Genetic and phenotypic divergence in an island bird: isolation by distance, by colonization or by adaptation?

Discerning the relative roles of adaptive and nonadaptive processes in generating differences among populations and species, as well as how these processes interact, is a fundamental aim in biology. Both genetic and phenotypic divergence across populations can be the product of limited dispersal and gradual genetic drift across populations (isolation by distance), of colonization history and founder effects (isolation by colonization) or of adaptation to different environments preventing migration between populations (isolation by adaptation). Here, we attempt to differentiate between these processes using island populations of Berthelot's pipit (Anthus berthelotii), a passerine bird endemic to three Atlantic archipelagos. Using microsatellite markers and approximate Bayesian computation, we reveal that the northward colonization of this species ca. 8500years ago resulted in genetic bottlenecks in the colonized archipelagos. We then show that high levels of genetic structure exist across archipelagos and that these are consistent with a pattern of isolation by colonization, but not with isolation by distance or adaptation. Finally, we show that substantial morphological divergence also exists and that this is strongly concordant with patterns of genetic structure and bottleneck history, but not with environmental differences or geographic distance. Overall, our data suggest that founder effects are responsible for both genetic and phenotypic changes across archipelagos. Our findings provide a rare example of how founder effects can persist over evolutionary timescales and suggest that they may play an important role in the early stages of speciation

Long-term in situ persistence of biodiversity in tropical sky islands revealed by landscape genomics

Tropical mountains are areas of high species richness and endemism. Two historical phenomena may have contributed to this: (1) fragmentation and isolation of habitats may have promoted the genetic differentiation of populations and increased the possibility of allopatric divergence and speciation, and; (2) the mountain areas may have allowed long-term population persistence during global climate fluctuations. These two phenomena have been studied using either species occurrence data or estimating species divergence times. However, only few studies have used intraspecific genetic data to analyse the mechanisms by which endemism may emerge at the microevolutionary scale. Here, we use landscape analysis of genomic SNP data sampled from two high-elevation plant species from an archipelago of tropical sky-islands (the Transmexican Volcanic Belt) to test for population genetic differentiation, synchronous demographic changes and habitat persistence. We show that genetic differentiation can be explained by the degree of glacial habitat connectivity among mountains, and that mountains have facilitated the persistence of populations throughout glacial/interglacial cycles. Our results support the ongoing role of tropical mountains as cradles for biodiversity by uncovering cryptic differentiation and limits to gene flow

Quantitative Genetic Effects of Bottlenecks: Experimental Evidence from a Wild Plant Species, Nigella degenii

Understanding the genetic consequences of changes in population size is fundamental in a variety of contexts, such as adaptation and conservation biology. In the study presented here, we have performed a replicated experiment with the plant Nigella degenii to explore the quantitative genetic effects of a single-founder bottleneck. In agreement with additive theory, the bottleneck reduced the mean (co)variance within lines and caused stochastic, line-specific changes in the genetic (co)variance structure. However, a significant portion of the (co)variance structure was conserved, and 2 characters—leaf and flower (sepal) size—turned out to be positively correlated in all data sets, indicating a potential for correlated evolution in these characters, even after a severe bottleneck. The hierarchical partitioning of genetic variance for flower size was in good agreement with predictions from additive theory, whereas the remaining characters showed an excess of within-line variance and a deficiency of among-line variance. The latter discrepancies were most likely a result of selection, given the small proportion of lines (23%) that remained viable until the end of the experiment. Our results suggest that bottlenecked populations of N. degenii generally have a lower adaptive potential than the ancestral population but also highlight the idiosyncratic nature of bottleneck effects

The effect of environmental heterogeneity on RPW8-mediated resistance to powdery mildews in Arabidopsis thaliana

Background and Aims: The biotic and abiotic environment of interacting hosts and parasites may vary considerably over small spatial and temporal scales. It is essential to understand how different environments affect host disease resistance because this determines frequency of disease and, importantly, heterogeneous environments can retard direct selection and potentially maintain genetic variation for resistance in natural populations. Methods: The effect of different temperatures and soil nutrient conditions on the outcome of infection by a pathogen was quantified in Arabidopsis thaliana. Expression levels of a gene conferring resistance to powdery mildews, RPW8, were compared with levels of disease to test a possible mechanism behind variation in resistance. Key Results: Most host genotypes changed from susceptible to resistant across environments with the ranking of genotypes differing between treatments. Transcription levels of RPW8 increased after infection and varied between environments, but there was no tight association between transcription and resistance levels. Conclusions: There is a strong potential for a heterogeneous environment to change the resistance capacity of A. thaliana genotypes and hence the direction and magnitude of selection in the presence of the pathogen. Possible causative links between resistance gene expression and disease resistance are discussed in light of the present results on RPW8

