Biology subjects

Ruegg, K.

Publications and source records attributed to Ruegg, K..

8 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

Recent hybridisation and ghost introgression among a trio of island passerines

Hybridisation between species was once considered a relatively uncommon occurrence but is now recognised to occur frequently across many different taxa. It can result in homogenisation of previously distinct forms, a potential conservation issue, but can also act as a catalyst for diversification through introgression and sharing of favourable genes. Repeated rounds of island colonisation followed by speciation result in secondary sympatry, with the potential for hybridisation between early and late arrivers. In the southwest Pacific, this situation has arisen in the avian family Zosteropidae (the white-eyes). Here we use whole genome sequencing of live birds and historical specimens to characterise hybridisation between three white-eye species on Norfolk Island: two island endemics, Zosterops tenuirostris and the now-extinct Zosterops albogularis, and Zosterops lateralis, which colonised the island in 1904. Despite over two million years of divergence between Z. lateralis and the two endemics, we provide genomic evidence of their hybridisation. First, we confirm the identities of three Z. lateralis x Z. tenuirostris hybrids and additionally identify one Z. lateralis x Z. albogularis hybrid. We also report asymmetric, genome-wide introgression from both endemics into Z. lateralis, with introgressed regions enriched for a range of potential functions. However, despite this introgression, species boundaries have been maintained, and the extant endemic Z. tenuirostris does not appear to be at risk of genetic extinction. Our work additionally demonstrates an unusual case of recent ghost introgression from the extinct Z. albogularis into Z. lateralis. This study sheds light on the genomic outcomes of secondary sympatry and its potential consequences for single-island endemics.

evolutionary biology↗

bioRxiv2026

Co-limitation by stable, dynamic and directional habitat features shapes climate vulnerability in an alpine specialist

Alpine ecosystems are among the most climate sensitive on Earth, yet logistical challenges and detection biases often impede robust assessment of alpine dependent species. We investigated habitat associations and density patterns of the Sierra Nevada subspecies of the Gray-crowned Rosy-Finch (Leucosticte tephrocotis dawsoni), an alpine obligate and regional endemic, over five breeding seasons from 2018 to 2022 using hierarchical distance sampling and mark-recapture distance sampling to explicitly account for imperfect detection and spatial heterogeneity. Density estimates tracked annual snowpack variation, ranging from 4.77 individuals/km{superscript 2} in a low snow year to 12.08 individuals/km{superscript 2} in a high snow year. Abundance was highest near persistent snow patches that provide foraging habitat and near cliffs that provide nesting substrate, and declined sharply above approximately 10% woody cover, with densities approaching zero beyond approximately 25%, indicating a steep ecological threshold. In contrast, the proportion of surveyed blocks with detections remained relatively stable across years. Together, these patterns indicate a three timescale co-limitation framework in which breeding habitat is shaped by static features (cliffs), dynamic annual drivers (snowpack), and longer-term directional change (woody encroachment). By linking population density to climate sensitive habitat features, this study provides a high-resolution abundance-based baseline for long term monitoring and offers a framework for evaluating climate vulnerability in alpine and other resource-limited systems. Open Research StatementData necessary to replicate the analyses and results presented in this manuscript will be archived in the Dryad Digital Repository upon acceptance, with no embargo on the material. The R code associated with this manuscript is not novel. All analyses use publicly available packages and functions without modification, including mrds (v2.3.0), unmarked (v1.2.5), tidyverse (v2.0.0), MuMIn (v1.47.5), and standard ggplot2 visualization tools. All code is properly cited within the manuscript and publicly available through CRAN. Complete analysis scripts will be archived in Dryad alongside the data upon acceptance to facilitate full reproducibility of results.

ecology↗

bioRxiv2025

Migration patterns and hybridization within the Asian stonechat complex in response to a major geographical barrier

