Prioritizing Populations for Conservation Using Phylogenetic Networks

In the face of inevitable future losses to biodiversity, ranking species by conservation priority seems more than prudent. Setting conservation priorities within species (i.e., at the population level) may be critical as species ranges become fragmented and connectivity declines. However, existing approaches to prioritization (e.g., scoring organisms by their expected genetic contribution) are based on phylogenetic trees, which may be poor representations of differentiation below the species level. In this paper we extend evolutionary isolation indices used in conservation planning from phylogenetic trees to phylogenetic networks. Such networks better represent population differentiation, and our extension allows populations to be ranked in order of their expected contribution to the set. We illustrate the approach using data from two imperiled species: the spotted owl Strix occidentalis in North America and the mountain pygmy-possum Burramys parvus in Australia. Using previously published mitochondrial and microsatellite data, we construct phylogenetic networks and score each population by its relative genetic distinctiveness. In both cases, our phylogenetic networks capture the geographic structure of each species: geographically peripheral populations harbor less-redundant genetic information, increasing their conservation rankings. We note that our approach can be used with all conservation-relevant distances (e.g., those based on whole-genome, ecological, or adaptive variation) and suggest it be added to the assortment of tools available to wildlife managers for allocating effort among threatened populations

Building a better ark: theoretical and analytical approaches for managing species at the population level

Biodiversity losses and limited resources may soon call for the preservation of key populations rather than entire species. However, successful population-level management requires both an understanding of where evolutionarily distinct taxa occur on the landscape and an efficient method for prioritizing taxa based on survey data. The present study addresses these needs. I begin by investigating the genetic identity and origins of red foxes (Vulpes vulpes) in North America’s Intermountain West. I then demonstrate a new approach for prioritizing populations that extends the metrics for evolutionary isolation from phylogenetic trees to phylogenetic networks, using two example species. Patterns of genetic differentiation for red foxes are consistent with endemism or natural range expansion in the Intermountain West, making this population a potential conservation target. Heuristic networks generated for spotted owls (Strix occidentalis) and mountain pygmy-possums (Burramys parvus) show how the approach can highlight peripheral populations that may merit increased conservation attention

Habitat selection by Pacific marten (Martes caurina) and other carnivores after wildfire and post-fire salvage logging

Wildfire and post-fire salvage logging are altering North American forests at an unprecedented rate. These disturbances affect key resources for wildlife across a range of spatial scales, from individual trees to entire landscapes. Habitat losses from fire threaten forest-specialist carnivores, such as Pacific marten (Martes caurina), that require closed, connected, and highly structured habitats. Salvage-logging, as a secondary disturbance, may amplify these impacts. Although marten use burned forests, the pattern and severity of landscape change strongly influence where these animals persist. In addition, fire-driven shifts in habitat structure and prey abundance may alter carnivore communities, restricting regionally-threatened specialist species like Canada lynx (Lynx canadensis) while benefitting generalists like coyotes (Canis latrans). I used a multi-scale approach to examine habitat selection by marten and other carnivores in north-central Washington, USA (burned in 2006) and central British Columbia, Canada (burned in 2010 and 2017). I also assessed these species’ responses to salvage-logging after the 2010 burn. I used snow tracking and forestry surveys to identify habitat features associated with marten foraging and scent-marking, and deployed GPS collars to characterize marten home ranges. Finally, I used winter track and camera surveys to explore the distribution of carnivores across these landscapes. Marten consistently relied on residual forest structure and avoided salvage-logged areas. Foraging marten selected sites with lower burn severity, greater canopy closure, more vertical structures (trees and snags), more saplings and shrubs, and greater moss/lichen cover than was generally available post-fire. When scent-marking, marten chose structurally complex sites with abundant deadfall or shrubs. Marten home ranges were closely associated with residual forest cover. More broadly, carnivore detection rates differed by burn severity: lynx selected unburned areas and marten selected lightly-burned areas, while coyotes and weasels (Mustela spp.) dominated in severely-burned and salvage-logged areas. My work indicates that burned forests with sufficient residual structure can support rich carnivore communities. However, it is also clear that salvage logging poses a major challenge to wildlife conservation. Lightly-burned areas provide critical post-fire habitat for marten in both Washington and British Columbia, and the retention of residual trees after wildfire should be a top management priority.Science, Irving K. Barber Faculty of (Okanagan)Biology, Department of (Okanagan)Graduat

Post-fire movements of Pacific marten (Martes caurina) depend on the severity of landscape change

Background Wildfires and forestry activities such as post-fire salvage logging are altering North American forests on a massive scale. Habitat change and fragmentation on forested landscapes may threaten forest specialists, such as Pacific marten (Martes caurina), that require closed, connected, and highly structured habitats. Although marten use burned landscapes, it is unclear how these animals respond to differing burn severities, or how well they tolerate additional landscape change from salvage logging. Methods We used snow tracking and GPS collars to examine marten movements in three large burns in north-central Washington, USA (burned in 2006) and central British Columbia, Canada (burned in 2010 and 2017). We also assessed marten habitat use in relation to areas salvage-logged in the 2010 burn. We evaluated marten path characteristics in relation to post-fire habitat quality, including shifts in behaviour when crossing severely-disturbed habitats. Using GPS locations, we investigated marten home range characteristics and habitat selection in relation to forest cover, burn severity, and salvage logging. Results Marten in the 2006 burn shifted from random to directed movement in areas burned at high severity; in BC, they chose highly straight paths when crossing salvage-blocks and meadows. Collared marten structured their home ranges around forest cover and burn severity, avoiding sparsely-covered habitats and selecting areas burned at low severity. Marten selected areas farther from roads in both Washington and BC, selected areas closer to water in the 2006 burn, and strongly avoided salvage-logged areas of the 2010 burn. Marten home ranges overlapped extensively, including two males tracked concurrently in the 2010 burn. Conclusions Areas burned at low severity provide critical habitat for marten post-fire. Encouragingly, our results indicate that both male and female marten can maintain home ranges in large burns and use a wide range of post-fire conditions. However, salvage-logged areas are not suitable for marten and may represent significant barriers to foraging and dispersal.Science, Irving K. Barber Faculty of (Okanagan)Biology, Department of (Okanagan)ReviewedFacult

Conservation prioritization of spotted owl (<i>Strix occidentalis</i>) populations.

<p>(a) Distribution of spotted owls in the United States and the populations sampled by Barrowclough <i>et al. </i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0088945#pone.0088945-Barrowclough2" target="_blank">[48]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0088945#pone.0088945-Barrowclough3" target="_blank">[51]</a>. Shaded areas denote suitable habitat based on forest cover data <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0088945#pone.0088945-US2" target="_blank">[73]</a>. Colors denote the subspecies <i>S. o. caurina</i> (blue), <i>S. o. occidentalis</i> (green), and <i>S. o. lucida</i> (orange). Populations 31 and 32 represent the <i>S. o. juanaphillipsae</i> subspecies in Mexico (range not shown). (b) NeighborNet of sampled populations based on mtDNA differentiation (pairwise Φ_ST values). (c) Histogram of SH values, highlighting the populations with the highest scores. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0088945#pone-0088945-t001" target="_blank">Table 1</a> for an explanation of abbreviations used.</p

Spotted owl populations sampled by Barrowclough <i>et al</i>. [48], [51] and ranked by Shapley value (SH) and heightened evolutionary distinctiveness (HED).

<p>Number of individuals (<i>n</i> ind.), number of haplotypes (<i>n</i> hap.), SH, and HED scores from the present study are reported.</p

Conservation prioritization of mountain pygmy-possum (<i>Burramys parvus</i>) populations.

<p>(a) Distribution of mountain pygmy-possums in Australia (gray inset), showing populations sampled by Mitrovski <i>et al. </i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0088945#pone.0088945-Mitrovski1" target="_blank">[58]</a>. Shaded areas denote suitable habitat above 1,400 m. (b) NeighborNet of sampled populations based on microsatellite differentiation (pairwise <i>F</i>_ST values). (c) Histograms of SH and HED values, highlighting the populations with the highest scores. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0088945#pone-0088945-t002" target="_blank">Table 2</a> for an explanation of abbreviations used.</p

Using pairwise distances to rank species or populations.

<p>Consider a hypothetical group of taxa (A)—a set of closely-related species or populations of a single species—that is distributed across several islands in an archipelago (B). Differences among the taxa, labeled <i>x1</i> through <i>x6</i>, can be organized into a pairwise distance matrix (C). We can represent this matrix either as a phylogenetic tree or as a phylogenetic network (D), where a set of weighted <i>splits</i> describes the relationships among the taxa (E). Altogether, these splits represent the group's phylogenetic diversity (PD). By selecting subsets of splits that exclude a given taxon, we can calculate each taxon's contribution to the total PD of the tree or network (F). The <i>Shapley metric</i> (SH) and <i>expected PD complementarity</i> (PD_c) are different approaches for ranking taxa based on split data. Note that the highest-scoring taxa (highlighted values) can differ considerably depending on the type of metric used and whether the splits come from a tree or network. We discuss the reasons for these differences and methods for ranking taxa in Section (<i>ii</i>) of the main text.</p

Mountain pygmy-possum populations sampled by Mitrovski <i>et al</i>. [58] and ranked by Shapley value (SH) and heightened evolutionary distinctiveness (HED).

<p>Number of individuals (<i>n</i> ind.), number of alleles (<i>n</i> all.), allelic richness (<i>r</i>), and adult population sizes (<i>N</i>) are reported from previously-published data. Probabilities of extinction (<i>p</i>i, with <i>P</i> = 0.4), SH, and HED scores from the present study are also shown.</p