Biology subjects

Kleindorfer, S.

Publications and source records attributed to Kleindorfer, S..

8 recordsLinked to original sources

bioRxiv2026

The BEAC, an epigenetic clock for birds

Epigenetic clocks are powerful tools for estimating both chronological and biological age, enabling the integration of age information into population monitoring, demographic modelling, and research on the ecophysiology and evolution of ageing. Most epigenetic clocks so far have been developed for mammals: here, we present the Bird Epigenetic Ageing Clock (BEAC) for estimating chronological age in avian species. BEAC was established based on genome-wide enzymatic methylation sequencing data of known-age king penguins (Aptenodytes patagonicus), and validated in nine other bird species. The BEAC collects age-informative signals into a bisulfite amplicon sequencing panel of 24 primer pairs, providing a highly accurate and cost-effective alternative to sequencing-intensive approaches. It achieved strong predictive performance in independent king penguin training (R{superscript 2}=0.88; MAE=1.7 years, n=78) and testing data (R{superscript 2}=0.79; MAE=2.3 years, n=41), with negligible batch effects, high longitudinal consistency, and resilience to reduced sample size or missing loci. Importantly, cross-species validation across 180 samples showed that BEAC reliably captures age-associated methylation signals in nine additional bird species across seven clades, demonstrating that a single set of loci can be predictive of ageing across multiple different bird species. BEAC offers a flexible, empirically validated tool and a transferable framework for developing epigenetic clocks in avian species, providing a highly valuable resource for eco-evolutionary studies of ageing in wild species.

molecular biology↗

bioRxiv2026

Sex-specific functions of duetting in the Galapagos Yellow Warbler (Setophaga petechia aureola)

In over a thousand avian species, pairs coordinate vocalizations to form duets. Songbirds may use calls (simple, non-learned vocalizations) and songs (complex, learned vocalizations) to answer their partners. In Galapagos Yellow Warblers (Setophaga petechia aureola), song answers in duets appear to have evolved recently in addition to older call answers. Here, we explored the structure and functions of duets in an observational study to understand why song answers in duets may have evolved. We first described the temporal structure of duets initiated by either sex. We then tested whether the distance between pair members, countersinging with neighbours, and timing relative to aggressive encounters predicted answering probability for each sex. Finally, we tested whether the behavioral context of call and song answers differed. We found that most duets were initiated by males, and call answers were almost exclusively given by females. Female answers were also more tightly coordinated than those of males. Female answering probability decreased with increasing distance between pair members, whereas male answering probability did not. In addition, females were less likely to answer with songs when farther from their mate. Females answering probability also increased slightly when their mates initiation was preceded by a neighbors song. Our results show some evidence in support of the joint resource defence hypothesis for female answers. On the other hand, the significance of song in female answers may be related to some other functions that we did not test here, such as signaling quality or commitment to the pair bond. Lay summaryWho turns a song into a duet? In Galapagos Yellow Warblers, it is usually the female: she answers her mates song with a tightly timed call or song. Male replies were rarer and less coordinated. While male replies didnt seem to have a function, female replies were used in territorial disputes with neighbours and may indicate joint ownership of a territory. Female song replies, on the other hand, may signal commitment to the pair bond.

animal behavior and cognition↗

bioRxiv2026

Asymmetric migration shapes genetic structure of the invasive avian vampire fly (Philornis downsi) across the Galapagos Islands.

Biological invasions on islands provide a natural framework to study how dispersal and connectivity influence evolutionary and ecological processes. The avian nest parasitic fly, Philornis downsi - first recorded in Darwins finch nests in 1997 - causes high mortality in endemic land birds, yet its inter-island and sex-specific patterns of dispersal and genetic structure remain poorly understood. We use low-coverage whole genome sequencing to investigate genome-wide patterns of genetic diversity, directional migration and effective population size in P. downsi across five major Galapagos Islands and its native range in mainland Ecuador. We find evidence for a genetic bottleneck in the Galapagos, isolation by distance, and evidence that the island closest to the Ecuadorian mainland, San Cristobal, is genetically divergent from the other four islands sampled, despite retaining the highest genetic diversity. No evidence was found for sex-biased dispersal; however, sex-biased genetic structure was detected using only markers from inferred autosomal scaffolds. We found asymmetric gene flow with higher migration rates from San Cristobal westward to the other islands, matching the direction of both southeast trade winds and major cargo shipping routes. Our results suggest both natural and human-mediated colonisation of P. downsi from the mainland through San Cristobal to the other islands, followed by high inter-island dispersal among closely situated sink islands. Our findings are critical for prioritising islands for control strategies that will reduce P. downsi impacts on vulnerable endemic birds and underscore the value of understanding directional migration patterns for managing invasive species in metapopulations.