Long-distance avian migration is thought to be under strong natural selection. Facing geographical barriers, migrants display various patterns considered to be adaptive. For example, they may detour along either side around the barrier or cross it, requiring specialized behavioral adaptations. Variations within closely related taxa are excellent sources for understanding the evolutionary background of migration and how barriers are shaping migration routes. In Asia, some species are assumed to have a migratory divide in response to the major geographical barrier, the Qinghai-Tibet Plateau (QTP), including the stonechat taxa (Siberian Stonechat Saxicola maurus maurus and Amur Stonechat S. stejnegeri). As they detour along either side of the QTP, these taxa are believed to disfavor a crossing over the highland. However, the more southernly distributed Tibetan Stonechat (S. m. przewalskii) breeds on the QTP, suggesting adaptation to high elevation. To investigate migration patterns and the potentially associated genetic differences, we studied migration routes and population genetics of four populations around the assumed migratory divide in Russia and Mongolia, and of one from the QTP in China. Our results confirmed the existence of a migratory divide between maurus and stejnegeri, albeit with extensive hybridization. We observed both the hypothesized western and eastern routes, but also found individuals employing intermediate routes crossing the QTP, of which two-thirds were clear hybrids. Meanwhile, przewalskii followed a highland-crossing route and was genetically differentiated from maurus and stejnegeri. The diverse migration routes among Asian stonechats show differential responses towards the geographical barrier. The intermediate route may be associated with hybridization, and its conditional viability may facilitate gene flow between maurus and stejnegeri. The Asian stonechat complex thus offers great opportunities for novel research of the genetics and evolution of migration. The specific evolutionary background associated with inhabiting and crossing the QTP can offer new perspectives in this field. Teaser textMigratory divides can arise in birds because alternative routes around migratory barriers would select for behaviors to restrict hybridization. Hybrids of parental types that employ alternative routes are hypothesized to embark on intermediate routes that would expose them to suboptimal conditions, resulting in post-zygotic reproductive isolation. However, this hypothesis is challenged when a sister taxon actually breeds on the geographical barrier. This is the case in the Asian stonechat complex that breeds near or on the Qinghai-Tibet Plateau (QTP), the roof of the world. We demonstrated a migratory divide in central Siberia to Mongolia for race maurus and stejnegeri, yet showed also evidence for extensive hybridization. Hybrids migrated along a newly discovered intermediate route, seemingly viable and overlaps with the migration trajectory of race przewalskii over the eastern part of the QTP. The Asian migratory divide relative to the QTP thus provided new insights to the evolution of landbird migration.

evolutionary biology↗

bioRxiv2024

Population genetic consequences of the seasonal migrations of birds

Differences in life history can cause co-distributed species to display discordant population genetic patterns. In high-latitude animals, evolutionary processes may be especially influenced by long-distance seasonal migration, a widespread adaptation to seasonality. Although migratory movements are intuitively linked to dispersal, their evolutionary genetic consequences remain poorly understood. Using [~]1700 genomes from 35 co-distributed boreal-breeding bird species, we reveal that most long-distance migrants exhibit spatial genetic structure, revealing evolutionary effects of philopatry rather than dispersal. We further demonstrate that migration distance and genetic diversity are strongly positively correlated in our study species. This striking relationship suggests that the adaptive seasonal shifts in biogeography that long-distance migratory species undergo each year lends them enhanced population stability that preserves genetic diversity relative to shorter-distance migrants that winter at higher latitudes. Our results suggest that the major impact of long-distance seasonal migration on population genetic evolution occurs through promotion of demographic stability, rather than facilitation of dispersal.

evolutionary biology↗

bioRxiv2020

Genetic variation reveals individual-level climate tracking across the full annual cycle of a migratory bird

