"To ensure the survival of all living beings in a rapidly changing environment, we need to adapt our conservation strategies. It's not just about the characteristics of species, but also their ability to adapt to changing conditions that will determine their fate and evolution."
Dumie Dissanayake
As an evolutionary biologist, my primary focus is on contemporary natural selection, which involves integrating field research and molecular studies with theoretical frameworks to better understand the complex mechanisms underlying species adaptation. Currently, my research is centered on the use of ecological, genetic, and genomic principles to investigate the evolution and adaptation of vertebrates in response to changing climatic conditions.
Moreover, my research interests extend to exploring the origin and evolution of species and identifying crucial evolutionary units to resolve critical challenges in species evolutionary biology and their conservation management. By utilizing advanced techniques and interdisciplinary approaches, my goal is to uncover new insights into the fundamental principles governing evolutionary processes and their broader implications for biodiversity conservation.
Moreover, my research interests extend to exploring the origin and evolution of species and identifying crucial evolutionary units to resolve critical challenges in species evolutionary biology and their conservation management. By utilizing advanced techniques and interdisciplinary approaches, my goal is to uncover new insights into the fundamental principles governing evolutionary processes and their broader implications for biodiversity conservation.
17/03/2022
Our article "Lineage diversity within a widespread endemic Australian skink to better inform conservation in response to regional-scale disturbance" has been published online in Ecology and Evolution.
Abstract
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.
Dissanayake, D. S., Holleley, C. E., Sumner, J., Melville, J., & Georges, A. (2022). Lineage diversity within a widespread endemic Australian skink to better inform conservation in response to regional‐scale disturbance. Ecology and Evolution, 12(3), e8627.
https://doi.org/10.1002/ece3.8627
Our article "Lineage diversity within a widespread endemic Australian skink to better inform conservation in response to regional-scale disturbance" has been published online in Ecology and Evolution.
Abstract
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.
Dissanayake, D. S., Holleley, C. E., Sumner, J., Melville, J., & Georges, A. (2022). Lineage diversity within a widespread endemic Australian skink to better inform conservation in response to regional‐scale disturbance. Ecology and Evolution, 12(3), e8627.
https://doi.org/10.1002/ece3.8627
11/10/2021
Our new manuscript about Effects of natural nest temperatures on sex reversal and sex ratios in an Australian alpine skink is out today!
Abstract
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.
https://www.nature.com/articles/s41598-021-99702-1
Dissanayake, D.S.B., Holleley, C.E. & Georges, A. Effects of natural nest temperatures on sex reversal and sex ratios in an Australian alpine skink. Sci Rep 11, 20093 (2021).
Our new manuscript about Effects of natural nest temperatures on sex reversal and sex ratios in an Australian alpine skink is out today!
Abstract
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.
https://www.nature.com/articles/s41598-021-99702-1
Dissanayake, D.S.B., Holleley, C.E. & Georges, A. Effects of natural nest temperatures on sex reversal and sex ratios in an Australian alpine skink. Sci Rep 11, 20093 (2021).
Our newest paper on Australian lizards are outstanding models for reproductive biology research is now published online in the Australian Journal of Zoology. Twenty-six Australian researchers contributed to this review article, and it was just amazing to work with them.
Abstract
Australian lizards are a diverse group distributed across the continent and inhabiting a wide range of environments. Together, they exhibit a remarkable diversity of reproductive morphologies, physiologies, and behaviours that is broadly representative of vertebrates in general. Many reproductive traits exhibited by Australian lizards have evolved independently in multiple lizard lineages, including sociality, complex signalling and mating systems, viviparity, and temperature-dependent sex determination. Australian lizards are thus outstanding model organisms for testing hypotheses about how reproductive traits function and evolve, and they provide an important basis of comparison with other animals that exhibit similar traits. We review how research on Australian lizard reproduction has contributed to answering broader evolutionary and ecological questions that apply to animals in general. We focus on reproductive traits, processes, and strategies that are important areas of current research, including behaviours and signalling involved in courtship; mechanisms involved in mating, egg production, and sperm competition; nesting and gestation; sex determination; and finally, birth in viviparous species. We use our review to identify important questions that emerge from an understanding of this body of research when considered holistically. Finally, we identify additional research questions within each topic that Australian lizards are well suited for reproductive biologists to address.
