The Fergana Valley Is an Isolate of Biodiversity: A Discussion of the Endemic Herpetofauna and Description of Two New Species of Alsophylax (Sauria: Gekkonidae) from Eastern Uzbekistan

The high level of endemism in Fergana Valley has been well documented in numerous studies for various groups of animals and plants. In a relatively small area, there are 45 endemic plant species, five endemic insect species, and five endemic reptile species. In surveying this area for data on distribution, abundance, acoustics, and genetic samples for species of reptiles, we discovered two new species of gecko from the genus Alsophylax. Phylogenetic analyses of mitochondrial DNA sequences indicate the relatives of these new species are the even-fingered gecko, Alsophylax pipiens, and the southern even-fingered gecko, Alsophylax laevis, located hundreds of kilometers to the northwest and southwest of the Fergana Valley. The threats to these new endemic species are significant given the amount of continued agricultural development that involves new territories previously considered "unsuitable" for any species of significance that is leading to the further reduction in, fragmentation of, and degradation of the remaining natural ecosystems in the Fergana Valley. The conservation of these rare and locally endemic species depends directly on the readiness of the state to create areas with IUCN I and II protection. The many studies documenting levels of endemism, along with the data published in this study, are the basis for the justification for state-protected areas in the Fergana Valley.

A new species of Hemiphyllodactylus (Squamata, Gekkonidae) from Ha Giang Province, Vietnam

An integrative analysis recovered a new species of the Hemiphyllodactylustypus group from a karst formation in Lung Cu Commune, Dong Van District, Ha Giang Province, northeastern Vietnam. Hemiphyllodactyluslungcuensissp. nov. is embedded within clade 6 of the typus group, bearing an uncorrected pairwise sequence divergence of 4.6-20.2% from all other species based on a 1,038 base pair segment of the mitochondrial NADH dehydrogenase subunit 2 gene (ND2). It is diagnosable from other species in clade 6 by statistically significant mean differences in normalized morphometric, meristic, and categorical characters. A multiple factor analysis using the three aforementioned character types recovered its unique, non-overlapping placement in morphospace as statistically significantly different from that of all other species in clade 6. The description of this new Hemiphyllodactylus species contributes to a growing body of literature underscoring the high degree of herpetological diversity and endemism in karst landscapes in Vietnam as well as in the genus Hemiphyllodactylus.

Two new species of Dixonius from Vietnam and Laos with a discussion of the taxonomy of Dixonius (Squamata, Gekkonidae)

Integrated analyses using maximum likelihood (ML), Bayesian inference (BI), principal component analysis (PCA), discriminate analysis of principal components (DAPC), multiple factor analysis (MFA), and analysis of variance (ANOVA) recovered two new diagnosable species of gekkonid lizards in the genus Dixonius, one from the Central Highlands, Gia Lai Province, Vietnam and another from the Vientiane Province, Laos. Phylogenetic analyses based on the mitochondrial NADH dehydrogenase subunit 2 gene (ND2) and adjacent tRNAs showed that Dixoniusgialaiensissp. nov. is the sister species of D.minhlei from Dong Nai Province, Vietnam and is nested within a clade that also includes the sister species D.siamensis and D.somchanhae. Dixoniusmuangfuangensissp. nov. is the sister species to D.lao from Khammouane Province, Laos and is embedded in a clade with D.vietnamensis, D.taoi, and undescribed species from Thailand. Multivariate (PCA, DAPC, and MFA) and univariate (ANOVA) analyses using combinations of 15 meristic (scale counts), six morphometric (measurements), and five categorical (color pattern and morphology) characters from 44 specimens encompassing all eight species of Dixonius from Vietnam and Laos clearly illustrate Dixoniusgialaiensissp. nov. and Dixoniusmuangfuangensissp. nov. are statistically different and discretely diagnosable from all closely related species of Dixonius. These integrative analyses also highlight additional taxonomic issues that remain unresolved within Dixonius and the need for additional studies. The discovery of these new species further emphasizes the underappreciated herpetological diversity of the genus Dixonius and illustrates the continued need for field work in these regions.

