Geology topics

Jonathan Q. Richmond

Publications and source records attributed to Jonathan Q. Richmond.

At least 19 recordsLinked to original sources

USGS2025

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. We confirmed an east–west phyletic division within the A. elegans complex that correlates with an ecotone between the Sonoran and Chihuahuan Deserts and pinpoint the separation to a ∼20 km area in southeastern Arizona, USA. Individuals recognized as A. e. occidentalis do not form a genetically cohesive unit within a more inclusive western clade that is sister to the endemic Arizona pacata in Baja California, México. We synonymize four subspecies circumscribed by the western clade and recognize a new species Arizona occidentalis to re-align the taxonomy with the phylogeographic structure. Most of the diversity within A. occidentalis occurs in California, with three major lineages corresponding separate desert biomes. We revise the conservation units within A. occidentalis to mirror these lineages and address concerns regarding habitat loss in transitional environments along the western edge of its range. This work underscores the importance of aligning taxonomy, evolutionary identity, and management units to design the most effective conservation strategies.

Molecular Phylogenetics and Evolution↗

USGS2024

Effects of temporal hydrologic shifts on the population biology of an endangered freshwater fish in a dryland river ecosystem

Species occupying dryland river ecosystems often experience “boom-and-bust” demographic cycles that coincide with shifts in habitat availability. Knowing whether declines are within natural thresholds versus those caused by acute human disturbance is critical for managing protected species. We investigated temporal shifts in abundance and habitat use of an endangered population of the threespine stickleback Gasterosteus aculeatus in southern California, where a Mediterranean climate leads to ephemeral habitat in one of the regions' least hydrologically modified rivers, the Santa Clara River. We conducted population surveys over a period of below-average rainfall in the upper watershed in Soledad Canyon, with predefined reaches surveyed multiple times per year to capture different hydrologic conditions. Abundances were stable across years but varied significantly depending on location, with some reaches remaining dry and others drying seasonally to varying degrees. Occupancy models showed that the presence of stable perennial reaches, drying regime, and other site-specific factors were important predictors of habitat use, and that certain reaches may be key to ensuring source-sink dynamics as flow dissipates over the dry season. Low occupancy in two sections was driven by different predominant mechanisms, one by diel cycles of evapotranspiration and the other by cattails ( Typha spp.), with both having greater effects during the hotter, drier parts of the year. As dryland river ecosystems are vulnerable to the effects of anthropogenic-induced climate change, this study demonstrates how temporal monitoring can delimit dry-state benchmarks for improving management interventions (i.e., translocation and habitat restoration) for protected species under conditions that are predicted to worsen in the coming years.

California↗

USGS2024

Variation in dietary ecology of two invasive American Bullfrog (Lithobates catesbeianus) populations in Southern California

Invasive American Bullfrogs (Lithobates catesbeianus) are a threat to native species in riparian ecosystems worldwide. They are indiscriminate predators consuming both vertebrate and invertebrate prey, negatively affecting biodiversity. Documenting the diet and feeding ecology of invasive L. catesbeianus can help management agencies identify affected species and facilitate eradication efforts. We present a dietary analysis of two invasive L. catesbeianus populations over multiple breeding seasons (2016–2020), elucidating ontogenetic changes in diet and dietary differences between sexes and habitats. This is the first study to analyze dietary variation from contemporary populations of invasive L. catesbeianus occupying different watersheds in Southern California, an area where their invasion presents acute conservation challenges. Our analysis of 667 gut contents shows that adult females had more prey in their guts than adult males, even though male and female body size was not significantly different. Adults were more likely than juveniles to consume vertebrate prey, and juveniles were more likely than adults to have empty stomachs. We also found that invasive Red Swamp Crayfish (Procambarus clarkii), made up a substantial portion of the diet of adult L. catesbeianus at the site where they were present. These results provide an important ecological context for designing mitigation actions that ameliorate the impacts of invasive L. catesbeianus.

