Species distribution modelling of the endangered Mahogany Glider (Petaurus gracilis) reveals key areas for targeted survey and conservation

The Mahogany Glider (Petaurus gracilis) is one of the most endangered marsupials in Australia. Its known distribution is an approximately 120 km strip of fragmented coastal woodland in north-east Queensland, from north of Townsville to the Tully area. Records are clustered in a number of well-surveyed areas, with significant areas of lowland habitat unsurveyed. Around 30% of historic records fall in areas that were subsequently cleared for farmland, and ongoing clearing and fragmentation of lowland sclerophyll forest continues within the potential distribution. Resolving the distribution is an urgent requirement to guide conservation but Mahogany Gliders are difficult to detect in the field. Species distribution modelling offers a technique for estimating the fine-scale distribution and for targeting further field survey and conservation efforts. We used known occurrence records (N = 481) to predict the distribution of Mahogany Gliders across the Wet Tropics bioregion. We used climatic, topographic and other environmental predictors to generate distribution models using Maxent and Random Forest algorithms, each with two bias correction methods. The predictions revealed that many unknown populations may exist within the currently defined distribution and in important areas beyond this (e.g. Hinchinbrook Island). There was reasonable congruence between models, and we include syntheses of the models to present the most likely current distribution. The most important predictor variables across the models were precipitation seasonality (high seasonality), elevation (generally <100 m), soil type (hydrosols) and vegetation type (including Eucalyptus and Melaleuca woodlands). Our results identify core habitat and reveal key areas that require targeted field surveys. Importantly, the predicted suitable habitat is highly fragmented and ongoing conservation efforts need to improve habitat connectivity and limit further fragmentation

Conservation genomics reveals fine-scale population structuring and recent declines in the Critically Endangered Australian Kuranda Treefrog

The Kuranda Treefrog occurs in tropical north-east Australia and is listed as Critically Endangered due to its small distribution and population size, with observed declines due to drought and human-associated impacts to habitat. Field surveys identified marked population declines in the mid-2000s, culminating in very low abundance at most sites in 2005 and 2006, followed by limited recovery. Here, samples from before (2001–2004) and after (2007–2009) this decline were analysed using 7132 neutral genome-wide SNPs to assess genetic connectivity among breeding sites, genetic erosion, and effective population size. We found a high level of genetic connectivity among breeding sites, but also structuring between the population at the eastern end of the distribution (Jumrum Creek) versus all other sites. Despite finding no detectable sign of genetic erosion between the two times periods, we observed a marked decrease in effective population size (Ne), from 1720 individuals pre-decline to 818 post-decline. This mirrors the decline detected in the field census data, but the magnitude of the decline suggested by the genetic data is greater. We conclude that the current effective population size for the Kuranda Treefrog remains around 800 adults, split equally between Jumrum Creek and all other sites combined. The Jumrum Creek habitat requires formal protection. Connectivity among all other sites must be maintained and improved through continued replanting of rainforest, and it is imperative that impacts to stream flow and water quality are carefully managed to maintain or increase population sizes and prevent genetic erosion

Evidence of a distinct stellar population in the counter-rotating core of NGC 1700

We find a distinct stellar population in the counter-rotating and kinematically decoupled core of the isolated massive elliptical galaxy NGC 1700. Coinciding with the edge of this core we find a significant change in the slope of the gradient of various representative absorption line indices. Our age estimate for this core is markedly younger than the main body of the galaxy. We find lower values for the age, metallicity and Mg/Fe abundance ratio in the center of this galaxy when we compare them with other isolated elliptical galaxies with similar velocity dispersion. We discuss the different possible scenarios that might have lead to the formation of this younger kinematically decoupled structure and conclude that, in light of our findings, the ingestion of a small stellar companion on a retrograde orbit is the most favoured.Comment: 13 pages, 5 figures, accepted for publication in ApJ

Dating the formation of the counter-rotating stellar disc in the spiral galaxy NGC 5719 by disentangling its stellar populations

