Habitat Preferences and Distribution Modelling of the Endangered Frog Pseudophilautus zorro

Amphibians are the most threatened group of vertebrates in the world. In Sri Lanka, 67% of the amphibians are threatened with extinction largely due to anthropogenic activities. Fundamental to the conservation of amphibians is an understanding of habitat preferences and fine scale distribution of species. Pseudophilautus zorro is an endangered, endemic frog species restricted to Kandy district, Sri Lanka. Thus, a study was initiated to assess the (a) habitat preferences (type of vegetation, leaf litter thickness (LLT), percentage of canopy cover (PCC)), (b) model the fundamental ecological niche to unravel potential areas of occupancy using Ecological niche modeling (ENM) and then to (c) estimate the extent of occurrence (EOO) and area of occupancy (AOO) of P. zorro with new locality data and predicted data. Fieldwork was conducted in Gannoruwa Forest Reserve, Udawattakele Forest Reserve and Hanthana Conservation Area from December 2016 to August 2017. Habitat preferences were determined by randomly placing quadrats in different habitats and assessing the number of individuals in each quadrat. Occurrence localities of P. zorro from published records and localities from this study were used for ENM in Maxent. At α=0.05level, the results indicate that there is a positive relationship (r=0.427, p≤0.013) between LLT and number of individuals of P. zorro in quadrats. However, there was no significant relationship (r=0.078, p≥0.666) between PCC and number of individuals of P. zorroin quadrats and no significant variation (p≥0.404) in the occurrences of P. zorro among the three habitat types (forest, mahogany and pine plantations) suggesting that vegetation type is not a major determinant of P. zorro distribution. ENM predicted highly suitable areas (suitability >75%) in the central province in the Kandy and Matale districts. The EOO and AOO of P. zorro with new occurrence data was 22 km2 and 4 km2respectively, and with predicted data, 1,229.34 km2 and 117 km2, indicating an increase in EOO and AOO. However, the increase in EOO and AOO should be interpreted with caution as the presence of P. zorro is yet to be physically confirmed in the predicted areas. The data on habitat preferences and predicted habitats will be useful in formulating in-situ and ex-situ conservation measures, and serves as a useful starting point for future studies on niche modeling of endangered amphibians and similar taxa in Sri Lanka.Keywords: Maxent, Fundamental ecological niche, Leaf litter thickness, Extent of occurrence, Area of occupanc

Species Composition and Diversity in two Selected Lowland Tropical Rainforests in Sri Lanka and their Relationships to Temperature and Precipitation

Tropical rainforests are characterised by high species diversity, which may be due to a range of factors such as climate, topography, soil properties and the level of disturbance, both natural and anthropogenic. This study focused on investigating the species composition, richness, diversity and their conservation status in lowland tropical rainforests at two selected locations in Sri Lanka and determining their relationships to temperature and precipitation. Two permanent one-hectare sampling plots each were established at the Kanneliya (KDN1 and KDN2) and Pitadeniya-Sinharaja (PTD1 and PTD2) Forest Reserves. All trees with dbh≥10 cm were enumerated. A total of 3,303 trees were recorded, representing 158 species from 91 genera and 53 families, with a total basal area of 196.26 m2. Most abundant plant species were Alstonia macrophylla in KDN1 (11.7% of trees with dbh≥10 cm), Syzygium grande in KDN2 (9.8%), Shorea affinis in PTD1 (15.8%) Mesua thwaitesii in PTD2 (17.5%). Cullenia rosayroana (7.2%) is the most abundant species within the whole study area. While 25 species were recorded in all four plots, 70 species were found in only one location. Genus Shorea (18.6%) is the most common including 12 different species and Dipterocarpaceae (21.9%) is the most common family including 19 species. KDN1 recorded 1,011 plants from 108 species, with 74.3% endemic, 12.8% native and 11.9% exotic species. Other study sites recorded only endemic (88% at KDN2, 83.7% at PTD1 and 82.3% at PTD2) and native species. In comparison to PTD, KDN recorded higher numbers of trees with dbh≥10 cm (Chi-square p<0.0001), species (p<0.0001) and genera (p=0.0091). KDN also recorded a higher number of families but the difference was not significant (p=0.358). All indices of species diversity (Shannon index, H and Simpson index, D), evenness (J) and richness (R) are higher at KDN. However, only the difference in D was statistically-significant at p=0.05. Multiple regression analysis using the stepwise procedure showed that the number of trees with dbh≥10 cm and the species number increased with increasing average annual air temperature (T) but decreased with annual total precipitation (P). On the other hand, the numbers of genera and families increased with decreasing P with T not having a significant influence. The two diversity indices, H and D, increased with decreasing P and increasing T. In contrast, increasing P decreased J and R whereas variation in T did not have a significant influence. These findings provide important insights in to dynamics plant diversity in response to environmental changes.Keywords: Species composition, Species diversity, Tropical rainforest

