Frontiers in identifying conservation units: from neutral markers to adaptive genetic variation

Land use and life history constrain adaptive genetic variation and reduce the capacity for climate change adaptation in turtles

BACKGROUND

Rapid anthropogenic climate change will require species to adapt to shifting environmental conditions, with successful adaptation dependent upon current patterns of genetic variation. While landscape genomic approaches allow for exploration of local adaptation in non-model systems, most landscape genomics studies of adaptive capacity are limited to exploratory identification of potentially important functional genes, often without a priori expectations as to the gene functions that may be most important for climate change responses. In this study, we integrated targeted sequencing of genes of known function and genotyping of single-nucleotide polymorphisms to examine spatial, environmental, and species-specific patterns of potential local adaptation in two co-occuring turtle species: the Blanding's turtle (Emydoidea blandingii) and the snapping turtle (Chelydra serpentina).

RESULTS

We documented divergent patterns of spatial clustering between neutral and putatively adaptive genetic variation in both species. Environmental associations varied among gene regions and between species, with stronger environmental associations detected for genes involved in stress response and for the more specialized Blanding's turtle. Land cover appeared to be more important than climate in shaping spatial variation in functional genes, indicating that human landscape alterations may affect adaptive capacity important for climate change responses.

CONCLUSIONS

Our study provides evidence that responses to climate change will be contingent on species-specific adaptive capacity and past history of exposure to human land cover change.

Genetic Variation and Population Differentiation in the Bovine Lymphocyte Antigen DRB3.2 Locus of South African Nguni Crossbred Cattle

Simple Summary

Indigenous cattle breeds are important to their native environment as they confer significant and often unique adaptability traits. The Nguni is one such breeds that is indigenous to the Southern African region. This breed confers resistance to thermal stress and diseases, amongst other factors. The bovine major histocompatibility complex is an important region, which codes for alleles that have been associated with a plethora of diseases. In the current study, the genetic diversity within this region was assessed in Nguni crossbred cattle. This was done to detect the gene pool of the Nguni breed, and to identify genes that might be important within this breed. The populations displayed a high degree of genetic diversity, and some alleles were common throughout the populations and accounted for a significant portion of the total alleles. This high genetic diversity could account for the great adaptability of the Nguni breed to Southern Africa.

Abstract

The bovine lymphocyte antigen (BoLA-DRB3) gene is an important region that codes for glycoproteins responsible for the initiation of an immune response. BoLA-DRB3 alleles have been demonstrated to be associated with disease resistance/tolerance. Therefore, great genetic diversity is correlated with better adaptation, fitness, and robustness. The current study was conducted to assess the population genetic structure of the BoLA-DRB3 gene in Nguni crossbred cattle using polymerase chain reaction-sequence based typing (PCR-SBT). High genetic diversity was detected, with 30 alleles, 11 of which are novel to the study. Alleles DRB3*0201, DRB3*0701, DRB*0901, and DRB*1601 were present in all populations and accounted for nearly around 50% of all observed alleles. A mean genetic diversity (H_E) of 0.93 was detected. The high overall genetic diversity is possibly associated with pathogen-assisted selection and heterozygote advantage. Such high diversity might explain the hardiness of the Nguni crossbred cattle to the Southern African region. Low population genetic structure was identified (F_ST = 0.01), suggesting possible gene flow between populations and retention of similar alleles. The study was undertaken to bridge the dearth of such studies in South African breeds and it is imperative for effective sustainability of indigenous breeds and the implementation of effective breeding strategies.

