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

Phylogeography of three high latitude resident corvids : Clark’s nutcracker (Nucifraga columbiana), Eurasian nutcracker (Nucifraga caryocatactes), and gray jay (Perisoreus canadensis)

High latitude resident bird species provide an unique opportunity to investigate patterns of postglacial and barrier-mediated dispersal. In this study, multiple genetic markers were used to understand postglacial colonization by and contemporary barriers to gene flow in three corvids. Clark’s nutcracker (Nucifraga columbiana), Eurasian nutcracker (N. caryocatactes), and gray jay (Perisoreus canadensis) are year-round resident northern hemisphere passerines with ranges encompassing previously glaciated and unglaciated regions and potential barriers to dispersal (e.g. mountain ranges). Using mitochondrial DNA control region sequences, we found limited geographic genetic structure and one glacial refugium in nutcrackers, contrasting with seven distinct genetic groups and five refugia for gray jays. Nuclear microsatellite markers revealed additional and contrasting patterns of near-panmixia in nutcrackers and multiple hierarchical breaks in gray jays. Genetic patterns are explained by differences in natural history traits, specifically food preferences, for these species

Forecasting the Cumulative Effects of Multiple Stressors on Breeding Habitat for a Steeply Declining Aerial Insectivorous Songbird, the Olive-sided Flycatcher (Contopus cooperi)

To halt ongoing loss in biodiversity, there is a need for landscape-level management recommendations that address cumulative impacts of anthropogenic and natural disturbances on wildlife habitat. We examined the cumulative effects of logging, roads, land-use change, fire, and bark beetle outbreaks on future habitat for olive-sided flycatcher (Contopus cooperi), a steeply declining aerial insectivorous songbird, in Canada’s western boreal forest. To predict the occurrence of olive-sided flycatcher we developed a suite of habitat suitability models using point count surveys (1997–2011) spatially- and temporally-matched with forest inventory data. Flycatcher occurrence was positively associated with small (∼10 ha) 10- to 20-year-old clearcuts, and with 10–100% tree mortality due to mountain pine beetle (Dendroctonus ponderosae) outbreaks, but we found no association with roads or distance to water. We used the parameter estimates from the best-fit habitat suitability models to inform spatially explicit state-and-transition simulation models to project change in habitat availability from 2020 to 2050 under six alternative scenarios (three management × two fire alternatives). The simulation models projected that the cumulative effects of land use conversion, forest harvesting, and fire will reduce the area of olive-sided flycatcher habitat by 16–18% under Business As Usual management scenarios and by 11–13% under scenarios that include protection of 30% of the land base. Scenarios limiting the size of all clearcuts to ≤10 ha resulted in a median habitat loss of 4–6%, but projections were highly variable. Under all three management alternatives, a 50% increase in fire frequency (expected due to climate change) exacerbated habitat loss. The projected losses of habitat in western boreal forest, even with an increase in protected areas, imply that reversing the ongoing population declines of olive-sided flycatcher and other migratory birds will require attention to forest management beyond protected areas. Further work should examine the effects of multiple stressors on the demographic mechanisms driving change in aerial insectivore populations, including stressors on the wintering grounds in South America, and should aim to adapt the design of protected areas and forest management policies to projected climate-driven increases in the size and frequency of wildfires.Fil: Norris, Andrea R.. Environment and Climate Change; CanadáFil: Frid, Leonardo. No especifíca;Fil: Debyser, Chloé. No especifíca;Fil: De Groot, Krista L.. Environment and Climate Change; CanadáFil: Thomas, Jeffrey. Environment and Climate Change; CanadáFil: Lee, Adam. Environment and Climate Change; CanadáFil: Dohms, Kimberly M.. Environment and Climate Change; CanadáFil: Robinson, Andrew. Environment and Climate Change; CanadáFil: Easton, Wendy. Environment and Climate Change; CanadáFil: Martin, Kathy. University of British Columbia; CanadáFil: Cockle, Kristina Louise. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Puerto Iguazú | Universidad Nacional de Misiones. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Puerto Iguazú; Argentin

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

Zombie journals: designing a technological infrastructure for a precarious graduate student journal

