Genomic implications of the repeated shift to self-fertilization across a species' geographic distribution.

The ability to self-fertilize often varies among closely related hermaphroditic plant species, though, variation can also exist within species. In the North American Arabidopsis lyrata, the shift from self-incompatibility (SI) to selfing established in multiple regions independently, mostly since recent postglacial range expansion. This has made the species an ideal model for the investigation of the genomic underpinnings of the breakdown of SI and its population genetic consequences. By comparing nearby selfing and outcrossing populations across the entire species' geographic distribution, we investigated variation at the self-incompatibility (S-)locus and across the genome. Furthermore, a diallel crossing experiment on one mixed-mating population was performed to gain insight in the genetics of mating system variation. We confirmed that the breakdown of SI had evolved in several S-locus backgrounds. The diallel suggested the involvement of binuclearly expressed parental genes with dominance relations. Though, the population-level genome-wide association study did not single out clear-cut candidate genes but several regions with one near the S-locus. On the implication side, selfing as compared to outcrossing populations had less than half of the genomic diversity, while the number of runs of homozygosity and their length scaled with the degree of inbreeding. The results highlight that mating system shifts to selfing, its genetic underpinning and the likely negative genomic consequences for evolutionary potential can be strongly interlinked with past range dynamics.

The genetic architecture of repeated local adaptation to climate in distantly related plants.

Closely related species often use the same genes to adapt to similar environments. However, we know little about why such genes possess increased adaptive potential and whether this is conserved across deeper evolutionary lineages. Adaptation to climate presents a natural laboratory to test these ideas, as even distantly related species must contend with similar stresses. Here, we re-analyse genomic data from thousands of individuals from 25 plant species as diverged as lodgepole pine and Arabidopsis (~300 Myr). We test for genetic repeatability based on within-species associations between allele frequencies in genes and variation in 21 climate variables. Our results demonstrate significant statistical evidence for genetic repeatability across deep time that is not expected under randomness, identifying a suite of 108 gene families (orthogroups) and gene functions that repeatedly drive local adaptation to climate. This set includes many orthogroups with well-known functions in abiotic stress response. Using gene co-expression networks to quantify pleiotropy, we find that orthogroups with stronger evidence for repeatability exhibit greater network centrality and broader expression across tissues (higher pleiotropy), contrary to the 'cost of complexity' theory. These gene families may be important in helping wild and crop species cope with future climate change, representing important candidates for future study.

Evolutionary potential under heat and drought stress at the southern range edge of North American Arabidopsis lyrata.

The warm edges of species' distributions are vulnerable to global warming. Evidence is the recent range retraction from there found in many species. It is unclear why populations cannot easily adapt to warmer, drier, or combined hot and dry conditions and locally persist. Here, we assessed the ability to adapt to these stressors in the temperate species Arabidopsis lyrata. We grew plants from replicate seed families of a central population with high genetic diversity under a temperature and precipitation regime typical of the low-latitude margin or under hotter and/or drier conditions within naturally occurring amplitudes. We then estimated genetic variance-covariance (G-) matrices of traits depicting growth and allocation as well as selection vectors to compare the predicted adaptation potential under the different climate-stress regimes. We found that the sum of genetic variances and genetic correlations were not significantly different under stress as compared to benign conditions. However, under drought and heat drought, the predicted ability to adapt was severely constrained due to strong selection and selection pointing in a direction with less multivariate genetic variation. The much-reduced ability to adapt to dry and hot-dry conditions is likely to reduce the persistence of populations at the low-latitude margin of the species' distribution and contribute to the local extinction of the species under further warming.

Negative interaction effect of heat and drought stress at the warm end of species distribution.

