R.K. Wayne's research while affiliated with University of California, Los Angeles and other places

Publications (793)

Article
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Environmental DNA (eDNA) metabarcoding is a powerful tool that can enhance marine ecosystem/biodiversity monitoring programs. Here we outline five important steps managers and researchers should consider when developing eDNA monitoring program: (1) select genes and primers to target taxa; (2) assemble or develop comprehensive barcode reference data...
Article
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We know much about pathogen evolution and the emergence of new disease strains, but less about host resistance and how it is signaled to other individuals and subsequently maintained. The cline in frequency of black-coated wolves (Canis lupus) across North America is hypothesized to result from a relationship with canine distemper virus (CDV) outbr...
Article
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The remarkable radiation of South American (SA) canids produced 10 extant species distributed across diverse habitats, including disparate forms such as the short-legged, hypercarnivorous bush dog and the long-legged, largely frugivorous maned wolf. Despite considerable research spanning nearly two centuries, many aspects of their evolutionary hist...
Article
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Brownfields are unused sites that contain hazardous substances due to previous commercial or industrial use. The sites are inhospitable for many organisms, but some fungi and microbes can tolerate and thrive in the nutrient-depleted and contaminated soils. However, few studies have characterized the impacts of long-term contamination on soil microb...
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The bobcat (Lynx rufus) is a medium-sized carnivore well adapted to various environments and an indicator species for landscape connectivity. It is one of the four species within the extant Lynx genus in the family Felidae. Because of its broad geographic distribution and central role in food webs, the bobcat is important for conservation. Here we...
Preprint
Biodiversity monitoring in conservation projects is essential to understand environmental status and recovery. However, traditional field surveys can be biased towards visual detection and/or focused on measuring the biodiversity of a limited set of taxa. Environmental DNA (eDNA) methods provide a new approach to biodiversity monitoring that has th...
Article
In cases of severe wildlife population decline, a key question is whether recovery efforts will be impeded by genetic factors, such as inbreeding depression. Decades of excess mortality from gillnet fishing have driven Mexico’s vaquita porpoise ( Phocoena sinus ) to ~10 remaining individuals. We analyzed whole-genome sequences from 20 vaquitas and...
Preprint
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Island ecosystems provide models to assess the impacts of isolation on population persistence. However, most studies of persistence have focused on a single species, without comparisons to other organisms they interact with in the ecosystem. The simple predator-prey system of moose and gray wolves on Isle Royale provides allows a direct contrast of...
Article
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Species that hibernate generally live longer than would be expected based solely on their body size. Hibernation is characterized by long periods of metabolic suppression (torpor) interspersed by short periods of increased metabolism (arousal). The torpor–arousal cycles occur multiple times during hibernation, and it has been suggested that process...
Article
The genetic consequences of species-wide declines are rarely quantified because the timing and extent of the decline varies across the species’ range. The sea otter (Enhydra lutris) is a unique model in this regard. Their dramatic decline from thousands to fewer than 100 individuals per population occurred range-wide and nearly simultaneously due t...
Article
Long-term studies of mountain lions (Puma concolor) in Southern California have documented persistent small population sizes and the lowest genetic variation of any mountain lion population, except for the Federally endangered mountain lion subspecies, the Florida panther (Puma concolor coryi). There is overwhelming molecular evidence supporting in...
Article
In North American gray wolves, black coat color is dominantly inherited via a 3 base pair coding deletion in the canine beta defensin 3 (CBD103) gene. This 3 base pair deletion, called the KB allele, was introduced through hybridization with dogs and subsequently underwent a selective sweep that increased its frequency in wild wolves. Despite appar...
Preprint
Full-text available
Species that hibernate live longer than would be expected based solely on their body size. Hibernation is characterized by long periods of metabolic suppression (torpor) interspersed by short periods of increased metabolism (arousal). The torpor-arousal cycles occur multiple times during hibernation, and it has been suggested that processes control...
Article
Full-text available
Ecosystems globally are under threat from ongoing anthropogenic environmental change. Effective conservation management requires more thorough biodiversity surveys that can reveal system‐level patterns and that can be applied rapidly across space and time. Using modern ecological models and community science, we integrate environmental DNA and Eart...