Reference genome of the rubber boa, Charina bottae (Serpentes: Boidae)

The rubber boa, Charina bottae is a semi-fossorial, cold-temperature adapted snake that ranges across the wetter and cooler ecoregions of the California Floristic Province. The rubber boa is 1 of 2 species in the family Boidae native to California and currently has 2 recognized subspecies, the Northern rubber boa C. bottae bottae and the Southern rubber boa C. bottae umbratica. Recent genomic work on C. bottae indicates that these 2 subspecies are collectively composed of 4 divergent lineages that separated during the late Miocene. Analysis of habitat suitability indicates that C. bottae umbratica montane sky-island populations from southern California will lose the majority of their habit over the next 70 yr, and is listed as Threatened under the California Endangered Species Act. Here, we report a new, chromosome-level assembly of C. bottae bottae as part of the California Conservation Genomics Project (CCGP). Consistent with the reference genome strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology to produce a de novo assembled genome. The assembly comprises 289 scaffolds covering 1,804,944,895 bp, has a contig N50 of 37.3 Mb, a scaffold N50 of 97 Mb, and BUSCO completeness score of 96.3%, and represents the first reference genome for the Boidae snake family. This genome will enable studies of genetic differentiation and connectivity among C. bottae bottae and C. bottae umbratica populations across California and help manage locally endemic lineages as they confront challenges from human-induced climate warming, droughts, and wildfires across California.

The biogeography of bent-toed geckos, Cyrtodactylus (Squamata: Gekkonidae)

The gekkonid genus Cyrtodactylus is the third largest vertebrate genus on the planet with well over 300 species that range across at least eight biogeographic regions from South Asia to Melanesia. The ecological and morphological plasticity within the genus, has contributed to its ability to disperse across ephemeral seaways, river systems, basins, land bridges, and mountain ranges-followed by in situ diversification within specific geographic areas. Ancestral ranges were reconstructed on a mitochondrial phylogeny with 346 described and undescribed species from which it was inferred that Cyrtodactylus evolved in a proto-Himalaya region during the early Eocene. From there, it dispersed to what is currently Indoburma and Indochina during the mid-Eocene-the latter becoming the first major center of origin for the remainder of the genus that seeded dispersals to the Indian subcontinent, Papua, and Sundaland. Sundaland became a second major center of radiation during the Oligocene and gave rise to a large number of species that radiated further within Sundaland and dispersed to Wallacea, the Philippines, and back to Indochina. One Papuan lineage dispersed west to recolonize and radiate in Sundaland. Currently, Indochina and Sundaland still harbor the vast majority of species of Cyrtodactylus.

Phylogenetic and multivariate analyses of Gekko smithii Gray, 1842 recover a new species from Peninsular Malaysia and support the resurrection of G. albomaculatus (Giebel, 1861) from Sumatra

Abstract

An integrative taxonomic analysis of Sundaic populations of Gekko smithii from the Thai-Malaya Peninsula, Sumatra, and Borneo recovered four deeply divergent mitochondrial lineages that are separated by major geographic barriers (mountains and seaways). Furthermore, they bear a number of concordant statistically significant differences in meristic and morphometric features, morphospatial separation in multivariate space, and discrete differences in color pattern. Gekko smithiisensu stricto is restricted to southern Thailand south of the Isthmus of Kra and Peninsular Malaysia west of the Banjaran (mountain range) Titiwangsa, being that the type locality is on Penang Island, Penang. Gekko hulksp. nov. is a new species from extreme southern Thailand and Peninsular Malaysia east of the Banjaran Titiwangsa and five east coast islands—the type locality being Pulau (island) Tioman, Pahang. Gekko cf. albofasciolatus is tentatively used to include Bornean populations west of the Iran Mountains in Sabah and Sarawak which, in the absence of molecular data, cannot unequivocally be separated morphologically from G. albofasciolatus from the type locality at Banjarmasin, Kalimantan, Indonesia east of the Iran Mountains. In the absence of molecular data, G. albomaculatus is resurrected to include mainland Sumatran, Nias Island, and Banyak Islands populations which, based on their morphology, cannot be separated from descriptions of G. albomaculatus from the type locality of Bangka Island, 15 km off the southeast coast of mainland Sumatra. Further integrative analyses of all Sumatran and Bornean populations are currently underway as well as the enigmatic Wallacean populations from Sulawesi. Data are presented that strongly suggest all references to G. smithii from Java stem from a 151 year-old misidentification of a specimen of G. gecko of unknown provenance. Additionally, there are no vouchered records of G. smithii from Myanmar. The phylogeographic patterns of Sundaic populations of the G. smithii complex are concordant with those of a plethora of other Sundaic lineages.

