Biology subjects

Prochazka, P.

Publications and source records attributed to Prochazka, P..

5 recordsLinked to original sources

bioRxiv2025

Signatures of genomic adaptation to Cuckoo brood parasitism in Reed Warbler hosts across Europe

Behaviour is a fundamental defence mechanism for animals facing enemies, yet its plasticity makes finding associated genomic evidence for coevolution challenging. As a solution, we apply landscape genomics methods more typically deployed with abiotic variables to a coevolutionary model system: Reed Warblers (Acrocephalus scirpaceus) and their Cuckoo (Cuculus canorus) brood parasites. Using continental sampling of genome-wide data from hosts breeding under varying brood parasitism rates, we reveal that gene flow varies among populations, and, controlling for variation due to environmental differences, identify genomic regions and putative genes that differ with exposure to brood parasitism. Therefore, our results suggest that variable host responses to selection are possible, even by highly mobile and connected populations, supporting long-held assumptions that behavioural defences may reflect genomic adaptation despite their plasticity. Further studies, including those linking genetic variation to individual-level behaviours involved in parental responses to brood parasitism, are required to confirm a genetic basis to specific coevolutionary adaptations, and to test for other biotic or abiotic variables potentially confounding with local parasitism rate.

evolutionary biology↗

bioRxiv2025

High genetic diversity and no detectable founder effects following a rapid range expansion of a long-distance migrant (Acrocephalus scirpaceus)

Many species are currently experiencing range shifts in response to changing environmental conditions, but with potentially serious genetic consequences. Repeated founder events and strong genetic drift are expected to erode genetic variation at the range front, reducing adaptive potential and slowing or even halting the expansion. However, the severity of these consequences for the more common and highly mobile species undergoing environment-driven range shifts (c.f. invasions) is less clear. Here we combined historical observations and contemporary movement data of the common reed warbler (Acrocephalus scirpaceus) with genomic evidence from across its European breeding range to (1) infer the origin and (2) quantify the genetic consequences of a recent and rapid northward range expansion. While there were no reductions in levels of nucleotide diversity or allelic richness, nor a signal of founder effect in the directionality index ({psi}), our combined dataset approach was able to infer an expansion origin from the southwest. Furthermore, we found that private allelic richness retained a slight but significant linear decline along the colonisation route. These results suggest that high dispersal capabilities can allow even philopatric species to avoid the loss of genetic diversity during rapid range expansions. Nevertheless, if multiple lines of evidence enable identification of an expansion pathway, we may still detect genetic signals of expansion.

evolutionary biology↗

bioRxiv2023

Geographic distribution of feather δ34S in Europe

Geographic distribution models of environmental stable isotopes (so called isoscapes) are widely employed in animal ecology, wildlife forensics and conservation. However, the application of isoscapes is limited to elements and regions for which the spatial patterns have been estimated. Here, we focused on the ubiquitous yet less commonly used stable sulfur isotopes ({delta}34S). To predict the European{delta} 34S isoscape, we used 242 feather samples from Eurasian Reed Warbler (Acrocephalus scirpaceus) formed at 69 European wetland sites. We quantified the relationships between sample{delta} 34S and environmental covariates using a random forest regression model and applied the model to predict the geographic distribution of{delta} 34S. We also quantified within-site variation in{delta} 34S and complementarity with other isotopes on both individual and isoscape levels. The predicted feather{delta} 34S isoscape shows only slight differences between the central and southern parts of Europe while the coastal regions were most enriched in 34S. The most important covariates of{delta} 34S were distance to coastline, surface elevation and atmospheric concentrations of SO2 gases. The absence of a systematic spatial pattern impedes the application of the{delta} 34S isoscape but high complementarity with other isoscapes advocates the combination of multiple isoscapes to increase precision of animal tracing. Feather{delta} 34S compositions showed considerable within-site variation with highest values in inland parts of Europe, likely attributed to wetland anaerobic conditions and redox sensitivity of sulfur. The complex European geography and topography as well as using{delta} 34S samples from wetlands may contribute to the absence of a systematic spatial gradient of{delta} 34S values in Europe. We thus encourage future studies to focus on the geographic distribution of{delta} 34S using tissues from diverse taxa collected in various habitats over large land masses in the world (i.e., Africa, South America or East Asia). Open Research statementSample metadata are stored and available for reuse in the AviSample Network database (https://avisample.net/: AS00001-AS00117; Brlik et al. 2022b). The information on the isotopic composition and geographic origin of feather samples used to produce the{delta} 34S isoscape, predicted feather{delta} 34S,{delta} 2H and{delta} 13C isoscapes are publicly available from the Zenodo data repository at https://doi.org/10.5281/zenodo.7315567 (Brlik et al. 2022c).

