Pathogen richness and abundance predict patterns of adaptive major histocompatibility complex variation in insular amphibians

The identification of the factors responsible for genetic variation and differentiation at adaptive loci can provide important insights into the evolutionary process and is crucial for the effective management of threatened species. We studied the impact of environmental viral richness and abundance on functional diversity and differentiation of the MHC class Ia locus in populations of the black‐spotted pond frog (Pelophylax nigromaculatus), an IUCN‐listed species, on 24 land‐bridge islands of the Zhoushan Archipelago and three nearby mainland sites. We found a high proportion of private MHC alleles in mainland and insular populations, corresponding to 32 distinct functional supertypes, and strong positive selection on MHC antigen‐binding sites in all populations. Viral pathogen diversity and abundance were reduced at island sites relative to the mainland, and islands housed distinctive viral communities. Standardized MHC diversity at island sites exceeded that found at neutral microsatellites, and the representation of key functional supertypes was positively correlated with the abundance of specific viruses in the environment (Frog virus 3 and Ambystoma tigrinum virus). These results indicate that pathogen‐driven diversifying selection can play an important role in maintaining functionally important MHC variation following island isolation, highlighting the importance of considering functionally important genetic variation and host–pathogen associations in conservation planning and management.     

Genetic structure of kestrel populations and colonization of the Cape Verde archipelago

Genetic diversity and population structure were studied in eight populations of the kestrel Falco tinnunculus to identify the genetic consequences of spatial distribution and to infer the colonization patterns of the Cape Verde archipelago. We studied genetic differentiation and gene flow among seven island populations and one mainland population using nine microsatellite loci. Within the archipelago, differentiation was strong and genetic diversity and heterozygosity were low but variable among populations. Two subspecies F. tinnunculus neglectus on the northwestern islands and F. tinnunculus alexandri on all the other islands were identified as genetically distinct units. F. t. alexandri could be further separated into two groups on eastern and southern islands. Populations are probably founded by birds originating from the mainland. Immigration is more likely to the eastern and southern populations, whereas the northwestern islands with the lowest genetic diversity and highest differentiation are likely to exhibit fewer founding events by immigrants. The number of founding events on each island may depend not only on geographical distance to neighbouring populations, but also on directional immigration due to the northeastern trade winds. This may explain differences in genetic differentiation and diversity between populations and subspecies and may enable allopatric speciation.     

Farmland habitat selection of wintering lesser kestrels in a Spanish pseudosteppe: implications for conservation strategies

The lesser kestrel Falco naumanni is a globally threatened species, whose breeding populations seem to have declined due to recent agricultural changes. However, nothing is known about habitat requirements during winter, despite the fact that several populations are overwintering in areas affected by agricultural transformations. We studied population size and habitat selection by wintering lesser kestrels in a Spanish pseudosteppe (Los Monegros), where traditional fallow systems for cereals are rapidly being replaced by intensive and/or irrigated crops. About 15% of the adult population wintered in the study area, as determined by systematic roadside counts compared with accurate censuses made during the breeding season. Wintering lesser kestrels preferred to forage on field margins and stubble, while avoiding abandoned fields, ploughs, scrubland, growing cereals and, mainly, the expanding irrigated crops. This work confirms the need to incorporate the habitat requirements of threatened species over their complete annual cycles; while breeding lesser kestrels scarcely use fallow (ploughed at that time), during the winter, fallow (stubble at that time) is their main foraging habitat. Both fallow land and the present agricultural calendar should be maintained to assure the conservation of wintering lesser kestrel populations.     

Informative content of melanin‐based plumage colour in adult Eurasian kestrels

Covariation between melanin‐based colorations and other phenotypic attributes has been rarely measured simultaneously in males and females. Such covariations and mechanisms mediating them have crucial importance determining the signalling function of these coloured ornaments in the two sexes. We examined the role of four melanin‐based coloured plumage patches as indicators of quality in both males and females of the sexually dimorphic and dichromatic Eurasian kestrel Falco tinnunculus. Previous kestrel studies have focused on the size of melanin plumage patches in either males or females as indicators of individual quality. Here, we used spectrophotometric measurements of three plumage patches and the size of another plumage patch to investigate the information content of multiple plumage colour traits in male and female kestrels. We found that females with bright plumage in the head and with high UV chroma in black parts of the rump showed good body condition and innate immunity. In addition, laying date was significantly explained by the intensity of the brown in the head of females. Meanwhile, in males we only found that individuals with greyer rumps showed better innate immunity. Altogether, our results indicate that, irrespective of the mechanism promoting covariation between coloration and individual quality, melanin‐based coloration can inform on individual quality in adult kestrels.     

