Mitochondrial genome and polymorphic microsatellite markers from the abyssal sponge Plenaster craigi Lim & Wiklund, 2017: tools for understanding the impact of deep-sea mining

A new genus and species of abyssal sponge commonly encrusting polymetallic nodules in the Clarion-Clipperton Zone, East Pacific Ocean

(2017) Swee-Cheng Lim et al.   SYSTEMATICS AND BIODIVERSITY

Population structure and connectivity in the Mediterranean sponge Ircinia fasciculata are affected by mass mortalities and hybridization

(2016) A Riesgo et al.   HEREDITY

Isolation and Characterization of Microsatellite DNA Markers in the Deep-Sea AmphipodParalicella tenuipesby Illumina MiSeq Sequencing

(2016) Heather Ritchie et al.   JOURNAL OF HEREDITY

A primer for use of genetic tools in selecting and testing the suitability of set-aside sites protected from deep-sea seafloor massive sulfide mining activities

(2016) Rachel E. Boschen et al.   OCEAN & COASTAL MANAGEMENT

The complete mitochondrial genome of sponge Tethya sp. (Demospongiae, Tethyida, Tethyidae)

(2016) Yuan Zhang et al.   Mitochondrial DNA Part B-Resources

Threatened by mining, polymetallic nodules are required to preserve abyssal epifauna

(2016) Ann Vanreusel et al.   Scientific Reports

Mitochondrial group I and group II introns in the sponge orders Agelasida and Axinellida

(2015) Dorothée Huchon et al.   BMC EVOLUTIONARY BIOLOGY

Proposal for a revised classification of the Demospongiae (Porifera)

(2015) Christine Morrow et al.   Frontiers in Zoology

Appearance matters: sedimentation effects on different sponge morphologies

(2015) M. Carmen Pineda et al.   JOURNAL OF THE MARINE BIOLOGICAL ASSOCIATION OF THE UNITED KINGDOM

Sediment impacts on marine sponges

(2015) James J. Bell et al.   MARINE POLLUTION BULLETIN

Deceptive Desmas: Molecular Phylogenetics Suggests a New Classification and Uncovers Convergent Evolution of Lithistid Demosponges

(2015) Astrid Schuster et al.   PLoS One

Genetic structure and diversity of the endangered bath spongeSpongia lamella

(2014) Rocío Pérez-Portela et al.   AQUATIC CONSERVATION-MARINE AND FRESHWATER ECOSYSTEMS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

A Mitochondrial Intron in a Verongid Sponge

(2014) Dirk Erpenbeck et al.   JOURNAL OF MOLECULAR EVOLUTION

OrganellarGenomeDRAW—a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets

(2013) Marc Lohse et al.   NUCLEIC ACIDS RESEARCH

From principles to practice: a spatial approach to systematic conservation planning in the deep sea

(2013) L. M. Wedding et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

Small inverted repeats drive mitochondrial genome evolution in Lake Baikal sponges

(2012) Dennis V. Lavrov et al.   GENE

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

Primer3—new capabilities and interfaces

(2012) Andreas Untergasser et al.   NUCLEIC ACIDS RESEARCH

Panmixia in a Fragmented and Unstable Environment: The Hydrothermal Shrimp Rimicaris exoculata Disperses Extensively along the Mid-Atlantic Ridge

(2012) Sara Teixeira et al.   PLoS One

ProtTest 3: fast selection of best-fit models of protein evolution

(2011) Diego Darriba et al.   BIOINFORMATICS

The spatial scale of genetic subdivision in populations of Ifremeria nautilei, a hydrothermal-vent gastropod from the southwest Pacific

(2011) Andrew D Thaler et al.   BMC EVOLUTIONARY BIOLOGY

Deep-sea nematode assemblage has not recovered 26 years after experimental mining of polymetallic nodules (Clarion-Clipperton Fracture Zone, Tropical Eastern Pacific)

(2011) Dmitry M. Miljutin et al.   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS

Genetic diversity of the imperilled bath sponge Spongia officinalis Linnaeus, 1759 across the Mediterranean Sea: patterns of population differentiation and implications for taxonomy and conservation

(2011) T. DAILIANIS et al.   MOLECULAR ECOLOGY

Congruence between nuclear and mitochondrial genes in Demospongiae: A new hypothesis for relationships within the G4 clade (Porifera: Demospongiae)

(2011) C.C. Morrow et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows

(2010) LAURENT EXCOFFIER et al.   Molecular Ecology Resources

FASconCAT: Convenient handling of data matrices

(2010) Patrick Kück et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

(2009) Nicolas Lartillot et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

The complete mitochondrial genome of the demosponge Negombata magnifica (Poecilosclerida)

(2008) Frida Belinky et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Reconstructing ordinal relationships in the Demospongiae using mitochondrial genomic data

(2008) Dennis V. Lavrov et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Seventeen New Complete mtDNA Sequences Reveal Extensive Mitochondrial Genome Evolution within the Demospongiae

(2008) Xiujuan Wang et al.   PLoS One

A Rapid Bootstrap Algorithm for the RAxML Web Servers

(2008) Alexandros Stamatakis et al.   SYSTEMATIC BIOLOGY