evolutionary biology↗

bioRxiv2025

Cultural and morphological divergence of Darwin's cactus finches (Geospiza scandens) across the Galapagos Islands

Understanding the divergence of cultural traits, such as bird song, provides critical insights into evolutionary processes. In geographically isolated populations, the divergence of traits associated with mate choice can lead to further genetic separation. This study investigates divergence in song syllable types, acoustic characteristics, singing behavior, and morphology in two allopatric populations of Darwins cactus finch (Geospiza scandens) on Floreana and Santa Cruz Islands in the Galapagos Archipelago. Using song recordings of 50 males, we identified 25 syllable types with no overlap between islands, indicating a complete divergence in syllable repertoires. Syllables of Floreana and Santa Cruz males diverged in the acoustic space largely due to broader frequency bandwidths on Floreana. Moreover, Floreana males had smaller beaks than Santa Cruz males. Despite acoustic and morphological divergence, singing behaviors - like syllable repetition rate and number of syllables per song - did not differ significantly. Both cultural processes, including drift and transmission biases, as well as selection on morphology could have contributed to the observed acoustic divergence. This study adds to a growing literature on the role of geographic separation in the accumulation of both cultural and morphological divergence between populations. Future research could interrogate speciation scenarios in cactus finches if populations cease to interbreed after secondary contact.

animal behavior and cognition↗

bioRxiv2025

Solo songs, duets, and territory defense across seasons in female Galapagos Yellow Warblers (Setophaga petechia aureola)

While the function of bird song has been well studied in male songbirds, the function of female song is less well understood. This is partly due to a historical view of females occupying a passive role compared with males, which led to ignoring female song even in some well-studied species. We report one such case in yellow warblers (Setophaga petechia), as no other study investigated female song in 35 years after the first documentation of solo female songs. We interrogate the seasonal patterns and functions of female song in Galapagos yellow warblers (Setophaga petechia aureola), in which females perform solo song and produce duets with their male social partners. We carried out simulated territory intrusions by broadcasting male, female, or duet songs during breeding and non-breeding seasons, and conducted a territory retention survey for over a year. We measured the association between aggressive response and singing behaviour, sex-specific patterns of response, and territory retention across years. Females sang mostly during the non-breeding season and predominantly in male-led duets. Although females were strongly aggressive towards female song playback, they gave the weakest singing response towards them. There was no association between female aggressive behaviour and song output in response to a simulated intruder. Moreover, the probability of territory retention across years was not explained by song output or aggression in response to intruders, though evidence for this was weak due to the small sample size. We suggest that female song in this year-round resident island system does not function for territory defense or intrasexual competition, but may have other functions. HighlightsO_LIGalapagos Yellow Warbler females produce solo songs and duets with their male partners. C_LIO_LIFemale song and aggression were mainly restricted to the non-breeding season. C_LIO_LIWhile females were equally aggressive to all intruders, they had the lowest song rate in response to females. C_LIO_LIIn contrast to males, aggressive behaviour didnt predict song output in females. C_LIO_LIFemale singing behaviour did not increase the probability of territory retention. C_LI

animal behavior and cognition↗

bioRxiv2024

Galapagos yellow warblers in low- and high-traffic environments differ in song plasticity in response to noise.

Acoustic communication between animals is increasingly disrupted by noise in human-altered environments making signals less effective. Birdsong is a signal used in agonistic interactions between territorial rivals, and birds may modify their song and singing behaviour in response to noise. However, if these modifications are still ineffective, this can lead to increased conflict between rivals. Here, we asked whether experimental traffic noise induces immediate changes in acoustic characteristics of song and aggressive behaviour in populations and territories that differ greatly in traffic noise exposure. We conducted simulated territorial intrusions on Galapagos yellow warblers (Setophaga petechia aureola) living on Santa Cruz (high traffic) and Floreana (low traffic) islands. Territories were either adjacent to the nearest road or at least 100 m away from it. We assessed the focal birds physical response levels and recorded their vocalisations in response to playback of conspecific song (control) and conspecific song coupled with traffic noise (noise treatment). We found that physical response levels mostly depended on treatment and distance to the nearest road: on both islands, birds living adjacent to the nearest road increased their aggression levels with experimental noise compared to control, while birds living farther away decreased their aggression levels. Birds on all islands irrespective of their distance to a road increased minimum frequency of their songs during the noise treatment. However, change in peak frequency and duration of their songs depended on the habitat they live in. Our results suggest behavioural flexibility in territorial responses and birdsong in response to traffic noise, which appears to depend at least in part on prior experience with traffic noise. HighlightsO_LIGalapagos yellow warblers modified their behaviour in response to traffic noise. C_LIO_LIBehavioural plasticity depended on the island and distance to the nearest road. C_LIO_LIBirds living close to a road increased their aggression in response to an intruder C_LIO_LIBirds living farther away from a road decreased their aggression. C_LI

