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Abstract Many migratory species, from monarch butterflies to wildebeest, express partial migration, where only a subset of a population migrates. This intraspecific variation is likely to have large ecological consequences. We studied the ecological consequences of partial migration in a salmonid fish,Oncorhynchus mykiss, in coastal streams in California, USA. One ecotype, steelhead trout, migrates to the ocean, whereas the other, rainbow trout, completes its lifecycle in freshwater. Migration has a strong genetic basis inO. mykiss. In one stream, we found differences in the frequency of migration‐linked genotypes below and above a waterfall barrier (migratory allele frequency of 60% below vs. 31% above). Below the waterfall, in the migratory‐dominated region, the density of young fish (<1 yr old) was approximately twice that in the resident‐dominated region above the waterfall (0.46 vs. 0.26 individuals/m2, respectively), presumably reflecting the higher fecundity of migratory females. Additionally, there were half as many older fish (>1 yr old) in pools downstream of the waterfall (0.05 vs. 0.13 individuals/m2). In a second stream, between‐year variation in the dominance of migratory vs. resident fish allowed us to explore differences in fish density and size structure through time, and we found a consistent pattern. In brief, when migratory genotypes dominated, we found higher densities of young fish and lower densities of older fish, resulting in a simpler size structure, compared to when resident genotypes dominated. Moreover, large resident trout had a slightly higher trophic position than young fish (3.92 vs. 3.42 in one creek and 3.77 vs. 3.17 in the other), quantified with stable isotope data. The difference in fish size structure did not generate trophic cascades. Partial migration is widespread among migratory populations, as is phenotypic divergence between resident and migratory forms, suggesting the potential for widespread ecological effects arising from this common form of intraspecific variation.
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Combining Individual‐Based Radio‐Tracking With Whole‐Genome Sequencing Data Reveals Candidate for Genetic Basis of Partial Migration in a Songbird
ABSTRACT Partial migration is a phenomenon where migratory and resident individuals of the same species co‐exist within a population, and has been linked to both intrinsic (e.g., genetic) as well as environmental factors. Here we investigated the genomic architecture of partial migration in the common blackbird, a songbird that comprises resident populations in the southern distribution range, partial migratory populations in central Europe, and exclusively migratory populations in northern and eastern Europe. We generated whole‐genome sequencing data for 60 individuals, each of which was phenotyped for migratory behavior using radio‐telemetry tracking. These individuals were sampled across the species' distribution range, including resident populations (Spain and France), obligate migrants (Russia), and a partial migratory population with equal numbers of migratory and resident individuals in Germany. We estimated genetic differentiation (FST) of single‐nucleotide variants (SNVs) in 2.5 kb windows between all possible population and migratory phenotype combinations, and focused our characterization on birds from the partial migratory population in Germany. Despite overall low differentiation within the partial migratory German population, we identified several outlier regions with elevated differentiation on four distinct chromosomes. The region with the highest relative and absolute differentiation was located on chromosome 9, overlappingPER2, which has previously been shown to be involved in the control of the circadian rhythm across vertebrates. While this region showed high levels of differentiation, no fixed variant could be identified, supporting the notion that a complex phenotype such as migratory behavior is likely controlled by a large number of genetic loci.
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- Award ID(s):
- 2143004
- PAR ID:
- 10573345
- Publisher / Repository:
- Wiley
- Date Published:
- Journal Name:
- Ecology and Evolution
- Volume:
- 15
- Issue:
- 1
- ISSN:
- 2045-7758
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Abstract Migration is driven by a combination of environmental and genetic factors, but many questions remain about those drivers. Potential interactions between genetic and environmental variants associated with different migratory phenotypes are rarely the focus of study. We pair low coverage whole genome resequencing with a de novo genome assembly to examine population structure, inbreeding, and the environmental factors associated with genetic differentiation between migratory and resident breeding phenotypes in a species of conservation concern, the western burrowing owl (Athene cunicularia hypugaea). Our analyses reveal a dichotomy in gene flow depending on whether the population is resident or migratory, with the former being genetically structured and the latter exhibiting no signs of structure. Among resident populations, we observed significantly higher genetic differentiation, significant isolation‐by‐distance, and significantly elevated inbreeding. Among migratory breeding groups, on the other hand, we observed lower genetic differentiation, no isolation‐by‐distance, and substantially lower inbreeding. Using genotype–environment association analysis, we find significant evidence for relationships between migratory phenotypes (i.e., migrant versus resident) and environmental variation associated with cold temperatures during the winter and barren, open habitats. In the regions of the genome most differentiated between migrants and residents, we find significant enrichment for genes associated with the metabolism of fats. This may be linked to the increased pressure on migrants to process and store fats more efficiently in preparation for and during migration. Our results provide a significant contribution toward understanding the evolution of migratory behavior and vital insight into ongoing conservation and management efforts for the western burrowing owl.more » « less
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Partial migration is a common phenomenon wherein populations include migratory and resident individuals. Whether an individual migrates or not has important ecological and management implications, particularly within protected populations. Within partially migratory populations of Oncorhynchus mykiss, migration is highly correlated with a specific genomic region, but it is unclear how well this region predicts migration at the individual level. Here, we relate sex and life history genotype, determined using >400 single nucleotide polymorphisms (SNPs) on the migratory-linked genomic region, to life history expression of marked juvenile O. mykiss from two tributaries to the South Fork Eel River, northern California. Most resident fish were resident genotypes (57% resident, 37% heterozygous, 6% migratory genotype) and male (78%). Most migratory fish were female (62%), but were a mixture of genotypes (30% resident, 45% heterozygous, 25% migratory genotype). Sex was more strongly correlated with life history expression than genotype, but the best-supported model included both. Resident genotypes regularly migrated, highlighting the importance of conserving the full suite of life history and genetic diversity in partially migratory populations.more » « less
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1002/ece3.70800
