Effect of species rarity on the accuracy of species distribution models for reptiles and amphibians in southern California

Aim Several studies have found that more accurate predictive models of species’ occurrences can be developed for rarer species; however, one recent study found the relationship between range size and model performance to be an artefact of sample prevalence, that is, the proportion of presence versus absence observations in the data used to train the model. We examined the effect of model type, species rarity class, species’ survey frequency, detectability and manipulated sample prevalence on the accuracy of distribution models developed for 30 reptile and amphibian species. Location Coastal southern California, USA. Methods Classification trees, generalized additive models and generalized linear models were developed using species presence and absence data from 420 locations. Model performance was measured using sensitivity, specificity and the area under the curve (AUC) of the receiver‐operating characteristic (ROC) plot based on twofold cross‐validation, or on bootstrapping. Predictors included climate, terrain, soil and vegetation variables. Species were assigned to rarity classes by experts. The data were sampled to generate subsets with varying ratios of presences and absences to test for the effect of sample prevalence. Join count statistics were used to characterize spatial dependence in the prediction errors. Results Species in classes with higher rarity were more accurately predicted than common species, and this effect was independent of sample prevalence. Although positive spatial autocorrelation remained in the prediction errors, it was weaker than was observed in the species occurrence data. The differences in accuracy among model types were slight. Main conclusions Using a variety of modelling methods, more accurate species distribution models were developed for rarer than for more common species. This was presumably because it is difficult to discriminate suitable from unsuitable habitat for habitat generalists, and not as an artefact of the effect of sample prevalence on model estimation.     

北京市两栖爬行动物空间分布格局及影响因素

基于遥感和野外调查数据,研究北京市两栖爬行动物空间分布格局及其影响因素。结果显示,北京记录两栖爬行动物2纲3目10科17属22种,其中,保护物种15种,占物种总数的68.19%。物种分布整体呈现由西北向东南递减的空间特征,西北部山区丰富度和相对多度较大,门头沟和延庆物种丰富度最大(14种),占调查物种总数的66.67%,优势种为中国林蛙、黑斑侧褶蛙、中华蟾蜍和山地麻蜥;门头沟、怀柔、房山分布了全市71.54%的种群数量;200-500 m海拔段物种丰富度最高(18种),主要生境为森林灌丛;物种数在6种以上的网格有11个,包括大滩、怀九河、百花山、拒马河、密云水库等。总体来看,物种种类和数量相较之前呈现减少趋势,而土地用途转换具有重要影响。1980-2018年,建设用地表现出以东西城为核心向外围扩张的趋势,侵占的农田占生态系统总转换面积的42.85%;城六区和平原区的主要物种为黑斑侧褶蛙和中华蟾蜍,少有中国林蛙分布。进一步分析两栖动物1500 m的迁徙距离内,森林灌丛和农田为主要的生境类型,城市扩张侵占了部分农田;同时,污染物的排放引起水体水质下降,特别是北运河水系,造成两栖动物的繁殖率降低和栖息地破坏。目前,北京市各类保护地虽覆盖两栖爬行动物种类的90.91%和数量的60.45%,但在怀柔宝山镇白河上段、密云水库来水的潮河上段辛庄桥、平谷洳河大兴庄镇-峪口镇等地,仍然存在较大的保护空缺。对此,建议开展长期定位观测,构建生物多样性观测网络,并探索建立高强度土地利用下的生物多样性保护机制,从而实现生物资源可持续利用。     

湖南省两栖、爬行动物物种多样性及其地理分布

物种多样性及其地理分布是制定野生动物保护对策的重要依据。两栖、爬行动物在生物演化的历史上占据着重要地位, 又是脊椎动物分类体系变动较大的类群。为了掌握湖南省两栖、爬行动物物种多样性现状, 促进湖南省生物多样性保护和野生动物管理工作, 我们参考分类学及分子生物系统学的最新研究成果, 系统地收集了近10多年来有关湖南省两栖、爬行动物分类的文献资料, 结合团队长期以来的野外调查数据, 对湖南省两栖、爬行动物名录进行了整理与更新(截止到2021年10月31日)。结果表明: 湖南省已记录两栖动物2目10科30属86种(含亚种), 爬行动物2目22科55属105种(含亚种), 其中中国特有种分别有62种和30种, 湖南省特有种分别有10种和4种。列入《国家重点保护野生动物名录》(2021)的两栖动物有11种, 爬行动物有10种; 列为《中国生物多样性红色名录》(2021)受威胁等级的两栖动物有20种, 爬行动物有30种。此外, 湖南省两栖、爬行动物区系特征明显, 以东洋界种类为主(81.2%), 广布种较少(18.8%), 无古北界种。在地理分布上, 湘南山地丘陵区、湘西北山地区是湖南省两栖、爬行动物物种丰富度较高的地区。     

