Lizard Environmental DNA

We have recently been experimenting with trying to obtain DNA from lizard environmental samples. The initial aim of which is to be able to identify the presence of lizard species based on fecal samples collected in the field. Currently we are using this work to identify the presence of the endangered blunt-nosed leopard lizard in the San Joaquin desert and the coastal range.

Today for first time we generated DNA sequence data from Lizard fecal samples collected in the field. This is no mean feat considering the harsh conditions (including high UV inundation).  We hope to build on this success to aid in monitoring and mapping of the species as well as other conservation efforts.another-male-gambelia


Salt Marsh Harvest Mouse meeting

Salt Marsh Harvest Mouse Working Group Nov 2016

We just had a really productive meeting of the salt marsh harvest mouse (SMHM) working group at Mare Island near Vallejo. Personnel were present from multiple agencies including DWR, USFWS, DFW, USGS, as well consulting groups and universities. It was particularly good to have Howard Shellhammer (the godfather of the salt marsh harvest research) there.

The first item on the list was a discussion of issues associated with the morphological identification of harvest mice collected in the field. Throughout much of the SMHM range the species is sympatric with the non-endangered western harvest mouse (WHM). The two species are morphologically very similar and there is a high % miss-identification rate, especially in south San Francisco Bay. If mice are incorrectly identified in the field this has obvious negative effects on required monitoring efforts, as well as any  associated research. My research group are currently working to develop an improved morphological key (based on animals genetically identified to species), and we used this opportunity to solicit input from the group.

Next up was we were given a look at the new central database for storing all trapping data on the SMHM from across its range. This database is intended for use by all agencies should prove really useful for storing data, as well as making accessible, for example to mine information on SMHM demography.

Finally, we set up subcommittees (such as SMHM Research and Recovery needs) that will provide recommendations to the Tidal Marsh recovery group.

Salt Marsh Harvest Mouse Conservation

We have just published our paper on the conservation genetics of the salt marsh harvest mouse (Statham et al. 2016 Conservation genetics of the endangered San Francisco Bay endemic salt marsh harvest mouse (Reithrodontomys raviventris). Conservation genetics; DOI 10.1007/s10592-016-0843-4).

In collaboration with state and federal agency partners we investigated a number of outstanding questions important to the conservation of the species. Despite finding harvest mice of ambiguous morphology and species, we found deep, ancient separation between the salt marsh harvest mouse and western harvest mouse, with no evidence of recent hybridization. We identified deep subdivision within the salt marsh harvest mouse, splitting mice in the south San Francisco bay from those in the two northern bay, consistent with recognized subspecies. We identified substantially lower diversity and effective population size in the range of the southern subspecies. This subspecies has also suffered the greatest from habitat loss and population fragmentation. Additionally, comparing our genetic species identification with the morphological species identification, we found that the ID rate in the southern San Francisco Bay, was just above 50%, which has ramifications for ongoing mouse monitoring and conservation work in the area.


This project was funded by California Dept. of Fish and Wildlife.

Molecular Ecology Final Posters

I am very proud of the students from Bio-178 Molecular Ecology who presented their posters at an open event at Sacramento State University as part of the culmination of their capstone projects. These projects provide an important opportunity for the students to engage in research while investigating novel questions. This year Dr. Shannon Datwyler and I supervised eight group projects. Students investigated the following: phylogeography of ringtails in California; subspecies status and population structure of California voles in the San Francisco Bay Area; molecular ecology of arbuscular mycorrhiza; sturgeon population structure in California; phylogeography of Penstemon species; and progenitor species of a polyploidy Penstemon species.

Salt Marsh Harvest Mouse

The salt marsh harvest mouse is a tiny rodent species endemic to the San Francisco Bay Area. It has suffered heavily due to habitat loss and fragmentation due to urbanization and conversion of land for other uses, which has contributed to the species being listed under the endangered species act. We are conducting genetic research on the species to aid conservation efforts.

We recently received a mouse that was recovered during ongoing monitoring efforts by management agencies. Luis Hernandez and I used this unfortunate event to improve our scientific understanding of the species.

Salt marsh harvest mouse
Salt marsh harvest mouse. That’s right, those are centimeters
salt marsh harvest mouse
Salt marsh harvest mouse

We dissected the animal to recover tissue and organs for our genetic analyses, as well as to store for future study. Hopefully this work will improve our understanding of adaptations associated with coping with differences in salinity in diet and water source throughout the Bay Area. This is particularly important in view of anticipated sea level rise, and precipitation changes associated with climate change.

Post organ recovery
Post organ recovery