Predator presence may benefit: kestrels protect curlew nests against nest predators

We studied whether the presence of breeding kestrels (Falco tinnunculus) affected nest predation and breeding habitat selection of curlews (Numenius arquata) on an open flat farmland area in western Finland. We searched for nests of curlews from an area of 6 km² during 1985–1993. For each nest found, we recorded the fate of the nest, and the distance to the nearest kestrel nest and to the nearest perch. We measured the impact of breeding kestrels on nest predation by constructing artificial curlew nests in the vicinity of ten kestrel nests in 1993. Curlew nests were closer to kestrel nests than expected from random distribution, eventhough kestrels fed on average 5.5% of curlew chick production. Predation risk by kestrels was lower than predation risk by corvids and other generalist predators, which predated 9% of curlew nests surviving farming practices and an unknown proportion of chicks. Artificial nest experiment showed that nest predation was lower close to kestrel nests than further away suggesting that the breeding association of curlews and kestrels was a behavioural adaptation against nest predation. Thus, the presence of a predator may sometimes be beneficial to prey, and prey animals have behavioural adaptations to these situations.     

Increase of heterozygosity in a growing population of lesser kestrels

The lesser kestrel (Falco naumanni) suffered a sharp population decline over much of its European distribution range in the middle of the twentieth century. Still declining in some areas, the species has recently experienced a notable population recovery in certain regions. We examined the genetic diversity variation in a growing population of lesser kestrels from Central Spain over a 6-year period (2000-2005). The population studied showed a rapid demographic expansion, increasing in the number of both breeding pairs and colonies. Annual average heterozygosity and allelic diversity increased and genetic similarity between potential mates decreased over the study period. Several immigrants regularly arrived in the study area and introduced new alleles into the local population, pointing to immigration as the main cause contributing to the observed genetic recovery.     

Does avian predation risk depress reproduction of voles?

Reproductive output and the growth of captive voles were quantified under high and low avian predation risk in a semi-natural experiment. Voles were exposed to Eurasian kestrels (Falco tinnunculus), the main avian predator of vole species studied (Clethrionomys glareolus, Microtus agrestis and M. rossiaemeridionalis). Vole pairs were housed in cages settled under nest-boxes occupied by breeding kestrels or in control cages settled under empty nest-boxes for 2 weeks. The experiment was conducted in mid-summer when kestrels had half-grown nestlings, because in that time hunting adults and begging nestlings produce noise and scats which may indicate significant predation threat to voles housed underneath the nest-boxes. The risk of kestrel predation did not have any obvious impact on pregnancy rates, mean litter sizes, or growth rates of kestrel-exposed voles compared with control voles studied. These results indicate that the risk of avian predation does not depress the reproductive investment of voles. Received: 3 November 1997 / Accepted: 16 February 1998     

Reduced MHC class II diversity in island compared to mainland populations of the black-footed rock-wallaby (<Emphasis Type="Italic">Petrogale lateralis lateralis</Emphasis>)

