Parasite‐mediated selection in a natural metapopulation of Daphnia magna

Parasite‐mediated selection varying across time and space in metapopulations is expected to result in host local adaptation and the maintenance of genetic diversity in disease‐related traits. However, nonadaptive processes like migration and extinction‐(re)colonization dynamics might interfere with adaptive evolution. Understanding how adaptive and nonadaptive processes interact to shape genetic variability in life‐history and disease‐related traits can provide important insights into their evolution in subdivided populations. Here we investigate signatures of spatially fluctuating, parasite‐mediated selection in a natural metapopulation of Daphnia magna. Host genotypes from infected and uninfected populations were genotyped at microsatellite markers, and phenotyped for life‐history and disease traits in common garden experiments. Combining phenotypic and genotypic data a Q_ST–F_ST‐like analysis was conducted to test for signatures of parasite mediated selection. We observed high variation within and among populations for phenotypic traits, but neither an indication of host local adaptation nor a cost of resistance. Infected populations have a higher gene diversity (Hs) than uninfected populations and Hs is strongly positively correlated with fitness. These results suggest a strong parasite effect on reducing population level inbreeding. We discuss how stochastic processes related to frequent extinction‐(re)colonization dynamics as well as host and parasite migration impede the evolution of resistance in the infected populations. We suggest that the genetic and phenotypic patterns of variation are a product of dynamic changes in the host gene pool caused by the interaction of colonization bottlenecks, inbreeding, immigration, hybrid vigor, rare host genotype advantage and parasitism. Our study highlights the effect of the parasite in ameliorating the negative fitness consequences caused by the high drift load in this metapopulation.     

Contemporary effective population and metapopulation size (Ne and meta‐Ne): comparison among three salmonids inhabiting a fragmented system and differing in gene flow and its asymmetries

We estimated local and metapopulation effective sizes ( and meta‐) for three coexisting salmonid species (Salmo salar, Salvelinus fontinalis, Salvelinus alpinus) inhabiting a freshwater system comprising seven interconnected lakes. First, we hypothesized that might be inversely related to within‐species population divergence as reported in an earlier study (i.e., F_ST: S. salar> S. fontinalis> S. alpinus). Using the approximate Bayesian computation method implemented in ONeSAMP, we found significant differences in () between species, consistent with a hierarchy of adult population sizes (). Using another method based on a measure of linkage disequilibrium (LDNE: ), we found more finite values for S. salar than for the other two salmonids, in line with the results above that indicate that S. salar exhibits the lowest among the three species. Considering subpopulations as open to migration (i.e., removing putative immigrants) led to only marginal and non‐significant changes in , suggesting that migration may be at equilibrium between genetically similar sources. Second, we hypothesized that meta‐ might be significantly smaller than the sum of local s (null model) if gene flow is asymmetric, varies among subpopulations, and is driven by common landscape features such as waterfalls. One ‘bottom‐up’ or numerical approach that explicitly incorporates variable and asymmetric migration rates showed this very pattern, while a number of analytical models provided meta‐ estimates that were not significantly different from the null model or from each other. Our study of three species inhabiting a shared environment highlights the importance and utility of differentiating species‐specific and landscape effects, not only on dispersal but also in the demography of wild populations as assessed through local s and meta‐s and their relevance in ecology, evolution and conservation.     

Soil CO2 efflux measurements in a mixed forest: impact of chamber disturbances,spatial variability and seasonal evolution