We present the results of the VLT/VIMOS integral-field spectroscopic observations of the inner 28"x28" (3.1 kpc x 3.1 kpc) of the interacting spiral NGC 5719, which is known to host two co-spatial counter-rotating stellar discs. At each position in the field of view, the observed galaxy spectrum is decomposed into the contributions of the spectra of two stellar and one ionised-gas components. We measure the kinematics and the line strengths of the Lick indices of the two stellar counter-rotating components. We model the data of each stellar component with single stellar population models that account for the alpha/Fe overabundance. We also derive the distribution and kinematics of the ionised-gas disc, that is associated with the younger, less rich in metals, more alpha-enhanced, and less luminous stellar component. They are both counter-rotating with respect the main stellar body of the galaxy. These findings prove the scenario where gas was accreted first by NGC 5719 onto a retrograde orbit from the large reservoir available in its neighbourhoods as the result of the interaction with its companion NGC 5713, and subsequently fuelled the in situ formation of the counter-rotating stellar disc.Comment: 5 pages, 4 figures. Accepted for publication in MNRAS letters. Reference list update

The first linkage map for Australo-Papuan Treefrogs (family: Pelodryadidae) reveals the sex-determination system of the Green-eyed Treefrog (Litoria serrata)

Amphibians represent a useful taxon to study the evolution of sex determination because of their highly variable sex-determination systems. However, the sex-determination system for many amphibian families remains unknown, in part because of a lack of genomic resources. Here, using an F1 family of Green-eyed Treefrogs (Litoria serrata), we produce the first genetic linkage map for any Australo-Papuan Treefrogs (family: Pelodryadidae). The resulting linkage map contains 8662 SNPs across 13 linkage groups. Using an independent set of sexed adults, we identify a small region in linkage group 6 matching an XY sex-determination system. These results suggest Litoria serrata possesses a male heterogametic system, with a candidate sex-determination locus on linkage group 6. Furthermore, this linkage map represents the first genomic resource for Australo-Papuan Treefrogs, an ecologically diverse family of over 220 species

Kinematic Signatures of Bulges Correlate with Bulge Morphologies and S\'ersic Index

We use the Marcario Low Resolution Spectrograph (LRS) at the Hobby-Eberly-Telescope (HET) to study the kinematics of pseudobulges and classical bulges in the nearby universe. We present major-axis rotational velocities, velocity dispersions, and h3 and h4 moments derived from high-resolution (sigma ~ 39 km/s) spectra for 45 S0 to Sc galaxies; for 27 of the galaxies we also present minor axis data. We combine our kinematics with bulge-to-disk decompositions. We demonstrate for the first time that purely kinematic diagnostics of the bulge dichotomy agree systematically with those based on S\'ersic index. Low S\'ersic index bulges have both increased rotational support (higher v/sigma values) and on average lower central velocity dispersions. Furthermore, we confirm that the same correlation also holds when visual morphologies are used to diagnose bulge type. The previously noted trend of photometrically flattened bulges to have shallower velocity dispersion profiles turns to be significant and systematic if the S\'ersic index is used to distinguish between pseudobulges and classical bulges. The correlation between h3 and v/sigma observed in elliptical galaxies is also observed in intermediate type galaxies, irrespective of bulge type. Finally, we present evidence for formerly undetected counter rotation in the two systems NGC 3945 and NGC 4736. Based on observations obtained with the Hobby-Eberly Telescope, which is a joint project of the University of Texas at Austin, the Pennsylvania State University, Stanford University, Ludwig-Maximilians-Universit\"at M\"unchen, and Georg-August-Universit\"at G\"ottingen.Comment: 49 pages, 16 figures. Accepted for publication in Ap

Stellar kinematics across the Hubble sequence in the CALIFA survey: general properties and aperture corrections

