The changing status of imperilled species in British Columbia

We assess the conservation status of all tree species in order to identify conservation gaps and prioritize genetic conservation efforts. A thorough assessment would consider genetic variation in each species across the species range, but for most tree species, such information is simply not available. For this reason, we used spatial variation associated with Biogeoclimatic Ecosystem Classification zones (BEC zones) representing different macroclimates as a proxy for adaptive genetic variation. We re-assessed the 2005 conservation status calculated in this manner using updated datasets collected in 2017, considered both in situ and ex situ conservation, and used an adjusted criterion for small-stature tree species. Results of our gap analysis revealed that overall, the native tree species in 89% of the conservation units (defined as species-by-biogeoclimatic-zone combinations) were well protected in situ. Of the 43 native tree species in the province, 12 species had conservation gaps in one or more biogeoclimatic zones. When in situ and ex situ conservation were considered jointly, the overall percentage of conservation units that were adequately protected improved to 91%. Needs for additional ex situ collections or in situ protection are discussed in terms of both BEC zones and individual species. In most cases, we recommend seed collection as the most feasible short-term option to cover gaps in protected area coverage.

In 2007, a new species of shrew, Sorex rohweri, was described from western Washington. We examined historical museum and recent voucher specimens to assess identification criteria and status of this new species in British Columbia. Most similar morphologically to Sorex cinereus and Sorex vagrans, S. rohweri can be identified by a combination of dental and skull traits. Three-group discriminant analyses of 100 specimens based on as few as 6 skull measurements correctly assigned 98% of individuals to the 3 species. The available records, consisting of 18 specimens from 13 locations, suggest that S. rohweri has a small range extent of about 360 km2 in the lower Fraser River basin confined to the south side of the Fraser River. The combination of the shrew's association with forested habitats in a region greatly affected by agricultural and urban development, the concentration of recent records from Burns Bog, a fragmented 3000-ha patch of natural habitat, and the isolation of the British Columbian population from populations in Washington make it a species of national conservation concern in Canada.

The only breeding colony of the American White Pelican (Pelecanus erythrorhynchos) in British Columbia is located at Stum Lake. The species in British Columbia. is designated “Endangered” and it is also included on the provincial “Red List.” As such, the Stum Lake colony has been monitored regularly since 1994, and older records of nest counts and pre-fledgling numbers date back as far as 1953. A marking program for pre-fledging American White Pelicans was conducted from 1968 to 1993. During recent surveys, censuses of nest depressions were obtained late in the breeding season; pre-fledged young were also enumerated. Based on nest counts, numbers at Stum Lake declined in the 1960s and remained more or less stationary throughout the 1970s and early 1980s. In the late 1980s and early 1990s, the number of nesting pairs increased dramatically; and in the past decade, numbers of breeding birds at Stum Lake has stabilized at the highest since monitoring began (1953). The mean number of pre-fledged young also shows an increasing trend from 1963 through 2002. The mean productivity at the breeding colony, however, was highest in the decade showing the largest growth, from 1983 to 1992; but it decreased in the past decade as total numbers of breeding birds continued to increase. The mean productivity of the breeding colony since monitoring began has been 0.62 ± 0.37 young nest-1, with annual rates varying from nil to 1.48 young nest per nest. Four breeding failures have been documented since 1960. The majority of the returns from the marking program were from west of the Continental Divide in British Columbia, Washington, California, Oregon, Idaho and Mexico.

In this article, discrete and stochastic changes in (effective) population size are incorporated into the spectral representation of a biallelic diffusion process for drift and small mutation rates. A forward algorithm inspired by Hidden-Markov-Model (HMM) literature is used to compute exact sample allele frequency spectra for three demographic scenarios: single changes in (effective) population size, boom-bust dynamics, and stochastic fluctuations in (effective) population size. An approach for fully agnostic demographic inference from these sample allele spectra is explored, and sufficient statistics for stepwise changes in population size are found. Further, convergence behaviours of the polymorphic sample spectra for population size changes on different time scales are examined and discussed within the context of inference of the effective population size. Joint visual assessment of the sample spectra and the temporal coefficients of the spectral decomposition of the forward diffusion process is found to be important in determining departure from equilibrium. Stochastic changes in (effective) population size are shown to shape sample spectra particularly strongly.

Plant species within the genus Vaccinium L. (Ericaceae) – including blueberries and their relatives – grow both naturally and as cultivated crops in British Columbia. Vaccinium cultivation is primarily undertaken in the southern areas of British Columbia, but there is growing interest in cultivating Vaccinium plants further north, particularly as the climate warms in northern parts of Canada. Vaccinium species are an important food source for humans and many other species, including insects. Much remains unclear about which insect species may pose a threat to these plants at northern latitudes, both now and in the future. We identified Vaccinium insect and other arthropod pest species through a literature review and used this list of species to inform and prioritize the collection of digitized occurrence records. We assessed the degree of risk each species poses to Vaccinium cultivation, and found that Rhopobota naevana (Hübner, 1817), the blackheaded fireworm (Lepidoptera: Tortricidae), is a Vaccinium pest of high concern in British Columbia, where it is a significant pest of cranberry. We used species distribution modelling (Maxent) to assess the distribution of R. naevana under both current and future climate change scenarios in British Columbia. Improving our understanding of pest distributions and how they may change in response to climate change is important for informing future pest risks for northern cultivation of wild Vaccinium and related crops in British Columbia and other northern regions of Canada.