Long‐term datasets: From descriptive to predictive data using ecoinformatics

This Special Feature includes contributions on data‐processing of large ecological datasets under the heading ecoinformatics. Herewith the latter term is now al so established in the Journal of Vegetation Science. Ecoinfomatics is introduced as a rapid growing field within community ecology which is generating exciting new developments in ecology and in particular vegetation ecology. In our field, ecoinformatics deals with the understanding of patterns of species distributions at local and regional scales, and on the assemblages of species in relation to their properties, the local environment and their distribution in the region. Community ecology using ecoinformatics is related to bioinformatics, community ecology, biogeography and macroecology. We make clear how ecoinformatics in vegetation science and particularly the IAVS Working Group on Ecoinformatics has developed from the work of the old Working Group for Data Processing which was active during the 1970s and 1980s. Recent developments, including the creation of TURBOVEG and Syn Bio Sys in Europa and VEGBANK in the USA, form a direct link with these pioneer activities, both scientifically and personally. The contributions collected in this Special Feature present examples of seco‐infeveral types of the use of databases and the application of programmes and models. The main types are the study of long‐term vegetation dynamics in different cases of primary and secondary succession and the understanding of successional developments in terms of species traits. Among the future developments of great significance we mention the use of a variety of different large datasets for the study of the distribution and ecology and conservation of rare and threatened species.     

Salmonella diversity associated with wild reptiles and amphibians in Spain

During the spring and summer of 2001, faeces from 166 wild reptiles (94 individuals) and amphibians (72 individuals) from 21 different species found in central Spain were examined for the presence of Salmonella. Thirty-nine reptiles (41.5%) yielded 48 Salmonella isolates, whereas all the amphibians examined were negative. Subspecies Salmonella enterica enterica (I) accounted for up to 50% of isolates. Fourteen isolates (29.2%) belonged to subspecies diarizonae (IIIb), six isolates (12.5%) to subspecies salamae (II), and four isolates (8.3%) to subspecies arizonae (IIIa). Twenty-seven different serotypes were identified. Serotypes Anatum (12.5%), Herzliya (8.3%), Abony, 18:l,v:z, 9,12:z29:1,5 and 38:z10:z53 (6.2%/each) were the most frequently isolated. A high percentage (39.6%) of isolates belonged to serotypes previously associated with environmental sources. Also, 37.5% of isolates belonged to serotypes which had been related to human cases of salmonellosis. From these data, it is concluded that wild reptiles, but apparently not amphibians, may represent an important reservoir of Salmonella in nature and have potential implications for public health.     

A predictive framework and review of the ecological impacts of exotic plant invasions on reptiles and amphibians

The invasive spread of exotic plants in native vegetation can pose serious threats to native faunal assemblages. This is of particular concern for reptiles and amphibians because they form a significant component of the world's vertebrate fauna, play a pivotal role in ecosystem functioning and are often neglected in biodiversity research. A framework to predict how exotic plant invasion will affect reptile and amphibian assemblages is imperative for conservation, management and the identification of research priorities. Here, we present a new predictive framework that integrates three mechanistic models. These models are based on exotic plant invasion altering: (1) habitat structure; (2) herbivory and predator‐prey interactions; (3) the reproductive success of reptile and amphibian species and assemblages. We present a series of testable predictions from these models that arise from the interplay over time among three exotic plant traits (growth form, area of coverage, taxonomic distinctiveness) and six traits of reptiles and amphibians (body size, lifespan, home range size, habitat specialisation, diet, reproductive strategy). A literature review provided robust empirical evidence of exotic plant impacts on reptiles and amphibians from each of the three model mechanisms. Evidence relating to the role of body size and diet was less clear‐cut, indicating the need for further research. The literature provided limited empirical support for many of the other model predictions. This was not, however, because findings contradicted our model predictions but because research in this area is sparse. In particular, the small number of studies specifically examining the effects of exotic plants on amphibians highlights the pressing need for quantitative research in this area. There is enormous scope for detailed empirical investigation of interactions between exotic plants and reptile and amphibian species and assemblages. The framework presented here and further testing of predictions will provide a basis for informing and prioritising environmental management and exotic plant control efforts.     

