More grist for the mill? Species delimitation in the genomic era and its implications for conservation

Stanton, David W. G.; Frandsen, Peter; Waples, Ryan K.; Heller, Rasmus; Russo, Isa‐Rita M.; Orozco‐terWengel, Pablo; Pedersen, Casper-Emil Tingskov; Siegismund, Hans R.; Bruford, Michael William

doi:10.1007/s10592-019-01149-5

Cited by 92 publications

(86 citation statements)

References 79 publications

(95 reference statements)

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“…Species delimitation, and hence the degree of separation between different groups of biological organisms, is a pivotal concept for modern biology, despite the fact that there is no universal agreement about the species concept itself (Stanton et al 2019). The universal species concept proposed by de Queiroz (2007) -i.e., that species represent separately evolving evolutionary lines without any other defining characterspotentially implies the impossibility of taxonomically defining characters at a general scale.…”

Section: Introductionmentioning

confidence: 99%

Fine-scale species delimitation: speciation in process and periodic patterns in nudibranch diversity

Korshunova

Malmberg²,

Prkić³

et al. 2020

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Using the nudibranch genus Amphorina as a model, ongoing speciation is demonstrated, as well as how periodic-like patterns in colouration can be included in an integrated method of fine-scale species delimitation. By combining several methods, including BPP analysis and the study of molecular, morphological, and ecological data from a large number of specimens within a broad geographic range from northern Europe to the Mediterranean, five species are recognised within the genus Amphorina, reviewed here for the first time. Two new species from the southwestern coast of Sweden are described, A. viriolasp. nov. and A. andrasp. nov. Evidence is provided of a recent speciation process between the two closely related, yet separate, species which inhabit the same geographic localities, but demonstrate strict water depth differentiation, with one species inhabiting the shallow brackish top layer above the halocline and the other species inhabiting the underlying saltier water. The results presented here are of relevance for currently debated issues such as conservation in relation to speciation, fine species delimitation, and integration of molecular, morphological and ecological information in biodiversity studies. The periodic approach to taxonomy has considerable practical potential for various organismal groups.

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Section: Introductionmentioning

confidence: 99%

Fine-scale species delimitation: speciation in process and periodic patterns in nudibranch diversity

Korshunova

Malmberg²,

Prkić³

et al. 2020

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“…The IUCN definition of a species is provided online: ‘A group of interbreeding individuals with common characteristics that produce fertile (capable of reproducing) offspring and which are not able to interbreed with other such groups, that is, a population that is reproductively isolated from others’ (https://www.iucn.org/downloads/en_iucn_glossary_definitions.pdf), which is essentially the BSC. Given discrepancies in defining ‘species’, some scientists have suggested that conservation biology would benefit the most by concentrating on assessing the adaptive potential of evolutionary significant units rather than engage in mental gymnastics about ‘species’ (Fraser & Bernatchez, 2001; Funk, McKay, Hohenlohe, & Allendorf, 2012; Mable, 2019; Stanton et al., 2019).…”

Section: Species Subspecies and Endangered Speciesmentioning

confidence: 99%

“…However, other academic publications question whether the taxonomy adopted by O'Connor et al. (2019) reflects the ‘most in‐depth analysis of genetic evidence’ (Petzold & Hassanin, 2020; Stanton et al., 2019), so the giraffe ‘taxonomic quandary’ (Bercovitch & Deacon, 2015) continues.…”

