Dataset Information

Characterisation of a transcriptome to find sequence differences between two differentially migrating subspecies of the willow warbler Phylloscopus trochilus.

ABSTRACT: BACKGROUND:Animal migration requires adaptations in morphological, physiological and behavioural traits. Several of these traits have been shown to possess a strong heritable component in birds, but little is known about their genetic architecture. Here we used 454 sequencing of brain-derived transcriptomes from two differentially migrating subspecies of the willow warbler Phylloscopus trochilus to detect genes potentially underlying traits associated with migration. RESULTS:The transcriptome sequencing resulted in 1.8 million reads following filtering steps. Most of the reads (84%) were successfully mapped to the genome of the zebra finch Taeniopygia gutatta. The mapped reads were situated within at least 12,101 predicted zebra finch genes, with the greatest sequencing depth in exons. Reads that were mapped to intergenic regions were generally located close to predicted genes and possibly located in uncharacterized untranslated regions (UTRs). Out of 85,000 single nucleotide polymorphisms (SNPs) with a minimum sequencing depth of eight reads from each of two subspecies-specific pools, only 55 showed high differentiation, confirming previous studies showing that most of the genetic variation is shared between the subspecies. Validation of a subset of the most highly differentiated SNPs using Sanger sequencing demonstrated that several of them also were differentiated between an independent set of individuals of each subspecies. These SNPs were clustered in two chromosome regions that are likely to be influenced by divergent selection between the subspecies and that could potentially be associated with adaptations to their different migratory strategies. CONCLUSIONS:Our study represents the first large-scale sequencing analysis aiming at detecting genes underlying migratory phenotypes in birds and provides new candidates for genes potentially involved in migration.

SUBMITTER: Lundberg M

PROVIDER: S-EPMC3660185 | biostudies-literature | 2013 May

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Characterisation of a transcriptome to find sequence differences between two differentially migrating subspecies of the willow warbler Phylloscopus trochilus.

Lundberg Max M Boss John J Canbäck Björn B Liedvogel Miriam M Larson Keith W KW Grahn Mats M Åkesson Susanne S Bensch Staffan S Wright Anthony A

BMC genomics 20130514

<h4>Background</h4>Animal migration requires adaptations in morphological, physiological and behavioural traits. Several of these traits have been shown to possess a strong heritable component in birds, but little is known about their genetic architecture. Here we used 454 sequencing of brain-derived transcriptomes from two differentially migrating subspecies of the willow warbler Phylloscopus trochilus to detect genes potentially underlying traits associated with migration.<h4>Results</h4>The t ...[more]

PMID: 23672489

Similar Datasets

Project description:BackgroundThe arrival of many species of migrant passerine in the European spring has shifted earlier over recent decades, attributed to climate change and rising temperatures in Europe and west Africa. Few studies have shown the effects of climate change in both hemispheres though many long-distance migrants use wintering grounds which span Africa. The migrants' arrival in Europe thus potentially reflects a combination of the conditions they experience across Africa. We examine if the timing of spring migration of a long-distance migrant, the Willow Warbler, is related to large-scale climate indices across Africa and Europe.MethodsUsing data from daily mistnetting from 1 April to 15 May in 1982-2017 at Bukowo (Poland, Baltic Sea coast), we developed an Annual Anomaly metric (AA, in days) to estimate how early or late Willow Warblers arrive each spring in relation to their multi-year average pattern. The Willow Warblers' spring passage advanced by 5.4 days over the 36 years. We modelled AA using 14 potential explanatory variables in multiple regression models. The variables were the calendar year and 13 large-scale indices of climate in Africa and Europe averaged over biologically meaningful periods of two to four months during the year before spring migration.ResultsThe best model explained 59% of the variation in AA with seven variables: Northern Atlantic Oscillation (two periods), Indian Ocean Dipole, Southern Oscillation Index, Sahel Precipitation Anomaly, Scandinavian Index and local mean temperatures. The study also confirmed that a long-term trend for Willow Warblers to arrive earlier in spring continued up to 2017.DiscussionOur results suggest that the timing of Willow Warbler spring migration at the Baltic Sea coast is related to a summation of the ecological conditions they had encountered over the previous year during breeding, migration south, wintering in Africa and migration north. We suggest these large-scale climate indices reflect ecological drivers for phenological changes in species with complex migration patterns and discuss the ways in which each of the seven climate indices could be related to spring migration at the Baltic Sea coast.

Project description:It is well established that differences in migratory behavior between populations of songbirds have a genetic basis but the actual genes underlying these traits remains largely unknown. In an attempt to identify such candidate genes we de novo assembled the genome of the willow warbler Phylloscopus trochilus, and used whole-genome resequencing and a SNP array to associate genomic variation with migratory phenotypes across two migratory divides around the Baltic Sea that separate SW migrating P. t. trochilus wintering in western Africa and SSE migrating P. t. acredula wintering in eastern and southern Africa. We found that the genomes of the two migratory phenotypes lack clear differences except for three highly differentiated regions located on chromosomes 1, 3, and 5 (containing 146, 135, and 53 genes, respectively). Within each migratory phenotype we found virtually no differences in allele frequencies for thousands of SNPs, even when comparing geographically distant populations breeding in Scandinavia and Far East Russia (>6000 km). In each of the three differentiated regions, multidimensional scaling-based clustering of SNP genotypes from more than 1100 individuals demonstrates the presence of distinct haplotype clusters that are associated with each migratory phenotype. In turn, this suggests that recombination is absent or rare between haplotypes, which could be explained by inversion polymorphisms. Whereas SNP alleles on chromosome 3 correlate with breeding altitude and latitude, the allele distribution within the regions on chromosomes 1 and 5 perfectly matches the geographical distribution of the migratory phenotypes. The most differentiated 10 kb windows and missense mutations within these differentiated regions are associated with genes involved in fatty acid synthesis, possibly representing physiological adaptations to the different migratory strategies. The ?200 genes in these regions, of which several lack described function, will direct future experimental and comparative studies in the search for genes that underlie important migratory traits.