We would like to thank the anonymous referee for constructive comments that helped improve some aspects of the original manuscript. We are also grateful to the DiskMass survey team for sharing their data with us for the spectral resolution tests, and to Marc Verheijen and Kyle Westfall in particular for in-depth discussions on the topic. This study makes use of the data provided by the Calar Alto Legacy Integral Field Area (CALIFA) survey (http://califa.caha.es). Based on observations collected at the Centro Astronómico Hispano Alemán (CAHA) at Calar Alto, operated jointly by the Max-Planck-Institut für Astronomie and the Instituto de Astrofísica de Andalucía (CSIC). CALIFA is the first legacy survey being performed at Calar Alto. The CALIFA collaboration would like to thank the IAA-CSIC and MPIA-MPG as major partners of the observatory, and CAHA itself, for the unique access to telescope time and support in manpower and infrastructures. The CALIFA collaboration thanks also the CAHA staff for the dedication to this project.We present the stellar kinematic maps of a large sample of galaxies from the integral-field spectroscopic survey CALIFA. The sample comprises 300 galaxies displaying a wide range of morphologies across the Hubble sequence, from ellipticals to late-type spirals. This dataset allows us to homogeneously extract stellar kinematics up to several effective radii. In this paper, we describe the level of completeness of this subset of galaxies with respect to the full CALIFA sample, as well as the virtues and limitations of the kinematic extraction compared to other well-known integral-field surveys. In addition, we provide averaged integrated velocity dispersion radial profiles for different galaxy types, which are particularly useful to apply aperture corrections for single aperture measurements or poorly resolved stellar kinematics of high-redshift sources. The work presented in this paper sets the basis for the study of more general properties of galaxies that will be explored in subsequent papers of the survey.J. F.-B. from grant AYA2013- 48226-C3-1-P from the Spanish Ministry of Economy and Competitiveness (MINECO). J.F.-B. and G.v.d.V. from the FP7 Marie Curie Actions of the European Commission, via the Initial Training Network DAGAL under REA grant agreement number 289313. J.M.-A. and V.W. acknowledge support from the European Research Council Starting Grant (SEDMorph P.I. V. Wild). P.S.-B. acknowledge financial support from the BASAL CATA Center for Astrophysics and Associated Technologies through grant PFB-06. R.M.G.D. from grant AYA2014-57490-P. R.G.-B, R.M.G.D. and E.P. acknowledge support from the project JA-FQM-2828. C.J.W. acknowledges support through the Marie Curie Career Integration Grant 303912. L.G. from the Ministry of Economy, Development, and Tourism’s Millennium Science Initiative through grant IC120009 awarded to The Millennium Institute of Astrophysics (MAS), and CONICYT through FONDECYT grant 3140566. I.M. from grant AYA2013-42227-P

The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation

Amphibians represent a diverse group of tetrapods, marked by deep divergence times between their three systematic orders and families. Studying amphibian biology through the genomics lens increases our understanding of the features of this animal class and that of other terrestrial vertebrates. The need for amphibian genomic resources is more urgent than ever due to the increasing threats to this group. Amphibians are one of the most imperiled taxonomic groups, with approximately 41% of species threatened with extinction due to habitat loss, changes in land use patterns, disease, climate change, and their synergistic efects. Amphibian genomic resources have provided a better understanding of ontogenetic diversity, tissue regeneration, diverse life history and reproductive modes, anti-predator strategies, and resilience and adaptive responses. They also serve as essential models for studying broad genomic traits, such as evolutionary genome expansions and contractions, as they exhibit the widest range of genome sizes among all animal taxa and possess multiple mechanisms of genetic sex determination. Despite these features, genome sequencing of amphibians has signifcantly lagged behind that of other vertebrates, primarily due to the challenges of assembling their large, repeat-rich genomes and the relative lack of societal support. The emergence of long-read sequencing technologies, combined with advanced molecular and computational techniques

Resolving distribution and population fragmentation in two leaf-tailed gecko species of north-east Australia: key steps in the conservation of microendemic species

North Queensland harbours many microendemic species. These species are of conservation concern due to their small and fragmented populations, coupled with threats such as fire and climate change. We aimed to resolve the distribution and population genetic structure in two localised Phyllurus leaf-tailed geckos: P. gulbaru and P. amnicola. We conducted field surveys to better resolve distributions, used Species Distribution Models (SDMs) to assess the potential distribution, and then used the SDMs to target further surveys. We also sequenced all populations for a mitochondrial gene to assess population genetic structure. Our surveys found additional small, isolated populations of both species, including significant range extensions. SDMs revealed the climatic and non-climatic variables that best predict the distribution of these species. Targeted surveys based on the SDMs found P. gulbaru at an additional two sites but failed to find either species at other sites, suggesting that we have broadly resolved their distributions. Genetic analysis revealed population genetic structuring in both species, including deeply divergent mitochondrial lineages. Current and potential threats are overlain on these results to determine conservation listings and identify management actions. More broadly, this study highlights how targeted surveys, SDMs, and genetic data can rapidly increase our knowledge of microendemic species, and direct management

Phyllurus pinnaclensis Hoskin & Bertola & Higgie 2019, sp. nov.

