Conserving a wetland butterfly: quantifying early lifestage survival through seasonal flooding, adult nectar, and habitat preference

Conservation of once thought extinct populations of Lycaena xanthoides in western Oregon will require specific information of how the butterfly interacts with its now rare wetland habitat. Three experiments were conducted to yield information directly applicable to wetland restoration work: (1) to quantify the survival of L. xanthoides eggs laid on inundated plants, (2) to quantify adult nectar preferences, (3) to investigate the role of adult resources and how butterflies assess habitat quality. Survival of eggs laid on inundated plants was nearly seven times lower than the survival of eggs laid on uninundated plants, indicating that eggs laid on plants that are seasonally flooded are a population sink. Adult L. xanthoides preferred an endemic native nectar plant, Grindelia integrifolia × nana, as an adult resource and used it approximately 88% of the time while other butterfly species preferred to nectar on the non-native Mentha pulegium. Adult L. xanthoides had a significantly greater short-term recapture rate in two restored study sites that had a high relative amount of Grindelia integrifolia × nana compared to a degraded site that lacked the preferred nectar source. Based on the results from the three small experiments, restoration of wetlands for L. xanthoides should concentrate plantings of host plant in non-flooded areas and propagate conspicuous patches of the preferred nectar plant.     

THE FEMALE GAMETOPHYTE OF THREE SPECIES OF GRINDELIA AND OF PRIONOPSIS CILIATA (COMPOSITAE)

In the four species studied, Grindelia stricta ssp. blakei, G. arizonica, G. lanceolata, and Prionopsis ciliata (Haplopappus ciliatus), the female gametophyte develops according to the Polygonum (normal) type from the chalazal megaspore of a row of four. In most cases only two antipodal cells are formed, the micropylar one originally containing two nuclei. The number of nuclei increases in both cells; one or both antipodal cells typically grow laterally into the integument, often extending to near the surface of the ovule. This resembles the condition previously reported in Grindelia squarrosa. Since the four species of Grindelia have similar antipodal outgrowths, such outgrowths may be considered typical for this genus. The fact that Prionopsis resembles Grindelia in regard to outgrowths from the antipodal cells and differs in this respect from typical Haplopappus helps to justify its separation from Haplopappus, and perhaps its suggested merger with Grindelia.     

Protecting a single endangered species and meeting multiple conservation goals: an approach with Guaiacum sanctum in Yucatan Peninsula,Mexico

Aim New protected areas should consider safeguarding high conservation value sites based on multiple criteria and not just the presence of a single endangered or charismatic species. However, the extent to which complementary criteria coincide is usually unknown. We use the case of Guaiacum sanctum (Zygopyllaceae), an endangered timber tree species, to explore whether the protection of forests where this species is most abundant would meet other complementary conservation goals, such as capturing regional plant biodiversity, protecting other threatened/endemic species or safeguarding ecosystem services. Location Yucatan Peninsula, southern Mexico. Methods We conducted an analysis of the structure, composition and diversity of tree communities (including stems ≥5 cm dbh) at eight G. sanctum forest sites. We identified endemic and threatened tree species and quantified above‐ground tree biomass and carbon storage in these G. sanctum forests. Results Guaiacum sanctum forests contain 35–59 tree species on plots as small as 1000 m². The species composition of tree communities changed rapidly (high β‐diversity) across soil boundaries and rainfall regimes. Twenty‐one endemic and eight threatened tree species were recorded in our inventories. Individuals of G. sanctum represented up to 55% of the above‐ground carbon for trees ≥5 cm dbh. The high basal area of G. sanctum forests plus the high wood density, abundance, large size and longevity (more than 500 years) of G. sanctum and other tree species enhance the potential importance of these forests for carbon storage. Main conclusions A conservation strategy focused on protecting important populations of G. sanctum in the Yucatan Peninsula would have significant co‐benefits for conservation of regional tree species biodiversity and provision of critical ecosystem services. Our study illustrates a multiple criteria approach useful for the selection of areas with high conservation value on the basis of endemic, threatened species, species richness and ecosystem services.     