A closed‐dynamic‐chamber system (CDCS) was used to measure the spatial and seasonal variability of the soil CO₂ efflux (F_s) in beech and in Douglas fir patches of the Vielsalm forest (Belgium). First the difference between natural and measured soil CO₂ efflux induced by the presence of the CDCS was studied. The impact on the measurements of the pressure difference between the outside (natural condition) and the inside of the chamber was found to be small (0.4%). The influence of wind disturbance in the closed chamber was tested by comparison with an open‐chamber system characterized by a different wind distribution. A very good correlation between the two systems was found (r² = 0.99) but the open system yielded slightly lower fluxes than the closed one (slope = 0.88 ± 0.05). A measurement procedure has been developed to minimize the effect of the other sources of perturbation. The spatial and seasonal evolution of the soil CO₂ efflux was obtained by performing regular measurements on 29 spots in the beech patch over a period of 12 months and on 24 spots in the Douglas fir patch over 8 months. For each spot, the experimental relationship between Fs and soil temperature was compared with the fitted line for an Arrhenius relationship with a soil temperature‐dependent activation energy. Soil temperature explains 73% of the seasonal variation for all the data. The spatial average of the soil CO₂ efflux at 10 °C (Fs₁₀) in the beech patch is 2.57 ± 0.41 μmol m^?2 s^?1, approximately twice the average in the Douglas fir patch recorded at 1.42 ± 0.22 μmol m^?2 s^?1. The litter fall analysis seems to indicate that soil organic matter quality and quantity may be one the reasons for this difference. Finally the annual soil CO₂ efflux was calculated for the beech and Douglas fir patches (870 ± 140 and 438 ± 68 gC m^?2 y^?1, respectively). The beech value would represent 92 ± 15% of the annual ecosystem respiration estimated from the eddy covariance measurements.     

Stability of European natural populations of Drosophila melanogaster with regard to the P–M system: a buffer zone made up of Q populations

Current natural populations of Drosophila melanogaster from Eurasia, Africa and Oceania were investigated with regard to the P–M system of hybrid dysgenesis, for both genetic properties (gonadal dysgenesis sterility analyses) and molecular characteristics (number of full-size elements and particular P element deletion-derivatives, the KP elements). Full-size and KP elements are, respectively, at the origin of two distinct regulation systems, the maternally transmitted P cytotype and the KP-mediated repression whose transmission is biparental. The results show both qualitative and quantitative differences in the geographical distribution of P elements. Comparison with distributions observed in 1980–1983 reveals a great stability of natural populations with regard to this system. In particular, the eastward gradient of P susceptibility previously described in Europe is still observed. This stability could result from the existence of a ’buffer zone’ made up of the French and bordering Q populations (with no P activity and completely regulating the transposition of active P elements). Indeed, in such populations repression mechanisms are redundant, as revealed by the study of repression inheritance. These populations are thus potentially able to limit the progression of P elements that occurs by step by step migrations. This distribution also allows us to enrich the P element invasion model, which can be divided into three steps: (1) a decrease in the number of full-size elements which coincides with an increase in the number of KP elements due to a regulatory role or a high transposition capacity; (2) an equilibrium, when the number of KP elements reaches a maximum and in which populations still have some full-size elements; (3) KP elements reduce in number in the absence of full-size elements allowing transposition, the populations losing their repression potential.     

Disentangling the spatial and temporal causes of decline in a bird population

The difficulties in understanding the underlying reasons of a population decline lie in the typical short duration of field studies, the often too small size already reached by a declining population or the multitude of environmental factors that may influence population trend. In this difficult context, useful demographic tools such as integrated population models (IPM) may help disentangling the main reasons for a population decline. To understand why a hoopoe Upupa epops population has declined, we followed a three step model analysis. We built an IPM structured with respect to habitat quality (approximated by the expected availability of mole crickets, the main prey in our population) and estimated the contributions of habitat‐specific demographic rates to population variation and decline. We quantified how much each demographic rate has decreased and investigated whether habitat quality influenced this decline. We tested how much weather conditions and research activities contributed to the decrease in the different demographic rates. The decline of the hoopoe population was mainly explained by a decrease in first‐year apparent survival and a reduced number of fledglings produced, particularly in habitats of high quality. Since a majority of pairs bred in habitats of the highest quality, the decrease in the production of locally recruited yearlings in high‐quality habitat was the main driver of the population decline despite a homogeneous drop of recruitment across habitats. Overall, the explanatory variables we tested only accounted for 19% of the decrease in the population growth rate. Among these variables, the effects of spring temperature (49% of the explained variance) contributed more to population decline than spring precipitation (36%) and research activities (maternal capture delay, 15%). This study shows the power of IPMs for identifying the vital rates involved in population declines and thus paves the way for targeted conservation and management actions.     

