Stabilizing selection and mitochondrial heteroplasmy in the Canada lynx (Lynx canadensis).

Mitochondrial DNA is commonly used in population genetic studies to investigate spatial structure, intraspecific variation, and phylogenetic relationships. The control region is the most rapidly evolving and largest non-coding region, but its analysis can be complicated by heteroplasmic signals of genome duplication in many mammals, including felids. Here, we describe the presence of heteroplasmy in the control region of Canada lynx (Lynx canadensis) through intra-individual sequence variation. Our results demonstrate multiple haplotypes of varying length in each lynx, resulting from different copy numbers of the repetitive sequence RS-2 and suggest possible heteroplasmic single nucleotide polymorphisms (SNPs) in both repetitive sequences RS-2 and RS-3. Intra-individual variation was only observed in the repetitive sequences while inter-individual variation was detected in the flanking regions outside of the repetitive sequences, indicating that heteroplasmic mutations are restricted to these repeat regions. Although each lynx displayed multiple haplotypes of varying length, we found the most common variant contained three complete copies of the RS-2 repeat unit, suggesting copy number is regulated by stabilizing selection. While genome duplication offers potential for increased diversity, heteroplasmy may lead to a selective advantage or detriment in the face of mitochondrial function and disease, which could have significant implications for wildlife populations experiencing decline (e.g., bottlenecks) as a result of habitat modification or climate change.

Population genomic analyses reveal a highly differentiated and endangered genetic cluster of northern goshawks (Accipiter gentilis laingi) in Haida Gwaii.

Accurate knowledge of geographic ranges and genetic relationships among populations is important when managing a species or population of conservation concern. Along the western coast of Canada, a subspecies of the northern goshawk (Accipiter gentilis laingi) is legally designated as Threatened. The range and distinctness of this form, in comparison with the broadly distributed North American subspecies (Accipiter gentilis atricapillus), is unclear. Given this morphological uncertainty, we analyzed genomic relationships in thousands of single nucleotide polymorphisms identified using genotyping-by-sequencing of high-quality genetic samples. Results revealed a genetically distinct population of northern goshawks on the archipelago of Haida Gwaii and subtle structuring among other North American sampling regions. We then developed genotyping assays for ten loci that are highly differentiated between the two main genetic clusters, allowing inclusion of hundreds of low-quality samples and confirming that the distinct genetic cluster is restricted to Haida Gwaii. As the laingi form was originally described as being based on Haida Gwaii (where the type specimen is from), further morphological analysis may result in this name being restricted to the Haida Gwaii genetic cluster. Regardless of taxonomic treatment, the distinct Haida Gwaii genetic cluster along with the small and declining population size of the Haida Gwaii population suggests a high risk of extinction of an ecologically and genetically distinct form of northern goshawk. Outside of Haida Gwaii, sampling regions along the coast of BC and southeast Alaska (often considered regions inhabited by laingi) show some subtle differentiation from other North American regions. These results will increase the effectiveness of conservation management of northern goshawks in northwestern North America. More broadly, other conservation-related studies of genetic variation may benefit from the two-step approach we employed that first surveys genomic variation using high-quality samples and then genotypes low-quality samples at particularly informative loci.

Temperate grassland songbird species accumulate incrementally along a gradient of primary productivity.

Global analyses of bird communities along elevation gradients suggest that bird diversity on arid mountains is primarily limited by water availability, not temperature or altitude. However, the mechanism by which water availability, and subsequently primary productivity, increases bird diversity is still unclear. Here we evaluate two possible mechanisms from species-energy theory. The more individuals hypothesis proposes that a higher availability of resources increases the total number of individuals that can be supported, and therefore the greater number of species that will be sampled. By contrast, the more specialization hypothesis proposes that increasing resource availability will permit specialists to exploit otherwise rare resources, thus increasing total diversity. We used 5 years of surveys of grassland songbird communities along an elevational gradient in British Columbia, Canada, to distinguish between these hypotheses. Vegetation changed markedly in composition along the gradient and contrary to the expectations of the more specialization hypothesis, bird community composition was remarkably constant. However, both total abundance and species richness of birds increased with increasing water availability to plants. When we used rarefaction to correct species richness for differences in total abundance, much of the increase in bird diversity was lost, consistent with the expectations of the more individuals hypothesis. Furthermore, high species richness was associated with reductions in territory size of common bird species, rather than the fine-scale spatial partitioning of the landscape. This suggests that bird diversity increases when greater resource availability allows higher densities rather than greater habitat specialization. These results help explain a pervasive global pattern in bird diversity on arid mountains, and suggest that in such landscapes conservation of grassland birds is strongly linked to climate and hydrology.

Pre-dispersal strategies by Quercus schottkyana to mitigate the effects of weevil infestation of acorns.

We investigated how pre-dispersal strategies may mitigate the effects of weevil infestation of acorns in a population of Quercus schottkyana, a dominant oak in Asian evergreen broad-leaved forests, and assess if weevil infestation contributes to low seedling recruitment. We counted the number of acorns produced, daily from the end of August to mid-late November for 9 years from 2006-2014. We also recorded the rate of acorn infestation by weevils and acorn germination rates of weekly collections. Annual acorn production was variable, but particularly low in 2011 and 2013. There was no trade-off between acorn production and acorn dry mass. However, acorns produced later in the season were significantly heavier. For most years: (i) the rate of weevil infestation was negatively density dependent (a greater proportion of acorns died with increased acorn density), (ii) the percentage germination of acorns was positively density dependent (proportionately more acorns germinated with increased density), and (iii) as the season progressed, the percentage of infested acorns declined while germination rates increased. Finally, (iv) maximum acorn production, percentage infestation and percentage germination were asynchronous. Although pre-dispersal mortality is important it is unlikely to be the primary factor leading to low recruitment of oak seedlings.

An experimental approach to addressing ecological questions related to the conservation of plant biodiversity in China.

We briefly introduce and describe seven questions related to community structure and biodiversity conservation that can be addressed using field experiments, and provide the context for using the vast geographic diversity, biodiversity, and network of Nature Reserves in China to perform these experiments. China is the world's third largest country, has a diverse topography, covers five climatic zones from cold-temperate to tropical, has 18 vegetation biomes ranging from Arctic/alpine tundra and desert to Tropical rain forest, and supports the richest biodiversity in the temperate northern hemisphere (>10% of the world total). But this tremendous natural resource is under relentless assault that threatens to destroy biodiversity and negatively impact the services ecosystems provide. In an attempt to prevent the loss of biodiversity, China has established 2729 nature reserves which cover 14.84% of the nation's area. Unfortunately underfunding, mismanagement, illegal activities, invasive species and global climate change threaten the effectiveness of these protected areas. Attention has focused on protecting species and their habitats before degradation and loss of either species or habitats occur. Here we argue that we must move beyond the simple protection of ecosystems, beyond their description, and by using experiments, try to understand how ecosystems work. This new understanding will allow us to design conservation programs, perform restoration of damaged or degraded areas, and address resource management concerns (e.g., agriculture, logging, mining, hunting) more effectively than with the current approach of ad hoc reactions to ecological and environmental problems. We argue that improving our understanding of nature can best be done using well designed, replicated, and typically manipulative field experiments.