Limited geographic genetic structure detected in a widespread Palearctic corvid, Nucifraga caryocatactes

Open accessThe Eurasian or spotted nutcracker (Nucifraga caryocatactes) is a widespread resident corvid found throughout the Palearctic fromCentral Europe to Japan. Characterized by periodic bouts of irruptive dispersal in search of Pinus seed crops, this species has potential for high levels of gene flow across its range. Previous analysis of 11 individuals did not find significant range-wide population genetic structure.We investigated population structure using 924 base pairs of mitochondrial DNA control region sequence data from 62 individuals from 12 populations distributed throughout the nutcracker’s range.We complemented this analysis by incorporating additional genetic data frompreviously published sequences.High levels of genetic diversity and limited population genetic structure were detected suggesting that potential barriers to dispersal do not restrict gene flow in nutcrackers.Ye

Multilocus genetic analysis and spatial modeling reveal complex population structure and history in a widespread resident North America passerine (Perisoreus canadensis)

Sherpa Romeo green journal. Open access article. Creative Commons Attribution 3.0 Unported License (CC BY 3.0) applies.An increasing body of studies of widely distributed, high latitude species shows a variety of refugial locations and population genetic patterns. We examined the effects of glaciations and dispersal barriers on the population genetic patterns of a widely distributed, high latitude, resident corvid, the gray jay (Perisoreus canadensis), using the highly variable mitochondrial DNA (mtDNA) control region and microsatellite markers combined with species distribution modeling. We sequenced 914 bp of mtDNA control region for 375 individuals from 37 populations and screened seven loci for 402 individuals from 27 populations across the gray jay range. We used species distribution modeling and a range of phylogeographic analyses (haplotype diversity, ΦST, SAMOVA, FST, Bayesian clustering analyses) to examine evolutionary history and population genetic structure. MtDNA and microsatellite markers revealed significant genetic differentiation among populations with high concordance between markers. Paleodistribution models supported at least five potential areas of suitable gray jay habitat during the last glacial maximum and revealed distributions similar to the gray jay’s contemporary during the last interglacial. Colonization from and prolonged isolation in multiple refugia is evident. Historical climatic fluctuations, the presence of multiple dispersal barriers, and highly restricted gene flow appear to be responsible for strong genetic diversification and differentiation in gray jays.Ye

Influence of landscape features on the microgeographic genetic structure of a resident songbird

Sherpa Romeo yellow journal. Pre-print or post-print onlyVariation in landscape features influence individual dispersal and as a result can affect both gene flow and genetic variation within and between populations. The landscape of British Columbia, Canada, is already highly heterogeneous due to natural ecological and geological transitions, but disturbance from human mediated processes has further fragmented continuous habitat, particularly in the central plateau region. In this study, we evaluated the effects of landscape heterogeneity on the genetic structure of a common resident songbird, the black-capped chickadee (Poecile atricapillus). Previous work revealed significant population structuring in British Columbia which could not be explained by physical barriers, so our aim was to assess the pattern of genetic structure at a microgeographic scale and determine the effect of different landscape features on genetic differentiation. A total of 399 individuals from 15 populations were genotyped for fourteen microsatellite loci revealing significant population structuring in this species. Individual and population based analyses revealed as many as nine genetic clusters with isolation in the north, the central plateau and the south. Moreover, a mixed modelling approach that accounted for non-independence of pairwise distance values revealed a significant effect of land cover and elevation resistance on genetic differentiation. These results suggest that barriers in the landscape influence dispersal which has led to the unexpectedly high levels of population isolation. Our study demonstrates theimportance of incorporating additional landscape features when interpreting patterns of population differentiation. Despite taking a microgeographic approach, our results have opened up additional questions concerning the processes influencing dispersal and gene flow at the local scale.Ye

Genetic population structure of black-browed and Campbell albatrosses, and implications for assigning provenance of birds killed in fisheries

