Why should mitochondria define species?

Abstract

More than a decade of DNA barcoding encompassing about five million specimens covering 100,000 animal species supports the generalization that mitochondrial DNA clusters largely overlap with species as defined by domain experts. Most barcode clustering reflects synonymous substitutions. What evolutionary mechanisms account for synonymous clusters being largely coincident with species? The answer depends on whether variants are phenotypically neutral. To the degree that variants are selectable, purifying selection limits variation within species and neighboring species may have distinct adaptive peaks. Phenotypically neutral variants are only subject to demographic processes—drift, lineage sorting, genetic hitchhiking, and bottlenecks. The evolution of modern humans has been studied from several disciplines with detail unique among animal species. Mitochondrial barcodes provide a commensurable way to compare modern humans to other animal species. Barcode variation in the modern human population is quantitatively similar to that within other animal species. Several convergent lines of evidence show that mitochondrial diversity in modern humans follows from sequence uniformity followed by the accumulation of largely neutral diversity during a population expansion that began approximately 100,000 years ago. A straightforward hypothesis is that the extant populations of almost all animal species have arrived at a similar result consequent to a similar process of expansion from mitochondrial uniformity within the last one to several hundred thousand years.

Species‐level predation network uncovers high prey specificity in a Neotropical army ant community

“…DNA barcoding relies on the premise that intraspecific sequence differences in a standardized gene fragment are generally smaller than interspecific ones (Meier, Zhang, & Ali, ; Stoeckle & Thaler, ; Wiemers & Fiedler, ). This allows clustering of barcode data into distinct genetic groups, which in most cases reflect actual species boundaries (Stoeckle & Thaler, ).…”

The Mitochondrial Genome–on Selective Constraints and Signatures at the Organism, Cell, and Single Mitochondrion Levels

“…As such transcripts overlap the coding regions of protein-coding genes, it is difficult to distinguish the potential functional impact of mutations in such elements. Despite all of the above, although it is possible to assess the potential impact of mutations that alter codons but not the amino acid code (the so-called silent mutations) by assessing codon bias index (Levin et al, 2013), only minor phenotypic effects have been demonstrated regarding such in the mitochondria, leading some researchers to argue for lack of selective signatures in most mtDNA mutations (Stoeckle and Thaler, 2018). Nevertheless, phenotypic impact of a mutation is not only limited to the subsequent gene function-an apparently silent mutation could alter a previously un-noticed regulatory element (Blumberg et al, 2018).…”

Phylogeography and demographic history of the black kite Milvus migrans, a widespread raptor in Eurasia, Australia and Africa

“…While it is difficult to isolate nuclear DNA of sufficient quality and quantity from moulted feathers, there are hundreds to thousands of copies of the mtDNA molecule, making it more readily available for analysis. Mitochondrial loci have been shown to be an efficient estimator of recent population divergence (Moore 1995, Zink and Barrowclough 2008, Hung et al 2016, DeSalle et al 2017, Stoeckle and Thaler 2018). While phylogenetic trees reconstructed from phenotypes and mitochondrial or nuclear loci can contradict each other (Griffiths et al 2004, Bensch et al 2006, Yeung et al 2011, Drovetski et al 2018, Harris et al 2018), our data on the geographic distribution of black kite haplogroups correlated well with subspecies ranges inferred from phenotype and migration pathways; hence, we consider that the phylogenetic tree based on the CytB gene fragment adequately reflects actual black kite phylogeny.…”