We assembled and annotated a chromosome-level genome for the Western Spadefoot, Spea hammondii (Anura, Scaphiopodidae) representing one of only three amphibians included in the California Conservation Genomics Project (CCGP). Spea hammondii is a vernal pool breeding anuran native to California and northwestern Baja California which has undergone both range contractions and local extirpations across its distribution, primarily due to habitat loss and degradation and drought. The species is recognized by the state of California as a Species of Special Concern and is proposed for listing under the United States Endangered Species Act. Using the established CCGP pipeline, this S. hammondii genome was produced using Pacific Biosciences HiFi long-reads and Omni-C proximity ligation, resulting in a de novo genome assembly 1.14 Gb in length, distributed across 479 scaffolds (scaffold N50 = 120.8 Mb; largest scaffold = 183.6 Mb) with a BUSCO completeness score of 90.9% using a conserved tetrapod ortholog set. Our assembly shows high base accuracy (quality value [QV] = 63.7) and low frameshift error in coding regions (QV 50.42). Annotation of this genome yielded 20,434 genes with a BUSCO completeness score of 94.7%. This genome assembly, in combination with range-wide resequencing data from CCGP, will facilitate statewide population genomic assessments to delineate conservation units, quantify inbreeding and genomic load, and test for adaptive variation associated with vernal pool hydrology and drought tolerance, all of which are important considerations in the proposed federal listing.
The transition from small genetic to genome-scale datasets for studying biodiversity has revealed that genetic exchange through introgressive hybridization is a widespread phenomenon in nature. Despite this, a lack of high-quality reference genomes for most non-model species limits our understanding of the impact of this process for many taxonomic groups. This restricts the range of insights that genomic tools can provide for conservation biologists, who often hope to employ genomic datasets to accurately identify historically isolated lineages to protect and to predict their evolutionary fate in the face of environmental change. Tiger whiptail lizards (Aspidoscelis tigris complex) are an abundant and important ecological component of ecosystems across the southwestern United States. In this study, we assembled and annotated a chromosome-level reference genome for A. t. stejnegeri from coastal California. We then used this reference genome to reconstruct patterns of speciation and admixture within the larger species complex, finding evidence that gene flow is widespread both geographically and across the genome.
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.
Most aspects of the lives of ectotherms are temperature dependent. Achieving the warmer body temperatures (Tb s) typically required for optimal performance can be particularly challenging for nocturnal ectotherms. Homonota darwinii-the world's southernmost gecko-is broadly distributed in southern Argentina (35-52 °S latitude) where cold climates over parts of its range likely pose an additional performance challenge for this nocturnal lizard. We hypothesized that the southernmost populations of this species would be the most thermally challenged, as evidenced by a decline in temperature-dependent sprint performance with increasing latitude. A temperature-dependent depression in locomotory performance may indicate suboptimal performance in other thermally dependent traits linked to fitness (e.g., foraging efficiency, metabolism). We measured sprint performance at five ecologically relevant Tb s for four populations spanning most of the latitudinal range of H. darwinii. We also recorded annual operative temperatures (Te s) at each site on the surface and in refuges used by the geckos. Sprint data indicated differences in maximum performance over the range of H. darwinii, but not the latitudinal decline predicted. Instead, sprint performance was likely influenced by climatic variability associated with each site's elevation. Geckos from most populations had a broad range of Tb s over which sprint performance was optimal, albeit twofold to threefold lower than other geckos. This is indicative of eurythermy, the ability to perform well over a wide range of temperatures. We discuss this finding in the context of alternative hypotheses concerning performance tradeoffs in nocturnal ectotherms.
I am excited to present this year’s Robert K. Johnson Award for Excellence in Service to the American Society of Ichthyologists and Herpetologists. This year’s Johnson Award committee members include Eric Hilton and Michael Douglas. The award honors Bob Johnson, who provided incredible service to the ASIH during his career until his death in 2000. Societies like the ASIH rely on the selfless service of our members. The Johnson Award is awarded to either an ichthyologist or a herpetologist in alternate years. This year’s award will be presented to a herpetologist. This year’s Johnson Award winner was unanimously selected by the committee for this recognition. Notably, the winner is still ‘‘mid-career’’ but has already accrued a service record that is worthy of recognition with this award. Providing such service to the ASIH while maintaining an excellent record of teaching, curating a collection, gaining funding and publishing in their field, and mentoring students is a model for the rest of us in the societies meeting at the JMIH. The awardee for 2019 has been active in ASIH since the 1990s when they were on the Committee for Graduate Student Participation and organized the Graduate Student Workshop, while also winning the ASIH Stoye Award for best student paper not once, but twice. Since then, the awardee has maintained continual presence on various committees for ASIH, including the JMIH Resolutions Committee, the Equal Participation Committee, and committees for the Johnson Award, the Fitch Award, and the Copeia Best Papers in Herpetology Award. Highlighting their commitment to the student members of the ASIH, the awardee has been a judge for the Stoye Awards, has chaired the Stoye and Storer award committees, has served on the Gaige Award committee, and co-organizes the Graduate Student–Professionals Speed-Networking Workshop. The awardee has also provided significant service to our Society’s publication by serving on the Copeia Review Implementation Committee, the Copeia Publications Policy Committee, and as the Copeia Book Review Editor for Herpetology. The awardee has been a central member of ASIH governance by serving two terms on the Board of Governors, as Co-Chair of the Long-Range Planning Committee branch of Executive Committee, and was on the ad hoc Committee for JMIH Code of Conduct. Our 2019 Robert K. Johnson awardee is Robert E. Espinoza.