ecology↗

bioRxiv2022

Genomic consequences of range expansion and colonisation in the reed warbler (Acrocephalus scirpaceus)

Range expansion is a common natural phenomenon, which may be intensified by human-induced drivers such as climate change and alterations of habitat. The genetic consequences of range expansion are potentially major, and it is important to study known cases of range expansion to understand how human activities affect contemporary evolution, and to learn more about the genetic adaptive potential of species. The reed warbler (Acrocephalus scirpaceus) is a long-distance migratory bird breeding in Eurasia and wintering south of Sahara. It is currently expanding its range northwards, likely as a consequence of climate change. Interestingly, however, reed warblers have also recently colonised new territory southwards, following habitat restoration at the southern range margin. In this study, we investigate the genetic consequences of these two-directional range expansions with RAD-seq, looking at 10 populations from north to south in Europe. We investigate population structure and genome diversity, and assess the role of selection in divergence between populations across the species range. We do not find evidence of strong genetic structure in the reed warbler populations, and the youngest edge populations do not exhibit any substantial loss in genetic diversity, suggesting ongoing gene flow. On a smaller scale, the edge populations are the most genetically distinct, and we identify environmental disparity, especially in precipitation variability, as the main barrier of gene flow, to a greater extent than geographic distance. We find no evidence that the loci involved in population divergence and adaptation in the core populations are the same that are involved in adaptation at the range edges. Using three genome scan methods to identify selection, we found 49 SNPs putatively under selection, of which 33 were located in introns of 28 unique genes. Most of these are correlated with differences in climatic variables of temperature and precipitation. Some genome scan outliers show signs of being part of nascent selective sweeps, especially one which is distinct for the northern range edge. Our results suggest that in the reed warbler, contemporary range expansion has had little effect on molecular diversity and has been rapidly followed by local adaptation to climatic conditions, which could further corroborate the rapid pace at which colonisation of novel environments has occurred both northwards and southwards.

evolutionary biology↗

bioRxiv2020

Automatic identification of bird females using egg phenotype

O_LIIdentification of individuals greatly contributes to understanding animal ecology and evolution, and in many cases can only be achieved using expensive and invasive techniques. Advances in computing technology offer alternative cost-effective techniques which are less invasive and can discriminate between individuals based on visual and/or acoustic cues. Here, we employ human assessment and an automatic analytical approach to predict the identity of common cuckoo (Cuculus canorus) females based on the appearance of their eggs. The cuckoos secretive brood parasitic strategy makes studying its life history very challenging. Eggs were analysed using calibrated digital photography for quantifying spotting pattern, size and shape, and spectrometry for measuring colour. Cuckoo females were identified from genetic sampling of their nestlings, allowing us to determine the accuracy of human and automatic female assignment. Finally, we used a novel same-different approach that uses both genetic and phenotypic information to assign eggs that were not genetically analysed. C_LIO_LIOur results supported the constant egg-type hypothesis, showing that individual cuckoo females lay eggs with a relatively constant appearance and that eggs laid by different females differ more than eggs laid by the same female. The accuracy of unsupervised hierarchical clustering was comparable to assessments of experienced human observers. Supervised random forest analysis showed better results, with higher cluster accuracy. Same-different analysis was able to assign 22 of 87 unidentified cuckoo eggs to seven already known females. C_LIO_LIOur study showed that egg appearance on its own is not sufficient for identification of individual cuckoo females. We therefore advocate genetic analysis to be used for this purpose. However, supervised analytical methods reliably assigned a relatively high number of eggs without genetic data to their mothers which can be used in conjunction with genetic testing as a cost-effective method for increasing sample sizes for eggs where genetic samples could not be obtained. C_LI

ecology↗