Taylor Edwards

The dazed and confused identity of Agassiz’s land tortoise, Gopherus agassizii (Testudines, Testudinidae) with the description of a new species, and its consequences for conservation

Abstract We investigate a cornucopia of problems associated with the identity of the desert tortoise, Gopherus agassizii (Cooper). The date of publication is found to be 1861, rather than 1863. Only one of the three original cotypes exists, and it is designated as the lectotype of the species. Another cotype is found to have been destroyed in the 1906 San Francisco earthquake and subsequent fire. The third is lost. The lectotype is genetically confirmed to be from California, and not Arizona, USA as sometimes reported. Maternally, the holotype of Gopherus lepidocephalus (Ottley & Velázques Solis. 1989) from the Cape Region of Baja California Sur, Mexico is also from the Mojavian population of the desert tortoise, and not from Tiburon Island, Sonora, Mexico as previously proposed. A suite of characters serve to diagnose tortoises west and north of the Colorado River, the Mojavian population, from those east and south of the river in Arizona, USA, and Sonora and Sinaloa, Mexico, the Sonoran population. Species recognition is warranted and because Gopherus lepidocephalus is from the Mojavian population, no names are available for the Sonoran species. Thus, a new species, Gopherus morafkai sp. n., is named and this action reduces the distribution of Gopherus agassizii to only 30% of its former range. This reduction has important implications for the conservation and protection of Gopherus agassizii, which may deserve a higher level of protection.

Implications of anthropogenic landscape change on inter-population movements of the desert tortoise (Gopherus agassizii)

In the Sonoran Desert of North America, populations of the desert tortoise (Gopherus agassizii) occur in rocky foothills throughout southwestern Arizona and northwestern Mexico. Although tortoise populations appear to be isolated from each other by low desert valleys, individuals occasionally move long distances between populations. Increasingly, these movements are hindered by habitat fragmentation due to anthropogenic landscape changes. We used molecular techniques and radiotelemetry to examine movement patterns of desert tortoises in southern Arizona. We collected blood samples from 170 individuals in nine mountain ranges and analyzed variability in seven microsatellite loci to determine genetic differentiation among populations. Gene flow estimates between populations indicate that populations exchanged individuals historically at a rate greater than one migrant per generation, and positive correlation between genetic and geographic distance of population pairs suggests that the limiting factor for gene flow among populations is isolation by distance. Life history traits of the desert tortoise, a long-lived species with delayed sexual maturity, may severely constrain the ability of small populations to respond to disturbances that increase adult mortality. Historic gene flow estimates among populations suggests that recovery of declining populations may rely heavily on the immigration of new individuals from adjacent mountain ranges. Management strategies compatible with the evolutionary history of gene flow among disjunct populations will help ensure the long-term persistence of Sonoran desert tortoise populations.

A Genetic Assessment of the Recovery Units for the Mojave Population of the Desert Tortoise, Gopherus agassizii

ABSTRACT In the 1994 Recovery Plan for the Mojave population of the desert tortoise, Gopherus agassizii, the US Fish and Wildlife Service established 6 recovery units by using the best available data on habitat use, behavior, morphology, and genetics. To further assess the validity of the recovery units, we analyzed genetic data by using mitochondrial deoxyribonucleic acid (mtDNA) sequences and nuclear DNA microsatellites. In total, 125 desert tortoises were sampled for mtDNA and 628 for microsatellites from 31 study sites, representing all recovery units and desert regions throughout the Mojave Desert in California and Utah, and the Colorado Desert of California. The mtDNA revealed a great divergence between the Mojave populations west of the Colorado River and those occurring east of the river in the Sonoran Desert of Arizona. Some divergence also occurred between northern and southern populations within the Mojave population. The microsatellites indicated a low frequency of private alleles and a significant correlation between genetic and geographic distance among 31 sample sites, which was consistent with an isolation-by-distance population structure. Regional genetic differentiation was complementary to the recovery units in the Recovery Plan. Most allelic frequencies in the recovery units differed. An assignment test correctly placed most individuals to their recovery unit of origin. Of the 6 recovery units, the Northeastern and the Upper Virgin River units showed the greatest differentiation; these units may have been relatively more isolated than other areas and should be managed accordingly. The Western Mojave Recovery Unit, by using the new genetic data, was redefined along regional boundaries into the Western Mojave, Central Mojave, and Southern Mojave recovery units. Large-scale translocations of tortoises and habitat disturbance throughout the 20th century may have contributed to the observed patterns of regional similarity.