A new species of crocodile newt from populations on opposite sides of the Ayeyarwady Basin, Myanmar, previously referred to as Tylototriton cf. verrucosus, is described on the basis of colour pattern, morphology and phylogenetic data from the mitochondrial gene ND2. Tylototriton panwaensis sp. nov. is most closely related to T. verrucosus + T. shanjing but bears a unique suite of colour pattern and morphological characters separating it from T. verrucosus and T. shanjing as well as the other geographically proximate species T. ngarsuensis and T. shanorum. Molecular and morphological data presented herein (that have been used elsewhere) continue to fuel the issue of separate specific allocation (or not) to T. verrucosus and T. shanjing but go no further to resolve the controversy. The description of this new species adds to a rapidly growing database of newly described species of amphibians and reptiles from the upland, mountainous regions of eastern Myanmar.
A phylogenetic taxonomy of species in the Cyrtodactylus peguensis group from the Ayeyarwady Basin of Myanmar is constructed based on color pattern, morphology, and molecular systematic analyses using the mitochondrial gene NADH dehydrogenase subunit 2. Newly collected samples from the type locality of C. peguensis and other localities indicate that this clade is endemic to central Myanmar and contains at least seven species, four of which are undescribed. Three species, including C. peguensis occur in the low hills of the Bago Yoma Range within the central portion of the Ayeyarwady Basin. Two of these, C. myintkyawthurai sp. nov. from the northern and central Bago Yoma and C. meersi sp. nov. which is syntopic with C. peguensis in the southern Bago Yoma are described herein. As more lowland hilly areas bordering, and within the Ayeyarwady Basin are surveyed, more new species of this group are likely to be discovered. These discoveries continue the recent surge of descriptions of new species of Cyrtodactylus that are being discovered in Myanmar.
A phylogenetic taxonomic analysis of a monophyletic subgroup of the salamandrid genus Tylototriton revealed that a newly discovered population from Ngar Su Village, 1 km south of Ywangan, Shan State, Myanmar is a new species and most closely related to T. shanorum from approximately 80 km to the west in the vicinity of Taunggyi, Shan State. Tylototriton ngarsuensis sp. nov. differs from other closely related species of Tylototriton on basis of varying combinations of characteristics associated with it shorter head, larger size, rib nodule morphology, and overall drab, very dark, coloration, along with its genetic differentiation. Tylototriton ngarsuensis sp. nov. also appears to breed later in the year than most other species. Unfortunately, this species like many other Asian newts, is being harvested for the pet and medicinal trade and given its restricted distribution, this could pose a serious threat to its long-term survival.
A phylogenetic taxonomic analysis indicates that a newly discovered population of Cyrtodactylus from the vicinity of Ywangan Town in the Shan Hills, Shan State, Myanmar is a new species (C. ywanganensis sp. nov.) and the earliest diverging member of the linnwayensis group within the previously defined Indochinese clade. The DIVALIKE+J model of a BioGeoBEARS biogeographic analysis indicates that the Indochinese clade evolved in the Shan Hills and Salween Basin of eastern Myanmar and dispersed into Indochina on at least three separate occasions from 18.6-13.4 mya. Once there, uplift of the Tenasserim Mountains and Thai Highlands created the intermedius group, the oldhami group, and C. tigroides of western and southern Thailand which form sister lineages to the linnwayensis group, yathepyanensis group, and the sinyineensis group, respectively, of eastern Myanmar. Diverging lineages within the Indochinese clade highlight the importance of the Thai Highlands and Tenasserim Mountains in that group's evolution and speciation. The discovery of C. ywanganensis sp. nov. in karstic habitats in the Shan Hills continues to underscore the unrealized karst-associated herpetological diversity of this vast, relatively unexplored, upland region and the need for additional field studies.
Learning that occurs in a field setting is a powerful experience that promotes the development of new generations of creative scientists, enhances environmental literacy, and instills social responsibility in our citizens. Institutional challenges to field studies include decreasing financial resources and increasing regulatory concerns. These are coupled with changing student interests, in particular the growing misconception that field study is not relevant to many biological careers. Collectively, these factors contribute to a significant decline in field-study opportunities for students and lack of pedagogical guidance for instructors interested in conducting field courses. Nature and culture are inextricably linked, and we all benefit from including diverse backgrounds and perspectives in field experiences. We suggest expanding the definition of "the field" to include human-influenced ecosystems, as well as more conventional natural habitats. More than ever, the world needs the passion, insight, and wisdom that come from field studies.
