Molecular phylogeny of the mud lobsters and mud shrimps (Crustacea: Decapoda: Thalassinidea) using nuclear 18S rDNA and mitochondrial 16S rDNA

Invertebrate Systematics 01/2002; 16:839-847. DOI: 10.1071/IS02012

ABSTRACT Partial sequences ,of the ,18S nuclear and 16S mitochondrial ,ribosomal ,genes were obtained for 14 species of thalassinidean shrimp (families Callianassidae, Laomediidae, Strahlaxiidae, Thalassinidae and Upogebiidae) and a further six species in related decapod infraorders (families Aeglidae, Astacidae, Lithodidae, Palinuridae, Raninidae and Scyllaridae). Maximum-likelihood and Bayesian analyses show equivocal support for the monophyly of the Thalassinidea, but show strong support for division of the infraorder into two major clades. This dichotomy separates representatives in the Upogebiidae, Laomediidae and Thalassinidae from those in the Strahlaxiidae and Callianassidae. The Laomediidae is shown to be paraphyletic, with the thalassinid species, Thalassina squamifera, being placed on a branch between Axianassa and a clade comprising Jaxea and Laomedia,

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    ABSTRACT: The names Gebiidea and Axiidea, erected by de Saint Laurent (1979), have priority over others for the two infraorders of shrimps previously included in Thalassinidea. Importantly, Thalassinidea are not monophyletic and the name should be replaced. Gebiidea and Axiidea, besides having priority and describing two monophyletic taxa, are now in common use (130 citations) and are more stable than alternative schemes proposed by Sakai (2005 and later). The history of the names of higher taxa applied to these groups is reviewed, and all family-group taxa listed.
    Crustaceana 09/2014; 87(10-10):1258-1272. DOI:10.1163/15685403-00003354 · 0.47 Impact Factor
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    ABSTRACT: A total of 75 specimens belonging to four species of thalassinoids were collected in the intertidal and estuarine zones of two localities along the Pacific coast of Mexico. Callianassa tabogensis is recorded for the first time in Mexico, and is transferred to the genus Neotrypaea. Material of Callichirus is assigned to Callichirus seilacheri with some doubts due to taxonomic problems related to this genus in the eastern Pacific. Neocallichirus cf. grandimana, an amphi-American species described for the western Atlantic and previously reported in Ecuador and along the Pacific coast of Panama and Colombia, is reported for the first time in Mexico. Upogebia dawsoni is recorded for the second time from the coast of Jalisco. An updated list of Axiidea and Gebiidea known from the Mexican Pacific is provided, including 35 species.
    Journal of the Marine Biological Association of the UK 03/2013; 94(02):369-388. DOI:10.1017/S0025315413001495 · 1.13 Impact Factor
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    ABSTRACT: Not much more than fifteen years ago, the first decapod phylogenies based on mitochondrial DNA (mtDNA) sequences revolutionized decapod phylogenetics. Initially, this method was accepted only reluctantly. However, a wider understanding of the methods, and the realization that credibility of specific branching patterns can be measured by statistic confidence values, allowed the recognition of molecular Systematics as just another phylogenetic approach, in which homologous characters are compared and interpreted in terms of apomorphic or plesiomorphic status, and best possible trees are calculated based on distances, parsimony, or likelihoods. Similar to morphological characters, some of the shared molecular characters can result from convergence, but the large quantity of potential characters to be compared (15,000-17,000 in mtDNA) promises to reveal phylogenetic signal. For many years, preference was given to mitochondrial genes among the molecular markers, because of the relative ease with which they can be amplified (stable and numerous copies per cell) and interpreted (because they are only maternally inherited and lack introns and recombination), and because of higher mutation rates and thus greater variability than nuclear DNA. More recently, some of these apparent advantages were interpreted as shortcomings of mtDNA, and the discovery of selective sweeps, mitochondrial introgressions, and nuclear copies of mtDNA (numts) have questioned the credibility of phylogenies based exclusively on mtDNA. Here, I revisit the history and importance of mtDNA-based phylogenies of decapods, present two examples of how numts can produce erroneous phylogenies, and emphasize the need for primer optimization for better PCR results and avoidance of numts. Mitochondrial DNA has distinct advantages and disadvantages and, if used in combination with other phylogenetic markers, is still a very effective tool for phylogenetic inference. In most cases, and when used with the necessary care, phylogenies and phylogeographies based on mtDNA will render absolutely reliable results that can be tested and confirmed with other molecular and non-molecular approaches.

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