Testing Taxon Tenacity of Tortoises: evidence for a geographical selection gradient at a secondary contact zone

Divergence in Regulatory Regions and Gene Duplications May Underlie Chronobiological Adaptation in Desert Tortoises

Many cellular processes and organismal behaviours are time-dependent, and asynchrony of these phenomena can facilitate speciation through reinforcement mechanisms. The Mojave and Sonoran desert tortoises (Gopherus agassizii and G. morafkai respectively) reside in adjoining deserts with distinct seasonal rainfall patterns and they exhibit asynchronous winter brumation and reproductive behaviours. We used whole genome sequencing of 21 individuals from the two tortoise species and an outgroup to understand genes potentially underlying these characteristics. Genes within the most diverged 1% of the genome (FST ≥ 0.63) with putatively functional variation showed extensive divergence in regulatory elements, particularly promoter regions. Such genes related to UV nucleotide excision repair, mitonuclear and homeostasis functions. Genes mediating chronobiological (cell cycle, circadian and circannual) processes were also among the most highly diverged regions (e.g., XPA and ZFHX3). Putative promoter variants had significant enrichment of genes related to regulatory machinery (ARC-Mediator complex), suggesting that transcriptional cascades driven by regulatory divergence may underlie the behavioural differences between these species, leading to asynchrony-based prezygotic isolation. Further investigation revealed extensive expansion of respiratory and intestinal mucins (MUC5B and MUC5AC) within Gopherus, particularly G. morafkai. This expansion could be a xeric-adaptation to water retention and/or contribute to differential Mycoplasma agassizii infection rates between the two species, as mucins help clear inhaled dust and bacterial. Overall, results highlight the diverse array of genetic changes underlying divergence, adaptation and reinforcement during speciation.

Move it or lose it: Predicted effects of culverts and population density on Mojave desert tortoise (Gopherus agassizii) connectivity

Roadways and railways can reduce wildlife movements across landscapes, negatively impacting population connectivity. Connectivity may be improved by structures that allow safe passage across linear barriers, but connectivity could be adversely influenced by low population densities. The Mojave desert tortoise is threatened by habitat loss, fragmentation, and population declines. The tortoise continues to decline as disturbance increases across the Mojave Desert in the southwestern United States. While underground crossing structures, like hydrological culverts, have begun receiving attention, population density has not been considered in tortoise connectivity. Our work asks a novel question: How do culverts and population density affect connectivity and potentially drive genetic and demographic patterns? To explore the role of culverts and population density, we used agent-based spatially explicit forward-in-time simulations of gene flow. We constructed resistance surfaces with a range of barriers to movement and representative of tortoise habitat with anthropogenic disturbance. We predicted connectivity under variable population densities. Simulations were run for 200 non-overlapping generations (3400 years) with 30 replicates using 20 microsatellite loci. We evaluated population genetic structure and diversity and found that culverts would not entirely negate the effects of linear barriers, but gene flow improved. Our results also indicated that density is important for connectivity. Low densities resulted in declines regardless of the landscape barrier scenario (> 75% population census size, > 97% effective population size). Results from our simulation using current anthropogenic disturbance predicted decreased population connectivity over time. Genetic and demographic effects were detectable within five generations (85 years) following disturbance with estimated losses in effective population size of 69%. The pronounced declines in effective population size indicate this could be a useful monitoring metric. We suggest management strategies that improve connectivity, such as roadside fencing tied to culverts, conservation areas in a connected network, and development restricted to disturbed areas.

‘Unscrambling’ the drivers of egg production in Agassiz’s desert tortoise: climate and individual attributes predict reproductive output

The ‘bet hedging’ life history strategy of long-lived iteroparous species reduces short-term reproductive output to minimize the risk of reproductive failure over a lifetime. For desert-dwelling ectotherms living in variable and unpredictable environments, reproductive output is further influenced by precipitation and temperature via effects on food availability and limits on activity. We assembled multiple (n = 12) data sets on egg production for the threatened Agassiz’s desert tortoise Gopherus agassizii across its range and used these data to build a range-wide predictive model of annual reproductive output as a function of annual weather variation and individual-level attributes (body size and prior-year reproductive status). Climate variables were more robust predictors of reproductive output than individual-level attributes, with overall reproductive output positively related to prior-year precipitation and an earlier start to the spring activity season, and negatively related to spring temperature extremes (monthly temperature range in March-April). Reproductive output was highest for individuals with larger body sizes that reproduced in the previous year. Expected annual reproductive output from 1990-2018 varied from 2-5 to 6-12 eggs female-1 yr-1 , with a weak decline in expected reproductive output over this time (p = 0.02). Climate-driven environmental variation in expected reproductive output was highly correlated across all 5 Recovery Units for this species (Pearson’s r > 0.9). Overall, our model suggests that climate change could strongly impact the reproductive output of Agassiz’s desert tortoise, and could have a negative population-level effect if precipitation is significantly reduced across the species’ range as predicted under some climate models.

