The santa cruz long-toed salamander (sclts) is a federally endangered amphibian occupying an extremely limited range in southern santa cruz and northern monterey counties, california

The U.S. Fish and Wildlife Service awarded a $246,632 Cooperative Endangered Species Conservation Fund (CFDA 15.615) grant to the California Department of Fish and Wildlife (CDFW). The grant supports a 3-year project (3/1/2024 - 2/28/2027) to conduct a comprehensive genetic health assessment of the federally endangered Santa Cruz long-toed salamander across its limited range in southern Santa Cruz and northern Monterey Counties, California.

The project will generate genomic data and population genetics analyses to: 1) determine if low recruitment reflects low genetic variation and inbreeding, 2) identify habitat characteristics supporting genetically robust populations, and 3) assess landscape connectivity and gene flow. Findings will inform management actions like identifying populations needing genetic rescue and dispersal corridors for habitat conservation. CDFW has sub-awarded part of the grant to the University of California, Los Angeles to support the genetic research and analyses.

The most recent recovery document lists only 23 breeding sites where the sclts is currently found, and recent surveys indicate that recruitment is insufficient to maintain historical population sizes at even the healthiest of these breeding ponds. Causes for recent declines include saltwater inundation, habitat fragmentation due to residential development, ecological succession within ponds, and negative effects of mosquito control. The comprehensive genetic health assessment proposed here spans the range of the sclts and will: 1) determine whether recent, low, recruitment reflects low genetic variation which can lead to inbreeding depression, 2) identify habitat characteristics that support the most genetically robust populations, and 3) assess current levels of landscape connectivity and gene flow within and between metapopulations, including the identification of potential dispersal corridors. Each of these outcomes has direct implications for management, including: 1) identifying populations with the lowest genetic variation that may benefit from genetic rescue, 2) providing managers with data on the habitat characteristics most associated with greatest genetic health, and 3) identifying movement corridors where conserving additional habitat would be most beneficial to the species. These outcomes will be achieved through a collaboration between the shaffer lab at university of california, LOS angeles (ucla) and the searcy lab at university of miami (UM), both of which have a long history of partnering with california department of fish and wildlife (cdfw) and united states fish and wildlife service (USFWS) on conserving california s at-risk reptiles and amphibians. Building upon recent tissue samples and habitat data collected in 2021 and 2022 by DR. Searcy as part of an ongoing section 6 funded project (F22AP00217 G2198107), researchers at ucla and UM will generate a comprehensive tissue library spanning the geographic range of sclts. Then, utilizing genomic tools developed specifically for this system, they will generate genomic data from the assembled tissue samples. By applying contemporary bioinformatics and landscape and population genetics software, the team will provide estimates of genetic variation, effective population size, and genetic differentiation for all sampled breeding ponds. Deliverables will include: 1) a ranked list of population health based on standing genetic variation, including recommendations for those in need of genetic rescue and a list of candidate source populations for genetic outcrossing, 2) a model identifying the habitat characteristics most strongly associated with genetic health and accompanying management recommendations for these habitat variables, and 3) digital maps illustrating current movement corridors and where additional habitat conservation would most likely bolster further genetic exchange. This project will directly carry out one of the recovery goals decided at the 2019 sclts expert s meeting, conduct current genetic sampling and analysis across the range to determine levels of differentiation amongmetapopulations and assess variation within ponds, and will use those data to inform three of the recommendedactions in 2019 5-year review: 1) investigate and implement a population augmentation program, 2) enhanceexisting and potential breeding ponds, and 3) restore upland and dispersal habitat.