Museomics help resolving the phylogeny of snowfinches (Aves, Passeridae, Montifringilla and allies).

Historical specimens from museum collections provide a valuable source of material also from remote areas or regions of conflict that are not easily accessible to scientists today. With this study, we are providing a taxon-complete phylogeny of snowfinches using historical DNA from whole skins of an endemic species from Afghanistan, the Afghan snowfinch, Pyrgilauda theresae. To resolve the strong conflict between previous phylogenetic hypotheses, we generated novel mitogenome sequences for selected taxa and genome-wide SNP data using ddRAD sequencing for all extant snowfinch species endemic to the Qinghai-Tibet Plateau (QTP) and for an extended intraspecific sampling of the sole Central and Western Palearctic snowfinch species (Montifringilla nivalis). Our phylogenetic reconstructions unanimously refuted the previously suggested paraphyly of genus Pyrgilauda. Misplacement of one species-level taxon (Onychostruthus tazcanowskii) in previous snowfinch phylogenies was undoubtedly inferred from chimeric mitogenomes that included heterospecific sequence information. Furthermore, comparison of novel and previously generated sequence data showed that the presumed sister-group relationship between M. nivalis and the QTP endemic M. henrici was suggested based on flawed taxonomy. Our phylogenetic reconstructions based on genome-wide SNP data and on mitogenomes were largely congruent and supported reciprocal monophyly of genera Montifringilla and Pyrgilauda with monotypic Onychostruthus being sister to the latter. The Afghan endemic P. theresae likely originated from a rather ancient Pliocene out-of-Tibet dispersal probably from a common ancestor with P. ruficollis. Our extended trans-Palearctic sampling for the white-winged snowfinch, M. nivalis, confirmed strong lineage divergence between an Asian and a European clade dated to 1.5 - 2.7 million years ago (mya). Genome-wide SNP data suggested subtle divergence among European samples from the Alps and from the Cantabrian mountains.

The great tit HapMap project: A continental-scale analysis of genomic variation in a songbird.

A major aim of evolutionary biology is to understand why patterns of genomic diversity vary within taxa and space. Large-scale genomic studies of widespread species are useful for studying how environment and demography shape patterns of genomic divergence. Here, we describe one of the most geographically comprehensive surveys of genomic variation in a wild vertebrate to date; the great tit (Parus major) HapMap project. We screened ca 500,000 SNP markers across 647 individuals from 29 populations, spanning ~30 degrees of latitude and 40 degrees of longitude - almost the entire geographical range of the European subspecies. Genome-wide variation was consistent with a recent colonisation across Europe from a South-East European refugium, with bottlenecks and reduced genetic diversity in island populations. Differentiation across the genome was highly heterogeneous, with clear 'islands of differentiation', even among populations with very low levels of genome-wide differentiation. Low local recombination rates were a strong predictor of high local genomic differentiation (FST), especially in island and peripheral mainland populations, suggesting that the interplay between genetic drift and recombination causes highly heterogeneous differentiation landscapes. We also detected genomic outlier regions that were confined to one or more peripheral great tit populations, probably as a result of recent directional selection at the species' range edges. Haplotype-based measures of selection were related to recombination rate, albeit less strongly, and highlighted population-specific sweeps that likely resulted from positive selection. Our study highlights how comprehensive screens of genomic variation in wild organisms can provide unique insights into spatio-temporal evolutionary dynamics.

Rural landscape dynamics over time and its consequences for habitat preference patterns of the grey partridge Perdix perdix.

Intensification of agricultural practices has drastically shaped farmland landscapes and generally caused a decline in spatial and temporal heterogeneity, thus leading to changes in habitat quality and food resources and a decline for most farmland birds Europe-wide. The relationship between complex landscape changes and habitat preferences of animals still remains poorly understood. Particularly, temporal and spatial changes in diversity may affect not only habitat choice but also population sizes. To answer that question, we have looked into a severely declining typical farmland bird species, the grey partridge Perdix perdix in a diverse farmland landscape near Vienna to investigate the specific habitat preferences in respect to the change of agricultural landscape over two decades and geographic scales. Using a dataset collected over 7.64 km² and between 2001 and 2017 around Vienna, we calculated Chesson's electivity index to study the partridge's change of habitat selection over time on two scales and between winter and spring in 2017. Although the farmland landscape underwent an ongoing diversification over the two decades, the grey partridges declined in numbers and shifted habitat use to less diverse habitats. During covey period in winter, partridges preferred also human infrastructure reservoirs such as roads and used more diverse areas with smaller fields than during breeding where they selected harvested fields but surprisingly, avoided hedges, fallow land and greening. Known as best partridge habitats, those structures when inappropriately managed might rather function as predator reservoirs. The avoidance behaviour may further be a consequence of increasing landscape structuring and edge effects by civilisation constructions. Besides, the loss in size and quality of partridge farmland is altered by crop choice and pesticides reducing plant and insect food. With declining breeding pairs, the grey partridge does not seem to adjust to these unsustainable landscape changes and farmland practices.

