Mikael Åkesson

Ten years of AFLP in ecology and evolution: why so few animals?

Researchers in the field of molecular ecology and evolution require versatile and low‐cost genetic typing methods. The AFLP (amplified fragment length polymorphism) method was introduced 10 years ago and shows many features that fulfil these requirements. With good quality genomic DNA at hand, it is relatively easy to generate anonymous multilocus DNA profiles in most species and the start‐up time before data can be generated is often less than a week. Built‐in dynamic, yet simple modifications make it possible to find a protocol suitable to the genome size of the species and to screen thousands of loci in hundreds of individuals for a relatively low cost. Until now, the method has primarily been applied in studies of plants, bacteria and fungi, with a strong bias towards economically important cultivated species and their pests. In this review we identify a number of research areas in the study of wild species of animals where the AFLP method, presently very much underused, should be a very valuable tool. These aspects include classical problems such as studies of population genetic structure and phylogenetic reconstructions, and also new challenges such as finding markers for genes governing adaptations in wild populations and modifications of the protocol that makes it possible to measure expression variation of multiple genes (cDNA‐AFLP) and the distribution of DNA methylation. We hope this review will help molecular ecologists to identify when AFLP is likely to be superior to other more established methods, such as microsatellites, SNP (single nucleotide polymorphism) analyses and multigene DNA sequencing.

Severe inbreeding depression in a wild wolf Canis lupus population

The difficulty of obtaining pedigrees for wild populations has hampered the possibility of demonstrating inbreeding depression in nature. In a small, naturally restored, wild population of grey wolves in Scandinavia, founded in 1983, we constructed a pedigree for 24 of the 28 breeding pairs established in the period 1983–2002. Ancestry for the breeding animals was determined through a combination of field data (snow tracking and radio telemetry) and DNA microsatellite analysis. The population was founded by only three individuals. The inbreeding coefficient F varied between 0.00 and 0.41 for wolves born during the study period. The number of surviving pups per litter during their first winter after birth was strongly correlated with inbreeding coefficients of pups (R2=0.39, p<0.001). This inbreeding depression was recalculated to match standard estimates of lethal equivalents (2B), corresponding to 6.04 (2.58–9.48, 95% CI) litter-size-reducing equivalents in this wolf population.

Microsatellite diversity predicts recruitment of sibling great reed warblers

Inbreeding increases the level of homozygosity, which in turn might depress fitness. In addition, individuals having the same inbreeding coefficient (e.g. siblings) vary in homozygosity. The potential fitness effects of variation in homozygosity that is unrelated to the inbreeding coefficient have seldom been examined. Here, we present evidence from wild birds that genetic variation at five microsatellite loci predicts the recruitment success of siblings. Dyads of full–sibling great reed warblers (Acrocephalus arundinaceus), one individual of which became a recruit to the natal population while the other did not return, were selected for the analysis. Each dyad was matched for sex and size. Local recruitment is strongly tied to fitness in great reed warblers as the majority of offspring die before adulthood, philopatry predominates among surviving individuals and emigrants have lower lifetime fitness. Paired tests showed that recruited individuals had higher individual heterozygosity and higher genetic diversity, which was measured as the mean squared distance between microsatellite alleles (mean d2), than their non–recruited siblings. These relationships suggest that the microsatellite markers, which are generally assumed to be neutral, cosegregated with genes exhibiting genetic variation for fitness.

DOES LINKAGE DISEQUILIBRIUM GENERATE HETEROZYGOSITY-FITNESS CORRELATIONS IN GREAT REED WARBLERS?