Description of two new species of <i>Hemiphyllodactylus</i> (Reptilia: Gekkonidae) from karst landscapes in Yunnan, China, highlights complex conservation needs

Karst habitats are hotspots of diversity and endemism. Their naturally fragmented distributions across broad geographic landscapes have led to the complex array of smaller evolutionary ecosystems that present unique challenges from a conservation perspective. Comprehensive biodiversity assessments of karst habitats have revealed that these ecosystems contain an almost unparalleled level of endemism, and many site-restricted species remain undescribed, thus posing considerable challenges for effective conservation management. Small rock-dwelling species, such as geckos, may be particularly prone to such isolation. In this paper, we discuss one such genus, i.e., Hemiphyllodactylus, and explore its diversity across karst landforms in Yunnan Province, southwestern China. Based on morphological and genetic data, we describe two new species of Hemiphyllodactylus from karst habitats in Simao District and Yanshan County. A phylogenetic tree for Hemiphyllodactylus was constructed using 1 039 base pairs (bp) of the mitochondrial NADH dehydrogenase subunit 2 gene (ND2). The Simao and Yanshan specimens can be distinguished from all other congeners within their respective subclades based on uncorrected genetic pairwise distances greater than 6.3% and 4.3% respectively, as well as significant morphological differences. The discovery and description of these two new species brings the total number of described Hemiphyllodactylus species in China to 14 and indicates many more undescribed species from unsurveyed karst regions await discovery. Our findings suggest that karst ecosystems in Yunnan support a higher diversity of Hemiphyllodactylus than previously known. This study also highlights the importance of karst ecosystems as refugia for site-specific endemic species and the need for heightened conservation efforts.

Convergent evolution of karst habitat preference and its ecomorphological correlation in three species of Bent-toed Geckos (Cyrtodactylus) from Peninsular Malaysia

Abstract

By studying ecomorophology in the context of phylogeny, researchers can parse out similarity due to common ancestry versus that due to convergence. This is especially true among relatively closely related species where both phylogenetic and environmental constraints may be operating simultaneously. We explored these issues among three karst-associated species from two lineages of Cyrtodactylus—the sworderi group from Peninsular Malaysia and the swamp clade from Peninsular Malaysia and western Indonesia of the agamensis group. A stochastic character mapping analysis using five different habitat preferences corroborated a larger previous analysis in recovering a general habitat preference as an ancestral condition for all habitat preferences and a karst habitat preference in C. guakanthanensis and C. gunungsenyumensis of the sworderi group and C. metropolis of the swamp clade as convergently evolved. Multivariate and univariate analyses of 10 morphometric characters revealed that the ecomorphological similarity between C. guakanthanensis and C. gunungsenyumensis of the sworderi group was also convergent. The ecomorphology of C. metropolis of the swamp clade was intermediate between a karst-adapted ecomorphology and a swamp-generalists ecomorphology. Of the 10 morphometric characters employed in this analysis, only three—head length, head width, and forelimb width—showed any signs of phylogenetic signal. Cyrtodactylus metropolis is hypothesized to be a recently refuged swamp-dwelling species that frequented the Batu Caves environments prior to urbanization of the surrounding swamp habitat to which it is now confined.

A new species of Hemiphyllodactylus Bleeker (Squamata: Gekkonidae) from Yunnan, China and its phylogenetic relationship to other congeners

A new species of the gekkonid genus Hemiphyllodactylus is described from forested karst hills near Zhutangxiang town, Lancang Lahu Autonomous County, Yunnan, China. Hemiphyllodactylus zhutangxiangensis sp. nov. is distinguished from all other congeners in morphology and an uncorrected pairwise sequence divergence of greater than 14% based on 1039 base pairs of the mitochondrial NADH dehydrogenase subunit 2 gene (ND2). The new species is defined by the following characters: a maximum SVL of 44.42 mm; 79 chin scales; enlarged postmentals; five circumnasal scales; 24 internasal scales; 811 supralabial scales; 811 infralabial scales; subdigital lamellae on fingers IIV (35)-(46)-(4 or 5)-(4 or 5); subdigital lamellae on toes IIV (4 or 5)-(4 or 5)-(46)-(4 or 5); dorsal scales 1115; ventral scales 57; 2023 continuous femoroprecloacal pores; having pale-grey base color on the body with various darker transverse dorsal blotches; a dark postorbital stripe extending to at least to the base of the neck; no dark dorsolateral or ventrolateral stripe on trunk; and postsacral marking bearing a dark fork-like pattern with anteriorly projecting arms. The new species brings the species total of Hemiphyllodactylus in China to 11.

