Jonathan Q. Richmond

Jonathan Q. Richmond
United States Geological Survey | USGS · Western Ecological Research Center, San Diego Field Station

MS, PhD

About

169
Publications
10,898
Reads
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942
Citations
Citations since 2017
39 Research Items
402 Citations
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2017201820192020202120222023020406080
Introduction
I work at the USGS Western Ecological Research Center, San Diego Field Station. My research varies widely but typically falls under evolutionary biology, conservation genetics, phylogenetic systematics, invasion biology, and general ecology. Current projects include studies on (1) a variety of reptile and amphibian species in the southwestern United States, Baja California, and Pacific Islands; (2) native freshwater fish species in Southern California; (3) and various non-native species.
Additional affiliations
September 2014 - December 2017
California State University, Fullerton
Position
  • PhD Student
Description
  • I am currently serving on a thesis committee for a Master's student at CSU Fullerton, Logan Fehrenbach. Logan is working on the physiological ecology of skinks in the Plestiodon skiltonianus species group.
November 2008 - December 2014
United States Geological Survey
Position
  • Wildlife Geneticist
February 2006 - October 2008
Cornell University
Position
  • PostDoc Position
Education
September 2000 - December 2005
University of Connecticut
Field of study
  • Zoology
September 1997 - May 2000
San Diego State University
Field of study
  • Evolutionary Biology
September 1989 - December 1993
University of California, Berkeley
Field of study
  • Integrative Biology

Publications

Publications (169)
Article
Full-text available
Context. Skinks comprise the dominant component of the terrestrial vertebrate fauna in Oceania, New Guinea, and Eastern Wallacea (ONGEW). However, knowledge of their diversity is incomplete, and their conservation needs are poorly understood. Aims. To explore the diversity and threat status of the skinks of ONGEW and identify knowledge gaps and con...
Article
Full-text available
Habitat loss, flood control infrastructure, and drought have left most of southern California and northern Baja California’s native freshwater fish near extinction, including the endangered unarmored threespine stickleback (Gasterosteus aculeatus williamsoni). This subspecies, an unusual morph lacking the typical lateral bony plates of the G. acule...
Article
The glossy snake (Arizona elegans) is a polytypic species broadly distributed across southwestern North America. The species occupies habitats ranging from California’s coastal chaparral to the shortgrass prairies of Texas and southeastern Nebraska, to the extensive arid scrublands of central México. Three subspecies are currently recognized in Cal...
Article
Full-text available
Abstract Identifying how natural (i.e., unaltered by human activity) and anthropogenic landscape variables influence contemporary functional connectivity in terrestrial organisms can elucidate the genetic consequences of environmental change. We examine population genetic structure and functional connectivity among populations of a declining specie...
Article
Full-text available
Conservation translocations, the human-mediated movement and release of a living organism for a conservation benefit, are increasingly recommended in species’ recovery plans as a technique for mitigating population declines or augmenting genetic diversity. However, translocation protocols for species with broad distributions may require regionally...
Article
Maintenance of genetic diversity at adaptive loci may facilitate invasions by non-native species by allowing populations to adapt to novel environments, despite the loss of diversity at neutral loci that typically occurs during founder events. To evaluate this prediction, we compared genetic diversity at MHC and cytochrome b (cytb) loci from 20 pop...
Article
Full-text available
We discuss the problems associated with beaver disturbance and its effects on conserving the region's native fauna and flora. We refute arguments underlying the claim that beaver is native to the region, and review paleontological, zooarchaeological, and historical survey data from renowned field biologists and naturalists over the past ~160 years...
Article
Full-text available
Rediscovery of living populations of a species that was presumed to be extirpated can generate new narratives for conservation in areas suffering from losses in biodiversity. We used field observations and DNA sequence data to verify the rediscovery of the Critically Endangered scincid lizard Emoia slevini on Dåno′, an islet off the coast of Guam i...
Article
Full-text available
Remote oceanic islands have high potential to harbor unique fauna and flora, but opportunities to conduct in-depth biotic surveys are often limited. Furthermore, underrepresentation of existing biodiversity in the literature has the potential to detract from conservation planning and action. Between 18 and 29 October 2018, we surveyed the terrestri...
