Within uncharacterized groups, DNA barcodes, short DNA sequences that are present in a wide range of species, can be used to assign organisms into species. We propose an automatic procedure that sorts the sequences into hypothetical species based on the barcode gap, which can be observed whenever the divergence among organisms belonging to the same species is smaller than divergence among organisms from different species. We use a range of prior intraspecific divergence to infer from the data a model-based one-sided confidence limit for intraspecific divergence. The method, called Automatic Barcode Gap Discovery (ABGD), then detects the barcode gap as the first significant gap beyond this limit and uses it to partition the data. Inference of the limit and gap detection are then recursively applied to previously obtained groups to get finer partitions until there is no further partitioning. Using six published data sets of metazoans, we show that ABGD is computationally efficient and performs well for standard prior maximum intraspecific divergences (a few per cent of divergence for the five data sets), except for one data set where less than three sequences per species were sampled. We further explore the theoretical limitations of ABGD through simulation of explicit speciation and population genetics scenarios. Our results emphasize in particular the sensitivity of the method to the presence of recent speciation events, via (unrealistically) high rates of speciation or large numbers of species. In conclusion, ABGD is fast, simple method to split a sequence alignment data set into candidate species that should be complemented with other evidence in an integrative taxonomic approach.

ABGD, Automatic Barcode Gap Discovery for primary species delimitation

The mitochondrial (mt) genome is, to date, the most extensively studied genomic system in insects, outnumbering nuclear genomes tenfold and representing all orders versus very few. Phylogenomic analysis methods have been tested extensively, identifying compositional bias and rate variation, both within and between lineages, as the principal issues confronting accurate analyses. Major studies at both inter- and intraordinal levels have contributed to our understanding of phylogenetic relationships within many groups. Genome rearrangements are an additional data type for defining relationships, with rearrangement synapomorphies identified across multiple orders and at many different taxonomic levels. Hymenoptera and Psocodea have greatly elevated rates of rearrangement offering both opportunities and pitfalls for identifying rearrangement synapomorphies in each group. Finally, insects are model systems for studying aberrant mt genomes, including truncated tRNAs and multichromosomal genomes. Greater integration of nuclear and mt genomic studies is necessary to further our understanding of insect genomic evolution.

Insect Mitochondrial Genomics: Implications for Evolution and Phylogeny

The statistical rigor of species delimitation has increased dramatically over the past decade. Coalescent theory provides powerful models for population genetic inference, and is now increasingly important in phylogenetics and speciation research. By applying probabilistic models, coalescent-based species delimitation provides clear and objective testing of alternative hypotheses of evolutionary independence. As acquisition of multilocus data becomes increasingly automated, coalescent-based species delimitation will improve the discovery, resolution, consistency, and stability of the taxonomy of species. Along with other tools and data types, coalescent-based species delimitation will play an important role in an integrative taxonomy that emphasizes the identification of species limits and the processes that have promoted lineage diversification.

https://faculty.washington.edu/leache/wordpress/wp-content/uploads/2014/06/2012TREE.pdf

Coalescent-based species delimitation in an integrative taxonomy

Background
DNA barcoding aims to provide an efficient method for species-level identifications using an array of species specific molecular tags derived from the 5′ region of the mitochondrial cytochrome c oxidase I (COI) gene. The efficiency of the method hinges on the degree of sequence divergence among species and species-level identifications are relatively straightforward when the average genetic distance among individuals within a species does not exceed the average genetic distance between sister species. Fishes constitute a highly diverse group of vertebrates that exhibit deep phenotypic changes during development. In this context, the identification of fish species is challenging and DNA barcoding provide new perspectives in ecology and systematics of fishes. Here we examined the degree to which DNA barcoding discriminate freshwater fish species from the well-known Canadian fauna, which currently encompasses nearly 200 species, some which are of high economic value like salmons and sturgeons.

