Improved phylogenomic sampling of free-living nematodes enhances resolution of higher-level nematode phylogeny

Smythe, Ashleigh B.; Holovachov, Oleksandr; Kocot, Kevin M.

doi:10.1186/s12862-019-1444-x

Cited by 94 publications

(152 citation statements)

References 95 publications

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“…Secondly, mitochondrial 12S rRNA showed that there was a close relationship between clades IV and V, which has also been found in studies using the 18S rRNA gene and the transcriptome [7,11,12,31]. However, compared to phylogenetic studies using whole mitochondrial genomes, clade V was more closely related to Ascaridida, whereas clade IV was a sister clade to the clade consisting of clade V and Ascaridida [8][9][10].…”

Section: Potential Utility Of Mitochondrial 12s Rrna Gene In Nematodesupporting

confidence: 61%

Evaluation and utility of mitochondrial ribosomal genes for molecular systematics of parasitic nematodes

Chan

Chaisiri

Morand

et al. 2020

Preprint

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Abstract Background Molecular advances have accelerated our understanding of nematode systematics and taxonomy. However, comparative analyzes between various genetic markers have led to discrepancies in nematode phylogenies. This study aimed to evaluate the suitability of using mitochondrial 12S and 16S ribosomal RNA genes for nematode molecular systematics. Methods To study the suitability of mitochondrial 12S and 16S ribosomal RNA genes as genetic markers for nematode molecular systematics, we compared them with the other commonly used genetic markers, nuclear internal transcribed spacer 1 and 2 regions, nuclear 18S and 28S ribosomal RNA genes, and mitochondrial cytochrome c oxidase subunit 1 gene. After that, phylum-wide primers for mitochondrial 12S and 16S ribosomal RNA genes were designed, and parasitic nematodes of humans and animals from 75 taxa with 21 representative species were inferred through phylogenetic analyzes. Phylogenetic analyzes were carried out using maximum likelihood and Bayesian inference algorithms. Results The phylogenetic relationships of nematodes based on the mitochondrial 12S rRNA gene supported the monophyly of nematodes in clades I, IV, and V, reinforcing the potential of this gene as a genetic marker for nematode systematics. In contrast, the mitochondrial 16S rRNA gene only supported the monophyly of clades I and V, providing evidence that the 12S rRNA gene is more suitable for nematode molecular systematics. In this study, subclades of clade III containing various nematode families were not monophyletic when the 16S or 12S rRNA gene was used as the genetic marker. This is similar to the phylogenetic relationship revealed by previous studies using whole mitochondrial genomes as genetic markers. Conclusions This study supports the use of the 12S rRNA gene as a genetic marker for studying the molecular systematics of nematodes to understand intra-phyla relationships. Phylum-wide primers for nematodes using mitochondrial ribosomal genes were prepared, which may enhance future studies. Furthermore, sufficient genetic variation in the mitochondrial 12S and 16S rRNA genes between species also allowed for accurate taxonomy to species level, revealing the potential of these two genes as genetic markers for DNA barcoding.

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Section: Potential Utility Of Mitochondrial 12s Rrna Gene In Nematodesupporting

confidence: 61%

Evaluation and utility of mitochondrial ribosomal genes for molecular systematics of parasitic nematodes

Chan

Chaisiri

Morand

et al. 2020

Preprint

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“…Publicly available protein sequences from complete genomes and assembled transcriptomes were downloaded when available. Dataset assembly and processing built on our established and routinely used bioinformatic pipeline 30,[64][65][66][67] with a number of modifications to help reduce possible exogenous contamination and low quality data (e.g., incorrectly translated gene predictions from Genescan; see below). Unassembled publicly available transcriptome data were digitally normalized and assembled using Trinity 68 .…”

Section: Molecular Laboratory Work One Specimen Of Laevipilina Antarmentioning

confidence: 99%

New data from Monoplacophora and a carefully-curated dataset resolve molluscan relationships