For migratory species, seasonal movements complicate local climate adaptation, as it is unclear whether individuals track climate niches across the annual cycle. In the migratory songbird yellow warbler (Setophaga petechia), we find a correlation between individual-level wintering and breeding precipitation but not temperature. Birds wintering in the driest regions of the Neotropics breed in the driest regions of North America. Individuals from drier regions also possess distinct morphologies and population responses to varying rainfall. We find a positive association between bill size and breeding season precipitation which, given documented climate-associated genomic variation, might reflect adaptation to local precipitation regimes. Relative abundance in the breeding range is linked to interannual fluctuations in precipitation, but the directionality of this response varies across geography. Together, our results suggest that variation in climate optima may exist across the breeding range of yellow warblers and provide a mechanism for selection across the annual cycle.

evolutionary biology↗

bioRxiv2019

The multiple population genetic and demographic routes to islands of genomic divergence

1. The way that organisms diverge into reproductively isolated species is a major question in biology. The recent accumulation of genomic data provides promising opportunities to understand the genomic landscape of divergence, which describes the distribution of differences across genomes. Genomic areas of unusually high differentiation have been called genomic islands of divergence. Their formation has been attributed to a variety of mechanisms, but a prominent hypothesis is that they result from divergent selection over a small portion of the genome, with surrounding areas homogenised by gene flow. Such islands have often been interpreted as being associated with divergence with gene flow. However other mechanisms related to genetic architecture and population history can also contribute to the formation of genomic islands of divergence.\n\n2. We currently lack a quantitative framework to examine the dynamics of genomic landscapes under the complex and nuanced conditions that are found in natural systems. Here, we develop an individual-based simulation to explore the dynamics of diverging genomes under various scenarios of gene flow, selection and genotype-phenotype maps.\n\n3. Our modelling results are consistent with empirical observations demonstrating the formation of genomic islands under genetic isolation. Importantly, we have quantified the range of conditions that produce genomic islands. We demonstrate that the initial level of genetic diversity, drift, time since divergence, linkage disequilibrium, strength of selection and gene flow are all important factors that can influence the formation of genomic islands. Because the accumulation of genomic differentiation over time tends to erode the signal of genomic islands, genomic islands are more likely to be observed in recently divergent taxa, although not all recently diverged taxa will necessarily exhibit islands of genomic divergence. Gene flow primarily slows the swamping of islands of divergence with time.\n\n4. By using this framework, further studies may explore the relative influence of particular suites of events that contribute to the emergence of genomic islands under sympatric, parapatric and allopatric conditions. This approach represents a novel tool to explore quantitative expectations of the speciation process, and should prove useful in elucidating past and projecting future genomic evolution of any taxa.

genomics↗

bioRxiv2018

A mathematical model of flow-mediated coagulation identifies factor V as a modifier of thrombin generation in hemophilia A

Hemophilia A is a bleeding disorder categorized as severe, mild, and moderate deficiencies in factor VIII (FVIII). Within these categories the variance in bleeding severity is significant and the origins unknown. The number of parameters that could modify bleeding are so numerous that experimental approaches are not feasible for considering all possible combinations. Consequently, we turn to a mathematical model of coagulation under flow to act as a screening tool to identify parameters that are most likely to enhance thrombin generation. We performed global sensitivity analysis on 110,000 simulations that varied coagulation factor levels by 50-150% of their normal values in humans while holding FVIII levels at 1%. These simulations identified low factor V (FV) levels as the strongest candidate, with additional enhancement when combined with high prothrombin levels. This prediction was confirmed in two experimental models: Partial FV inhibition boosted fibrin deposition in flow assays performed at 100 1/s on collagen-tissue factor surfaces using whole blood from individuals with mild and moderate FVIII deficiencies. Low FV (~50%) or partial FV inhibition also augmented thrombin generation in FVIII-inhibited or FVIII-deficient plasma in calibrated automated thrombography. These effects were amplified by high prothrombin levels in both experimental models. Our mathematical model suggests a mechanism in which FV and FVIII compete to bind to factor Xa to initiate thrombin generation in low FV, FVIII-deficient blood. This unexpected result was made possible by a mechanistic mathematical model, providing an example of the potential of such models in making predictions in complex biological networks.

systems biology↗