Applications of next-generation sequencing to phylogeography and phylogenetics

McCormack, John E.; Hird, Sarah M.; Zellmer, Amanda J.; Carstens, Bryan C.; Brumfield, Robb T.

doi:10.1016/j.ympev.2011.12.007

Cited by 568 publications

(488 citation statements)

References 133 publications

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“…Konstanz GeCKo, Glasgow Polyomics, and illumina). Therefore, combined with the availability of new approaches to reduce genome representation, genomic projects are now feasible even on quite tight budgets Sboner et al, 2011;McCormack et al, 2013;Recknagel et al, 2015) and for the first time are less than or on par with the cost of approaches like microsatellite genotyping on ABI. This opens up great possibilities for ecological and evolutionary researchers of salmonids in the wild (Box 1).…”

Section: Tools For Ecological Genomicsmentioning

confidence: 99%

Genomic tools for new insights to variation, adaptation, and evolution in the salmonid fishes: a perspective for charr

Elmer

2016

Hydrobiologia

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The past few years have seen an absolute revolution in genomic technologies and their potential applications to ecology and evolutionary biology research. Such advances open up a range of opportunities for research on non-model organisms and individuals drawn from wild populations. This has resulted in exciting new research seeking to identify the genetic polymorphisms important in adaptation and speciation and how they are organised within the genome. Building on this, there is great interest in the extent to which similar evolutionary patterns are found across multiple populations, particularly whether consistent genetic mechanisms are associated with recurrent phenotypes. A powerful context for disentangling these mechanisms is to focus on highly diverse radiations, where phenotypes vary in and across environments. Therefore, the high diversity found within and among species of salmonid fishes such as charr (Salvelinus) make for an ideal 'non'-model for genomic research. This paper outlines some of the current approaches available in ecological genomics and highlights some recent advances in salmonid research. It also suggests avenues for the sort of predictions that can be derived from ecological genomics, with the aim of understanding the genetics behind the fantastic diversity of salmonid fishes.Keywords Ecological genomics Á Transcriptomics Á Speciation Á Genetic mapping Á Salmonid fishes Á Charr Recent advances in the field of molecular biology have exciting implications for research on the ecology and evolution of natural populations. Particularly, high throughput 'next-generation' sequencing (NGS) (also known as 'second-generation', or 'massively parallel' sequencing) can generate huge amounts of genomic or transcriptomic data on almost any organism. NGS is dramatically decreasing in cost and the associated tools and pipelines are within reach of even modest research groups. This is therefore becoming an invaluable tool for understanding the origins and maintenance of biodiversity. These exciting new approaches can address long-standing questions in evolutionary biology, such as: What is the genetic basis of adaptations? How do closely related species differ? Why are some lineages more diverse than others?The challenge for 'omics' of non-model organisms now shifts away from raw data generation to focusing on informative evolutionary, ecological, and environmental contexts in order to most efficiently and

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Section: Tools For Ecological Genomicsmentioning

confidence: 99%

Genomic tools for new insights to variation, adaptation, and evolution in the salmonid fishes: a perspective for charr

Elmer

2016

Hydrobiologia

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“…Recent advances in next-generation sequencing have resulted in novel of obtaining and analysing large amounts of data [16][17][18][19]. Two recent studies used next-generation data to examine relationships among lineages of Lepidoptera [20,21], but neither study included butterflies.…”

Section: Introductionmentioning

confidence: 99%

Phylogenomics provides strong evidence for relationships of butterflies and moths

2014

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Butterflies and moths constitute some of the most popular and charismatic insects. Lepidoptera include approximately 160 000 described species, many of which are important model organisms. Previous studies on the evolution of Lepidoptera did not confidently place butterflies, and many relationships among superfamilies in the megadiverse clade Ditrysia remain largely uncertain. We generated a molecular dataset with 46 taxa, combining 33 new transcriptomes with 13 available genomes, transcriptomes and expressed sequence tags (ESTs). Using HaMStR with a Lepidoptera-specific coreorthologue set of single copy loci, we identified 2696 genes for inclusion into the phylogenomic analysis. Nucleotides and amino acids of the all-gene, alltaxon dataset yielded nearly identical, well-supported trees. Monophyly of butterflies (Papilionoidea) was strongly supported, and the group included skippers (Hesperiidae) and the enigmatic butterfly-moths (Hedylidae). Butterflies were placed sister to the remaining obtectomeran Lepidoptera, and the latter was grouped with greater than or equal to 87% bootstrap support. Establishing confident relationships among the four most diverse macroheteroceran superfamilies was previously challenging, but we recovered 100% bootstrap support for the following relationships: ((Geometroidea, Noctuoidea), (Bombycoidea, Lasiocampoidea)). We present the first robust, transcriptome-based tree of Lepidoptera that strongly contradicts historical placement of butterflies, and provide an evolutionary framework for genomic, developmental and ecological studies on this diverse insect order.

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“…Future DNA sequencing studies will now be relatively easier to implement using newly available next‐generation high‐throughput amplicon sequencing technologies (McCormack, Hird, Zellmer, Carstens, & Brumfield, 2013). However, it should be noted that many of the haplotypes detected in our study differed by a single base in 710 bp of mtDNA sequence, so smaller amplicons would not allow detection of the same level of population differentiation as found here.…”

Section: Discussionmentioning

confidence: 99%

Screening mitochondrial DNA sequence variation as an alternative method for tracking established and outbreak populations of Queensland fruit fly at the species southern range limit

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Malipatil

Semeraro

et al. 2017

Ecology and Evolution

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Understanding the relationship between incursions of insect pests and established populations is critical to implementing effective control. Studies of genetic variation can provide powerful tools to examine potential invasion pathways and longevity of individual pest outbreaks. The major fruit fly pest in eastern Australia, Queensland fruit fly Bactrocera tryoni (Froggatt), has been subject to significant long‐term quarantine and population reduction control measures in the major horticulture production areas of southeastern Australia, at the species southern range limit. Previous studies have employed microsatellite markers to estimate gene flow between populations across this region. In this study, we used an independent genetic marker, mitochondrial DNA (mtDNA) sequences, to screen genetic variation in established and adjacent outbreak populations in southeastern Australia. During the study period, favorable environmental conditions resulted in multiple outbreaks, which appeared genetically distinctive and relatively geographically localized, implying minimal dispersal between simultaneous outbreaks. Populations in established regions were found to occur over much larger areas. Screening mtDNA (female) lineages proved to be an effective alternative genetic tool to assist in understanding fruit fly population dynamics and provide another possible molecular method that could now be employed for better understanding of the ecology and evolution of this and other pest species.

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Applications of next-generation sequencing to phylogeography and phylogenetics

Cited by 568 publications

References 133 publications

Genomic tools for new insights to variation, adaptation, and evolution in the salmonid fishes: a perspective for charr

Genomic tools for new insights to variation, adaptation, and evolution in the salmonid fishes: a perspective for charr

Phylogenomics provides strong evidence for relationships of butterflies and moths

Screening mitochondrial DNA sequence variation as an alternative method for tracking established and outbreak populations of Queensland fruit fly at the species southern range limit

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