Quantifying development to inform management of Mojave and Sonoran desert tortoise habitat in the American southwest

Two tortoise species native to the American southwest have experienced significant habitat loss from development and are vulnerable to ongoing threats associated with continued development. Mojave desert tortoises Gopherus agassizii are listed as threatened under the US Endangered Species Act, and Sonoran desert tortoises G. morafkai are protected in Arizona (USA) and Mexico. Substantial habitat for both species occurs on multiple-use public lands, where development associated with traditional and renewable energy production, recreation, and other activities is likely to continue. Our goal was to quantify development to inform and evaluate actions implemented to protect and manage desert tortoise habitat. We quantified a landscape-level index of development across the Mojave and Sonoran desert tortoise ranges using models of potential habitat for each species (152485 total observations). We used 13 years of Mojave desert tortoise monitoring data (4732 observations) to inform the levels and spatial scales at which tortoises may be affected by development. Most (66-70%) desert tortoise habitat has some development within 1 km. Development levels on desert tortoise habitat are lower inside versus outside areas protected by actions at national, state, and local levels, suggesting that protection efforts may be having the desired effects and providing a needed baseline for future effectiveness evaluations. Of the relatively undeveloped desert tortoise habitat, 43% (74030 km2) occurs outside of existing protections. These lands are managed by multiple federal, state, and local entities and private landowners, and may provide opportunities for future land acquisition or protection, including as mitigation for energy development on public lands.

A spatially explicit hierarchical model to characterize population viability

Many of the processes that govern the viability of animal populations vary spatially, yet population viability analyses (PVAs) that account explicitly for spatial variation are rare. We develop a PVA model that incorporates autocorrelation into the analysis of local demographic information to produce spatially explicit estimates of demography and viability at relatively fine spatial scales across a large spatial extent. We use a hierarchical, spatial, autoregressive model for capture-recapture data from multiple locations to obtain spatially explicit estimates of adult survival (ϕ_ad ), juvenile survival (ϕ_juv ), and juvenile-to-adult transition rates (ψ), and a spatial autoregressive model for recruitment data from multiple locations to obtain spatially explicit estimates of recruitment (R). We combine local estimates of demographic rates in stage-structured population models to estimate the rate of population change (λ), then use estimates of λ (and its uncertainty) to forecast changes in local abundance and produce spatially explicit estimates of viability (probability of extirpation, P_ex ). We apply the model to demographic data for the Sonoran desert tortoise (Gopherus morafkai) collected across its geographic range in Arizona. There was modest spatial variation in λ^ (0.94-1.03), which reflected spatial variation in ϕ^ad (0.85-0.95), ϕ^juv (0.70-0.89), and ψ^ (0.07-0.13). Recruitment data were too sparse for spatially explicit estimates; therefore, we used a range-wide estimate ( R^  = 0.32 1-yr-old females per female per year). Spatial patterns in demographic rates were complex, but ϕ^ad , ϕ^juv , and λ^ tended to be lower and ψ^ higher in the northwestern portion of the range. Spatial patterns in P_ex varied with local abundance. For local abundances >500, P_ex was near zero (<0.05) across most of the range after 100 yr; as abundances decreased, however, P_ex approached one in the northwestern portion of the range and remained low elsewhere. When local abundances were <50, western and southern populations were vulnerable (P_ex  > 0.25). This approach to PVA offers the potential to reveal spatial patterns in demography and viability that can inform conservation and management at multiple spatial scales, provide insight into scale-related investigations in population ecology, and improve basic ecological knowledge of landscape-level phenomena.

Landscape limits gene flow and drives population structure in Agassiz's desert tortoise (Gopherus agassizii)

Distance, environmental heterogeneity and local adaptation can strongly influence population structure and connectivity. Understanding how these factors shape the genomic landscape of threatened species is a major goal in conservation genomics and wildlife management. Herein, we use thousands (6,859) of single nucleotide polymorphism markers and spatial data from hundreds of individuals (n = 646) to re-evaluate the population structure of Agassiz's desert tortoise (Gopherus agassizii). Analyses resolve from 4 to 8 spatially well-defined clusters across the range. Western, central, and southern populations within the Western Mojave recovery unit are consistent throughout, while analyses sometimes merge other recovery units depending on the level of clustering. Causal modeling consistently associates genetic connectivity with least-cost distance, based on multiple landscape features associated with tortoise habitat, better than geographic distance. Some features include elevation, soil depth, rock volume, precipitation, and vegetation coverage, suggesting that physical, climatic, and biotic landscape features have played a strong evolutionary role restricting gene flow between populations. Further, 12 highly differentiated outlier loci have associated functions that may be involved with neurogenesis, wound healing, lipid metabolism, and possibly vitellogenesis. Together, these findings have important implications for recovery programs, such as translocations, population augmentation, reproduction in captivity and the identification of ecologically important genes, opening new venues for conservation genomics in desert tortoises.

