The landscape of genomic structural variation in Indigenous Australians.

Indigenous Australians harbour rich and unique genomic diversity. However, Aboriginal and Torres Strait Islander ancestries are historically under-represented in genomics research and almost completely missing from reference datasets1-3. Addressing this representation gap is critical, both to advance our understanding of global human genomic diversity and as a prerequisite for ensuring equitable outcomes in genomic medicine. Here we apply population-scale whole-genome long-read sequencing4 to profile genomic structural variation across four remote Indigenous communities. We uncover an abundance of large insertion-deletion variants (20-49 bp; n = 136,797), structural variants (50 b-50 kb; n = 159,912) and regions of variable copy number (>50 kb; n = 156). The majority of variants are composed of tandem repeat or interspersed mobile element sequences (up to 90%) and have not been previously annotated (up to 62%). A large fraction of structural variants appear to be exclusive to Indigenous Australians (12% lower-bound estimate) and most of these are found in only a single community, underscoring the need for broad and deep sampling to achieve a comprehensive catalogue of genomic structural variation across the Australian continent. Finally, we explore short tandem repeats throughout the genome to characterize allelic diversity at 50 known disease loci5, uncover hundreds of novel repeat expansion sites within protein-coding genes, and identify unique patterns of diversity and constraint among short tandem repeat sequences. Our study sheds new light on the dimensions and dynamics of genomic structural variation within and beyond Australia.

Metabolic consequences of sex reversal in two lizard species: a test of the like-genotype and like-phenotype hypotheses.

Vertebrate sex is typically determined genetically, but in many ectotherms sex can be determined by genes (genetic sex determination, GSD), temperature (temperature-dependent sex determination, TSD), or interactions between genes and temperature during development. TSD may involve GSD systems with either male or female heterogamety (XX/XY or ZZ/ZW) where temperature overrides chromosomal sex determination to cause a mismatch between genetic sex and phenotypic sex (sex reversal). In these temperature-sensitive lineages, phylogenetic investigations point to recurrent evolutionary shifts between genotypic and temperature-dependent sex determination. These evolutionary transitions in sex determination can occur rapidly if selection favours the reversed sex over the concordant phenotypic sex. To investigate the consequences of sex reversal on offspring phenotypes, we measured two energy-driven traits (metabolism and growth) and 6 month survival in two species of reptile with different patterns of temperature-induced sex reversal. Male sex reversal occurs in Bassiana duperreyi when chromosomal females (female XX) develop male phenotypes (maleSR XX), while female sex reversal occurs in Pogona vitticeps when chromosomal males (male ZZ) develop female phenotypes (femaleSR ZZ). We show metabolism in maleSR XX was like that of male XY; that is, reflective of phenotypic sex and lower than genotypic sex. In contrast, for Pogona vitticeps, femaleSR ZZ metabolism was intermediate between male ZZ and female ZW metabolic rate. For both species, our data indicate that differences in metabolism become more apparent as individuals become larger. Our findings provide some evidence for an energetic advantage from sex reversal in both species but do not exclude energetic processes as a constraint on the distribution of sex reversal in nature.

Lineage diversity within a widespread endemic Australian skink to better inform conservation in response to regional-scale disturbance.

Much attention is paid in conservation planning to the concept of a species, to ensure comparability across studies and regions when classifying taxa against criteria of endangerment and setting priorities for action. However, various jurisdictions now allow taxonomic ranks below the level of species and nontaxonomic intraspecific divisions to be factored into conservation planning-subspecies, key populations, evolutionarily significant units, or designatable units. Understanding patterns of genetic diversity and its distribution across the landscape is a key component in the identification of species boundaries and determination of substantial geographic structure within species. A total of 12,532 reliable polymorphic SNP loci were generated from 63 populations (286 individuals) covering the distribution of the Australian eastern three-lined skink, Bassiana duperreyi, to assess genetic population structure in the form of diagnosable lineages and their distribution across the landscape, with particular reference to the recent catastrophic bushfires of eastern Australia. Five well-supported diagnosable operational taxonomic units (OTUs) existed within B. duperreyi. Low levels of divergence of B. duperreyi between mainland Australia and Tasmania (no fixed allelic differences) support the notion of episodic exchange of alleles across Bass Strait (ca 60 m, 25 Kya) during periods of low sea level during the Upper Pleistocene rather than the much longer period of isolation (1.7 My) indicated by earlier studies using mitochondrial sequence variation. Our study provides foundational work for the detailed taxonomic re-evaluation of this species complex and the need for biodiversity assessment to include an examination of cryptic species and/or cryptic diversity below the level of species. Such information on lineage diversity within species and its distribution in the context of disturbance at a regional scale can be factored into conservation planning regardless of whether a decision is made to formally diagnose new species taxonomically and nomenclaturally.

