Mitochondrial DNA analyses of the saltwater crocodile (Crocodylus porosus) from the Northern Territory of Australia

Luck, Naomi L.; Thomas, Kristen C.; Morin-Adeline, Victoria; Barwick, Sophie; Chong, Amanda Y; Carpenter, Eliza L.; Wan, LinXiao; Willet, Cali E.; Langford-Salisbury, Shannan M.; Abdelsayd, Mary; Ang, Rachel A.; Atkinson, Sarah; Barcelo, Fabian G.; Booth, Melanie E.; Bradbury, Emma J.; Branighan, Thomas L.; Brown, Jennifer M.; Castillo, Lesley; Chandler, Nichola D.; Chong, Josephine; Collits, Kimberly J.; Cook, Emma; Cruz, Rachel; Farrugia, Claire A.; Fletcher, Jessica L.; Fletcher, Sophie; Gamaliel, Nicole S.; Gurr, Jessica; Hallett, Nathan J.; Hargreaves, Grace; Harris, Teresa; Hollings, Samantha; Hopcroft, R.; Johinke, Danielle; Kern, Pippa; Kiddell, Jane L.; Kilby, Kristen E.; Kragic, Borjana; Kwan, Jacqueline H.; Lee, Joseph I.; Liang, Jennifer M.; Lillie, Mette; Lui, Belle C.; Luk, Sharon W.; Lun, Kwok H.; Marshall, Kate L. A.; Marzec, Jolanta A.; Masters, Kellie T.; Mazurkijevic, Laura J.; Medlock, Jeremy; Meoli, Christopher C.; Morris, Katrina M.; Noh, Yvonne H.; Okazaki, Hideki; Orourke, Tamara J.; Payne, Elyssa; Powell, D. J.; Quinlivan, Antonia R.; Reeves, Thomas; Robson, Kate; Royle, Leah J.; Stevenson, Ryan O; Sellens, Teigan; Sun, ZiChen; Sutton, Amanda L.; Swan, Amelia B.; Tang, Jihong; Tinker, Jarrod E.; Tomlinson, Suzanne C.; Wilkin, Tessa; Wright, Anthony R.; Xiao, Sam T.; Yang, Jessica; Yee, Christine; Jaratlerdsiri, Weerachai; Isberg, Sally R.; Miles, Lee G.; Higgins, Damien P.; Lane, Amanda; Gongora, Jaime

doi:10.1071/zo12008

Cited by 6 publications

(2 citation statements)

References 36 publications

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“…The study reveals that the variability in the 1,806 bp of mtDNA analysed here is low. The low level of variation in the mtDNA sequences is concordant with reports of low levels of mtDNA variation reported in other crocodilian species (Bloor et al, 2015;Glen et al, 2002;Luck et al, 2012;Posso-Pelaez et al, 2018;Ray et al, 2004). However, the homogeneity of the hypervariable control region is unusual.…”

Section: Discussionsupporting

confidence: 87%

Mitochondrial DNA analysis reveals extremely low genetic diversity in a managed population of the Critically Endangered Gharial (Gavialis gangeticus, Gmelin, 1789)

Sharma¹

2020

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A decline in the numbers of threatened species is often reversed by reintroduction with the aim of repopulating or strengthening the population to reduce the risk of extinction. The success of reintroduction programs is associated with demographic and genetic monitoring of the reintroduced populations. We undertook a genetic assessment of the Critically Endangered gharial (Gavialis gangeticus) to assess the current level of genetic variation using three partial mitochondrial (mt) DNA regions: cytochrome b, cytochrome c oxidase subunit-I and the control region. We sequenced 103 samples collected across 14 nesting sites. A low level of mtDNA variation was observed in the sampled population (hd = 0.462 ± 0.048; Pi = 0.00029 ± 0.00004). Only five distinct haplotypes were observed in three segregating sites. This is the first assessment of the genetic variation in the wild gharial population to be made using mtDNA. Homogeneity in the 520 bp hypervariable control region of the crocodilian mtDNA is reported here for the first time. The low mitochondrial diversity and no genetic structure in the sampled population is indicative of a genetic bottleneck, the founder effect and probably associated with humanassisted augmentation of the population of the gharial. An extremely low level of genetic variation in the largest gharial population highlights the vulnerability of the gharial population in the wild and calls for immediate genetic assessment of other gharial populations so that a robust conservation plan focusing on connectivity and enhanced protection can be developed for the long-term persistence of the gharial in the wild.

