Fitness benefits of genetic rescue despite chromosomal differences in an endangered pocket mouse.

Two-thirds of Earth's species have undergone population declines, leaving many vulnerable to genomic erosion and inbreeding depression. Genetic rescue can boost the fitness of small populations, but perceived risks of outbreeding depression can limit its use. We quantified these trade-offs in hundreds of endangered Pacific pocket mice () by combining whole-genome sequences with fitness data.

Desert ecosystems shape diversification in glossy snakes (genus Arizona) requiring a re-alignment of evolutionary and conservation units.

Subspecies are often targets for conservation, yet many lack the genetic data necessary to validate their status as distinctive evolutionary lineages. In 2016, conservationists faced this issue when designating the California glossy snake, Arizona elegans occidentalis, as a Species of Special Concern in California, a decision prompted by population declines and habitat loss but absent of genetic information about its evolutionary integrity. To address this knowledge gap, we collected genomic and mitochondrial data from a rangewide sample of the Arizona elegans complex (n = 257) and characterized genetic structure at varying spatial scales.

Genome Resources-A chromosome-Level genome assembly for the long-nosed leopard lizard, Gambelia wislizenii, the first reference genome for the lizard family crotaphytidae.

We report on an annotated chromosome-level genome assembly for the long-nosed leopard lizard, Gambelia wislizenii, as part of the California Conservation Genomics Project (CCGP). All seventeen species of reptiles, including two turtles, seven lizards, and seven snakes targeted for reference genome sequencing by the CCGP are now complete and posted on NCBI, and this paper is the third of seven CCGP lizard release papers to be published. It is also the first species of the family Crotaphytidae to have a released reference genome.

A chromosome-level reference genome assembly for Gilbert's skink Plestiodon gilberti.

Advances in genomic studies are revealing that gene flow between species is more frequent than previously understood, although the ways in which hybridization can bias gene flow across species boundaries or the extent to which introgression might be adaptive remain unexplored in most systems. We report on an annotated chromosome-level genome assembly for the Gilbert's skink, Plestiodon gilberti, one of 18 clades of reptiles and amphibians selected for reference genome sequencing in the California Conservation Genomics Project (CCGP). This assembly was produced using Pacific Biosciences HiFi long reads and Omni-C proximity ligation data.

Independent and interactive effects of disease and methylmercury on demographic rates across multiple amphibian populations.

Disease, alone or combined with other stressors such as habitat loss and contaminants, affects wildlife populations worldwide. However, interactions among stressors and how they affect demography and populations remain poorly understood. The amphibian chytrid fungus (Batrachochytrium dendrobatidis; Bd) is a sometimes-lethal pathogen linked with population declines and extirpations of amphibians globally.

Reference genome of the Gophersnake, Pituophis catenifer (Serpentes: Colubridae).

The Gophersnake, Pituophis catenifer, is a habitat generalist that ranges throughout the western half of the United States and southward into México. Five of the six subspecies, P. catenifer affinis (Sonoran Gophersnake), P.

Genomic discordance throws a wrench in the parallel speciation hypothesis for scincid lizards.

Parallel evolution of the same reproductive isolation barrier within a taxon is an indicator of ecology's role in speciation (i.e., parallel speciation), yet spatiotemporal variability in the efficacy of the barrier can present challenges to retracing how it evolved.

Iguanas rafted more than 8,000 km from North America to Fiji.

Founder-event speciation can occur when one or more organisms colonize a distant, unoccupied area via long-distance dispersal, leading to the evolution of a new species lineage. Species radiations established by long-distance, and especially transoceanic, dispersal can cause substantial shifts in regional biodiversity. Here, we investigate the occurrence and timing of the greatest known long-distance oceanic dispersal event in the history of terrestrial vertebrates-the rafting of iguanas from North America to Fiji.

Intrinsic and environmental drivers of pairwise cohesion in wild Canis social groups.

Animals within social groups respond to costs and benefits of sociality by adjusting the proportion of time they spend in close proximity to other individuals in the group (cohesion). Variation in cohesion between individuals, in turn, shapes important group-level processes such as subgroup formation and fission-fusion dynamics. Although critical to animal sociality, a comprehensive understanding of the factors influencing cohesion remains a gap in our knowledge of cooperative behavior in animals.

Amphibian richness, rarity, threats, and conservation prospects across the U.S. National Park System.

We assessed amphibian diversity, rarity, and threats across the National Park System (U.S.A.

A new species of Choleoeimeria (Apicomplexa: Eimeriidae) from the invasive curious skink, Carlia ailanpalai (Sauria: Scincidae) from Guam, U.S. Territory.

The curious skink, Carlia ailanpalai Zug, occurs in the main group of the Admiralty Islands of Papua New Guinea but has also successfully invaded Guam, the Marianas, Yap, and Kosrae. A single coccidian, Eimeria zugi McAllister, Duszynski, Fisher, & Austin, 2013 was described from C. ailanpalai from Papua New Guinea.

A New Isosporan (Apicomplexa: Eimeriidae) from the Pacific Blue-Tailed Skink, Emoia caeruleocauda (Sauria: Scincidae: Eugongylinae), from Guam, U.S. Territory.