Mating system,population growth,and management scenario for Kalanchoe pinnata in an invaded seasonally dry tropical forest

Ecological invasions are a major issue worldwide, where successful invasion depends on traits that facilitate dispersion, establishment, and population growth. The nonnative succulent plant Kalanchoe pinnata, reported as invasive in some countries, is widespread in remnants of seasonally dry tropical forest on a volcanic outcrop with high conservation value in east‐central Mexico where we assessed its mating system and demographic growth and identified management strategies. To understand its local mating system, we conducted hand‐pollination treatments, germination, and survival experiments. Based on the experimental data, we constructed a life‐stage population matrix, identified the key traits for population growth, weighted the contributions of vegetative and sexual reproduction, and evaluated management scenarios. Hand‐pollination treatments had slight effects on fruit and seed setting, as well as on germination. With natural pollination treatment, the successful germination of seeds from only 2/39 fruit suggests occasional effective natural cross‐pollination. The ratios of the metrics for self‐ and cross‐pollinated flowers suggest that K. pinnata is partially self‐compatible. Most of the pollinated flowers developed into fruit, but the seed germination and seedling survival rates were low. Thus, vegetative propagation and juvenile survival are the main drivers of population growth. Simulations of a virtual K. pinnata population suggest that an intense and sustained weeding campaign will reduce the population within at least 10 years. Synthesis and applications. The study population is partially self‐compatible, but sexual reproduction by K. pinnata is limited at the study site, and population growth is supported by vegetative propagation and juvenile survival. Demographic modeling provides key insights and realistic forecasts on invasion process and therefore is useful to design management strategies.     

Red and blond Mangalitza pigs display a signature of divergent directional selection in the SLC45A2 gene

The Mangalitza lard‐type pig breed is well known for its fat appearance and curly hair, and it is mainly distributed in Eastern Europe. Four main lines were created in the nineteenth century by artificial selection: Blond Mangalitza, Black Mangalitza, Swallow‐Belly Mangalitza and Red Mangalitza. The Swallow‐Belly line has a black coat combined with yellow‐blond throat and underbelly. In the current work, we aimed to investigate if the colourations of Mangalitza pigs are genetically determined by one or a few loci whose frequencies have been modified by artificial selection. The results of selection scans, with Hap FLK and BayeScan , and of a GWAS for coat colour highlighted the existence of one region on SSC16 (18–20 Mb) with potential effects on hair pigmentation (Red vs. Blond contrast). The analysis of the gene content of this region allowed us to detect the solute carrier family 45 member 2 (SLC45A2) locus as a candidate gene for this trait. The polymorphism of the SLC45A2 locus has been associated with reduced levels or the absence of melanin in several mammalian species. The genotyping of four missense polymorphisms evidenced that rs341599992:G > A and rs693695020:G > A SNPs are strongly but not fully associated with the red and blond coat colours of Mangalitza pigs, a result that was confirmed by performing a haplotype association test. The near fixation of alternative SLC45A2 genotypes in Red and Blond Mangalitza pigs provides a compelling example of the consequences of a divergent directional selection for coat colour in a domestic species.     

Stage‐dependent responses to emergent habitat heterogeneity: consequences for a predatory insect population in a coffee agroecosystem

Interactions among members of biological communities can create spatial patterns that effectively generate habitat heterogeneity for other members in the community, and this heterogeneity might be crucial for their persistence. For example, stage‐dependent vulnerability of a predatory lady beetle to aggression of the ant, Azteca instabilis, creates two habitat types that are utilized differently by the immature and adult life stages of the beetle. Due to a mutualistic association between A. instabilis and the hemipteran Coccus viridis – which is A. orbigera main prey in the area – only plants around ant nests have high C. viridis populations. Here, we report on a series of surveys at three different scales aimed at detecting how the presence and clustered distribution of ant nests affect the distribution of the different life stages of this predatory lady beetle in a coffee farm in Chiapas, Mexico. Both beetle adults and larvae were more abundant in areas with ant nests, but adults were restricted to the peripheries of highest ant activity and outside the reach of coffee bushes containing the highest densities of lady beetle larvae. The abundance of adult beetles located around trees with ants increased with the size of the ant nest clusters but the relationship is not significant for larvae. Thus, we suggest that A. orbigera undergoes an ontogenetic niche shift, not through shifting prey species, but through stage‐specific vulnerability differences against a competitor that renders areas of abundant prey populations inaccessible for adults but not for larvae. Together with evidence presented elsewhere, this study shows how an important predator is not only dependent on the existence of two qualitatively distinct habitat types, but also on the spatial distribution of these habitats. We suggest that this dependency arises due to the different responses that the predator's life stages have to this emergent spatial pattern.     