/pdf/identifying-canadian-freshwater-fishes-through-dna-barcodes-fih50art9t.pdf

Identifying Canadian Freshwater Fishes through DNA Barcodes

Most apomictic root-knot nematodes (RKN; Meloidogyne spp.) have host ranges that encompass the majority of flowering plants, and M. incognita is possibly the world's most damaging crop pathogen. The ancestors, age, and origins of the polyphagous RKN are obscure, but there is increasing evidence that M. incognita, M. javanica, and M. arenaria are closely related, heterogeneous species with a recent, hybrid (reticulate) origin. If so, they must owe much of their current worldwide distributions to spread by agriculture. Host resistance appears to be generally durable in the field, but laboratory studies suggest that apomixis does not prevent evolution in response to selection by a parasitic bacterium (Pasteuria penetrans) and host resistance. Maintaining general fitness may be the evolutionary priority for most populations of polyphagous RKN, and a wide host range, important in the field but not in the laboratory, may be conserved by apomixis. Several factors may help confer a wide host range, including suppression of host resistance, perhaps as a consequence of the strength of the induced susceptible response. Resistance genes effective against RKN appear not to have resulted from coevolution. Rates of juvenile invasion and/or development are low in many wild and some crop plants, with the result that they are both poor hosts and sustain less damage. Overall, it is suggested that greater coordination, particularly of fundamental research, is required.

Apomictic, polyphagous root-knot nematodes: exceptionally successful and damaging biotrophic root pathogens.

The recently introduced term ‘integrative taxonomy’ refers to taxonomy that integrates all available data sources to frame species limits. We survey current taxonomic methods available to delimit species that integrate a variety of data, including molecular and morphological characters. A literature review of empirical studies using the term ‘integrative taxonomy’ assessed the kinds of data being used to frame species limits, and methods of integration. Almost all studies are qualitative and comparative – we are a long way from a repeatable, quantitative method of truly ‘integrative taxonomy’. The usual methods for integrating data in phylogenetic and population genetic paradigms are not appropriate for integrative taxonomy, either because of the diverse range of data used or because of the special challenges that arise when working at the species/population boundary. We identify two challenges that, if met, will facilitate the development of a more complete toolkit and a more robust research programme in integrative taxonomy using species tree approaches. We propose the term ‘iterative taxonomy’ for current practice that treats species boundaries as hypotheses to be tested with new evidence. A search for biological or evolutionary explanations for discordant evidence can be used to distinguish between competing species boundary hypotheses. We identify two recent empirical examples that use the process of iterative taxonomy.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-3113.2010.00558.x

Integrative taxonomy, or iterative taxonomy?

The utility of cytochrome oxidase I (COI) DNA barcodes for the identifica- tion of nine species of forensically important blowflies of the genus Chrysomya (Diptera: Calliphoridae), from Australia, was tested A 658-bp fragment of the COI gene was sequenced from 56 specimens, representing all nine Chrysomya species and three cal- liphorid outgroups Nucleotide sequence divergences were calculated using the Kimura- two-parameter distance model and a neighbour-joining (NJ) analysis was performed to provide a graphic display of the patterns of divergence among the species All species were resolved as reciprocally monophyletic on the NJ tree Mean intraspecific and inter- specific sequence divergences were 0097% (range 0 - 0612%, standard error (SE) = 0119%) and 6499% (range 0458 - 9254%, SE = 1864%), respectively In one case, a specimen that was identified morphologically was recovered with its sister species on the NJ tree The hybrid status of this specimen was established by sequence analysis of the second ribosomal internal transcribed spacer (ITS2) In another instance, this nu- clear region was used to verify four cases of specimen misidentification that had been highlighted by the COI analysis The COI barcode sequence was found to be suitable for the identification of Chrysomya species from the east coast of Australia

http://forensicentomologist.com/wp-content/uploads/2008/05/coi-barcodes-for-forensically-important-flies.pdf

Using COI barcodes to identify forensically and medically important blowflies.

https://ro.uow.edu.au/cgi/viewcontent.cgi?article=8050&context=scipapers

Leigh A. Nelson

Papers

Integrative taxonomy, or iterative taxonomy?

Using COI barcodes to identify forensically and medically important blowflies.

Beyond barcoding: A mitochondrial genomics approach to molecular phylogenetics and diagnostics of blowflies (Diptera: Calliphoridae)

Relationship of climate and soil characteristics to geographical distribution of Meloidogyne species in agricultural soils.

Identification of forensically important Chrysomya (Diptera: Calliphoridae) species using the second ribosomal internal transcribed spacer (ITS2).