Many animal populations that are endangered in mainland areas exist in stable island populations, which have the potential to act as an “ark” in case of mainland population declines. Previous studies have found neutral genetic variation in such species to be up to an order of magnitude lower in island compared to mainland populations. If low genetic variation is prevalent across fitness-related loci, this would reduce the effectiveness of island populations as a source of individuals to supplement declining mainland populations or re-establish extinct mainland populations. One such species, the black-footed rock-wallaby (Petrogale lateralis lateralis), exists within fragmented mainland populations and small island populations off Western Australia. We examined sequence variation in this species within a fitness-related locus under positive selection, the MHC class II DAB β1 locus. The mainland populations displayed greater levels of allelic diversity (4–7 alleles) than the island population, despite being small and isolated, and contained at least two DAB gene copies. The island population displayed low allelic diversity (2 alleles) and fewer alleles per individual in comparison to mainland populations, and probably possesses only one DAB gene copy. The patterns of DAB diversity suggested that the island population has a markedly lower level of genetic variation than the mainland populations, in concordance with results from microsatellites (genotyped in a previous study), but preserved unique alleles which were not found in mainland populations. Where possible, conservation actions should pool individuals from multiple populations, not only island populations, for translocation programs, and focus on preventing further declines in mainland populations.     

Isolation and characterization of polymorphic microsatellite markers in lesser kestrel (Falco naumanni) and cross-amplification in common kestrel (Falco tinnunculus)

Lesser kestrel, Falco naumanni, is a colonial and migratory species breeding in part of the Mediterranean Basin and part of central Asia and north-east of China and Mongolia. This species is catalogued in IUCN red list category as vulnerable. Twenty microsatellite loci were selected from libraries enriched in AC or AG tandem repeats and specific PCR were devised from their flanking sequences. Most microsatellites (14) were found polymorphic among 30 individuals of F. naumanni representing 20 reproduction areas of the species in the region of Extremadura, Spain. Polymorphisms were detected by size variation of the amplified loci, which allele number and observed heterozygosity ranged from 3 to 20 and from 0.300 to 0.933, respectively. Cross-species amplification showed that 13 of selected loci were also found polymorphic in common kestrel species (Falco tinnunculus). Novel polymorphic microsatellites will serve to conservation studies in lesser kestrel.     

Genetic structure in insular and mainland populations of house sparrows (Passer domesticus) and their hemosporidian parasites

Small and isolated populations usually exhibit low levels of genetic variability, and thus, they are expected to have a lower capacity to adapt to changes in environmental conditions, such as exposure to pathogens and parasites. Comparing the genetic variability of selectively neutral versus functional loci allows one to assess the evolutionary history of populations and their future evolutionary potential. The genes of the major histocompatibility complex (MHC) control immune recognition of parasites, and their unusually high diversity is genes which is likely driven by parasite‐mediated balancing selection. Here, we examined diversity and differentiation of neutral microsatellite loci and functional MHC class I genes in house sparrows (Passer domesticus), living in six insular and six mainland populations, and we aimed to determine whether their diversity or differentiation correlates with the diversity and the prevalence of infection of hemosporidian parasites. We found that island bird populations tended to have lower neutral genetic variability, whereas MHC variability gene was similar between island and mainland populations. Similarly, island populations tended to show greater genetic differentiation than mainland populations, especially at microsatellite markers. The maintenance of MHC genetic diversity and its less marked structure in the island populations could be attributed to balancing‐selection. The greater MHC differentiation among populations was negatively correlated with similarity in blood parasites (prevalence and diversity of parasite strains) between populations. Even at low prevalence and small geographical scale, haemosporidian parasites might contribute to structure the variability of immune genes among populations of hosts.     

Allelic diversity at the Mhc-DQA locus of woodmouse populations (Apodemus sylvaticus) present in the islands and mainland of the northern Mediterranean

Aim Polymorphism at neutral markers and at MHC loci in rodent populations living on islands is generally low. The main genetic factors that may contribute to a reduced level of genetic variability are genetic drift, reduced gene flow and founder events. We investigated the pattern of polymorphism at the second exon of the Mhc‐DQA gene in island populations of Apodemus sylvaticus and in their mainland counterparts to investigate the pattern of MHC polymorphism in a phylogeographical context and to assess the impact of insularity on diversity at this locus. Location Eight north Mediterranean populations of Apodemus sylvaticus were studied, including five island populations (Majorca, Minorca, Porquerolles, Port‐Cros and Sicily) and three mainland populations. Methods cDNA sequencing and nucleotide sequences analyses. Synonymous and non‐synonymous substitutions were examined at the PBR and non‐PBR sites. The DQA allelic distribution in populations was compared with the woodmouse phylogeography. Results This study presents novel DQA alleles. High polymorphism of the DQA locus is recorded in natural populations of A. sylvaticus with 13 alleles being widely distributed irrespective of the geographical origin and palaeoclimatic history of populations. The DQA locus does not show the expected pattern for non‐synonymous substitutions at the PBR sites. However, island populations show a weak loss of polymorphism in comparison with their mainland counterparts. Main conclusions The DQA locus in the woodmouse seems to be subject to weak selection and does not allow resolution of phylogeographical relationships among European woodmouse populations. The presence of at least three alleles in island populations and the maintenance of five alleles between the two European lineages over 1.5 Myr suggest that balancing selection may act within populations, and more precisely within island populations, to maintain genetic variability. This study shows that phylogeographical studies are a prerequisite for any genetic investigation of selected genes in natural populations.     