Late-successional biological soil crusts in a biodiversity hotspot: an example of congruency in species richness

Understanding the biodiversity of functionally important communities in Earth’s ecosystems is vital in the apportionment of limited ecosystem management funds and efforts. In southern California shrublands, which lie in a global biodiversity hotspot, biological soil crusts (BSCs) confer critical ecosystem services; however, their biodiversity remains unknown. In this study, six sites (n = 4 each, 25 m²) were established along a mediterranean shrubland environmental gradient in southern California. Here, the biodiversity of all BSC-forming lichens and bryophytes was evaluated, related to environmental traits along the gradient, and compared to species richness among North American ecosystems supporting BSCs (data from previous studies). In total, 59 BSC-forming lichens and bryophytes were observed, including the very rare Sarcogyne crustacea, a rare moss, and five endemic lichen species. Over half (61%) of the species observed were found at a single site. Along the gradient, species evenness of late-successional BSC was related to dew point and elevation, and both evenness and richness were related to distance to coast. Using an ordination analysis, five distinct late-successional BSC communities were identified: Riversidian, Spike moss, Casperian, Alisian, and Lagunian. Twenty-five lichens and 19 bryophytes are newly reported for North American BSC-forming organisms, now comprising ~1/2 of the North American total. BSCs in North American hot and cold deserts were approximately 4.0 and 2.4 times less species rich than BSCs found in southern California shrublands, respectively. Given the anthropogenic impacts on quality and distribution of California mediterranean shrublands, our results show that these sites represent important refugia of BSC species in this globally important region.     

Plantlet recruitment is the key demographic transition in invasion by Kalanchoe daigremontiana

Biological invasions have a great impact on biodiversity and ecosystem functioning worldwide. Kalanchoe daigremontiana is a noxious invasive plant in arid zones. Besides being toxic for domestic animals and wildlife, this species inhibits the growth of native plants. Its rapid proliferation in Cerro Saroche National Park (Venezuela) is of great concern because this area hosts several species endemic to the scarce arid zones in the Caribbean. The traits of K. daigremontiana that contribute to its invasive success are unknown. Based on empirical data, we derived a stage structured, stochastic and density-dependent model, to identify characteristics relevant for its establishment. Sensitivity analyses revealed that the establishment of K. daigremontiana depends exclusively on plantlet recruitment. Because asexual plantlets reproduce in less than 1 year populations are able to increase rapidly during the initial phases of invasion, when extinction risks are higher. Sexual seedlings, on the contrary, require a minimum of 3 years to reproduce. As a result, seedling recruitment contributes little to the transient dynamics of the population and therefore cannot warrant the successful establishment of the species. Simulations of various management strategies show that eradication through plant removal may only be achieved if harvest begins shortly after introduction. If a rapid response is not possible, reducing the survival and growth rates of plantlets through biological control is an alternative option. Thus, a strict control of dispersal of plantlets by humans and a continuous monitoring of new invasions should be the first priority for reducing further impact on native species.     

Production, use and fate of Chilean brown seaweeds: re-sources for a sustainable fishery

Chile is an important producer of brown seaweeds representing 10% of world supply. Landings of Chilean kelp fluctuated between 40,000 t.year⁻¹ in the early ‘80s to 250,000 t.year⁻¹ more recently. Commercialized algae come from natural populations and no mass-cultures of involved species have been established. Four species of brown algae are commercially collected in the country: Lessonia trabeculata, L. nigrescens, Macrocystis pyrifera and M. integrifolia. Since 2000, the demand of alginate sources and food for cultivated abalones dramatically raised the harvesting of these species. Direct evaluations of Lessonia spp. and Macrocystis standing-stocks were made along 700 km of coast in northern Chile. Lessonia spp. estimated populations exceed 900,000 t, whereas M. integrifolia does not exceed 300 t. The insights provided indicate that sustainability of Chilean kelp subjected to intense harvesting would require management programs including the following bio-ecological recommendations: (1) to harvest the entire plant including the holdfast; (2) to harvest plants larger than 20 cm in diameter; (3) to harvest plants sparsely, selecting mayor specimens; (4) rotation of harvesting areas; and (5) for Macrocystis, to cut the canopy 1–2 m from the surface. They must be implemented in a National Program of Kelp Management, elaborated by government, scientists, fisherman, and industry.     