Abstract Heterozygosity‐fitness correlations (HFCs) at noncoding genetic markers are commonly assumed to reflect fitness effects of heterozygosity at genomewide distributed genes in partially inbred populations. However, in populations with much linkage disequilibrium (LD), HFCs may arise also as a consequence of selection on fitness loci in the local chromosomal vicinity of the markers. Recent data suggest that relatively high levels of LD may prevail in many ecological situations. Consequently, LD may be an important factor, together with partial inbreeding, in causing HFCs in natural populations. In the present study, we evaluate whether LD can generate HFCs in a small and newly founded population of great reed warblers (Acrocephalus arundinaceus). For this purpose dyads of full siblings of which only one individual survived to adult age (i.e., returned to breed at the study area) were scored at 19 microsatellite loci, and at a gene region of hypothesized importance for survival, the major histocompatibility complex (MHC). By examining siblings, we controlled for variation in the inbreeding coefficient and thus excluded genome‐wide fitness effects in our analyses. We found that recruited individuals had significantly higher multilocus heterozygosity (MLH), and mean d2 (a microsatellite‐specific variable), than their nonrecruited siblings. There was a tendency for the survivors to have a more diverse MHC than the nonsurvivors. Single‐locus analyses showed that the strength of the genotype‐survival association was especially pronounced at four microsatellite loci. By using genotype data from the entire breeding population, we detected significant LD between five of 162 pairs of microsatellite loci after accounting for multiple tests. Our present finding of a significant within‐family multilocus heterozygosity‐survival association in a nonequilibrium population supports the view that LD generates HFCs in natural populations.

Selection for Heterozygosity Gives Hope to a Wild Population of Inbred Wolves

Recent analyses have questioned the usefulness of heterozygosity estimates as measures of the inbreeding coefficient (f), a finding that may have dramatic consequences for the management of endangered populations. We confirm that f and heterozygosity is poorly correlated in a wild and highly inbred wolf population. Yet, our data show that for each level of f, it was the most heterozygous wolves that established themselves as breeders, a selection process that seems to have decelerated the loss of heterozygosity in the population despite a steady increase of f. The markers contributing to the positive relationship between heterozygosity and breeding success were found to be located on different chromosomes, but there was a substantial amount of linkage disequilibrium in the population, indicating that the markers are reflecting heterozygosity over relatively wide genomic regions. Following our results we recommend that management programs of endangered populations include estimates of both f and heterozygosity, as they may contribute with complementary information about population viability.

Linkage mapping reveals sex-dimorphic map distances in a passerine bird

Linkage maps are lacking for many highly influential model organisms in evolutionary research, including all passerine birds. Consequently, their full potential as research models is severely hampered. Here, we provide a partial linkage map and give novel estimates of sex-specific recombination rates in a passerine bird, the great reed warbler (Acrocephalus arundinaceus). Linkage analysis of genotypic data at 51 autosomal microsatellites and seven markers on the Z-chromosome (one of the sex chromosomes) from an extended pedigree resulted in 12 linkage groups with 2–8 loci. A striking feature of the map was the pronounced sex-dimorphism: males had a substantially lower recombination rate than females, which resulted in a suppressed autosomal map in males (sum of linkage groups: 110.2 cM) compared to females (237.2 cM; female/male map ratio: 2.15). The sex-specific recombination rates will facilitate the building of a denser linkage map and cast light on hypotheses about sex-specific recombination rates.

Estimating heritabilities and genetic correlations: comparing the 'animal model' with parent-offspring regression using data from a natural population.

Quantitative genetic parameters are nowadays more frequently estimated with restricted maximum likelihood using the ‘animal model’ than with traditional methods such as parent-offspring regressions. These methods have however rarely been evaluated using equivalent data sets. We compare heritabilities and genetic correlations from animal model and parent-offspring analyses, respectively, using data on eight morphological traits in the great reed warbler (Acrocephalus arundinaceus). Animal models were run using either mean trait values or individual repeated measurements to be able to separate between effects of including more extended pedigree information and effects of replicated sampling from the same individuals. We show that the inclusion of more pedigree information by the use of mean traits animal models had limited effect on the standard error and magnitude of heritabilities. In contrast, the use of repeated measures animal model generally had a positive effect on the sampling accuracy and resulted in lower heritabilities; the latter due to lower additive variance and higher phenotypic variance. For most trait combinations, both animal model methods gave genetic correlations that were lower than the parent-offspring estimates, whereas the standard errors were lower only for the mean traits animal model. We conclude that differences in heritabilities between the animal model and parent-offspring regressions were mostly due to the inclusion of individual replicates to the animal model rather than the inclusion of more extended pedigree information. Genetic correlations were, on the other hand, primarily affected by the inclusion of more pedigree information. This study is to our knowledge the most comprehensive empirical evaluation of the performance of the animal model in relation to parent-offspring regressions in a wild population. Our conclusions should be valuable for reconciliation of data obtained in earlier studies as well as for future meta-analyses utilizing estimates from both traditional methods and the animal model.