Divergence with gene flow in a population of thermophilic bacteria: a potential role for spatially varying selection

A fundamental goal of evolutionary biology is to understand how ecological diversity arises and is maintained in natural populations. We have investigated the contributions of gene flow and divergent selection to the distribution of genetic variation in an ecologically differentiated population of a thermophilic cyanobacterium (Mastigocladus laminosus) found along the temperature gradient of a nitrogen‐limited stream in Yellowstone National Park. For most loci sampled, gene flow appears to be sufficient to prevent substantial genetic divergence. However, one locus (rfbC) exhibited a comparatively low migration rate as well as other signatures expected for a gene experiencing spatially varying selection, including an excess of common variants, an elevated level of polymorphism and extreme genetic differentiation along the gradient. rfbC is part of an expression island involved in the production of the polysaccharide component of the protective envelope of the heterocyst, the specialized nitrogen‐fixing cell of these bacteria. SNP genotyping in the vicinity of rfbC revealed a ~5‐kbp region including a gene content polymorphism that is tightly associated with environmental temperature and therefore likely contains the target of selection. Two genes have been deleted both in the predominant haplotype found in the downstream region of White Creek and in strains from other Yellowstone populations of M. laminosus, which may result in the production of heterocysts with different envelope properties. This study implicates spatially varying selection in the maintenance of variation related to thermal performance at White Creek despite on‐going or recent gene flow.     

Loci under selection during multiple range expansions of an invasive plant are mostly population specific,but patterns are associated with climate

Identifying the genes underlying rapid evolutionary changes, describing their function and ascertaining the environmental pressures that determine fitness are the central elements needed for understanding of evolutionary processes and phenotypic changes that improve the fitness of populations. It has been hypothesized that rapid adaptive changes in new environments may contribute to the rapid spread and success of invasive plants and animals. As yet, studies of adaptation during invasion are scarce, as is knowledge of the genes underlying adaptation, especially in multiple replicated invasions. Here, we quantified how genotype frequencies change during invasions, resulting in rapid evolution of naturalized populations. We used six fully replicated common garden experiments in Brazil where Pinus taeda (loblolly pine) was introduced at the same time, in the same numbers, from the same seed sources, and has formed naturalized populations expanding outward from the plantations. We used a combination of nonparametric, population genetics and multivariate statistics to detect changes in genotype frequencies along each of the six naturalization gradients and their association with climate as well as shifts in allele frequencies compared to the source populations. Results show 25 genes with significant shifts in genotype frequencies. Six genes had shifts in more than one population. Climate explained 25% of the variation in the groups of genes under selection across all locations, but specific genes under strong selection during invasions did not show climate‐related convergence. In conclusion, we detected rapid evolutionary changes during invasive range expansions, but the particular gene‐level patterns of evolution may be population specific.     

Seasonal and individual predictors of diet in a free‐ranging population of mandrills

Deciphering the dietary habits of a species is central to understanding its ecology, resource requirements, and the evolution of its life history traits. Detailed information on how primates use their environment to address their nutritional needs is available for many primate species. Such basic, but necessary data are, however, fragmented for secretive primates, especially regarding direct behavioral observations of individuals. In this study, we evaluated the impact of seasonality and demographic characteristics on diet and feeding habits in the only free‐ranging population of habituated mandrills (Mandrillus sphinx), a forest‐dwelling species inhabiting the dense humid forests of Central Africa. We collected fine‐grained quantitative data on feeding behavior of 57 individually‐recognized animals of both sexes and different age classes during a 17‐month period. We identified most consumed plant species and determined their abundance in the habitat of the studied mandrills. We showed that diet in this species was extremely diverse and included approximately 150 different plant species, but also mushrooms, invertebrates, and vertebrates. This omnivorous and highly diverse diet presented, however, a clear frugivorous tendency. While we identified three food items largely consumed throughout the year, we also found a strong seasonal signature on diet that was partly, but not only, related to food availability. Age and sex also influenced feeding habits with some feeding specializations according to the individual categories considered and their associated nutritional needs. Our quantitative data provide a basis for future studies examining the nutritional and mineral content of food items, which will further elucidate important aspects of the ecology of this little studied forest primate.     