Cold Code: the global initiative to DNA barcode amphibians and nonavian reptiles

DNA barcoding facilitates the identification of species and the estimation of biodiversity by using nucleotide sequences, usually from the mitochondrial genome. Most studies accomplish this task by using the gene encoding cytochrome oxidase subunit I (COI; Entrez COX1). Within this barcoding framework, many taxonomic initiatives exist, such as those specializing in fishes, birds, mammals, and fungi. Other efforts center on regions, such as the Arctic, or on other topics, such as health. DNA barcoding initiatives exist for all groups of vertebrates except for amphibians and nonavian reptiles. We announce the formation of Cold Code, the international initiative to DNA barcode all species of these ‘cold‐blooded’ vertebrates. The project has a Steering Committee, Coordinators, and a home page. To facilitate Cold Code, the Kunming Institute of Zoology, Chinese Academy of Sciences will sequence COI for the first 10 specimens of a species at no cost to the steward of the tissues.     

Sleep in amphibians and reptiles: a review and a preliminary analysis of evolutionary patterns

Despite the ubiquitous nature of sleep, its functions remain a mystery. In an attempt to address this, many researchers have studied behavioural and electrophysiological phenomena associated with sleep in a diversity of animals. The great majority of vertebrates and invertebrates display a phase of immobility that could be considered as a sort of sleep. Terrestrial mammals and birds, both homeotherms, show two sleep states with distinct behavioural and electrophysiological features. However, whether these features have evolved independently in each clade or were inherited from a common ancestor remains unknown. Unfortunately, amphibians and reptiles, key taxa in understanding the evolution of sleep given their position at the base of the tetrapod and amniote tree, respectively, remain poorly studied in the context of sleep. This review presents an overview of what is known about sleep in amphibians and reptiles and uses the existing data to provide a preliminary analysis of the evolution of behavioural and electrophysiological features of sleep in amphibians and reptiles. We also discuss the problems associated with analysing existing data, as well as the difficulty in inferring homologies of sleep stages based on limited data in the context of an essentially mammalian‐centric definition of sleep. Finally, we highlight the importance of developing comparative approaches to sleep research that may benefit from the great diversity of species with different ecologies and morphologies in order to understand the evolution and functions of sleep.     

Thermal biology mediates responses of amphibians and reptiles to habitat modification

Human activities often replace native forests with warmer, modified habitats that represent novel thermal environments for biodiversity. Reducing biodiversity loss hinges upon identifying which species are most sensitive to the environmental conditions that result from habitat modification. Drawing on case studies and a meta‐analysis, we examined whether observed and modelled thermal traits, including heat tolerances, variation in body temperatures, and evaporative water loss, explained variation in sensitivity of ectotherms to habitat modification. Low heat tolerances of lizards and amphibians and high evaporative water loss of amphibians were associated with increased sensitivity to habitat modification, often explaining more variation than non‐thermal traits. Heat tolerances alone explained 24–66% (mean = 38%) of the variation in species responses, and these trends were largely consistent across geographic locations and spatial scales. As habitat modification alters local microclimates, the thermal biology of species will likely play a key role in the reassembly of terrestrial communities.     

