Preliminary phylogenetic analysis of selected subterranean amphipod crustaceans, using small subunit rDNA gene sequences

Könemann, Stefan; Englisch, Ulrike

doi:10.1078/1439-6092-00011

Cited by 47 publications

(19 citation statements)

References 13 publications

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“…First, we sequenced our 16 local species, using 2 individuals of each species for portions of 3 genes: mitochondrial cytochrome c oxidase subunit I (COI) and 16S rRNA, and nuclear 18S rRNA. The 18S gene has been widely used in crustacean phylogenetics generally, and in peracarid [23], isopod [24], and amphipod phylogenetics in particular [25], [26], [27]. This combination of 3 genes has also been used previously in a study of Lake Baikal amphipods [28].…”

Section: Methodsmentioning

confidence: 99%

Phylogeny as a Proxy for Ecology in Seagrass Amphipods: Which Traits Are Most Conserved?

Best

Stachowicz

2013

PLoS ONE

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Increasingly, studies of community assembly and ecosystem function combine trait data and phylogenetic relationships to gain novel insight into the ecological and evolutionary constraints on community dynamics. However, the key to interpreting these two types of information is an understanding of the extent to which traits are phylogenetically conserved. In this study, we develop the necessary framework for community phylogenetics approaches in a system of marine crustacean herbivores that play an important role in the ecosystem functioning of seagrass systems worldwide. For 16 species of amphipods and isopods, we (1) reconstructed phylogenetic relationships using COI, 16S, and 18S sequences and Bayesian analyses, (2) measured traits that are potentially important for assembling species between and within habitats, and (3) compared the degree to which each of these traits are evolutionarily conserved. Despite poor phylogenetic resolution for the order Amphipoda as a whole, we resolved almost all of the topology for the species in our system, and used a sampling of ultrametric trees from the posterior distribution to account for remaining uncertainty in topology and branch lengths. We found that traits varied widely in their degree of phylogenetic signal. Body mass, fecundity, and tube building showed very strong phylogenetic signal, and temperature tolerance and feeding traits showed much less. As such, the degree of signal was not predictable based on whether the trait is related to environmental filtering or to resource partitioning. Further, we found that even with strong phylogenetic signal in body size, (which may have large impacts on ecosystem function), the predictive relationship between phylogenetic diversity and ecosystem function is not straightforward. We show that patterns of phylogenetic diversity in communities of seagrass mesograzers could lead to a variety of interpretations and predictions, and that detailed study of trait similarities and differences will be necessary to interpret these patterns.

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Section: Methodsmentioning

confidence: 99%

Phylogeny as a Proxy for Ecology in Seagrass Amphipods: Which Traits Are Most Conserved?

Best

Stachowicz

2013

PLoS ONE

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“…Meland and Willassen found that despite independent modes of evolution, mitochondrial COI and hypervariable regions V4 and V7 of nuclear 18S share comparable phylogenetic structure in mysids, with 18S sequence divergence averaging 1.31% compared to an average of 33% for COI sequence uncorrected pair-wise distances (2004). Englisch and Koenemann (2001) reported uncorrected 18S pair-wise sequence differences to average 1.3% between different amphipod species in a genus.…”

Section: S Rdna As a Species-level Molecular Marker For Leucothoidaementioning

confidence: 99%

“…Some examples of crustaceans for which molecular phylogenies have been based at least partially on 18S rDNA include brachyuran crabs (Spears et al, 1992;Spears and Abele, 2000), branchiopod crustaceans (Crease and Taylor, 1998), subterranean gammaridean amphipods (Englisch and Koenemann, 2001), onychopod cladocerans (Cristescu and Hebert, 2002), Ostracoda (Yamaguchi and Endo, 2003), and oniscidean isopods (Raupach et al, 2009). …”

Section: S Rdna As a Species-level Molecular Marker For Leucothoidaementioning

confidence: 99%

Nuclear 18S rDNA As A Species-Level Molecular Marker for Leucothoidae (Amphipoda)

White

2011

Journal of Crustacean Biology

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) Rising Star Program, Trans-disciplinary Organization for Subtropical Island Studies (TRO-SIS), University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa, Japan 903-0213 A B S T R A C T Leucothoid amphipods were investigated using nuclear 18S ribosomal DNA sequences. Analysis of sequences from eight species in two genera supported the current morphological species designations and the separation of the family into two clades. Additionally, an anamorph-leucomorph connection has been confirmed with molecular sequence data that demonstrated both morphologies conclusively belonged to the same species, Anamixis vanga Thomas, 1997. Analyses suggest that morphology is reflecting the genetic evolutionary history of the family. Levels of sequence divergence are compared for 18S rDNA and COI mitochondrial DNA in Leucothoidae.

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“…PCR amplifications of partial mitochondrial COI and 16S and nuclear 18S were performed in 10 µl reactions containing 0.25 μL BSA, 0.5 μL dNTP (2.5 mM each), 1 μL 10x NH 4 reaction buffer, 0.3 μL of each primer (10 μM), 0.5 μL MgCl 2 (50 mM), 0.1 μL DNA Polymerase (5 U/μL; Bioline, Taunton, MA, USA), and 2 μL of template DNA. The following primers were used: 18Sfw (Englisch & Koenemann 2001) and 18L (Halanych et al 1995) for amplifying partially sequences of 18SrDNA, LCO1490 and HCO2198 (Folmer et al 1994) for mitochondrial COI, and either 16Ssf and 16Ssr (Tsang et al 2009, Tsang pers. comm.…”

Section: Genetic Analysismentioning

confidence: 99%

Spionidae (Annelida: ‘Polychaeta’: Canalipalpata) from Lizard Island, Great Barrier Reef, Australia: the genera Malacoceros, Scolelepis, Spio, Microspio, and Spiophanes

Meißner

Götting

2015

Zootaxa

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Seven species belonging to the spionid genera Malacoceros, Scolelepis, Spio, Microspio, and Spiophanes were found during the polychaete workshop on Lizard Island in August 2013. One species is new to science and named Scolelepis inversa n. sp., another Scolelepis species is probably also a new species but was represented in our samples by only a single specimen and not formally described. All other species have been reported previously from Australia. Species diagnoses of all species found during the workshop and of Scolelepis balihaiensis Hartmann-Schröder, 1979, Microspio microcera (Dorsey, 1977) and M. minuta (Hartmann-Schröder, 1962) have been critically reviewed and amended based on the study of type material. The potential synonymy of Microspio minuta (Hartmann-Schröder, 1962) and M. microcera (Dorsey, 1977) is discussed. The new combination Spio jirkovi (Sikorski, 1992) proposed by Sikorski (2013) is returned to Malacoceros. We added DNA barcodes for five species collected in the Lizard Island area to public databases which will be useful in future phylogenetic and phylogeographic studies. For Microspio we provide the first sequence data for this genus.

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Preliminary phylogenetic analysis of selected subterranean amphipod crustaceans, using small subunit rDNA gene sequences

Cited by 47 publications

References 13 publications

Phylogeny as a Proxy for Ecology in Seagrass Amphipods: Which Traits Are Most Conserved?

Phylogeny as a Proxy for Ecology in Seagrass Amphipods: Which Traits Are Most Conserved?

Nuclear 18S rDNA As A Species-Level Molecular Marker for Leucothoidae (Amphipoda)

Spionidae (Annelida: ‘Polychaeta’: Canalipalpata) from Lizard Island, Great Barrier Reef, Australia: the genera Malacoceros, Scolelepis, Spio, Microspio, and Spiophanes

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