Preprint
Full-text available
Species that hibernate live longer than would be expected based solely on their body size. Hibernation is characterized by long periods of metabolic suppression (torpor) interspersed by short periods of increased metabolism (arousal). The torpor-arousal cycles occur multiple times during hibernation, and it has been suggested that processes control...
Article
Full-text available
Dire wolves are considered to be one of the most common and widespread large carnivores in Pleistocene America¹, yet relatively little is known about their evolution or extinction. Here, to reconstruct the evolutionary history of dire wolves, we sequenced five genomes from sub-fossil remains dating from 13,000 to more than 50,000 years ago. Our res...
Article
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Climate change is leading to habitat shifts that threaten species persistence throughout California's unique ecosystems. Baseline biodiversity data would provide opportunities for habitats to be managed under short-term and long-term environmental change. Aiming to provide biodiversity data, the UC Conservation Genomics Consortium launched the Cali...
Article
Aim The majority of work done to gather information on the Earth's biodiversity has been carried out using in‐situ data, with known issues related to epistemology (e.g., species determination and taxonomy), spatial uncertainty, logistics (time and costs), among others. An alternative way to gather information about spatial ecosystem variability is...
Preprint
Aim The majority of work done to gather information on Earth diversity has been carried out by in-situ data, with known issues related to epistemology (e.g., species determination and taxonomy), spatial uncertainty, logistics (time and costs), among others. An alternative way to gather information about spatial ecosystem variability is the use of s...
Preprint
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ABSTRACT Aging is often perceived as a degenerative process caused by random accrual of cellular damage over time. In spite of this, age can be accurately estimated by epigenetic clocks based on DNA methylation profiles from almost any tissue of the body. Since such pan-tissue epigenetic clocks have been successfully developed for several different...
Article
Large percentages of abnormal sperm, termed teratospermia, are associated with poor fertility in cats, many of which are threatened with extinction from their natural habitats. Even normal appearing spermatozoa from felids with teratospermia may have a compromised capacity for motility and fertilization indicating there are factors affecting the fe...
Preprint
Full-text available
In North American gray wolves, black coat color is dominantly inherited via a three base pair coding deletion in the canine beta defensin 3 ( CBD103 ) gene. This three base pair deletion, called the K B allele, was introduced through hybridization with dogs and subsequently underwent a selective sweep that increased its frequency in wild wolves. De...
Article
Full-text available
Human‐driven habitat fragmentation and loss have led to a proliferation of small and isolated plant and animal populations with high risk of extinction. One of the main threats to extinction in these populations is inbreeding depression, which is primarily caused by recessive deleterious mutations becoming homozygous due to inbreeding. The typical...
Article
Full-text available
Mojave Desert springs are fragile ecosystems, hosting endemic plants and animals, which are threatened by the increasing human demand for water and climate change. To develop management practices that will protect the groundwater‐dependent ecosystems at Mojave Desert springs, real‐time, low‐cost biodiversity monitoring, and assessments are required...
Article
Full-text available
A key step in supporting our students and addressing problems of student persistence and retention in STEM fields lies in shifting the focus from "what" we teach to "how" we teach it. Student success and persistence in STEM are known to increase when (a) active-learning strategies are used effectively in the classroom (Freeman et al., 2014; Haak, H...
Article
Full-text available
A key step in supporting our students and addressing problems of student persistence and retention in STEM fields lies in shifting the focus from "what" we teach to "how" we teach it. Student success and persistence in STEM are known to increase when (a) active-learning strategies are used effectively in the classroom (Freeman et al., 2014; Haak, H...
Article
Full-text available
The grey wolf (Canis lupus) is one of the most widely distributed mammals in which a variety of distinct populations have been described. However, given their currently fragmented distribution and recent history of human-induced population decline, little is known about the events that led to their differentiation. Based on the analysis of whole ca...
Preprint
Full-text available
Unique ecosystems globally are under threat from ongoing anthropogenic environmental change. Effective conservation management requires more thorough biodiversity surveys that can reveal system-level patterns and that can be applied rapidly across space and time. We offer a way to use environmental DNA, community science and remote sensing together...