From cognitive to neural models of working memory

Working memory refers to the temporary retention of information that was just experienced or just retrieved from long-term memory but no longer exists in the external environment. These internal representations are short-lived, but can be stored for longer periods of time through active maintenance or rehearsal strategies, and can be subjected to various operations that manipulate the information in such a way that makes it useful for goal-directed behaviour. Empirical studies of working memory using neuroscientific techniques, such as neuronal recordings in monkeys or functional neuroimaging in humans, have advanced our knowledge of the underlying neural mechanisms of working memory. This rich dataset can be reconciled with behavioural findings derived from investigating the cognitive mechanisms underlying working memory. In this paper, I review the progress that has been made towards this effort by illustrating how investigations of the neural mechanisms underlying working memory can be influenced by cognitive models and, in turn, how cognitive models can be shaped and modified by neuroscientific data. One conclusion that arises from this research is that working memory can be viewed as neither a unitary nor a dedicated system. A network of brain regions, including the prefrontal cortex (PFC), is critical for the active maintenance of internal representations that are necessary for goal-directed behaviour. Thus, working memory is not localized to a single brain region but probably is an emergent property of the functional interactions between the PFC and the rest of the brain.     

Ascaridoid nematodes of amphibians and reptiles: Ophidascaris Baylis, 1920

The genus Ophidascaris is revised and divided into five groups of species. A key for the species groups is provided. Group 1 (‘filaria’ group) occurs in pythons and a key is provided for differentiating eight species based on fresh and preserved specimens and on developmental patterns. O. papillifera (Linstow, 1898) is redescribed from the type-specimens and is considered to be close or identical to O. niuginiensis, for which Candoia carinatus is recorded as a new host. A key for the differentiation of species in Groups 2 to 5 is based on preserved specimens only. Group 2 (‘obconica’ group) contains (i) O. obconica and O. trichuriformis [= caballeroi] in South American colubrids (further investigation will probably show that O. trichuriformis is a synonym of O. obconica); new host records are Xenodon severus, X. neuwiedii, X. colubrinus, Leptodeira annulata, Thamnodynastes pallidus, Leimadophis poecilogyrus and Boa constrictor; (ii) O. ashi n. sp. (new species name for ‘O. labiatopapillosa’) in North American colubrids, new host records are Nerodia valida, Heterodon nasicus and Storeria occipitomaculata; (iii) O. mombasica in African colubrids; new host records are Psammophis phillipsii and P. sibilans; (iv) O. solenopoion in Madagascan colubrids; (v) O. pyrrhus in Australian elapids; new host records are Cacophis squamulosus, Cryptophis nigrescens, Demansia atra, D. olivacea, Hemiaspis signata, Hoplocephalus bitorquatus, H. stephensi, H. bungaroides and Tropedechis carinatus, it is also recorded in Australia in the colubrid Styporhyncus mairii (new host record) and in Demansia papuensis papuensis and D. olivacea papuensis in Papua New Guinea; (vi) O. piscatori in Asian colubrids; (vii) O. excavata [? = schikhobalovi] in Agkistrodon spp. and possibly other aquatic snakes in Asia; new host record is Agkistrodon halys blomhoffi. Group 3 (‘radiosa’ group) in African viperids contains O. radiosa [ = intorta] in Bitis spp. Specimens from Atheris nitschei, Causus rhombeatus and the colubrid Boaedon lineatus were similar, but showed differences indicating possibility of other species in this group. Group 4 (‘najae’ group) in African elapids and Asian elapids and colubrids contains O. najae [ = daubaylisi]; new host records are Ophiophagus hannah, Boiga cyanea, Elaphe carinata. Group 5 (‘arndti’ group) in South American crotalids and colubrids contains O. arndti [ = travassosi and sprenti] in Crotalus spp. and Bothrops spp.; new host record is B. atrox in Panama. No morphological differentiation except size could be detected between O. arndti in crotalines and O. sicki in colubrids, but in view of difference in the feeding habits of their host, both species names were tentatively sustained; new host records for O. sicki are Xenodon neuwiedii, Leimadophis poecilogyrus, Pseudoboa cloelia, Philodryas patagoniensis and Micrurus frontalis; O. ochoteranai was regarded as a species inquirenda. The following species previously placed in Amplicaecum are placed in Ophidascaris; excavata Hsu & Hoeppli, 1931; schikhobalovi Mozgovoy, 1950; robertsi Sprent & Mines, 1960; longispiculum Oshmarin & Demshin, 1972; orientalis Wang, 1965. The position of Ophidascaris in relation to other ascaridoids is discussed: it is placed within the subfamily Ascaridinae sensu Sprent (1983) containing all other ascaridoids of terrestrial animals. It is concluded that Ophidascaris is in a relatively recent stage of evolution. The most likely centre of dispersal for the genus appears to have been Central Africa with spread in one direction to Asia and thence to the New World and in another direction to Madagascar and Australia.     