Van Dyke, J.U., Thompson, M.B., Burridge, C.P., Castelli, M.A., Clulow, S., Dissanayake, D.S., Dong, C.M., Doody, J.S., Edwards, D.L., Ezaz, T. and Friesen, C.R., 2021. Australian lizards are outstanding models for reproductive biology research. Australian Journal of Zoology.
Our review article on Temperature-Induced Sex Reversal in Reptiles: Prevalence, Discovery, and Evolutionary Implications came out today in Sexual Development.
Abstract
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.
Abstract
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.
We have been a featured guest on the nature heredity podcast on our recent work on lizard sex reversal in the Australian high country.
You can hear the podcast here:
https://play.acast.com/s/heredity-podcast-naturecom-science-feeds/reversingsex
or read more about the project here
http://georges.biomatix.org/blog/post/lizard-sex-reversal
or go to the original article
https://doi.org/10.1038/s41437-021-00406-z
Abstract
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.
You can hear the podcast here:
https://play.acast.com/s/heredity-podcast-naturecom-science-feeds/reversingsex
or read more about the project here
http://georges.biomatix.org/blog/post/lizard-sex-reversal
or go to the original article
https://doi.org/10.1038/s41437-021-00406-z
Abstract
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.
MY PHD THESIS HAS BEEN SUBMITTED - 16/07/2021
I've just submitted my Ph.D. thesis for examination. What an amazing journey the last 4 years have been! Thesis scientific contributions: 69501words, 256pages, 4 published manuscripts, 2 in review, 1 to be submitted, and 2 data sets sitting on my desk to complete.Thank you so much to all my supervisors, collaborators, funding bodies & friends! Just hope my examiners like my work!
I've just submitted my Ph.D. thesis for examination. What an amazing journey the last 4 years have been! Thesis scientific contributions: 69501words, 256pages, 4 published manuscripts, 2 in review, 1 to be submitted, and 2 data sets sitting on my desk to complete.Thank you so much to all my supervisors, collaborators, funding bodies & friends! Just hope my examiners like my work!
Happy to share our recent paper that came out today in Heredity.
We examined populations of Bassiana duperreyi along an elevational gradient from the seasonally snow-covered Australian Alps down to the coast of Victoria. Our paper published recently in Heredity found that the highest frequency of sex reversal occurred at alpine locations and decreased in frequency to zero with decreasing elevation. We also show that, as the frequency of sex reversal occurs, populations risk jettisoning the Y chromosome as they evolve to achieve parity in the phenotypic sex ratio. If this occurred, as is likely in isolated populations at the highest elevation sites, the populations would transition from GSD to TSD.
Abstract
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.
Dissanayake, D.S.B., Holleley, C.E., Deakin, J.E., Georges, A. High elevation increases the risk of Y chromosome loss in Alpine skink populations with sex reversal. Heredity (2021).
We examined populations of Bassiana duperreyi along an elevational gradient from the seasonally snow-covered Australian Alps down to the coast of Victoria. Our paper published recently in Heredity found that the highest frequency of sex reversal occurred at alpine locations and decreased in frequency to zero with decreasing elevation. We also show that, as the frequency of sex reversal occurs, populations risk jettisoning the Y chromosome as they evolve to achieve parity in the phenotypic sex ratio. If this occurred, as is likely in isolated populations at the highest elevation sites, the populations would transition from GSD to TSD.
Abstract
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.
Dissanayake, D.S.B., Holleley, C.E., Deakin, J.E., Georges, A. High elevation increases the risk of Y chromosome loss in Alpine skink populations with sex reversal. Heredity (2021).
New site records published today in Taprobanica, The Journal of Asian Biodiversity
Round-eared tube-nosed bat (Murina cyclotis) from Southwest Sri Lanka.
http://file.taprobanica.org/238_murina_cyclotis...
Lesser large-footed Bat (Myotis hasseltii) from Southwest Sri Lanka.
http://file.taprobanica.org/239_myotis_hasseltii...