Article
The invasiveness of nonnative taxa can vary across a landscape due to environmental gradients, suggesting that location-dependent management strategies may be more effective at reducing spread compared to a “one size fits all” approach across the entire introduced range. Using bait stations placed along linear transects within habitat preserves, we...
Book
As the world population grows, so does the demand for food, putting unprecedented pressure on agricultural lands. At the same time, climate change, soil degradation, and water scarcity mean that productivity of many of these lands is deteriorating. In many desert dryland regions, drinking wells are drying up and the land above them is sinking, soil...
Article
Niche breadth and position can influence diversification among closely related species or populations, yet limited empirical data exist concerning the predictability of the outcomes. We explored the effects of these factors on the evolution of the Emoia atrocostata species group, an insular radiation of lizards in the western Pacific Ocean and Indo...
Article
Niche breadth and position can influence diversification among closely related species or populations, yet limited empirical data exist concerning the predictability of the outcomes. We explored the effects of these factors on the evolution of the Emoia atrocostata species group, an insular radiation of lizards in the western Pacific Ocean and Indo...
Article
Full-text available
Noninvasive fecal sampling combined with genetic analysis is a technique allowing the study of elusive or otherwise difficult to monitor species without the need for direct contact. Although this method is widely used in birds and mammals, it has never been successfully applied on a large scale in reptiles. The blunt‐nosed leopard lizard (Gambelia...
Article
Full-text available
A recent global trend toward retirement of farmland presents opportunities to reclaim habitat for threatened and endangered species. We examine habitat restoration opportunities in one of the world's most converted landscapes, California's San Joaquin Desert (SJD). Despite the presence of 35 threatened and endangered species, agricultural expansion...
Data
Summary of resurvey effort for two apparently extirpated historical record locations at or near the historical northern range margin of Gambelia sila. (XLSX)
Data
Comparison of realized climatic niches for Gambelia sila and all three species in the genus Gambelia. Other members of the genus occupy hotter and drier environments than are available to G. sila in the San Joaquin Desert (see also S2 Fig). Occurrence data were thinned to one record per 30-arcsecond climate grid cell. Climate data were extracted fr...
Data
Ensemble habitat suitability surfaces generated for this study. Zipped file includes GeoTIFF files representing continuous and binary historical habitat suitability for Gambelia sila (see text). (ZIP)
Data
Discussion of potential impact of climate change. (PDF)
Data
Hours of restriction during the breeding season (left) and hours of activity during the active season (right). Hours of restriction are average number of hours per day during the breeding season (AMJJ) that operative environmental temperatures are too hot for Gambelia sila to be active above ground. Hours of activity are number of hours per day dur...
Data
Modeled change in habitat suitability over time for four future climate scenarios. Climate scenarios were selected to represent a range of potential future conditions, combining two global circulation models with two emission scenarios. The global circulation models predict either a relatively hot and dry future (MIROC-ESM) or a relatively warm and...
Data
Change in climatic niche of Gambelia sila from the historical era to modern era with respect to actual evapotranspiration (AET). The distribution of all distinct G. sila record locations on intact habitat has shifted toward sites with lower AET from the historical (pre-1960) to modern (1995 or after) periods. (TIFF)
Data
Threatened, endangered, extinct, and extirpated species of the San Joaquin Desert. List includes 42 species with occurrence records that fall within the boundary of the San Joaquin Desert (sensu Germano et al., 2011). SSC indicates a California species of special concern. (XLSX)
Data
Locations of some recent Gambelia sila habitat destruction. This list is by no means comprehensive. It is a partial list of locations where the authors and collaborators have observed habitat loss in the course of other work duties. Examining historical aerial imagery in the vicinity of many of these disturbances reveals additional instances of hab...