Geographic range limits of species are often a reflection of their ecological niche limits. In many organisms, important niche limits that coincide with distribution limits are warm and warm-dry conditions. We investigated the effects of heat and drought, as they can occur at the warm end of distribution. In a greenhouse experiment, we raised North American Arabidopsis lyrata from the centre of its distribution as well as from low- and high-latitude limits under average and extreme conditions. We assessed plant growth and development, as well as leaf and root functional traits, and tested for a decline in performance and selection acting on growth, leaf, and root traits. Drought and heat, when applied alone, lowered plant performance, while combined stress caused synergistically negative effects. Plants from high latitudes did not survive under combined stress, whereas plants originating from central and low latitudes had low to moderate survival, indicating divergent adaptation. Traits positively associated with survival under drought, with or without heat, were delayed and slowed growth, though plastic responses in these traits were generally antagonistic to the direction of selection. In line, higher tolerance of stress in southern populations did not involve aspects of growth but rather a higher root-to-shoot ratio and thinner leaves. In conclusion, combined heat and drought, as can occur at southern range edges and presumably more so under global change, seriously impede the long-term persistence of A. lyrata, even though they impose selection and populations may adapt, though under likely interference by considerable maladaptive plasticity.

Asynchronous life cycles contribute to reproductive isolation between two Alpine butterflies.

Geographic isolation often leads to the emergence of distinct genetic lineages that are at least partially reproductively isolated. Zones of secondary contact between such lineages are natural experiments that allow investigation of how reproductive isolation evolves and co-existence is maintained. While temporal isolation through allochrony has been suggested to promote reproductive isolation in sympatry, its potential for isolation upon secondary contact is far less understood. Sampling two contact zones of a pair of mainly allopatric Alpine butterflies over several years and taking advantage of museum samples, we show that the contact zones have remained geographically stable over several decades. Furthermore, they seem to be maintained by the asynchronous life cycles of the two butterflies, with one reaching adulthood primarily in even and the other primarily in odd years. Genomic inferences document that allochrony is leaky and that gene flow from allopatric sites scales with the degree of geographic isolation. Overall, we show that allochrony has the potential to contribute to the maintenance of secondary contact zones of lineages that diverged in allopatry.

Intraspecific variation in reproductive barriers between two closely related Arabidopsis sister species.

Reproductive isolation (RI) is a critical component of speciation and varies strongly in timing and strength among different sister taxa, depending on, for example the geography of speciation and divergence time. However, these factors may also produce variation in timing and strength among populations within species. Here we tested for variation in the expression of RI among replicate population pairs between the sister taxa Arabidopsis lyrata subsp. lyrata and A. arenicola. While the former is predominantly outcrossing, the latter is predominantly selfing. We focused on intrinsic prezygotic and postzygotic RI as both species occur largely in allopatry. We assessed RI by performing within-population crosses and interspecific between-population crosses, and by raising offspring. RI was generally high between all interspecific population pairs, but it varied in timing and strength depending on population history. Prezygotic isolation was strongest between the closest-related population pair, while early postzygotic isolation was high for all other population pairs. Furthermore, the timing and strength of RI depended strongly on cross direction. Our study provides empirical support that reproductive barriers between species are highly variable among population pairs and asymmetric within population pairs, and this variation seems to follow patterns typically described across species pairs.

Recent speciation associated with range expansion and a shift to self-fertilization in North American Arabidopsis.

The main processes classically evoked for promoting reproductive isolation and speciation are geographic separation reducing gene flow among populations, divergent selection, and chance genomic change. In a case study, we present evidence that the additional factors of climate change, range expansion and a shift in mating towards inbreeding can initiate the processes leading to parapatric speciation. At the end of the last Pleistocene glaciation cycle, the North American plant Arabidopsis lyrata expanded its range and concomitantly lost its reproductive mode of outcrossing multiple times. We show that in one of the newly colonized areas, the self-fertilizing recolonization lineage of A. lyrata gave rise to selfing A. arenicola, which expanded its range to subarctic and arctic Canada and Greenland, while the parental species remained restricted to temperate North America. Despite the vast range expansion by the new species, mutational load did not increase, probably because of selfing and quasi-clonal selection. We conclude that such peripheral parapatric speciation combined with range expansion and inbreeding may be an important but so far overlooked mode of speciation.

Cryptic population structure at the northern range margin of the service tree Sorbus domestica.