Patterns of Orthoptera abundance and lesser kestrel conservation in arable landscapes

The lesser kestrel Falco naumanni experienced a marked decline during the second half of the 20th century due to changes in land use that influenced breeding success by reducing the abundance and quality of prey. However, the factors governing spatial and temporal variation of prey abundance around lesser kestrel colonies has not yet been investigated. We sampled Orthoptera abundance in the main crop types and edge habitats surrounding six lesser kestrel colonies in southern Spain. Samplings focused on Orthoptera because they constitute the main prey during the nestling period. Only those Orthoptera species that are known to be preyed by lesser kestrels were considered in this study. We found differences in prey density among localities, and crop types. Semi-natural habitats such as grasslands, fallow land, and field margins held the highest densities. However, prey abundance showed a complex pattern that was not possible to explain solely on the basis of crop composition around colonies. Factors determining productivity in individual fields like soil type and productivity or biocide input, and mean size of agricultural fields contributed to explain this complex pattern of prey abundance. Our results highlight the key role of semi-natural and edge habitats in farmed landscapes as prey reservoirs and corridors. Higher conservation priorities for these habitats are suggested to benefit foraging lesser kestrels, but many other farmland species that also experienced steep population declines due to decreasing food supply resulting from modern agriculture.     

Climate determinants of breeding and wintering ranges of lesser kestrels in Italy and predicted impacts of climate change

Climate warming would theoretically create conditions for the breeding range expansion of pseudo‐steppe Mediterranean and long‐distance migrant species and provide the possibility for these to overwinter in the same breeding areas. However, contemporary changes in rainfall regimes might have negative effects on the climate suitability and in turn, shrink species potential range. The lesser kestrel Falco naumanni is highly sensitive to rainfall oscillations and has recently extended its Italian breeding range towards northern latitudes and increasing its wintering records. We modelled the effects of temperature and rainfall on current and future climate suitability for lesser kestrels in both the breeding and wintering periods by using MaxEnt. Models were based on the distribution of 298 colonies and 40 wintering records. Future climate suitability was assessed under eight different scenarios. Spring rainfall amount resulted as the main determinant of breeding climate suitability, so its predicted reduction will determine a shrinkage in suitable areas (–42.10% in 2050; –32.07% in 2070). Specifically, the 66.05% of Italian colonies will be outside the climatically suitable area by 2050. However wide areas, suitable under current climate conditions, are still not occupied by lesser kestrel and allow the potential expansion of its Italian breeding range in the short term. Temperature seasonality mainly determined the species’ winter climate suitability, which is overall predicted to boost in the next decades (+145.03% in 2050; and +123.91% in 2070). All but one future scenarios predicted a northward shift of about 40 km for both breeding and wintering climate suitability. Despite its recent expansion, we have found that climate change will pose conservation concerns for the Italian breeding population of lesser kestrels. Indeed, changes in non‐climate factors will also outline the future suitability of the Italian range for lesser kestrels in both seasons with effects that might both strengthen or mitigate climate effects.     

