Persistence of historical population structure in an endangered species despite near‐complete biome conversion in California's San Joaquin Desert

Parsing variance by marker type: Testing biogeographic hypotheses and differential contribution of historical processes to population structure in a desert lizard

A fundamental goal of population genetic studies is to identify historical biogeographic patterns and understand the processes that generate them. However, localized demographic events can skew population genetic inference. Assessing populations with multiple types of genetic markers, each with unique mutation rates and responses to changes in population size, can help to identify potentially confounding population-specific demographic processes. Here, we compared population structure and connectivity inferred from microsatellites and restriction site-associated DNA loci among 17 populations of an arid-specialist lizard, the desert night lizard, Xantusia vigilis, in central California to test among historical processes structuring population genetic diversity. We found that both marker types yielded generally concordant insights into population genetic structure including a major phylogenetic break maintained between two populations separated by less than 10 km, suggesting that either marker type could be used to understand generalized demographic patterns across the region for management purposes. However, we also found that the effects of demography on marker discordance could be used to elucidate population histories and distinguish among competing biogeographic hypotheses. Our results suggest that comparisons of within-population diversity across marker types provide powerful opportunities for leveraging marker discordance, particularly for understanding the creation and maintenance of contact zones among clades.

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.

Genetic Rescue and the Plight of Ponui Hybrids

Long-term sustainable and resilient populations is a key goal of conservation. How to best achieve this is controversial. There are, for instance, polarized views concerning the fitness and conservation value of hybrid populations founded through multi-origin translocations. A classic example concerns Apteryx (kiwi) in New Zealand. The A. mantelli of Ponui Island constitute a hybrid population where the birds are highly successful in their island habitat. A key dilemma for managers is understanding the reason for this success. Are the hybrid birds of Ponui Island of “no future conservation value” as recently asserted, or do they represent an outstanding example of genetic rescue and an important resource for future translocations? There has been a paradigm shift in scientific thinking concerning hybrids, but the ecological significance of admixed genomes remains difficult to assess. This limits what we can currently predict in conservation science. New understanding from genome science challenges the sufficiency of population genetic models to inform decision making and suggests instead that the contrasting outcomes of hybridization, “outbreeding depression” and “heterosis,” require understanding additional factors that modulate gene and protein expression and how these factors are influenced by the environment. We discuss these findings and the investigations that might help us to better understand the birds of Ponui, inform conservation management of kiwi and provide insight relevant for the future survival of Apteryx.

Natural history collections are critical resources for contemporary and future studies of urban evolution

Urban environments are among the fastest changing habitats on the planet, and this change has evolutionary implications for the organisms inhabiting them. Herein, we demonstrate that natural history collections are critical resources for urban evolution studies. The specimens housed in these collections provide great potential for diverse types of urban evolution research, and strategic deposition of specimens and other materials from contemporary studies will determine the resources and research questions available to future urban evolutionary biologists. As natural history collections are windows into the past, they provide a crucial historical timescale for urban evolution research. While the importance of museum collections for research is generally appreciated, their utility in the study of urban evolution has not been explicitly evaluated. Here, we: (a) demonstrate that museum collections can greatly enhance urban evolution studies, (b) review patterns of specimen use and deposition in the urban evolution literature, (c) analyze how urban versus rural and native versus nonnative vertebrate species are being deposited in museum collections, and (d) make recommendations to researchers, museum professionals, scientific journal editors, funding agencies, permitting agencies, and professional societies to improve archiving policies. Our analyses of recent urban evolution studies reveal that museum specimens can be used for diverse research questions, but they are used infrequently. Further, although nearly all studies we analyzed generated resources that could be deposited in natural history collections (e.g., collected specimens), a minority (12%) of studies actually did so. Depositing such resources in collections is crucial to allow the scientific community to verify, replicate, and/or re-visit prior research. Therefore, to ensure that adequate museum resources are available for future urban evolutionary biology research, the research community-from practicing biologists to funding agencies and professional societies-must make adjustments that prioritize the collection and deposition of urban specimens.