Wrong place,wrong time: climate change‐induced range shift across fragmented habitat causes maladaptation and declined population size in a modelled bird species

Many species are locally adapted to decreased habitat quality at their range margins, and therefore show genetic differences throughout their ranges. Under contemporary climate change, range shifts may affect evolutionary processes at the expanding range margin due to founder events. In addition, populations that are affected by such founder events will, in the course of time, become located in the range centre. Recent studies investigated evolutionary changes at the expanding range margin, but have not assessed eventual effects across the species' range. We explored the possible influence of range shift on the level of adaptation throughout the species' total range. For this we used a spatially explicit, individual‐based simulation model of a woodland bird, parameterized after the middle spotted woodpecker ( Dendrocopos medius) in fragmented habitat. We simulated its range under climate change, and incorporated genetic differences at a single locus that determined the individual's degree of adaptation to optimal temperature conditions. Generalist individuals had a large thermal tolerance, but relatively low overall fitness, whereas climate specialists had high fitness combined with a small thermal tolerance. In equilibrium, the populations in the range centre were comprised of the specialists, whereas the generalists dominated the margins. In contrast, under temperature increase, the generalist numbers increased at the expanding margin and eventually also occupied the centre of the shifting range, whereas the specialists were located in the retracting margins. This was caused by founder events and led to overall maladaptation of the species, which resulted in a reduced metapopulation size and thus impeded the species' persistence. We therefore found no evidence for a complementary effect of local adaptation and range shifts on species' survival. Instead, we showed that founder events can cause local maladaptation which can amplify throughout the species' range, and, as such, hamper the species' persistence under climate change.     

Growth and phosphate uptake kinetics of the cyanobacterium,Cylindrospermopsis raciborskii (Cyanophyceae) in throughflow cultures

• 1 Cylindrospermopsis raciborskii occupies a rapidly expanding geographical area. Its invasive success challenges eutrophication control in many lakes. To understand better the load‐dependent behaviour of this nitrogen fixing cyanobacterium under in situ conditions, we studied P‐dependent growth of a C. raciborskii strain under continuous and pulsed P supply.
• 2 The Droop model reasonably described P‐dependent growth in the continuously supplied chemostats. Large P pulses, however, caused a delay in growth and cells subject to P pulses grew slower than their counterparts with the same P quota supplied continuously.
• 3 The kinetics of P uptake indicated that C. raciborskii is opportunistic with respect to P. Its high excess P storage capacity after a saturating P pulse (Q_ex=95 µg P [mg C]^‐1) and P‐specific uptake capacity (U_max = V_max/Q_P=150–1200) are indicative of storage adaptation. At the same time, the affinity of the P uptake system (U_max/K = 800–4000) is also high.
• 4 Rate of leakage exceeded that of the steady state net P uptake by one to two orders of magnitude. Growth affinity of C. raciborskii (µ_max/K_µ≈ 20) was relatively low, presumably due to the substantial leakage.
• 5 The dynamics of the particular water body determine which trait contributes most to competitive success of C. raciborskii. In deep lakes with vertical nutrient gradients, the cyanobacterium may rely primarily on its high P storage capacity, which is coupled to a lack of short‐term feedback inhibition and efficient buoyancy regulation. In lakes without such gradients, high P uptake affinity may be vitally important.

     

Finding needles in a genomic haystack: targeted capture identifies clear signatures of selection in a nonmodel plant species

