Organellar DNA continues to provide a rich source of information in the genomics era

Abstract

Next-generation sequencing (NGS) and genomics continue to transform how biologists address fundamental questions in ecology and evolution. The quantity of data that can be generated quickly and cheaply enable researchers to interrogate genomes for hundreds or thousands of loci that can be used for evolutionary inference. This phenomenon had led to an important paradigm shift in how phylogenetic, phylogeographic, and population genomic studies are designed.Historically, mitochondrial DNA (mtDNA) was the primary molecular marker used to estimate evolutionary history and demographic parameters in animals (Avise, 2000;Avise et al., 1987), whereas chloroplast markers were used extensively in plant phylogenetics and phylogeography (Bonatelli et al., 2013;Hickerson et al., 2010;Soltis et al., 1997). Subsequently, microsatellites became a popular multilocus, fragment-based method used to investigate population structure in the nuclear genome. More recently, methods and markers such as RADseq and its derivatives (Baird et al., 2008;Elshire et al., 2011;Peterson et al., 2012), ultraconserved elements (UCEs; Faircloth et al., 2012), anchored hybrid enrichment (AHEs;Lemmon et al., 2012), transcriptomes, and whole genomes have emerged to take full advantage of the power of NGS technologies. The potential resolution provided by thousands of loci is impressive, but not without challenges. Issues with assembly, paralogy, variant calling, phasing, and sequencing errors can all impact subsequent evolutionary inference. Another major issue that can impact these genomic

Piecing the barcoding puzzle of Palearctic water frogs (Pelophylax) sheds light on amphibian biogeography and global invasions

“…Despite well‐known limitations (Rubinoff et al., 2006), single gene barcoding shall continue to provide essential information, even in the era of genomics (Blair, 2023). By combining decades of barcoding efforts in a meta‐analysis framework, we revisit the diversification of Palearctic water frogs in space and time to appraise its evolution, diversity and biological invasions.…”

Creating, curating and evaluating a mitogenomic reference database to improve regional species identification using environmental DNA

“…While we should strive to create reference databases of full nuclear genomes for all organisms on the planet, nuclear DNA may not turn up reliably in extraorganismal eDNA from aggregating, nonspawning metazoans (Jensen et al, 2021; Olson et al, 2012), making nuclear reference sequence databases less useful for eDNA applications. There will therefore always be a need for mitogenomic reference data, and much can still be gleaned from complete mitogenomes on their own (Blair, 2023).…”

Editorial 2024

“…In a reversal from the early days of phylogeography and genomics, many population studies report on variation in the nuclear genome only. As noted by Blair (2023), this is an unfortunate oversight since organellar information can be useful for species identification, as well as for addressing important questions such dispersal mechanisms and the evolution of species limits. Blanchet et al (2023) put forward a framework-based on analyses of phylogenetically conserved candidate genes and associated functional traits-for investigating eco-evolutionary processes across biological scales.…”

“…In a reversal from the early days of phylogeography and genomics, many population studies report on variation in the nuclear genome only. As noted by Blair (2023), this is an unfortunate oversight since organellar information can be useful for species identification, as well as for addressing important questions such dispersal mechanisms and the evolution of species limits. Blanchet et al.…”