Diversification rates and phenotypic evolution in venomous snakes (Elapidae)

Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited.The relationship between rates of diversification and of body size change (a common proxy for phenotypic evolution) was investigated across Elapidae, the largest radiation of highly venomous snakes. Time-calibrated phylogenetic trees for 175 species of elapids (more than 50% of known taxa) were constructed using seven mitochondrial and nuclear genes. Analyses using these trees revealed no evidence for a link between speciation rates and changes in body size. Two clades (Hydrophis, Micrurus) show anomalously high rates of diversification within Elapidae, yet exhibit rates of body size evolution almost identical to the general elapid ‘background’ rate. Although correlations between speciation rates and rates of body size change exist in certain groups (e.g. ray-finned fishes, passerine birds), the two processes appear to be uncoupled in elapid snakes. There is also no detectable shift in diversification dynamics associated with the colonization of Australasia, which is surprising given that elapids appear to be the first clade of venomous snakes to reach the continent

Evaluating the drivers of Indo-Pacific biodiversity: speciation and dispersal of sea snakes (Elapidae: Hydrophiinae)

Aim: There are several competing hypotheses to explain the high species richness of the Indo-Australian Archipelago (IAA) marine biodiversity hotspot centred within Southeast (SE) Asia. We use phylogenetic methods to provide a novel perspective on this problem using viviparous sea snakes, a group with high species richness in the IAA that is highly distinct from other taxa previously studied, both phylogenetically (Reptilia, Amniota) and biologically (e.g. viviparity and direct development). Location: Indian Ocean and the West Pacific. Methods: We used likelihood and Bayesian methods to reconstruct a multi-locus time-calibrated phylogeny for c. 70% of viviparous sea snake species, many sampled from multiple localities in Australasia, Southeast Asia and the Indian Ocean. We then compared rates and temporal concordance of inferred vicariance and dispersal events between marine basins using several approaches including new Bayesian analyses that allow for clade-specific and event-specific dispersal rates. Results: Phylogenetic analyses and novel Bayesian biogeographical reconstructions indicate that viviparous sea snakes underwent rapid speciation after colonizing SE Asia c. 3 million years ago. Most of the SE Asian sea snake diversity is the result of in situ speciation, most consistent with the ‘centre of origin’ and ‘centre of refuge’ models for biodiversity hotspots. There is also speciation at the periphery, or entirely outside SE Asia; however, contrary to predictions of the ‘accumulation’ and ‘overlap’ models, these new outlying taxa do not preferentially disperse back into SE Asia. Instead, lineages are equally likely to disperse either into or away from SE Asia. Main conclusion: The high diversity of sea snakes in SE Asia (and hence the IAA) is mostly explained by in situ speciation rather than accumulation or overlap. Most speciation events are contemporaneous with sea level changes that generated and dissolved barriers between marine basins during the last 2.5 million years.Kanishka D.B. Ukuwela, Michael S.Y. Lee, Arne R. Rasmussen, Anslem de Silva, Mumpuni, Bryan G. Fry, Parviz Ghezellou, Mohsen Rezaie-Atagholipour, and Kate L. Sander

Spectral diversification and trans-species allelic polymorphism during the land-to-sea transition in snakes

