Neutral Loci Research Articles

Genetic Diversity and Divergence among Bighorn Sheep from Reintroduced Herds in Washington and Idaho

ABSTRACTBighorn sheep (Ovis canadensis) populations in the western United States have undergone widespread declines and extirpations since the late nineteenth century as a consequence of introduced diseases, competition with livestock, and unregulated hunting. Washington, Idaho, USA, and British Columbia, Canada were historically thought to be occupied by 2 bighorn lineages or subspecies: Rocky Mountain (O. c. canadensis) and California (O. c. californiana). The putative California lineage was completely extirpated in the United States, and reintroductions to reestablish populations were sourced directly or indirectly from a single region in southern British Columbia. Restoration efforts have attempted to maintain the diversity and divergence of these 2 lineages, sometimes referred to as subspecies although taxonomic classifications have changed over time. In this study we describe genetic variation in a subset of native and reintroduced herds of California and Rocky Mountain bighorn sheep. We examined genetic diversity and divergence between bighorn sheep herds using 15 microsatellite loci, including 4 loci linked to genes involved in immune function. We analyzed 504 samples from reintroduced herds in Washington (n = 10 California herds, n = 4 Rocky Mountain herds) and Idaho (n = 5 California), and source herds in Oregon (n = 1 Rocky Mountain) and British Columbia (n = 5 California, 1 Rocky Mountain). Genetic structure reflected known reintroduction history, and geographic proximity also was associated with decreased genetic divergence. Herds in Washington and Idaho sourced from California bighorn sheep were less genetically diverse than those sourced from Rocky Mountain herds. Also, levels of relatedness within and across California herds were higher than in Rocky Mountain herds and similar to what would be expected for full and half siblings. Lower diversity and higher relatedness among California herds is a concern for long‐term fitness and likely related to past population bottlenecks, fewer source populations, and management history, such as entirely sourcing California herds from British Columbia. Genetic divergence of neutral loci between California and Rocky Mountain herds was greater than that of adaptive loci, potentially indicating that balancing selection has maintained similar genetic diversity across lineages in loci associated with immune and other adaptive functions. Thus, we recommend future reintroductions and augmentations should continue to use source populations from the appropriate California or Rocky Mountain lineage to avoid potential outbreeding depression and maintain possible adaptive differences. This could be accomplished by obtaining sheep from ≥1 source within the genetic lineage, while avoiding sourcing from admixed herds. Future work encompassing a broader geographic sampling of populations and a greater portion of the genome is necessary to better evaluate the degree to which contemporary divergence between lineages is associated with recent founder effects and genetic isolation or evolutionary adaptation. © 2021 The Wildlife Society

Synthetic counter-selection markers and their application in genetic modification of Synechococcus elongatus UTEX2973.

Due to its robustness to environmental stresses and fast growth, Synechococcus elongatus UTEX2973 is developed as a new model for researches on cyanobacterial molecular biology and biotechnology. However, systematic genetic modifications of S. elongatus UTEX2973 were hindered by the lack of effective genetic manipulation tools, especially available counter-selection markers. Here, six synthetic counter-selection markers (SCOMs) were assembled by fusing six toxin genes from either Escherichia coli or cyanobacteria with a theophylline-inducible promoter. The SCOMs containing SYNPCC7002_G0085 from Synechococcus sp. PCC7002 or mazF from E. coli were proved to be inducible by theophylline in S. elongatus UTEX2973. By using the mazF-based SCOM, the neutral locus 1 and 23 small regulatory RNAs were completely deleted from the genome of S. elongatusUTEX2973 after one round of selection with both kanamycin and theophylline. The genetic tools developed in this work will facilitate future researches on molecular genetics and synthetic biology in S. elongatus UTEX2973. KEY POINTS: • Two inducible counter-selection markers are lethal to S. elongatus UTEX2973. • The counter-selection marker benefits the gene targeting in S. elongatus UTEX2973. • Twentry-three small regulatory RNAs were fully deleted via the novel gene targeting method.