It is often assumed that the northern peripheral populations of species’ ranges are genetically depauperate due in part to founder effects from postglacial colonization. The majority of federally protected plant species are peripheral in Canada, yet we have little information about their patterns of genetic diversity and structure. In British Columbia, the majority of these protected plant species occur in two threatened habitats: the Garry oak and Okanagan shrub-steppe ecosystems. Using universal noncoding chloroplast DNA markers, we investigated genetic diversity and genetic structure in four rare and common plant species pairs inhabiting these two ecosystems. We found that rare species had lower genetic diversity than their common congeners, and detected contrasting patterns of regional diversity and structure based on ecosystem. Species from the Garry oak ecosystem showed lower genetic diversity in the northern deglaciated region and significant differentiation between regions, likely due to limited dispersal between Vancouver Island and the mainland. Species from the Okanagan shrub-steppe, however, tended to have uniform diversity across their range and lack regional structure. This study provides an important first look at the phylogeographic patterns of four rare plant species in British Columbia.

Population size and population growth rate respond to changes in vital rates like survival and fertility. In deterministic environments change in population growth rate alone determines change in population size. In random environments, population size at any time t is a random variable so that change in population size obeys a probability distribution. We analytically show that, in a density-independent population, the proportional change in population size with respect to a small proportional change in a vital rate has an asymptotic normal distribution. Its mean grows linearly at a rate equal to the elasticity of the long-term stochastic growth rate λS while the standard deviation scales as \(\sqrt t\). Consequently, a vital rate with a larger elasticity of λS may produce a larger mean change in population size compared to one with a smaller elasticity of λS. But a given percentage change in population size may be more likely when the vital rate with smaller elasticity is perturbed. Hence, the response of population size to perturbation of a vital rate depends not only on the elasticity of the population growth rate but also on the variance in change in population size. Our results provide a formula to calculate the probability that population size changes by a given percentage that works well even for short time periods.

Molecular-assisted alpha taxonomy using COI-5P and rbcL-3P was employed to reassess species diversity for the Rhodymeniales (Rhodophyta) in British Columbia. A total of 563 collections from British Columbia were resolved as 16 genetic species groups, whereas 13 were previously reported. Collections attributed to Botryocladia pseudodichotoma from British Columbia were resolved as distinct from collections of that species from California (type locality) and were assigned to Botryocladia hawkesii sp. nov. DNA sequence data also resolved an additional species of Fryeella. Although two species of Gloiocladia were recognized, genetic analyses resolved three: G. fryeana, G. laciniata, and Gloiocladia vigneaultii sp. nov. Data also resolved Gloiocladia media comb. nov. from California. For the genus Rhodymenia, where two species were expected, DNA sequence data resolved four. Both R. californica and R. pacifica were confirmed in British Columbia, whereas some collections field-identified as R. californica were genetically distinct and assigned to the novel species, Rhodymenia bamfieldensis sp. nov. Some collections initially identified as R. pacifica were assigned to the resurrected species R. rhizoides. Anatomical development for the monospecific genus Minium was also reassessed owing to that taxon’s assignment to the Fryeellaceae. Our investigation clarified the number of rhodymenialean species in British Columbia and resolved taxonomic and distributional uncertainties associated with some of these taxa.

In human populations, the relative levels of neutral diversity on the X and autosomes differ markedly from each other and from the naïve theoretical expectation of 3/4. Here we propose an explanation for these differences based on new theory about the effects of sex-specific life history and given pedigree-based estimates of the dependence of human mutation rates on sex and age. We demonstrate that life history effects, particularly longer generation times in males than in females, are expected to have had multiple effects on human X-to-autosome (X:A) diversity ratios, as a result of male-biased mutation rates, the equilibrium X:A ratio of effective population sizes, and the differential responses to changes in population size. We also show that the standard approach of using divergence between species to correct for male mutation bias results in biased estimates of X:A effective population size ratios. We obtain alternative estimates using pedigree-based estimates of the male mutation bias, which reveal that X:A ratios of effective population sizes are considerably greater than previously appreciated. Finally, we find that the joint effects of historical changes in life history and population size can explain the observed X:A diversity ratios in extant human populations. Our results suggest that ancestral human populations were highly polygynous, that non-African populations experienced a substantial reduction in polygyny and/or increase in the male-to-female ratio of generation times around the Out-of-Africa bottleneck, and that current diversity levels were affected by fairly recent changes in sex-specific life history.