Snakes are descended from highly visual lizards [1] , but have limited (probably dichromatic) colour vision attributed to a dim-light lifestyle of early snake ancestors [2–4]. The living species of front-fanged elapids, however, are ecologically very diverse, with ~300 terrestrial species (cobras, taipans, etc.) and ~60 fully marine sea snakes, plus eight independently marine, amphibious sea kraits [1]. Here, we investigate the evolution of spectral sensitivity in elapids by analyzing their opsin genes (which are responsible for sensitivity to UV and visible light), retinal photoreceptors, and ocular lenses. We found that sea snakes underwent rapid adaptive diversification of their visual pigments when compared with their terrestrial and amphibious relatives. The three opsins present in snakes (SWS1, LWS, RH1) have evolved under positive selection in elapids, and in sea snakes have undergone multiple shifts in spectral sensitivity towards the longer wavelengths that dominate below the sea surface. Several distantly related Hydrophis sea snakes are polymorphic for shortwave sensitive visual pigment encoded by alleles of SWS1. This spectral site polymorphism is expected to confer expanded ‘UV-Blue’ spectral sensitivity and is estimated to have persisted twice as long as the predicted survival time for selectively neutral nuclear alleles. We suggest that this polymorphism is adaptively maintained across Hydrophis species via balancing selection, similarly to the LWS polymorphism that confers allelic trichromacy in some primates. Diving sea snakes thus appear to share parallel mechanisms of color vision diversification with fruit-eating primates

Description of the tadpole of Hylarana aurantiaca (Anura:Ranidae) from Sri Lanka

Presently 105 species of amphibians are known from Sri Lanka and the family Ranidae is represented by three species (Meegaskumbura and Manamendraarachchi, 2007). The genus Hylarana is represented by three species: the endemic H. gracilis, and H. aurantiaca and H. temporalis which also occur in South India (Pethiyagoda et al. 2006). Despite Hylarana aurantiaca being a common frog species in the low and mid elevations of the wet regions in Sri Lanka and India, its tadpole stages are poorly known. In this paper the tadpole of H. aurantiaca is described from specimens reared from spawn collected from central Sri Lanka.Kanishka D.B. Ukuwel

The presence of Polypedates cruciger tadpoles reduces the growth of Duttaphrynus melanostictus tadpoles under laboratory conditions

Competition is one of the main types of interactions in ecological communities. Interspecific competition of many organisms including anuran tadpoles has been demonstrated in numerous previous studies. However, a few studies have also shown that interspecific competition is absent or insignificant in certain tadpole communities. In this study, we conducted experiments to assess whether the presence of one species of tadpole affects the growth of another species. We selected tadpoles of two commonly co-occurring species of anurans in Sri Lanka: Duttaphrynus melanostictus and Polypedates cruciger. The length and width of tadpoles were used as a measure of growth. The laboratory experiments revealed that the presence of P. cruciger tadpoles negatively impacted the growth of D. melanostictus tadpoles. Tadpoles of D. melanostictus that were raised with P. cruciger tadpoles (treatment) were significantly smaller than those raised with conspecifics (control). P. cruciger tadpoles that were raised with D. melanostictus tadpoles were significantly bigger than those raised with conspecifics. We believe that these effects are due to the superiority of P. cruciger tadpoles to D. melanostictus tadpoles in terms of competition.Kanishka D. B. Ukuwela and Kithsiri B. Ranawanahttp://www.herpetologynotes.seh-herpetology.org/contents4.htm

Systematics, evolution and biogeography of viviparous sea snakes of the Indo-Pacific.