Integrating genomics in population models to forecast translocation success

Whole‐genome sequencing is revolutionizing our understanding of organismal biology, including adaptations likely to influence demographic performance in different environments. Excitement over the potential of genomics to inform population dynamics has prompted multiple conservation applications, including genomics‐based decision‐making for translocation efforts. Despite interest in applying genomics to improve translocations, there is a critical research gap: we lack an understanding of how genomic differences translate into population dynamics in the real world. We review how genomics and genetics data could be used to inform organismal performance, including examples of how adaptive and neutral loci have been quantified in a translocation context, and future applications. Next, we discuss three main drivers of population dynamics: demographic structure, spatial barriers to movement, and introgression, and their consequences for translocations informed by genomic data. Finally, we provide a practical guide to different types of models, including size‐structured and spatial models, that could be modified to include genomics data. We then propose a framework to improve translocation success by repeatedly developing, selecting, and validating forecasting models. By integrating lab‐based and field‐collected data with model‐driven research, our iterative framework could address long‐standing challenges in restoration ecology, such as when selecting locally adapted genotypes will aid translocation of plants and animals.

Population genomics and conservation of Gila Trout (Oncorhynchus gilae)

Many salmonid species exist in highly structured and isolated populations, and are susceptible to habitat fragmentation and disturbances. Gila Trout (Oncorhynchus gilae) is a threatened species found in the Southwestern United States, and is managed to preserve relict populations (i.e., lineages) distributed across a fragmented landscape. We evaluated genomic variation within and among remaining lineages of Gila Trout using RADseq to assess how drift and selection have structured populations using neutral and outlier loci. We also examined whether a signature of hybridization was evident in relict populations. Gila Trout lineages were significantly differentiated from one another and were characterized by low effective population sizes. However, most lineages maintained genomic diversity and are potentially adapted to local conditions. Hybridization with non-native Rainbow Trout (O. mykiss) was not detected in any lineage. All lineages have experienced population bottlenecks associated with mortality from drought and severe wildfires. Current management strategies should be reevaluated and adapted to better account for long-term effects of climate change. Specifically, we suggest reconnecting some populations via dendritic stream networks to facilitate natural dispersal in a metapopulation context. This would allow natural genetic mixing on the landscape and potentially increase adaptive potential. Furthermore, genetic rescue should be implemented to preserve integrity of the unique Spruce Creek lineage that is currently compromised by extremely low diversity.

Whiteness and preference perception of white light sources: A case study at 5500 K with positive and negative Duv values

Recent studies reported a series of neutral loci for white lighting, which showed significant differences when the correlated colour temperature was greater than 4000 K. Several were located above the Planckian locus while others were located below. In addition, some researchers indicated that the whiteness of lighting correlates with colour preference (i.e. visual appreciation on the colour rendition of lighting) but that conclusion is not in full accordance with certain individual results of preference or whiteness evaluation. To investigate the perceived whiteness and colour preference in a viewing cabinet, two visual experiments were carried out. The light sources adopted in both the experiments were eight sources of 5500 K, that included four with constant positive Duv values (~0.004) and four having constant negative Duv values (~− 0.006). The illuminance levels were approximately 200 lux while the Color Rendering Index (CRI) values were in range of 85–91. The results showed that sources of negative Duvs obtained higher values of whiteness assessment and their colour rendition was preferred by observers. The findings also strengthen the opinion that, for practical conditions with a constant CCT and acceptable CRI values, the Duv value could be considered as an effective indicator for colour preference judgement.

Can We Compare Effect Size of Spatial Genetic Structure Between Studies and Species Using Moran Eigenvector Maps?