1.Previous genetic studies found evidence of at least three distinct groups of black-browed Thalassarche melanophris and Campbell Thalassarche impavida albatrosses in the Southern Ocean. Almost 350 individuals including samples from additional breeding sites on the Falkland Islands and South Georgia Island were screened using mitochondrial DNA. 2.The new sequence data using lineage specific PCR primers provided further support for the taxonomic split of T. melanophris and T. impavida and separate management of the two distinct T. melanophris groups. 3.In total, 207 black-browed albatrosses killed in longline fisheries were screened. Approximately 93% of the bycaught birds from the Falkland Islands belonged to the Falkland mtDNA group and the remaining birds had mtDNA from the Widespread T. melanophris group; these proportions were similar to those in the local Falklands breeding population. The South African and South Georgia bycatch samples predominantly comprised the Widespread T. melanophris group, with only one bird from each area containing Falkland mtDNA. Lastly, 81% of the albatrosses bycaught off New Zealand had T. impavida mtDNA and the remaining four birds were Widespread T. melanophris. These differences in bycatch composition matched what is known from tracking and banding data about the at-sea distribution of black-browed albatrosses. 4.Based on the mtDNA results and current population trends, consideration should be given to assigning regional IUCN status for the different breeding populations

Do phylogeny and habitat influence admixture among four North American chickadee (family: Paridae) species?

Accepted author manuscriptHybridization is an important aspect of speciation, yet questions remain about the ecological and environmental factors that influence hybridization among wild populations. We used microsatellite genotyping data and collected land cover and environmental data for four North American chickadee species: black-capped Poecile atricapillus, mountain P. gambeli, chestnut-backed P. rufescens and boreal P. hudsonicus chickadees. Combining these datasets, we sought to examine whether there is evidence of admixture between four widely distributed North American chickadee species; whether admixture takes place more often between more closely related species pairs or between species pairs with more similar ecological preferences; and whether certain habitat types have higher rates of admixture than others. We detected admixture for five of the six species pairs analyzed (chestnut-backed–mountain chickadee pair showed no evidence of admixture), and found rates of admixture varied geographically, and within taxa pairs. Admixture was higher among less closely related species than more closely related species, although habitat similarity was not a significant predictor. Finally, rates of admixture were higher in urban parkland habitats than deciduous, mixed or coniferous forest habitats. Our work indicates admixture occurs frequently among North American parids, and habitat and environmental variation may play an important role in the frequency and geographic distribution of hybridization.Ye

Comparative phylogeographic analysis suggests a shared history among eastern North American boreal forest birds

Accepted author manuscriptPhylogeographic structure within high-latitude North American birds is likely shaped by a history of isolation in refugia during Pleistocene glaciations. Previous studies of individual species have come to diverse conclusions regarding the number and location of likely refugia, but no studies have explicitly tested for biogeographic concordance in a comparative phylogeographic framework. Here we use a hierarchical approximate Bayesian computation analysis of mitochondrial DNA sequences from 653 individuals of 6 bird species that are currently co-distributed in the boreal forest of North America to test for biogeographic congruence. We find support for congruent phylogeographic patterns across species, with shallow divergence dating to the Holocene within each species. Combining genetic results with paleodistribution modeling, we propose that these species shared a single Pleistocene refugium south of the ice sheets in eastern North America. Additionally, we assess modern geographic genetic structure within species, focusing on Newfoundland and disjunct high-elevation populations at the southern periphery of ranges. We find evidence for a “periphery effect” in some species with significant genetic structure among peripheral populations and between peripheral and central populations. Our results suggest that reduced gene flow among peripheral populations, rather than discordant biogeographic histories, can explain the small differences in genetic structure and levels of genetic diversity among co-distributed boreal forest birdsYe

Cryptic genetic diversity and cytonuclear discordance characterize contact among Canada Jay (Perisoreus canadensis) morphotypes in western North America