Chocolate pipistrelle (Hypsugo affinis) from Hantana, Sri Lanka, after 87 years.
http://file.taprobanica.org/240_hypsugo_affinis...
Published on 28 November 2020 in Taprobanica, The Journal of Asian Biodiversity
Authors: Gayan Mithra Edirisinghe , Dinesh Eransake Gabadage, Madhava Botejue, Thilina Surasinghe, Prasanna Chandika, Duminda Dissanayake, Sameera Akmeemana & S. Yaddehige
Round-eared tube-nosed bat (Murina cyclotis) from Southwest Sri Lanka.
http://file.taprobanica.org/238_murina_cyclotis...
Lesser large-footed Bat (Myotis hasseltii) from Southwest Sri Lanka.
http://file.taprobanica.org/239_myotis_hasseltii...
Chocolate pipistrelle (Hypsugo affinis) from Hantana, Sri Lanka, after 87 years.
http://file.taprobanica.org/240_hypsugo_affinis...
Published on 28 November 2020 in Taprobanica, The Journal of Asian Biodiversity
Authors: Gayan Mithra Edirisinghe , Dinesh Eransake Gabadage, Madhava Botejue, Thilina Surasinghe, Prasanna Chandika, Duminda Dissanayake, Sameera Akmeemana & S. Yaddehige
Happy to share our recent paper came out today in BMC Genomics.
With the development of next-generation sequencing technologies, new methods have been developed for screening sex-linked DNA and various approaches have been used to identify sex-linked markers in non-classical model organisms.
Here, we report an in silico approach to isolate sex-specific markers based on sequence unique to the Y or W chromosome, analogous to genomic representational difference analysis (gRDA). Subtractive genomic approaches have been used to identify targets in various human bacterial pathogens and identify potential tumor antigen candidates and cancer-specific genes. Our study is the first to apply the subtraction approach for identifying the Y chromosome-specific sequence in a reptile, the Bassiana duperreyi.
Here, we use low depth whole-genome sequencing of a male and a female B. duperreyi to apply an in silico whole-genome subtraction approach and develop new practical markers, useful in ongoing studies of this species in the laboratory and the wild.
Abstract
Homologous sex chromosomes can differentiate over time because recombination is suppressed in the region of the sex determining locus, leading to the accumulation of repeats, progressive loss of genes that lack differential influence on the sexes and sequence divergence on the hemizygous homolog. Divergence in the non-recombining regions leads to the accumulation of Y or W specific sequence useful for developing sex-linked markers. Here we use in silico whole-genome subtraction to identify putative sex-linked sequences in the scincid lizard Bassiana duperreyi which has heteromorphic XY sex chromosomes. We generated 96.7 × 109 150 bp paired-end genomic sequence reads from a XY male and 81.4 × 109 paired-end reads from an XX female for in silico whole genome subtraction to yield Y enriched contigs. We identified 7 reliable markers which were validated as Y chromosome specific by polymerase chain reaction (PCR) against a panel of 20 males and 20 females. The sex of B. duperreyi can be reversed by low temperatures (XX genotype reversed to a male phenotype). We have developed sex-specific markers to identify the underlying genotypic sex and its concordance or discordance with phenotypic sex in wild populations of B. duperreyi. Our pipeline can be applied to isolate Y or W chromosome-specific sequences of any organism and is not restricted to sequence residing within single-copy genes. This study greatly improves our knowledge of the Y chromosome in B. duperreyi and will enhance future studies of reptile sex determination and sex chromosome evolution.Dissanayake, D.S.B., Holleley, C.E., Hill, L.K. et al. Identification of Y chromosome markers in the eastern three-lined skink (Bassiana duperreyi) using in silico whole genome subtraction. BMC Genomics 21, 667 (2020).
https://bmcgenomics.biomedcentral.com/.../s12864-020-07071-2
With the development of next-generation sequencing technologies, new methods have been developed for screening sex-linked DNA and various approaches have been used to identify sex-linked markers in non-classical model organisms.
Here, we report an in silico approach to isolate sex-specific markers based on sequence unique to the Y or W chromosome, analogous to genomic representational difference analysis (gRDA). Subtractive genomic approaches have been used to identify targets in various human bacterial pathogens and identify potential tumor antigen candidates and cancer-specific genes. Our study is the first to apply the subtraction approach for identifying the Y chromosome-specific sequence in a reptile, the Bassiana duperreyi.