Elevational trends in life histories: revising the pace-of-life framework.

Life-history traits in birds, such as lifespan, age at maturity, and rate of reproduction, vary across environments and in combinations imposed by trade-offs and limitations of physiological mechanisms. A plethora of studies have described the diversity of traits and hypothesized selection pressures shaping components of the survival-reproduction trade-off. Life-history variation appears to fall along a slow-fast continuum, with slow pace characterized by higher investment in survival over reproduction and fast pace characterized by higher investment in reproduction over survival. The Pace-of-Life Syndrome (POLS) is a framework to describe the slow-fast axis of variation in life-history traits and physiological traits. The POLS corresponds to latitudinal gradients, with tropical birds exhibiting a slow pace of life. We examined four possible ways that the traits of high-elevation birds might correspond to the POLS continuum: (i) rapid pace, (ii) tropical slow pace, (iii) novel elevational pace, or (iv) constrained pace. Recent studies reveal that birds breeding at high elevations in temperate zones exhibit a combination of traits creating a unique elevational pace of life with a central trade-off similar to a slow pace but physiological trade-offs more similar to a fast pace. A paucity of studies prevents consideration of the possibility of a constrained pace of life. We propose extending the POLS framework to include trait variation of elevational clines to help to investigate complexity in global geographic patterns.

Testing mechanisms of Bergmann's rule: phenotypic decline but no genetic change in body size in three passerine bird populations.

Bergmann's rule predicts a decrease in body size with increasing temperature and has much empirical support. Surprisingly, we know very little about whether "Bergmann size clines" are due to a genetic response or are a consequence of phenotypic plasticity. Here, we use data on body size (mass and tarsus length) from three long-term (1979-2008) study populations of great tits (Parus major) that experienced a temperature increase to examine mechanisms behind Bergmann's rule. We show that adult body mass decreased over the study period in all populations and that tarsus length increased in one population. Both body mass and tarsus length were heritable and under weak positive directional selection, predicting an increase, rather than a decrease, in body mass. There was no support for microevolutionary change, and thus the observed declines in body mass were likely a result of phenotypic plasticity. Interestingly, this plasticity was not in direct response to temperature changes but seemed to be due to changes in prey dynamics. Our results caution against interpreting recent phenotypic body size declines as adaptive evolutionary responses to temperature changes and highlight the importance of considering alternative environmental factors when testing size clines.

Hematozoa in endemic subspecies of common kestrel in the Cape Verde Islands.

We examined 130 Common Kestrel (Falco tinnunculus) representing two endemic subspecies and nine resident island populations on the Cape Verde archipelago between 1996 and 1999 to study diversity, prevalence, and intensity of hematozoa. Hematozoan diversity was very low; we detected only Plasmodium fallax, a species that is rarely found in Falconoformes, and, possibly, Haemoproteus brachiatus. Moreover, prevalence of Plasmodium fallax was low (1.5%) with a mean intensity of infection of 0.05 protozoa/10(-3) erythrocytes. Only one bird (0.8%) was infected with a gametocyte that was most likely Haemoproteus brachiatus; the intensity in this infected bird was 1.5 protozoa/10(-3) erythrocytes. A single parasite or two parasites were observed in blood smears in four additional birds, but identification to genus was not possible. This is the first record of blood parasites in birds on the Cape Verde Archipelago. The low prevalence of these parasites might be because of arid and less-favorable conditions for the pathogen's vectors. The sedentary nature and high level of isolation of the island kestrel populations are also factors that could decrease the probability of infection.