Environmental drivers behind the genetic differentiation in mountain chickadees (Poecile gambeli).

Anthropogenic climate change has a large impact on wildlife populations and the scale of the impacts has been increasing. In this study, we utilised 3dRAD sequence data to investigate genetic divergence and identify the environmental drivers of genetic differentiation between 12 populations of mountain chickadees, family Paridae, sampled across North America. To examine patterns of genetic variation across the range, we conducted a discriminant analysis of principal components (DAPC), admixture analysis, and calculated pairwise Fst values. The DAPC revealed four clusters: southern California, eastern Rocky Mountains, northwestern Rocky Mountains, and Oregon/northern California. We then used BayeScEnv to highlight significant outlier SNPs associated with the five environmental variables. We identified over 150 genes linked to outlier SNPs associated with more than 15 pathways, including stress response and circadian rhythm. We also found a strong signal of isolation by distance and local temperature was highly correlated with genetic distance. Maxent simulations showed a northward range shift over the next 50 years and a decrease in suitable habitat, highlighting the need for immediate conservation action.

Habitat and climate influence hybridization among three genetically distinct Canada jay (Perisoreus canadensis) morphotypes in an avian hybrid zone complex.

Examining the frequency and distribution of hybrids across contact zones provide insights into the factors mediating hybridization. In this study, we examined the effect of habitat and climate on hybridization patterns for three phenotypically, genetically, and ecologically distinct groups of the Canada jay (Perisoreus canadensis) in a secondary contact zone in western North America. Additionally, we tested whether the frequency of hybridization involving the three groups (referred to as Boreal, Pacific and Rocky Mountain morphotypes) is similar across the hybrid zones or whether some pairs have hybridized more frequently than others. We reanalyzed microsatellite, mtDNA and plumage data, and new microsatellite and plumage data for 526 individuals to identify putative genetic and phenotypic hybrids. The genetically and phenotypically distinct groups are associated with different habitats and occupy distinct climate niches across the contact zone. Most putative genetic hybrids (86%) had Rocky Mountain ancestry. Hybrids were observed most commonly in intermediate climate niches and in habitats where Engelmann spruce (Picea engelmannii) overlaps broadly with boreal and subalpine tree species. Our finding that hybrids occupy intermediate climate niches relative to parental morphotypes matches patterns for other plant and animal species found in this region. This study demonstrates how habitat and climate influence hybridization patterns in areas of secondary contact and adds to the growing body of research on tri-species hybrid zones.

Do habitat and elevation promote hybridization during secondary contact between three genetically distinct groups of warbling vireo (Vireo gilvus)?

Following postglacial expansion, secondary contact can occur between genetically distinct lineages. These genetic lineages may be associated with specific habitat or environmental variables and therefore, their distributions in secondary contact could reflect such conditions within these areas. Here we used mtDNA, microsatellite, and morphological data to study three genetically distinct groups of warbling vireo (Vireo gilvus) and investigate the role that elevation and habitat play in their distributions. We studied two main contact zones and within each contact zone, we examined two separate transects. Across the Great Plains contact zone, we found that hybridization between eastern and western groups occurs along a habitat and elevational gradient, whereas hybridization across the Rocky Mountain contact zone was not as closely associated with habitat or elevation. Hybrids in the Great Plains contact zone were more common in transitional areas between deciduous and mixed-wood forests, and at lower elevations (<1000 m). Hybridization patterns were similar along both Great Plains transects indicating that habitat and elevation play a role in hybridization between distinct eastern and western genetic groups. The observed patterns suggest adaptation to different habitats, perhaps originating during isolation in multiple Pleistocene refugia, is facilitating hybridization in areas where habitat types overlap.

Living on the edge: comparative phylogeography and phylogenetics of Oreohelix land snails at their range edge in Western Canada.

