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Journal ArticleDOI

Mitochondrial DNA sequences reveal extensive cryptic diversity within a western American springsnail.

TLDR
The finding that P. micrococcus contains multiple, genetically distinct and geographically restricted lineages suggests that diversification within this highly speciose aquatic genus has been structured in large part by the operation of terrestrial barriers to gene flow.
Abstract
We analysed cytochrome c oxidase subunit I and NADH dehydrogenase subunit I sequence variation among 29 populations of a widely ranging southwestern springsnail (Pyrgulopsis micrococcus) and 18 regional congeners. Cladistic analyses of these sequences depict P. micrococcus as a polyphyletic composite of five well-supported clades. Sequence divergences among these clades and subclades imply the possible occurrence of as many as seven or eight cryptic species in addition to P. micrococcus. Our finding that P. micrococcus contains multiple, genetically distinct and geographically restricted lineages suggests that diversification within this highly speciose aquatic genus has been structured in large part by the operation of terrestrial barriers to gene flow. However, these sequence data also indicate that recent dispersal among hydrographically separated areas has occurred within one of these lineages, which we attribute to passive transport on migratory waterbirds.

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

TL;DR: This study 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, and revealed extraordinary levels of cryptic diversity and endemism.
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Multiple-stressor effects on stream invertebrates: DNA barcoding reveals contrasting responses of cryptic mayfly species

TL;DR: In this paper, the authors used DNA barcoding of the mitochondrial cytochrome c oxidase subunit I gene (COI) to investigate species-specific responses to environmental stressors.
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Habitat type predicts genetic population differentiation in freshwater invertebrates

TL;DR: It is found that lentic invertebrates exhibit, on average, lower genetic population differentiation than lotic species, and proposes that such differences should occur in a number of other habitat types that differ in spatio‐temporal stability.
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Independent colonization and extensive cryptic speciation of freshwater amphipods in the isolated groundwater springs of Australia's Great Artesian Basin

TL;DR: The authors used mitochondrial DNA and allozyme data to unravel a complicated history of isolation, extinction and dispersal among spring amphipod populations across the Great Artesian Basin (GAB) in arid inland Australia.
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A gleam in the dark: Phylogenetic species delimitation in the confusing spring-snail genus Bythinella Moquin-Tandon, 1856 (Gastropoda: Rissooidea: Amnicolidae)

TL;DR: The results strongly suggest that classical morphological descriptors may not constitute valid specific criteria within Bythinella, and support a complex scenario of invasions of subterranean habitats, as illustrated by the syntopy of several mitochondrial lineages or the conflicting evolutionary histories between COI and ITS1 in caves.
References
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Journal ArticleDOI

Clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

TL;DR: The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved and modifications are incorporated into a new program, CLUSTAL W, which is freely available.
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The neighbor-joining method: a new method for reconstructing phylogenetic trees.

TL;DR: The neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods for reconstructing phylogenetic trees from evolutionary distance data.
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Confidence limits on phylogenies: an approach using the bootstrap.

TL;DR: The recently‐developed statistical method known as the “bootstrap” can be used to place confidence intervals on phylogenies and shows significant evidence for a group if it is defined by three or more characters.
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MRBAYES: Bayesian inference of phylogenetic trees

TL;DR: The program MRBAYES performs Bayesian inference of phylogeny using a variant of Markov chain Monte Carlo, and an executable is available at http://brahms.rochester.edu/software.html.
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MODELTEST: testing the model of DNA substitution.

TL;DR: The program MODELTEST uses log likelihood scores to establish the model of DNA evolution that best fits the data.
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