Biology subjects

Irestedt, M.

Publications and source records attributed to Irestedt, M..

15 recordsLinked to original sources

bioRxiv2026

The road to nowhere: geolocation-by-genotype traces large-scale yellow-browed warbler vagrancy to central Siberia

Vagrant animals - individuals found far outside their normal range - offer powerful natural experiments for understanding migratory mechanisms. The yellow-browed warbler (Phylloscopus inornatus) provides perhaps the best-yet example, typically migrating from Siberia to South/Southeast Asia yet found in increasingly large numbers in Western Europe. This represents a strikingly unresolved evolutionary puzzle: why do so many migrants consistently move in almost the complete wrong direction? A critical first step toward solving this enigma is determining where these birds come from. If vagrants came from the proximal western range edge this would imply simple disorientation, whilst a more easterly origin could imply large-scale reverse misorientation. Here, we develop a geolocation-by-genotype algorithm for low-coverage whole-genome resequencing data collected from feathers. Our method identifies spatially informative SNPs; clusters them to account for covariance in allele frequency through space; and employs a bootstrapped maximum-likelihood framework to estimate spatial origin with uncertainty. Applied to more than 80 European-caught birds, our results place their origin in central Siberia (118{degrees}E; 89-134{degrees}E [95% CI]); over 2000km east of the western range edge. These results suggest mass misorientation in a near-reverse direction, and highlight the yellow-browed warbler as an exceptional system for probing the mechanism, ontogeny and evolution of migration.

animal behavior and cognition↗

bioRxiv2026

Bioclimatic variables influence the strength of purifying selection on mitochondrial DNA in an avian clade (Aves: Piciformes)

Mitochondrial loci were for long considered as markers of choice to reconstruct phylogenies. The development of high-throughput sequencing over the past two decades fostered the sequencing of mitogenomes, allowing further macroevolutionary questions to be tested. Several biological traits of birds (e.g. body mass, migration distances) have been related to mitochondrial substitution rates. Environmental parameters in ectothermics vertebrates, and potentially in endotherms, have been further suggested to impact substitution rates for specific taxa or loci. Yet, the relative importance of biological traits versus bioclimatic variables is unknown because the former were not systematically controlled for in studies that underlined the effect of the bioclimatic variables. To assess the importance of bioclimatic variables on selection regimes, we analysed the thirteen mitochondrial protein-coding genes for 176 Piciformes (toucans, honeyguides, woodpeckers), a clade with homogeneous life-history traits that can be found in diverse bioclimatic environments. Our analyses highlighted a negative relationship between temperature annual range and the non synonymous to synonymous substitutions ratio. The higher purifying selection in temperate environments may be a result of the strong constraints on maintaining an optimal metabolism in broader climatic variations. Our results further highlight that care should be taken when applying general mitochondrial clocks to estimate divergence times among avian lineages distributed in different climatic conditions.

evolutionary biology↗

bioRxiv2025

Programmed DNA elimination drives rapid genomic innovation in two thirds of all bird species

Bird genomes are among the most stable in terms of synteny and gene content across vertebrates. However, germline-restricted chromosomes (GRCs) represent a striking exception where programmed DNA elimination confines large-scale genomic changes to the germline. GRCs are known to occur in songbirds (oscines), but have been studied only in a few species of Passerides such as the zebra finch, the key model for passerine genomics. Their presence and evolutionary dynamics in most major passerine lineages remain largely unexplored, with suboscines entirely unexamined by cytogenetic or genomic methods. Here, we present the most comprehensive comparative analysis of GRCs to date, spanning 44 million years of passerine evolution. By generating the first germline reference genomes of an oscine and a suboscine, 22 novel germline draft genomes spanning nearly all major passerine lineages and a germline draft genome of a parrot outgroup, we show that the GRC is likely present in 6,700 passerine species. Our results reveal that the GRC evolves rapidly and distinctly from the standard A chromosomes (autosomes and sex chromosomes), yet retains functionally important, selectively maintained genes. We observed gene and repeat turnover occuring orders of magnitude faster than on the A chromosomes. Some GRC genes, such as cpeb1 and pim1, are widespread from an ancient duplication. In contrast, other GRC genes, like mfsd2b and bmp15, have been independently duplicated onto the GRC multiple times, suggesting adaptive constraints. The discovery of zglp1 on the zebra finch GRC, initially copied from chromosome 30 and subsequently lost from it, indicates functional replacement, where the GRC permits gene loss from the standard genome. As the GRC harbors the only zglp1 copy in most of the [~]4000 Passerides species, GRC loss would compromise essential germline functions. Our findings establish the GRC as a genomic innovator driving rapid germline evolution. This fact highlights its evolutionary significance for passerine diversification and suggests that programmed DNA elimination may be an overlooked yet phylogenetically widespread mechanism in many understudied animal lineages.

