Evaluating gene flow using selected markers: a case study.

The extent to which an organism is locally adapted in an environmental pocket depends on the selection intensities inside and outside the pocket, on migration, and on the size of the pocket. When two or more loci are involved in this local adaptation, measuring their frequency gradients and their linkage disequilbria allows one to disentangle the forces-migration and selection-acting on the system. We apply this method to the case of a local adaptation to organophosphate insecticides in the mosquito Culex pipiens pipiens in southern France. The study of two different resistance loci allowed us to estimate with support limits gene flow as well as selection pressure on insecticide resistance and the fitness costs associated with each locus. These estimates permit us to pinpoint the conditions for the maintenance of this pocket of adaptation as well as the effect of the interaction between the two resistance loci.     

Migration/selection balance and ecotypic differentiation in the mosquito Culex pipiens

Ecotypic differentiation is well described in the mosquito Culex pipiens , separating populations breeding in subterranean and human-made sites (hypogeous habitat) from those in open-air sites (epigeous habitat). The pattern of population differentiation observed at the Aat-1 locus has been suspected to be associated with such ecotypic differentiation via habitat-dependent selection, but this supposition is still the subject of debate in the literature. We analysed differentiation patterns for Aat-1 and another four loci among populations from both habitat types in the French Alps. We showed that the Aat-1^A allele is favoured within hypogeous habitats but selected against within epigeous habitats. Comparisons of our results with other data reported in the literature indicate that the Aat-1^A allele is generally evolving under habitat-differential selection, but that the precise balance of migration and selection that determines equilibrium allele frequencies varies greatly across Europe. The nature of this habitat-dependent selection, and its resulting (geographically varying) equilibrium point, are discussed in relation to the biology of this mosquito species.     

Identifying adaptive genetic divergence among populations from genome scans

The identification of signatures of natural selection in genomic surveys has become an area of intense research, stimulated by the increasing ease with which genetic markers can be typed. Loci identified as subject to selection may be functionally important, and hence (weak) candidates for involvement in disease causation. They can also be useful in determining the adaptive differentiation of populations, and exploring hypotheses about speciation. Adaptive differentiation has traditionally been identified from differences in allele frequencies among different populations, summarised by an estimate of FST. Low outliers relative to an appropriate neutral population-genetics model indicate loci subject to balancing selection, whereas high outliers suggest adaptive (directional) selection. However, the problem of identifying statistically significant departures from neutrality is complicated by confounding effects on the distribution of FST estimates, and current methods have not yet been tested in large-scale simulation experiments. Here, we simulate data from a structured population at many unlinked, diallelic loci that are predominantly neutral but with some loci subject to adaptive or balancing selection. We develop a hierarchical-Bayesian method, implemented via Markov chain Monte Carlo (MCMC), and assess its performance in distinguishing the loci simulated under selection from the neutral loci. We also compare this performance with that of a frequentist method, based on moment-based estimates of FST. We find that both methods can identify loci subject to adaptive selection when the selection coefficient is at least five times the migration rate. Neither method could reliably distinguish loci under balancing selection in our simulations, even when the selection coefficient is twenty times the migration rate.     

Population structure in Mediterranean islands and risk of genetic invasion in Culexpipiens L. (Diptera: Culicidae)

The mosquito Culex pipiens is subjected to organophosphate treatments in both Corsica and southern Sardinia, but the resistance gene A2-B2, which is currently in a worldwide expansion, has only reached Sardinia. In order to understand this situation, the genetic structure of populations sampled in Sardinia and Corsica was assessed using 15 isozymes. Two loci (HK1 and HK2) were not taken into account because of the possibility of selection. For trie other loci, statistical independence was not rejected for all possible pairs, and no deviation from Hardy-Weinberg expectations was apparent. Low but significant genie differentiation was present between Corsica and Sardinia, as well as between northern and southern Sardinia, despite a large number of effective migrants per generation. These results are discussed in the context of the high probability of extinction/recolonization of breeding sites, the flight migration ability of this mosquito, and the pleiotropic cost of insecticide resistances genes. It is concluded that A2-B2 resistance is unlikely to reach Corsica from southern Sardinia, unless accidental human transportation occurs.     