Data
Density plots for 11 candidate predictor variables. Shown are Gambelia sila occurrence locations and background sampling locations used for parameterizing our models. Occurrence data was thinned to one record per 1-km grid cell. Old locations on developed habitat were not included. (TIFF)
Data
Habitat suitability in the Westlands Water District peaks on alkaline soils located in the western portions of the district. Under a settlement negotiated with the federal government at least 405 km2 of farmland in Westlands Water District will be permanently retired, including 70–210 km2 of formerly suitable habitat for Gambelia sila. The thick bo...
Data
Biases and critiques of previous species distribution models for San Joaquin Desert species. (XLSX)
Data
Information on 11 candidate predictor variables evaluated for their strength in determining habitat quality and distribution. (XLSX)
Data
Locations of Gambelia sila occurrence observed on retired agricultural lands. Scars from former ploughing are clearly visible on aerial imagery of these sites. (XLSX)
Preprint
Full-text available
A recent global trend toward retirement of farmland presents opportunities to reclaim habitat for threatened and endangered species. We examine habitat restoration opportunities in one of the world’s most converted landscapes, California’s San Joaquin Desert (SJD). Despite the presence of 35 threatened and endangered species, agricultural expansion...
Preprint
Full-text available
A recent global trend toward retirement of farmland presents opportunities to reclaim habitat for threatened and endangered species. We examine habitat restoration opportunities in one of the world’s most converted landscapes, California’s San Joaquin Desert (SJD). Despite the presence of 35 threatened and endangered species, agricultural expansion...
Article
Full-text available
Striking faunal turnover across Asia and Australasia, most famously along the eastern edge of the Sunda Shelf or 'Wallace's Line', has been a focus of biogeographic research for over 150 years. Here, we investigate the origins of a highly threatened endemic lizard fauna (four species) on Christmas Island. Despite occurring less 350 km south of the...
Preprint
Full-text available
Aim: Habitat loss has been the greatest historical driver of species extinctions. A recent global trend toward retirement of marginally productive agricultural lands presents opportunities to reclaim critical habitat for endangered species. We examine habitat restoration opportunities in the context of historical sources of habitat loss, including...
Article
Full-text available
Life history adaptations and spatial configuration of metapopulation networks allow certain species to persist in extreme fluctuating environments, yet long-term stability within these systems relies on the maintenance of linkage habitat. Degradation of such linkages in urban riverscapes can disrupt this dynamic in aquatic species, leading to incre...
Article
Full-text available
Southern California has experienced widespread amphibian declines since the 1960s. One species, the Vulnerable California red-legged frog Rana draytonii , is now considered to be extirpated from most of southern California. In February 2017 a population of R. draytonii was discovered in the southern foothills of the San Bernardino Mountains of Rive...
Article
The islands of East Melanesia have generated key insights into speciation processes and community assembly. However, when and how these islands began to form, emerge and accumulate endemic taxa remains poorly understood. Here, we show that two divergent lineages within the world’s most diverse genus of geckos (Cyrtodactylus) occur in the Solomon Is...
Article
Genomic responses to habitat conversion can be rapid, providing wildlife managers with time-limited opportunities to enact recovery efforts that use population connectivity information that reflects pre-disturbance landscapes. Such opportunities may still exist for the endemic fauna and flora of California's San Joaquin Desert, where biome conversi...
Chapter
Full-text available
Accumulating baseline knowledge of Samoa's’ reptiles is clearing a pathway forward in conserving and managing this largely regionally endemic fauna. We conducted a rapid biodiversity assessment (BIORAP) for reptiles at four main survey sites in Samoa between 16 July and 2 August 2016. Sites were located within three key biodiversity areas (KBAs) fo...
Article
Full-text available
We characterized the species richness, diversity, and distribution of amphibians and reptiles inhabiting El Monte Valley, a heavily disturbed, alluvium-filled basin within the lower San Diego River in Lakeside, California. This rare habitat type in coastal southern California is designated as a critical sand resource by the state of California and...
Article
We used microsatellites and mtDNA sequences to examine the mixed effects of geophysical, habitat, and contemporary urban barriers on the genetics of threatened Alameda Striped Racers (Coluber lateralis euryxanthus), a species with close ties to declining coastal scrub and chaparral habitat in the eastern San Francisco Bay area of California. We use...