Climate change has aroused interest in planting warm- and drought-adapted trees in managed forests and urban areas. An option is to focus on tree species that occur naturally, but have centers of distribution in warmer and drier areas. However, in order to protect the species pool of genetic diversity, efforts of planting and promotion should be informed by knowledge on the local genetic diversity. Here, we studied the macro- and micro-scale population genetic structure of the rare European fruit tree Sorbus domestica at its northern range margin, in western Switzerland. New microsatellite data were combined with published data from across the European distribution of the species. Analyses revealed the presence of mainly one of two species-wide ancestral clusters, i.e., the western European cluster, with evidence that it consists of two cryptic sub-clusters. Average pairwise F ST of 0.118 was low across the range, and only allelic richness was reduced in the northern margin compared to more southern and southeastern areas of Europe. Based on our finding of considerable genetic diversity of the species in western and northern Switzerland, we suggest that a national propagation program should focus on collecting seeds from natural, high-density tree stands and propagate locally. More generally, our study shows that rare tree species in marginal areas of their distributions do not necessarily have low genetic diversity or heightened levels of inbreeding, and in those cases probably need no assisted migration in efforts to propagate them.

Reduced pollinator service in small populations of Arabidopsis lyrata at its southern range limit.

Even though a high fraction of angiosperm plants depends on animal pollinators for sexual reproduction, little is known how pollinator service changes across the ranges of plant species and whether it may contribute to range limits. Here, we tested for variation in pollinator service in the North American Arabidopsis lyrata from its southern to northern range edge and evaluated the driving mechanisms. We monitored insect pollinators using time-lapse cameras in 13 populations over two years and spotted 67 pollinating insect taxa, indicating the generalist nature of this plant-pollinator system. Pollinator service was highest at intermediate local flower densities and higher in large compared to small plant populations. Southern populations had generally smaller population sizes, and visitation rate and pollination ratio decreased with latitude. We also found that pollinator visitation was positively correlated with the richness of other flowering plants. This study indicates that plant populations at southern range edges receive only marginal pollinator service if they are small, and the effect of lower pollination is also detectable within populations across the range when the local flower density is low. Results, therefore, suggest the potential for an Allee effect in pollination that manifests itself across spatial scales.

Trait divergence and trade-offs among Brassicaceae species differing in elevational distribution.

Species have restricted geographic distributions and the causes are still largely unknown. Temperature has long been associated with distribution limits, suggesting that there are ubiquitous constraints to the evolution of the climate niche. Here, we investigated the traits involved in such constraints by macroevolutionary comparisons involving 100 Brassicaceae species differing in elevational distribution. Plants were grown under three temperature treatments (regular frost, mild, regular heat) and phenotyped for phenological, morphological, and thermal resistance traits. Trait values were analyzed by assessing the effect of temperature and elevational distribution, by comparing models of evolutionary trajectories, and by correlative approaches to identify trade-offs. Analyses pointed to size, leaf morphology, and growth under heat as among the most discriminating traits between low- and high-elevation species, with high-elevation species growing faster under the occurrence of regular heat bouts, at the cost of reduced size. Mixed models and evolutionary models supported adaptive divergence for these traits, and correlation analysis indicated their involvement in moderate trade-offs. Finally, we found asymmetry in trait evolution, with evolvability across traits being 50% less constrained under regular frost. Overall, results suggest that trade-offs between traits under adaptive divergence contribute to the disparate distribution of species along the elevational gradient.

Environment dependence of the expression of mutational load and species' range limits.

Theoretical and empirical research on the causes of species' range limits suggest the contribution of several intrinsic and extrinsic factors, with potentially complex interactions among them. An intrinsic factor proposed by recent theory is mutational load increasing towards range edges because of genetic drift. Furthermore, environmental quality may decline towards range edges and enhance the expression of load. Here, we tested whether the expression of mutational load associated with range limits in the North American plant Arabidopsis lyrata was enhanced under stressful environmental conditions by comparing the performance of within- versus between-population crosses at common garden sites across the species' distribution and beyond. Heterosis, reflecting the expression of load, increased with heightened estimates of genomic load and with environmental stress caused by warming, but the interaction was not significant. We conclude that range-edge populations suffer from a twofold genetic Allee effect caused by increased mutational load and stress-dependent load linked to general heterozygote deficiency, but there is no synergistic effect between them.

A review on trade-offs at the warm and cold ends of geographical distributions.