&lt;i&gt;Phyllurus pinnaclensis&lt;/i&gt; sp. nov. &lt;p&gt;Pinnacles Leaf-tailed Gecko&lt;/p&gt; &lt;p&gt;(Figs 2, 3, 4A, 5A)&lt;/p&gt; &lt;p&gt; &lt;b&gt;Material examined. Holotype.&lt;/b&gt; QMJ96418, adult male, The Pinnacles (19.410&deg;S, 146.614&deg;E), 2 November 2015, C. J. Hoskin &amp; M. Higgie. &lt;b&gt;Paratypes.&lt;/b&gt; None.&lt;/p&gt; &lt;p&gt; &lt;b&gt;Diagnosis.&lt;/b&gt; Distinguished from congeners by the following characters: cylindrical, tapering tail; rostral scale partially divided by a single groove; high internasal count (7&ndash;10, typically 9 or 10); high subdigital lamellae count under the 4 th toe (19&ndash;21); original tail long (&gt; 85% SVL) and largely devoid of tubercles after the basal quarter.&lt;/p&gt; &lt;p&gt; &lt;b&gt;Etymology.&lt;/b&gt; Refers to The Pinnacles, the locality to which this species appears to be restricted.&lt;/p&gt; &lt;p&gt; &lt;b&gt; Description of holotype. &lt;i&gt;Measurements and scale counts.&lt;/i&gt;&lt;/b&gt; SVL = 85.22 mm, T (original) = 74.28 mm, TW = 6.94 mm, TD = 4.90 mm, AG = 38.76 mm, NL = 17.32 mm, HL = 22.69 mm, HW = 19.18 mm, HD = 8.20 mm, S = 10.98 mm, L1 = 37.90 mm, FLL = 16.00 mm, L2 = 49.10 mm, HLL = 19.10 mm, internasals = 10, supralabials = 16 (left side) and 15 (right side), infralabials = 15, subdigital lamellae under fingers (listed 1 st &ndash;5 th) = 12, 14, 17, 17, 16, subdigital lamellae under toes (listed 1 st &ndash;5 th) = 13, 17, 19, 20, 20. &lt;b&gt; &lt;i&gt;Head&lt;/i&gt;.&lt;/b&gt; Large, depressed, triangular; covered in very small granules with larger, pale, conical tubercles at back and sides of head (Figs 2A, 3, 4A); a bony ridge with larger granules extends forward from upper anterior margin of each eye towards naris (Fig. 3); skin of head co-ossified with skull; deep, vertical groove partially (25%) dividing rostral scale (Fig. 5A); rostral not in contact with nostril; 10 scales along the dorsal margin of rostral shield (Fig. 5A); first supralabial scale taller than wide, remaining supralabials broad and steadily decreasing in size; first infralabial scale taller than wide, remaining infralabials broad and steadily decreasing in size; granular scales of chin and throat largest along the edge of the mental and infralabials (particularly abutting infralabials 1&ndash;3) and diminishing in size to minute granules on the throat; ear opening inconspicuous, elliptical, vertical, much less than half as large as eye. &lt;i&gt;Neck.&lt;/i&gt; Broad; covered in small granules that are intermixed with larger pale conical tubercles, including prominent, sharp tubercles on the back of the head and anterior neck (Figs 2A, 3, 4A). &lt;i&gt;Body.&lt;/i&gt; Depressed, covered in small granules; flank granules intermixed with larger pale, conical tubercles (Figs 2A, 3, 4A); tubercles on back very small; ventral surface covered in even, smooth, fine granules, with no enlarged tubercles; preanal pores absent; large testicular bulge; conspicuous cloacal &lsquo;spurs&rsquo;, consisting of a cluster of white triangular scales, on the anterior-lateral margin (Fig. 4A); axilla deeply invaginated. &lt;i&gt;Limbs.&lt;/i&gt; Long and very slender, covered in small pointed tubercles dorsally (Figs 2A, 3, 4A); lacking enlarged tubercles on ventral surface; digits strongly compressed distally; dorsal surface of hands, feet and digits without enlarged conical tubercles (Fig. 3). &lt;i&gt;Original tail.