Viviparous sea snakes are an exceptionally diverse radiation of secondarily marine reptiles that inhabit the shallow tropical and subtropical waters of the Indian and Pacific Oceans with the peak diversity in the Indo-Australian Archipelago (IAA). Although sea snake biology, natural history and diversity are relatively well known, they have a highly unstable taxonomy, and poorly understood evolutionary and biogeographic histories. This thesis examined the systematics, species limits, historical biogeography and diversification of Indo-Pacific viviparous sea snakes using molecular phylogenetics and a combination of external and internal morphological characters. In the second chapter of this thesis, I describe a highly distinctive new species of viviparous sea snake from shallow estuarine waters of the Gulf of Carpentaria, northern Australia. Molecular analyses placed the new species, named ‘rough scaled’ sea snake, Hydrophis donaldi, as a deeply divergent lineage within the Hydrophis subgroup. A multi-locus analysis and a morphological examination of the dangerously venomous and widely distributed ‘beaked’ sea snakes, Hydrophis schistosus, in the third chapter showed that they actually consist of two separate species in Asia and Australia that are not each other’s closest relatives. This finding suggested that the beaked sea snakes represent an extreme case of convergent phenotypic evolution in response to similar dietary specialisations, providing important implications for snakebite management. In the third chapter of this thesis I investigated how past and present barriers to dispersal caused by historical geoclimatic events in the IWP have influenced fine-scale population genetic structure and speciation in the widely distributed ‘spine-bellied’ sea snake, Hydrophis curtus. Analyses of mitochondrial and nuclear sequences and microsatellite variation sampled across the IWP strongly indicated population subdivision in H. curtus with a deep species level genetic break across the Indian Ocean and West Pacific. These findings further demonstrated that the Indo-Pacific biogeographic barrier in the Plio-Pleistocene may have a significant role in generation of biodiversity in the IAA. Phylogenetic analyses and biogeographic reconstructions of Indo-West Pacific (IWP) viviparous sea snakes in chapter four indicate that despite their origins in Australasia, sea snakes underwent an explosive in-situ radiation during the last 2.5 to 0.3 million years after colonizing Southeast Asia with subsequent dispersals to Australasia and the Indian Ocean. The high speciation rates in the core Hydrophis group and allopatric population divergence between the Indian and Pacific Oceans indicate an association with the Pleistocene sea level changes. Together these findings provide important insights to the origins and maintenance of high biodiversity in this marine biodiversity hotspot. Findings on species boundaries, endemism and population structure in this thesis will directly benefit sea snake conservation and marine reserve management in the IWP. However, a need for more basic systematic studies on sea snakes is strongly implied by the discovery of cryptic lineages and the new species. The inability of temporal diversification patterns to explain the rapid speciation of Hydrophis suggests that non-geographic speciation might be a major driving force in sea snake speciation. Hence other avenues of research (e.g niche relationships, adaptation genomics) may provide possible explanations to the high species diversity.Thesis (Ph.D.) -- University of Adelaide, School of Earth & Environmental Sciences, 201

A survey on the amphibians of Ambagamuwa, a tropical wet midland area in Sri Lanka

A survey to assess the amphibian diversity of Ambagamuwa area in the mid-hills of Sri Lanka was carried out from January-February 2003 and in August 2007. Five different habitat types including gardens, primary forests, secondary forests, paddy fields and tea plantations were systematically sampled and investigated for amphibians. The survey revealed a total of 19 amphibian species with eleven of them endemic to the island and nine of them listed in the 2007 IUCN red list of threatened species. Two new frog species of the genus Philautus were discovered in this area. The overall existence of a high number of threatened species and the possible existence of so far undiscovered species strikes the importance of an urgent conservation of this area.D.M. Nayana Pradeep Kumara & Kanishka D.B. Ukuwel

Hydrophis donaldi (Elapidae, Hydrophiinae), a highly distinctive new species of sea snake from northern Australia

A new species of viviparous sea snake, Hydrophis donaldi sp. nov. (Hydrophiinae), is described from the Gulf of Carpentaria, northern Australia. Molecular analyses reveal this species as a deeply divergent lineage within the Hydrophis subgroup, and separate it from all other sampled taxa by fixed nucleotide substitutions at three independent mitochondrial and nuclear loci. The new species is assigned to Hydrophis based on the current morphological diagnosis of this large but paraphyletic genus, and is distinguished from all other Hydrophis species and closely allied genera by a combination of morphological characters relating to scalation, colour pattern and osteology. Using current keys for sea snakes, H. donaldi sp. nov. might be mistaken for H. coggeri, H. sibauensis or H. torquatus diadema but it is readily distinguished from these species by a higher number of bands on the body and tail, lower ventral count, strongly spinous body scales, and a wider, more rounded head. Sea snakes have been sampled intensively in the Gulf of Carpentaria due to their vulnerability to bycatch in the region’s commercial prawn-trawl fisheries. That this highly distinctive new species has evaded discovery in the region until now is surprising, but might be explained by its habitat preferences. All known specimens of H. donaldi sp. nov. were found in estuarine habitats that are relatively poorly surveyed and are not targeted by commercial fisheries.Kanishka D. B. Ukuwela, Kate L. Sanders & Bryan G. Fr