Phylogenetic partitioning of the third-largest vertebrate genus in the world, Cyrtodactylus Gray, 1827 (Reptilia; Squamata; Gekkonidae) and its relevance to taxonomy and conservation

The gekkonid genus Cyrtodactylus is the third most speciose vertebrate genus in the world, containing well over 300 species that collectively range from South Asia to Melanesia across some of the most diverse landscapes and imperiled habitats on the planet. A genus-wide phylogeny of the group has never been presented because researchers working on different groups were using different genetic markers to construct phylogenies that could not be integrated. We present here Maximum likelihood and Bayesian inference mitochondrial and mito-nuclear phylogenies incorporating of 310 species that include dozens of species that had never been included in a genus-wide analysis. Based on the mitochondrial phylogeny, we partition Cyrtodactylus into 31 well-supported monophyletic species groups which, if used as recommended herein, will increase the information content of future integrative taxonomic analyses that continue to add new species to this genus at an ever-increasing annual rate. Data presented here reiterate the outcome of several previous studies indicating that Cyrtodactylus comprises an unprecedented number of narrow-range endemics restricted to single mountain tops, small islands, or karst formations that still remain unprotected. This phylogeny can provide a platform for various comparative ecological studies that can be integrated with conservation management programs across the broad diversity of landscapes and habitats occupied by this genus. Additionally, these data indicate that the true number of Cyrtodactylus remains substantially underrepresented.

Phylogenetic partitioning of the third-largest vertebrate genus in the world, Cyrtodactylus Gray, 1827 (Reptilia; Squamata; Gekkonidae) and its relevance to taxonomy and conservation

The gekkonid genus Cyrtodactylus is the third most speciose vertebrate genus in the world, containing well over 300 species that collectively range from South Asia to Melanesia across some of the most diverse landscapes and imperiled habitats on the planet. A genus-wide phylogeny of the group has never been presented because researchers working on different groups were using different genetic markers to construct phylogenies that could not be integrated. We present here Maximum likelihood and Bayesian inference mitochondrial and mito-nuclear phylogenies incorporating of 310 species that include dozens of species that had never been included in a genus-wide analysis. Based on the mitochondrial phylogeny, we partition Cyrtodactylus into 31 well-supported monophyletic species groups which, if used as recommended herein, will increase the information content of future integrative taxonomic analyses that continue to add new species to this genus at an ever-increasing annual rate. Data presented here reiterate the outcome of several previous studies indicating that Cyrtodactylus comprises an unprecedented number of narrow-range endemics restricted to single mountain tops, small islands, or karst formations that still remain unprotected. This phylogeny can provide a platform for various comparative ecological studies that can be integrated with conservation management programs across the broad diversity of landscapes and habitats occupied by this genus. Additionally, these data indicate that the true number of Cyrtodactylus remains substantially underrepresented.

The Results of Four Recent Joint Expeditions to the Gobi Desert: Lacertids and Agamids

The National University of Mongolia, the Mongolian State University of Education, the University of Nebraska, and the University of Kansas conducted four collaborative expeditions between 2010 and 2014, resulting in accounts for all species of lacertid and agamid, except Phrynocephalus kulagini. These expeditions resulted in a range extension for Eremias arguta and the collection of specimens and tissues across 134 unique localities. In this paper we summarize the species of the Agamidae (Paralaudakia stoliczkana, Ph. hispidus, Ph. helioscopus, and Ph. versicolor) and Lacertidae (E. argus, E. arguta, E. dzungarica, E. multiocellata, E. przewalskii, and E. vermiculata) that were collected during these four expeditions. Further, we provide a summary of all species within these two families in Mongolia. Finally, we discuss issues of Wallacean and Linnaean shortfalls for the herpetofauna of the Mongolian Gobi Desert, and provide future directions for studies of community assemblages and population genetics of reptile species in the region.