Major histocompatibility complex B variability in Korean native chicken breeds

Adaptive genetic variations have direct influences on the fitness traits of the animal. The major histocompatibility complex B (MHC-B) region is responsible for adaptive and innate immune responses in chickens. In native Korean chicken breeds, no information on serologically defined B haplotypes is available. We investigated the MHC-B diversity in 5 restored lines of Korean native chicken and Ogye chicken breeds using a recently described MHC-B single-nucleotide polymorphism (SNP) panel and the MHC-linked LEI0258 variable number of tandem repeat marker. High SNP haplotype diversity was observed in Korean native chicken breeds with an average of 9.7 MHC-B SNP haplotypes per line. The total number of haplotypes ranged from 6 to 12 per line, and population-specific haplotypes ranged from 3 to 4. A total of 41 BSNP haplotypes, including 26 novel population-specific haplotypes and 15 common haplotypes, were reported over all populations. The 15 common haplotypes included 7 novel and 8 previously reported standard haplotypes. Selection and breeding evidence supports the observation of common haplotypes between the Korean native chicken and exotic breeds. Similarly, the LEI0258 marker showed allele variation, between 193 bp and 474 bp having 5 to 8 alleles per population. Some of these alleles (193, 249, 309, and 443 bp) were shared and more frequently observed. Comparison between SNP haplotypes and LEI0258 allele sizes for the same samples showed that some LEI0258 allele sizes correspond to more than one BSNP haplotype. The use of the MHC-B SNP panel greatly enhances the identification of MHC diversity compared with the sole use of the LEI0258 marker in native chicken populations.

Species-specific genetic variation in response to deep-sea environmental variation amongst Vulnerable Marine Ecosystem indicator taxa

Understanding the ecological processes that shape spatial genetic patterns of population structure is critical for understanding evolutionary dynamics and defining significant evolutionary and management units in the deep sea. Here, the role of environmental factors (topographic, physico-chemical and biological) in shaping the population genetic structure of four deep-sea habitat-forming species (one sponge - Poecillastra laminaris, three corals - Goniocorella dumosa, Madrepora oculata, Solenosmilia variabilis) was investigated using seascape genetics. Genetic data (nuclear and mitochondrial sequences and microsatellite multilocus genotypes) and environmental variables were employed to build individual-based and population-level models. The results indicated that environmental factors affected genetic variation differently amongst the species, as well as at different geographic scales. For individual-based analyses, different environmental variables explained genetic variation in P. laminaris (dissolved oxygen), G. dumosa (dynamic topography), M. oculata (sea surface temperature and surface water primary productivity), and S. variabilis (tidal current speed). At the population level, factors related to current and food source explained the regional genetic structure in all four species, whilst at the geomorphic features level, factors related to food source and topography were most important. Environmental variation in these parameters may be acting as barriers to gene flow at different scales. This study highlights the utility of seascape genetic studies to better understand the processes shaping the genetic structure of organisms, and to identify environmental factors that can be used to locate sites for the protection of deep-sea Vulnerable Marine Ecosystems.

Role of oceanography in shaping the genetic structure in the North Pacific hake Merluccius productus

Determining the relative influence of biotic and abiotic factors on genetic connectivity among populations remains a major challenge in evolutionary biology and in the management and conservation of species. North Pacific hake (Merluccius productus) inhabits upwelling regions in the California Current ecosystem from the Gulf of California to the Gulf of Alaska. In this study, we examined mitochondrial DNA (mtDNA) and microsatellite variation to estimate levels of genetic differentiation of M. productus in relation to the role of oceanographic features as potential barriers to gene flow. Samples were obtained from nine sites spanning a large part of the geographic range of the species, from Puget Sound, Washington to Costa Rica. The microsatellite results revealed three genetically discrete populations: one spanning the eastern Pacific coast, and two apparently resident populations circumscribed to the Puget Sound and the northern Gulf of California (F_ST = 0.032, p = 0.036). Cytochrome b sequence data indicated that isolation between the Puget Sound and northern Gulf of California populations from the coastal Pacific were recent phenomena (18.5 kyr for Puget Sound and 40 kyr for the northern Gulf of California). Oceanographic data obtained from the Gulf of California support the hypothesis that permanent fronts within the region, and strong gradients at the entrance to the Gulf of California act as barriers to gene flow. A seascape genetics approach found significant genetic–environment associations, where the daytime sea surface temperature and chlorophyll concentrations were the best predictive variables for the observed genetic differentiation. Considering the potential causes of genetic isolation among the three populations, e.g. spawning areas in different latitudes associated with upwelling processes, oceanographic barriers, asymmetric migration and specialized diet, oceanographic barriers appear to be a likely mechanism restricting gene flow.