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Section: Discussionsupporting

confidence: 87%

Mitochondrial DNA analysis reveals extremely low genetic diversity in a managed population of the Critically Endangered Gharial (Gavialis gangeticus, Gmelin, 1789)

Sharma¹

2020

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“…The proportion of sequences from each of the CERV clades did not appear to vary from the overall average proportion of sequences recovered across all locations (Table 1). Although recent genetic studies have revealed some level of diversity among animals from the same or similar sampling locations [29,30], a comparison with the current dataset was not possible as different regions of the genome (mtDNA and gene coding regions) were used in these studies.…”

Section: Resultsmentioning

confidence: 99%

Strong purifying selection in endogenous retroviruses in the saltwater crocodile (Crocodylus porosus) in the Northern Territory of Australia

Chong

Atkinson

Isberg³

et al. 2012

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BackgroundEndogenous retroviruses (ERVs) are remnants of exogenous retroviruses that have integrated into the nuclear DNA of a germ-line cell. Here we present the results of a survey into the ERV complement of Crocodylus porosus, the saltwater crocodile, representing 45 individuals from 17 sampling locations in the Northern Territory of Australia. These retroelements were compared with published ERVs from other species of Crocodylia (Crocodilians; alligators, caimans, gharials and crocodiles) as well as representatives from other vertebrates. This study represents one of the first in-depth studies of ERVs within a single reptilian species shedding light on the diversity of ERVs and proliferation mechanisms in crocodilians.ResultsAnalyses of the retroviral pro-pol gene region have corroborated the presence of two major clades of ERVs in C. porosus and revealed 18 potentially functional fragments out of the 227 recovered that encode intact pro-pol ORFs. Interestingly, we have identified some patterns of diversification among those ERVs as well as a novel sequence that suggests the presence of an additional retroviral genus in C. porosus. In addition, considerable diversity but low genetic divergence within one of the C. porosus ERV lineages was identified.ConclusionsWe propose that the ERV complement of C. porosus has come about through a combination of recent infections and replication of ancestral ERVs. Strong purifying selection acting on these clades suggests that this activity is recent or still occurring in the genome of this species. The discovery of potentially functional elements is an interesting development that warrants further investigation.

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MHC class I of saltwater crocodiles (Crocodylus porosus): polymorphism and balancing selection

et al. 2012

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Saltwater crocodiles are in high demand for the production of luxury fashion items. However, their susceptibility to disease incurs substantial losses and it is hoped to be able to genetically select these animals for disease resistance. So far, this has only been enabled by phenotypic selection. Investigating the major histocompatibility complex (MHC) could provide insight into the ability of an individual to respond to pathogens acting as a selective pressure on the host. Here, we assessed genetic diversity and a role of selection in shaping the diversity of MHC class I exon 3 among 42 saltwater crocodiles from nine river basins in the Northern Territory, Australia. We generated 640 sequences using cloning and sequencing methods and identified 43 MHC variants among them. Phylogenetic analyses clustered these variants into two major clades, which may suggest two gene lineages. We found the number of variants within an individual varying between one and seven, indicating that there are at least four gene loci in this species. Selection detection analyses revealed an elevated ratio of nonsynonymous to synonymous substitutions (mean = 1.152 per codon), suggesting balancing selection. Population differentiation analyses revealed that the MHC did not show structuring among the river basins, and there were some shared variants among them. This may be a result of possible gene flow and/or similar selection pressures among populations. These findings provide background knowledge to identify potential MHC markers, which could be used for selecting genetically variable individuals for future disease associations. All MHC class I exon 3 sequences reported in this paper were submitted to the GenBank database with following accession numbers: HQ008785-HQ008789, HQ008791-HQ008798, HQ008808-HQ008815, HQ008824, HQ008826-HQ008830, HQ008835, HQ008839, HQ008842-HQ008850, and JX023536-JX023540.

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Mitochondrial DNA analyses of the saltwater crocodile (Crocodylus porosus) from the Northern Territory of Australia

Cited by 6 publications

References 36 publications

Mitochondrial DNA analysis reveals extremely low genetic diversity in a managed population of the Critically Endangered Gharial (Gavialis gangeticus, Gmelin, 1789)

Mitochondrial DNA analysis reveals extremely low genetic diversity in a managed population of the Critically Endangered Gharial (Gavialis gangeticus, Gmelin, 1789)

Strong purifying selection in endogenous retroviruses in the saltwater crocodile (Crocodylus porosus) in the Northern Territory of Australia

MHC class I of saltwater crocodiles (Crocodylus porosus): polymorphism and balancing selection

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