Kocot

Poustka

Stöger

et al. 2020

Sci Rep

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Relationships among the major lineages of Mollusca have long been debated. Morphological studies have considered the rarely collected Monoplacophora (tryblidia) to have several plesiomorphic molluscan traits. the phylogenetic position of this group is contentious as morphologists have generally placed this clade as the sister taxon of the rest of conchifera whereas earlier molecular studies supported a clade of Monoplacophora + polyplacophora (Serialia) and phylogenomic studies have generally recovered a clade of Monoplacophora + cephalopoda. phylogenomic studies have also strongly supported a clade including Gastropoda, Bivalvia, and Scaphopoda, but relationships among these taxa have been inconsistent. in order to resolve conchiferan relationships and improve understanding of early molluscan evolution, we carefully curated a high-quality data matrix and conducted phylogenomic analyses with broad taxon sampling including newly sequenced genomic data from the monoplacophoran Laevipilina antarctica. Whereas a partitioned maximum likelihood (ML) analysis using site-homogeneous models recovered Monoplacophora sister to cephalopoda with moderate support, both ML and Bayesian inference (Bi) analyses using mixture models recovered Monoplacophora sister to all other conchiferans with strong support. A supertree approach also recovered Monoplacophora as the sister taxon of a clade composed of the rest of conchifera. Gastropoda was recovered as the sister taxon of Scaphopoda in most analyses, which was strongly supported when mixture models were used. A molecular clock based on our Bi topology dates diversification of Mollusca to ~546 MYA (+/− 6 MYA) and Conchifera to ~540 MYA (+/− 9 MYA), generally consistent with previous work employing nuclear housekeeping genes. these results provide important resolution of conchiferan mollusc phylogeny and offer new insights into ancestral character states of major mollusc clades. Mollusca is the second most diverse animal phylum whose members exhibit an incredible array of body shapes and sizes. Many molluscs have important ecological roles in marine, freshwater, and terrestrial environments and others are culturally and/or economically important as a source of food, jewellery, or dye 1. Despite their diversity and importance, understanding of early molluscan evolution remains incomplete and several conflicting phylogenetic hypotheses 1-9 have been proposed regarding relationships among the eight major clades (i.e., classes): Bivalvia (clams, scallops, oysters, etc.), Caudofoveata (Chaetodermomorpha), Cephalopoda (octopuses, squids, and Nautilus), Gastropoda (snails and slugs), Monoplacophora (Tryblidia; deep-sea, limpet-like molluscs), Polyplacophora (chitons), Scaphopoda (tusk shells), and Solenogastres (Neomeniomorpha). Within Conchifera (Bivalvia, Cephalopoda, Gastropoda, Monoplacophora, and Scaphopoda), the clade of molluscs with uni-or bivalved shells, the deep-sea limpet-like Monoplacophora has long been thought to be important to understanding early molluscan evolution 5,10-...

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“…5 0 and 3 0 sequences terminal to the enzymatic domains were excluded. Under a general timereversible (GTR) model, designating Loa loa as outgroup a priori [38,39], and setting the number of rate categories that maximized the likelihood of the tree a posteriori, we performed 200 independent inferences from each matrix, with node support on the final trees estimated from 1000 bootstrap pseudoreplicates. In a second approach, we performed Bayesian inference from DNA sequences of enzymatic domains, including third codon positions, and specifying a codon model of substitution, as implemented in MRBAYES v. 3.2.6 [40].…”

Section: (B) Reconstruction Of Switch-gene Historiesmentioning

confidence: 99%

Regulators of an ancient polyphenism evolved through episodic protein divergence and parallel gene radiations

Biddle

Ragsdale

2020

Proc. R. Soc. B.

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Polyphenism is a form of developmental plasticity that transduces environmental cues into discontinuous, often disparate phenotypes. In some cases, polyphenism has been attributed to facilitating morphological diversification and even the evolution of novel traits. However, this process is predicated on the origins and evolutionary maintenance of genetic mechanisms that specify alternate developmental networks. When and how regulatory loci arise and change, specifically before and throughout the history of a polyphenism, is little understood. Here, we establish a phylogenetic and comparative molecular context for two dynamically evolving genes, eud-1 and seud-1 , which regulate polyphenism in the nematode Pristionchus pacificus . This species is dimorphic in its adult feeding-structures, allowing individuals to become microbivores or facultative predators depending on the environment. Although polyphenism regulation is increasingly well understood in P. pacificus , the polyphenism is far older than this species and has diversified morphologically to enable an array of ecological functions across polyphenic lineages. To bring this taxonomic diversity into a comparative context, we reconstructed the histories of eud-1 and seud-1 relative to the origin and diversification of polyphenism, finding that homologues of both genes have undergone lineage-specific radiations across polyphenic taxa. Further, we detected signatures of episodic diversifying selection on eud-1 , particularly in early diplogastrid lineages. Lastly, transgenic rescue experiments suggest that the gene's product has functionally diverged from its orthologue's in a non-polyphenic outgroup. In summary, we provide a comparative framework for the molecular components of a plasticity switch, enabling studies of how polyphenism, its regulation, and ultimately its targets evolve.

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Improved phylogenomic sampling of free-living nematodes enhances resolution of higher-level nematode phylogeny

Cited by 94 publications

References 95 publications

Evaluation and utility of mitochondrial ribosomal genes for molecular systematics of parasitic nematodes

Evaluation and utility of mitochondrial ribosomal genes for molecular systematics of parasitic nematodes

New data from Monoplacophora and a carefully-curated dataset resolve molluscan relationships

Regulators of an ancient polyphenism evolved through episodic protein divergence and parallel gene radiations

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