Phylogeography of the reticulated python (Malayopython reticulatus ssp.): Conservation implications for the worlds' most traded snake species

As an important economic natural resource in Southeast Asia, reticulated pythons (Malayopython reticulatus ssp.) are primarily harvested from the wild for their skins-which are prized in the luxury leather goods industry. Trade dynamics of this CITES Appendix II listed species are complex and management approaches on the country or regional level appear obscure. Little is known about the actual geographic point-of-harvest of snakes, how genetic diversity is partitioned across the species range, how current harvest levels may affect the genetic viability of populations, and whether genetic structure could (or should) be accounted for when managing harvest quotas. As an initial survey, we use mitochondrial sequence data to define the broad-scale geographic structure of genetic diversity across a significant portion of the reticulated python's native range. Preliminary results reveal: (1) prominent phylogenetic structure across populations east and west of Huxley's modification of Wallace's line. Thirty-four haplotypes were apportioned across two geographically distinct groups, estimated to be moderately (5.2%); (2) Philippine, Bornean and Sulawesian populations appear to cluster distinctly; (3) individuals from Ambon Island suggest recent human introduction. Malayopython reticulatus is currently managed as a single taxonomic unit across Southeast Asia yet these initial results may justify special management considerations of the Philippine populations as a phylogenetically distinct unit, that warrants further examination. In Indonesia, genetic structure does not conform tightly to political boundaries and therefore we advocate the precautionary designation and use of Evolutionary Significant Units within Malayopython reticulatus, to inform and guide regional adaptive management plans.

Comparison of the effectiveness of ISJ and SSR markers and detection of outlier loci in conservation genetics of Pulsatilla patens populations

BACKGROUND

Research into the protection of rare and endangered plant species involves genetic analyses to determine their genetic variation and genetic structure. Various categories of genetic markers are used for this purpose. Microsatellites, also known as simple sequence repeats (SSR), are the most popular category of markers in population genetics research. In most cases, microsatellites account for a large part of the noncoding DNA and exert a neutral effect on the genome. Neutrality is a desirable feature in evaluations of genetic differences between populations, but it does not support analyses of a population's ability to adapt to a given environment or its evolutionary potential. Despite the numerous advantages of microsatellites, non-neutral markers may supply important information in conservation genetics research. They are used to evaluate adaptation to specific environmental conditions and a population's adaptive potential. The aim of this study was to compare the level of genetic variation in Pulsatilla patens populations revealed by neutral SSR markers and putatively adaptive ISJ markers (intron-exon splice junction).

METHODS

The experiment was conducted on 14 Polish populations of P. patens and three P. patens populations from the nearby region of Vitebsk in Belarus. A total of 345 individuals were examined. Analyses were performed with the use of eight SSR primers specific to P. patens and three ISJ primers.

RESULTS

SSR markers revealed a higher level of genetic variation than ISJ markers (He = 0.609, He = 0.145, respectively). An analysis of molecular variance (AMOVA) revealed that, the overall genetic diversity between the analyzed populations defined by parameters FST and Φ PT for SSR (20%) and Φ PT for ISJ (21%) markers was similar. Analysis conducted in the Structure program divided analyzed populations into two groups (SSR loci) and three groups (ISJ markers). Mantel test revealed correlations between the geographic distance and genetic diversity of Polish populations of P. patens for ISJ markers, but not for SSR markers.

CONCLUSIONS

The results of the present study suggest that ISJ markers can complement the analyses based on SSRs. However, neutral and adaptive markers should not be alternatively applied. Neutral microsatellite markers cannot depict the full range of genetic variation in a population because they do not enable to analyze functional variation. Although ISJ markers are less polymorphic, they can contribute to the reliability of analyses based on SSRs.