‘Same procedure as last year?‘ Repeatedly tracked swifts show individual consistency in migration pattern in successive years

Individual migration pattern during non‐breeding season is still a black box in many migratory birds. However, knowledge on both individual level and population level in migration and overwintering is fundamental to understand the life cycle of these birds and the constraints affecting them. We showed in a highly aerial migrant, the common swift Apus apus, that repeatedly tracked birds breeding at one site in Germany used the same individual‐specific migration routes and wintering areas in subsequent years. In contrast, different individuals from the same breeding colony showed diverse movement patterns during non‐breeding season suggesting that several suitable areas for overwintering coexist. We found lower variation in timing of autumn and spring migration within than between individuals. Our findings provide first indication of individual consistency but between‐individual variation in migration pattern in a small non‐passerine bird revealed by geolocators. This supports that swifts have diverse but individual‐specific ‘step‐by‐step’ migration patterns revealing high flexibility through individual strategies.     

Combining genetic markers and stable isotopes to reveal population connectivity and migration patterns in a neotropical migrant,Wilson's warbler (Wilsonia pusilla)

We used results from the analysis of microsatellite DNA variation and hydrogen stable-isotope ratios to characterize the population structure of a neotropical migrant passerine, the Wilson's warbler (Wilsonia pusilla). The resulting information was then used to infer migration patterns and population connectivity between breeding grounds in North America and overwintering areas in Mexico and Central America. The microsatellite data revealed genetic structure across the North American continent; populations in the west were found to significantly differ from the east. Minimal genetic structure was observed among western sites. The lack of isolation by distance and low variance in FST values suggests that gene flow could play an ongoing role in limiting genetic differentiation among sites in the western part of the distribution. However, additional information including estimates of effective population size and the proximity of the population to equilibrium is required before the role of gene flow can be assessed fully. Analysis of isotope data showed a negative relationship between latitude and hydrogen isotope ratios in breeding ground individuals. There was a positive relationship between wintering ground latitude and hydrogen isotope ratios for individuals that were genetically western in origin. This is consistent with a leapfrog pattern of migration, in which genetically western birds from the northernmost breeding areas overwinter at the most southerly locations in Central America. Additionally, isotopic ratios of western birds suggest that coastal breeders overwinter in western Mexico, while western birds from further inland and at high elevations overwinter in eastern Mexico. Using information from both genetic an isotopic approaches will probably be useful for identifying patterns of migration and population connectivity between breeding and overwintering areas, both important issues for conservation efforts, and may also contribute to investigation of the evolution of migration.     

Migration rates, frequency-dependent selection and the self-incompatibility locus in Leavenworthia (brassicaceae)

Loci subject to negative frequency-dependent selection are expected to exhibit higher effective migration rates compared to reference loci. Although the number of gene copies transferred between populations by migration is the same for all genes, those subject to negative frequency-dependent selection are more likely to be retained in the immigrant population because rare alleles are selectively favored. So far, evidence for this prediction has been indirect, based on summary statistics rather than on migration rate estimates. Here, we introduce an approximate Bayesian procedure to jointly estimate migration rates at two predefined sets of loci between two populations. We applied the procedure to compare migration rate estimates at the self-incompatibility locus (S-locus) with that at 10 reference loci in two plant species, Leavenworthia alabamica and L. crassa (Brassicaceae). The maximum likelihood estimate for the proportion of migrants (m) was four times higher at the S-locus than at reference loci, but the difference was not statistically significant. Lack of significance might be due to insufficient data, but perhaps also to the recent divergence of the two species (311 ka), because we also show using simulations that the effective migration rate at the S-locus is expected to increase with increasing divergence time. These findings aid in understanding the evolutionary dynamics of negative frequency-dependent selection and they suggest that divergence time should be accounted for when employing migration rates to help detect negative frequency-dependent selection.     