As the field of landscape genetics is progressing toward comparative empirical studies and meta-analysis, it is important to know how best to compare the strength of spatial genetic structure between studies and species. Moran’s Eigenvector Maps are a promising method that does not make an assumption of isolation-by-distance in a homogeneous environment but can discern cryptic structure that may result from multiple processes operating in heterogeneous landscapes. MEMgene uses spatial filters from Moran’s Eigenvector Maps as predictor variables to explain variation in a genetic distance matrix, and it returns adjusted R2 as a measure of the amount of genetic variation that is spatially structured. However, it is unclear whether, and under which conditions, this value can be used to compare the degree of spatial genetic structure (effect size) between studies. This study addresses the fundamental question of comparability at two levels: between independent studies (meta-analysis mode) and between species sampled at the same locations (comparative mode). We used published datasets containing 9,900 haploid, biallelic, neutral loci simulated on a quasi-continuous, square landscape under four demographic scenarios (island model, isolation-by-distance, expansion from one or two refugia). We varied the genetic resolution (number of individuals and loci) and the number of random sampling locations. We considered two measures of effect size, the MEMgene adjusted R2 and multivariate Moran’s I, which is related to Moran’s Eigenvector Maps. Both metrics were highly sensitive to the number of locations, even when using standardized effect sizes, SES, and the number of individuals sampled per location, but not to the number of loci. In comparative mode, using the same Moran Eigenvector Maps for all species, even those with missing values at some sampling locations, reduced bias due to the number of locations under isolation-by-distance (stationary process) but increased it under expansion from one or two refugia (non-stationary process). More robust measures of effect size need to be developed before the strength of spatial genetic structure can be accurately compared, either in a meta-analysis of independent empirical studies or within a comparative, multispecies landscape genetic study.

Opportunities and challenges in assessing climate change vulnerability through genomics

By investigating how past selection has affected allele frequencies across space, genomic tools are providing new insights into adaptive evolutionary processes. Now researchers are considering how this genomic information can be used to predict the future vulnerability of species under climate change. Genomic vulnerability assessments show promise, but challenges remain.

Type and intensity of surrounding human land use, not local environment, shape genetic structure of a native grassland plant.

Landscape heterogeneity can shape genetic structure and functional connectivity of populations. When this heterogeneity imposes variable costs of moving across the landscape, populations can be structured according to a pattern of "isolation by resistance" (IBR). At the same time, divergent local environmental filters can limit gene flow, creating an alternative pattern of "isolation by environment" (IBE). Here, we evaluate IBR and IBE in the insect-pollinated, biennial plant Sabatia angularis (L.) Pursh (Gentianaceae) across serpentine grasslands in the fragmented landscape of SE Pennsylvania, USA using ~4500 neutral SNP loci. Specifically, we test the extent to which radical alteration of the landscape matrix by humans has fundamentally altered the cost of movement, imprinting a pattern of IBR dictated by land use type and intensity, and the potential for IBE in relation to a gradient of heavy metal concentrations found in serpentine soil. We reveal a strong signal of IBR and a weak signal of IBE across sites, indicating the greater importance of the landscape matrix in shaping genetic structure of S.angularis populations in the study region. Based on Circuitscape and least cost path approaches, we find that both low- and high-intensity urbanization resist gene flow by orders of magnitude greater than "natural" habitats, although resistance to low-intensity urbanization weakens at larger spatial scales. While cropland presents a substantially lower barrier than urban development, cumulative human land use surrounding populations predicts within-population genetic diversity and inbreeding in S.angularis. Our results emphasize the role of forest buffers and corridors in facilitating gene flow between serpentine grassland patches and averting local extinction of plant populations.

Genomic vulnerability to rapid climate warming in a tree species with a long generation time.

The ongoing increase in global temperature affects biodiversity, especially in mountain regions where climate change is exacerbated. As sessile, long-lived organisms, trees are especially challenged in terms of adapting to rapid climate change. Here, we show that low rates of allele frequency shifts in Swiss stone pine (Pinus cembra) occurring near the treeline result in high genomic vulnerability to future climate warming, presumably due to the species' long generation time. Using exome sequencing data from adult and juvenile cohorts in the Swiss Alps, we found an average rate of allele frequency shift of 1.23×10-2 /generation (i.e. 40years) at presumably neutral loci, with similar rates for putatively adaptive loci associated with temperature (0.96×10-2 /generation) and precipitation (0.91×10-2 /generation). These recent shifts were corroborated by forward-in-time simulations at neutral and adaptive loci. Additionally, in juvenile trees at the colonisation front we detected alleles putatively beneficial under a future warmer and drier climate. Notably, the observed past rate of allele frequency shift in temperature-associated loci was decidedly lower than the estimated average rate of 6.29×10-2 /generation needed to match a moderate future climate scenario (RCP4.5). Our findings suggest that species with long generation times may have difficulty keeping up with the rapid climate change occurring in high mountain areas and thus are prone to local extinction in their current main elevation range.