animal behavior and cognition↗

bioRxiv2024

Genomic introgression between critically endangered and stable species of Darwin's tree finches on the Galapagos Islands

Natural hybridisation among rare or endangered species and stable congenerics is increasingly topical for the conservation of species-level diversity under anthropogenic impacts. Evidence for beneficial genes being introgressed into or selected for in hybrids raises concurrent questions about its evolutionary significance. In Darwins tree finches on the island of Floreana (Galapagos Islands, Ecuador), the Critically Endangered medium tree finch (Camarhynchus pauper) undergoes introgression with the stable small tree finch (Camarhynchus parvulus), and hybrids regularly backcross with C. parvulus. Earlier studies in 2005-2013 documented an increase in the frequency of Camarhynchus hybridisation on Floreana using field-based and microsatellite data. With single nucleotide polymorphism (SNP) data from the same Floreana tree finches sampled in 2005 and 2013 (n = 95), we examine genome-wide divergence across parental and hybrid birds and evidence for selection in hybrids. In assessing previous estimates of introgression we found that just 18% of previously assigned hybrid birds based on microsatellites were assigned to hybrids using SNPs. Over half of the previously assigned hybrids (63%) were reassigned to C. parvulus, though parental species showed concordance with prior assignments. Of 4869 private alleles found in hybrid birds, 348 were at a high frequency ([≥]0.30) that exceeded their parental species of origin 89-96% of the time. Across the two years, 3436 (70.6%) private alleles underwent a substantial ([≥]0.30) allele frequency increase or decrease. Of these, 28 private alleles were identified as candidate loci under selection via local PCA genome scans and outlier tests. Alleles were annotated to genes associated with inflammation, immunity, brain function and development. We provide evidence that introgression among a critically endangered and stable species of Darwins tree finch is being retained by selection across years and may aid in the retention of genetic diversity in birds threatened with extinction.

evolutionary biology↗

bioRxiv2021

Gene flow between two thick-billed grasswren subspecies with low dispersal creates a genomic pattern of isolation-by-distance

ContextIn the era of the Anthropocene, habitat loss and environmental change threaten the persistence of many species. Genotyping-By-Sequencing (GBS) is a useful molecular tool for understanding how patterns of gene flow are associated with contemporary habitat distributions that may be affected by environmental change. Two parapatric subspecies of the threatened thick-billed grasswren (TBGW; Amytornis modestus) more frequently occur in different plant communities. As such, a preference for plant community type could reduce subspecific introgression and increase genetic diversity at the parapatric boundary. AimsWe aimed to measure gene flow within and among two TBGW subspecies and tested whether divergent genomic markers were associated with plant community type. MethodsWe sequenced 118 individuals from either of the two TBGW subspecies or in the region of parapatry and identified 7583 SNPs through ddRADseq. Key resultsWe found evidence of asymmetric gene flow and a genomic pattern of isolation-by-distance. There were sixteen genomic outliers correlated with plant community type (regardless of location). ConclusionsThese findings show that plant community type does not prevent introgression in one subspecies (A. m. raglessi), but low dispersal and habitat heterogeneity could contribute to the maintenance of distinct subspecific morphotypes. Local adaptation in different plant community types could also provide a mechanism for future divergence. ImplicationsWe suggest subspecific introgression could increase genetic variation and the adaptive potential of the species, facilitating species persistence under conditions of climate change. Introgression between grasswren subspeciesCharacterising gene flow facilitates conservation management. This study used genomic markers to measure gene flow between thick-billed grasswren subspecies and found results that support taxonomic identification of the two subspecies and suggests grasswrens have low dispersal and may benefit from increased genetic diversity. Recognition of models of divergence with gene flow will be necessary for future conservation management.

evolutionary biology↗