Annual Cycle and Migration Strategies of a Trans-Saharan Migratory Songbird: A Geolocator Study in the Great Reed Warbler

Recent technological advancements now allow us to obtain geographical position data for a wide range of animal movements. Here we used light-level geolocators to study the annual migration cycle in great reed warblers (Acrocephalus arundinaceus), a passerine bird breeding in Eurasia and wintering in sub-Saharan Africa. We were specifically interested in seasonal strategies in routes and schedules of migration. We found that the great reed warblers (all males, no females were included) migrated from the Swedish breeding site in early August. After spending up to three weeks at scattered stopover sites in central to south-eastern Europe, they resumed migration and crossed the Mediterranean Sea and Sahara Desert without lengthy stopovers. They then spread out over a large overwintering area and each bird utilised two (or even three) main wintering sites that were spatially separated by a distinct mid-winter movement. Spring migration initiation date differed widely between individuals (1-27 April). Several males took a more westerly route over the Sahara in spring than in autumn, and in general there were fewer long-distance travels and more frequent shorter stopovers, including one in northern Africa, in spring. The shorter stopovers made spring migration on average faster than autumn migration. There was a strong correlation between the spring departure dates from wintering sites and the arrival dates at the breeding ground. All males had a high migration speed in spring despite large variation in departure dates, indicating a time-minimization strategy to achieve an early arrival at the breeding site; the latter being decisive for high reproductive success in great reed warblers. Our results have important implications for the understanding of long-distance migrants’ ability to predict conditions at distant breeding sites and adapt to rapid environmental change.

Heritability of resting metabolic rate in a wild population of blue tits

We report the first study with the aim to estimate heritability in a wild population, a nest box breeding population of blue tits. We estimated heritability as well as genetic and phenotypic correlations of resting metabolic rate (RMR), body mass and tarsus length with an animal model based on data from a split cross‐fostering experiment with brood size manipulations. RMR and body mass, but not tarsus length, showed significant levels of explained variation but for different underlying reasons. In body mass, the contribution to the explained variation is mainly because of a strong brood effect, while in RMR it is mainly because of a high heritability. The additive variance in RMR was significant and the heritability was estimated to 0.59. The estimates of heritability of body mass (0.08) and tarsus length (0.00) were both low and based on nonsignificant additive variances. Thus, given the low heritability (and additive variances) in body mass and tarsus length the potential for direct selection on RMR independent of the two traits is high in this population. However, the strong phenotypic correlation between RMR and mass (0.643 ± 0.079) was partly accounted for by a potentially strong, although highly uncertain, genetic correlation (1.178 ± 0.456) between the two traits. This indicates that the additive variance of body mass, although low, might still somewhat constrain the independent evolvability of RMR.

A strong quantitative trait locus for wing length on chromosome 2 in a wild population of great reed warblers.

Wing length is a key character for essential behaviours related to bird flight such as migration and foraging. In the present study, we initiate the search for the genes underlying wing length in birds by studying a long-distance migrant, the great reed warbler (Acrocephalus arundinaceus). In this species wing length is an evolutionary interesting trait with pronounced latitudinal gradient and sex-specific selection regimes in local populations. We performed a quantitative trait locus (QTL) scan for wing length in great reed warblers using phenotypic, genotypic, pedigree and linkage map data from our long-term study population in Sweden. We applied the linkage analysis mapping method implemented in GridQTL (a new web-based software) and detected a genome-wide significant QTL for wing length on chromosome 2, to our knowledge, the first detected QTL in wild birds. The QTL extended over 25 cM and accounted for a substantial part (37%) of the phenotypic variance of the trait. A genome scan for tarsus length (a body-size-related trait) did not show any signal, implying that the wing-length QTL on chromosome 2 was not associated with body size. Our results provide a first important step into understanding the genetic architecture of avian wing length, and give opportunities to study the evolutionary dynamics of wing length at the locus level.