&lt;/i&gt; Long, cylindrical, tapering (Figs 2A, 4A); slightly depressed at base; distal quarter of tail a very narrow attenuated tip, terminating with a minute, rounded, white 'knob'; dorsal surface covered in minute granules and fine tubercles; prominent enlarged spinose tubercles restricted to the basal quarter; ventral surface smooth with a mosaic of fine round scales. &lt;i&gt;Colour pattern in spirit&lt;/i&gt; (Fig. 4A). Dorsal base colour tan, with irregular dark brown blotches on head, body and limbs; blotches largest on body and neck, smallest on head; eyelids bluish grey; pale band from lower anterior margin of eye diagonally to midway along jaw, and similar pale band from lower posterior margin of eye diagonally to just behind jaw; pale &lsquo;band&rsquo; anterior to base of tail, and inconspicuous, irregular, pale transverse &lsquo;bars&rsquo; on back; top of hands and feet pale; most digits strongly banded; inner anterior digit almost completely white; original tail finely mottled light brown, with five prominent, regular, bright white transverse bands and fine white &lsquo;knob&rsquo; on tip; all ventral surfaces pale cream, with a few light brown smudges on throat, underside of limbs and testicular bulge. &lt;i&gt;Colour pattern in life.&lt;/i&gt; As above but base colour of body much lighter (whitish grey) and brown stippling on tail darker (Figs 2A, 3).&lt;/p&gt; &lt;p&gt;Note: Abbreviations of measurements are: SVL, Snout to vent length; AG, axilla to groin length; FL, forearm length; HLL, lower hindlimb length; T(O), original tail length; T(R), regenerated tail length; TW(O), original tail width; TD(O), original tail depth; HW, head width; HL, head length; HD, head depth; S, snout length; NL, neck length. See Methods for definitions.&lt;/p&gt; &lt;p&gt; &lt;b&gt;Field data.&lt;/b&gt; Data was collected from an additional nine individuals in the field. &lt;i&gt;Morphometrics and scalation.&lt;/i&gt; See Table 1. &lt;i&gt;Original tail.&lt;/i&gt; Shape as for holotype but slightly more depressed at base in some individuals. Tail colouration generally as for holotype, with all (N = 7) individuals having five prominent white bands (excluding white tip). Two of these individuals also had one or two less conspicuous thin, pale bands on tail. In most individuals, base colour (between the white bands) is darker than for holotype, generally almost black.&lt;/p&gt; &lt;p&gt; &lt;i&gt;Regenerated tail&lt;/i&gt; (Fig. 2B). Slightly depressed, cylindrical, bulbous at base and tapering to tip; covered with uniform granules aligned in fine concentric rings for the full length of the tail; no spinose tubercles. Regenerated tail heavily mottled dark brown on a tan base colour. &lt;i&gt;Colour pattern.&lt;/i&gt; As described for the holotype but with the following variation. Base colour of some individuals is brown, giving the whole animal a much darker appearance (e.g., Fig. 2B). Some individuals, have prominent pale spots or blotches on the dorsal surfaces of the body, head and limbs; in juveniles and subadults these are bright white. Variation in tail colour pattern described immediately above.&lt;/p&gt; &lt;p&gt; &lt;b&gt;Comparison.&lt;/b&gt; &lt;i&gt;Phyllurus pinnaclensis&lt;/i&gt; &lt;b&gt;sp. nov.