BACKGROUND: The biodiversity and distributions of terrestrial snails at local and regional scales are influenced by their low vagility and microhabitat specificity. The accessibility of large-bodied species and their characteristically high levels of genetic polymorphism make them excellent ecological and evolutionary models for studies on the phylogeography, phylogenetics, and conservation of organisms in fragmented populations. This study aims to elucidate the biodiversity, systematics, and distributions of genetic lineages within the genus Oreohelix at the northern and western periphery of their range. RESULTS: We found four mitochondrial clades, three of which are putative subspecies of Oreohelix subrudis. One clade was geographically widespread, occurring within numerous sites in Cypress Hills and in the Rocky Mountains, a second was geographically restricted to the Rocky Mountains in Alberta, and a third was restricted to the Cypress Hills region. A fourth clade was the small-bodied species, O. cooperi. ITS2 sequence and screening data revealed three genetic clusters, of which one was O. cooperi. Cluster 1 contained most individuals in COI clade X and some from clade B and cluster 2 was predominantly made up of individuals from COI clades B and B' and a few from clade X. ITS2 alleles were shared in a narrow contact zone between two COI clades, suggestive of hybridization between the two. CONCLUSIONS: A sky island known as Cypress Hills, in southeastern Alberta, Canada, is a biodiversity hotspot for terrestrial land snails in the genus Oreohelix. The observed phylogeographic patterns likely reflect reproductive isolation during the Last Glacial Maximum, followed by secondary contact due to passive, long-range dispersal resulting from low vagility, local adaptation, and complex glacial history.

Author Correction: The influence of latitude, geographic distance, and habitat discontinuities on genetic variation in a high latitude montane species.

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.

The influence of latitude, geographic distance, and habitat discontinuities on genetic variation in a high latitude montane species.

Examining the factors that influence contemporary genetic patterns is important given the alarming rate at which natural environments are changing. In particular habitat fragmentation and climate change are expected to influence the distribution and diversity of natural populations. In this study we used both mitochondrial control region (mtDNA) and microsatellite data to answer the following questions about genetic diversity and divergence in mountain chickadees (Poecile gambeli) a resident bird species in western North America: (1) Do populations exhibit similar levels of genetic diversity across the range? (2) What is the genetic affinity of western populations in Oregon and Washington? (3) Do genetic patterns exhibit isolation by distance, or are genetic patterns more heavily influenced by habitat discontinuity? We tested the effects of isolation by distance and habitat distribution on genetic structure by analyzing 266 samples from 17 sites across western Canada and the United States. We found a near significant relationship between genetic diversity and latitude, however, our results indicate that overall, latitude is not a strong predictor of genetic diversity. Our analyses of populations in Oregon and Washington revealed a mismatch between patterns detected with mtDNA and microsatellite data. In particular, Washington clustered with the Coast Range/Cascades/Rocky Mountain mtDNA group, but with populations in southern Oregon/California based on microsatellite data. These results suggest the presence of a contact zone in Washington between the two mtDNA clades Coast Range/Cascades/Rocky Mountain and southern Oregon/California clades. Finally, our study revealed a greater effect of isolation by distance than isolation by habitat for both mtDNA and microsatellite data. Overall the isolation by distance signal was greater for mtDNA than microsatellite patterns. The greater signal of isolation by distance on mtDNA patterns likely reflects the strong effects of Pleistocene glaciations in shaping genetic patterns in western North America.

Cryofixation during live-imaging enables millisecond time-correlated light and electron microscopy.

Correlating live-cell imaging with electron microscopy is among the most promising approaches to relate dynamic functions of cells or small organisms to their underlying ultrastructure. The time correlation between light and electron micrographs, however, is limited by the sample handling and fixation required for electron microscopy. Current cryofixation methods require a sample transfer step from the light microscope to a dedicated instrument for cryofixation. This transfer step introduces a time lapse of one second or more between live imaging and the fixed state, which is studied by electron microscopy. In this work, we cryofix Caenorhabditis elegans directly within the light microscope field of view, enabling millisecond time-correlated live imaging and electron microscopy. With our approach, the time-correlation is limited only by the sample cooling rate. C. elegans was used as a model system to establish compatibility of in situ cryofixation and subsequent transmission electron microscopy (TEM). TEM images of in situ cryofixed C. elegans show that the ultrastructure of the sample was well preserved with this method. We expect that the ability to correlate live imaging and electron microscopy at the millisecond scale will enable new paradigms to study biological processes across length scales based on real-time selection and arrest of a desired state. LAY DESCRIPTION: Researchers seek to link cellular functions to their smallest structural components. Currently this requires correlation of two imaging techniques, live imaging and electron microscopy. Current correlative methods, however, have limited time resolution due to the sample preparation procedures for electron microscopy. Following live imaging, samples are transferred from the light microscope to a cryofixation, or ultra-fast freezing, instrument. The biological process progresses until the sample freezes, 1 second or more after the last live image. In this work, samples are cryofixed directly within the light microscope field of view. By eliminating the transfer step, time correlation between light and electron microscopy images of our samples is limited only by the freezing rate to the order of milliseconds rather than seconds.