Slender salamanders (genus Batrachoseps) reveal Southern California to be a center for the diversification, persistence, and introduction of salamander lineages

Background

The southern California biodiversity hotspot has had a complex geological history, with both plate tectonic forces and sea level changes repeatedly reconfiguring the region, and likely driving both lineage splittings and extinctions. Here we investigate patterns of genetic divergence in two species of slender salamanders (Plethodontidae: Batrachoseps) in this region. The complex geological history in combination with several organismal traits led us to predict that these species harbor multiple ancient mitochondrial lineages endemic to southern California. These species belong to a clade characterized by fine-scale mitochondrial structure, which has been shown to track ancient splits. Both focal species, Batrachoseps major and B. nigriventris, are relatively widely distributed in southern California, and estimated to have persisted there across millions of years. Recently several extralimital populations of Batrachoseps were found in the San Joaquin Valley of California, a former desert area that has been extensively modified for agriculture. The origins of these populations are unknown, but based on morphology, they are hypothesized to result from human-mediated introductions of B. major.

Methods

We sequenced the mitochondrial gene cytochrome b from a geographically comprehensive sampling of the mitochondrial lineages of B. major and B. nigriventris that are endemic to southern California. We used phylogenetic analyses to characterize phylogeographic structure and identify mitochondrial contact zones. We also included the San Joaquin Valley samples to test whether they resulted from introductions. We used a bootstrap resampling approach to compare the strength of isolation-by-distance in both Batrachoseps species and four other salamander species with which they co-occur in southern California.

Results

The northern lineage of B. major harbors at least eight deeply differentiated, geographically cohesive mitochondrial subclades. We identify geographic contact between many of these mtDNA lineages and some biogeographic features that are concordant with lineage boundaries. Batrachoseps nigriventris also has multiple deeply differentiated clades within the region. Comparative analyses highlight the smaller spatial scales over which mitochondrial divergence accumulates in Batrachoseps relative to most other salamander species in southern California. The extralimital populations of Batrachoseps from the San Joaquin Valley are assigned to B. major and are shown to result from at least two independent introductions from different source populations. We also suggest that B. major on Catalina Island, where it is considered native, may be the result of an introduction. Some of the same traits that facilitate the build-up of deep phylogeographic structure in Batrachoseps likely also contribute to its propensity for introductions, and we anticipate that additional introduced populations will be discovered.

Detecting geospatial patterns of Plasmodium falciparum parasite migration in Cambodia using optimized estimated effective migration surfaces

BACKGROUND

Understanding the genetic structure of natural populations provides insight into the demographic and adaptive processes that have affected those populations. Such information, particularly when integrated with geospatial data, can have translational applications for a variety of fields, including public health. Estimated effective migration surfaces (EEMS) is an approach that allows visualization of the spatial patterns in genomic data to understand population structure and migration. In this study, we developed a workflow to optimize the resolution of spatial grids used to generate EEMS migration maps and applied this optimized workflow to estimate migration of Plasmodium falciparum in Cambodia and bordering regions of Thailand and Vietnam.

METHODS

The optimal density of EEMS grids was determined based on a new workflow created using density clustering to define genomic clusters and the spatial distance between genomic clusters. Topological skeletons were used to capture the spatial distribution for each genomic cluster and to determine the EEMS grid density; i.e., both genomic and spatial clustering were used to guide the optimization of EEMS grids. Model accuracy for migration estimates using the optimized workflow was tested and compared to grid resolutions selected without the optimized workflow. As a test case, the optimized workflow was applied to genomic data generated from P. falciparum sampled in Cambodia and bordering regions, and migration maps were compared to estimates of malaria endemicity, as well as geographic properties of the study area, as a means of validating observed migration patterns.

RESULTS

Optimized grids displayed both high model accuracy and reduced computing time compared to grid densities selected in an unguided manner. In addition, EEMS migration maps generated for P. falciparum using the optimized grid corresponded to estimates of malaria endemicity and geographic properties of the study region that might be expected to impact malaria parasite migration, supporting the validity of the observed migration patterns.

CONCLUSIONS

Optimized grids reduce spatial uncertainty in the EEMS contours that can result from user-defined parameters, such as the resolution of the spatial grid used in the model. This workflow will be useful to a broad range of EEMS users as it can be applied to analyses involving other organisms of interest and geographic areas.