Teasing apart neutral and adaptive genomic processes and identifying loci that are targets of selection can be difficult, particularly for nonmodel species that lack a reference genome. However, identifying such loci and the factors driving selection have the potential to greatly assist conservation and restoration practices, especially for the management of species in the face of contemporary and future climate change. Here, we focus on assessing adaptive genomic variation within a nonmodel plant species, the narrow‐leaf hopbush (Dodonaea viscosa ssp. angustissima), commonly used for restoration in Australia. We used a hybrid‐capture target enrichment approach to selectively sequence 970 genes across 17 populations along a latitudinal gradient from 30°S to 36°S. We analysed 8462 single‐nucleotide polymorphisms (SNPs) for F_ST outliers as well as associations with environmental variables. Using three different methods, we found 55 SNPs with significant correlations to temperature and water availability, and 38 SNPs to elevation. Genes containing SNPs identified as under environmental selection were diverse, including aquaporin and abscisic acid genes, as well as genes with ontologies relating to responses to environmental stressors such as water deprivation and salt stress. Redundancy analysis demonstrated that only a small proportion of the total genetic variance was explained by environmental variables. We demonstrate that selection has led to clines in allele frequencies in a number of functional genes, including those linked to leaf shape and stomatal variation, which have been previously observed to vary along the sampled environmental cline. Using our approach, gene regions subject to environmental selection can be readily identified for nonmodel organisms.     

Seasonal synchrony of life cycles between the exotic predator,Pseudoscymnus tsugae (Coleoptera: Coccinellidae) and its prey,the hemlock woolly adelgid Adelges tsugae (Homoptera:Adelgidae)

1 The seasonal synchrony between the exotic predator, Pseudoscymnus tsugae and its prey, the hemlock woolly adelgid, Adelges tsugae, was investigated in field cages and in the forest in Connecticut, U.S.A. from 1997–1999. 2 In early spring, egg to adult development took 45 d at 18.7 °C, 39.7 d at 20.2 °C and 31.5 d at 22.7 °C. Earliest emerging F1 adults mated and oviposited in the same year. whereas F1 and F2 females emerging later in the summer mated and reserved most of their egg complement for the following year. 3 A second generation of P. tsugae is possible in Connecticut but may be delayed by cool mid‐spring temperatures. Individuals of three generations of P. tsugae, including overwintering survivors, may coexist in July and August and adults can be found year‐round with A. tsugae in infested hemlock forests. 4 A linear regression model for development from egg to adult under field temperatures gave good agreement with results from constant temperature findings. The model predicted a lower development threshold of 9.5 °C and a sum of effective temperatures of 405 day °C. Development time of P. tsugae is shorter relative to its prey A. tsugae and generation time ratios of predator to prey was 0.16–0.5, with an advantage conferred on the coccinellid. 5 Overwintering ability and behaviour were determined in 1998–1999 and adults remained on infested hemlock branches throughout a mild winter, becoming reproductively active in mid‐April. Peak oviposition period extended from April to July, in synchrony with peak oviposition and developing stages of two generations of A. tsugae.     

Interactions between a pollinating seed predator and its host plant: the role of environmental context within a population

Plant–insect interactions often are important for plant reproduction, but the outcome of these interactions may vary with environmental context. Pollinating seed predators have positive and negative effects on host plant reproduction, and the interaction outcome is predicted to vary with density or abundance of the partners. We studied the interaction between Silene stellata, an herbaceous perennial, and Hadena ectypa, its specialized pollinating seed predator. Silene stellata is only facultatively dependent upon H. ectypa for pollination because other nocturnal moth co‐pollinators are equally effective at pollen transfer. We hypothesized that for plants without conspecific neighbors, H. ectypa would have higher visitation rates compared to co‐pollinators, and the plants would experience lower levels of H. ectypa pollen deposition. We predicted similar oviposition throughout the study site but greater H. ectypa predation in the area without conspecific neighbors compared to plants embedded in a naturally high density area. We found that H. ectypa had consistently higher visitation than moth co‐pollinators in all host plant contexts. However, H. ectypa pollinator importance declined in areas with low conspecific density because of reduced pollen deposition, resulting in lower seed set. Conversely, oviposition was similar across the study site independent of host plant density. Greater likelihood of very high fruit predation combined with lower pollination by H. ectypa resulted in reduced S. stellata female reproductive success in areas with low conspecific density. Our results demonstrate local context dependency of the outcomes of pollinating seed predator interactions with conspecific host plant density within a population.     