Increased yield stability of field-grown winter barley (Hordeum vulgare L.) varietal mixtures through ecological processes

Crop variety mixtures have the potential to increase yield stability in highly variable and unpredictable environments, yet knowledge of the specific mechanisms underlying enhanced yield stability has been limited. Ecological processes in genetically diverse crops were investigated by conducting field trials with winter barley varieties (Hordeum vulgare), grown as monocultures or as three-way mixtures in fungicide treated and untreated plots at three sites. Mixtures achieved yields comparable to the best performing monocultures whilst enhancing yield stability despite being subject to multiple predicted and unpredicted abiotic and biotic stresses including brown rust (Puccinia hordei) and lodging. There was compensation through competitive release because the most competitive variety overyielded in mixtures thereby compensating for less competitive varieties. Facilitation was also identified as an important ecological process within mixtures by reducing lodging. This study indicates that crop varietal mixtures have the capacity to stabilise productivity even when environmental conditions and stresses are not predicted in advance. Varietal mixtures provide a means of increasing crop genetic diversity without the need for extensive breeding efforts. They may confer enhanced resilience to environmental stresses and thus be a desirable component of future cropping systems for sustainable arable farming

Molecular techniques reveal cryptic life history and demographic processes of a critically endangered marine turtle

The concept of ‘effective population size’ (Ne), which quantifies how quickly a population will lose genetic variability, is one of the most important contributions of theoretical evolutionary biology to practical conservation management. Ne is often much lower than actual population size: how much so depends on key life history and demographic parameters, such as mating systems and population connectivity, that often remain unknown for species of conservation concern. Molecular techniques allow the indirect study of these parameters, as well as the estimation of current and historical Ne. Here, we use genotyping to assess the genetic health of an important population of the critically endangered hawksbill turtle (Eretmochelys imbricata), a slow-to-mature, difficult-to-observe species with a long history of severe overhunting. Our results were surprisingly positive: we found that the study population, located in the Republic of Seychelles, Indian Ocean, has a relatively large Ne, estimated to exceed 1000, and showed no evidence of a recent reduction in Ne (i.e. no genetic bottleneck). Furthermore, molecular inferences suggest the species' mating system is conducive to maintaining a large Ne, with a relatively large and widely distributed male population promoting considerable gene flow amongst nesting sites across the Seychelles area. This may also be reinforced by the movement of females between nesting sites. Our study underlines how molecular techniques can help to inform conservation biology. In this case our results suggest that this important hawksbill population is starting from a relatively strong position as it faces new challenges, such as global climate change

Comparative analyses of population structure in two subspecies of Nigella degenii: evidence for diversifying selection on pollen-colour dimorphisms

Flower color can be a major determinant of plant fitness, not only because of preferential visitation by pollinators but also because of pleiotropic relationships between the expression of floral pigments and biochemically related compounds that influence vegetative performance variables. Different environments may therefore favor different pigmentation phenotypes. We examined whether spatially varying selection has played a major role in shaping large-scale patterns of differentiation in two subspecies of Nigella degenii (Ranunculaceae), with particular emphasis on pollen color. The two subspecies appear to have been genetically isolated for substantial periods of time and, therefore, provide a "replicated test" for the effect of natural selection. Estimates of population structure based on a suite of floral and vegetative characters were compared with the corresponding data for amplified fragment length polymorphism (AFLP) markers, which were assumed to be selectively neutral. We found low levels of genetic structure within the subspecies using both the AFLP markers (F-ST <= 0.05) and quantitative characters (Q(ST) <= 0.15), with no statistically significant differences between the two measures. There is, therefore, no evidence of diversifying selection being important in structuring variation in quantitative characters within each of the two subspecies. In contrast, estimates of differentiation in pollen color (F-ST <= 0.10) significantly exceeded the neutral expectations (estimated from AFLP data), Suggesting that local adaptation has played a key role in the evolution of this monogenic character