California↗

USGS2023

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. cranial horns, dorsoventrally compressed body, cryptic coloration, and blood squirting from the orbital sinuses), and status as Species of Special Concern in California. Rangewide decline since the early 20th century, the basis of its conservation status, has been driven mainly by habitat conversion, over-collecting, and invasion of a non-native ant that displaces its native ant prey base. Here, we report on a scaffold-level genome assembly for P. blainvillii as part of the California Conservation Genomics Project (CCGP), produced using Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology. The de novo assembly has 78 scaffolds, a total length of ~2.21 Gb, a scaffold N50 length of ~352 Mb, and BUSCO score of 97.4%. This is the second species of Phrynosoma for which a reference genome has been assembled and represents a considerable improvement in terms of contiguity and completeness. Combined with the landscape genomics data being compiled by the CCGP, this assembly will help strategize efforts to maintain and/or restore local genetic diversity, where interventions like genetic rescue, translocation, and strategic land preservation may be the only means by which P. blainvillii and other low-vagility species can survive in the fragmented habitats of California.

California↗

USGS2023

Skinks of Oceania, New Guinea, and Eastern Wallacea: An underexplored biodiversity hotspot

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 conservation needs. Methods: We compiled a list of all skink species occurring in the region and their threat categories designated by the International Union for Conservation of Nature. We used available genetic sequences deposited in the National Center for Biotechnology Information’s GenBank to generate a phylogeny of the region’s skinks. We then assessed their diversity within geographical sub-divisions and compared to other reptile taxa in the region. Key results: Approximately 300 species of skinks occur in ONGEW, making it the second largest global hotspot of skink diversity following Australia. Many phylogenetic relationships remain unresolved, and many species and genera are in need of taxonomic revision. One in five species are threatened with extinction, a higher proportion than almost all reptile families in the region. Conclusions: ONGEW contain a large proportion of global skink diversity on <1% of the Earth’s landmass. Many are endemic and face risks such as habitat loss and invasive predators. Yet, little is known about them, and many species require taxonomic revision and threat level re-assessment. Implications: The skinks of ONGEW are a diverse yet underexplored group of terrestrial vertebrates, with many species likely facing extreme risks in the near future. Further research is needed to understand the threats they face and how to protect them.

Pacific Conservation Biology↗

USGS2023

Prioritizing the risk and management of introduced species in a landscape with high indigenous biodiversity

Risk analysis protocols for prioritizing the management of non-native species are numerous, yet few incorporate risk and management in the same analysis or accommodate a broad diversity of taxa outside of a specific geographic area. We adapted a protocol that accounts for these factors to address non-native animal species in the Southern California/Northern Baja California Coast Ecoregion near the international border in San Diego County, an area with high indigenous biodiversity and high numbers of species of conservation concern. This stepwise, semi-quantitative protocol is applicable to any animal group in any predefined geographic area, relies on consensus-building among taxonomic experts, and has been vetted through previous use and in peer-reviewed literature. Our results show that the final prioritization was driven mainly by management feasibility, with top-ranked species having multitrophic effects that favor other non-native invaders over native residents. Conditions within the assessment area required some modification to the protocol as it was originally designed, namely a shift in emphasis from eradication to control, given that eradication is implausible for most non-native species in the assessment area. We call attention to taxon-specific issues that surfaced during the analysis, identify areas for improvement in this first-ever risk assessment for invasive animal species in the Natural Communities Conservation Plan/Habitat Conservation Plan (NCCP/HCP) reserve system of San Diego County, and provide suggestions for further refinement of the protocol. This study builds on the effort to standardize risk analysis for invasive species globally, given that many of the same invaders present threats to indigenous biodiversity worldwide.

California↗

USGS2022

Genetic structure and historic demography of endangered unarmoured threespine stickleback at southern latitudes signals a potential new management approach