Here, we use low depth whole-genome sequencing of a male and a female B. duperreyi to apply an in silico whole-genome subtraction approach and develop new practical markers, useful in ongoing studies of this species in the laboratory and the wild.
Abstract
Homologous sex chromosomes can differentiate over time because recombination is suppressed in the region of the sex determining locus, leading to the accumulation of repeats, progressive loss of genes that lack differential influence on the sexes and sequence divergence on the hemizygous homolog. Divergence in the non-recombining regions leads to the accumulation of Y or W specific sequence useful for developing sex-linked markers. Here we use in silico whole-genome subtraction to identify putative sex-linked sequences in the scincid lizard Bassiana duperreyi which has heteromorphic XY sex chromosomes. We generated 96.7 × 109 150 bp paired-end genomic sequence reads from a XY male and 81.4 × 109 paired-end reads from an XX female for in silico whole genome subtraction to yield Y enriched contigs. We identified 7 reliable markers which were validated as Y chromosome specific by polymerase chain reaction (PCR) against a panel of 20 males and 20 females. The sex of B. duperreyi can be reversed by low temperatures (XX genotype reversed to a male phenotype). We have developed sex-specific markers to identify the underlying genotypic sex and its concordance or discordance with phenotypic sex in wild populations of B. duperreyi. Our pipeline can be applied to isolate Y or W chromosome-specific sequences of any organism and is not restricted to sequence residing within single-copy genes. This study greatly improves our knowledge of the Y chromosome in B. duperreyi and will enhance future studies of reptile sex determination and sex chromosome evolution.Dissanayake, D.S.B., Holleley, C.E., Hill, L.K. et al. Identification of Y chromosome markers in the eastern three-lined skink (Bassiana duperreyi) using in silico whole genome subtraction. BMC Genomics 21, 667 (2020).
https://bmcgenomics.biomedcentral.com/.../s12864-020-07071-2
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Great to see the Centre for Conservation Ecology and Genetics at U Canberra on Twitter! Just follow us if you want to see some of the astonishing research in conservation, ecology, and genetics/genomics!
https://twitter.com/UC_CCEG/status/1369452767576788999?s=20 Photo credit: @UniCanberra #UniCBR Institute for Applied Ecology, University of Canberra |
Happy to share our recent paper came out today in Genome Biology and Evolution which identifies sex chromosomes in the Yellow-bellied water skink (Eulamprus heatwolei) in Australia. This species was previously reported, to great fanfare, as a viviparous lizard with temperature-dependent sex determination. Here we discovered the present of XY chromosomes and that the Y chromosomal region is 79-116 million-years-old and shared between Yellow-bellied water skink and Spotted skinks (Niveoscincus ocellatus). 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.
Abstract
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.
Paola Cornejo-Páramo, Duminda S B Dissanayake, Andrés Lira-Noriega, Mónica L Martínez-Pacheco, Armando Acosta, Ciro Ramírez-Suástegui, Fausto R Méndez-de-la-Cruz, Tamás Székely, Araxi O Urrutia, Arthur Georges, Diego Cortez, Viviparous Reptile Regarded to Have Temperature-Dependent Sex Determination Has Old XY Chromosomes, Genome Biology and Evolution, Volume 12, Issue 6, June 2020, Pages 924–930, https://doi.org/10.1093/gbe/evaa104
Abstract
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.
Paola Cornejo-Páramo, Duminda S B Dissanayake, Andrés Lira-Noriega, Mónica L Martínez-Pacheco, Armando Acosta, Ciro Ramírez-Suástegui, Fausto R Méndez-de-la-Cruz, Tamás Székely, Araxi O Urrutia, Arthur Georges, Diego Cortez, Viviparous Reptile Regarded to Have Temperature-Dependent Sex Determination Has Old XY Chromosomes, Genome Biology and Evolution, Volume 12, Issue 6, June 2020, Pages 924–930, https://doi.org/10.1093/gbe/evaa104
© 2017 by Duminda Dissanayake Last update 11 Oct 2021