Climate-induced phenological shifts may have serious consequences for organisms and populations, but it is challenging to link such shifts to demographic change. Here, we present an overview of current methodological approaches for studying the demographic consequences of phenological shifts, based on a literature survey of 62 studies on diverse taxa. The majority of these studies (66%) were conducted using an approach that linked phenological shifts to demography through the measurement of vital rates (survival, growth, and fecundity). About 18% of the studies used a population-based approach that linked the phenological shifts to changes in population size, and 16% took a combined approach by considering changes in both vital rates and population size. Birds and mammals were overrepresented in studies of the demographic consequences of phenological shifts, compared to their occurrence in nature, while insects were heavily underrepresented. The effects of phenological shifts often varied according to the particular vital rate under consideration, in many cases even within a single species. In the few studies that examined changes in phenology together with both vital rate and population data, the changes in vital rates did not always predict changes in population size. To better understand the ultimate causes of population-level effects we argue that further study is needed on density-dependent aspects of population dynamics and on the sensitivity of population dynamics to perturbations in vital rates. We encourage re searchers to observe multiple vital rates throughout organisms' life-cycles in order to enable more meaningful examination of the consequences of phenological shifts for population dynamics. (Less)

Recent deep-water surveys of the continental slope in the Bering Sea and the eastern North Pacific, conducted by the US National Marine Fisheries Service, Alaska Fisheries Science Center, and Fisheries and Oceans Canada, have broadened our understanding of the ichthyofauna in the region. Herein, we report significant new records of 2 species of skates based on morphological and molecular data. For Bathyraja spinosissima, the White Skate, we describe 2 specimens: a neonate male that constitutes a northern range extension for the species to Alaska in the Bering Sea; and an adult male representing a new record for the species in British Columbia. For B. microtrachys, the Fine-spined Skate, we describe 5 males taken in a single haul that represent the 1st record of the species in British Columbia. These specimens had been previously misidentified as B. violacea, the Okhotsk Skate, a species known only from the western Aleutian Islands and the western North Pacific.

Observations of birds in the Bylot Island region from 1979 to 1997, with emphasis on the southwest part of the island each summer since 1989, revealed an avifauna composed of 63 species, of which 35 were breeding. Thirteen species are new records for the region, including one for the Northwest Territories (black-headed gull, Larus ridibundus) and two for the Canadian Arctic Archipelago (killdeer, Charadrius vociferus; mew gull, Larus canus). Two species, Canada goose (Brant canadensis) and red knot (Calidris canutus), were also confirmed as breeders for the first time in the region. A summary of these avifaunal observations, along with a review of previous observations made in the region, allows changes in population size and status of individual species to be identified. These records combined with those from earlier studies give a total of 74 species for the Bylot Island region, 45 confirmed as breeders. This makes the avian community in the area one of the most diverse known north of 70° N latitude in the Canadian Arctic Archipelago.

Monitoring changes in animal population size is rarely possible through complete censuses; frequently, the only feasible means of monitoring changes in population size is to use counts of animals obtained by skilled observers as indices to abundance. Analysis of changes in population size can be severely biased if factors related to the acquisition of data are not adequately controlled for. In particular, we identify two types of observer effects: these correspond to baseline differences in observer competence and to changes through time in the ability of individual observers. We present a family of models for count data in which the first of these observer effects is treated as a nuisance parameter. Conditioning on totals of negative binomial counts yields a Dirichlet compound multinomial vector for each observer. Quasi-likelihood is used to estimate parameters related to population trajectory and other parameters of interest; model selection is carried out on the basis of Akaike's information criterion. An example is presented using data on Wood thrush from the North American Breeding Bird Survey.

Recently, new methods have been developed for estimating the current and recent changes in effective population sizes. Based on the methods, the effective population sizes of Korean populations were estimated using data from the Korean Association Resource (KARE) project. The overall changes in the population sizes of the total populations were similar to CHB (Han Chinese in Beijing, China) and JPT (Japanese in Tokyo, Japan) of the HapMap project. There were no differences in past changes in population sizes with a comparison between an urban area and a rural area. Age-dependent current and recent effective population sizes represent the modern history of Korean populations, including the effects of World War II, the Korean War, and urbanization. The oldest age group showed that the population growth of Koreans had already been substantial at least since the end of the 19th century.

Understanding and predicting population abundance is a major challenge confronting scientists. Several genetic models have been developed using microsatellite markers to estimate the present and ancestral effective population sizes. However, to get an overview on the evolution of population requires that past fluctuation of population size be traceable. To address the question, we developed a new model estimating the past changes of effective population size from microsatellite by resolving coalescence theory and using approximate likelihoods in a Monte Carlo Markov Chain approach. The efficiency of the model and its sensitivity to gene flow and to assumptions on the mutational process were checked using simulated data and analysis. The model was found especially useful to provide evidence of transient changes of population size in the past. The times at which some past demographic events cannot be detected because they are too ancient and the risk that gene flow may suggest the false detection of a bottleneck are discussed considering the distribution of coalescence times. The method was applied on real data sets from several Atlantic salmon populations. The method called VarEff (Variation of Effective size) was implemented in the R package VarEff and is made available at https://qgsp.jouy.inra.fr and at http://cran.r-project.org/web/packages/VarEff.