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. 2022 Apr 18:10:e13285.
doi: 10.7717/peerj.13285. eCollection 2022.

How many single-copy orthologous genes from whole genomes reveal deep gastropod relationships?

Zeyuan Chen  1   2 , Michael Schrödl  1   2   3
Affiliations

How many single-copy orthologous genes from whole genomes reveal deep gastropod relationships?

Zeyuan Chen et al. PeerJ. .

Abstract

The Gastropoda contains 80% of existing mollusks and is the most diverse animal class second only to the Insecta. However, the deep phylogeny of gastropods has been controversial for a long time. Especially the position of Patellogastropoda is a major uncertainty. Morphology and some mitochondria studies concluded that Patellogastropoda is likely to be sister to all other gastropods (Orthogastropoda hypothesis), while transcriptomic and other mitogenomic studies indicated that Patellogastropoda and Vetigastropoda are sister taxa (Psilogastropoda). With the release of high-quality genomes, orthologous genes can be better identified and serve as powerful candidates for phylogenetic analysis. The question is, given the current limitations on the taxon sampling side, how many markers are needed to provide robust results. Here, we identified single-copy orthologous genes (SOGs) from 14 gastropods species with whole genomes available which cover five main gastropod subclasses. We generated different datasets from 395 to 1610 SOGs by allowing species missing in different levels. We constructed gene trees of each SOG, and inferred species trees from different collections of gene trees. We found as the number of SOGs increased, the inferred topology changed from Patellogastropoda being sister to all other gastropods to Patellogastropoda being sister to Vetigastropoda + Neomphalina (Psilogastropoda s.l.), with considerable support. Our study thus rejects the Orthogastropoda concept showing that the selection of the representative species and use of sufficient informative sites greatly influence the analysis of deep gastropod phylogeny.

Keywords: Conflicting topologies; Gene tree; Mollusca; Orthogastropoda; Patellogastropoda; Phylogeny; Whole genomes.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Figure 1
Figure 1. The four data sets used to infer gastropod relationships.
The first data set includes single-copy orthologous genes (SOGs) identified in all 16 species per SOG and results in 395 SOGs. 933, 1,331, 1,610 SOGs were identified while allowed 1–3 species missing per SOG respectively. The blue line represents SOGs identified by each species, and the black vertical line represents the missing of that gene in the corresponding species. The dots below represent the number of SOGs occupied by corresponding species under different degrees of species missing.
Figure 2
Figure 2. The gastropod relationships constructed with different data sets and the corresponding posterior probabilities of different topology.
H: Heterobranchia, C: Caenogastropoda, V: Vetigastropoda, N: Neomphalina, P: Patellogastropoda, B: Bivalve.
Figure 3
Figure 3. Gastropod phylogeny inferred from 847 single-copy orthologous genes (SOGs) identified from 15 species except C. consors.
Bootstrap support percentages are indicated for each internal branch. Branch length is marked with blue numbers.
See this image and copyright information in PMC

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