genomics↗

bioRxiv2023

Species-specific dynamics may cause deviations from general biogeographical predictions - evidence from a population genomics study of a New Guinean endemic passerine bird family (Melampittidae).

New Guinea, the largest tropical island, is topographically complex and is dominated by a large central mountain range surrounded by multiple smaller isolated mountain regions along its perimeter. The island is biologically hyper-diverse and harbours an avifauna with many species found only there. The family Melampittidae is endemic to New Guinea and consists of two monotypic genera: Melampitta lugubris (Lesser Melampitta) and Megalampitta gigantea (Greater Melampitta). Both Melampitta species have scattered and disconnected distributions across New Guinea in the central mountain range and in some of the outlying ranges. While M. lugubris is common and found in most montane regions of the island, M. gigantaea is elusive and known from only six localities in isolated pockets on New Guinea with very specific habitats of limestone and sinkholes. In this project, we apply museomics to determine the population structure and demographic history of these two species. We re-sequenced the genomes of all seven known M. gigantaea samples housed in museum collections as well as 24 M. lugubris samples from across its distribution. By comparing population structure between the two species, we investigate to what extent habitat dependence, such as in M. gigantaea, may affect population connectivity. Phylogenetic and population genomic analyses, as well as acoustic differentiation, revealed that M. gigantaea consists of a single population in contrast to M. lugubris that shows much stronger population structure across the island. This work sheds new light on the mechanisms that have shaped the intriguing distribution of the two species within this family and is a prime example of the importance of museum collections for genomic studies of poorly known and rare species.

evolutionary biology↗

bioRxiv2023

Inbreeding or outbreeding depression? How to manage an endangered and locally adapted population of red grouse Lagopus scotica

The balance between the inbreeding and outbreeding continuum is a fundamental debate within conservation genomics. To inform this debate we use genome wide data to show that inbreeding is higher in Irish red grouse (Lagopus scotica) and that this smaller and isolated population exhibits divergence from the British. Outlier analysis identified divergence in several genomic regions linked to genes coding for ecologically important traits such as phenotypic differences in plumage colour and sequence divergence among coding regions in the melanin pathway. We also find differences among immune genes and loci involved in food intake and energy control. The two populations thus appear locally adapted. Divergence between the source and the target population when used for conservation aided restocking may have negative consequences if locally adapted alleles are swamped and/or maladapted genotypes are introduced, leading to outbreeding depression. While avoiding inbreeding by maintaining large populations is important, our study illustrates that conservationists and managers should also consider population divergence and local adaptation. We argue against translocations among Ireland and Britain as a conservation strategy. The results of our study demonstrate the value of focusing on local populations and habitat management when aiming to enhance the conservation status of specific species.

genomics↗

bioRxiv2023

Introgression underlies phylogenetic uncertainty but not parallel plumage evolution in a recent songbird radiation

