Marine turtle mitogenome phylogenetics and evolution

Duchêne, Sebastián; Frey, Amy; Alfaro-Núñez, Alonzo; Dutton, Peter H.; Gilbert, M. Thomas P.; Morin, Phillip A.

doi:10.1016/j.ympev.2012.06.010

Cited by 91 publications

(164 citation statements)

References 59 publications

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“…Finalmente el haplotipo 4 (H4) presentó la inserción de 8 bases (posición 36 al 42 y la posición 46). La utilización de la herramienta BLAST de GenBank mostró que el haplotipo 1 fue registrado en Galápagos (Número de acceso JX454978.1) y México (JX454974.1) por Duchene et al (2012); además de estar descrito en individuos de Japón (AB485794.1) por Nishizawa et al (2010). Finalmente los haplotipos 2, 3 y 4 no han sido reportados en la base de datos.…”

Section: Análisis Genéticounclassified

Estudio poblacional y genético de la tortuga Chelonia mydas agassizii (Sauria: Cheloniidae) en la Playa Chinchorro, Arica, Chile

Véliz

Salinas

Sielfeld

et al. 2014

Rev. biol. mar. oceanogr.

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Section: Análisis Genéticounclassified

Estudio poblacional y genético de la tortuga Chelonia mydas agassizii (Sauria: Cheloniidae) en la Playa Chinchorro, Arica, Chile

Véliz

Salinas

Sielfeld

et al. 2014

Rev. biol. mar. oceanogr.

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“…The taxonomy of marine turtles is now well-established based on both nuclear and mitochondrial genes (Naro-Maciel et al, 2008;Duchêne et al, 2012), yet population genetic and phylogeographic studies continue to reveal complex population structuring within each species. Such studies inform both broad scale contemporary patterns of geographic variation, as well as inferring historic patterns that led to the current distribution of genetic variation.…”

Section: Evolutionary History and Phylogeographymentioning

confidence: 99%

“…For mtDNA, this began with the development of primers that target an extended control region sequence (i.e., 766 vs. 490 bp; Shamblin et al, 2012b), and recently extended to identification of diagnostic variants in other mtDNA regions (Shamblin et al, 2012a;Tikochinski et al, 2012) and whole mitogenome sequencing (Duchêne et al, 2012). In cases where there is not extensive haplotype sharing among rookeries, the extended control region sequence can effectively identify natal origin of foraging turtles (LeRoux et al, 2012).…”

Section: Expansion Of Molecular Markersmentioning

confidence: 99%

“…For example, in addition to DNA sequencing HTS techniques, RNA sequencing (RNASeq) can be employed to quantify gene expression (in lieu of lower throughput techniques such as quantitative PCR) and conduct functional genomics studies. Although to date HTS has been more widely used in other wildlife taxa (e.g., mammals and fish; Shafer et al, 2015;Cammen et al, 2016), in marine turtles HTS approaches have been used to construct the complete green turtle reference genome (Wang et al, 2013), generate mitogenomes of all seven marine turtle species for phylogenetic analyses (Duchêne et al, 2012), and discover SNPs for green, hawksbill and loggerhead turtles (Hancock-Hanser et al, 2013;Komoroske et al, 2016). While HTS approaches effectively eliminate bottlenecks in data production, challenges in data quality and interpretation can remain, particularly for wildlife species with limited genomic resources.…”

Section: High-throughput Sequencingmentioning

confidence: 99%

“…These resources allow researchers to share both code and data, complimenting public genomic databases such as NCBI, the UCSC Genome Browser and Ensembl. For example, marine turtle mitogenome analysis, SNP discovery and genotyping scripts, as well as the complete green turtle reference genome, mitogenomes for all species, and targeted capture array probe sequences are now publically available (see data accessibility links in Duchêne et al, 2012;Hancock-Hanser et al, 2013;Wang et al, 2013).…”

Section: Open Source Software and Reproducibility Initiativesmentioning

confidence: 99%

See 2 more Smart Citations

Advances in the Application of Genetics in Marine Turtle Biology and Conservation

et al. 2017

Self Cite

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Marine turtles migrate across long distances, exhibit complex life histories, and occupy habitats that are difficult to observe. These factors present substantial challenges to understanding fundamental aspects of their biology or assessing human impacts, many of which are important for the effective conservation of these threatened and endangered species. The early development and application of genetic tools made important contributions to understanding marine turtle population and evolutionary biology, such as providing evidence of regional natal homing by breeding adults, establishing connectivity between rookeries and foraging habitats, and determining phylogeography and broad scale stock structure for most marine turtle species. Recent innovations in molecular technologies, statistical methods, and creative application of genetic tools have significantly built upon this knowledge to address key questions in marine turtle biology and conservation management. Here, we evaluate the latest major advances and potential of marine turtle genetic applications, including improved resolution and large-scale syntheses of population structure, connectivity and phylogeography, estimation of key demographic rates such as age to maturity and operational or breeding sex ratios, insight into reproductive strategies and behavior, and assessment of differential human impacts among populations. We then discuss remaining challenges and emerging capabilities, such as rapid, multiplexed genotyping, and investigation of the genomic underpinnings of adaptive variation afforded by high-throughput sequencing technologies.

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Phylogeography, genetic stocks, and conservation implications for an Australian endemic marine turtle

FitzSimmons

Pittard

McIntyre

et al. 2020

Aquatic Conservation

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Identification of the geographic extent of population boundaries, the distribution of genetic lineages, and the amount of genetic exchange among breeding groups is needed for effective conservation of vulnerable marine migratory species. This is particularly true of the flatback turtle (Natator depressus), which only breeds in Australia but has extensive migrations that can include international waters. This study investigated the phylogeography and genetic structure among 17 flatback turtle rookeries across their range by sequencing an 810 bp portion of the mitochondrial DNA in 889 samples and genotyping 10 microsatellite loci in 598 samples. There was low phylogenetic divergence among haplotypes and evidence of recent population expansion, likely in the late Pleistocene. A predominant haplotype was found across all rookeries, but other haplotype groups were regionally specific. In general, there was agreement in patterns of genetic differentiation in the mitochondrial DNA and microsatellite data, and in some pairwise comparisons a higher mutation rate of microsatellites provided stronger evidence of differentiation. These results suggest natal philopatry operates in the choice of breeding locations for males as well as females. Evidence of genetic connectivity among neighbouring rookeries led to the identification of seven genetic stocks. Geographic boundaries of rookeries used by genetic stocks varied widely (160–1,300 km), highlighting a need for field studies to better understand movement patterns. Hierarchical analysis of molecular variance identified significant genetic differentiation based upon genetic stock, nesting phenology (summer vs. winter nesters), and a west–east discontinuity across Torres Strait. A pattern of isolation by distance was identified, which was most strongly observed in the microsatellite data. In combination with tagging and telemetry studies, these results will allow better quantification of stock‐specific threats along migratory routes and in foraging habitats. Implications of climate change will be stock specific and may depend upon the extent of genetic connectivity between neighbouring stocks.

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Marine turtle mitogenome phylogenetics and evolution

Cited by 91 publications

References 59 publications

Estudio poblacional y genético de la tortuga Chelonia mydas agassizii (Sauria: Cheloniidae) en la Playa Chinchorro, Arica, Chile

Estudio poblacional y genético de la tortuga Chelonia mydas agassizii (Sauria: Cheloniidae) en la Playa Chinchorro, Arica, Chile

Advances in the Application of Genetics in Marine Turtle Biology and Conservation

Phylogeography, genetic stocks, and conservation implications for an Australian endemic marine turtle

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