Using Genome-Wide SNP Discovery and Genotyping to Reveal the Main Source of Population Differentiation in Nothofagus dombeyi (Mirb.) Oerst. in Chile

Within a woody plant species, environmental heterogeneity has the potential to influence the distribution of genetic variation among populations through several evolutionary processes. In some species, a relationship between environmental characteristics and the distribution of genotypes can be detected, showing the importance of natural selection as the main source of differentiation. Nothofagus dombeyi (Mirb.) Oerst. (Nothofagaceae) is an endemic tree species occurring both in Chile and in Argentina temperate forests. Postglacial history has been studied with chloroplast DNA and evolutionary forces shaping genetic variation patterns have been analysed with isozymes but fine-scale genetic diversity studies are needed. The study of demographic and selection histories in Nothofagus dombeyi requires more informative markers such as single nucleotide polymorphisms (SNP). Genotyping-by-Sequencing tools now allow studying thousands of SNP markers at reasonable prices in nonmodel species. We investigated more than 10 K SNP loci for signatures of local adaptation and showed that interrogation of genomic resources can identify shifts in genetic diversity and putative adaptive signals in this nonmodel woody species.

Why and how might genetic and phylogenetic diversity be reflected in the identification of key biodiversity areas?

‘Key biodiversity areas' are defined as sites contributing significantly to the global persistence of biodiversity. The identification of these sites builds from existing approaches based on measures of species and ecosystem diversity and process. Here, we therefore build from the work of Sgró et al. (2011 Evol. Appl.4, 326–337. (doi:10.1111/j.1752-4571.2010.00157.x)) to extend a framework for how components of genetic diversity might be considered in the identification of key biodiversity areas. We make three recommendations to inform the ongoing process of consolidating a key biodiversity areas standard: (i) thresholds for the threatened species criterion currently consider a site's share of a threatened species' population; expand these to include the proportion of the species' genetic diversity unique to a site; (ii) expand criterion for ‘threatened species' to consider ‘threatened taxa’ and (iii) expand the centre of endemism criterion to identify as key biodiversity areas those sites holding a threshold proportion of the compositional or phylogenetic diversity of species (within a taxonomic group) whose restricted ranges collectively define a centre of endemism. We also recommend consideration of occurrence of EDGE species (i.e. threatened phylogenetic diversity) in key biodiversity areas to prioritize species-specific conservation actions among sites.

Comparative genomics for biodiversity conservation

Genomic approaches are gathering momentum in biology and emerging opportunities lie in the creative use of comparative molecular methods for revealing the processes that influence diversity of wildlife. However, few comparative genomic studies are performed with explicit and specific objectives to aid conservation of wild populations. Here I provide a brief overview of comparative genomic approaches that offer specific benefits to biodiversity conservation. Because conservation examples are few, I draw on research from other areas to demonstrate how comparing genomic data across taxa may be used to inform the characterisation of conservation units and studies of hybridisation, as well as studies that provide conservation outcomes from a better understanding of the drivers of divergence. A comparative approach can also provide valuable insight into the threatening processes that impact rare species, such as emerging diseases and their management in conservation. In addition to these opportunities, I note areas where additional research is warranted. Overall, comparing and contrasting the genomic composition of threatened and other species provide several useful tools for helping to preserve the molecular biodiversity of the global ecosystem.

Selection and phylogenetics of salmonid MHC class I: wild brown trout (Salmo trutta) differ from a non-native introduced strain

We tested how variation at a gene of adaptive importance, MHC class I (UBA), in a wild, endemic Salmo trutta population compared to that in both a previously studied non-native S. trutta population and a co-habiting Salmo salar population (a sister species). High allelic diversity is observed and allelic divergence is much higher than that noted previously for co-habiting S. salar. Recombination was found to be important to population-level divergence. The α1 and α2 domains of UBA demonstrate ancient lineages but novel lineages are also identified at both domains in this work. We also find examples of recombination between UBA and the non-classical locus, ULA. Evidence for strong diversifying selection was found at a discrete suite of S. trutta UBA amino acid sites. The pattern was found to contrast with that found in re-analysed UBA data from an artificially stocked S. trutta population.

