Genomic methods take the plunge: recent advances in high-throughput sequencing of marine mammals

Kristina M. Cammen; Kimberly R. Andrews; Emma L. Carroll; Andrew David Foote; Emily Humble; Jane I. Khudyakov; Marie Louis; Michael R. McGowen; Morten Tange Olsen; Amy M. van Cise

doi:10.1093/jhered/esw044

Genomic methods take the plunge: recent advances in high-throughput sequencing of marine mammals

Kristina M. Cammen, Kimberly R. Andrews, Emma L. Carroll, Andrew David Foote, Emily Humble, Jane I. Khudyakov, Marie Louis, Michael R. McGowen, Morten Tange Olsen, Amy M. van Cise

27 Citationer (Scopus)

Abstract

The dramatic increase in the application of genomic techniques to non-model organisms (NMOs) over the past decade has yielded numerous valuable contributions to evolutionary biology and ecology, many of which would not have been possible with traditional genetic markers. We review this recent progression with a particular focus on genomic studies of marine mammals, a group of taxa that represent key macroevolutionary transitions from terrestrial to marine environments and for which available genomic resources have recently undergone notable rapid growth. Genomic studies of NMOs utilize an expanding range of approaches, including whole genome sequencing, restriction site-associated DNA sequencing, array-based sequencing of single nucleotide polymorphisms and target sequence probes (e.g., exomes), and transcriptome sequencing. These approaches generate different types and quantities of data, and many can be applied with limited or no prior genomic resources, thus overcoming one traditional limitation of research on NMOs. Within marine mammals, such studies have thus far yielded significant contributions to the fields of phylogenomics and comparative genomics, as well as enabled investigations of fitness, demography, and population structure. Here we review the primary options for generating genomic data, introduce several emerging techniques, and discuss the suitability of each approach for different applications in the study of NMOs.

Originalsprog	Engelsk
Tidsskrift	Journal of Heredity
Vol/bind	107
Udgave nummer	6
Sider (fra-til)	481-495
Antal sider	15
ISSN	0022-1503
DOI	https://doi.org/10.1093/jhered/esw044
Status	Udgivet - nov. 2016

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10.1093/jhered/esw044

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title = "Genomic methods take the plunge: recent advances in high-throughput sequencing of marine mammals",

abstract = "The dramatic increase in the application of genomic techniques to non-model organisms (NMOs) over the past decade has yielded numerous valuable contributions to evolutionary biology and ecology, many of which would not have been possible with traditional genetic markers. We review this recent progression with a particular focus on genomic studies of marine mammals, a group of taxa that represent key macroevolutionary transitions from terrestrial to marine environments and for which available genomic resources have recently undergone notable rapid growth. Genomic studies of NMOs utilize an expanding range of approaches, including whole genome sequencing, restriction site-associated DNA sequencing, array-based sequencing of single nucleotide polymorphisms and target sequence probes (e.g., exomes), and transcriptome sequencing. These approaches generate different types and quantities of data, and many can be applied with limited or no prior genomic resources, thus overcoming one traditional limitation of research on NMOs. Within marine mammals, such studies have thus far yielded significant contributions to the fields of phylogenomics and comparative genomics, as well as enabled investigations of fitness, demography, and population structure. Here we review the primary options for generating genomic data, introduce several emerging techniques, and discuss the suitability of each approach for different applications in the study of NMOs.",

author = "Cammen, {Kristina M.} and Andrews, {Kimberly R.} and Carroll, {Emma L.} and Foote, {Andrew David} and Emily Humble and Khudyakov, {Jane I.} and Marie Louis and McGowen, {Michael R.} and Olsen, {Morten Tange} and {van Cise}, {Amy M.}",

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T2 - recent advances in high-throughput sequencing of marine mammals

AU - Cammen, Kristina M.

AU - Andrews, Kimberly R.

AU - Carroll, Emma L.

AU - Foote, Andrew David

AU - Humble, Emily

AU - Khudyakov, Jane I.

AU - Louis, Marie

AU - McGowen, Michael R.

AU - Olsen, Morten Tange

AU - van Cise, Amy M.

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N2 - The dramatic increase in the application of genomic techniques to non-model organisms (NMOs) over the past decade has yielded numerous valuable contributions to evolutionary biology and ecology, many of which would not have been possible with traditional genetic markers. We review this recent progression with a particular focus on genomic studies of marine mammals, a group of taxa that represent key macroevolutionary transitions from terrestrial to marine environments and for which available genomic resources have recently undergone notable rapid growth. Genomic studies of NMOs utilize an expanding range of approaches, including whole genome sequencing, restriction site-associated DNA sequencing, array-based sequencing of single nucleotide polymorphisms and target sequence probes (e.g., exomes), and transcriptome sequencing. These approaches generate different types and quantities of data, and many can be applied with limited or no prior genomic resources, thus overcoming one traditional limitation of research on NMOs. Within marine mammals, such studies have thus far yielded significant contributions to the fields of phylogenomics and comparative genomics, as well as enabled investigations of fitness, demography, and population structure. Here we review the primary options for generating genomic data, introduce several emerging techniques, and discuss the suitability of each approach for different applications in the study of NMOs.

AB - The dramatic increase in the application of genomic techniques to non-model organisms (NMOs) over the past decade has yielded numerous valuable contributions to evolutionary biology and ecology, many of which would not have been possible with traditional genetic markers. We review this recent progression with a particular focus on genomic studies of marine mammals, a group of taxa that represent key macroevolutionary transitions from terrestrial to marine environments and for which available genomic resources have recently undergone notable rapid growth. Genomic studies of NMOs utilize an expanding range of approaches, including whole genome sequencing, restriction site-associated DNA sequencing, array-based sequencing of single nucleotide polymorphisms and target sequence probes (e.g., exomes), and transcriptome sequencing. These approaches generate different types and quantities of data, and many can be applied with limited or no prior genomic resources, thus overcoming one traditional limitation of research on NMOs. Within marine mammals, such studies have thus far yielded significant contributions to the fields of phylogenomics and comparative genomics, as well as enabled investigations of fitness, demography, and population structure. Here we review the primary options for generating genomic data, introduce several emerging techniques, and discuss the suitability of each approach for different applications in the study of NMOs.

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JO - Journal of Heredity

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