Disease management at the wildlife‐livestock interface: Using whole‐genome sequencing to study the role of elk in Mycobacterium bovis transmission in Michigan,USA

The role of wildlife in the persistence and spread of livestock diseases is difficult to quantify and control. These difficulties are exacerbated when several wildlife species are potentially involved. Bovine tuberculosis (bTB), caused by Mycobacterium bovis, has experienced an ecological shift in Michigan, with spillover from cattle leading to an endemically infected white‐tailed deer (deer) population. It has potentially substantial implications for the health and well‐being of both wildlife and livestock and incurs a significant economic cost to industry and government. Deer are known to act as a reservoir of infection, with evidence of M. bovis transmission to sympatric elk and cattle populations. However, the role of elk in the circulation of M. bovis is uncertain; they are few in number, but range further than deer, so may enable long distance spread. Combining Whole Genome Sequences (WGS) for M. bovis isolates from exceptionally well‐observed populations of elk, deer and cattle with spatiotemporal locations, we use spatial and Bayesian phylogenetic analyses to show strong spatiotemporal admixture of M. bovis isolates. Clustering of bTB in elk and cattle suggests either intraspecies transmission within the two populations, or exposure to a common source. However, there is no support for significant pathogen transfer amongst elk and cattle, and our data are in accordance with existing evidence that interspecies transmission in Michigan is likely only maintained by deer. This study demonstrates the value of whole genome population studies of M. bovis transmission at the wildlife‐livestock interface, providing insights into bTB management in an endemic system.     

Mismatches between supply and demand in wildlife tourism: Insights for assessing cultural ecosystem services

Assessing cultural ecosystem services provided by biodiversity requires a combination of ecological and social approaches. In this study, we investigated the capacity of large African mammal species to provide the cultural ecosystem service of wildlife tourism by using a supply and demand framework. First, we tested the relationship between supply and demand for large mammal species in wildlife tourism. Second, we tested whether the trophic level and body size of mammals influenced the mismatch between supply and demand, and whether the patterns of mismatches were consistent among four protected areas (PAs) in three Southern African countries. To quantify supply of species, we counted large mammals along 196 five km road transects within the four PAs; to estimate demand, we gathered 651 face-to-face questionnaires of wildlife tourists and distinguished between their expectation and hope to see specific species. Results show that a higher supply of large mammal species increased the expectation to see a species (linear regression slope β = 0.28, p < 0.01), whereas supply did not affect the hopes to see a specific species (β = −0.04, p = 0.63). Analyses of mismatches revealed that predator species were more demanded in relation to their supply than ungulates. Finally, we found that the demands of wildlife tourists for mammal species in relation to their supply were consistent across the four PAs. Supply-demand analyses reveal that species’ traits, in particular trophic level, shape the hopes of wildlife tourists to see specific mammal species. We propose that the quantification of supply-demand mismatches can be used to identify charismatic species and relevant species’ traits, and can be applied for wildlife tourism assessments within as well as across regions. Supply-demand analyses provide a useful framework and deliver indicators for better assessing cultural ecosystem services involving wildlife and nature-based tourism, and can be used for conservation management.     

Population genomics study for the conservation management of the endangered shrub Abeliophyllum distichum

Natural monuments are IUCN Category III protected areas that play an important role in biodiversity conservation as they provide species refuge and allow species migration. Despite their status, natural monuments are often confined to cultural and fragmented landscapes due to anthropogenic land-use demands. In this population genomic study, we surveyed 11 populations of the endemic shrub Abeliophyllum distichum Nakai (Oleaceae), including five natural monument habitats, covering its range-wide distribution in South Korea. Using 2,254 SNPs as markers, our results showed a mean expected heterozygosity (He) of 0.319, with populations in the central distribution showing significantly higher He than those at the periphery. There was no significant heterozygote deficiency and inbreeding among studied populations overall (F_{IS =} ?0.098), except for a single natural monument population (GS-NM147). Population structure and differentiation was moderate to high (F_ST?=?0.196), while recent gene flow between populations appeared weak, which can be attributed to the fragmented distribution and the outcrossing mating system of the heterostylous plant. Based on these findings, we provide suggestions for the population conservation and management of this endangered species.

     

Population genetic structure of the endemic rosewoods Dalbergia cochinchinensis and D. oliveri at a regional scale reflects the Indochinese landscape and life‐history traits

