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Background High-quality genomic resources facilitate investigations into behavioral ecology, morphological and physiological adaptations, and the evolution of genomic architecture. Lizards in the genus Sceloporus have a long history as important ecological, evolutionary, and physiological models, making them a valuable target for the development of genomic resources. Findings We present a high-quality chromosome-level reference genome assembly, SceUnd1.0 (using 10X Genomics Chromium, HiC, and Pacific Biosciences data), and tissue/developmental stage transcriptomes for the eastern fence lizard, Sceloporus undulatus. We performed synteny analysis with other snake and lizard assemblies to identify broad patterns of chromosome evolution including the fusion of micro- and macrochromosomes. We also used this new assembly to provide improved reference-based genome assemblies for 34 additional Sceloporus species. Finally, we used RNAseq and whole-genome resequencing data to compare 3 assemblies, each representing an increased level of cost and effort: Supernova Assembly with data from 10X Genomics Chromium, HiRise Assembly that added data from HiC, and PBJelly Assembly that added data from Pacific Biosciences sequencing. We found that the Supernova Assembly contained the full genome and was a suitable reference for RNAseq and single-nucleotide polymorphism calling, but the chromosome-level scaffolds provided by the addition of HiC data allowed synteny and whole-genome association mapping analyses. The subsequent addition of PacBio data doubled the contig N50 but provided negligible gains in scaffold length. Conclusions These new genomic resources provide valuable tools for advanced molecular analysis of an organism that has become a model in physiology and evolutionary ecology.

Davis, Hayden R., Grismer, L. Lee, Klabacka, Randy L., Muin, Mohd Abdul, Quah, Evan S. H., Anuar, Shahrul, Wood Jr, Perry L., Sites, Jack W. (2016): The phylogenetic relationships of a new Stream Toad of the genus Ansonia Stoliczka, 1870 (Anura: Bufonidae) from a montane region in Peninsular Malaysia. Zootaxa 4103 (2): 137-153, DOI: http://doi.org/10.11646/zootaxa.4103.2.4

Ansonia smeagol sp. nov. The Precious Stream-Toad Fig. 3 A Holotype. Adult female (LSUHC 12124) collected on 16 March 2015 from Genting Highlands, Malaysia (3 �� 25 ��� 26.32 ��� N; 101 �� 47 ��� 35.52 ���, 1218 m in elevation) by Lee Grismer, Perry L. Wood JR., Brandon T. Burch, Anthony J. Cobos, Matthew L. Murdoch, and Hayden R. Davis. Paratypes. All nine paratypes have the same collection data as the holotype (LSUHC 12122, 12123, 12125, 12126, 11641, 11645, 12076, 12078, 12270). LSUHC 12248 is the only male. Diagnosis. Ansonia smeagol sp. nov. is assigned to the genus Ansonia based on its phylogenetic placement and the following morphological characteristics: small body size; slender limbs; no parotoid glands; weak subarticular tubercles; and membranous foot webbing. It can be differentiated from all other species of Ansonia by the combination of the following characters: SVL 24.6���27.4 mm in females; snout projecting beyond lower jaw; tympanum visible; white tubercle at rictus; finger and toe tips rounded; presence of inner and outer metatarsal tubercle; presence of gular spotting; faint presence of crossbars on hind limbs; and the faint presence of a middorsal stripe extending from the tip of the snout to the interscapular region. Description of holotype. Adult female, SVL 27.3 mm; head longer than wide (HL/HW= 1.02); snout shorter than wide (SL/SW= 0.68), extending beyond lower jaw, dorsally convex with a midline depression; canthus rostralis distinct; nares open laterally just below canthus, nearly terminal on snout; distance between nares smaller than snout length (IND /SL= 0.93) and snout width (IND /SW= 0.63); eyes large, slightly protruding beyond labials in dorsal view, diameter slightly larger than snout length (ED/SL= 1.07), less than one-half the size of interorbital distance (ED/IOD= 0.40); tympanum fairly distinct, circular with horizontal axis being shorter than eye diameter (TD/ED= 0.45); choanae subcircular, separated by a distance larger than their diameter; vomerine ridge and teeth absent; tongue narrow, ending in median point, posterior one-half free. continued. Forelimbs and fingers long and slender; finger length from shortest to longest: I, II, IV, III; basal webbing not extending beyond proximal subarticular tubercle; fingertips rounded, slightly dilated but not forming discs; subarticular tubercles distinct; inner and outer metacarpal tubercles distinct, oval, raised, inner slightly smaller than outer. Hindlimbs and toes are long and slender (CL/SVL= 0.29), foot longer than tibia (PL/CL= 1.33); toe length from longest to shortest: I, II, III, V, IV; webbing formula: I 1, II ��- 2, III 1 ��- 2, IV 3 ��- 3.7, V 1.5; tips rounded, dilated but not forming discs; subarticular tubercles distinct; inner tubercle