No Population Genetic Structure of Skipjack Tuna (Katsuwonus pelamis) in the Tropical Western and Central Pacific Assessed Using Single Nucleotide Polymorphisms

Skipjack tuna (Katsuwonus pelamis) has historically been considered panmictic at the ocean basin scale because of the species’ life history and substantial absolute population size. However, recent advances in population genomics have enabled scientists to demonstrate population structure in other species that were likewise traditionally assumed to be panmictic. Accordingly, we used DArTseq, a proprietary platform of reduced-representation genome sequencing developed by Diversity Arrays Technology (DArTech) to genotype 222 skipjack tuna from 9 sample groups collected across 6 exclusive economic zones (EEZs) and over 6 years in the tropical Western and Central Pacific Ocean. This is one of the most fine-scale population genetics assessments of skipjack tuna to date. We found several statistically significant pairwise FST comparisons using purportedly neutral loci, but very little indication of structure based on observed and expected heterozygosity, effective population size, a Mantel test, AMOVA, numerous genetic clustering and population assignment tests, and exploration of correlation with oceanographic features. Significant pairwise FST values were often shallow and resulted in uncertainty about their biological significance. Furthermore, a test of the hypothesis that the geographic and temporal distribution of the potentially adaptive genetic diversity may depict cryptic fine scale structure using two different outlier detection methods, could not reject panmixia based on estimates of fixation indices and two clustering software. Our results support the presence of a single population of skipjack tuna in the tropical Western and Central Pacific Ocean, but highly recommend the expansion of the study area, in latitude, longitude, and seasonality, before drawing any global conclusions.

Life-stage-dependent supergene haplotype frequencies and metapopulation neutral genetic patterns of Atlantic cod, Gadus morhua, from Canada's Northern cod stock region and adjacent areas.

Among highly migratory fish species, nursery areas occupied by juveniles often differ from adult habitats. To better understand the spatial dynamics of Canada's Northern cod stock, juveniles caught off the east coast of Newfoundland and Labrador were compared to adults from the same region as well as individuals from other areas in Atlantic Canada using double-digest restriction site-associated DNA sequencing-derived single nucleotide polymorphisms. A reduced proportion of homozygotes with a chromosomal inversion located in linkage group 1 (LG1) was detected between juvenile and adult samples in the Northern cod stock region, potentially indicating age-dependent habitat use or ontogenetic selection for attributes associated with the many genes located in LG1. No selectively neutral genetic differences were found between samples from the Northern cod stock; nevertheless, significant differences were found between some of these samples and cod collected from St. Pierre Bank, Bay of Fundy, Browns Bank and the southern Scotian Shelf. Clustering analysis of variants at neutral loci provided evidence for three major genetic units: (a) the Newfoundland Atlantic Coast, (b) eastern and southern Gulf of St. Lawrence and Burgeo Bank and (c) the Bay of Fundy, Browns Bank and southern Scotian Shelf. Both adaptive and neutral population structure within the Northern cod stock should be considered by managers to promote demographic rebuilding of the stock.

Population Genetic Structure and Connectivity of the European Lobster Homarus gammarus in the Adriatic and Mediterranean Seas.

Highly selective fishing has the potential to permanently change the characteristics within a population and could drive the decline of genetic diversity. European lobster is an intensively fished crustacean species in the Adriatic Sea which reaches high market value. Since knowledge of population structure and dynamics is important for effective fisheries management, in this study, we used 14 neutral microsatellites loci and partial mitochondrial COI region sequencing to explore population connectivity and genetic structure by comparing samples from the Adriatic Sea and the adjacent basins of the Mediterranean Sea. The obtained results suggest that neutral genetic diversity has not been significantly affected by decrease in population size due to overfishing, habitat degradation and other anthropogenic activities. Global genetic differentiation across all populations was low (FST = 0.0062). Populations from the Adriatic Sea were panmictic, while genetic differentiation was found among populations from different Mediterranean basins. Observed gene flow for European lobster suggest that populations in the north eastern Adriatic act as a source for surrounding areas, emphasizing the need to protect these populations by establishing interconnected MPAs that will be beneficial for both fisheries and conservation management.