Article
Full-text available
We used microsatellites and mtDNA sequences to examine the mixed effects of geophysical, habitat, and contemporary urban barriers on the genetics of threatened Alameda Striped Racers (Coluber lateralis euryxanthus), a species with close ties to declining coastal scrub and chaparral habitat in the eastern San Francisco Bay area of California. We use...
Article
Full-text available
We used microsatellites and mtDNA sequences to examine the mixed effects of geophysical, habitat, and contemporary urban barriers on the genetics of threatened Alameda Striped Racers (Coluber lateralis euryxanthus), a species with close ties to declining coastal scrub and chaparral habitat in the eastern San Francisco Bay area of California. We use...
Article
Full-text available
The California Red-legged Frog (Rana draytonii) is a threatened species in the United States that has undergone population declines, especially in southern California. Due to the lack of information on the status of Mexican populations, we surveyed for the presence of R. draytonii in Baja California and assessed possible threats to population persi...
Article
Full-text available
Multiple host introductions to the same non-native environment have the potential to complete life cycles of parasites incidentally transported with them. Our goal was to identify a recently detected parasitic flatworm in the invasive Brown Treesnake (Boiga irregularis) on the remote Pacific island of Guam. We considered possible factors influencin...
Article
Full-text available
Adaptation to different thermal environments has the potential to cause evolutionary changes that are sufficient to drive ecological speciation. Here, we examine whether climate-based niche divergence in lizards of the Plestiodon skiltonianus species complex is consistent with the outcomes of such a process. Previous work on this group shows that a...
Data
Table S3. Specimen data used in these analyses.
Data
Methods S1. Niche Models and niche differentiation. Results S1. Detailed results from paleo‐distributions and spatial overlap analyses. Results S2. Detailed results from niche differentiation tests. Figure S1. Niches and Niche Dynamics. Figure S2. Correlative niche models current and paleo distributions. Figure S3. Niche Overlap. Table S1. Bi...
Poster
Full-text available
We assessed the distribution and threats to Rana draytonii populations in Baja California, Mexico. Previous records dated from 1889 to 2006, with the Sierra San Pedro Mártir accounting for 90% of the records. We conducted surveys at 40 sites during 2013-2014. We observed R. draytonii at ten locations in three watersheds (San Rafael, San Telmo and S...
Chapter
Full-text available
In this study, we describe the current species composition of the herpetofauna on Nauru (2013), building on the data collected in Buden (2008). This included confirmation of previously known terrestrial reptiles, identifying undocumented species that may naturally occur on the island, and identifying newly established invasive species. A second obj...
Article
Full-text available
The brown treesnake (Boiga irregularis) population on the Pacific island of Guam has reached iconic status as one of the most destructive invasive species of modern times, yet no published works have used genetic data to identify a source population. We used DNA sequence data from multiple genetic markers and coalescent-based phylogenetic methods t...
Article
Full-text available
Abstract Much remains to be understood about the evolutionary history and contemporary landscape genetics of unarmored threespine stickleback in southern California, where populations collectively referred to as Gasterosteus aculeatus williamsoni have severely declined over the past 70? years and are now endangered. We used mitochondrial sequence a...
Article
Full-text available
Populations forming the edge of a species range are often imperiled by isolation and low genetic diversity, with proximity to human population centers being a major determinant of edge stability in modern landscapes. Since the 1960s, the California red-legged frog (Rana draytonii) has undergone extensive declines in heavily urbanized southern Calif...
Data
Figure S1. Unrooted neighbor‐joining tree based on the pairwise Cavalli‐Sforza chord distances. Table S1. Locus labels, primer sequences, fluorescent dyes, and multiplex PCR mixes for the 15 microsatellite sequences used in this study. Table S2. Summary statistics for the microsatellites developed for R. draytonii. Table S3. Pairwise F ST values...
Article
Full-text available
Comparative studies of major histocompatibility complex (MHC) genes across vertebrate species can reveal the evolutionary processes that shape the structure and function of immune regulatory proteins. In this study, we characterized MHC class I sequences from six frog species representing three anuran families (Hylidae, Centrolenidae and Ranidae)....