Evolution of habitat preference in 243 species of Bent-toed geckos (Genus Cyrtodactylus Gray, 1827) with a discussion of karst habitat conservation

Understanding the processes that underpin adaptive evolutionary shifts within major taxonomic groups has long been a research directive among many evolutionary biologists. Such phenomena are best studied in large monophyletic groups that occupy a broad range of habitats where repeated exposure to novel ecological opportunities has happened independently over time in different lineages. The gekkonid genus Cyrtodactylus is just such a lineage with approximately 300 species that range from South Asia to Melanesia and occupy a vast array of habitats. Ancestral state reconstructions using a stochastic character mapping analysis of nine different habitat preferences were employed across a phylogeny composed of 76% of the known species of Cyrtodactylus. This was done in order to ascertain which habitat preference is the ancestral condition and from that condition, the transition frequency to more derived habitat preferences. The results indicate that a general habitat preference is the ancestral condition for Cyrtodactylus and the frequency of transitioning from a general habitat preference to anything more specialized occurs approximately four times more often than the reverse. Species showing extreme morphological and/or ecological specializations generally do not give rise to species bearing other habitat preferences. The evolution of different habitat preferences is generally restricted to clades that tend to occur in specific geographic regions. The largest radiations in the genus occur in rocky habitats (granite and karst), indicating that the transition from a general habitat preference to a granite or karst-dwelling life style may be ecologically uncomplicated. Two large, unrelated clades of karst-associated species are centered in northern Indochina and the largest clade of granite-associated species occurs on the Thai-Malay Peninsula. Smaller, independent radiations of clades bearing other habitat preferences occur throughout the tree and across the broad distribution of the genus. With the exception of a general habitat preference, the data show that karst-associated species far out-number all others (29.6% vs. 0.4%-10.2%, respectively) and the common reference to karstic regions as "imperiled arcs of biodiversity" is not only misleading but potentially dangerous. Karstic regions are not simply refugia harboring the remnants of local biodiversity but are foci of speciation that continue to generate the most speciose, independent, radiations across the genus. Unfortunately, karstic landscapes are some of the most imperiled and least protected habitats on the planet and these data continue to underscore the urgent need for their conservation.

A new insular species of the Cyrtodactylus intermedius (Squamata: Gekkonidae) group from Cambodia with a discussion of habitat preference and ecomorphology

An integrative taxonomic analysis based on mitochondrial and morphological data recovered the population of Cyrtodactylus on Koh Rong Island, Preah Sihanouk Province, Cambodiaa as an endemic insular species belonging to the Cyrtodactylus intermedius group. This brings the number of species in the C. intermedius group to at least 10 and the number of species in Cambodia to at least seven. Species of this relatively small group vary widely in habitat preference, occurring in general, terrestrial, karstic, or granitic habitats. Ancestral character state mapping recovered a general habitat preference as the ancestral condition from which all others independently evolved even though this did not covary with morphology. The description of another new species of reptile from Cambodia continues to underscore the potentially significant amount of unrealized biodiversity in Indochina and Southeast Asia and the continued need for field surveys in unexplored or poorly explored areas.

Rivers of Indochina as potential drivers of lineage diversification in the spotted flying lizard (Draco maculatus) species complex

Southeast Asia hosts a rich concentration of biodiversity within multiple biodiversity hotspots. Indochina, a region with remarkably high levels of in situ diversification, possesses five major rivers (Ayeyarwady, Chiang Mai, Mekong, Red, and Salween), several of which coincide with phylogenetic breaks of terrestrial taxa. Draco maculatus possesses a range that stretches across Indochina, which widespread geographic distribution along with potential discrete variation within subspecies alludes to the possibility of this taxon constituting multiple divergent lineages. Using sequence data from three mitochondrial (12S, 16S, and ND2) and three nuclear (BDNF, CMOS, and PNN) genes, we provide the first estimated phylogeny of this hypothesized species complex and examine its phylogeographic architecture with maximum likelihood and Bayes factor delimitation (BFD) approaches. Our results support multiple divergent lineages with phylogenetic breaks coincident with rivers, indicating that river barriers may be contributing to the elevated levels of in situ diversification of Indochina.