Horizontal genetic exchange of chromosomally encoded markers between Campylobacter jejuni cells.

Many epidemiological studies provide us with the evidence of horizontal gene transfer (HGT) contributing to the bacterial genomic diversity that benefits the bacterial populations with increased ability to adapt to the dynamic environments. Campylobacter jejuni, a major cause of acute enteritis in the U.S., often linked with severe post-infection neuropathies, has been reported to exhibit a non-clonal population structure and comparatively higher strain-level genetic variation. In this study, we provide evidence of the HGT of chromosomally encoded genetic markers between C. jejuni cells in the biphasic MH medium. We used two C. jejuni NCTC-11168 mutants harbouring distinct antibiotic-resistance genes [chloramphenicol (Cm) and kanamycin (Km)] present at two different neutral genomic loci. Cultures of both marker strains were mixed together and incubated for 5 hrs, then plated on MH agar plates supplemented with both antibiotics. The recombinant cells with double antibiotic markers were generated at the frequency of 0.02811 ± 0.0035% of the parental strains. PCR assays using locus-specific primers confirmed that transfer of the antibiotic-resistance genes was through homologous recombination. Also, the addition of chicken cecal content increased the recombination efficiency approximately up to 10-fold as compared to the biphasic MH medium (control) at P < 0.05. Furthermore, treating the co-culture with DNase I decreased the available DNA, which in turn significantly reduced recombination efficiency by 99.92% (P < 0.05). We used the cell-free supernatant of 16 hrs-culture of Wild-type C. jejuni as a template for PCR and found DNA sequences from six different genomic regions were easily amplified, indicating the presence of released chromosomal DNA in the culture supernatant. Our findings suggest that HGT in C. jejuni is facilitated in the chicken gut environment contributing to in vivo genomic diversity. Additionally, C. jejuni might have an active mechanism to release its chromosomal DNA into the extracellular environment, further expediting HGT in C. jejuni populations.

Mixed support for gene flow as a constraint to local adaptation and contributor to the limited geographic range of an endemic salamander

Understanding mechanisms that underlie species range limits is at the core of evolutionary ecology. Asymmetric gene flow between larger core populations and smaller edge populations can swamp local adaptation at the range edge and inhibit further range expansion. However, empirical tests of this theory are exceedingly rare. We tested the hypothesis that asymmetric gene flow can constrain local adaptation and thereby species' range limits in an endemic US salamander (Ambystoma barbouri) by determining if gene flow is asymmetric between the core and peripheries of the species' geographic distribution and testing whether local adaptation is swamped at range edges with a reciprocal transplant experiment. Using putatively neutral loci from populations across three core-to-edge transects that covered nearly the entire species' geographic range, we found evidence for asymmetric, core-to-edge gene flow along western and northern transects, but not along a southern transect. Subsequently, the reciprocal transplant experiment suggested that northern and western edge populations are locally adapted despite experiencing asymmetric gene flow, yet have lower fitness in their respective home regions than those of centre population. Conversely, southern populations exhibit low deme quality, experiencing high mortality regardless of where they were reared, probably due to harsher edge habitat conditions. Consequently, we provide rare species-wide evidence that local adaptation can occur despite asymmetric gene flow, though migration from the core may prohibit range expansion by reducing fitness in edge populations. Further, our multitransect study shows that multiple, nonmutually exclusive mechanisms can lead to range limits within a single species.

The Spatial Signature of Introgression After a Biological Invasion With Hybridization