Section: How Many Species Of Giraffe Are There?mentioning

confidence: 99%

Giraffe taxonomy, geographic distribution and conservation

Bercovitch

2020

Afr J Ecol

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The conservation implications of taxonomic pedigrees and geographic distributions are substantial because the two entities are inseparable when the goal is saving biodiversity and ecosystems. Yet, neither Latin nomenclature nor animal movement patterns are static over time because modifications result as more data are collected.Scientists have recently reassessed both the taxonomy and geographic range of giraffes, Giraffa camelopardalis. Evidence has been presented that giraffes ought to be classified into anywhere from one to nine species, and that their continent-wide ranging area has compressed by about 6%. A systematic, comprehensive, and critical evaluation of the literature supports the suggestion that the conventional taxonomy of giraffes is due for an overhaul, but serious doubts exist regarding the inference that their geographic range in Africa has altered in the last few years. Sharing competing viewpoints about taxonomy and geographic ranges in the academic literature can be productive, but becomes counter-productive, and detrimental to conservation management plans and programmes, when scientists prematurely proclaim and promote questionable 'new' findings. K E Y W O R D Sconservation, endangered species, geographic range, giraffe, taxonomy | 151 BERCOVITCH nomenclature. Strangely, the word 'species' is absent from the Glossary in The Origin of Species (Darwin, 1859). Charles Darwin was too meticulous to have inadvertently omitted the word. Rather than define the term, he explained it (pp. 45-46): '…no clear line of demarcation has as yet been drawn between species and sub-species or between sub-species and well-marked varieties, or between lesser varieties and individual differences. These differences blend into each other by an insensible series…I look at the term species as one arbitrarily given, for the sake of convenience, to a set of individuals closely resembling each other'.As recognised by Darwin, organisms exist in nature, but species do not. Evolution is dynamic, speciation is unstoppable, and continued data collection combined with the development of new methods translates into periodic revisions of taxonomy. Because 'species' do not exist as entities in nature, and because of differences in scientific definitions and perspectives as to what defines a 'species' or 'subspe-

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“…It now has a more contemporaneous meaning, defined primarily by population genomic data, and represents a conservation unit isolated demographically from other such units (Mussmann, Douglas, Chafin, & Douglas, 2019; Palsbøll, Bérubé, & Allendorf, 2014). While genomic data clearly hold great potential for elucidating the evolutionary process, arguments must still be resolved before they become a de facto diagnostic tool for species delineation (Stanton et al., 2019). For example, genomic techniques were unsuccessful in unraveling a hybrid complex among Darwin's finches in the Galapagos (Zink & Vázguez‐Miranda, 2019).…”

Section: Introductionmentioning

confidence: 99%

Gene flow and species delimitation in fishes of Western North America: Flannelmouth (Catostomus latipinnis) and Bluehead sucker (C. Pantosteus discobolus)

Bangs

Douglas

Chafin

2020

Ecology and Evolution

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The delimitation of species boundaries, particularly those obscured by reticulation, is a critical step in contemporary biodiversity assessment. It is especially relevant for conservation and management of indigenous fishes in western North America, represented herein by two species with dissimilar life histories codistributed in the highly modified Colorado River (i.e., flannelmouth sucker, Catostomus latipinnis; bluehead sucker, C. (Pantosteus) discobolus). To quantify phylogenomic patterns and examine proposed taxonomic revisions, we first employed double‐digest restriction site‐associated DNA sequencing (ddRAD), yielding 39,755 unlinked SNPs across 139 samples. These were subsequently evaluated with multiple analytical approaches and by contrasting life history data. Three phylogenetic methods and a Bayesian assignment test highlighted similar phylogenomic patterns in each, but with considerable difference in presumed times of divergence. Three lineages were detected in bluehead sucker, supporting elevation of C. (P.) virescens to species status and recognizing C. (P.) discobolus yarrowi (Zuni bluehead sucker) as a discrete entity. Admixture in the latter necessitated a reevaluation of its contemporary and historic distributions, underscoring how biodiversity identification can be confounded by complex evolutionary histories. In addition, we defined three separate flannelmouth sucker lineages as ESUs (evolutionarily significant units), given limited phenotypic and genetic differentiation, contemporary isolation, and lack of concordance (per the genealogical concordance component of the phylogenetic species concept). Introgression was diagnosed in both species, with the Little Colorado and Virgin rivers in particular. Our diagnostic methods, and the agreement of our SNPs with previous morphological, enzymatic, and mitochondrial work, allowed us to partition complex evolutionary histories into requisite components, such as isolation versus secondary contact.

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More grist for the mill? Species delimitation in the genomic era and its implications for conservation

Cited by 92 publications

References 79 publications

Fine-scale species delimitation: speciation in process and periodic patterns in nudibranch diversity

Fine-scale species delimitation: speciation in process and periodic patterns in nudibranch diversity

Giraffe taxonomy, geographic distribution and conservation

Gene flow and species delimitation in fishes of Western North America: Flannelmouth (Catostomus latipinnis) and Bluehead sucker (C. Pantosteus discobolus)

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