Purpose: Nothing is known about coccidians (Apicomplexa: Eimeriidae) from the Pacific blue-tailed skink, Emoia caeruleocauda. Here, we report mensural and morphometric data on a new species of Isospora from E. caeruleocauda from Guam, US Territory.

A Dataset of Amphibian Species in U.S. National Parks.

National parks and other protected areas are important for preserving landscapes and biodiversity worldwide. An essential component of the mission of the United States (U.S.

Chromosome-Level Genome Assembly of the Blacktail Brush Lizard, Urosaurus nigricaudus, Reveals Dosage Compensation in an Endemic Lizard.

Urosaurus nigricaudus is a phrynosomatid lizard endemic to the Baja California Peninsula in Mexico. This work presents a chromosome-level genome assembly and annotation from a male individual. We used PacBio long reads and HiRise scaffolding to generate a high-quality genomic assembly of 1.

Broad-Scale Assessment of Methylmercury in Adult Amphibians.

Mercury (Hg) is a toxic contaminant that has been mobilized and distributed worldwide and is a threat to many wildlife species. Amphibians are facing unprecedented global declines due to many threats including contaminants. While the biphasic life history of many amphibians creates a potential nexus for methylmercury (MeHg) exposure in aquatic habitats and subsequent health effects, the broad-scale distribution of MeHg exposure in amphibians remains unknown.

Fecal metabarcoding of the endangered Pacific pocket mouse () reveals a diverse and forb rich diet that reflects local habitat availability.

Information on diet breadth and preference can assist in understanding links between food resources and population growth and inform habitat restoration for rare herbivores. We assessed the diet of the endangered Pacific pocket mouse using metabarcoding of fecal samples and compared it to plant community composition in long-term study plots in two populations on Marine Corps Base Camp Pendleton, San Diego County, CA. Fecal samples ( = 221) were collected between spring 2016 and fall 2017 during monthly live-trap surveys.

Native amphibian toxin reduces invasive crayfish feeding with potential benefits to stream biodiversity.

Background: Biodiversity is generally reduced when non-native species invade an ecosystem. Invasive crayfish, Procambarus clarkii, populate California freshwater streams, and in the Santa Monica Mountains (Los Angeles, USA), their introduction has led to trophic cascades due to omnivorous feeding behavior and a rapid rate of population growth. The native California newt, Taricha torosa, possesses a neurotoxin, tetrodotoxin (TTX), that affects freshwater animal behavior.

A reference genome assembly for the continentally distributed ring-necked snake, Diadophis punctatus.

Snakes in the family Colubridae include more than 2,000 currently recognized species, and comprise roughly 75% of the global snake species diversity on Earth. For such a spectacular radiation, colubrid snakes remain poorly understood ecologically and genetically. Two subfamilies, Colubrinae (788 species) and Dipsadinae (833 species), comprise the bulk of colubrid species richness.

A genome assembly for the southern Pacific rattlesnake, Crotalus oreganus helleri, in the western rattlesnake species complex.

Rattlesnakes play important roles in their ecosystems by regulating prey populations, are involved in complex coevolutionary dynamics with their prey, and exhibit a variety of unusual adaptations, including maternal care, heat-sensing pit organs, hinged fangs, and medically-significant venoms. The western rattlesnake (Crotalus oreganus) is one of the widest ranging rattlesnake species, with a distribution from British Columbia, where it is listed as threatened, to Baja California and east across the Great Basin to western Wyoming, Colorado and New Mexico. Here, we report a new reference genome assembly for one of six currently recognized subspecies, C.

Assembly of the largest squamate reference genome to date: The western fence lizard, Sceloporus occidentalis.

Spiny lizards (genus Sceloporus) have long served as important systems for studies of behavior, thermal physiology, dietary ecology, vector biology, speciation, and biogeography. The western fence lizard, Sceloporus occidentalis, is found across most of the major biogeographical regions in the western United States and northern Baja California, Mexico, inhabiting a wide range of habitats, from grassland to chaparral to open woodlands. As small ectotherms, Sceloporus lizards are particularly vulnerable to climate change, and S.

Reference genome of an iconic lizard in western North America, Blainville's horned lizard Phrynosoma blainvillii.

Genome assemblies are increasingly being used to identify adaptive genetic variation that can help prioritize the population management of protected species. This approach may be particularly relevant to species like Blainville's horned lizard, Phrynosoma blainvillii, due to its specialized diet on noxious harvester ants, numerous adaptative traits for avoiding predation (e.g.

Habitat connectivity and host relatedness influence virus spread across an urbanising landscape in a fragmentation-sensitive carnivore.

Spatially heterogeneous landscape factors such as urbanisation can have substantial effects on the severity and spread of wildlife diseases. However, research linking patterns of pathogen transmission to landscape features remains rare. Using a combination of phylogeographic and machine learning approaches, we tested the influence of landscape and host factors on feline immunodeficiency virus (FIV) genetic variation and spread among bobcats () sampled from coastal southern California.