Shorter migration distances associated with higher winter temperatures suggest a mechanism for advancing nesting phenology of American kestrels Falco sparverius

Global climate change has affected avian migration patterns and nesting phenology. Changes in one phase of a bird's cycle will most likely affect other stages, but few studies focus simultaneously on multiple life‐history events. We used western North American ringing records and Christmas Bird Counts to examine whether changes in migration patterns were concordant with advancing American kestrel Falco sparverius nesting phenology. Consistent with previous findings, male kestrels migrated shorter distances than female kestrels, and kestrels nesting in southern latitudes migrated shorter distances than kestrels nesting in more northern areas. In addition, kestrel migration distance decreased significantly from 1960 to 2009 and was negatively associated with winter minimum temperatures. Christmas Birds Counts from the same time period showed increasing indices of overwintering kestrel abundance in northern states (Washington, Idaho, and Utah), where winter minimum temperatures have increased significantly, and concomitant decreases in southern states (California and Arizona). Finally, changes in nesting phenology of kestrels in southwestern Idaho were best explained by warmer winters, not springs. Warmer winters may decrease energetic demands on migrants by allowing for shorter migration distances, decreasing thermoregulatory costs, or both. Decreased energy demands during winter may allow birds to gain resources necessary for reproduction earlier in the nesting season. Higher winter temperatures that decrease (former) constraints on early nesting may be a particularly important mechanism leading to advancing nesting phenology for species with strong seasonal declines in fecundity or intense early season competition for high‐quality nesting areas.     

Selection from parasites favours immunogenetic diversity but not divergence among locally adapted host populations

The unprecedented polymorphism in the major histocompatibility complex (MHC) genes is thought to be maintained by balancing selection from parasites. However, do parasites also drive divergence at MHC loci between host populations, or do the effects of balancing selection maintain similarities among populations? We examined MHC variation in populations of the livebearing fish Poecilia mexicana and characterized their parasite communities. Poecilia mexicana populations in the Cueva del Azufre system are locally adapted to darkness and the presence of toxic hydrogen sulphide, representing highly divergent ecotypes or incipient species. Parasite communities differed significantly across populations, and populations with higher parasite loads had higher levels of diversity at class II MHC genes. However, despite different parasite communities, marked divergence in adaptive traits and in neutral genetic markers, we found MHC alleles to be remarkably similar among host populations. Our findings indicate that balancing selection from parasites maintains immunogenetic diversity of hosts, but this process does not promote MHC divergence in this system. On the contrary, we suggest that balancing selection on immunogenetic loci may outweigh divergent selection causing divergence, thereby hindering host divergence and speciation. Our findings support the hypothesis that balancing selection maintains MHC similarities among lineages during and after speciation (trans‐species evolution).     

A molecular phylogeny of African kestrels with reference to divergence across the Indian Ocean

In this paper we examine the evolutionary relationships of kestrels from mainland Africa, Indian Ocean islands and related areas. We construct a molecular phylogeny of African kestrels, using approximately 1.0 kb of mitochondrial cytochrome b sequence. Our molecular results support an Old World origin for typical kestrels and an ancient divergence of kestrels into the New World, and indicate a more recent radiation of kestrels from Africa via Madagascar towards Mauritius and the Seychelles. Phylogenetic placement of the Australian kestrel suggests a recent origin from African kestrel stock. We compare evolutionary relationships based on kestrel plumage pattern and morphology to our molecular results for the African and Indian Ocean kestrels, and reveal some consistency with the different island forms. We apply a range of published avian cytochrome b substitution rates to our data, as an alternative to internal calibration of a molecular clock arising from incomplete paleontological information. We align these divergence estimates to the geological history of Indian Ocean island formation inferred from potassium-argon dating methods. The arrival of kestrels on Mauritius appears consistent with the cessation of volcanic activity on Mauritius. The estimated time and route of divergence of the Seychelles kestrel from Madagascar may be compatible with the emergence of smaller islands during Pleistocene sea level fluctuations.     