Indochina is a biodiversity hot spot and harbors a high number of endemic species, most of which are poorly studied. This study explores the genetic structure and reproductive system of the threatened endemic timber species Dalbergia cochinchinensis and Dalbergia oliveri using microsatellite data from populations across Indochina and relates it to landscape characteristics and life‐history traits. We found that the major water bodies in the region, Mekong and Tonle Sap, represented barriers to gene flow and that higher levels of genetic diversity were found in populations in the center of the distribution area, particularly in Cambodia. We suggest that this pattern is ancient, reflecting the demographic history of the species and possible location of refugia during earlier time periods with limited forest cover, which was supported by signs of old genetic bottlenecks. The D. oliveri populations had generally high levels of genetic diversity (mean H_e = 0.73), but also strong genetic differentiation among populations (global G_ST = 0.13), while D. cochinchinensis had a moderate level of genetic diversity (mean H_e = 0.55), and an even stronger level of differentiation (global G_ST = 0.25). These differences in genetic structure can be accounted for by a higher level of gene flow in D. oliveri due to a higher dispersal capacity, but also by the broader distribution area for D. oliveri, and the pioneer characteristics of D. cochinchinensis. This study represents the first detailed analysis of landscape genetics for tree species in Indochina, and the found patterns might be common for other species with similar ecology.     

Genetic variation in Plethodon cinereus and Plethodon hubrichti from in and around a contact zone

Climate change poses several challenges to biological communities including changes in the frequency of encounters between closely related congeners as a result of range shifts. When climate change leads to increased hybridization, hybrid dysfunction or genetic swamping may increase extinction risk—particularly in range‐restricted species with low vagility. The Peaks of Otter Salamander, Plethodon hubrichti, is a fully terrestrial woodland salamander that is restricted to ~18 km of ridgeline in the mountains of southwestern Virginia, and its range is surrounded by the abundant and widespread Eastern Red‐backed Salamander, Plethodon cinereus. In order to determine whether these two species are hybridizing and how their range limits may be shifting, we assessed variation at eight microsatellite loci and a 1,008 bp region of Cytochrome B in both species at allopatric reference sites and within a contact zone. Our results show that hybridization between P. hubrichti and P. cinereus either does not occur or is very rare. However, we find that diversity and differentiation are substantially higher in the mountaintop endemic P. hubrichti than in the widespread P. cinereus, despite similar movement ability for the two species as assessed by a homing experiment. Furthermore, estimation of divergence times between reference and contact zone populations via approximate Bayesian computation is consistent with the idea that P. cinereus has expanded into the range of P. hubrichti. Given the apparent recent colonization of the contact zone by P. cinereus, future monitoring of P. cinereus range limits should be a priority for the management of P. hubrichti populations.     

Segregation of male‐sterility alleles across a species boundary

Hybrid zones may serve as bridges permitting gene flow between species, including alleles influencing the evolution of breeding systems. Using greenhouse crosses, we assessed the likelihood that a hybrid zone could serve as a conduit for transfer of nuclear male‐sterility alleles between a gynodioecious species and a hermaphroditic species with very rare females in some populations. Segregation patterns in progeny of crosses between rare females of hermaphroditic Schiedea menziesii and hermaphroditic plants of gynodioecious Schiedea salicaria heterozygous at the male‐sterility locus, and between female S. salicaria and hermaphroditic plants from the hybrid zone, were used to determine whether male‐sterility was controlled at the same locus in the parental species and the hybrid zone. Segregations of females and hermaphrodites in approximately equal ratios from many of the crosses indicate that the same nuclear male‐sterility allele occurs in the parent species and the hybrid zone. These rare male‐sterility alleles in S. menziesii may result from gene flow from S. salicaria through the hybrid zone, presumably facilitated by wind pollination in S. salicaria. Alternatively, rare male‐sterility alleles might result from a reversal from gynodioecy to hermaphroditism in S. menziesii, or possibly de novo evolution of male sterility. Phylogenetic analysis indicates that some species of Schiedea have probably evolved separate sexes independently, but not in the lineage containing S. salicaria and S. menziesii. High levels of selfing and expression of strong inbreeding depression in S. menziesii, which together should favour females in populations, argue against a reversal from gynodioecy to hermaphroditism in S. menziesii.     

Plant fecundity and pre-dispersal reproductive losses in a common and a rare Euphorbia species (Euphorbiaceae)

Comparative studies on the reproductive biology of closely related plant species have provided valuable information to understand the causes and consequences of common-rare differences with possible applications for the management of threatened populations. The magnitude and spatiotemporal variability of seed production and pre-dispersal reproductive losses were studied for 3 years in the rare endemic Euphorbia welwitschii and in its widespread congener E. characias. The factors responsible for a decrease in potential seed production in these species were the lack of a functional ovary in the cyathium, ovary and fruit abortion, seed predation by insects and seed abortion. In E. characias, the moth Acroclita subsequana was also responsible for minor reproductive losses. The proportion of male cyathia varied significantly between seasons, populations and species, being consistently higher in E. characias than in E. welwitschii. Reproductive losses that resulted in ovary, fruit and seed abortion affected mostly the endemic species and were heavier in the populations located near the sea due to local adverse climatic conditions. Seed predators inflicted higher reproductive losses to the endemic species than to its widespread congener and their impact was particularly heavy at Risco. The two Euphorbia species differed markedly in cyathia production, with E. welwitschii producing systematically a lower number of cyathia than its widespread congener and this, together with higher levels of ovary, fruit and seed abortion, seemed to be the main reasons for the low reproductive output of this rare species.     