Open access article. Creative Commons Attribution Non-commercial License (CC-BY-NC) applies.Background: The Meeting of the Minds graduate student journal is edited primarily by students from our Masters programme. This means that our editorial board is subject to high annual turnover and that our technological infrastructure and workflow needed to be easy to train for, accommodate differing levels of technological skill and editorial interest, and provide archiving that did not require a continuing interest in the journal by future generations of students. Analysis: This article provides a detailed and comparative account of the "off-the-shelf" systems and software used in developing the journal with an explanation of the rationale behind our choices. Conclusion and implications: The choices we made can be adopted by other journals interested in a low-cost, "future-proof" approach to developing a publishing infrastructure.Ye

"Let's start a journal!": the multidisciplinary graduate student journal as educational opportunity

Sherpa Romeo green journal. Open access article. Creative Commons Attribution 4.0 International License (CC BY 4.0) applies.The University of Lethbridge is a medium-sized, primarily undergraduate, comprehensive research university on the Canadian Prairies in Alberta. It has a small but growing graduate school, within which most students are studying at the masters level. For many years, the graduate student elected representative body, the Graduate Students Association (GSA), has sponsored an annual refereed conference, Meeting of the Minds. In 2015 the GSA decided to supplement this conference with an accompanying journal, also called Meeting of the Minds. This article discusses the lessons learned in establishing this journal and overseeing its first two years of operations (and first year of publication). The article concentrates on two sets of problems: 1) philosophical, economic, and sociological issues that arose at the conceptual level while establishing a multidisciplinary, institution-focused graduate journal; and 2) technical, bibliographic, organizational, and economic issues encountered in attempting to address these conceptual concerns and ensure the long-term viability of the research accepted and published. Although the journal was not able to solve all the problems that arose during the first two years of operation, several solutions on the organizational, technological, economic, and bibliographic levels were developed that might be used by others establishing similar scholar- or student-led journals.Ye

Molecular Markers Reveal Limited Population Genetic Structure in a North American Corvid, Clark’s Nutcracker (<i>Nucifraga columbiana</i>)

<div><p>The genetic impact of barriers and Pleistocene glaciations on high latitude resident species has not been widely investigated. The Clark’s nutcracker is an endemic North American corvid closely associated with <i>Pinus</i>-dominated forests. The nutcracker’s encompasses known barriers to dispersal for other species, and glaciated and unglaciated areas. Clark’s nutcrackers also irruptively disperse long distances in search of pine seed crops, creating the potential for gene flow among populations. Using the highly variable mitochondrial DNA control region, seven microsatellite loci, and species distribution modeling, we examined the effects of glaciations and dispersal barriers on population genetic patterns and population structure of nutcrackers. We sequenced 900 bp of mitochondrial control region for 169 individuals from 15 populations and analysed seven polymorphic microsatellite loci for 13 populations across the Clark’s nutcracker range. We used species distribution modeling and a range of phylogeographic analyses to examine evolutionary history. Clark’s nutcracker populations are not highly differentiated throughout their range, suggesting high levels of gene flow among populations, though we did find some evidence of isolation by distance and peripheral isolation. Our analyses suggested expansion from a single refugium after the last glacial maximum, but patterns of genetic diversity and paleodistribution modeling of suitable habitat were inconclusive as to the location of this refugium. Potential barriers to dispersal (e.g. mountain ranges) do not appear to restrict gene flow in Clark’s nutcracker, and postglacial expansion likely occurred quickly from a single refugium located south of the ice sheets.</p> </div

Clark’s nutcracker mitochondrial DNA haplotype network.

<p><b>Legend</b>: Maximum parsimony network constructed using a median joining algorithm and post-processed with a maximum parsimony procedure for a 900 base pair fragment of mitochondrial control region from 169 Clark’s nutcrackers across North America. Each colour represents a different population (<i>n</i> = 15). Circle size is proportional to number of individuals with that haplotype. Haplotypes represented as pie charts include individuals from multiple populations with pie segments proportional to the number of individuals from each population. Capital letters are those assigned to shared haplotypes (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0079621#pone-0079621-t003" target="_blank">Table 3</a>). Small black circles represent inferred nodes. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0079621#pone-0079621-t001" target="_blank">Table 1</a> for population abbreviations.</p

Mantel test of isolation by distance for mitochondrial DNA.

<p><b>Legend</b>: <i>R</i>² = 0.082, <i>P</i> = 0.040. Each point represents one population pairwise Φ_ST/ (1- Φ_ST) plotted against geographic distance between paired populations. </p