Utility of arginine kinase for resolution of phylogenetic relationships among brachyuran genera and families

Mahon, Brian C.; Neigel, Joseph E.

doi:10.1016/j.ympev.2008.05.005

Cited by 26 publications

(10 citation statements)

References 37 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Various reasons might explain the discrepancy between the expected power and the observed utility of the genes observed herein, as well as in previous studies (e.g. Mahon & Neigel, 2008;Klopfstein et al, 2010). For instance, PI analysis requires the forcing of a single optimal tree during the analysis, and the tree is assumed to depict the true evolutionary relationship among the species studied (Townsend, 2007).…”

Section: Mtdna Markersmentioning

confidence: 60%

“…Discrepancies between informativeness (as predicted by PI profiles) and the observed performance of genes has been previously noted by other authors that have compared the utility of COI and one nuclear gene (arginine kinase, AK ) in brachyuran crabs (Mahon & Neigel, ), and COI and two different nuclear gene segments (the D2 and D3 regions of 28S ) in parasitoid wasps (Klopfstein et al ., ). Various reasons might explain the discrepancy between the expected power and the observed utility of the genes observed herein, as well as in previous studies (e.g.…”

Section: Discussionmentioning

confidence: 86%

“…The software PhyDesign imple-ments this method and estimates the net PI of one or more markers by measuring the probability that a substitution occurs along an internode, and is not later masked by a subsequent substitution (Townsend, 2007). The method above is considered much more powerful to assess the utility of molecular markers than other methods that measure PI based on pairwise and saturation curves (Grant & Kluge, 2003;Fong & Fujita, 2011; but see Mahon & Neigel, 2008;Klopfstein, Kropf & Quicke, 2010).…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Exploring phylogenetic informativeness and nuclear copies of mitochondrial DNA (numts) in three commonly used mitochondrial genes: mitochondrial phylogeny of peppermint, cleaner, and semi-terrestrial shrimps (Caridea:Lysmata,Exhippolysmata, andMerguia)

Baeza

Fuentes²

2013

Zool J Linn Soc

View full text Add to dashboard Cite

Of paramount importance to studies that profit from molecular trees is the accuracy and robustness of the reconstructed phylogenies. Causes of systematic error that can mislead phylogenetic methods include nuclear copies of mitochondrial DNA (numts) and low phylogenetic informativeness (PI). Herein, numts and PI were explored in three mitochondrial genes commonly used for phylogenetic reconstruction: 16S, 12S, and cytochrome c oxidase I (COI). Shrimps from the genera Lysmata, Exhippolysmata, and Merguia were used as a model system. The existence of: (1) multiple bands on gels of COI and 12S polymerase chain reaction (PCR) products from various species; (2) double peaks, background noise, and ambiguity in sequence chromatograms of COI and 12S PCR products that produced a single clear band in other species; and (3) indels, stop codons, and considerable composition bias in COI‐like cloned sequences of one problematic species (Lysmata seticaudata), was interpreted as evidence of pervasive non‐functional nuclear copies of mitochondrial DNA (numts) of the targeted COI (and probably 12S) mtDNA fragment. The information content of the three mtDNA markers studied was investigated using PI profiling, spectral analysis, and neighbour‐nets. Marker‐specific PI profiles suggested that the COI marker has the highest information content and greatest power for resolving both shallow and deep nodes in trees depicting the phylogenetic relationship among the species studied. Nonetheless, spectral analysis of splits and neighbour‐nets suggested that the 16S and 12S markers were equally or even more powerful than the COI marker for resolving nodes at all phylogenetic levels. Altogether, these analyses suggest that all three mtDNA markers are equally useful for resolving phylogenetic relationships in the shrimps studied, and that PI profiling is not necessarily useful to estimate overall gene utility. A ‘total‐evidence’ phylogenetic analysis that included 34 species and used a concatenated data set of 1403 characters (from reliable 16S, 12S and COI sequences), demonstrated that the genus Lysmata is paraphyletic, and that the monophyletic clade comprising species of Lysmata and Exhippolysmata can be divided into four well‐supported subclades (Neotropical, Cleaner, Cosmopolitan, and Morphovariable). © 2013 The Linnean Society of London

show abstract

Section: Mtdna Markersmentioning

confidence: 60%

Section: Discussionmentioning

confidence: 86%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Exploring phylogenetic informativeness and nuclear copies of mitochondrial DNA (numts) in three commonly used mitochondrial genes: mitochondrial phylogeny of peppermint, cleaner, and semi-terrestrial shrimps (Caridea:Lysmata,Exhippolysmata, andMerguia)

Baeza

Fuentes²

2013

Zool J Linn Soc

View full text Add to dashboard Cite

show abstract

“…( M. ) longisignalis and U. ( M. ) minax (Mahon & Neigel, 2008), implying a close relationship between U. ( M. ) longisignalis , U.…”