Accepted author manuscriptThree distinct Canada jay (Perisoreus canadensis) morphotypes with easily recognizable plumage traits come into contact in western North America. Recent work demonstrated high genetic structure across the species’ range; however, patterns of genetic variation in these contact zones remain unknown. We categorized 605 individuals into one of three morphotypes (Pacific, Rocky Mountain, and Boreal) based on plumage, and genotyped individuals at the mtDNA control region and 12 microsatellite loci to assess the extent of hybridization between morphotypes. Our data showed cryptic genetic diversity and high cytonuclear discordance among morphotypes within contact zones, which is likely the result of recent and historical admixture. The distributions of the Boreal and Pacific morphotypes each showed a strong association with a single, distinct genetic group, whereas the Rocky Mountain morphotype exhibited higher genetic diversity and was associated with multiple genotypes. Our analyses show the importance of considering both plumage and genetic traits when examining contact zones between closely related taxa. Finally the data presented in this study reaffirm that the Pacific morphotype is distinct from the Boreal and Rocky Mountain morphotypes based on genetic, phenotypic and ecological data, indicating that the Pacific morphotype should be re-elevated to a full species.Ye

Telomere length measurement by qPCR in birds is affected by storage method of blood samples

Given the potential role of telomeres as biomarkers of individual health and ageing, there is an increasing interest in studying telomere dynamics in a wider range of taxa in the fields of ecology and evolutionary biology. Measuring telomere length across the lifespan in wild animal systems is essential for testing these hypotheses, and may be aided by archived blood samples collected as part of longitudinal field studies. However, sample collection, storage, and DNA extraction methods may influence telomere length measurement, and it may, therefore, be difficult to balance consistency in sampling protocol with making the most of available samples. We used two complementary approaches to examine the impacts of sample storage method on measurements of relative telomere length (RTL) by qPCR, particularly focusing on FTA (Flinders Technology Associates) cards as a long-term storage solution. We used blood samples from wandering albatrosses collected over 14 years and stored in three different ways (n = 179), and also blood samples from captive zebra finches (n = 30) that were each stored using three different methods. Sample storage method influenced RTL in both studies, and samples on FTA cards had significantly shorter RTL measurements. There was no significant correlation between RTL measured in zebra finch blood on FTA cards and the same samples stored either as frozen whole blood or as extracted DNA. These results highlight the importance of consistency of sampling protocol, particularly in the context of long-term field studies, and suggest that FTA cards should not be used as a long-term storage solution to measure RTL without validation

Monitoring regulatory T cells in clinical samples: consensus on an essential marker set and gating strategy for regulatory T cell analysis by flow cytometry

Regulatory T cell (Treg)-mediated immunosuppression is considered a major obstacle for successful cancer immunotherapy. The association between clinical outcome and Tregs is being studied extensively in clinical trials, but unfortunately, no consensus has been reached about (a) the markers and (b) the gating strategy required to define human Tregs in this context, making it difficult to draw final conclusions. Therefore, we have organized an international workshop on the detection and functional testing of Tregs with leading experts in the field, and 40 participants discussing different analyses and the importance of different markers and context in which Tregs were analyzed. This resulted in a rationally composed ranking list of “Treg markers”. Subsequently, the proposed Treg markers were tested to get insight into the overlap/differences between the most frequently used Treg definitions and their utility for Treg detection in various human tissues. Here, we conclude that the CD3, CD4, CD25, CD127, and FoxP3 markers are the minimally required markers to define human Treg cells. Staining for Ki67 and CD45RA showed to provide additional information on the activation status of Tregs. The use of markers was validated in a series of PBMC from healthy donors and cancer patients, as well as in tumor-draining lymph nodes and freshly isolated tumors. In conclusion, we propose an essential marker set comprising antibodies to CD3, CD4, CD25, CD127, Foxp3, Ki67, and CD45RA and a corresponding robust gating strategy for the context-dependent analysis of Tregs by flow cytometry