Variable detours in long‐distance migration across ecological barriers and their relation to habitat availability at ground

Migration detours, the spatial deviation from the shortest route, are a widespread phenomenon in migratory species, especially if barriers must be crossed. Moving longer distances causes additional efforts in energy and time, and to be adaptive, this should be counterbalanced by favorable condition en route. We compared migration patterns of nightingales that travelled along different flyways from their European breeding sites to the African nonbreeding sites. We tested for deviations from shortest routes and related the observed and expected routes to the habitat availability at ground during autumn and spring migration. All individuals flew detours of varying extent. Detours were largest and seasonally consistent in western flyway birds, whereas birds on the central and eastern flyways showed less detours during autumn migration, but large detours during spring migration (eastern flyway birds). Neither migration durations nor the time of arrival at destination were related to the lengths of detours. Arrival at the breeding site was nearly synchronous in birds flying different detours. Flying detours increased the potential availability of suitable broad‐scale habitats en route only along the western flyway. Habitat availability on observed routes remained similar or even decreased for individuals flying detours on the central or the eastern flyway as compared to shortest routes. Thus, broad‐scale habitat distribution may partially explain detour performance, but the weak detour‐habitat association along central and eastern flyways suggests that other factors shape detour extent regionally. Prime candidate factors are the distribution of small suitable habitat patches at local scale as well as winds specific for the region and altitude.     

Fitness costs of insecticide resistance in natural breeding sites of the mosquito Culex pipiens

Genetic changes conferring adaptation to a new environment may induce a fitness cost in the previous environment. Although this prediction has been verified in laboratory conditions, few studies have tried to document this cost directly in natural populations. Here, we evaluated the pleiotropic effects of insecticide resistance on putative fitness components of the mosquito Culex pipiens. Experiments using different larval densities were performed during the summer in two natural breeding sites. Two loci that possess alleles conferring organophosphate (OP) resistance were considered: ace-1 coding for an acetylcholinesterase (AChE1, the OP target) and Ester, a 'super locus" including two closely linked loci coding for esterases A and B. Resistance ace-1 alleles coding for a modified AChE1 were associated with a longer development time and shorter wing length. The pleiotropic effects of two resistance alleles Ester1 and Ester4 coding for the overproduced esterases A1 and A4-B4, respectively, were more variable. Both A1 and A4-B4 reduced wing length, although only A1 was associated with a longer preimaginal stage. The fluctuating asymmetry (FA) of the wing did not respond to the presence or to the interaction of resistance alleles at the two loci at any of the density levels tested. Conversely, the FA of one wing section decreased when larval density increased. This may be the consequence of selection against less developmentally stable individuals. The results are discussed in relation to the local evolution of insecticide resistance genes.     

Photoperiodic response may facilitate adaptation to climatic change in long-distance migratory birds

Recent climatic change is causing spring events in northern temperate regions to occur earlier in the year. As a result, migratory birds returning from tropical wintering sites may arrive too late to take full advantage of the food resources on their breeding grounds. Under these conditions, selection will favour earlier spring arrival that could be achieved by overwintering closer to the breeding grounds. However, it is unknown how daylength conditions at higher latitudes will affect the timing of life cycle stages. Here, we show in three species of Palaearctic-African migratory songbirds that a shortening of migration distance induces an advancement of springtime activities. Birds exposed to daylengths simulating migration to and wintering in southern Europe considerably advanced their spring migratory activity and testicular development. This response to the novel photoperiodic environment will enable birds wintering further north to advance spring arrival and to start breeding earlier. Thus, phenotypic flexibility in response to the photoperiod may reinforce selection for shorter migration distance if spring temperatures continue to rise.     