Predicting establishment success for alien reptiles and amphibians: a role for climate matching

We examined data comprising 1,028 successful and 967 failed introduction records for 596 species of alien reptiles and amphibians around the world to test for factors influencing establishment success. We found significant variations between families and between genera. The number of jurisdictions where a species was introduced was a significant predictor of the probability the species had established in at least one jurisdiction. All species that had been introduced to more than 10 jurisdictions (34 species) had established at least one alien population. We also conducted more detailed quantitative comparisons for successful (69 species) and failed (116 species) introductions to three jurisdictions (Great Britain, California and Florida) to test for associations with climate match, geographic range size, and history of establishment success elsewhere. Relative to failed species, successful species had better climate matches between the jurisdiction where they were introduced and their geographic range elsewhere in the world. Successful species were also more likely to have high establishment success rates elsewhere in the world. Cross-validations indicated our full model correctly categorized establishment success with 78–80% accuracy. Our findings may guide risk assessments for the import of live alien reptiles and amphibians to reduce the rate new species establish in the wild.     

Thermal niche predicts tolerance to habitat conversion in tropical amphibians and reptiles

Habitat conversion is a major driver of the biodiversity crisis, yet why some species undergo local extinction while others thrive under novel conditions remains unclear. We suggest that focusing on species' niches, rather than traits, may provide the predictive power needed to forecast biodiversity change. We first examine two Neotropical frog congeners with drastically different affinities to deforestation and document how thermal niche explains deforestation tolerance. The more deforestation‐tolerant species is associated with warmer macroclimates across Costa Rica, and warmer microclimates within landscapes. Further, in laboratory experiments, the more deforestation‐tolerant species has critical thermal limits, and a jumping performance optimum, shifted ~2 °C warmer than those of the more forest‐affiliated species, corresponding to the ~3 °C difference in daytime maximum temperature that these species experience between habitats. Crucially, neither species strictly specializes on either habitat – instead habitat use is governed by regional environmental temperature. Both species track temperature along an elevational gradient, and shift their habitat use from cooler forest at lower elevations to warmer deforested pastures upslope. To generalize these conclusions, we expand our analysis to the entire mid‐elevational herpetological community of southern Costa Rica. We assess the climatological affinities of 33 amphibian and reptile species, showing that across both taxonomic classes, thermal niche predicts presence in deforested habitat as well as or better than many commonly used traits. These data suggest that warm‐adapted species carry a significant survival advantage amidst the synergistic impacts of land‐use conversion and climate change.     

The behavioral responses of amphibians and reptiles to microgravity on parabolic flights

In the present study, we exposed 53 animals from 23 different species of amphibians and reptiles to microgravity (mug). This nearly doubles the number of amphibians and reptiles observed so far in mug. The animals were flown on a parabolic flight, which provided 20-25s of mug, to better characterize behavioral reactions to abrupt exposure to mug. Highly fossorial limbless caecilians and amphisbaenians showed relatively limited movement in mug. Limbed quadrupedal reptiles that were non-arboreal in the genera Leiocephalus, Anolis, and Scincella showed the typical righting response and enormous amounts of body motion and tail rotation, which we interpreted as both righting responses and futile actions to grasp the substrate. Both arboreal and non-arboreal geckos in the genera Uroplatus, Palmatogecko, Stenodactylus, Tarentola, and Eublepharis instead showed a skydiving posture previously reported for highly arboreal anurans. Some snakes, in the genera Thamnophis and Elaphe, which typically thrashed and rolled in mug, managed to knot their own bodies with their tails and immediately became quiescent. This suggests that these reptiles gave stable physical contact, which would indicate that they were not falling, primacy over vestibular input that indicated that they were in freefall. The fact that they became quiet upon self-embrace further suggests a failure to distinguish self from non-self. The patterns of behavior seen in amphibians and reptiles in mug can be explained in light of their normal ecology and taxonomic relations.