Development of a Species Status Assessment Process for Decisions under the U.S. Endangered Species Act

Decisions under the U.S. Endangered Species Act (ESA) require scientific input on the risk that the species will become extinct. A series of critiques on the role of science in ESA decisions have called for improved consistency and transparency in species risk assessments and clear distinctions between science input and policy application. To address the critiques and document the emerging practice of the U.S. Fish and Wildlife Service (USFWS), we outline an assessment process based on principles and practices of risk and decision analyses that results in a scientific report on species status. The species status assessment (SSA) process has three successive stages: 1) document the life history and ecological relationships of the species in question to provide the foundation for the assessment, 2) describe and hypothesize causes for the current condition of the species, and 3) forecast the species' future condition. The future condition refers to the ability of a species to sustain populations in the wild under plausible future scenarios. The scenarios help explore the species' response to future environmental stressors and to assess the potential for conservation to intervene to improve its status. The SSA process incorporates modeling and scenario planning for prediction of extinction risk and applies the conservation biology principles of representation, resiliency, and redundancy to evaluate the current and future condition. The SSA results in a scientific report distinct from policy application, which contributes to streamlined, transparent, and consistent decision-making and allows for greater technical participation by experts outside of the USFWS, for example, by state natural resource agencies. We present two case studies based on assessments of the eastern massasauga rattlesnake Sistrurus catenatus and the Sonoran Desert tortoise Gopherus morafkai to illustrate the process. The SSA builds upon the past threat-focused assessment by including systematic and explicit analyses of a species' future response to stressors and conservation, and as a result, we believe it provides an improved scientific analysis for ESA decisions.

The evolution of different maternal investment strategies in two closely related desert vertebrates

We compared egg size phenotypes and tested several predictions from the optimal egg size (OES) and bet-hedging theories in two North American desert-dwelling sister tortoise taxa, Gopherus agassizii and G. morafkai, that inhabit different climate spaces: relatively unpredictable and more predictable climate spaces, respectively. Observed patterns in both species differed from the predictions of OES in several ways. Mean egg size increased with maternal body size in both species. Mean egg size was inversely related to clutch order in G. agassizii, a strategy more consistent with the within-generation hypothesis arising out of bet-hedging theory or a constraint in egg investment due to resource availability, and contrary to theories of density dependence, which posit that increasing hatchling competition from later season clutches should drive selection for larger eggs. We provide empirical evidence that one species, G. agassizii, employs a bet-hedging strategy that is a combination of two different bet-hedging hypotheses. Additionally, we found some evidence for G. morafkai employing a conservative bet-hedging strategy. (e.g., lack of intra- and interclutch variation in egg size relative to body size). Our novel adaptive hypothesis suggests the possibility that natural selection favors smaller offspring in late-season clutches because they experience a more benign environment or less energetically challenging environmental conditions (i.e., winter) than early clutch progeny, that emerge under harsher and more energetically challenging environmental conditions (i.e., summer). We also discuss alternative hypotheses of sexually antagonistic selection, which arise from the trade-offs of son versus daughter production that might have different optima depending on clutch order and variation in temperature-dependent sex determination (TSD) among clutches. Resolution of these hypotheses will require long-term data on fitness of sons versus daughters as a function of incubation environment, data as yet unavailable for any species with TSD.

Assessing models of speciation under different biogeographic scenarios; an empirical study using multi-locus and RNA-seq analyses

Evolutionary biology often seeks to decipher the drivers of speciation, and much debate persists over the relative importance of isolation and gene flow in the formation of new species. Genetic studies of closely related species can assess if gene flow was present during speciation, because signatures of past introgression often persist in the genome. We test hypotheses on which mechanisms of speciation drove diversity among three distinct lineages of desert tortoise in the genus Gopherus. These lineages offer a powerful system to study speciation, because different biogeographic patterns (physical vs. ecological segregation) are observed at opposing ends of their distributions. We use 82 samples collected from 38 sites, representing the entire species' distribution and generate sequence data for mtDNA and four nuclear loci. A multilocus phylogenetic analysis in *BEAST estimates the species tree. RNA‐seq data yield 20,126 synonymous variants from 7665 contigs from two individuals of each of the three lineages. Analyses of these data using the demographic inference package ∂a∂i serve to test the null hypothesis of no gene flow during divergence. The best‐fit demographic model for the three taxa is concordant with the *BEAST species tree, and the ∂a∂i analysis does not indicate gene flow among any of the three lineages during their divergence. These analyses suggest that divergence among the lineages occurred in the absence of gene flow and in this scenario the genetic signature of ecological isolation (parapatric model) cannot be differentiated from geographic isolation (allopatric model).