Testosterone,migration distance,and migratory timing in song sparrows Melospiza melodia

In seasonally migratory animals, migration distance often varies substantially within populations such that individuals breeding at the same site may overwinter different distances from the breeding grounds. Shorter migration may allow earlier return to the breeding grounds, which may be particularly advantageous to males competing to acquire a breeding territory. However, little is known about potential mechanisms that may mediate migration distance. We investigated naturally-occurring variation in androgen levels at the time of arrival to the breeding site and its relationship to overwintering latitude in male and female song sparrows (Melospiza melodia). We used stable isotope analysis of hydrogen (δ²H) in winter-grown claw tissue to infer relative overwintering latitude (migration distance), combined with 14 years of capture records from a long-term study population to infer the arrival timing of males versus females. Relative to females, males had higher circulating androgen levels, migrated shorter distances, and were more likely to be caught early in the breeding season. Males that migrate short distances may benefit from early arrival at the breeding grounds, allowing them to establish a breeding territory. Even after controlling for sex and date, androgen levels were highest in individuals that migrated shorter distances. Our findings indicate that androgens and migration distance are correlated traits within and between sexes that may reflect individual variation within an integrated phenotype in which testosterone has correlated effects on behavioral traits such as migration.     

Fitness Consequences of Timing of Migration and Breeding in Cormorants

In most bird species timing of breeding affects reproductive success whereby early breeding is favoured. In migratory species migration time, especially arrival at the breeding grounds, and breeding time are expected to be correlated. Consequently, migration time should also have fitness consequences. However, in contrast to breeding time, evidence for fitness consequences of migration time is much more limited. Climate change has been shown to negatively affect the synchrony between trophic levels thereby leading to directional selection on timing but again direct evidence in avian migration time is scarce. We here analysed fitness consequences of migration and breeding time in great cormorants and tested whether climate change has led to increased selection on timing using a long-term data set from a breeding colony on the island of Vorsø (Denmark). Reproductive success, measured as number of fledglings, correlated with breeding time and arrival time at the colony and declined during the season. This seasonal decline became steeper during the study period for both migration and breeding time and was positively correlated to winter/spring climate, i.e. selection was stronger after warmer winters/springs. However, the increasing selection pressure on timing seems to be unrelated to climate change as the climatic variables that were related to selection strength did not increase during the study period. There is indirect evidence that phenology or abundances of preferred prey species have changed which could have altered selection on timing of migration and breeding.     

Evolution of winter molting strategies in European and North American migratory passerines

Molt is critical for birds as it replaces damaged feathers and worn plumage, enhancing flight performance, thermoregulation, and communication. In passerines, molt generally occurs on the breeding grounds during the postbreeding period once a year. However, some species of migrant passerines that breed in the Nearctic and Western Palearctic regions have evolved different molting strategies that involve molting on the overwintering grounds. Some species forego molt on the breeding grounds and instead complete their prebasic molt on the overwintering grounds. Other species molt some or all feathers a second time (prealternate molt) during the overwintering period. Using phylogenetic analyses, we explored the potential drivers of the evolution of winter molts in Nearctic and Western Palearctic breeding passerines. Our results indicate an association between longer photoperiods and the presence of prebasic and prealternate molts on the overwintering grounds for both Nearctic and Western Palearctic species. We also found a relationship between prealternate molt and generalist and water habitats for Western Palearctic species. Finally, the complete prealternate molt in Western Palearctic passerines was linked to longer days on the overwintering grounds and longer migration distance. Longer days may favor the evolution of winter prebasic molt by increasing the time window when birds can absorb essential nutrients for molt. Alternatively, for birds undertaking a prealternate molt at the end of the overwintering period, longer days may increase exposure to feather‐degrading ultra‐violet radiation, necessitating the replacement of feathers. Our study underlines the importance of the overwintering grounds in the critical process of molt for many passerines that breed in the Nearctic and Western Palearctic regions.     

