Development of a multilocus-based approach for sponge (phylum Porifera) identification: refinement and limitations

Yang, Qi; Franco, Christopher M. M.; Sorokin, Shirley J.; Zhang, Wei

doi:10.1038/srep41422

Cited by 25 publications

(29 citation statements)

References 61 publications

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“…Despite highlighting the polyphyletic nature of Haplosclerida, applying a multilocus based approach using ribosomal and mitochondrial markers continues to prove as a useful tool in resolving the taxonomy between congeneric species. Recently this approach has been used across a wide taxonomic range of sponges (Erpenbeck et al, 2016; Yang et al, 2017). These methods are useful as a first pass assessment of classification for a wide range diversity of sponges, to be subsequently integrated with morphological systematics.…”

Section: Discussionmentioning

confidence: 99%

Molecular and morphological congruence of three new crypticNeopetrosiaspp. in the Caribbean

Vicente

Ríos

Zea

et al. 2019

PeerJ

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Neopetrosia proxima (Porifera: Demospongiae: Haplosclerida) is described as a morphologically variable sponge common on shallow reefs of the Caribbean. However, the range of morphological and reproductive variation within putative N. proxima led us to hypothesize that such variability may be indicative of cryptic species rather than plasticity. Using DNA sequences and morphological characters we confirmed the presence of three previously undescribed species of Neopetrosia. Morphological differences of each new congener were best resolved by partial gene sequences of the mitochondrial cytochrome oxidase subunit 1 over nuclear ones (18S rRNA and 28S rRNA). Several new characters for Neopetrosia were revealed by each new species. For example, N. dendrocrevacea sp. nov. and N. cristata sp. nov. showed the presence of grooves on the surface of the sponge body that converge at the oscula, and a more disorganized skeleton than previously defined for the genus. N. sigmafera sp. nov. adds the (1) presence of sigma microscleres, (2) significantly wider/longer oxeas (>200 μm), and (3) the presence of parenchymella larvae. Sampling of conspecifics throughout several locations in the Caribbean revealed larger spicules in habitats closer to the continental shelf than those in remote island locations. Our study highlights the importance of integrating molecular and morphological systematics for the discrimination of new Neopetrosia spp. despite belonging to one of several polyphyletic groups (families, genera) within the current definition of the order Haplosclerida.

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Section: Discussionmentioning

confidence: 99%

Molecular and morphological congruence of three new crypticNeopetrosiaspp. in the Caribbean

Vicente

Ríos

Zea

et al. 2019

PeerJ

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“…The specimens were identified according to their molecular classification in conjunction with the morphological characterization following our previously developed protocol 30 . They are Aplysina archeri with accession number KJ620395 38 , Halichondria okadai - KJ801656 38 , Igernella notabilis – KJ620376 38 , and Tedania tubulifera - KJ620377 38 , which belong to four different orders Verongida, Suberitida, Poecilosclerida, and Dendroceratida, respectively.…”

Section: Methodsmentioning

confidence: 99%

Uncovering the hidden marine sponge microbiome by applying a multi-primer approach

Yang

Franco

Zhang

2019

Sci Rep

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Marine sponges (phylum Porifera) are hosts to microorganisms that make up to 40–60% of the mesohyl volume. The challenge is to characterise this microbial diversity more comprehensively. To accomplish this, a new method was for the first time proposed to obtain sequence coverage of all the variable regions of the 16S rRNA gene to analyze the amplicon-based microbiomes of four representative sponge species belonging to different orders. The five primer sets targeting nine variable regions of the 16S rRNA gene revealed a significant increase in microbiome coverage of 29.5% of phylum level OTUs and 35.5% class level OTUs compared to the community revealed by the commonly used V4 region-specific primer set alone. Among the resulting OTUs, 52.6% and 61.3% were unaffiliated, including candidate OTUs, at the phylum and class levels, respectively, which demonstrated a substantially superior performance in uncovering taxonomic ‘blind spots’. Overall, a more complete sponge microbiome profile was achieved by this multi-primer approach, given the significant improvement of microbial taxonomic coverage and the enhanced capacity to uncover novel microbial taxa. This multi-primer approach represents a fundamental and practical change from the conventional single primer set amplicon-based microbiome approach, and can be broadly applicable to other microbiome studies.

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“…Despite highlighting the polyphyletic nature of Haplosclerida, applying a multi-locus based approach using ribosomal and mitochondrial markers continues to prove as a useful tool in resolving the taxonomy between congeneric species. Recently this approach has been used across a wide taxonomic range of sponges (Erpenbeck et al 2016;Yang et al 2017). These methods are useful as a first pass assessment of classification for a wide range diversity of sponges, to be subsequently integrated with morphological systematics.…”

Section: Discussionmentioning

confidence: 99%

Peer Review #1 of "Molecular and morphological congruence of three new cryptic Neopetrosia spp. in the Caribbean (v0.1)"

2019

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Neopetrosia proxima (Porifera: Demospongiae: Haplosclerida) is described as a morphologically variable sponge common on shallow reefs of the Caribbean. However, the range of morphological and reproductive variation within putative N. proxima led us to hypothesize that such variability may be indicative of cryptic species rather than plasticity. Using DNA sequences and morphological characters we confirmed the presence of three previously undescribed species of Neopetrosia. Morphological differences of each new congener were best resolved by partial gene sequences of the mitochondrial cytochrome oxidase subunit 1 (COI) over nuclear ones (18S rRNA and 28S rRNA). Several new characters for Neopetrosia were revealed by each new species. For example, Neopetrosia dendrocrevacea sp. nov. and Neopetrosia cristata sp. nov. showed the presence of grooves on the surface of the sponge body that converge at the oscula, and a more disorganized skeleton than previously defined for the genus. Neopetrosia sigmafera sp. nov. adds the 1) presence of sigma microscleres, 2) significantly wider/longer oxeas (>200 µm), and 3) the presence of parenchymella larvae. Sampling of conspecifics throughout several locations in the Caribbean revealed larger spicules in habitats closer to the continental shelf than those in remote island locations. Our study highlights the importance of integrating molecular and morphological systematics for the discrimination of new Neopetrosia spp. despite belonging to one of several polyphyletic groups (families, genera) within the current definition of the order Haplosclerida.

show abstract

Development of a multilocus-based approach for sponge (phylum Porifera) identification: refinement and limitations

Cited by 25 publications

References 61 publications

Molecular and morphological congruence of three new crypticNeopetrosiaspp. in the Caribbean

Molecular and morphological congruence of three new crypticNeopetrosiaspp. in the Caribbean

Uncovering the hidden marine sponge microbiome by applying a multi-primer approach

Peer Review #1 of "Molecular and morphological congruence of three new cryptic Neopetrosia spp. in the Caribbean (v0.1)"

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