Instances of parallel phenotypic evolution offer great opportunities to understand the evolutionary processes underlying phenotypic changes. However, confirming parallel phenotypic evolution and studying its causes requires a robust phylogenetic framework. One such example is the "black-and-white wagtails", a group of five species in the songbird genus Motacilla: one species, the White Wagtail (M. alba), shows wide intra-specific plumage variation, while the four others form two pairs of very similar-looking species (African Pied Wagtail M. aguimp + Mekong Wagtail M. samveasnae and Japanese Wagtail M. grandis + White-browed Wagtail M. maderaspatensis, respectively). However, the two species in each of these pairs were not recovered as sisters in previous phylogenetic inferences. Their relationships varied depending on the markers used, suggesting that gene tree heterogeneity might have hampered accurate phylogenetic inference. Here, we use whole genome resequencing data to explore the phylogenetic relationships within this group, with a special emphasis on characterizing the extent of gene tree heterogeneity and its underlying causes. We first used multispecies coalescent methods to generate a "complete evidence" phylogenetic hypothesis based on genome-wide variants, while accounting for incomplete lineage sorting and introgression. We then investigated the variation in phylogenetic signal across the genome, to quantify the extent of discordance across genomic regions, and test its underlying causes. We found that wagtail genomes are mosaics of regions supporting variable genealogies, because of ILS and inter-specific introgression. The most common topology across the genome, supporting M. alba and M. aguimp as sister species, appears to be influenced by ancient introgression. Additionally, we inferred another ancient introgression event, between M. alba and M. grandis. By combining results from multiple analyses, we propose a phylogenetic network for the black-and-white wagtails that confirms that similar phenotypes evolved in non-sister lineages, supporting parallel plumage evolution. Furthermore, the inferred reticulations do not connect species with similar plumage coloration, suggesting that introgression does not underlie parallel plumage evolution in this group. Our results demonstrate the importance of investigation of genome-wide patterns of gene tree heterogeneity to help understanding the mechanisms underlying phenotypic evolution.

evolutionary biology↗

bioRxiv2022

The formation of the Indo-Pacific montane avifauna

Mountain biotas have considerable conservation and research importance, but the formation of montane communities remains incompletely understood. Study of Indo-Pacific island faunas has inspired two main hypotheses for the generation of montane diversity. The first posits that montane populations arise via direct colonization from other mountain areas, while the second invokes recruitment from adjacent lowland populations. We sought to reconcile these apparently conflicting hypotheses by asking whether a species ancestral geographic origin determines its mode of mountain colonization. To this end, island-dwelling passerine birds at the faunal crossroads between Eurasia and Australo-Papua provide an ideal study system. We recovered the phylogenetic relationships of the regions montane species, and used this information to reconstruct their ancestral geographic ranges, elevational ranges, and migratory behavior. We also performed genomic population studies of three super-dispersive montane species/clades with broad island distributions. Eurasian-origin species populated archipelagos via direct colonization between mountains. This mode of colonization appears related to ancestral adaptations to cold and seasonal Palearctic climates, specifically short-distance migration. Australo-Papuan-origin mountain populations, by contrast, evolved from lowland ancestors, and highland distribution mostly precludes their further colonization of island mountains. The patterns and processes revealed for this group are compatible with taxon cycles, a hypothesized process of lowland lineage expansion followed by montane relictualization. Collectively, our analyses explain much of the distributional variation within a complex biological system, and provide a synthesis of two seemingly discordant hypotheses for montane community formation.

evolutionary biology↗

bioRxiv2022

Population genomics of the island thrush elucidates one of earth's great archipelagic radiations

Tropical islands are renowned as natural laboratories for evolutionary study. Lineage radiations across tropical archipelagos are ideal systems for investigating how colonization, speciation, and extinction processes shape biodiversity patterns. The expansion of the island thrush across the Indo-Pacific represents one of the largest yet most perplexing island radiations of any songbird species. The island thrush exhibits a complex mosaic of pronounced plumage variation across its range, and is arguably the worlds most polytypic bird. It is a sedentary species largely restricted to mountain forests, yet it has colonized a vast island region spanning a quarter of the globe. We conducted comprehensive sampling of island thrush populations and obtained genome-wide SNP data, which we used to reconstruct its phylogeny, population structure, gene flow, and demographic history. The island thrush evolved from migratory Palearctic ancestors and radiated explosively across the Indo-Pacific during the Pleistocene, with numerous instances of gene flow between populations. Its bewildering plumage variation masks a biogeographically intuitive stepping stone colonization path from the Philippines through the Greater Sundas, Wallacea and New Guinea to Polynesia. The island thrushs success in colonizing Indo-Pacific mountains can be understood in light of its ancestral mobility and adaptation to cool climates; however, shifts in elevational range, degree of plumage variation and apparent dispersal rates in the eastern part of its range raise further intriguing questions about its biology.