Geographic structure of genetic variation in the Parachute Gecko Ptychozoon lionotum Annandale, 1905 across Indochina and Sundaland with descriptions of three new species

An integrative taxonomic analysis of the Ptychozoon lionotum group across its range in Indochina and Sundaland recovers P. lionotum sensu lato Annandale, 1905 as paraphyletic with respect to P. popaense Grismer, Wood, Thura, Grismer, Brown, Stuart, 2018a and composed of four allopatric, genetically divergent, ND2 mitochondrial lineages. Multivariate and univariate analyses of continuous and discrete morphological and color pattern characters statistically and discretely diagnose each lineage from one another and together, with maximum likelihood and Bayesian inference analyses, provide the foundation for the recognition of each lineage as a new species-hypotheses corroborated with a Generalized Mixed Yule Coalescent species delimitation analysis. Ptychozoon cicakterbang sp. nov. ranges throughout Peninsular Malaysia to Pulau Natuna Besar, Indonesia; P. kabkaebin sp. nov. is endemic to northern and central Laos; and P. tokehos sp. nov. ranges from southern Thailand south of the Isthmus of Kra northward to Chiang Mai, fringing the Chao Phraya Basin and ranging southward through Cambodia to southern Vietnam. Ptychozoon lionotum sensu stricto ranges from northwestern Laos through southern Myanmar to eastern India. The phylogeographic structure within each species varies considerably with P. lionotum s.s. showing no genetic divergence across its 1,100 km range compared to P. cicakterbang sp. nov. showing upwards of 8.2% sequence divergence between syntopic individuals. Significant phylogeographic structure exists within P. tokehos sp. nov. and increased sampling throughout Thailand may require additional taxonomic changes within this species.

The Eurasian invasion: phylogenomic data reveal multiple Southeast Asian origins for Indian Dragon Lizards

BACKGROUND

The Indian Tectonic Plate split from Gondwanaland approximately 120 MYA and set the Indian subcontinent on a ~ 100 million year collision course with Eurasia. Many phylogenetic studies have demonstrated the Indian subcontinent brought with it an array of endemic faunas that evolved in situ during its journey, suggesting this isolated subcontinent served as a source of biodiversity subsequent to its collision with Eurasia. However, recent molecular studies suggest that Eurasia may have served as the faunal source for some of India's biodiversity, colonizing the subcontinent through land bridges between India and Eurasia during the early to middle Eocene (~35-40 MYA). In this study we investigate whether the Draconinae subfamily of the lizard family Agamidae is of Eurasian or Indian origin, using a multi locus Sanger dataset and a novel dataset of 4536 ultraconserved nuclear element loci.

RESULTS

Results from our phylogenetic and biogeographic analyses revealed support for two independent colonizations of India from Eurasian ancestors during the early to late Eocene prior to the subcontinent's hard collision with Eurasia.

CONCLUSION

These results are consistent with other faunal groups and new geologic models that suggest ephemeral Eocene land bridges may have allowed for dispersal and exchange of floras and faunas between India and Eurasia during the Eocene.

First record of Batrachochytrium dendrobatidis infecting four frog families from Peninsular Malaysia

The fungal pathogen Batrachochytrium dendrobatidis (Bd) infects amphibians on every continent where they occur and is linked to the decline of over 200 amphibian species worldwide. At present, only three published Bd surveys exist for mainland Asia, and Bd has been detected in South Korea alone. In this article, we report the first survey for Bd in Peninsular Malaysia. We swabbed 127 individuals from the six amphibian families that occur on Peninsular Malaysia, including two orders, 27 genera, and 47 species. We detected Bd on 10 out of 127 individuals from four of five states and five of 11 localities, placing the 95% confidence interval for overall prevalence at 4-14%. We detected no variation in Bd prevalence among regions, elevations, or taxonomic groups. The infection intensity ranged from 1 to 157,000 genome equivalents. The presence of Bd infections in native species without clinical signs of disease suggests that Bd may be endemic to the region. Alternately, Bd may have been introduced from non-native amphibians because of the substantial amphibian food trade in Peninsular Malaysia. Under both scenarios, management efforts should be implemented to limit the spread of non-native Bd and protect the tremendous amphibian diversity in Peninsular Malaysia.