Project description:BackgroundHigh-latitude bird migration has evolved after the last glaciation, in less than 10,000-15,000 years. Migrating songbirds rely on an endogenous migratory program, encoding timing, fueling, and routes, but it is still unknown which compass mechanism they use on migration. We used geolocators to track the migration of willow warblers (Phylloscopus trochilus yakutensis) from their eastern part of the range in Russia to wintering areas in sub-Saharan Africa. Our aim was to investigate if the autumn migration route can be explained by a simple compass mechanism, based on celestial or geomagnetic information, or whether migration is undertaken as a sequence of differential migratory paths possibly involving a map sense. We compared the recorded migratory routes for our tracked birds with simulated routes obtained from different compass mechanisms.ResultsThe three tracked males were very similar in the routes they took to their final wintering sites in southern Tanzania or northern Mozambique, in their use of stopover sites and in the overall timing of migration. None of the tested compass mechanisms could explain the birds' routes to the first stopover area in southwest Asia or to the destination in Southeast Africa without modifications. Our compass mechanism simulations suggest that the simplest scenarios congruent with the observed routes are based on either an inclination or a sun compass, assuming two sequential steps.ConclusionsThe birds may follow a magnetoclinic route coinciding closely with the tracks by first moving west, i.e. closer to the goal, and thereafter follow a constant apparent angle of inclination to the stopover site. An alternative would be to use the sun compass, but with time-adjustments along the initial part of the migration to the first stopover, and thereafter depart along a new course to the winter destination. A combination of the two mechanisms cannot be ruled out, but needs to be confirmed in future studies.

Project description:INTRODUCTION:In contact zones, genetic mixing of two taxa can be restricted by prezygotic (e.g. assortative mating) or postzygotic (lower fitness of hybrid offspring) barriers, or a combination of the two. A hybrid zone between two willow warbler subspecies (Phylloscopus trochilus trochilus, P. t. acredula) with distinctive migratory strategies occurs in central Sweden. These subspecies exhibit differences in migratory direction and distance, resulting in geographically distinct wintering areas in Africa. The subspecies may have diverged from a common refuge after the last ice age, and neutral genetic markers are homogeneous across their range. By contrast, several phenotypic traits and genetic markers of two chromosomal regions previously identified show steep clines across the divide. The evolutionary forces that maintain this migratory divide remain unknown. Here we use plumage colour, morphology, genetic markers and feather stable nitrogen-isotopes (? (15)N) to assess if assortative mating between migratory phenotypes could be acting as a possible mechanism for keeping the two forms genetically separate and maintaining the migratory divide. We colour-ringed a willow warbler breeding population in the central part of the hybrid zone and observed the breeding population to assess phenotypic and genotypic traits of social pairs. RESULTS:Our data suggest that wintering area and genetic ancestry had an effect on male arrival time to the breeding grounds which could contribute to assortment. However, evidence for assortative mating could not be detected based on a comparison of plumage colour, morphology and ? (15)N between social mates. CONCLUSION:This finding was strengthened by analyses of subspecies-specific genetic markers, which allowed us to identify the presence of a large proportion of potential hybrids and backcrosses at the study site. Our results supported the hypothesis that pre-mating isolation in willow warblers is weak, resulting in extensive hybridisation across the migratory divide.

Project description:Backgrounds:Geographic regions, where two closely related taxa with different migration routes come into contact, are known as migratory divides. Hybrids originating from migratory divides are hypothesized to migrate intermediately relative to the parental populations. Few studies have tested this hypothesis in wild birds, and only in hybrids that have completed the migration back to the breeding grounds. Here, we make use of the well-established migration routes of willow warblers (Phylloscopus trochilus), for which the subspecies trochilus and acredula have migration-associated genetic markers on chromosomes 1 and 5. The genetic approach enabled us to analyze the geographic distribution of juveniles during their first autumn migration, predicting that hybrids should be more frequent in the central flyway over Italy than along the typical SW routes of trochilus and SE routes of acredula. Methods:Blood and feather samples were collected from wintering birds in Africa (n =?69), and from juveniles during autumn migration in Portugal (n =?33), Italy (n =?38) and Bulgaria (n =?32). Genotyping was carried out by qPCR SNP assays, on one SNP each on chromosome 1 (SNP 65) and chromosome 5 (SNP 285). Both these SNPs have alternative alleles that are highly fixed (>?97%) in each of the subspecies. Results:The observed combined genotypes of the two SNPs were associated with the known migration routes and wintering distributions of trochilus and acredula, respectively. We found hybrids (HH) among the juveniles in Italy (5/38) and in Portugal (2/33). The proportion of hybrids in Italy was significantly higher than expected from a background rate of hybrid genotypes (1.5%) in allopatric populations of the subspecies. Conclusions:Our genetic approach to assign individuals to subspecies and hybrids allowed us to investigate migration direction in juvenile birds on their first migration, which should better reflect the innate migratory direction than studies restricted to successful migrants. The excess of hybrids in Italy, suggests that they employ an intermediate route relative to the parental populations. Our qPCR SNP genotyping method is efficient for processing large sample sizes, and will therefore be useful in migration research of species with known population genetic structure.

Dataset Information

Characterisation of a transcriptome to find sequence differences between two differentially migrating subspecies of the willow warbler Phylloscopus trochilus.

Publications

Characterisation of a transcriptome to find sequence differences between two differentially migrating subspecies of the willow warbler Phylloscopus trochilus.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets