Effect of Geography and Captivity on Scat Bacterial Communities in the Imperiled Channel Island Fox

With developing understanding that host-associated microbiota play significant roles in individual health and fitness, taking an interdisciplinary approach combining microbiome research with conservation science is increasingly favored. Here we establish the scat microbiome of the imperiled Channel Island fox (Urocyon littoralis) and examine the effects of geography and captivity on the variation in bacterial communities. Using high throughput 16S rRNA gene amplicon sequencing, we discovered distinct bacterial communities in each island fox subspecies. Weight, timing of the sample collection, and sex contributed to the geographic patterns. We uncovered significant taxonomic differences and an overall decrease in bacterial diversity in captive versus wild foxes. Understanding the drivers of microbial variation in this system provides a valuable lens through which to evaluate the health and conservation of these genetically depauperate foxes. The island-specific bacterial community baselines established in this study can make monitoring island fox health easier and understanding the implications of inter-island translocation clearer. The decrease in bacterial diversity within captive foxes could lead to losses in the functional services normally provided by commensal microbes and suggests that zoos and captive breeding programs would benefit from maintaining microbial diversity.

Diet of a threatened endemic fox reveals variation in sandy beach resource use on California Channel Islands

The coastal zone provides foraging opportunities for insular populations of terrestrial mammals, allowing for expanded habitat use, increased dietary breadth, and locally higher population densities. We examined the use of sandy beach resources by the threatened island fox (Urocyon littoralis) on the California Channel Islands using scat analysis, surveys of potential prey, beach habitat attributes, and stable isotope analysis. Consumption of beach invertebrates, primarily intertidal talitrid amphipods (Megalorchestia spp.) by island fox varied with abundance of these prey across sites. Distance-based linear modeling revealed that abundance of giant kelp (Macrocystis pyrifera) wrack, rather than beach physical attributes, explained the largest amount of variation in talitrid amphipod abundance and biomass across beaches. δ13C and δ15N values of fox whisker (vibrissae) segments suggested individualism in diet, with generally low δ13C and δ15N values of some foxes consistent with specializing on primarily terrestrial foods, contrasting with the higher isotope values of other individuals that suggested a sustained use of sandy beach resources, the importance of which varied over time. Abundant allochthonous marine resources on beaches, including inputs of giant kelp, may expand habitat use and diet breadth of the island fox, increasing population resilience during declines in terrestrial resources associated with climate variability and long-term climate change.

Body size and shape in insular environments and applications of the island rule in biological anthropology

The discovery of small-bodied hominin fossils in 2004 on the island of Flores, Indonesia, unearthed a large debate within biological anthropology. This debate has exemplified that there are questions and research areas that biological anthropologists do not understand about island evolution. To improve understanding on the causes and products of evolution within island areas for biological anthropologists, this dissertation addresses three overarching research areas relevant to the biological anthropology community. The first is an analysis of how primate body sizes vary on islands, with interpretations that are anchored in the evolutionary history of body sizes of primates. Primates that initially evolved body sizes to survive within a frugivorous niche, with elongated life spans to improve survival in unpredictable environments, have body sizes distributed among islands in relation to the presence of absence of these pressures. Smaller islands contain more large, bodied primates overall, whereas larger islands contain more small-bodied ones. Second, an analysis of island fox body size and shape indicates that island foxes have reduced body sizes and divergent skeletal traits compared to mainland, closely related counterparts. Distinct body proportions are likely due to selection because allometric scaling of limb lengths to body mass are divergent for the island fox. Further, the island fox is not a scaled down version of the mainland fox, with limbs decreasing in size at a faster rate compared to the mainland. Last, an investigation on the diversity of two human populations in the Baja California peninsula demonstrates that Amerindians who migrated to and survived in these regions were impacted by ecogeographic pressures in different degrees, likely related to access to resources. Heat-adapted skeletal traits are apparent in both human populations who inhabited this hot desert, but body size is distinct for the two groups. Body size is smaller for individuals with less access to marine resources and increased susceptibility to periods of drought and starvation. Body size is larger for humans with convenient access to oceanic and terrestrial resources. These studies demonstrate that primates, omnivores, and humans are not immune to the effects of insularity as has been suggested. Rather, interpreting body size and shape alterations requires contextualizing the organism with their evolutionary histories and subsequent interactions within the island areas. Body size alterations are the result of shifting selective pressures from competing with other community members to competing with other individuals within a population over finite resources. As such, body shape can also be divergent compared to closely related mainland counterparts due to adaptation to local ecogeographic pressures. Skeletal traits of organisms need to be interpreted in relation to their migratory journeys and adaptation to local ecogeographic pressures within the island. For humans, contextualizing these variables with cultural and behavioral characteristics is imperative to understand a body size response within a sociocultural omnivorous niche.

Effect of Geography and Captivity on Scat Bacterial Communities in the Imperiled Channel Island Fox

Background With developing understanding that host-associated microbiota play significant roles in individual health and fitness, taking an interdisciplinary approach combining microbiome research with conservation science is increasingly favored. Here we establish the scat microbiome of the imperiled Channel Island fox (Urocyon littoralis) and look at the effects of geography and captivity on the variation in bacterial communities. Results Using high throughput 16S rRNA gene amplicon sequencing, we discovered distinct bacterial communities in each island fox subspecies. Weight, timing of the sample collection, and sex contributed to the geographic patterns. We uncovered significant taxonomic differences and an overall decrease in bacterial diversity in captive versus wild foxes. Conclusions Understanding the drivers of microbial variation in this system provides a valuable lens through which to evaluate the health and conservation of these genetically depauperate foxes. The island-specific bacterial community baselines established in this study can make monitoring island fox health easier and understanding the implications of inter-island translocation clearer. The decrease in bacterial diversity within captive foxes could lead to losses in the functional services normally provided by commensal microbes and suggests that zoos and captive breeding programs would benefit from maintaining microbial diversity.

Notes from the Santa Cruz Island Reserve

This chapter presents the author's field notes from the Santa Cruz Island Reserve. The author was particularly interested in studying island foxes. Lacking natural predators, island foxes tend not to find humans intimidating, indeed appearing tame even though they are technically wild. The island fox is currently on the rebound from endangered status. There were two thousand foxes on Santa Cruz Island in 1994, but canine distemper and golden eagle predation reduced the numbers to under 135 by 2000. The author was also interested in the endangered plants, the red-tailed hawk, the anise swallowtail, and the island scrub-jays. Not only is the island scrub-jay endemic, occurring only on the island, but it is also the only insular land bird in either the United States or Canada. The explanation for this is that scrub-jays seem incapable of crossing significant amounts of water.

Unbiased Estimation of Linkage Disequilibrium from Unphased Data

Linkage disequilibrium (LD) is used to infer evolutionary history, to identify genomic regions under selection, and to dissect the relationship between genotype and phenotype. In each case, we require accurate estimates of LD statistics from sequencing data. Unphased data present a challenge because multilocus haplotypes cannot be inferred exactly. Widely used estimators for the common statistics r2 and D2 exhibit large and variable upward biases that complicate interpretation and comparison across cohorts. Here, we show how to find unbiased estimators for a wide range of two-locus statistics, including D2, for both single and multiple randomly mating populations. These unbiased statistics are particularly well suited to estimate effective population sizes from unlinked loci in small populations. We develop a simple inference pipeline and use it to refine estimates of recent effective population sizes of the threatened Channel Island Fox populations.