Asymmetric nanofluidic grating detector for differential refractive index measurement and biosensing.

Measuring small changes in refractive index can provide both sensitive and contactless information on molecule concentration or process conditions for a wide range of applications. However, refractive index measurements are easily perturbed by non-specific background signals, such as temperature changes or non-specific binding. Here, we present an optofluidic device for measuring refractive index with direct background subtraction within a single measurement. The device is comprised of two interdigitated arrays of nanofluidic channels designed to form an optical grating. Optical path differences between the two sets of channels can be measured directly via an intensity ratio within the diffraction pattern that forms when the grating is illuminated by a collimated laser beam. Our results show that no calibration or biasing is required if the unit cell of the grating is designed with an appropriate built-in asymmetry. In proof-of-concept experiments we attained a noise level equivalent to ∼10-5 refractive index units (30 Hz sampling rate, 4 min measurement interval). Furthermore, we show that the accumulation of biomolecules on the surface of the nanochannels can be measured in real-time. Because of its simplicity and robustness, we expect that this inherently differential measurement concept will find many applications in ultra-low volume analytical systems, biosensors, and portable devices.

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

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 because of 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 that 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 the importance of incorporating 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.

Influence of ecological and geological features on rangewide patterns of genetic structure in a widespread passerine.

Geological and ecological features restrict dispersal and gene flow, leading to isolated populations. Dispersal barriers can be obvious physical structures in the landscape; however microgeographic differences can also lead to genetic isolation. Our study examined dispersal barriers at both macro- and micro-geographical scales in the black-capped chickadee, a resident North American songbird. Although birds have high dispersal potential, evidence suggests dispersal is restricted by barriers. The chickadee's range encompasses a number of physiological features which may impede movement and lead to divergence. Analyses of 913 individuals from 34 sampling sites across the entire range using 11 microsatellite loci revealed as many as 13 genetic clusters. Populations in the east were largely panmictic whereas populations in the western portion of the range showed significant genetic structure, which often coincided with large mountain ranges, such as the Cascade and Rocky Mountains, as well as areas of unsuitable habitat. Unlike populations in the central and southern Rockies, populations on either side of the northern Rockies were not genetically distinct. Furthermore, Northeast Oregon represents a forested island within the Great Basin; genetically isolated from all other populations. Substructuring at the microgeographical scale was also evident within the Fraser Plateau of central British Columbia, and in the southeast Rockies where no obvious physical barriers are present, suggesting additional factors may be impeding dispersal and gene flow. Dispersal barriers are therefore not restricted to large physical structures, although mountain ranges and large water bodies do play a large role in structuring populations in this study.

X-ray scattering experiments with high-flux X-ray source coupled rapid mixing microchannel device and their potential for high-flux neutron scattering investigations.

Small-angle X-ray scattering provides global, shape-sensitive structural information about macromolecules in solution. Its extension to time dimension in the form of time-resolved SAXS investigations and combination with other time-resolved biophysical methods contributes immensely to the study of protein dynamics. TR-SAXS can also provide unique information about the global structures of transient intermediates during protein dynamics. An experimental set-up with low protein consumption is essential for an extensive use of TR-SAXS experiments on protein dynamics. In this direction, a newly developed 20-microchannel microfluidic continuous-flow mixer was combined with SAXS. With this set-up, we demonstrate ubiquitin unfolding dynamics after rapid mixing with the chaotropic agent Guanidinium-HCl within milliseconds using only ∼ 40 nanoliters of the protein sample per scattering image. It is suggested that, in the future, this new TR-SAXS platform will help to increase the use of time-resolved small-angle X-ray scattering, wide-angle X-ray scattering and neutron scattering experiments for studying protein dynamics in the early millisecond regime. The potential research field for this set-up includes protein folding, protein misfolding, aggregation in amyloidogenic diseases, function of intrinsically disordered proteins and various protein-ligand interactions.

When east meets west: population structure of a high-latitude resident species, the boreal chickadee (Poecile hudsonicus).

