Biodiversity estimates and ecological interpretations of meiofaunal communities are biased by the taxonomic approach

Accurate assessments of biodiversity are crucial to advising ecosystem-monitoring programs and understanding ecosystem function. Nevertheless, a standard operating procedure to assess biodiversity accurately and consistently has not been established. This is especially true for meiofauna, a diverse community (>20 phyla) of small benthic invertebrates that have fundamental ecological roles. Recent studies show that metabarcoding is a cost-effective and timeeffective method to estimate meiofauna biodiversity, in contrast to morphological-based taxonomy. Here, we compare biodiversity assessments of a diverse meiofaunal community derived by applying multiple taxonomic methods based on comparative morphology, molecular phylogenetic analysis, DNA barcoding of individual specimens, and metabarcoding of environmental DNA. We show that biodiversity estimates are strongly biased across taxonomic methods and phyla. Such biases affect understanding of community structures and ecological interpretations. This study supports the urgency of improving aspects of environmental high-throughput sequencing and the value of taxonomists in correctly understanding biodiversity estimates

Meiofauna as a valuable bioindicator of climate change in the polar regions

Establishing robust estimates of polar marine biodiversity is important for interpreting future changes in the Arctic; however, despite a recent increase in scientific expeditions, this region remains relatively underexplored. Particularly overlooked in biodiversity assessments are small species, such as protists, fungi, and many small invertebrates that are collectively known as meiofauna. These species contribute to the foundation of food webs and are crucial for the survival of larger species that are economically and socially important. The application of high-throughput sequencing methodologies has proven effective for biomonitoring small metazoan species but has sparingly been applied in the Arctic. We used a metabarcoding approach to assess the diversity of sea ice and sediment-associated metazoans from Utqiaġvik (Barrow), Alaska. Sea ice and sediment samples were collected six times over eight months (January through August) encompassing three seasons (winter, spring, and summer) from polar night to ice-out in August. Biodiversity was assessed as both richness and community composition by incorporating incidence data and phylogenetic distance. Environmental conditions associated with ice, sediment, water, and snow were measured and tested for possible correlations with biodiversity estimates. We found a high number of taxa distributed locally, suggesting that metabarcoding can be effectively applied to Arctic biomonitoring programs. In addition, these results show that season and habitat are significant predictors of meiofaunal biodiversity, supporting hypotheses that meiofauna can be used as a valuable indicator of climate change

Comparative mitochondrial genomics in Nematoda reveal astonishing variation in compositional biases and substitution rates indicative of multi-level selection

Abstract Background Nematodes are the most abundant and diverse metazoans on Earth, and are known to significantly affect ecosystem functioning. A better understanding of their biology and ecology, including potential adaptations to diverse habitats and lifestyles, is key to understanding their response to global change scenarios. Mitochondrial genomes offer high species level characterization, low cost of sequencing, and an ease of data handling that can provide insights into nematode evolutionary pressures. Results Generally, nematode mitochondrial genomes exhibited similar structural characteristics (e.g., gene size and GC content), but displayed remarkable variability around these general patterns. Compositional strand biases showed strong codon position specific G skews and relationships with nematode life traits (especially parasitic feeding habits) equal to or greater than with predicted phylogeny. On average, nematode mitochondrial genomes showed low non-synonymous substitution rates, but also high clade specific deviations from these means. Despite the presence of significant mutational saturation, non-synonymous (dN) and synonymous (dS) substitution rates could still be significantly explained by feeding habit and/or habitat. Low ratios of dN:dS rates, particularly associated with the parasitic lifestyles, suggested the presence of strong purifying selection. Conclusions Nematode mitochondrial genomes demonstrated a capacity to accumulate diversity in composition, structure, and content while still maintaining functional genes. Moreover, they demonstrated a capacity for rapid evolutionary change pointing to a potential interaction between multi-level selection pressures and rapid evolution. In conclusion, this study helps establish a background for our understanding of the potential evolutionary pressures shaping nematode mitochondrial genomes, while outlining likely routes of future inquiry

The Mitochondrial Genomes of the Nudibranch Mollusks, Melibe leonina and Tritonia diomedea, and Their Impact on Gastropod Phylogeny.