On the origin of sweet potato (Ipomoea batatas (L.) Lam.) genetic diversity in New Guinea, a secondary centre of diversity

New Guinea is considered the most important secondary centre of diversity for sweet potato (Ipomoea batatas). We analysed nuclear and chloroplast genetic diversity of 417 New Guinea sweet potato landraces, representing agro-morphological diversity collected throughout the island, and compared this diversity with that in tropical America. The molecular data reveal moderate diversity across all accessions analysed, lower than that found in tropical America. Nuclear data confirm previous results, suggesting that New Guinea landraces are principally derived from the Northern neotropical genepool (Camote and Batata lines, from the Caribbean and Central America). However, chloroplast data suggest that South American clones (early Kumara line clones or, more probably, later reintroductions) were also introduced into New Guinea and then recombined with existing genotypes. The frequency distribution of pairwise distances between New Guinea landraces suggests that sexual reproduction, rather than somaclonal variation, has played a predominant role in the diversification of sweet potato. The frequent incorporation of plants issued from true seed by farmers, and the geographical and cultural barriers constraining crop diffusion in this topographically and linguistically heterogeneous island, has led to the accumulation of an impressive number of variants. As the diversification of sweet potato in New Guinea is primarily the result of farmers' management of the reproductive biology of their crop, we argue that on-farm conservation programmes that implement distribution of core samples (clones representing the useful diversity of the species) and promote on-farm selection of locally adapted variants may allow local communities to fashion relatively autonomous strategies for coping with ongoing global change.

Genetic evidence for restricted dispersal along continuous altitudinal gradients in a climate change-sensitive mammal: the American Pika

When faced with rapidly changing environments, wildlife species are left to adapt, disperse or disappear. Consequently, there is value in investigating the connectivity of populations of species inhabiting different environments in order to evaluate dispersal as a potential strategy for persistence in the face of climate change. Here, we begin to investigate the processes that shape genetic variation within American pika populations from the northern periphery of their range, the central Coast Mountains of British Columbia, Canada. At these latitudes, pikas inhabit sharp elevation gradients ranging from sea level to 1500 m, providing an excellent system for studying the effects of local environmental conditions on pika population genetic structure and gene flow. We found low levels of neutral genetic variation compared to previous studies from more southerly latitudes, consistent with the relatively recent post-glacial colonization of the study location. Moreover, significant levels of inbreeding and marked genetic structure were detected within and among sites. Although low levels of recent gene flow were revealed among elevations within a transect, potentially admixed individuals and first generation migrants were identified using discriminant analysis of principal components between populations separated by less than five kilometers at the same elevations. There was no evidence for historical population decline, yet there was signal for recent demographic contractions, possibly resulting from environmental stochasticity. Correlative analyses revealed an association between patterns of genetic variation and annual heat-to-moisture ratio, mean annual precipitation, precipitation as snow and mean maximum summer temperature. Changes in climatic regimes forecasted for the region may thus potentially increase the rate of population extirpation by further reducing dispersal between sites. Consequently, American pika may have to rely on local adaptations or phenotypic plasticity in order to survive predicted climate changes, although additional studies are required to investigate the evolutionary potential of this climate change sensitive species.

Population genetics of the Halys pit viper (Gloydius halys) at the northern distribution limit in Siberia

We studied the genetic structure and diversity of a vulnerable population of the Halys pit viper (Gloydius halys) living at the northern distribution limit of the species (Novosibirsk Region, West Siberia, Russia) and fairly isolated from the nearest known locations (180-200 km). 157 snakes from three locations (separated by 5-11 km) were genotyped using 8 microsatellite loci. In addition, nucleotide sequences of a mitochondrial marker gene (ND4) were obtained from 30 individuals. Two mitochondrial haplotypes differing by one synonymous substitution could be detected. Haplotype H1 had a prevalence of 96.7%. High levels of genetic diversity (mean ) were detected and no evidence of a recent bottleneck in any sampling site could be discovered. We found that G. halys exhibits a low, although significant, level of genetic differentiation on a fine geographic scale (overall FST = 0.013). The degree of differentiation is comparably low with regard to values reported for other vipers and more similar to those in Colubridae. In addition, using local based FST estimates, we detected a significant difference in the extent of genetic drift between the centrally located and marginal local populations as predicted by the stepping-stone model of migration. Thus, from a short-term perspective, primary attention should be given to the peripheral local populations, due to limited immigration and stronger influence of genetic drift. Since all habitat patches are situated along the river and have a linear order it is important to preserve each habitat site to maintain gene flow across the metapopulation.

