Biology subjects

Carling, M. D.

Publications and source records attributed to Carling, M. D..

5 recordsLinked to original sources

bioRxiv2025

A chromosome-scale genome assembly for Clark's Nutcracker (Nucifraga columbiana)

Focal and intelligent passerine songbirds, corvids (Aves: Corvidae) have served as models for research on the genomics of hybridization and cognition. Clarks Nutcracker (Nucifraga columbiana), the sole North American member of its genus, is distributed in mountain forests from northern Mexico to northern British Columbia. A seed predator, N. columbiana is highly reliant on pine nuts from Pinus spp. conifers, which it both consumes directly from cones and caches for future use. Because cached seeds are often forgotten or abandoned, it is a major seed disperser for high elevation pines--in particular Whitebark Pine P. albicaulis. Previous studies of genetic variation in Clarks Nutcracker found range-wide panmixia and generally high levels of heterozygosity at a handful of nuclear and mitochondrial loci, potentially due to seasonal elevational movements and long term dispersal. An earlier genome assembly from low-coverage short read data was highly fragmented and has not to date been used as the basis for population-level resequencing. Here we report on the first chromosome-scale genome assembly for N. colombiana. We generated long-read sequencing and genome conformation mapping data from tissues sampled from a male N. columbiana individual in Wyoming, USA. These data were assembled into a highly contiguous and complete assembly, which showed strong chromosomal synteny with New Caledonian crow (Corvus moneduloides). This genome has relatively low heterozygosity compared to other Corvid genomes and to previous population-level heterozygosity estimates for the species. We also found evidence of a long-term decline in effective population size dating back to the Pleistocene, after accounting for a technical artifact common to demographic inference using the pairwise sequential Markovian coalescent. These findings raise concerns about the future viability of the species and its mutualist P. albicaulis; we hope the assembly will motivate further comparative and conservation genomics research.

genomics↗

bioRxiv2022

Thermal acclimation in a non-migratory songbird occurs via changes to thermogenic capacity, but not conductance

Thermoregulatory performance can be modified through changes in various subordinate traits, including thermal conductance, basal and summit metabolic rates, and body composition. We investigated physiological differences between black-capped chickadees (Poecile atricapillus) acclimated for six weeks to cold (-5{degrees}C) or control (25{degrees}C) environments (n = 7 per treatment) by measuring traits that affect thermal balance. We made repeated measurements of basal and summit metabolic rates via flow-through respirometry and body composition using quantitative magnetic resonance of live birds. At the end of the acclimation, we measured thermal conductance of the combined feathers and skins. Cold-acclimated birds had a higher summit metabolic rate, reflecting a greater capacity for endogenous heat generation, and an increased lean mass. However, birds did not alter their thermal conductance. These results suggest that, while birds can use multiple mechanisms to acclimate to their thermal environment, they use a subset of potential changes over varying timescales.

physiology↗

bioRxiv2022

Geographic variability of hybridization between Red-breasted and Red-naped Sapsuckers

Hybrid zones reveal the strength of reproductive isolation between populations undergoing speciation and are thus a key tool used in evolutionary biology research. Multiple replicate transects across the same hybrid zone offer further insight into the dynamics of hybridization in different environments, clarifying the role of extrinsic forces on the speciation process. Red-breasted and Red-naped Sapsuckers (Sphyrapicus ruber and S. nuchalis) have a long zone of contact over approximately 1,600 km from central British Columbia, Canada to central California, USA. We compared Genotyping-by-Sequencing data from three independent sapsucker hybrid zone transects to compare hybridization dynamics between the same species under variable geoclimatic conditions. We then generated geographic clines of the genomic data to compare hybrid zone widths and used Random Forest models and linear regression to assess the relationship between climate and sapsucker ancestry along each transect. Our results show variation in symmetry and directionality of back crossing, patterns often indicative of moving hybrid zones. We note variable cline widths among transects, indicating differences in the selection maintaining hybrid zone dynamics. Furthermore, Random Forest models identified different variables in close association with sapsucker ancestry across each transect. These results indicate a lack of repeatability across replicate transects and a strong influence of the local environment on hybrid zone dynamics.

evolutionary biology↗

bioRxiv2021

Haemosporidian infection does not alter aerobic performance in the Pink-sided Junco (Junco hyemalis mearnsi)

Avian haemosporidia are blood parasites that can have dramatic fitness consequences on their hosts, including largescale population declines when introduced to naive hosts. Yet the physiological effects that accompany haemosporidian infection and underlie these fitness decrements are poorly characterized in most wild birds. Because haemosporidia destroy host red blood cells and consume host hemoglobin, they are predicted to have detrimental impacts on avian blood-oxygen transport and, as a result, reduce aerobic performance. However, the documented effects of infection on avian hematological traits vary across species and no effects have been demonstrated on avian aerobic performance to date. Here we quantified the physiological effects of haemosporidian infections on wild Pink-sided Juncos (Junco hyemalis mearnsi) breeding in northwestern Wyoming, USA. We assayed hematological traits (hemoglobin concentration and hematocrit) and aerobic performance (resting and summit metabolic rates, thermogenic endurance, and aerobic scope), then screened individuals for haemosporidian infection post-hoc (n = 106 adult juncos). We found that infection status did not correlate with any of the physiological indices that we measured, suggesting there is little cost of haemosporidian infection on either junco aerobic performance or energy budgets. Our results highlight the need for more studies of haemosporidia infections in a broader range of species and in a wider array of environmental contexts.

physiology↗

bioRxiv2020

Temperature heterogeneity correlates with intraspecific variation in physiological flexibility in a small endotherm

Phenotypic flexibility allows individuals to reversibly modify trait values and theory predicts an individuals relative degree of flexibility positively correlates with the environmental heterogeneity it experiences. We tested this prediction by integrating surveys of population genetic and physiological variation with thermal acclimation experiments and indices of environmental heterogeneity in the Dark-eyed Junco (Junco hyemalis) and its congeners. We combined measures of thermogenic capacity for ~300 individuals, >21,000 single nucleotide polymorphisms genotyped in 192 individuals, and laboratory acclimations replicated on five populations. We found that Junco populations: (1) differ in their thermal performance responses to temperature variation in situ; (2) exhibit intra-specific variation in their thermogenic flexibility in the laboratory that correlates with heterogeneity in their native thermal environment; and (3) harbor genetic variation that also correlates with temperature heterogeneity. These results provide comprehensive support that phenotypic flexibility corresponds with environmental heterogeneity and highlight its importance for coping with environmental change.

evolutionary biology↗