Conservation genetics of two island endemic Ribes spp. (Grossulariaceae) of Sardinia: survival or extinction?

Measuring levels of population genetic diversity is an important step for assessing the conservation status of rare or endangered plant species and implementing appropriate conservation strategies. Populations of Ribes multiflorum subsp. sandalioticum and R. sardoum, two endangered endemic species from Sardinia, representing the whole genus on the island, were investigated using ISSR and SSR markers to determine levels and structure of genetic variability in their natural populations. Results indicated medium to low genetic diversity at the population level: Nei's gene diversity for ISSR markers ranged from 0.0840 to 0.1316; the expected heterozygosity (H_E) for SSR ranged from 0.4281 to 0.7012. In addition, only one remnant population of R. sardoum showed a high level of inbreeding, in accordance with its very small size. Regarding the structure of the six R. sandalioticum populations, both principal coordinates analysis (PCoA) and STRUCTURE analysis of ISSR and SSR data highlighted low population structure, although two populations appeared to be clearly distinct from the others. The genetic pattern of the two taxa associated with their different ecological positions indicated resilience of R. sandalioticum populations in fresh and humid habitats and uncertain future resistance for the residual R. sardoum population in xeric calcareous stands. Hence, this study highlights the importance of an integrated conservation approach (genetic plus in situ and ex situ conservation studies/measures) for activating management programmes in these endemic and threatened taxa that can be considered as crop wild relatives of cultivated Ribes species.     

Genetic diversity and distribution patterns of diploid and polyploid hybrid water frog populations (Pelophylax esculentus complex) across Europe

Polyploidization is a rare yet sometimes successful way for animals to rapidly create geno‐ and phenotypes that may colonize new habitats and quickly adapt to environmental changes. In this study, we use water frogs of the Pelophylax esculentus complex, comprising two species (Pelophylax lessonae, genotype LL; Pelophylax ridibundus, RR) and various diploid (LR) and triploid (LLR, LRR) hybrid forms, summarized as P. esculentus, as a model for studying recent hybridization and polyploidization in the context of speciation. Specifically, we compared the geographic distribution and genetic diversity of diploid and triploid hybrids across Europe to understand their origin, maintenance and potential role in hybrid speciation. We found that different hybrid and parental genotypes are not evenly distributed across Europe. Rather, their genetic diversity is structured by latitude and longitude and the presence/absence of parental species but not of triploids. Highest genetic diversity was observed in central and eastern Europe, the lowest in the northwestern parts of Europe. This gradient can be explained by the decrease in genetic diversity during postglacial expansion from southeastern glacial refuge areas. Genealogical relationships calculated on the basis of microsatellite data clearly indicate that hybrids are of multiple origin and include a huge variety of parental genomes. Water frogs in mixed‐ploidy populations without any parental species (i.e. all‐hybrid populations) can be viewed as evolutionary units that may be on their way towards hybrid speciation. Maintenance of such all‐hybrid populations requires a continuous exchange of genomes between diploids and triploids, but scenarios for alternative evolutionary trajectories are discussed.     

Use of simple remote sensing tools to expedite surveys for rare tiger beetles (Insecta: Coleoptera: Cicindelidae)

Tiger beetles (Insecta: Coleoptera: Cicindelidae) often occupy small patches of suitable habitat in otherwise unsuitable landscapes. Such patches are easily overlooked, which may lead to underestimates of both the number of occurrences and the overall population size. In this study, simple World Wide Web-based tools (Google Earth and Microsoft Terraserver) were used to search high-resolution satellite imagery for patches of suitable habitat for globally and regionally rare tiger beetles on a 3,278 ha wildlife refuge in Maryland, USA. This tract is largely forested but contains scattered small open areas of sand and clay soils that are potential habitat for tiger beetles of conservation concern. Visual inspection of remotely sensed imagery resulted in the identification of 19 potential habitat patches, 15 of which yielded tiger beetle populations when surveyed on the ground. The number of species of tiger beetles recorded from this tract was increased from 3 to 8 and two new sites were discovered for the state sensitive species Cicindela scutellaris rugifrons Dejean. In addition, a small population of C. splendida Hentz was discovered, a species last reported from Maryland in 1948. The technique described here shows great promise for locating small patches of potential tiger beetle habitat in otherwise unsuitable landscapes.     