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 unarmoured threespine stickleback ( Gasterosteus aculeatus williamsoni ). This subspecies, an unusual morph lacking the typical lateral bony plates of the G. aculeatus complex, occurs at arid southern latitudes in the eastern Pacific Ocean and survives in only three inland locations. Managers have lacked molecular data to answer basic questions about the ancestry and genetic distinctiveness of unarmoured populations. These data could be used to prioritize conservation efforts. We sampled G. aculeatus from 36 localities and used microsatellites and whole genome data to place unarmoured populations within the broader evolutionary context of G. aculeatus across southern California/northern Baja California. We identified three genetic groups with none consisting solely of unarmoured populations. Unlike G. aculeatus at northern latitudes, where Pleistocene glaciation has produced similar historical demographic profiles across populations, we found markedly different demographics depending on sampling location, with inland unarmoured populations showing steeper population declines and lower heterozygosity compared to low armoured populations in coastal lagoons. One exception involved the only high elevation population in the region, where the demography and alleles of unarmoured fish were similar to low armoured populations near the coast, exposing one of several cases of artificial translocation. Our results suggest that the current “management-by-phenotype” approach, based on lateral plates, is incidentally protecting the most imperilled populations; however, redirecting efforts toward evolutionary units, regardless of phenotype, may more effectively preserve adaptive potential.

Baja California, California↗

USGS2022

Natural and anthropogenic landscape factors shape functional connectivity of an ecological specialist in urban Southern California

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 species, the Blainville's horned lizard ( Phrynosoma blainvillii ), in the urbanized landscape of the Greater Los Angeles Area in Southern California, USA. Using single nucleotide polymorphism data, we assessed genetic structure among populations occurring at the interface of two abutting evolutionary lineages, and at a fine scale among habitat fragments within the heavily urbanized area. Based on the ecology of P. blainvillii , we predicted which environmental variables influence population structure and gene flow and used gravity models to distinguish among hypotheses to best explain population connectivity. Our results show evidence of admixture between two evolutionary lineages and strong population genetic structure across small habitat fragments. We also show that topography, microclimate, and soil and vegetation types are important predictors of functional connectivity, and that anthropogenic disturbance, including recent fire history and urban development, are key factors impacting contemporary population dynamics. Examining how natural and anthropogenic sources of landscape variation affect contemporary population genetics is critical to understanding how to best manage sensitive species in a rapidly changing landscape.

California↗

USGS2022

Reference genome of the California glossy snake, Arizona elegans occidentalis: A declining California Species of Special Concern

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 California, one of which is afforded state-level protection based on the extensive loss and modification of its preferred alluvial coastal scrub and inland desert habitat. We report the first genome assembly of A. elegans occidentalis as part of the California Conservation Genomics Project (CCGP). Consistent with the reference genome strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technologies to produce a de novo assembled genome. The assembly comprises a total of 140 scaffolds spanning 1,842,602,218 base pairs, has a contig NG50 of 61 Mb, a scaffold NG50 of 136 Mb, and a BUSCO complete score of 95.9%, and is one of the most complete snake genome assemblies. The A. e. occidentalis genome will be a key tool for understanding the genomic diversity and the basis of adaptations within this species and close relatives within the hyperdiverse snake family Colubridae.

California↗

USGS2022

Taking the leap: A binational translocation effort to close the 420-km gap in the Baja California lineage of the California red-legged frog (Rana draytonii)

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 specific considerations to increase success, as environmental gradients may pose different constraints on population establishment and persistence in different parts of the range. Here we report on ongoing, genetically informed translocations of a threatened amphibian, California red-legged frog ( Rana draytonii ), from Baja California, México, to extirpated parts of the range in southern California in the United States, where contemporary stressors related to urbanization, invasive species, and aridification add to the natural environmental challenges already present for amphibians at this ‘warm edge’ of the range. We describe the collaborative binational planning required to jumpstart the effort, the fine-tuning of protocols for collection, transport, headstarting, and release of individuals, and results of multiple translocations, where time will tell whether the successes to date have reached their full potential. The steps outlined in this paper can serve as a template to inform future conservation translocations of imperiled amphibians across the U.S./México border, where the phylogenetics, historical biogeography and future habitat availability of a focal species are blind to political boundaries and critical to guiding recovery actions across the range.