Species' range limits are ubiquitous. This suggests that the evolution of the ecological niche is constrained in general and at the edges of distributions in particular. While there may be many ecological and genetic reasons for this phenomenon, here we focus on the potential role of trade-offs. We performed a literature search on evidence for trade-offs associated with geographical or elevational range limits. The majority of trade-offs were reported as relevant at either the cold end of species' distribution (n = 19), the warm or dry end (n = 19) or both together (n = 14). One common type of trade-off involved accelerating growth or development (27%), often at the cost of small size. Another common type involved resistance to or tolerance of climatic extremes that occur at certain periods of the year (64%), often at the cost of small size or reduced growth. Trade-offs overlapped with some of the classic trade-offs reported in life-history evolution or thermal adaptation. The results highlight several general insights about species' niches and ranges, and we outline how future research should better integrate the ecological context and test for the presence of microevolutionary trade-offs. This article is part of the theme issue 'Species' ranges in the face of changing environments (Part II)'.

Niche breadth and elevational range size: a comparative study on Middle-European Brassicaceae species.

High-elevation species are predicted to have larger elevational ranges compared with species of lower elevations. The reasoning is that temperature variability is greater at higher elevation, selecting for wider niche breadth and more plastic genotypes. We used macroevolutionary comparisons involving 90 Brassicaceae species of the central Alps to test for associations among median elevation of occurrence, elevational range size and thermal variability over space and time on the one hand, and their associations with performance breadth or trait plasticity on the other hand. Performance breadth and trait plasticity were estimated by raising replicate plants per species under three temperature treatments (mild, recurrent frost, recurrent heat). Against prediction, we found that mid-elevation species had the largest elevational ranges, and their ranges were associated with increased spatial thermal variability. Nevertheless, variability in the thermal regime was positively associated neither with niche breadth nor with plasticity. Evidence for adaptive constraints was limited to a trade-off between acclimation-based increases in frost and heat resistance, and phylogenetic niche conservatism for median elevation of occurrence and temporal thermal variability. Results suggest that large elevational range size is associated with divergent adaptation within species, but not with more niche breadth or trait plasticity. This article is part of the theme issue 'Species' ranges in the face of changing environments (part I)'.

Conservation genetics as a management tool: The five best-supported paradigms to assist the management of threatened species.

About 50 y ago, Crow and Kimura [An Introduction to Population Genetics Theory (1970)] and Ohta and Kimura [Genet. Res. 22, 201-204 (1973)] laid the foundations of conservation genetics by predicting the relationship between population size and genetic marker diversity. This work sparked an enormous research effort investigating the importance of population dynamics, in particular small population size, for population mean performance, population viability, and evolutionary potential. In light of a recent perspective [J. C. Teixeira, C. D. Huber, Proc. Natl. Acad. Sci. U.S.A. 118, 10 (2021)] that challenges some fundamental assumptions in conservation genetics, it is timely to summarize what the field has achieved, what robust patterns have emerged, and worthwhile future research directions. We consider theory and methodological breakthroughs that have helped management, and we outline some fundamental and applied challenges for conservation genetics.

Drivers of linkage disequilibrium across a species' geographic range.

While linkage disequilibrium (LD) is an important parameter in genetics and evolutionary biology, the drivers of LD remain elusive. Using whole-genome sequences from across a species' range, we assessed the impact of demographic history and mating system on LD. Both range expansion and a shift from outcrossing to selfing in North American Arabidopsis lyrata were associated with increased average genome-wide LD. Our results indicate that range expansion increases short-distance LD at the farthest range edges by about the same amount as a shift to selfing. However, the extent over which LD in genic regions unfolds was shorter for range expansion compared to selfing. Linkage among putatively neutral variants and between neutral and deleterious variants increased to a similar degree with range expansion, providing support that genome-wide LD was positively associated with mutational load. As a consequence, LD combined with mutational load may decelerate range expansions and set range limits. Finally, a small number of genes were identified as LD outliers, suggesting that they experience selection by either of the two demographic processes. These included genes involved in flowering and photoperiod for range expansion, and the self-incompatibility locus for mating system.

Demographic Processes Linked to Genetic Diversity and Positive Selection across a Species' Range.