Congruent population genetic structure but differing depths of divergence for three alpine stoneflies with similar ecology and geographic distributions

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Comparison of a common and rare species of Mimosa (Mimosaceae) in Central Brazil

Abstract The aim of this study was to verify differences in the biology of a common widespread species (Mimosa claussenii Benth.) and three rare endemics (Mimosa decorticans Barneby, M. heringeri Barneby, and M. setosissima Taub.). We studied three populations of M. claussenii and one population of each rare species at four localities in central Brazil. We compared the population structure, phenology, fruit set, seed predation, germination, establishment and root/shoot ratio in these six populations. The endemic species occurred in higher densities and smaller individuals were more abundant. When in sympatry, the rare and common species showed a significant negative correlation of density. Mimosa claussenii occurred in drier and rocky environments, whereas M. decorticans and M. setosissima occurred in moister habitats. Rare species had higher levels of fruit set, more viable seeds per individual, and heavier seeds. Mimosa setosissima had the highest level of germination and establishment rate, but did not survive away from its endemism centre. The common species had a higher root/shoot ratio. Overall, the biological aspects studied indicated an advantage in reproductive biology for the rare in relation to the common species. The small geographical range of the rare species may be related to edaphic isolation and climatic changes in the Quaternary.     

Heterogeneous microcommunities and ecosystem multifunctionality in seminatural grasslands under three management modes

Increasing attention has been paid to the relationship between biodiversity and ecosystem functioning (BEF) because of the rapid increase in species loss. However, over the past 20 years, most BEF studies only focused on the effect of species diversity on one or a few ecosystem functions, and only a few studies focused on ecosystem multifunctionality (i.e., the simultaneous provision of several ecosystem functions). Grassland ecosystems have important economic, environmental, and esthetic value; thus, this study focused on the heterogeneous microcommunities in grasslands under three management modes. The multifunctionality index (M‐index) was assessed at community and microcommunity scales, and the relationship between species diversity and multifunctionality was investigated. The communities were found to be respectively composed of one, three, and six microcommunities in grazing, clipping, and enclosure management, based on a two‐way indicator species analysis (TWINSPAN) and detrended correspondence analysis (DCA) for community structure. Biodiversity and soil indicators showed an apparent degradation of the grazing community, which had the worst M‐index. Clipping and enclosure communities showed no significant difference in biodiversity indices, soil variables, and M‐index; however, these indices were clearly different among microcommunities. Therefore, the microcommunity scale may be suitable to investigate the relationship between vegetation and multifunctionality in seminatural grassland ecosystems. Dominant species richness had more explanatory power for ecosystem multifunctionality than subdominant species richness, rare species richness, and the number of all species. Therefore, it is important to distinguish the role and rank of different species in the species richness–multifunctionality model; otherwise, the model might include redundant and unclear information. Communities with more codominant species whose distribution is also even might have better multifunctionality.     

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

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 predisturbance landscapes. Despite near‐complete biome conversion, such opportunities may still exist for the endemic fauna and flora of California's San Joaquin Desert, but comprehensive genetic data sets are lacking for nearly all species in the region. To fill this knowledge gap, we studied the rangewide population structure of the endangered blunt‐nosed leopard lizard Gambelia sila, a San Joaquin Desert endemic, using restriction site‐associated DNA (RAD), microsatellite and mtDNA data to test whether admixture patterns and estimates of effective migration surfaces (EEMS) can identify land areas with high population connectivity prior to the conversion of native xeric habitats. Clustering and phylogenetic analyses indicate a recent shared history between numerous isolated populations and EEMS reveals latent signals of corridors and barriers to gene flow over areas now replaced by agriculture and urbanization. Conflicting histories between the mtDNA and nuclear genomes are consistent with hybridization with the sister species G. wislizenii, raising important questions about where legal protection should end at the southern range limit of G. sila. Comparative analysis of different data sets also adds to a growing list of advantages in using RAD loci for genetic studies of rare species. We demonstrate how the results of this work can serve as an evolutionary guidance tool for managing endemic, arid‐adapted taxa in one of the world's most compromised landscapes.