variation reflect both the historical origins (as demonstrated by biochemical markers) and adaptation through natural selection (as indicated by provenance research). Existing populations probably still retain significant elements of adaptive variation; though this will vary according to species, with some showing close correlation between patterns of adaptive variation and environmental factors and others being more plastic. Indigenous genepools have been modified by fragmentation, changes in the forest environment, and introduction of foreign material, much of which is maladapted to upland sites. With some exceptions, the levels of genetic variation in existing indigenous populations comprise an adequate basis for restoring and expanding native woodland. The current undiscriminating use of continental provenances needs to be strongly discouraged; but equally restricting choice of seed sources to the most local provenances can also be inappropriate. Use of Scottish material from the same region and similar site type as the planting site needs to be encouraged. Current genetic management measures are rudimentary and fail to address adequately key issues of provenance choice, genetic conservation, seed supply or provision of selected or improved material, especially in broadleaves. Changes in legislation, regulation, seed supply, advice and research are proposed to address these shortcomings. The need for more provenance research is highlighted.

Genecological variation corresponding to Forest Ecosystem Classification vegetation and soil types for jack pine and black spruce from northwestern Ontario

A preliminary study was undertaken to reveal ecotypic differentiation in jack pine and black spruce corresponding to ecological land classification groups. Seed sources of jack pine (64) and black spruce (68) from northwestern Ontario were classified according to Vegetation Types (V-Types) and Soil Types (S-Types) defined by the Forest Ecosystem Classification (FEC) developed by the Ontario Ministry of Natural Resources and Forestry Canada for northwestern Ontario. Two short-term common garden field trials and a greenhouse trial were established for each species. Significant differences were present among ecological groupings of seed sources for both species. These differences were expressed according to V-Types and S-Types based on first, second, and third year heights as well as needle flushing dates for jack pine and second year growth increments for black spruce. Rank differences among the groups based on FEC V-Types and S-Types were generally consistent for each of the two species although certain groups showed rank reversals at the two field trials. Apparently, selection pressures corresponding to different FEC V-Types and S-Types have resulted in a detectable pattern of adaptive variation for both jack pine and black spruce in northwestern Ontario. However, the management implications for these two species are uncertain since additional tests are required to verify these results.