Not as the crow flies: a historical explanation for circuitous migration in Swainson's thrush (Catharus ustulatus)

Many migratory songbirds follow circuitous migratory routes instead of taking the shortest path between overwintering and breeding areas. Here, we study the migration patterns in Swainson's thrush (Catharus ustulatus), a neartic-neotropical migrant songbird, using molecular genetic approaches. This species is presently separated into genetically distinct coastal and continental populations that diverged during the Late Pleistocene (as indicated by molecular dating), yet appear to have retained ancestral patterns of migration. Low nucleotide diversity, a star-like haplotype phylogeny and unimodal mismatch distributions all support the hypothesis that both the coastal and the continental populations have undergone recent demographic expansions. Nearctic-neotropical banding and genetic data show nearly complete segregation of migratory routes and of overwintering locations: coastal populations migrate along the Pacific Coast to overwintering sites in Central America and Mexico, whereas continental populations migrate along an eastern route to overwintering sites in Panama and South America. Nearctic-neotropical banding data also show that continental birds north, northwest and east of this migratory divide fly thousands of miles east before turning south. We conclude that circuitous migration in the Swainson's thrush is an artefact of a Late Pleistocene range expansion.     

Maximum-likelihood estimation of migration rates and effective population numbers in two populations using a coalescent approach.

A new method for the estimation of migration rates and effective population sizes is described. It uses a maximum-likelihood framework based on coalescence theory. The parameters are estimated by Metropolis-Hastings importance sampling. In a two-population model this method estimates four parameters: the effective population size and the immigration rate for each population relative to the mutation rate. Summarizing over loci can be done by assuming either that the mutation rate is the same for all loci or that the mutation rates are gamma distributed among loci but the same for all sites of a locus. The estimates are as good as or better than those from an optimized FST-based measure. The program is available on the World Wide Web at http://evolution.genetics. washington.edu/lamarc.html/.     

Influence of environmental conditions at spawning sites and migration routes on adaptive variation and population connectivity in Chinook salmon

Many species that undergo long breeding migrations, such as anadromous fishes, face highly heterogeneous environments along their migration corridors and at their spawning sites. These environmental challenges encountered at different life stages may act as strong selective pressures and drive local adaptation. However, the relative influence of environmental conditions along the migration corridor compared with the conditions at spawning sites on driving selection is still unknown. In this study, we performed genome–environment associations (GEA) to understand the relationship between landscape and environmental conditions driving selection in seven populations of the anadromous Chinook salmon (Oncorhynchus tshawytscha)—a species of important economic, social, cultural, and ecological value—in the Columbia River basin. We extracted environmental variables for the shared migration corridors and at distinct spawning sites for each population, and used a Pool‐seq approach to perform whole genome resequencing. Bayesian and univariate GEA tests with migration‐specific and spawning site‐specific environmental variables indicated many more candidate SNPs associated with environmental conditions at the migration corridor compared with spawning sites. Specifically, temperature, precipitation, terrain roughness, and elevation variables of the migration corridor were the most significant drivers of environmental selection. Additional analyses of neutral loci revealed two distinct clusters representing populations from different geographic regions of the drainage that also exhibit differences in adult migration timing (summer vs. fall). Tests for genomic regions under selection revealed a strong peak on chromosome 28, corresponding to the GREB1L/ROCK1 region that has been identified previously in salmonids as a region associated with adult migration timing. Our results show that environmental variation experienced throughout migration corridors imposed a greater selective pressure on Chinook salmon than environmental conditions at spawning sites.     

Likelihood analysis of ongoing gene flow and historical association

Abstract.— We develop a Monte Carlo-based likelihood method for estimating migration rates and population divergence times from data at unlinked loci at which mutation rates are sufficiently low that, in the recent past, the effects of mutation can be ignored. The method is applicable to restriction fragment length polymorphisms (RFLPs) and single nucleotide polymorphisms (SNPs) sampled from a subdivided population. The method produces joint maximum-likelihood estimates of the migration rate and the time of population divergence, both scaled by population size, and provides a framework in which to test either for no ongoing gene flow or for population divergence in the distant past. We show the method performs well and provides reasonably accurate estimates of parameters even when the assumptions under which those estimates are obtained are not completely satisfied. Furthermore, we show that, provided that the number of polymorphic loci is sufficiently large, there is some power to distinguish between ongoing gene flow and historical association as causes of genetic similarity between pairs of populations.     