Species delimitation with gene flow: A methodological comparison and population genomics approach to elucidate cryptic species boundaries in Malaysian Torrent Frogs

Accurately delimiting species boundaries is a nontrivial undertaking that can have significant effects on downstream inferences. We compared the efficacy of commonly used species delimitation methods (SDMs) and a population genomics approach based on genomewide single‐nucleotide polymorphisms (SNPs) to assess lineage separation in the Malaysian Torrent Frog Complex currently recognized as a single species (Amolops larutensis). First, we used morphological, mitochondrial DNA and genomewide SNPs to identify putative species boundaries by implementing noncoalescent and coalescent‐based SDMs (mPTP, iBPP, BFD*). We then tested the validity of putative boundaries by estimating spatiotemporal gene flow (fastsimcoal2 , ABBA‐BABA) to assess the extent of genetic isolation among putative species. Our results show that the A. larutensis complex runs the gamut of the speciation continuum from highly divergent, genetically isolated lineages (mean F_st = 0.9) to differentiating populations involving recent gene flow (mean F_st = 0.05; N_m > 5). As expected, SDMs were effective at delimiting divergent lineages in the absence of gene flow but overestimated species in the presence of marked population structure and gene flow. However, using a population genomics approach and the concept of species as separately evolving metapopulation lineages as the only necessary property of a species, we were able to objectively elucidate cryptic species boundaries in the presence of past and present gene flow. This study does not discount the utility of SDMs but highlights the danger of violating model assumptions and the importance of carefully considering methods that appropriately fit the diversification history of a particular system.     

Gene flow,linked selection,and divergent sorting of ancient polymorphism shape genomic divergence landscape in a group of edaphic specialists

Interpreting the formation of genomic variation landscape, especially genomic regions with elevated differentiation (i.e. islands), is fundamental to a better understanding of the genomic consequences of adaptation and speciation. Edaphic islands provide excellent systems for understanding the interplay of gene flow and selection in driving population divergence and speciation. However, discerning the relative contribution of these factors that modify patterns of genomic variation remains difficult. We analysed 132 genomes from five recently divergent species in Primulina genus, with four species distributed in Karst limestone habitats and the fifth one growing in Danxia habitats. We demonstrated that both gene flow and linked selection have contributed to genome-wide variation landscape, where genomic regions with elevated differentiation (i.e., islands) were largely derived by divergent sorting of ancient polymorphism. Specifically, we identified several lineage-specific genomic islands that might have facilitated adaptation of P. suichuanensis to Danxia habitats. Our study is amongst the first cases disentangling evolutionary processes that shape genomic variation of plant specialists, and demonstrates the important role of ancient polymorphism in the formation of genomic islands that potentially mediate adaptation and speciation of endemic plants in special soil habitats.     

A genomic assessment of population structure and gene flow in an aquatic salamander identifies the roles of spatial scale,barriers, and river architecture

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Clock gene polymorphism,migratory behaviour and geographic distribution: a comparative study of trans‐Saharan migratory birds

Migratory behaviour is controlled by endogenous circannual rhythms that are synchronized by external cues, such as photoperiod. Investigations on the genetic basis of circannual rhythmicity in vertebrates have highlighted that variation at candidate ‘circadian clock’ genes may play a major role in regulating photoperiodic responses and timing of life cycle events, such as reproduction and migration. In this comparative study of 23 trans‐Saharan migratory bird species, we investigated the relationships between species‐level genetic variation at two candidate genes, Clock and Adcyap1, and species’ traits related to migration and geographic distribution, including timing of spring migration across the Mediterranean Sea, migration distance and breeding latitude. Consistently with previous evidence showing latitudinal clines in ‘circadian clock’ genotype frequencies, Clock allele size increased with breeding latitude across species. However, early‐ and late‐migrating species had similar Clock allele size. Species migrating over longer distances, showing delayed spring migration and smaller phenotypic variance in spring migration timing, had significantly reduced Clock (but not Adcyap1) gene diversity. Phylogenetic confirmatory path analysis suggested that migration date and distance were the most important variables directly affecting Clock gene diversity. Hence, our study supports the hypothesis that Clock allele size increases poleward as a consequence of adaptation to the photoperiodic regime of the breeding areas. Moreover, we show that long‐distance migration is associated with lower Clock diversity, coherently with strong stabilizing selection acting on timing of life cycle events in long‐distance migratory species, likely resulting from the time constraints imposed by late spring migration.