Section: Discussionmentioning

confidence: 94%

The geographic structure of morphological variation in eight species of fiddler crabs (Ocypodidae: genus Uca) from the eastern United States and Mexico

Hopkins

Thurman

2010

Biological Journal of the Linnean Society

View full text Add to dashboard Cite

Species with larger geographic distributions are more likely to encounter a greater variety of environmental conditions and barriers to gene flow than geographically-restricted species. Thus, even closely-related species with similar life-history strategies might vary in degree and geographic structure of variation if they differ in geographic range size. In the present study, we investigated this using samples collected across the geographic ranges of eight species of fiddler crabs (Crustacea: Uca) from the Atlantic and Gulf coasts of North America. Morphological variation in the carapace was assessed using geometric morphometric analysis of 945 specimens. Although the eight Uca species exhibit different degrees of intraspecific variation, widespread species do not necessarily exhibit more intraspecific or geographic variation in carapace morphology. Instead, species with more intraspecific variation show stronger morphological divergence among populations. This morphological divergence is partly a result of allometric growth coupled with differences in maximum body size among populations. On average, 10% of total within-species variation is attributable to allometry. Possible drivers of the remaining morphological differences among populations include gene flow mediated by ocean currents and plastic responses to various environmental stimuli, with isolation-by-distance playing a less important role. The results obtained indicate that morphological divergence among populations can occur over shorter distances than expected based on dispersal potential.

show abstract

“…The recent work of Ng et al (2008) on the extant brachyurans was a step forward in the reorganization of the Majoidea, not only because it contributed to settling many pending taxonomic or nomenclatural issues, but also because it clearly pinpointed those in need of further revision. Although the monophyly of the Majoidea is consensual (Hultgren & Stachowicz 2008), the incorporation of molecular and larval morphology data into phylogenetic reconstructions showed that the internal placement of some families and genera is still far from being resolved (Marques & Pohle 2003;Hultgren & Stachowicz 2008;Mahon & Neigel 2008;Hultgren et al 2009).…”

Section: Introductionmentioning

confidence: 99%

Phylogeography and phylogeny of the genus Acanthonyx (Decapoda, Epialtidae) in the north‐east Atlantic and Mediterranean

et al. 2017

View full text Add to dashboard Cite

The genus Acanthonyx Latreille, 1828 (Majoidea, Epialtidae) contains 17 or 18 known species, depending on competing taxonomic views, that are widely distributed across the world. Morphologically, most species look superficially alike, and therefore, similar taxonomic concepts have been described under different names. Consequently, there is today a considerable list of synonyms, which further complicates the taxonomy of the genus Acanthonyx. In this study, we conducted a phylogeographical and phylogenetic analysis of populations of the genus Acanthonyx in the NE Atlantic, Mediterranean and Macaronesia using the mitochondrial cytochrome oxidase subunit I (COI) and the nuclear 28S rRNA loci. Our phylogenetic and phylogeographical results revealed that Acanthonyx lunulatus sensu lato is a complex of three distinct lineages: one corresponding to the previously described Acanthonyx brevifrons, another to A. lunulatus sensu stricto and a third to a yet undescribed group. Whereas our results confirms that A. brevifrons deserves the status of a species, as it can be easily distinguishable from A. lunulatus by a few morphological traits, we could not find any such traits suitable for the discrimination between A. lunulatus sensu stricto and the third lineage. Furthermore, the degree of COI divergence between this lineage and A. lunulatus is below average levels for Decapoda species. Yet, no shared haplotypes have been detected between them. The differences found in the nuclear gene (indels), together with the sympatric occurrence of the two forms, prompt for a more detailed analysis of this group. Overall, the results show that significant genetic differentiation between specimens with similar morphology occurs in the Epialtidae, thus reinforcing the importance of combining morphological and genetic tools to fully resolve the taxonomy of these decapods.

show abstract

Utility of arginine kinase for resolution of phylogenetic relationships among brachyuran genera and families

Cited by 26 publications

References 37 publications

Exploring phylogenetic informativeness and nuclear copies of mitochondrial DNA (numts) in three commonly used mitochondrial genes: mitochondrial phylogeny of peppermint, cleaner, and semi-terrestrial shrimps (Caridea:Lysmata,Exhippolysmata, andMerguia)

Exploring phylogenetic informativeness and nuclear copies of mitochondrial DNA (numts) in three commonly used mitochondrial genes: mitochondrial phylogeny of peppermint, cleaner, and semi-terrestrial shrimps (Caridea:Lysmata,Exhippolysmata, andMerguia)

The geographic structure of morphological variation in eight species of fiddler crabs (Ocypodidae: genus Uca) from the eastern United States and Mexico

Phylogeography and phylogeny of the genus Acanthonyx (Decapoda, Epialtidae) in the north‐east Atlantic and Mediterranean

Contact Info

Product

Resources

About