The population genetic structure of northern boreal species has been strongly influenced both by the Quaternary glaciations and the presence of contemporary barriers, such as mountain ranges and rivers. We used a combination of mitochondrial DNA (mtDNA), nuclear microsatellites and spatial distribution modelling to study the population genetic structure of the boreal chickadee (Poecile hudsonicus), a resident passerine, and to investigate whether historical or contemporary barriers have influenced this northern species. MtDNA data showed evidence of eastern and western groups, with secondary admixture occurring in central Canada. This suggests that the boreal chickadee probably persisted in multiple glacial refugia, one in Beringia and at least one in the east. Palaeo-distribution modelling identified suitable habitat in Beringia (Alaska), Atlantic Canada and the southern United States, and correspond to divergence dates of 60-96 kya. Pairwise FST values for both mtDNA and microsatellites were significant for all comparisons involving Newfoundland, though mtDNA data suggest a more recent separation. Furthermore, unlike mtDNA data, nuclear data support population connectivity among the continental populations, possibly due to male-biased dispersal. Although both are significant, the isolation-by-distance signal is much stronger for mtDNA (r(2)=0.51) than for microsatellites (r(2)=0.05), supporting the hypothesis of male-biased dispersal. The population structure of the boreal chickadee was influenced by isolation in multiple refugia and contemporary barriers. In addition to geographical distance, physical barriers such as the Strait of Belle Isle and northern mountains in Alaska are restricting gene flow, whereas the Rocky Mountains in the west are a porous barrier.

Population genetic structure and its implications for adaptive variation in memory and the hippocampus on a continental scale in food-caching black-capped chickadees.

Food-caching birds rely on stored food to survive the winter, and spatial memory has been shown to be critical in successful cache recovery. Both spatial memory and the hippocampus, an area of the brain involved in spatial memory, exhibit significant geographic variation linked to climate-based environmental harshness and the potential reliance on food caches for survival. Such geographic variation has been suggested to have a heritable basis associated with differential selection. Here, we ask whether population genetic differentiation and potential isolation among multiple populations of food-caching black-capped chickadees is associated with differences in memory and hippocampal morphology by exploring population genetic structure within and among groups of populations that are divergent to different degrees in hippocampal morphology. Using mitochondrial DNA and 583 AFLP loci, we found that population divergence in hippocampal morphology is not significantly associated with neutral genetic divergence or geographic distance, but instead is significantly associated with differences in winter climate. These results are consistent with variation in a history of natural selection on memory and hippocampal morphology that creates and maintains differences in these traits regardless of population genetic structure and likely associated gene flow.

Suspended microchannel resonators with piezoresistive sensors.

Precision frequency detection has enabled the suspended microchannel resonator (SMR) to weigh single living cells, single nanoparticles, and adsorbed protein layers in fluid. To date, the SMR resonance frequency has been determined optically, which requires the use of an external laser and photodiode and cannot be easily arrayed for multiplexed measurements. Here we demonstrate the first electronic detection of SMR resonance frequency by fabricating piezoresistive sensors using ion implantation into single crystal silicon resonators. To validate the piezoresistive SMR, buoyant mass histograms of budding yeast cells and a mixture of 1.6, 2.0, 2.5, and 3.0 µm diameter polystyrene beads are measured. For SMRs designed to weigh micron-sized particles and cells, the mass resolution achieved with piezoresistive detection (∼3.4 fg in a 1 kHz bandwidth) is comparable to what can be achieved by the conventional optical-lever detector. Eliminating the need for expensive and delicate optical components will enable new uses for the SMR in both multiplexed and field deployable applications.

Dosing accuracy of commonly used disposable insulin pens.

OBJECTIVE: The present study aimed to assess the dosing accuracy of commonly used disposable insulin pens including SoloStar (SR)*, FlexPen (FP) dagger, Next Generation FlexPen (NGFP) dagger, and KwikPen (KP) double dagger. It is the first comparative study covering the whole dosing range from 1 U to 60 U. It also covers the accuracy of SR at 80 U. RESEARCH DESIGN AND METHOD: A total of sixty insulin pens from two lots of each pen type were used. From each pen 1 U, 10 U, 30 U, 40 U, 60 U and 80 U were dispensed in random order. The 80 U dose was only evaluated for the SR as the other insulin pens do not deliver this dose in one injection. The actual doses were determined gravimetrically taking density of the different insulin preparations into account. The evaluation of dose accuracy was based on the regulations of the International Organization for Standardization (DIN EN ISO 11608-1:2000). RESULTS: All tested insulin pens met the requirements for accuracy with none of the single values at all dose levels being outside the defined range of the ISO recommendations (1 +/- 1 U, 10 +/- 1 U, 30 +/- 1.5 U, 40 +/- 2 U, 60 +/- 3 U and 80 +/- 4 U). For the investigated dosage levels the absolute average deviation of all insulin pens ranged between 0.09 and 0.81 U. CONCLUSION: The present study demonstrates an excellent dosing accuracy for all tested insulin pens, with no clinically relevant differences between the products.

