Transposable elements mark a repeat‐rich region associated with migratory phenotypes of willow warblers (<i>Phylloscopus trochilus</i>)

Caballero-López, Violeta; Lundberg, Max; Sokolovskis, Kristaps; Bensch, Staffan

doi:10.1111/mec.16292

Cited by 18 publications

(22 citation statements)

References 77 publications

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“…This role in helping the species adapt to environmental conditions was similarly discovered for fish diadromy, which is the migration between freshwater and the sea, in a study that investigated genomes of 24 fish species ( Carotti et al, 2021 ). Similar adaptions have also been observed for the migratory phenotype of birds such as willow warblers ( Caballero-López et al, 2022 ), and in the relationship between sociality and genomic architecture in snapping shrimps, Synalpheus ( Chak et al, 2021 ). Further, ancestral state construction suggested that TEs propagated the transition to eusociality ( Chak et al, 2021 ).…”

Section: Systematic Functions Of Transposable Elementssupporting

confidence: 67%

The Role of Transposable Elements in Sexual Development

Chiang

DeRosa

Park

et al. 2022

Front. Behav. Neurosci.

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Up to 50% of most mammalian genomes are made up of transposable elements (TEs) that have the potential to mobilize around the genome. Despite this prevalence, research on TEs is only beginning to gain traction within the field of neuroscience. While TEs have long been regarded as “junk” or parasitic DNA, it has become evident that they are adaptive DNA and RNA regulatory elements. In addition to their vital role in normal development, TEs can also interact with steroid receptors, which are key elements to sexual development. In this review, we provide an overview of the involvement of TEs in processes related to sexual development- from TE activity in the germline to TE accumulation in sex chromosomes. Moreover, we highlight sex differences in TE activity and their regulation of genes related to sexual development. Finally, we speculate on the epigenetic mechanisms that may govern TEs’ role in sexual development. In this context, we emphasize the need to further the understanding of sexual development through the lens of TEs including in a variety of organs at different developmental stages, their molecular networks, and evolution.

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Section: Systematic Functions Of Transposable Elementssupporting

confidence: 67%

The Role of Transposable Elements in Sexual Development

Chiang

DeRosa

Park

et al. 2022

Front. Behav. Neurosci.

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“…2 a and 3 ). Unlike the InvP-Ch1 and InvP-Ch5 that are chromosomal inversions the MARB-a is a repeat-rich block with a varying copy number of a specific TE 15 . Thus, our present genotyping protocol can only score for absence (<7 copies of TE) or presence (>7 copies of TE) of MARB-a (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…In total, we retrieved data from 72 individuals of which 51 are from the migratory divide. Each bird was blood sampled upon recapture and genotyped for InvP-Ch1, InvP-Ch5 16 and presence or absence of MARB-a 15 .…”

Section: Introductionmentioning

confidence: 99%

Migration direction in a songbird explained by two loci

et al. 2023

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Migratory routes and remote wintering quarters in birds are often species and even population specific. It has been known for decades that songbirds mainly migrate solitarily, and that the migration direction is genetically controlled. Yet, the underlying genetic mechanisms remain unknown. To investigate the genetic basis of migration direction, we track genotyped willow warblers Phylloscopus trochilus from a migratory divide in Sweden, where South-West migrating, and South-East migrating subspecies form a hybrid swarm. We find evidence that migration direction follows a dominant inheritance pattern with epistatic interaction between two loci explaining 74% of variation. Consequently, most hybrids migrate similarly to one of the parental subspecies, and therefore do not suffer from the cost of following an inferior, intermediate route. This has significant implications for understanding the selection processes that maintain narrow migratory divides.

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“…However, the relationship between DNA sequence variation and epigenome variation is likely complicated by variants that are difficult to detect or quantify. For example, copy number variants and transposable element insertions may be important and inheritable DNA sequence variants, but detecting these remains difficult particularly in non-model organisms (Caballero-Lopez et al, 2021). When these undetected sequence variants are important to a measured phenotype and co-vary with epigenome variants, this may give the false impression that the trait is solely epigenetically inherited; if this happens frequently across the genome this will, perhaps falsely, suggest that sequence variation is not strongly related to epigenetic variation (Heard and Martienssen, 2014).…”

Section: Does Dna Sequence Diversity Relate To Epigenome Diversity An...mentioning

confidence: 99%

Epigenetics in Ecology, Evolution, and Conservation

et al. 2022

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Epigenetic variation is often characterized by modifications to DNA that do not alter the underlying nucleotide sequence, but can influence behavior, morphology, and physiological phenotypes by affecting gene expression and protein synthesis. In this review, we consider how the emerging field of ecological epigenetics (eco-epi) aims to use epigenetic variation to explain ecologically relevant phenotypic variation and predict evolutionary trajectories that are important in conservation. Here, we focus on how epigenetic data have contributed to our understanding of wild populations, including plants, animals, and fungi. First, we identified published eco-epi literature and found that there was limited taxonomic and ecosystem coverage and that, by necessity of available technology, these studies have most often focused on the summarized epigenome rather than locus- or nucleotide-level epigenome characteristics. We also found that while many studies focused on adaptation and heritability of the epigenome, the field has thematically expanded into topics such as disease ecology and epigenome-based ageing of individuals. In the second part of our synthesis, we discuss key insights that have emerged from the epigenetic field broadly and use these to preview the path toward integration of epigenetics into ecology. Specifically, we suggest moving focus to nucleotide-level differences in the epigenome rather than whole-epigenome data and that we incorporate several facets of epigenome characterization (e.g., methylation, chromatin structure). Finally, we also suggest that incorporation of behavior and stress data will be critical to the process of fully integrating eco-epi data into ecology, conservation, and evolutionary biology.

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Transposable elements mark a repeat‐rich region associated with migratory phenotypes of willow warblers (Phylloscopus trochilus)

Abstract: This is an open access article under the terms of the Creat ive Commo ns Attri butio n-NonCo mmerc ial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.

Cited by 18 publications

References 77 publications

The Role of Transposable Elements in Sexual Development

The Role of Transposable Elements in Sexual Development

Migration direction in a songbird explained by two loci

Epigenetics in Ecology, Evolution, and Conservation

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