Demography determines the strength of genetic drift, which generally reduces genetic variation and the efficacy of selection. Here, we disentangled the importance of demographic processes at a local scale (census size and mating system) and at a species-range scale (old split between population clusters, recolonization after the last glaciation cycle, and admixture) in determining within-population genomic diversity and genomic signatures of positive selection. Analyses were based on re-sequence data from 52 populations of North American Arabidopsis lyrata collected across its entire distribution. The mating system and range dynamics since the last glaciation cycle explained around 60% of the variation in genomic diversity among populations and 52% of the variation in the signature of positive selection. Diversity was lowest in selfing compared with outcrossing populations and in areas further away from glacial refugia. In parallel, reduced positive selection was found in selfing populations and in populations with a longer route of postglacial range expansion. The signature of positive selection was also reduced in populations without admixture. We conclude that recent range expansion can have a profound influence on diversity in coding and non-coding DNA, similar in magnitude to the shift toward selfing. Distribution limits may in fact be caused by reduced effective population size and compromised positive selection in recently colonized parts of the range.

Expressed mutational load increases toward the edge of a species' geographic range.

There is no general explanation for why species have restricted geographic distributions. One hypothesis posits that range expansion or increasing scarcity of suitable habitat results in accumulation of mutational load due to enhanced genetic drift, which constrains population performance toward range limits and further expansion. We tested this hypothesis in the North American plant, Arabidopsis lyrata. We experimentally assessed mutational load by crossing plants of 20 populations from across the entire species range and by raising the offspring of within- and between-population crosses at five common garden sites within and beyond the range. Offspring performance was tracked over three growing seasons. The heterosis effect, depicting expressed mutational load, was increased in populations with heightened genomic estimates of load, longer expansion distance or long-term isolation, and a selfing mating system. The decline in performance of within-population crosses amounted to 80%. Mutation accumulation due to past range expansion and long-term isolation of populations in the area of range margins is therefore a strong determinant of population-mean performance, and the magnitude of effect may be sufficient to cause range limits.

Lineage-specific adaptation to climate involves flowering time in North American Arabidopsis lyrata.

Adaptation to local climatic conditions is commonly found within species, but whether it involves the same intraspecific genomic variants is unknown. We studied this question in North American Arabidopsis lyrata, whose current distribution is shaped by post-glacial range expansion from two refugia, resulting in two distinct genetic clusters covering comparable climatic gradients. Using pooled whole-genome sequence data of 41 outcrossing populations, we identified loci associated with three niche-determining climatic variables in the two clusters and compared these outliers. Little evidence was found for parallelism in climate adaptation for single nucleotide polymorphisms (SNPs) and for genes with an accumulation of outlier SNPs. Significantly increased selection coefficients supported them as candidates of climate adaptation. However, the fraction of gene ontology (GO) terms shared between clusters was higher compared to outlier SNPs and outlier genes, suggesting that selection acts on similar pathways but not necessarily the same genes. Enriched GO terms involved responses to abiotic and biotic stress, circadian rhythm and development, with flower development and reproduction being among the most frequently detected. In line with GO enrichment, regulators of flowering time were detected as outlier genes. Our results suggest that while adaptation to environmental gradients on the genomic level are lineage-specific in A. lyrata, similar biological processes seem to be involved. Differential loss of standing genetic variation, probably driven by genetic drift, can in part account for the lack of parallel evolution on the genomic level.

A Practical Guide to the Study of Distribution Limits.

Factors that limit the geographic distribution of species are broadly important in ecology and evolutionary biology, and understanding distribution limits is imperative for predicting how species will respond to environmental change. Good data indicate that factors such as dispersal limitation, small effective population size, and isolation are sometimes important. But empirical research highlights no single factor that explains the ubiquity of distribution limits. In this article, we outline a guide to tackling distribution limits that integrates established causes, such as dispersal limitation and spatial environmental heterogeneity, with understudied causes, such as mutational load and genetic or developmental integration of traits limiting niche expansion. We highlight how modeling and quantitative genetic and genomic analyses can provide insight into sources of distribution limits. Our practical guide provides a framework for considering the many factors likely to determine species distributions and how the different approaches can be integrated to predict distribution limits using eco-evolutionary modeling. The framework should also help predict distribution limits of invasive species and of species under climate change.