Vertebrate taxa with entirely unisexual populations are composed of females that reproduce without fertilization and are generally of hybrid origin. At least 23 vertebrate families have unisexual lineages. Within squamate reptiles, >40 uniparental species have been described from five major lineages: acrodont iguanians, Gekkota, Serpentes, Scincomorpha, and Varanidae. Pleurodont iguanians include >1100 species, all of which have gonochoristic reproduction. Here we report the discovery of a new unisexual lizard from the liolaemid genus Liolaemus, a species-rich (∼260 species) clade distributed over most of southern South American. The new species, Liolaemus parthenos, is the only known all-female triploid pleurodont iguanian. The structural chromosome heteromorphisms of the karyotypes support the hypothesis that L. parthenos is the product of a hybrid origin. Based on morphology, the new species is assignable to the L. boulengeri group (sensu Abdala, 2007), and phylogenetic analyses of mitochondrial DNA indicate that L. parthenos is nested within L. darwinii, suggesting that the latter is the maternal ancestor of this species. Additional data are needed to identify the patrilineal ancestor.
Effective and targeted conservation action requires detailed information about species, their distribution, systematics and ecology as well as the distribution of threat processes which affect them. Knowledge of reptilian diversity remains surprisingly disparate, and innovative means of gaining rapid insight into the status of reptiles are needed in order to highlight urgent conservation cases and inform environmental policy with appropriate biodiversity information in a timely manner. We present the first ever global analysis of extinction risk in reptiles, based on a random representative sample of 1500 species (16% of all currently known species). To our knowledge, our results provide the first analysis of the global conservation status and distribution patterns of reptiles and the threats affecting them, highlighting conservation priorities and knowledge gaps which need to be addressed urgently to ensure the continued survival of the world’s reptiles. Nearly one in five reptilian species are threatened with extinction, with another one in five species classed as Data Deficient. The proportion of threatened reptile species is highest in freshwater environments, tropical regions and on oceanic islands, while data deficiency was highest in tropical areas, such as Central Africa and Southeast Asia, and among fossorial reptiles. Our results emphasise the need for research attention to be focussed on tropical areas which are experiencing the most dramatic rates of habitat loss, on fossorial reptiles for which there is a chronic lack of data, and on certain taxa such as snakes for which extinction risk may currently be underestimated due to lack of population information. Conservation actions specifically need to mitigate the effects of human-induced habitat loss and harvesting, which are the predominant threats to reptiles.
(1) We measured thermal tolerances (critical thermal minimum, CTmin and panting threshold, Tpant) for four populations of Homonota darwinii spanning most of the latitudinal range of the species. (2) CTmin differed across populations, but not latitudinally as predicted, likely because latitude was not as good a proxy for operative temperatures (Te). (3) Some populations had subzero CTmin indicating supercooling or freeze tolerance—the first time either phenomenon has been reported for a gecko. (4) Tpant did not differ significantly among populations. (5) The thermal tolerance breadth appears to be correlated with thermal variability in the environment. (6) Annual Te data indicate gecko retreats play a crucial role in surviving extreme surface temperatures (<0 or >50°C).
Herbivory is generally thought to be restricted to reptiles with large body sizes that live in warm climates. We show that Liolaemus poecilochromus is primarily herbivorous (>80% plants in diet) even as juveniles, making them the smallest herbivorous reptile known. We detected relatively few differences in diet between the sexes, despite male-biased sexual dimorphism in head and body size. Adults consumed more mites and flowers than juveniles, and we detected a weak ontogenetic shift from omnivory to herbivory that is attributable to the lower volumetric consumption of plants by juvenile males. We discuss the abiotic and biotic conditions that likely selected for herbivory in this and other small-bodied, high-elevation Liolaemus. Herbivoría en general se cree que se limita a los reptiles con cuerpos grandes que viven en climas cálidos. Mostramos que Liolaemus poecilochromus es principalmente herbívora (>80% de plantas en la dieta) incluso los juveniles, convirtiéndolo por esto en el reptil herbívoro más pequeño conocido. Asimismo, detectamos pocas diferencias en la dieta entre los sexos, a pesar del dimorfismo sexual a favor de los machos en el tamaño de la cabeza y el cuerpo. Los adultos consumen más ácaros y flores que los juveniles, por otro lado se detectó un cambio ontogenético débil de omnivoria a herbivoría en los machos juveniles, debido a su bajo consumo de plantas. Discutimos las condiciones abióticas y bióticas que probablemente favorecieron la herbivoría en este y otros Liolaemus de cuerpo pequeño y alta elevación.