Diet of Crotalus lepidus klauberi (Banded Rock Rattlesnake)

Abstract We describe the diet of Crotalus lepidus klauberi (Banded Rock Rattlesnake) using samples collected in the field and from museum specimens, as well as several records from unpublished reports. Most records (approximately 91%) were from the northern Sierra Madrean Archipelago. Diet consisted of 55.4% lizards, 28.3% scolopendromorph centipedes, 13.8% mammals, 1.9% birds, and 0.6% snakes. Sceloporus spp. comprised 92.4% of lizards. Extrapolation suggests that Sceloporus jarrovii represents 82.3% of lizard records. Diet was independent of geographic distribution (mountain range), sex, source of sample (stomach vs. intestine/feces), and age class. However, predator snout–vent length differed significantly among prey types; snakes that ate birds were longest, followed in turn by those that ate mammals, lizards, and centipedes. Collection date also differed significantly among prey classes; the mean date for centipede records was later than the mean date for squamate, bird, or mammal records. We found no difference in the elevation of collection sites among prey classes.

Polyandry and multiple paternities in the threatened Agassiz's desert tortoise, Gopherus agassizii

We used data from 17 to 20 microsatellite markers to investigate the incidence of multiple paternities in wild Agassiz’s desert tortoises, Gopherus agassizii. Neonates were sampled from clutches of eggs laid by wild mothers in nesting enclosures at Edwards Air Force Base and at the Marine Corps Air Ground Combat Center, California. We genotyped 28 clutches from 26 females sampling an average of six neonates per clutch. The number of paternal alleles was used to determine the minimum number of sires for each clutch. Based on conservative criteria requiring evidence from at least two loci to determine multiple paternity, a minimum of 64% of females were polyandrous, while a minimum of 57% of clutches were sired by multiple males. This formed one of the highest incidences of multiple paternities recorded to date in any species of tortoise. The high number of microsatellite loci involved in the analyses allowed detection of multiple paternities in clutches where this may have been missed if fewer loci were used. Our results highlighted the potential pitfalls of quantitatively comparing paternity studies based on differing sampling strategies. Finally, we summarized the conservation implications of the high rate of multiple paternities in this threatened species.

Tracing Genetic Lineages of Captive Desert Tortoises in Arizona

Abstract We genotyped 180 captive desert tortoises (Gopherus agassizii) from Kingman (n  =  45), Phoenix (n  =  113), and Tucson (n  =  22), Arizona, USA, to determine if the genetic lineage of captives is associated with that of wild tortoises in the local area (Sonoran Desert). We tested all samples for 16 short tandem repeats and sequenced 1,109 base pairs of mitochondrial DNA (mtDNA). To determine genetic origin, we performed assignment tests against a reference database of 997 desert tortoise samples collected throughout the Mojave and Sonoran Deserts. We found that >40% of our Arizona captive samples were genetically of Mojave Desert or hybrid origin, with the percentage of individuals exhibiting the Mojave genotype increasing as the sample locations approached the California, USA, border. In Phoenix, 11.5% were Sonoran–Mojave crosses, and 8.8% were hybrids between desert tortoise and Texas tortoise (G. berlandieri). Our findings present many potential implications for wild tortoises in the Sonoran Desert of Arizona. Escaped or released captive tortoises with Mojave or hybrid genotypes have the potential to affect the genetic composition of Sonoran wild populations. Genotyping captive desert tortoises could be used to inform the adoption process, and thereby provide additional protection to native desert-tortoise populations in Arizona.

The desert tortoise trichotomy: Mexico hosts a third, new sister-species of tortoise in the Gopherus morafkai-G. agassizii group.