Baja California, California↗

USGS2021

Impacts of a non-indigenous ecosystem engineer, the American beaver (Castor canadensis), in a biodiversity hotspot

Non-native species having high per capita impacts in invaded communities are those that modulate resource availability and alter disturbance regimes in ways that are biologically incompatible with the native biota. In areas where it has been introduced by humans, American beaver ( Castor canadensis ) is an iconic example of such species due to its capacity to alter trophic dynamics of entire ecosystems and create new invasional pathways for other non-native species. The species is problematic in several watersheds within the Southern California-Northern Baja California Coast Ecoregion, a recognized hotspot of biodiversity, due to its ability to modify habitat in ways that favor invasive predators and competitors over the region's native species and habitat. Beaver was deliberately introduced across California in the mid-1900s and generally accepted as non-native to the region up to the early 2000s; however, articles promoting the idea that beaver may be a natural resident have gained traction in recent years, due in large part to the species' charismatic nature rather than by presentation of sound evidence. Here, 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 to show that no evidence exists that beaver arrived by any means other than deliberate human introduction. Managing this ecosystem engineer has potential to reduce the richness and abundance of other non-native species because the novel, engineered habitat now supporting these species would diminish in beaver-occupied watersheds. At the same time, hydrologic functionality would shift toward more natural, ephemeral conditions that favor the regions' native species while suppressing the dominance of the most insidious invaders.

California↗

USGS2021

Range eclipse leads to tenuous survival of a rare lizard species on a barrier atoll

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 in the southern Mariana Islands, where for > 20 years it had been considered possibly extirpated. Endemic to the Marianas, E. slevini has declined throughout its range and no longer occurs on as many as five islands from which it was historically known, most likely because of interactions with invasive species and loss of native forest. Our results show that individuals from Dåno′, the type locality for E. slevini , are genetically similar but not identical to E. slevini on Sarigan and Alamagan to the north, and that E. slevini is a close evolutionary relative to another congener in the southern Marianas that is currently recognized as E moia atrocostata but probably represents an undescribed species in this archipelago. We also show that other, more broadly distributed species of Emoia occurring on Dåno′ are distant relatives to E. slevini and the Mariana lineage of E. atrocostata , providing further evidence of the distinctiveness of these taxa. The rediscovery of E. slevini on Dåno′ following rodent eradication and culling of a population of monitor lizards suggests that management of invasive species is key to the recovery of this skink in the Mariana Islands, and that a range eclipse on the larger neighbouring island of Guam best explains why the rediscovery took place at the periphery of the species’ historic range. A Chamorro abstract can be found in the supplementary material.

Dåno′, Guam↗

USGS2021

New faunal records from a World Heritage Site in danger: Rennell Island, Solomon Islands

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 terrestrial vertebrates of East Rennell, a UNESCO World Heritage Site in Solomon Islands. We documented 56 species, including 15 squamates, 13 mammals, and 38 birds, and present four new vertebrate records for the island: Stephan's emerald dove ( Chalcophaps stephani ), Maluku myotis ( Myotis moluccarum ), littoral skink ( Emoia atrocostata ) and brahminy blindsnake ( Indotyphlops braminus ). East Rennell was designated a World Heritage site for its significant on-going ecological and biological processes, and importance for the study of island biogeography. The new records presented here provide evidence that continued field studies combined with DNA analysis will continue to uncover even greater endemic biodiversity. Rennell is currently experiencing major habitat destruction in parts of the island that are not under World Heritage protection, and we anticipate collateral damage will likely extend into protected areas. Our survey also underscores the incredible vertebrate biodiversity that stands to be lost unless conservation actions and local community needs are intertwined to promote beneficial outcomes on both fronts.

Pacific Science↗

USGS2021

Predictability of invasive Argentine ant distribution across Mediterranean ecoregions of southern California

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 tested for effects of ecoregion, vegetation, soil moisture, habitat edge type (i.e., moisture source), and distance from edges on the presence of the invasive Argentine ant Linepithema humile in San Diego County, California, a region with high indigenous biodiversity and numerous rare and protected species. Our results showed an inverse relationship between the presence of native ant species and the presence of the Argentine ant across ecoregions, with the latter reaching peak abundance in the coastal terrace. Argentine ant presence was negatively associated with distance from all edge types regardless of location, but the magnitude of this effect varied among ecoregions. In the xeric foothill and inland valleys, the probability of occurrence was nearly 0 at distances of 200 m and 750 m from moisture edges, respectively, whereas in the coastal terrace, the probability remained above 0.80 at distances up to 1.25 km. When compared to previous studies at different spatial scales, these findings provide an alternative perspective on the invasiveness of the Argentine ant at the landscape level. Our results further suggest that efforts to control spread in regions with a Mediterranean climate may be more successful in inland areas, where the ant is likely to have lower environmental tolerance and native ant species may be better able to generate biotic resistance. In contrast, different tactics and expectations may be necessary for coastal areas, where the same constraints are diminished or absent.