Article
One of the most enduring surprises about the genetic history of Late Pleistocene populations is that continuity is often disturbed by upheaval. In fact, studies that support population continuity are increasingly rare in humans, a variety of vertebrate taxa, and vascular plants (Hofreiter & Stewart, 2009; Burbrink et al., 2016). Perhaps such contin...
Article
The red wolf (Canis rufus), a legally recognized and severely endangered wolf, is known to interbreed with coyotes (C. latrans). Declared extirpated in the wild in 1980, red wolves were reintroduced to North Carolina nearly a decade later. Interbreeding with coyotes was thought to be restricted to a narrow geographic region adjacent to the reintrod...
Article
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An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Article
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Pumas are the most widely distributed felid in the Western Hemisphere. Increasingly, however, human persecution and habitat loss are isolating puma populations. To explore the genomic consequences of this isolation, we assemble a draft puma genome and a geographically broad panel of resequenced individuals. We estimate that the lineage leading to p...
Article
Knowledge of mutation rates is crucial for calibrating population genetics models of demographic history in units of years. However, mutation rates remain challenging to estimate because of the need to identify extremely rare events. We estimated the nuclear mutation rate in wolves by identifying de novo mutations in a pedigree of seven wolves. Put...
Article
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Dogs are the most phenotypically diverse mammalian species, and they possess more known heritable disorders than any other non-human mammal. Efforts to catalog and characterize genetic variation across well-chosen populations of canines are necessary to advance our understanding of their evolutionary history and genetic architecture. To date, no or...
Preprint
Full-text available
Environmental DNA (eDNA) metabarcoding is emerging as a biomonitoring tool available to the citizen science community that promises to augment or replace photographic observation. However, eDNA results and photographic observations have rarely been compared to document their individual or combined power. Here, we use eDNA multilocus metabarcoding,...
Preprint
Full-text available
Human-driven habitat fragmentation and loss have led to a proliferation of small and isolated plant and animal populations with high risk of extinction. One of the main threats to extinction in these populations is inbreeding depression, which is primarily caused by the exposure of recessive deleterious mutations as homozygous by inbreeding. The ty...
Article
Despite its recent invasion into the marine realm, the sea otter (Enhydra lutris) has evolved a suite of adaptations for life in cold coastal waters, including limb modifications and dense insulating fur. This uniquely dense coat led to the near-extinction of sea otters during the 18th-20th century fur trade and an extreme population bottleneck. We...
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Within the Canidae, the African wild dog (Lycaon pictus) is the most specialized with regards to cursorial adaptations (specialized for running), having only four digits on their forefeet. In addition, this species is one of the few canids considered to be an obligate meat-eater, possessing a robust dentition for taking down large prey, and display...
Article
During the late Pleistocene, isolated lineages of hominins exchanged genes thus influencing genomic variation in humans in both the past and present. However, the dynamics of this genetic exchange and associated phenotypic consequences through time remain poorly understood. Gene exchange across divergent lineages can result in myriad outcomes arisi...
Article
Psychological stress induced by exposure to predators has complex effects on the behaviour and physiology of prey species. This includes potential influences on gene expression mediated via stress-responsive physiological pathways such as the sympathetic nervous system and hypothalamus–pituitary–adrenal (HPA) axis. Laboratory studies have documente...
Article
The demographic history of dogs is complex, involving multiple bottlenecks, admixture events and artificial selection. However, existing genetic studies have not explored variance in the number of reproducing males and females, and whether it has changed across evolutionary time. While male-biased mating practices, such as male-biased migration and...
Article
Full-text available
Context Urbanization is a substantial force shaping the genetic and demographic structure of natural populations. Urban development and major highways can limit animal movements, and thus gene flow, even in highly mobile species. Characterizing varying species responses to human activity and fragmentation is important for maintaining genetic contin...
Article
Full-text available
1.Environmental DNA (eDNA) metabarcoding is a promising method to monitor species and community diversity that is rapid, affordable, and non‐invasive. Longstanding needs of the eDNA community are modular informatics tools, comprehensive and customizable reference databases, flexibility across high‐throughput sequencing platforms, fast multilocus me...