Historical Population Size Change and Differentiation of Relict Populations of the Endangered Giant Kangaroo Rat

From a conservation management perspective it is important to understand how genetic diversity is partitioned across a species' range, including 1) identification of evolutionarily distinct units versus those recently isolated through anthropogenic activities and 2) the relative genetic contributions among components of fragmented (meta)populations. To address these questions, we investigated the phylogeography and metapopulation structure among relict populations of the endangered giant kangaroo rat (Dipodomys ingens) in the highly altered San Joaquin Desert Ecosystem. This keystone species underwent a ~97% range reduction over the past century, resulting in a current range that is highly fragmented, with 2 dominant northern and southern populations occurring 150 km apart. We sequenced >800 bp of mitochondrial DNA and genotyped 17 nuclear microsatellites in >275 D. ingens to assess the evolutionary relationship of these populations as well as the genetic structure within the northern metapopulation. A Bayesian Skyline Plot indicated that the species experienced a demographic expansion toward the end of the Pleistocene, with a recent population decline. Northern and southern D. ingens split 1857-13 443 years ago, prior to the massive conversion of the San Joaquin Valley to irrigated agriculture. We recommend that the northern and southern populations of D. ingens be re-classified as distinct population segments under the United States Endangered Species Act. We also observed population structure and asymmetrical migration within northern D. ingens where the Tumey Hills acted as a source contributing gene flow to all peripheral populations. This emphasized the importance of this location in the conservation of the metapopulation as a whole.

Habitat restoration opportunities, climatic niche contraction, and conservation biogeography in California's San Joaquin Desert

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 continues to drive habitat loss in the SJD, even as marginal farmland is retired. Over the next decades a combination of factors, including salinization, climate change, and historical groundwater overdraft, are projected to lead to the retirement of more than 2,000 km2 of farmland in the SJD. To promote strategic habitat protection and restoration, we conducted a quantitative assessment of habitat loss and fragmentation, habitat suitability, climatic niche stability, climate change impacts, habitat protection, and reintroduction opportunities for an umbrella species of the SJD, the endangered blunt-nosed leopard lizard (Gambelia sila). We use our suitability models, in conjunction with modern and historical land use maps, to estimate the historical and modern rate of habitat loss to development. The estimated amount of habitat lost since the species became protected under endangered species law in 1967 is greater than the total amount of habitat currently protected through public ownership and conservation easement. We document climatic niche contraction and associated range contraction away from the more mesic margins of the species' historical distribution, driven by the anthropogenic introduction of exotic grasses and forbs. The impact of exotic species on G. sila range dynamics appears to be still unfolding. Finally, we use NASA fallowed area maps to identify 610 km2 of fallowed or retired agricultural land with high potential to again serve as habitat. We discuss conservation strategies in light of the potential for habitat restoration and multiple drivers of ongoing and historical habitat loss.

Evaluating methods to visualize patterns of genetic differentiation on a landscape

With advances in sequencing technology, research in the field of landscape genetics can now be conducted at unprecedented spatial and genomic scales. This has been especially evident when using sequence data to visualize patterns of genetic differentiation across a landscape due to demographic history, including changes in migration. Two recent model-based visualization methods that can highlight unusual patterns of genetic differentiation across a landscape, SpaceMix and EEMS, are increasingly used. While SpaceMix's model can infer long-distance migration, EEMS' model is more sensitive to short-distance changes in genetic differentiation, and it is unclear how these differences may affect their results in various situations. Here, we compare SpaceMix and EEMS side by side using landscape genetics simulations representing different migration scenarios. While both methods excel when patterns of simulated migration closely match their underlying models, they can produce either un-intuitive or misleading results when the simulated migration patterns match their models less well, and this may be difficult to assess in empirical data sets. We also introduce unbundled principal components (un-PC), a fast, model-free method to visualize patterns of genetic differentiation by combining principal components analysis (PCA), which is already used in many landscape genetics studies, with the locations of sampled individuals. Un-PC has characteristics of both SpaceMix and EEMS and works well with simulated and empirical data. Finally, we introduce msLandscape, a collection of tools that streamline the creation of customizable landscape-scale simulations using the popular coalescent simulator ms and conversion of the simulated data for use with un-PC, SpaceMix and EEMS.