DNA Barcoding Methods for Invertebrates

Evans, Nathaniel; Paulay, Gustav

doi:10.1007/978-1-61779-591-6_4

Cited by 32 publications

(24 citation statements)

References 145 publications

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“…In practice, different regions of DNA are necessary to provide adequate species identification across lineages. The plastid and nuclear loci indicated here are the most broadly used DNA barcodes for major groups of organisms, including algae [88], land plants [4,89], fungi [5], invertebrates [6], amphibians [7], fish [90], birds [70], and mammals [87,91]. Abbreviations: COI, cytochrome oxidase I; ITS, internal transcribed spacer.…”

Section: Box 1 Building the Dna Barcode Library Using Sanger Sequencingmentioning

confidence: 99%

“…The DNA barcode loci now most commonly used for plants [a combination of plastid rbcL, matK, and trnH-psbA with nuclear internal transcribed spacer (ITS)] and fungi (nuclear ITS) may never be as efficient and successful in identification as CO1 in animals. However, even for some groups of animals (e.g., some invertebrates [6], amphibians, and reptiles [7]), CO1 works poorly and other gene regions are being used as DNA barcodes ( Figure 1). …”

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confidence: 99%

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DNA barcodes for ecology, evolution, and conservation

Kress

García‐Robledo

Uriarte

et al. 2015

Trends in Ecology & Evolution

439

336

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Section: Box 1 Building the Dna Barcode Library Using Sanger Sequencingmentioning

confidence: 99%

mentioning

confidence: 99%

DNA barcodes for ecology, evolution, and conservation

Kress

García‐Robledo

Uriarte

et al. 2015

Trends in Ecology & Evolution

439

336

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“…marinus . In the absence of any differences in the mitochondrial genome or at least at the COI locus—a fast‐evolving locus often used as a species‐level barcode (Evans & Paulay, )—our interpretation of these results is that there has been a recent and rapid speciation event, and likely concomitant selection for traits associated with different habitats: wider carapace and the lack of natatory fringes in Pa. laevimanus (similar to other intertidal Pachygrapsus species) and rounder carapace and natatory fringes in Pl. marinus (similar to other Planes species).…”

Section: Discussionmentioning

confidence: 75%

“…marinus. In the absence of any differences in the mitochondrial genome or at least at the COI locus-a fast-evolving locus often used as a species-level barcode (Evans & Paulay, 2012)-our interpretation of these results is that there has been a (Pfaller & Gil, 2016) or the same sea turtle (Frick et al, 2011) yet do not interbreed. Identifying the factors that both promote hybridization in specific areas and deter hybridization elsewhere would shed light on the mechanisms underlying the maintenance and merger of species diversity on a broader scale (Abbott et al, 2013;Barton, 2001).…”

Section: Low Species Diversity In Rafting Crabsmentioning

confidence: 84%

Hitchhiking the high seas: Global genomics of rafting crabs

Pfaller

Payton

Bjorndal

et al. 2019

Ecology and Evolution

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Population differentiation and diversification depend in large part on the ability and propensity of organisms to successfully disperse. However, our understanding of these processes in organisms with high dispersal ability is biased by the limited genetic resolution offered by traditional genotypic markers. Many neustonic animals disperse not only as pelagic larvae, but also as juveniles and adults while drifting or rafting at the surface of the open ocean. In theory, the heightened dispersal ability of these animals should limit opportunities for species diversification and population differentiation. To test these predictions, we used next‐generation sequencing of genomewide restriction‐site‐associated DNA tags (RADseq) and traditional mitochondrial DNA sequencing, to investigate the species‐level relationships and global population structure of Planes crabs collected from oceanic flotsam and sea turtles. Our results indicate that species diversity in this clade is low—likely three closely related species—with no evidence of cryptic or undescribed species. Moreover, our results indicate weak population differentiation among widely separated aggregations with genetic indices showing only subtle genetic discontinuities across all oceans of the world (RADseq F ST = 0.08–0.16). The results of this study provide unprecedented resolution of the systematics and global biogeography of this group and contribute valuable information to our understanding of how theoretical dispersal potential relates to actual population differentiation and diversification among marine organisms. Moreover, these results demonstrate the limitations of single gene analyses and the value of genomic‐level resolution for estimating contemporary population structure in organisms with large, highly connected populations.

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“…All PCR, sequencing, and analytics were carried out at the Laboratories of Analytical Biology at the National Museum of Natural History, Smithsonian Institution. Mitochondrial COI barcode region and partial sequences of 12S and 16S rRNA were obtained by standard protocols (see Evans and Paulay 2012). Unaligned sequences for at least one type specimen of each new species were accessioned to GenBank along with archival data for the respective voucher specimens listed in Table 1.…”

Section: Methodsmentioning

confidence: 99%

A revision of “blanket-hermit crabs” of the genus Paguropsis Henderson, 1888, with the description of a new genus and five new species (Crustacea, Anomura, Diogenidae)

Lemaitre

Rahayu

Komai

2018

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For 130 years the diogenid genus Paguropsis Henderson, 1888 was considered monotypic for an unusual species, P. typica Henderson, 1888, described from the Philippines and seldom reported since. Although scantly studied, this species is known to live in striking symbiosis with a colonial sea anemone that the hermit can stretch back and forth like a blanket over its cephalic shield and part of cephalothoracic appendages, and thus the common name “blanket-crab”. During a study of paguroid collections obtained during recent French-sponsored biodiversity campaigns in the Indo-West Pacific, numerous specimens assignable to Paguropsis were encountered. Analysis and comparison with types and other historical specimens deposited in various museums revealed the existence of five undescribed species. Discovery of these new species, together with the observation of anatomical characters previously undocumented or poorly described, including coloration, required a revision of the genus Paguropsis. The name Chlaenopagurus andersoni Alcock & McArdle, 1901, considered by Alcock (1905) a junior synonym of P. typica, proved to be a valid species and is resurrected as P. andersoni (Alcock, 1899). In two of the new species, the shape of the gills, length/width of exopod of maxilliped 3, width and shape of sternite XI (of pereopods 3), and armature of the dactyls and fixed fingers of the chelate pereopods 4, were found to be characters so markedly different from P. typica and other species discovered that a new genus for them, Paguropsina gen. n., is justified. As result, the genus Paguropsis is found to contain five species: P. typica, P. andersoni, P. confusa sp. n., P. gigas sp. n., and P. lacinia sp. n. Herein, Paguropsina gen. n., is proposed and diagnosed for two new species, P. pistillata gen. et sp. n., and P. inermis gen. et sp. n.; Paguropsis is redefined, P. typica and its previously believed junior synonym, P. andersoni, are redescribed. All species are illustrated, and color photographs provided. Also included are a summary of the biogeography of the two genera and all species; remarks on the significance of the unusual morphology; and remarks on knowledge of the symbiotic anemones used by the species. To complement the morphological descriptions and assist in future population and phylogenetic investigations, molecular data for mitochondrial COI barcode region and partial sequences of 12S and 16S rRNA are reported. A preliminary phylogenetic analysis using molecular data distinctly shows support for the separation of the species into two clades, one with all five species of Paguropsis, and another with the two species Paguropsina gen. n.

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DNA Barcoding Methods for Invertebrates

Cited by 32 publications

References 145 publications

DNA barcodes for ecology, evolution, and conservation

DNA barcodes for ecology, evolution, and conservation

Hitchhiking the high seas: Global genomics of rafting crabs

A revision of “blanket-hermit crabs” of the genus Paguropsis Henderson, 1888, with the description of a new genus and five new species (Crustacea, Anomura, Diogenidae)

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