California↗

USGS2021

Genetic considerations for rewilding the San Joaquin Desert

Genetic data are a powerful and important tool for guiding rewilding efforts and for monitoring the recovery outcomes of those efforts. When used in conjunction with historic species’ distribution records and predictive habitat suitability modeling, genetic information adds a key piece to the puzzle that will increase the probability of successful ecosystem restoration.

California↗

USGS2020

Influence of niche breadth and position on the historical biogeography of seafaring scincid lizards

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-Australasia composed of both endemic and widespread species that differ in niche occupancy. We used molecular data and phylogeographical diffusion models to estimate the timing and patterns of range expansion, and ancestral reconstruction methods to infer shifts in ecology. We show evidence of multidirectional spread from a centre of origin in western Micronesia, and that the phyletic diversity of the group is derived from a putative habitat specialist that survives in the littoral zone. This species is composed of paraphyletic lineages that represent stages or possible endpoints in the continuum toward speciation. Several descendant species have transitioned to either strand or interior forest habitat, but only on remote islands with depauperate terrestrial faunas. Our results suggest that the atrocostata group might be in the early phases of a Wilsonian taxon cycle and that the capacity to tolerate salt stress has promoted dispersal and colonization of remote oceanic islands. Divergence itself, however, is largely driven by geographical isolation rather than shifts in ecology.

Biological Journal of the Linnean Society↗

USGS2019

Noninvasive identification of cryptic herpetofauna from fecal samples: A novel approach pairing conservation dog surveys and genetic analysis

Noninvasive fecal sampling combined with genetic analysis is a powerful technique allowing the study of elusive or otherwise difficult to monitor species without the need for direct contact. While 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 sila) is an endangered species endemic to the San Joaquin Desert of California. Presently, acquiring data on G. sila for research and management involves more traditional methods such as live capture to obtain tissue samples for DNA analysis, or observation via visual surveys, which are also used for regulatory monitoring in accordance with wildlife agency protocols. Here we describe an innovative approach for gathering additional information, that combines use of conservation detection dogs trained to locate G. sila scat samples with genetic analysis for identifying and distinguishing among sympatric lizard species. We developed two PCR assays that produce fluorescently labelled amplicons of species-specific fragment length for six lizard species in the study area. Using these assays we genetically identifed to species 78% (255 of 327) of samples collected by dog-handler teams across four years. The majority of the genetically identifed samples (82.4%; 210 of 255) were confirmed as originating from G. sila. Beyond the immediate application of these techniques for the study and monitoring of G. sila, our ability to recover usable DNA and to differentiate among a diverse group of lizards highlights the broad potential of our methodology for noninvasive sampling in reptiles.

California↗

USGS2018

Insular biogeographic origins and high phylogenetic distinctiveness for a recently depleted lizard fauna from Christmas Island, Australia

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 Sunda Shelf, this fauna mostly comprises species from clades centred on the more distant regions of Wallacea, the Pacific and Australia (more than 1000 km east). The three most divergent lineages show Miocene (approx. 23–5 Ma) divergences from sampled relatives; and have recently become extinct or extinct in the wild, likely owing to the recent introduction of a southeast Asian snake ( Lycodon capucinus ). Insular distributions, deep phylogenetic divergence and recent decline suggest that rather than dispersal ability or recent origins, environmental and biotic barriers have impeded these lineages from diversifying on the continental Sunda Shelf, and thereby, reinforced faunal differentiation across Wallace's Line. Our new phylogenetically informed perspective further highlights the rapid loss of ancient lineages that has occurred on Christmas Island, and underlines how the evolutionary divergence and vulnerability of many island-associated lineages may continue to be underestimated.

Christmas Island↗