elongate, raised; outer tubercle raised, oval, slightly smaller than inner. Upper eyelid, interorbital region, and dorsal part of snout and canthus covered in small, raised tubercles bearing keratinized tips; interorbital ridges absent; few randomly dispersed tubercles present on lores; single row of small spinules on upper lip and outer margin of upper eyelid; large tubercle just above rictus, posterior to tympanum; supratympanic fold and parotoid gland absent; back, flanks, and dorsal part of limbs bearing irregularly spaced large and small tubercles bearing white or brown keratinized spinules; entire ventral surface except for manus and pes covered with fine, evenly spaced spinules that are most dense around rictal and pectoral region; and ventral surface finely granular in both males and females. Coloration in life (Fig. 3 A). Dorsal ground color is dark brown to black; flanks bearing randomly arranged, white patches; large, white tubercle at rictus with a smaller, white tubercle present between rictus and posterior upper labial tubercles on left side of head but absent on right; four small, white patches on upper, right lip and three small, white patches on upper, left lip; white patches on ventral side of mandible, near the vent, and on anterior portion of thigh; and ventral portion of thigh much lighter than other parts of body. Variations (Fig. 4). All paratypes closely resembled the holotype in both coloration and pattern. Apart from one paratype (LSUHC 12125), the ventral portion of the thigh was not lighter in coloration than the rest of the ventral surface. The same paratype also showed a higher prominence of white spotting on the ventral portion of the body. None of the paratypes had a tubercle anterior to the large, white tubercle at the rictus, as was seen in the holotype. Measurements showing the variation in size within the type series are shown in Table 4. Comparisons. Morphological data for species comparisons were obtained from Wood et al. (2008) and the material examined (Appendix). Ansonia smeagol sp. nov. forms a monophyletic group with A. jeetsukumarani, A. lumut, A. malayana, and A. penangensis (Fig. 3). Ansonia smeagol sp. nov. differs from A. lumut by having a slightly smaller SVL (24.6���27.4 mm versus 27.7���31.6 mm in females, respectively), lacking a large yellow tubercle at the angle of the jaw, lacking a dorsolateral row of enlarged tubercles, and having a coarsely granular abdomen. It is differentiated from A. jeetsukumarani by lacking a dorsolateral row of enlarged tubercles, having an inner metatarsal tubercle, and the absence of orange coloration on the flanks and orange banding on the limbs. It differs from A. malayana by lacking a large yellow tubercle at the angle of the jaw, the absence of a light orange coloration on limbs and dorsum, and the absence of an ���X��� pattern on the dorsum. It differs from A. penangensis by its smaller SVL (24.6 mm versus 37.2 mm in females), the absence of a tarsal ridge, and the absence of orange bands on the limbs. Comparisons to all other Ansonia species can be found in Table 3. Distribution and natural history. Ansonia smeagol sp. nov. is only known to occur in the upland regions of the Titiwangsa Mountain Range (1218m in elevation) at Genting Highlands. Four of the specimens were found between 2000 and 2300 hrs in a small drainage ditch at the side of a dirt road, next to a muddy slope covered by hill dipterocarp forest. Five other specimens were found on top of the leaf litter, in a closed canopy forest (Fig. 5). Both localities were in the vicinity (50���200 m) of a large, fast-flowing rocky stream with various side pools. The holotype and four out of the eight paratypes were collected during the month of March, three of which were gravid indicating that March falls within this species��� reproductive season. Etymology. The specific epithet is a noun in apposition in reference to ������Sm��agol������, a fictional character created by J. R. R. Tolkien in The Hobbit (1937). Sm��agol is an upland, semiaquatic, large-eyed, creature inhabiting the Misty Mountains of Middle Earth who has long, thin limbs bearing digits with bulbous tips, large webbed feet, and large protruding eyes���characters found in the new population being described herein., Published as part of Davis, Hayden R., Grismer, L. Lee, Klabacka, Randy L., Muin, Mohd Abdul, Quah, Evan S. H., Anuar, Shahrul, Wood Jr, Perry L. & Sites, Jack W., 2016, The phylogenetic relationships of a new Stream Toad of the genus Ansonia Stoliczka, 1870 (Anura: Bufonidae) from a montane region in Peninsular Malaysia, pp. 137-153 in Zootaxa 4103 (2) on pages 148-150, DOI: 10.11646/zootaxa.4103.2.4, http://zenodo.org/record/263920, {"references":["Wood, Jr., P. L., Grismer, L. L., Ahmad, N. & Senawi, J. (2008) Two new species of torrent-dwelling toads Ansonia Stoliczka, 1870 (Anura: Bufonidae) from Peninsular Malaysia. Herpetologica, 64 (3), 321 - 340. http: // dx. doi. org / 10.1655 / 07 - 065.1"]}