Mechanisms of population differentiation in seabirds.

Despite recent advances in population genetic theory and empirical research, the extent of genetic differentiation among natural populations of animals remains difficult to predict. We reviewed studies of geographic variation in mitochondrial DNA in seabirds to test the importance of various factors in generating population genetic and phylogeographic structure. The extent of population genetic and phylogeographic structure varies extensively among species. Species fragmented by land or ice invariably exhibit population genetic structure and most also have phylogeographic structure. However, many populations (26 of 37) display genetic structure in the absence of land, suggesting that other barriers to gene flow exist. In these populations, the extent of genetic structure is best explained by nonbreeding distribution: almost all species with two or more population-specific nonbreeding areas (or seasons) have phylogeographic structure, and all species that are resident at or near breeding colonies year-round have population genetic structure. Geographic distance between colonies and foraging range appeared to have a weak influence on the extent of population genetic structure, but little evidence was found for an effect of colony dispersion or population bottlenecks. In two species (Galapagos petrel, Pterodroma phaeopygia, and Xantus's murrelet, Synthliboramphus hypoleucus), population genetic structure, and even phylogeographic structure, exist in the absence of any recognizable physical or nonphysical barrier, suggesting that other selective or behavioural processes such as philopatry may limit gene flow. Retained ancestral variation may be masking barriers to dispersal in some species, especially at high latitudes. Allopatric speciation undoubtedly occurs in this group, but reproductive isolation also appears to have evolved through founder-induced speciation, and there is strong evidence that parapatric and sympatric speciation occur. While many questions remain unanswered, results of the present review should aid conservation efforts by enabling managers to predict the extent of population differentiation in species that have not yet been studied using molecular markers, and, thus, enable the identification of management units and evolutionary significant units for conservation.

Global population structure and taxonomy of the wandering albatross species complex.

A recent taxonomic revision of wandering albatross elevated each of the four subspecies to species. We used mitochondrial DNA and nine microsatellite markers to study the phylogenetic relationships of three species (Diomedea antipodensis, D. exulans and D. gibsoni) in the wandering albatross complex. A small number of samples from a fourth species, D. dabbenena, were analysed using mitochondrial DNA only. Mitochondrial DNA sequence analyses indicated the presence of three distinct groups within the wandering albatross complex: D. exulans, D. dabbenena and D. antipodensis/D. gibsoni. Although no fixed differences were found between D. antipodensis and D. gibsoni, a significant difference in the frequency of a single restriction site was detected using random fragment length polymorphism. Microsatellite analyses using nine variable loci, showed that D. exulans, D. antipodensis and D. gibsoni were genetically differentiated. Despite the widespread distribution of D. exulans, we did not detect any genetic differentiation among populations breeding on different island groups. The lower level of genetic differentiation between D. antipodensis and D. gibsoni should be reclassified as D. antipodensis. Within the context of the current taxonomy, these combined data support three species: D. dabbenena, D. exulans and D. antipodensis.

Unravelling dispersal patterns in an expanding population of a highly mobile seabird, the northern fulmar (Fulmarus glacialis).

The northern fulmar (Fulmarus glacialis) is an abundant seabird whose Northeast Atlantic population has expanded dramatically over the past 100 years. Archaeological evidence suggests that Iceland and St Kilda were the ancestral populations from which essentially all other colonies in the region were derived. We collected samples from seven breeding colonies around the North Atlantic and used mitochondrial DNA analysis to ask whether population structure was present and, if so, where there was evidence about which colony was the dominant source population. Our data reveal a pattern consistent with isolation by distance, suggesting that, even though capable of flying great distances, most birds return to breed either at their own or neighbouring colonies. Interestingly, although most colonizers appear to have come originally from Iceland, our analysis also identifies St Kilda as a possible source. However, this secondary pattern appears to be largely an artefact, and can be attributed to the low haplotype diversity on St Kilda which yields a much clearer isolation by distance signal than that generated by birds dispersing from Iceland, where haplotype diversity is extremely high. Consequently, we urge caution when interpreting patterns in which populations vary greatly in the genetic diversity they harbour.