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

Invertebrate Systematics 01/2002; 16(6):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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Available from: Christopher Tudge, Sep 27, 2015
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    • "One mitochondrial (16S) and three nuclear genes (18S, 28S, H3) were selected due to their range of phylogenetic utility (Toon et al. 2009). The nuclear ribosomal genes 18S and 28S resolve deeper-level relationships while the nuclear protein-coding gene, H3, and mitochondrial ribosomal gene fragment, 16S, show informative resolution in family, genus, and species-level studies (Spears et al. 1992, 1994; Giribet et al. 1996; Schubart et al. 2000; Stillman & Reeb 2001; Tudge & Cunningham 2002; Porter et al. 2005; Mantelatto et al. 2006, 2007; Robles et al. 2007, 2009; Bracken et al. 2009a,b; Felder & Robles 2009). Since we are exploring relationships over a broad range of taxonomic levels (infraorder to species), the genes were concatenated and partitioned in the final analyses. "
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    ABSTRACT: Ever since discovery of the anchialine shrimp, Procaris ascensionis Chace & Manning 1972, there has been debate as to its systematic position in relationship to other shrimp-like decapods. Several morphological characters have suggested a close affinity among Procarididae, Dendrobranchiata and Stenopodidea, whereas other physical features unite Procarididae with Caridea. Few molecular studies have examined the phylogenetic position of procaridid shrimp due to limited available material for genetic analyses. Those studies show procaridids as sister to carideans but lack sufficient taxon and locus sampling to validate the relationship. Here, we present a molecular phylogeny of selected individuals across decapod infraorders and superfamilies to clarify the phylogenetic position of procaridid shrimp. One mitochondrial (16S) and three nuclear genes (18S, 28S, H3) have been chosen to elucidate relationships. We used Bayesian molecular dating methods implemented in multidivtime to estimate and compare the divergence times among procaridids and other lineages. Findings secure the placement of the procaridids as a sister clade to carideans. Results provide evidence for the recognition of procaridids as a separate infraorder (Procarididea Felgenhauer & Abele 1983) within the Decapoda on the basis of molecular and morphological data. Yes Yes
    Zoologica Scripta 03/2010; 39(2). DOI:10.1111/j.1463-6409.2009.00410.x · 3.22 Impact Factor
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    • "Their single thalassinid and single upogebiid did not group together as representatives of Gebiidea, but poor internodal support makes their positioning questionable. Our molecular analysis argues against monophyly of the infraorder Thalassinidea, thus supporting conclusions of de Saint Laurent (1979a, b), Tudge et al. (2002), and Sakai & Sawada (2006), though not for the same reasons. Rooted to the Caridea, we find that the thalassinideans are distributed among two clades for which the rank of infraorder is more appropriate than superfamily, as the latter could imply membership in the same infraorder. "
    Decapod Crustacean Phylogenetics .(Crustacean Issues, 18)., Edited by Martin, J.W., Crandall, K.A., Felder, D.L., 06/2009: chapter Molecular phylogeny of the Thalassinidea based on nuclear and mitochondrial genes: pages 309-326; Taylor & Francis/CRC., ISBN: 978-1-4200-9258-5
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    • "Only in Crandall et al. (1995) and Crandall & Fitzpatrick (1996), and in subsequent papers on crayfish Systematics and phylogeny (Ponniah & Hughes 1998; Lawler & Crandall 1998), was there an explicit goal to establish molecular Systematics, which only Spears et al. (1992) had undertaken previously for decapods, by proposing phylogenetic relationships among brachyuran crabs using nuclear 18S. This slowly changed as species descriptions became based on, or were accompanied by, mitochondrial DNA data (Daniels et al. 1998; Schubart et al. 1998b, 1999; Gusmao et al. 2000; Macpherson & Machordom 2001, Daniels et al. 2001; Guinot et al. 2002; Guinot & Hurtado 2003; Gillikin & Schubart 2004; Lin et al. 2004, and later papers), when species were synonymized based on mtDNA in the absence of morphological characters (Shih et al. 2004; Robles et al. 2007; Mantelatto et al. 2007), and especially when phylogenetic relationships within genera and families were reconstructed with mtDNA in order to establish new taxonomic classifications (Schubart et al. 2000a, 2002; Kitaura et al. 2002; Tudge & Cunningham 2002; Chu et al. 2003; Lavery et al. 2004; Klaus et al. 2006; Schubart et al. 2006). Only recently, mtDNA has been used as part of multi-locus studies to reconstruct phylogenies at higher levels within decapod Crustacea (Ahyong & O'Meally 2004; Porter et al. 2005; Daniels et al. 2006). "
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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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