Article
Full-text available
The observation that small isolated populations often suffer reduced fitness from inbreeding depression has guided conservation theory and practice for decades. However, investigating the genome-wide dynamics associated with inbreeding depression in natural populations is only now feasible with relatively inexpensive sequencing technology and annot...
Article
Over the past two decades, new molecular genetic tech- niques have had substantial impacts on the fields of ecology, evolution and conservation. However, our cur- rent toolbox of genetic methodologies remains inadequate for answering many questions and there are significant technological and analytical limitations. We review the possible uses of si...
Article
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The causes and consequences of vertebrate natal dispersal have been studied extensively, yet little is known about the molecular mechanisms involved. We used RNA-seq to quantify transcriptomic gene expression in blood of wild yellow-bellied marmots (Marmota flaviventer) prior to dispersing from or remaining philopatric to their natal colony. We tes...
Article
Full-text available
The resolution of conservation genetic analyses has been limited until recently due to technological and computational challenges associated with genotyping multiple loci at once. In this review, we focus on how the development of high-throughput genotyping methods have enabled conservation genomics studies of wolves in North America. The gray wolf...
Preprint
Full-text available
Global change is leading to habitat shifts that threaten species persistence throughout California's unique ecosystems. Baseline biodiversity data provide opportunities for ecosystems to be managed for community complexity and connectivity. In 2017, the University of California Conservation Genomics Consortium launched the California Environmental...
Preprint
Full-text available
1. Environmental DNA (eDNA) metabarcoding is a promising method to monitor species and community diversity that is rapid, affordable, and non-invasive. Longstanding needs of the eDNA community are modular informatics tools, comprehensive and customizable reference databases, flexibility across high-throughput sequencing platforms, fast multilocus m...
Preprint
Full-text available
Introduction paragraph/Abstract Across the geographic range of mountain lions, which includes much of North and South America, populations have become increasingly isolated due to human persecution and habitat loss. To explore the genomic consequences of these processes, we assembled a high-quality mountain lion genome and analyzed a panel of reseq...
Preprint
Full-text available
The observation that small, isolated populations often suffer reduced fitness as a result of inbreeding depression has guided conservation theory and practice for decades. However, investigating the genome-wide dynamics associated with inbreeding depression in natural populations is only now feasible with relatively inexpensive sequencing technolog...
Article
The recovery and persistence of rare and endangered species are often threatened by genetic factors, such as the accumulation of deleterious mutations, loss of adaptive potential, and inbreeding depression [1]. Island foxes (Urocyon littoralis), the dwarfed descendants of mainland gray foxes (Urocyon cinereoargenteus), have inhabited California's C...
Preprint
During the late Pleistocene, genetically isolated lineages of hominins exchanged genes thus influencing genomic variation in humans in both the past and present. However, the dynamics of this genetic exchange and the associated phenotypic consequences through time remain poorly understood. Gene exchange across divergent lineages can result in myria...
Preprint
Full-text available
Studies of genetic variation have shown that the demographic history of dogs has been extremely complex, involving multiple bottleneck and admixture events. However, existing studies have not explored the variance in the number of reproducing males and females, and whether it has changed across evolutionary time. While male-biased mating practices,...
Article
Full-text available
Here we assess admixture during natural re-colonization and the resulting distribution of genetic variation based on mitochondrial haplotypes and 18,508 neutral nuclear SNPs. We utilize niche modelling to define ecotype boundaries and find little correspondence with genetic partitions that may reflect recent colonization from multiple sources. The...
Article
Full-text available
Pigmentation is often used to understand how natural selection affects genetic variation in wild populations since it can have a simple genetic basis, and can affect a variety of fitness-related traits (e.g., camouflage, thermoregulation, and sexual display). In gray wolves, the K locus, a β-defensin gene, causes black coat color via a dominantly i...
Data
Raw data and averaged data for the specimens that had the same geographic location, for all dimension and pigmentation traits of Didelphis virginiana
Data
List of all Didelphis virginiana museum specimens of used in our study