The phylogenetic relationships among certain groups of gastropods have remained unresolved in recent studies, especially in the diverse subclass Opisthobranchia, where nudibranchs have been poorly represented. Here we present the complete mitochondrial genomes of Melibe leonina and Tritonia diomedea (more recently named T. tetraquetra), two nudibranchs from the unrepresented Cladobranchia group, and report on the resulting phylogenetic analyses. Both genomes coded for the typical thirteen protein-coding genes, twenty-two transfer RNAs, and two ribosomal RNAs seen in other species. The twelve-nucleotide deletion previously reported for the cytochrome oxidase 1 gene in several other Melibe species was further clarified as three separate deletion events. These deletions were not present in any opisthobranchs examined in our study, including the newly sequenced M. leonina or T. diomedea, suggesting that these previously reported deletions may represent more recently divergent taxa. Analysis of the secondary structures for all twenty-two tRNAs of both M. leonina and T. diomedea indicated truncated d arms for the two serine tRNAs, as seen in some other heterobranchs. In addition, the serine 1 tRNA in T. diomedea contained an anticodon not yet reported in any other gastropod. For phylogenetic analysis, we used the thirteen protein-coding genes from the mitochondrial genomes of M. leonina, T. diomedea, and seventy-one other gastropods. Phylogenetic analyses were performed for both the class Gastropoda and the subclass Opisthobranchia. Both Bayesian and maximum likelihood analyses resulted in similar tree topologies. In the Opisthobranchia, the five orders represented in our study were monophyletic (Anaspidea, Cephalaspidea, Notaspidea, Nudibranchia, Sacoglossa). In Gastropoda, two of the three traditional subclasses, Opisthobranchia and Pulmonata, were not monophyletic. In contrast, four of the more recently named gastropod clades (Vetigastropoda, Neritimorpha, Caenogastropoda, and Heterobranchia) were all monophyletic, and thus appear to be better classifications for this diverse group

Bayesian and maximum likelihood consensus tree for gastropod phylogeny.

<p>All deep nodes for Bayesian and maximum likelihood analyses were identical, and are illustrated here as a consensus tree showing the relationship among the major gastropod groups. The more recently distinguished gastropod groups are all monophyletic and are highly supported. Posterior probability and bootstrap values are located at the nodes.</p

Cytochrome oxidase 1 sequence differences in <i>Melibe</i> genus.

<p>Nucleotide (A) and amino acid (B) alignments of a portion of the cytochrome oxidase 1 gene for <i>M</i>. <i>leonina</i> and other members of the <i>Melibe</i> genus indicate that <i>M</i>. <i>leonina</i> lacks the twelve nucleotide deletion present in other species.</p

Bayesian analysis of gastropod phylogeny, based on amino acid alignment of 72 gastropods.

<p>Posterior probability values indicate the confidence of each node. The bivalve, <i>Venustaconcha ellipsiformis</i>, was used an outgroup. The traditional subclasses are highlighted (pulmonates in red, opisthobranchs in green, and prosobranchs in blue). Two of the three traditional subclasses (pulmonates and opisthobranchs) were not monophyletic. In contrast, the four more recently distinguished gastropod groups (Heterobranchia, Caenogastropoda, Vetigastropoda, and Neritimorpha) were all monophyletic.</p

The complete mitochondrial genomes of <i>Melibe leonina</i> (A) and <i>Tritonia diomedea</i> (B).

<p>Both mitochondrial genomes were found to code for the expected 22 transfer RNA, 13 protein-coding genes, and a short and large ribosomal subunit. The 13 protein-coding gene order was found to be identical to all other opisthobranchs.</p

Gastropod mitochondrial genomes used in this study.

<p>(*) indicates a classification that was not supported by this study.</p><p>Gastropod mitochondrial genomes used in this study.</p

Maximum likelihood analysis of gastropod phylogeny, based on amino acid alignment of 72 gastropods.

<p>Bootstrap support values indicate the confidence of each node. The bivalve, <i>Venustaconcha ellipsiformis</i>, was used an outgroup. Colors as in Fig 6. While there are minor differences compared to the Bayesian analysis (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0127519#pone.0127519.g005" target="_blank">Fig 5</a>), the topology of major groups is the same (see consensus in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0127519#pone.0127519.g007" target="_blank">Fig 7</a>).</p