Effects of natural nest temperatures on sex reversal and sex ratios in an Australian alpine skink.

Altered climate regimes have the capacity to affect the physiology, development, ecology and behaviour of organisms dramatically, with consequential changes in individual fitness and so the ability of populations to persist under climatic change. More directly, extreme temperatures can directly skew the population sex ratio in some species, with substantial demographic consequences that influence the rate of population decline and recovery rates. In contrast, this is particularly true for species whose sex is determined entirely by temperature (TSD). The recent discovery of sex reversal in species with genotypic sex determination (GSD) due to extreme environmental temperatures in the wild broadens the range of species vulnerable to changing environmental temperatures through an influence on primary sex ratio. Here we document the levels of sex reversal in nests of the Australian alpine three-lined skink (Bassiana duperreyi), a species with sex chromosomes and sex reversal at temperatures below 20 °C and variation in rates of sex reversal with elevation. The frequency of sex reversal in nests of B. duperreyi ranged from 28.6% at the highest, coolest locations to zero at the lowest, warmest locations. Sex reversal in this alpine skink makes it a sensitive indicator of climate change, both in terms of changes in average temperatures and in terms of climatic variability.

Temperature-Induced Sex Reversal in Reptiles: Prevalence, Discovery, and Evolutionary Implications.

Sex reversal is the process by which an individual develops a phenotypic sex that is discordant with its chromosomal or genotypic sex. It occurs in many lineages of ectothermic vertebrates, such as fish, amphibians, and at least one agamid and one scincid reptile species. Sex reversal is usually triggered by an environmental cue that alters the genetically determined process of sexual differentiation, but it can also be caused by exposure to exogenous chemicals, hormones, or pollutants. Despite the occurrence of both temperature-dependent sex determination (TSD) and genetic sex determination (GSD) broadly among reptiles, only 2 species of squamates have thus far been demonstrated to possess sex reversal in nature (GSD with overriding thermal influence). The lack of species with unambiguously identified sex reversal is not necessarily a reflection of a low incidence of this trait among reptiles. Indeed, sex reversal may be relatively common in reptiles, but little is known of its prevalence, the mechanisms by which it occurs, or the consequences of sex reversal for species in the wild under a changing climate. In this review, we present a roadmap to the discovery of sex reversal in reptiles, outlining the various techniques that allow new occurrences of sex reversal to be identified, the molecular mechanisms that may be involved in sex reversal and how to identify them, and approaches for assessing the impacts of sex reversal in wild populations. We discuss the evolutionary implications of sex reversal and use the central bearded dragon (Pogona vitticeps) and the eastern three-lined skink (Bassiana duperreyi) as examples of how species with opposing patterns of sex reversal may be impacted differently by our rapidly changing climate. Ultimately, this review serves to highlight the importance of understanding sex reversal both in the laboratory and in wild populations and proposes practical solutions to foster future research.

High elevation increases the risk of Y chromosome loss in Alpine skink populations with sex reversal.

The view that has genotypic sex determination and environmental sex determination as mutually exclusive states in fishes and reptiles has been contradicted by the discovery that chromosomal sex and environmental influences can co-exist within the same species, hinting at a continuum of intermediate states. Systems where genes and the environment interact to determine sex present the opportunity for sex reversal to occur, where the phenotypic sex is the opposite of that predicted by their sex chromosome complement. The skink Bassiana duperreyi has XX/XY sex chromosomes with sex reversal of the XX genotype to a male phenotype, in laboratory experiments, and in field nests, in response to exposure to cold incubation temperatures. Here we studied the frequency of sex reversal in adult populations of B. duperreyi in response to climatic variation, using elevation as a surrogate for environmental temperatures. We demonstrate sex reversal in the wild for the first time in adults of a reptile species with XX/XY sex determination. The highest frequency of sex reversal occurred at the highest coolest elevation location, Mt Ginini (18.46%) and decreased in frequency to zero with decreasing elevation. We model the impact of this under Fisher's frequency-dependent selection to show that, at the highest elevations, populations risk the loss of the Y chromosome and a transition to temperature-dependent sex determination. This study contributes to our understanding of the risks of extinction from climate change in species subject to sex reversal by temperature, and will provide focus for future research to test on-the-ground management strategies to mitigate the effects of climate in local populations.