Applications and implications of neutral versus non-neutral markers in molecular ecology

The field of molecular ecology has expanded enormously in the past two decades, largely because of the growing ease with which neutral molecular genetic data can be obtained from virtually any taxonomic group. However, there is also a growing awareness that neutral molecular data can provide only partial insight into parameters such as genetic diversity, local adaptation, evolutionary potential, effective population size, and taxonomic designations. Here we review some of the applications of neutral versus adaptive markers in molecular ecology, discuss some of the advantages that can be obtained by supplementing studies of molecular ecology with data from non-neutral molecular markers, and summarize new methods that are enabling researchers to generate data from genes that are under selection.

Phylogeography, genetic structure and population divergence time of cheetahs in Africa and Asia: evidence for long-term geographic isolates

The cheetah (Acinonyx jubatus) has been described as a species with low levels of genetic variation. This has been suggested to be the consequence of a demographic bottleneck 10 000–12 000 years ago (ya) and also led to the assumption that only small genetic differences exist between the described subspecies. However, analysing mitochondrial DNA and microsatellites in cheetah samples from most of the historic range of the species we found relatively deep phylogeographic breaks between some of the investigated populations, and most of the methods assessed divergence time estimates predating the postulated bottleneck. Mitochondrial DNA monophyly and overall levels of genetic differentiation support the distinctiveness of Northern-East African cheetahs (Acinonyx jubatus soemmeringii). Moreover, combining archaeozoological and contemporary samples, we show that Asiatic cheetahs (Acinonyx jubatus venaticus) are unambiguously separated from African subspecies. Divergence time estimates from mitochondrial and nuclear data place the split between Asiatic and Southern African cheetahs (Acinonyx jubatus jubatus) at 32 000–67 000 ya using an average mammalian microsatellite mutation rate and at 4700–44 000 ya employing human microsatellite mutation rates. Cheetahs are vulnerable to extinction globally and critically endangered in their Asiatic range, where the last 70–110 individuals survive only in Iran. We demonstrate that these extant Iranian cheetahs are an autochthonous monophyletic population and the last representatives of the Asiatic subspecies A. j. venaticus. We advocate that conservation strategies should consider the uncovered independent evolutionary histories of Asiatic and African cheetahs, as well as among some African subspecies. This would facilitate the dual conservation priorities of maintaining locally adapted ecotypes and genetic diversity.

Building evolutionary resilience for conserving biodiversity under climate change

Evolution occurs rapidly and is an ongoing process in our environments. Evolutionary principles need to be built into conservation efforts, particularly given the stressful conditions organisms are increasingly likely to experience because of climate change and ongoing habitat fragmentation. The concept of evolutionary resilience is a way of emphasizing evolutionary processes in conservation and landscape planning. From an evolutionary perspective, landscapes need to allow in situ selection and capture high levels of genetic variation essential for responding to the direct and indirect effects of climate change. We summarize ideas that need to be considered in planning for evolutionary resilience and suggest how they might be incorporated into policy and management to ensure that resilience is maintained in the face of environmental degradation.

Rapid selection against inbreeding in a wild population of a rare frog

Populations that are small and isolated can be threatened through loss of fitness due to inbreeding. Nevertheless, an increased frequency of recessive homozygotes could increase the efficiency of selection against deleterious mutants, thus reducing inbreeding depression. In wild populations, observations of evolutionary changes determined by selection against inbreeding are few. We used microsatellite DNA markers to compare the genetic features of tadpoles immediately after hatch with those of metamorphosing froglets belonging to the same cohort in a small, isolated population of the threatened frog Rana latastei. Within a generation, the inbreeding coefficient (F_IS) decreased: at hatch, F_IS was significantly >0, whereas F_IS was <0 after metamorphosis. Furthermore, heterozygosity increased and allelic frequencies changed over time, resulting in the loss of genotypes at metamorphosis that were present in hatchlings. One microsatellite locus exhibited atypically large F_ST values, suggesting it might be linked to a locus under selection. These results support the hypothesis that strong selection against the most inbred genotypes occurred among early life-history stages in our population. Selective forces can promote changes that can affect population dynamics and should be considered in conservation planning.