evolutionary biology↗

bioRxiv2022

The hidden structural variability in avian genomes

Structural variants (SVs) are DNA mutations that can have relevant effects at micro- and macro-evolutionary scales. The detection of SVs is largely limited by the type and quality of sequencing technologies adopted, therefore genetic variability linked to SVs may remain undiscovered, especially in complex repetitive genomic regions. In this study, we used a combination of long-read and linked-read genome assemblies to investigate the occurrence of insertions and deletions across the chromosomes of 14 species of birds-of-paradise and two species of estrildid finches including highly repetitive W chromosomes. The species sampling encompasses most genera and representatives from all major clades of birds-of-paradise, allowing comparisons between individuals of the same species, genus, and family. We found the highest densities of SVs to be located on the microchromosomes and on the female-specific W chromosome. Genome assemblies of multiple individuals from the same species allowed us to compare the levels of genetic variability linked to SVs and single nucleotide polymorphisms (SNPs) on the W and other chromosomes. Our results demonstrate that the avian W chromosome harbours more genetic variability than previously thought and that its structure is shaped by the continuous accumulation and turnover of transposable element insertions, especially endogenous retroviruses.

evolutionary biology↗

bioRxiv2021

Historical climate change and megafaunal extinctions linked to genetic diversity declines in shorebirds

Understanding the relative contributions of historical and anthropogenic factors to declines in genetic diversity is important for informing conservation action. Using genome-wide DNA of fresh and historic specimens, including that of two species widely thought to be extinct, we investigated fluctuations in genetic diversity and present the first complete phylogenomic tree for all nine species of the threatened shorebird genus Numenius, known as whimbrels and curlews. Most species faced sharp declines in effective population size, a proxy for genetic diversity, soon after the Last Glacial Maximum (around 20,000 years ago). These declines occurred prior to the Anthropocene and in spite of an increase in breeding area predicted by environmental niche modelling, suggesting that they were not caused by climatic or recent anthropogenic factors. Crucially, these genetic diversity declines coincide with mass extinctions of mammalian megafauna in the Northern Hemisphere. Demise of ecosystem-engineering megafauna which maintained open habitats would have been detrimental for grassland and tundra-breeding Numenius shorebirds. Our work suggests that the impact of historical factors such as megafaunal extinction may have had wider repercussions on present-day population dynamics of open habitat biota than previously appreciated.

evolutionary biology↗

bioRxiv2020

Complex population structure of the Atlantic puffin revealed by whole genome analyses

The factors underlying gene flow and genomic population structure in vagile seabirds are notoriously difficult to understand due to their complex ecology with diverse dispersal barriers and extensive periods at sea. Yet, such understanding is vital for conservation management of seabirds that are globally declining at alarming rates. Here, we elucidate the population structure of the Atlantic puffin (Fratercula arctica) by assembling its reference genome and analyzing genome-wide resequencing data of 72 individuals from 12 colonies. We identify four large, genetically distinct clusters, observe isolation-by-distance between colonies within these clusters, and obtain evidence for a secondary contact zone. These observations disagree with the current taxonomy, and show that a complex set of contemporary biotic factors impede gene flow over different spatial scales. Our results highlight the power of whole genome data to reveal unexpected population structure in vagile marine seabirds and its value for seabird taxonomy, evolution and conservation.

genomics↗

bioRxiv2020

The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities

It is a broadly observed pattern that the non-recombining regions of sex-limited chromosomes (Y and W) accumulate more repeats than the rest of the genome, even in species like birds with a low genome-wide repeat content. Here we show that in birds with highly heteromorphic sex chromosomes, the W chromosome has a transposable element (TE) density of >55% compared to the genome-wide density of <10%, and contains over half of all full-length (thus potentially active) endogenous retroviruses (ERVs) of the entire genome. Using RNA-seq and protein mass spectrometry data, we were able to detect signatures of female-specific ERV expression. We hypothesise that the avian W chromosome acts as a refugium for active ERVs, likely leading to female-biased mutational load that may influence female physiology similar to the "toxic-Y" effect in Drosophila. Furthermore, Haldanes rule predicts that the heterogametic sex has reduced fertility in hybrids. We propose that the excess of W-linked active ERVs over the rest of the genome may be an additional explanatory variable for Haldanes rule, with consequences for genetic incompatibilities between species through TE/repressor mismatches in hybrids. Together, our results suggest that the sequence content of female-specific W chromosomes can have effects far beyond sex determination and gene dosage.