Major histocompatibility complex class II genetic variation in forest musk deer (Moschus berezovskii) in China

The major histocompatibility complex (MHC) plays an important role in the immune system of vertebrates. We used the second exon of four MHC class II genes (DRA, DQA1, DQA2 and DRB3) to assess the overall MHC variation in forest musk deer (Moschus berezovskii). We also compared the MHC variation in captive and wild populations. We observed 22 alleles at four loci (four at DRA, four at DQA1, four at DQA2 and 10 at DRB3), 15 of which were newly identified alleles. Results suggest that forest musk deer maintain relatively high MHC variation, which may result from balancing selection. Moreover, considerable diversity was observed at the DRA locus. We found a high frequency of Mobe‐DRA*02, Mobe‐DQA1*01 and Mobe‐DQA2*05 alleles, which may be important for pathogen resistance. A Ewens–Watterson test showed that the DRB3 locus in the wild population had experienced recent balancing selection. We detected a small divergence at the DRA locus, suggesting the effect of weak positive selection on the DRA gene. Alternatively, this locus may be young and not yet adapted a wide spectrum of alleles for pathogen resistance. The significant heterozygosity deficit observed at the DQA1 and DRB3 loci in the captive population and at all four loci in the wild population may be the result of a population bottleneck. Additionally, MHC genetic diversity was higher in the wild population than in the captive, suggesting that the wild population may have the ability to respond to a wider range of pathogens.     

Adaptive divergence despite strong genetic drift: genomic analysis of the evolutionary mechanisms causing genetic differentiation in the island fox (Urocyon littoralis)

The evolutionary mechanisms generating the tremendous biodiversity of islands have long fascinated evolutionary biologists. Genetic drift and divergent selection are predicted to be strong on islands and both could drive population divergence and speciation. Alternatively, strong genetic drift may preclude adaptation. We conducted a genomic analysis to test the roles of genetic drift and divergent selection in causing genetic differentiation among populations of the island fox (Urocyon littoralis). This species consists of six subspecies, each of which occupies a different California Channel Island. Analysis of 5293 SNP loci generated using Restriction‐site Associated DNA (RAD) sequencing found support for genetic drift as the dominant evolutionary mechanism driving population divergence among island fox populations. In particular, populations had exceptionally low genetic variation, small N_e (range = 2.1–89.7; median = 19.4), and significant genetic signatures of bottlenecks. Moreover, islands with the lowest genetic variation (and, by inference, the strongest historical genetic drift) were most genetically differentiated from mainland grey foxes, and vice versa, indicating genetic drift drives genome‐wide divergence. Nonetheless, outlier tests identified 3.6–6.6% of loci as high F_ST outliers, suggesting that despite strong genetic drift, divergent selection contributes to population divergence. Patterns of similarity among populations based on high F_ST outliers mirrored patterns based on morphology, providing additional evidence that outliers reflect adaptive divergence. Extremely low genetic variation and small N_e in some island fox populations, particularly on San Nicolas Island, suggest that they may be vulnerable to fixation of deleterious alleles, decreased fitness and reduced adaptive potential.     

Impact of historical founder effects and a recent bottleneck on MHC variability in Commander Arctic foxes (Vulpes lagopus)

Populations of Arctic foxes (Vulpes lagopus) have been isolated on two of the Commander Islands (Bering and Mednyi) from the circumpolar distributed mainland population since the Pleistocene. In 1970-1980, an epizootic outbreak of mange caused a severe population decline on Mednyi Island. Genes of the major histocompatibility complex (MHC) play a primary role in infectious disease resistance. The main objectives of our study were to compare contemporary variation of MHC class II in mainland and island Arctic foxes, and to document the effects of the isolation and the recent bottleneck on MHC polymorphism by analyzing samples from historical and contemporary Arctic foxes. In 184 individuals, we found 25 unique MHC class II DRB and DQB alleles, and identified evidence of balancing selection maintaining allelic lineages over time at both loci. Twenty different MHC alleles were observed in mainland foxes and eight in Bering Island foxes. The historical Mednyi population contained five alleles and all contemporary individuals were monomorphic at both DRB and DQB. Our data indicate that despite positive and diversifying selection leading to elevated rates of amino acid replacement in functionally important antigen-binding sites, below a certain population size, balancing selection may not be strong enough to maintain genetic diversity in functionally important genes. This may have important fitness consequences and might explain the high pathogen susceptibility in some island populations. This is the first study that compares MHC diversity before and after a bottleneck in a wild canid population using DNA from museum samples.