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.

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Identifying Canadian Freshwater Fishes through DNA Barcodes

We DNA barcoded 2,597 parasitoid wasps belonging to 6 microgastrine braconid genera reared from parapatric tropical dry forest, cloud forest, and rain forest in Area de Conservacion Guanacaste (ACG) in northwestern Costa Rica and combined these data with records of caterpillar hosts and morphological analyses. We asked whether barcoding and morphology discover the same provisional species and whether the biological entities revealed by our analysis are congruent with wasp host specificity. Morphological analysis revealed 171 provisional species, but barcoding exposed an additional 142 provisional species; 95% of the total is likely to be undescribed. These 313 provisional species are extraordinarily host specific; more than 90% attack only 1 or 2 species of caterpillars out of more than 3,500 species sampled. The most extreme case of overlooked diversity is the morphospecies Apanteles leucostigmus. This minute black wasp with a distinctive white wing stigma was thought to parasitize 32 species of ACG hesperiid caterpillars, but barcoding revealed 36 provisional species, each attacking one or a very few closely related species of caterpillars. When host records and/or within-ACG distributions suggested that DNA barcoding had missed a species-pair, or when provisional species were separated only by slight differences in their barcodes, we examined nuclear sequences to test hypotheses of presumptive species boundaries and to further probe host specificity. Our iterative process of combining morphological analysis, ecology, and DNA barcoding and reiteratively using specimens maintained in permanent collections has resulted in a much more fine-scaled understanding of parasitoid diversity and host specificity than any one of these elements could have produced on its own.

https://www.pnas.org/content/pnas/105/34/12359.full.pdf

Extreme diversity of tropical parasitoid wasps exposed by iterative integration of natural history, DNA barcoding, morphology, and collections

The species concept is the cornerstone of biodiversity science, and any paradigm shift in the delimitation of species affects many research fields. Many biologists now are embracing a new "species" paradigm as separately evolving populations using different delimitation criteria. Individual criteria can emerge during different periods of speciation; some may never evolve. As such, a paradigm shift in the species concept relates to this inherent heterogeneity in the speciation process and species category-which is fundamentally overlooked in biodiversity research. Cryptic species fall within this paradigm shift: they are continuously being reported from diverse animal phyla but are poorly considered in current tests of ecological and evolutionary theory. The aim of this review is to integrate cryptic species in biodiversity science. In the first section, we address that the absence of morphological diversification is an evolutionary phenomenon, a "process" counterpart to the long-studied mechanisms of morphological diversification. In the next section regarding taxonomy, we show that molecular delimitation of cryptic species is heavily biased towards distance-based methods. We also stress the importance of formally naming of cryptic species for better integration into research fields that use species as units of analysis. Finally, we show that incorporating cryptic species leads to novel insights regarding biodiversity patterns and processes, including large-scale biodiversity assessments, geographic variation in species distribution and species coexistence. It is time for incorporating multicriteria species approaches aiming to understand speciation across space and taxa, thus allowing integration into biodiversity conservation while accommodating for species uncertainty.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/mec.14486

Cryptic species as a window into the paradigm shift of the species concept

Amphipods are brooding peracaridan crustaceans whose young undergo direct development, with no independent larval dispersal stage. Most species are epibenthic, benthic, or subterranean. There are some 1,870 amphipod species and subspecies recognized from fresh or inland waters worldwide at the end of 2005. This accounts for 20% of the total known amphipod diversity. The actual diversity may still be several-fold. Amphipods are most abundant in cool and temperate environments; they are particularly diversified in subterranean environments and in running waters (fragmented habitats), and in temperate ancient lakes, but are notably rare in the tropics. Of the described freshwater taxa 70% are Palearctic, 13% Nearctic, 7% Neotropical, 6% Australasian and 3% Afrotropical. Approximately 45% of the taxa are subterranean; subterranean diversity is highest in the karst landscapes of Central and Southern Europe (e.g., Niphargidae), North America (Crangonyctidae), and Australia (Paramelitidae). The majority of Palearctic epigean amphipods are in the superfamily Gammaroidea, whereas talitroid amphipods (Hyalella) account for all Neotropic and much of the Nearctic epigean fauna. Major concentrations of endemic species diversity occur in Southern Europe, Lake Baikal, the Ponto-Caspian basin, Southern Australia (including Tasmania), and the south-eastern USA. Endemic family diversity is similarly centered in the Western Palearctic and Lake Baikal. Freshwater amphipods are greatly polyphyletic, continental invasions have taken place repeatedly in different time frames and regions of the world. In the recent decades, human mediated invasions of Ponto-Caspian amphipods have had great impacts on European fluvial ecosystems.

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Global diversity of amphipods (Amphipoda; Crustacea) in freshwater

DNA barcodes, like traditional sources of taxonomic information, are potentially powerful heuristics in the identification of described species but require mindful analytical interpretation. The role of DNA barcoding in generating hypotheses of new taxa in need of formal taxonomic treatment is discussed, and it is emphasized that the recursive process of character evaluation is both necessary and best served by understanding the empirical mechanics of the discovery process. These undertakings carry enormous ramifications not only for the translation of DNA sequence data into taxonomic information but also for our comprehension of the magnitude of species diversity and its disappearance. This paper examines the potential strengths and pitfalls of integrating DNA sequence data, specifically in the form of DNA barcodes as they are currently generated and analyzed, with taxonomic practice.

Integrating DNA barcode data and taxonomic practice: Determination, discovery, and description

DNA barcoding has revealed unrecognized species in several animal groups. In this study we have employed DNA barcoding to examine Hyalella, a taxonomically difficult genus of amphipod crustaceans, from sites in the southern Great Basin of California and Nevada, USA. We assessed the extent of species diversity using a species screening threshold (SST) set at 10 times the average intrapopulation cytochrome c oxidase subunit I (COI) haplotype divergence. Despite the fact that this threshold approach is more conservative in delineating provisional species than the phylogenetic species concept, our analyses revealed extraordinary levels of cryptic diversity and endemism. The SST discriminated two provisional species within Hyalella sandra, and 33 provisional species within Hyalella azteca. COI nucleotide divergences among these provisional species ranged from 4.4% to 29.9%. These results have important implications for the conservation of life in desert springs - habitats that are threatened as a result of groundwater over-exploitation.

Doug L. Threloff

Papers

DNA barcoding reveals extraordinary cryptic diversity in an amphipod genus: implications for desert spring conservation

Genetic zoogeography of the Hyalella azteca species complex in the Great Basin: Rapid rates of molecular diversification in desert springs