evolutionary biology↗

bioRxiv2019

Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird-of-paradise

Genome assemblies are currently being produced at an impressive rate by consortia and individual laboratories. The low costs and increasing efficiency of sequencing technologies have opened up a whole new world of genomic biodiversity. Although these technologies generate high-quality genome assemblies, there are still genomic regions difficult to assemble, like repetitive elements and GC-rich regions (genomic "dark matter"). In this study, we compare the efficiency of currently used sequencing technologies (short/linked/long reads and proximity ligation maps) and combinations thereof in assembling genomic dark matter starting from the same sample. By adopting different de-novo assembly strategies, we were able to compare each individual draft assembly to a curated multiplatform one and identify the nature of the previously missing dark matter with a particular focus on transposable elements, multi-copy MHC genes, and GC-rich regions. Thanks to this multiplatform approach, we demonstrate the feasibility of producing a high-quality chromosome-level assembly for a non-model organism (paradise crow) for which only suboptimal samples are available. Our approach was able to reconstruct complex chromosomes like the repeat-rich W sex chromosome and several GC-rich microchromosomes. Telomere-to-telomere assemblies are not a reality yet for most organisms, but by leveraging technology choice it is possible to minimize genome assembly gaps for downstream analysis. We provide a roadmap to tailor sequencing projects around the completeness of both the coding and non-coding parts of the genomes.

genomics↗

bioRxiv2018

Dynamic evolutionary history and gene content of sex chromosomes across diverse songbirds

Songbirds have a species number almost equivalent to that of mammals, and are classic models for studying mechanisms of speciation and sexual selection. Sex chromosomes are hotspots of both processes, yet their evolutionary history in songbirds remains unclear. To elucidate that, we characterize female genomes of 11 songbird species having ZW sex chromosomes, with 5 genomes of bird-of-paradise species newly produced in this work. We conclude that songbird sex chromosomes have undergone at least four steps of recombination suppression before their species radiation, producing a gradient pattern of pairwise sequence divergence termed evolutionary strata. Interestingly, the latest stratum probably emerged due to a songbird-specific burst of retrotransposon CR1-E1 elements at its boundary, or chromosome inversion on the W chromosome. The formation of evolutionary strata has reshaped the genomic architecture of both sex chromosomes. We find stepwise variations of Z-linked inversions, repeat and GC contents, as well as W-linked gene loss rate that are associated with the age of strata. Over 30 W-linked genes have been preserved for their essential functions, indicated by their higher and broader expression of orthologs in lizard than those of other sex-linked genes. We also find a different degree of accelerated evolution of Z-linked genes vs. autosomal genes among different species, potentially reflecting their diversified intensity of sexual selection. Our results uncover the dynamic evolutionary history of songbird sex chromosomes, and provide novel insights into the mechanisms of recombination suppression.

evolutionary biology↗

bioRxiv2018

Comparative Genomics and Genome Evolution in Birds-of-paradise

BackgroundThe diverse array of phenotypes and lekking behaviors in birds-of-paradise have long excited scientists and laymen alike. Remarkably, almost nothing is known about the genomics underlying this iconic radiation. Currently, there are 41 recognized species of birds-of-paradise, most of which live on the islands of New Guinea. In this study we sequenced genomes of representatives from all five major clades recognized within the birds-of-paradise family (Paradisaeidae). Our aim was to characterize genomic changes that may have been important for the evolution of the groups extensive phenotypic diversity.\n\nResultsWe sequenced three de novo genomes and re-sequenced two additional genomes representing all major clades within the birds-of-paradise. We found genes important for coloration, morphology and feather development to be under positive selection. GO enrichment of positively selected genes on the branch leading to the birds-of-paradise shows an enrichment for collagen, glycogen synthesis and regulation, eye development and other categories. In the core birds-of-paradise, we found GO categories for startle response (response to predators) and olfactory receptor activity to be enriched among the gene families expanding significantly faster compared to the other birds in our study. Furthermore, we found novel families of retrovirus-like retrotransposons active in all three de novo genomes since the early diversification of the birds-of-paradise group, which could have potentially played a role in the evolution of this fascinating group of birds.\n\nConclusionHere we provide a first glimpse into the genomic changes underlying the evolution of birds-of-paradise. Our aim was to use comparative genomics to study to what degree the genomic landscape of birds-of-paradise deviates from other closely related passerine birds. Given the extreme phenotypic diversity in this family, our prediction was that genomes should be able to reveal features important for the evolution of this amazing radiation. Overall, we found a strong signal for evolution on mechanisms important for coloration, morphology, sensory systems, as well as genome structure.

genomics↗