Linkage disequilibrium and recombination rate estimates in the self-incompatibility region of Arabidopsis lyrata

Genetic diversity is unusually high at loci in the S-locus region of the self-incompatible species of the flowering plant, Arabidopsis lyrata, not just in the S loci themselves, but also at two nearby loci. In a previous study of a single natural population from Iceland, we attributed this elevated polymorphism to linkage disequilibrium (LD) between variants at loci close to the S locus and the S alleles, which are maintained in the population by balancing selection. With the four S-flanking loci whose diversity we previously studied, we could not determine the extent of the region linked to the S loci in which neutral sites are affected. We also could not exclude the possibility of a population bottleneck, or of admixture, as causes of the LD. We have now studied four more distant loci flanking the S-locus region, and more populations, and we analyze the results using a theoretical model of the effect of balancing selection on diversity at linked neutral sites within and between different functional S-allelic classes. In the model, diversity is a function of the number of selectively maintained alleles and the recombination distances from the selectively maintained sites. We use the model to estimate the number of different functional S alleles, their turnover rate, and recombination rates between the S-locus region and other loci. Our estimates suggest that there is a small region of very low recombination surrounding the S-locus region.     

Precise direct tracking and remote sensing reveal the use of forest islands as roost sites by Purple Martins during migration

Direct tracking methods in combination with remote sensing data allow examination of habitat use by birds during migration. Species that roost communally during migration, such as some swallows, form large aggregations that can attract both avian and terrestrial predators. However, the extent to which they might use patchy habitats that could reduce predation risk during migration is unknown. We tested the hypothesis that Purple Martins (Progne subis) use forest islands (patches of suitable forest habitat surrounded by unsuitable habitat) as roost sites during migration between breeding sites in North America and overwintering sites in South America. We used high‐precision (< 10 m), archival GPS units deployed and retrieved during the 2015 and 2016 breeding seasons, respectively, at 12 colonies located across eastern North America. We found that Purple Martins roosted in forest islands more often than expected based on availability during both spring and fall migration. Despite an apparent association with urban habitats by Purple Martins based on observational and radar data in North America during the fall, the roost locations we identified during spring and fall migration were not more closely associated with urban areas than random locations. The use of forest islands during both spring and fall migration suggest that Purple Martins may use these habitats to reduce predation risk during migration. Our results suggest that some species of birds may use similar habitats as stopover sites during migration and that patches of forest habitat may be important conservation targets for Purple Martins and other species. Identifying habitat use during migration represents an important advance in support of full annual‐cycle conservation of Purple Martins and other migratory species with declining populations.     

Climate conditions and resource availability drive return elevational migrations in a single-brooded insect

Seasonal elevational migrations have important implications for life-history evolution and ecological responses to environmental change. However, for most species, particularly invertebrates, evidence is still scarce for the existence of such migrations, as well as for the potential causes. We tested the extent to which seasonal abundance patterns in central Spain for overwintering (breeding) and summer (non-breeding) individuals of the butterfly Gonepteryx rhamni were consistent with three hypotheses explaining elevational migration: resource limitation (host plant and flower availability), physiological constraints of weather (maximum temperatures) and habitat limitation (forest cover for overwintering). For overwintering adults, abundance was positively associated with host plant density during two intensive survey seasons (2007–2008), and the elevational distribution was relatively stable over a 7-year period (2006–2012). The elevational distribution of summer adults was highly variable, apparently related both to temperature and habitat type. Sites occupied by adults in the summer were on average 3 °C cooler than their breeding sites, and abundance showed negative associations with summer temperature, and positive associations with forest cover and host plant density in 2007 and 2008. The results suggest that the extent of uphill migration in summer could be driven by different factors, depending on the year, and are mostly consistent with the physiological constraint and habitat limitation hypotheses. In contrast, the patterns for overwintering adults suggest that downhill migration can be explained by resource availability. Climate change could generate bottlenecks in the populations of elevational migrant species by constraining the area of specific seasonal habitat networks or by reducing the proximity of environments used at different times of year.