Abstract Desert tortoises (Testudines; Testudinidae; Gopherus agassizii group) have an extensive distribution throughout the Mojave, Colorado, and Sonoran desert regions. Not surprisingly, they exhibit a tremendous amount of ecological, behavioral, morphological and genetic variation. Gopherus agassizii was considered a single species for almost 150 years but recently the species was split into the nominate form and Morafka’s desert tortoise, Gopherus morafkai, the latter occurring south and east of the Colorado River. Whereas a large body of literature focuses on tortoises in the United States, a dearth of investigations exists for Mexican animals. Notwithstanding, Mexican populations of desert tortoises in the southern part of the range of Gopherus morafkai are distinct, particularly where the tortoises occur in tropical thornscrub and tropical deciduous forest. Recent studies have shed light on the ecology, morphology and genetics of these southern ‘desert’ tortoises. All evidence warrants recognition of this clade as a distinctive taxon and herein we describe it as Gopherus evgoodei sp. n. The description of the new species significantly reduces and limits the distribution of Gopherus morafkai to desertscrub habitat only. By contrast, Gopherus evgoodei sp. n. occurs in thornscrub and tropical deciduous forests only and this leaves it with the smallest range of the three sister species. We present conservation implications for the newly described Gopherus evgoodei, which already faces impending threats.

Genetic assessments and parentage analysis of captive Bolson tortoises (Gopherus flavomarginatus) inform their "rewilding" in New Mexico.

The Bolson tortoise (Gopherus flavomarginatus) is the first species of extirpated megafauna to be repatriated into the United States. In September 2006, 30 individuals were translocated from Arizona to New Mexico with the long-term objective of restoring wild populations via captive propagation. We evaluated mtDNA sequences and allelic diversity among 11 microsatellite loci from the captive population and archived samples collected from wild individuals in Durango, Mexico (n = 28). Both populations exhibited very low genetic diversity and the captive population captured roughly 97.5% of the total wild diversity, making it a promising founder population. Genetic screening of other captive animals (n = 26) potentially suitable for reintroduction uncovered multiple hybrid G. flavomarginatus×G. polyphemus, which were ineligible for repatriation; only three of these individuals were verified as purebred G. flavomarginatus. We used these genetic data to inform mate pairing, reduce the potential for inbreeding and to monitor the maintenance of genetic diversity in the captive population. After six years of successful propagation, we analyzed the parentage of 241 hatchlings to assess the maintenance of genetic diversity. Not all adults contributed equally to successive generations. Most yearly cohorts of hatchlings failed to capture the diversity of the parental population. However, overlapping generations of tortoises helped to alleviate genetic loss because the entire six-year cohort of hatchlings contained the allelic diversity of the parental population. Polyandry and sperm storage occurred in the captives and future management strategies must consider such events.

STR/microsatellite primers for the desert tortoise, Gopherus agassizii, and its congeners

The desert tortoise, Gopherus agassizii, is a threatened species native to the North American desert southwest and is recognized as having genetically distinct Mojave and Sonoran desert populations. The Mojave Desert population is federally listed as threatened under the Endangered Species Act and the Sonoran Desert population is fully protected under Mexican and United States state laws. We identified nine dinucleotide STR loci in the desert tortoise and tested their efficacy in 80 samples from both the Sonoran and Mojave deserts. One locus exhibited low allelic variation (4 alleles) while seven were highly variable (8–16 alleles). One locus exhibited a unique allele in congeners (G. flavomarginatus and G. berlandieri).

The Agassiz’s desert tortoise genome provides a resource for the conservation of a threatened species

Agassiz’s desert tortoise (Gopherus agassizii) is a long-lived species native to the Mojave Desert and is listed as threatened under the US Endangered Species Act. To aid conservation efforts for preserving the genetic diversity of this species, we generated a whole genome reference sequence with an annotation based on deep transcriptome sequences of adult skeletal muscle, lung, brain, and blood. The draft genome assembly for G. agassizii has a scaffold N50 length of 252 kbp and a total length of 2.4 Gbp. Genome annotation reveals 20,172 protein-coding genes in the G. agassizii assembly, and that gene structure is more similar to chicken than other turtles. We provide a series of comparative analyses demonstrating (1) that turtles are among the slowest-evolving genome-enabled reptiles, (2) amino acid changes in genes controlling desert tortoise traits such as shell development, longevity and osmoregulation, and (3) fixed variants across the Gopherus species complex in genes related to desert adaptations, including circadian rhythm and innate immune response. This G. agassizii genome reference and annotation is the first such resource for any tortoise, and will serve as a foundation for future analysis of the genetic basis of adaptations to the desert environment, allow for investigation into genomic factors affecting tortoise health, disease and longevity, and serve as a valuable resource for additional studies in this species complex.