&lt;/b&gt; could only be confused with congeners with a cylindrical, tapering tail. Of these, it is readily distinguished from &lt;i&gt;P. caudiannulatus&lt;/i&gt; Covacevich, 1975 and &lt;i&gt;P. kabikabi&lt;/i&gt; Couper, Hamley &amp; Hoskin, 2008 by a partially divided rostral scale (&lt;i&gt;versus&lt;/i&gt; completely divided). From &lt;i&gt;P. gulbaru&lt;/i&gt;, it is distinguished by a high internasal count (&lt;i&gt;P. gulbaru&lt;/i&gt; mean 6.5, range 5&ndash;8; &lt;i&gt;P. pinnaclensis&lt;/i&gt; &lt;b&gt;sp. nov.&lt;/b&gt; mean 9.1, range 7&ndash;10); high subdigital lamellae count under the 4 th toe (&lt;i&gt;P. gulbaru&lt;/i&gt; mean 17.9, range 16&ndash;19; &lt;i&gt;P. pinnaclensis&lt;/i&gt; &lt;b&gt;sp. nov.&lt;/b&gt; mean 20.0, range 19&ndash;21); longer original tail (&lt;i&gt;P. gulbaru&lt;/i&gt; T/SVL mean 0.80, range 0.71&ndash;0.84; &lt;i&gt;P. pinnaclensis&lt;/i&gt; &lt;b&gt;sp. nov.&lt;/b&gt; T/SVL mean 0.90, range 0.88&ndash;0.91) and regenerated tail (&lt;i&gt;P. gulbaru&lt;/i&gt; T/SVL mean 0.61, range 0.50&ndash;0.71; &lt;i&gt;P. pinnaclensis&lt;/i&gt; &lt;b&gt;sp. nov.&lt;/b&gt; T/SVL mean 0.73; range 0.73) (Table 1); and original tail largely devoid of prominent tubercles past the basal quarter (&lt;i&gt;versus&lt;/i&gt; prominent tubercles on at least basal half in &lt;i&gt;P. gulbaru&lt;/i&gt;). A relatively straightforward and near-diagnostic trait to assess in the field is the number of internasals, with&gt; 90% of &lt;i&gt;P. gulbaru&lt;/i&gt; individuals (N = 36) having &lt;8 (5&ndash;7) and 90% of &lt;i&gt;P. pinnaclensis&lt;/i&gt; &lt;b&gt;sp. nov.&lt;/b&gt; (N = 10) having&gt; 8 (9&ndash;10; but one aberrant individual had 7).&lt;/p&gt; &lt;p&gt; &lt;b&gt;Genetics.&lt;/b&gt; Approximately 6.4% divergent from &lt;i&gt;P. gulbaru&lt;/i&gt; for ND2 mtDNA (Fig. 1).&lt;/p&gt; &lt;p&gt; &lt;b&gt;Distribution.&lt;/b&gt; Appears to be restricted to The Pinnacles, 25 km south-west of Townsville (Fig. 1). Known from three areas of habitat on the western and southern Pinnacles (Fig. 1). Each of these small patches of habitat is isolated by unsuitable habitat that is too dry and/or not sufficiently rocky. Surveys of rainforest habitat in the northeastern Pinnacles (-19.397, 146.642) have failed to find &lt;i&gt;P. pinnaclensis&lt;/i&gt; &lt;b&gt;sp. nov.&lt;/b&gt;. This area has very high suitability in the SDM (dark green pixel in north-east Pinnacles in Figure 1) but the rock in this area is probably not sufficiently layered to have provided long-term climatic buffering. Potentially suitable rocky rainforest gullies in the south-eastern Pinnacles have not yet been surveyed.&lt;/p&gt; &lt;p&gt; &lt;b&gt;Habitat and habits.&lt;/b&gt; Layered rock with associated rainforest (&lsquo;vine-forest&rsquo;) vegetation. One site consists of piled, angular rock (Fig. 6A) associated with a gully, another site consists of piled, rounded, granite boulders along a gully (Fig. 6B), and the third site consists of deeply piled, granite boulders along a gully and adjacent slopes. At all sites, &lt;i&gt;P. pinnaclensis&lt;/i&gt; &lt;b&gt;sp. nov.&lt;/b&gt; was found on rock surfaces at night (Fig. 6B).&lt;/p&gt;Published as part of &lt;i&gt;Hoskin, Conrad J., Bertola, Lorenzo V. &amp; Higgie, Megan, 2019, A new species of Phyllurus leaf-tailed gecko (Lacertilia: Carphodactylidae) from The Pinnacles, north-east Australia, pp. 127-139 in Zootaxa 4576 (1)&lt;/i&gt; on pages 130-132, DOI: 10.11646/zootaxa.4576.1.6, &lt;a href="http://zenodo.org/record/2624732"&gt;http://zenodo.org/record/2624732&lt;/a&gt