Viviparous Reptile Regarded to Have Temperature-Dependent Sex Determination Has Old XY Chromosomes.

The water skinks Eulamprus tympanum and Eulamprus heatwolei show thermally induced sex determination where elevated temperatures give rise to male offspring. Paradoxically, Eulamprus species reproduce in temperatures of 12-15 °C making them outliers when compared with reptiles that use temperature as a cue for sex determination. Moreover, these two species are among the very few viviparous reptiles reported to have thermally induced sex determination. Thus, we tested whether these skinks possess undetected sex chromosomes with thermal override. We produced transcriptome and genome data for E. heatwolei. We found that E. heatwolei presents XY chromosomes that include 14 gametologs with regulatory functions. The Y chromosomal region is 79-116 Myr old and shared between water and spotted skinks. Our work provides clear evidence that climate could be useful to predict the type of sex determination systems in reptiles and it also indicates that viviparity is strictly associated with sex chromosomes.

Morphology and Molecular Characterization of Parabronema smithii (Cobbold, 1882) (Nematoda: Habronematidae) from Wild Asian Elephant (Elephas maximus maximus) of Sri Lanka.

PURPOSE: The aim of the present study was to carry out a detailed study of morphological features and to determine the phylogenetic position of Parabronema smithii (Cobbold, 1882) found in wild elephants in Sri Lanka. METHODS: Adult worms were collected from stomach ulcers at postmortem examination of wild elephants in the Udawalawe National Park, Sri Lanka. The detailed morphology of P. smithii was studied using light microscopy and, for the first time, scanning electron microscopy. Fifteen morphological characteristics were investigated. The phylogenetic analysis was conducted using the second internal transcribed spacer region (ITS2), and portions of the large subunit ribosomal DNA (28S) and cytochrome c oxidase subunit 1 (cox1). Furthermore, the present study provides a comparison of morphology and morphometrics of Parabronema species that occur in different hosts. CONCLUSION: Parabronema smithii isolated from wild elephants exhibited the key morphological features. Phylogenetic analysis of selected genes revealed that P. smithii is closely associated with P. skrjabini and Habronema spp. Findings of the present study enhance our understanding of the biology and taxonomy of P. smithii in wild elephant in Sri Lanka and will contribute to future phylogeographic studies.

The Venom of Spectacled Cobra (Elapidae: Naja naja): In Vitro Study from Distinct Geographical Origins in Sri Lanka.

Several countries residing envenomation due to Naja naja had revealed a disparity in the venom composition according to their geographic location and Sri Lankan cobra still lacks the evidence to support this. Therefore, the current study was focused on addressing relationship between the histopathological changes according to geographic variation of Sri Lankan N. naja venom. The histopathological changes in vital organs and muscle tissues following intramuscular administration of venom of N. naja were studied using BALB/c mice. The median lethal dose of venom of N. naja in the present study was determined to be 0.55, 0.66, 0.68, 0.62, and 0.7 mg/kg for North (NRP), Central (CRP), Western, Southern, and Sabaragamuwa Regional Population venoms, respectively. Histopathological changes were observed in different levels in vital organs and muscle tissues of mice. NRP accompanied significantly higher infiltration of inflammatory and necrotic cells into skeletal muscle and CRP venom demonstrated high level of cardiotoxic effects comparing to other regions. This study revealed a certain extent of variations in the pathological effects of N. naja venom samples according to their geographical distribution.

Hematological and plasma biochemical parameters in a wild population of Naja naja (Linnaeus, 1758) in Sri Lanka.

BACKGROUND: Hematological studies of any animal species comprise an important diagnostic method in veterinary medicine and an essential tool for the conservation of species. In Sri Lanka, this essential technique has been ignored in studies of many species including reptiles. The aim of the present work was to establish a reference range of hematological values and morphological characterization of wild spectacled cobras (Naja naja) in Sri Lanka in order to provide a diagnostic tool in the assessment of health condition in reptiles and to diagnose diseases in wild populations. METHODS: Blood samples were collected from the ventral caudal vein of 30 wild-caught Naja naja (18 males and 12 females). Hematological analyses were performed using manual standard methods. RESULTS: Several hematological parameters were examined and their mean values were: red blood cell count 0.581 ± 0.035 × 106/µL in males; 0.4950 ± 0.0408 × 106/µL in females; white blood cell count 12.45 ± 1.32 × 103/µL in males; 11.98 ± 1.62 × 103/µL in females; PCV (%) in males was 30.11 ± 1.93 and in females was 23.41 ± 1.67; hemoglobin (g/dL) was 7.6 ± 0.89 in males and 6.62 ± 1.49 in females; plasma protein (g/dL) was 5.11 ± 0.75 in males and 3.25 ± 0.74 in females; whereas cholesterol (mg/mL) was 4.09 ± 0.12 in males and 3.78 ± 0.42 in females. There were no significant differences in hematological parameters between the two genders except for erythrocyte count, thrombocyte count, hematocrit, hemoglobin, plasma protein, percentage of azurophil and heterophil. Intracellular parasites were not found in any of the studied specimens. CONCLUSION: Hematological and plasma biochemical parameters indicated a difference between geographically isolated populations and some values were significantly different between the two genders. These hematological results provide a reference range for Sri Lankan population of adult Naja naja.