The accumulation of genome-wide molecular data has emphasized the important role of hybridization in the evolution of many organisms, which may carry introgressed genomic segments resulting from past admixture events with other taxa. Despite a number of examples of hybridization occurring during biological invasions, the resulting spatial patterns of genomic introgression remain poorly understood. Preliminary simulation studies have suggested a heterogeneous spatial level of introgression for invasive taxa after range expansion. We investigated in detail the robustness of this pattern and its persistence over time for both invasive and local organisms. Using spatially explicit simulations, we explored the spatial distribution of introgression across the area of colonization of an invasive taxon hybridizing with a local taxon. The general pattern for neutral loci supported by our results is an increasing introgression of local genes into the invasive taxon with the increase in the distance from the source of the invasion and a decreasing introgression of invasive genes into the local taxon. However, we also show there is some variation in this general trend depending on the scenario investigated. Spatial heterogeneity of introgression within a given taxon is thus an expected neutral pattern in structured populations after a biological invasion with a low to moderate amount of hybridization. We further show that this pattern is consistent with published empirical observations. Using additional simulations, we argue that the spatial pattern of Neanderthal introgression in modern humans, which has been documented to be higher in Asia than in Europe, can be explained by a model of hybridization with Neanderthals in Eurasia during the range expansion of modern humans from Africa. Our results support the view that weak hybridization during range expansion may explain spatially heterogeneous introgression patterns without the need to invoke selection.

Supporting Fisheries Management With Genomic Tools: A Case Study of Kingklip (Genypterus capensis) Off Southern Africa

Kingklip, Genypterus capensis, is one of southern Africa’s most valuable demersal fisheries resources, with a wide geographic distribution spanning South Africa and Namibia. Previous studies have provided evidence for multiple stocks in South Africa, but the extent of stock structuring across the Southern African region remains unclear. In this study we genotyped over 40 000 SNPs to characterise the spatial distribution of genomic variation for G. capensis throughout its core distribution. Results suggest that fish sampled at the northernmost range (off central Namibia) are characterised by the lower genomic diversity, although the region was characterised by the highest number of private SNPs, suggesting some degree of geographic isolation. Using neutral and putative outlier loci independently, we show that Kingklip exhibits three population clusters, “northern Benguela”, “southern Benguela” and South African “South Coast”. Population differentiation was observed only using “outlier” loci, suggesting that local adaptation might be one of the main drivers of the observed differentiation. Overall, our research provides novel insights into the regional dynamics that can support the sustainable long-term exploitation of this valuable fisheries resource.

Habitat fragmentation differentially shapes neutral and immune gene variation in a tropical bird species.

Habitat fragmentation is a major cause of biodiversity loss, responsible for an alteration of intraspecific patterns of neutral genetic diversity and structure. Although neutral genetic variation can be informative for demographic inferences, it may be a poor predictor of adaptive genetic diversity and thus of the consequences of habitat fragmentation on selective evolutionary processes. In this context, we contrasted patterns of genetic diversity and structure of neutral loci (microsatellites) and immune genes (i.e., toll-like receptors) in an understorey bird species, the wedge-billed woodcreeper Glyphorynchus spirurus. The objectives were (1) to investigate forest fragmentation effects on population genetic diversity, (2) to disentangle the relative role of demography (genetic drift and migration) and selection, and (3) to assess whether immunogenetic patterns could be associated with variation of ectoparasite (i.e., ticks) pressures. Our results revealed an erosion of neutral genetic diversity and a substantial genetic differentiation among fragmented populations, resulting from a decrease in landscape connectivity and leading to the divergence of distinct genetic pools at a small spatial scale. Patterns of genetic diversity observed for TLR4 and TLR5 were concordant with neutral genetic patterns, whereas those observed for TLR3 and TLR21 were discordant. This result underlines that the dominant evolutionary force shaping immunogenetic diversity (genetic drift vs. selection) may be different depending on loci considered. Finally, tick prevalence was higher in fragmented environments. We discussed the hypothesis that pathogen selective pressures may contribute to maintain adaptive genetic diversity despite the negative demographic effect of habitat fragmentation on neutral genetic diversity.

Fine-scale spatial and temporal genomic variation among Dungeness crab Cancer magister larval recruits in the California Current Ecosystem