Hematological and plasma biochemical parameters in a wild population of Naja naja (Linnaeus, 1758) in Sri Lanka

Abstract Background Hematological studies of any animal species comprise an important diagnostic method in veterinary medicine and an essential tool for the conservation of species. In Sri Lanka, this essential technique has been ignored in studies of many species including reptiles. The aim of the present work was to establish a reference range of hematological values and morphological characterization of wild spectacled cobras (Naja naja) in Sri Lanka in order to provide a diagnostic tool in the assessment of health condition in reptiles and to diagnose diseases in wild populations. Methods Blood samples were collected from the ventral caudal vein of 30 wild-caught Naja naja (18 males and 12 females). Hematological analyses were performed using manual standard methods. Results Several hematological parameters were examined and their mean values were: red blood cell count 0.581 ± 0.035 × 106/L in males; 0.4950 ± 0.0408 × 106/L in females; white blood cell count 12.45 ± 1.32 × 103/L in males; 11.98 ± 1.62 × 103/L in females; PCV (%) in males was 30.11 ± 1.93 and in females was 23.41 ± 1.67; hemoglobin (g/dL) was 7.6 ± 0.89 in males and 6.62 ± 1.49 in females; plasma protein (g/dL) was 5.11 ± 0.75 in males and 3.25 ± 0.74 in females; whereas cholesterol (mg/mL) was 4.09 ± 0.12 in males and 3.78 ± 0.42 in females. There were no significant differences in hematological parameters between the two genders except for erythrocyte count, thrombocyte count, hematocrit, hemoglobin, plasma protein, percentage of azurophil and heterophil. Intracellular parasites were not found in any of the studied specimens. Conclusion Hematological and plasma biochemical parameters indicated a difference between geographically isolated populations and some values were significantly different between the two genders. These hematological results provide a reference range for Sri Lankan population of adult Naja naja.

Hematological and plasma biochemical parameters in a wild population of Naja naja (Linnaeus, 1758) in Sri Lanka

Background Hematological studies of any animal species comprise an important diagnostic method in veterinary medicine and an essential tool for the conservation of species. In Sri Lanka, this essential technique has been ignored in studies of many species including reptiles. The aim of the present work was to establish a reference range of hematological values and morphological characterization of wild spectacled cobras (Naja naja) in Sri Lanka in order to provide a diagnostic tool in the assessment of health condition in reptiles and to diagnose diseases in wild populations. Methods Blood samples were collected from the ventral caudal vein of 30 wild-caught Naja naja (18 males and 12 females). Hematological analyses were performed using manual standard methods. Results Several hematological parameters were examined and their mean values were: red blood cell count 0.581 ± 0.035 × 106/μL in males; 0.4950 ± 0.0408 × 106/μL in females; white blood cell count 12.45 ± 1.32 × 103/μL in males; 11.98 ± 1.62 × 103/μL in females; PCV (%) in males was 30.11 ± 1.93 and in females was 23.41 ± 1.67; hemoglobin (g/dL) was 7.6 ± 0.89 in males and 6.62 ± 1.49 in females; plasma protein (g/dL) was 5.11 ± 0.75 in males and 3.25 ± 0.74 in females; whereas cholesterol (mg/mL) was 4.09 ± 0.12 in males and 3.78 ± 0.42 in females. There were no significant differences in hematological parameters between the two genders except for erythrocyte count, thrombocyte count, hematocrit, hemoglobin, plasma protein, percentage of azurophil and heterophil. Intracellular parasites were not found in any of the studied specimens. Conclusion Hematological and plasma biochemical parameters indicated a difference between geographically isolated populations and some values were significantly different between the two genders. These hematological results provide a reference range for Sri Lankan population of adult Naja naja.(AU)