Dynamic marine environments can shape complex spatial and temporal patterns in the population connectivity of marine species, and this is often exemplified in species with long larval phases. Here, we used a genotyping-by-sequencing (GBS) approach to examine fine-scale spatial and temporal genomic variation among Dungeness crabCancer magisterlarval recruits sampled in the California Current Ecosystem. Specifically, we compared samples collected during expected- and late-season recruitment time periods within 2 consecutive years (2017 and 2018) at 2 sites in Oregon, USA (Yaquina Bay and Coos Bay). Evidence was found for high gene flow between the expected- and late-season recruits within each year and at both sites based on 1389 neutral loci. In contrast, strong genetic differentiation was observed between these 2 groups within each year and at both sites based on variation at 2 putatively adaptive loci. Contrary to prediction, the magnitude of genetic differentiation between these 2 seasonal groups was greater in 2017 when the Pacific Decadal Oscillation was stronger, upwelling was weaker, and the spring transition was later. Spatial genetic variation was not observed within 2017 or 2018. Comparing across years, expected- and late-season groups were differentiated at putatively adaptive loci. Interestingly, strong genetic differentiation was also observed between late-season groups across years. We found no evidence for cohesive larval dispersal among recruits based on genetic relatedness estimates. Overall, our findings provide evidence for high connectivity within Dungeness crab, but suggest that selective pressures and ocean conditions influence the genetic composition of larval recruits both intra- and inter-annually.

Individual-based dendrogenomic analysis of forest dieback driven by extreme droughts

Droughts driven by global change are triggering worldwide forest dieback, a phenomenon that is predicted to worsen. We combined genome-wide single nucleotide polymorphisms (SNPs) and dendrochronological approaches to assess genetically-based individual tree vulnerability to past extreme droughts that caused massive mortality of coihue (Nothofagus dombeyi (Mirb.) Blume) forests in northern Patagonia, Argentina. We collected fresh leaves and wood cores from pairs of trees, one with a healthy crown (HC) and another with a partially affected crown (PA), at four sites impacted by droughts in 1998, 2008, and 2014. We used dendrochronological techniques to estimate parameters in terms of growth trends due to drought and genomic analysis to assess the relationship of genomic variation with water stress. While 5155 neutral loci did not differentiate PA from HC trees, a set of 33 adaptive SNPs did, 8 of which were related to water stress. Association analysis between genomic variants and dendrophenotypic traits yielded 6 SNPs that were associated with a growth measure as resilience to cope with drought. Our preliminary results indicate that susceptibility to drought in N. dombeyi could be determined at the genomic level. The combination of these approaches provides a framework for the identification and analysis of candidate genes for stress response in non-model species.

Management of Genetic Diversity in the Era of Genomics.

Management of genetic diversity aims to (i) maintain heterozygosity, which ameliorates inbreeding depression and loss of genetic variation at loci that may become of importance in the future; and (ii) avoid genetic drift, which prevents deleterious recessives (e.g., rare disease alleles) from drifting to high frequency, and prevents random drift of (functional) traits. In the genomics era, genomics data allow for many alternative measures of inbreeding and genomic relationships. Genomic relationships/inbreeding can be classified into (i) homozygosity/heterozygosity based (e.g., molecular kinship matrix); (ii) genetic drift-based, i.e., changes of allele frequencies; or (iii) IBD-based, i.e., SNPs are used in linkage analyses to identify IBD segments. Here, alternative measures of inbreeding/relationship were used to manage genetic diversity in genomic optimal contribution (GOC) selection schemes. Contrary to classic inbreeding theory, it was found that drift and homozygosity-based inbreeding could differ substantially in GOC schemes unless diversity management was based upon IBD. When using a homozygosity-based measure of relationship, the inbreeding management resulted in allele frequency changes toward 0.5 giving a low rate of increase in homozygosity for the panel used for management, but not for unmanaged neutral loci, at the expense of a high genetic drift. When genomic relationship matrices were based on drift, following VanRaden and as in GCTA, drift was low at the expense of a high rate of increase in homozygosity. The use of IBD-based relationship matrices for inbreeding management limited both drift and the homozygosity-based rate of inbreeding to their target values. Genetic improvement per percent of inbreeding was highest when GOC used IBD-based relationships irrespective of the inbreeding measure used. Genomic relationships based on runs of homozygosity resulted in very high initial improvement per percent of inbreeding, but also in substantial discrepancies between drift and homozygosity-based rates of inbreeding, and resulted in a drift that exceeded its target value. The discrepancy between drift and homozygosity-based rates of inbreeding was caused by a covariance between initial allele frequency and the subsequent change in frequency, which becomes stronger when using data from whole genome sequence.