Rates and relations of mitochondrial genome evolution across the Echinoidea, with special focus on the superfamily Odontophora

Abstract

In order to better characterize the placement of genus Tripneustes, as a representative of the Toxopneustidae family within the broader sea urchin mitochondrial (MT) phylogeny, the complete MT genome of Tripneustes gratilla was generated and compared with all published echinoid MT genomes currently available on NCBI GenBank. The MT genome phylogeny supports the existence of the superfamily Odontophora (consisting of the families Strongylocentrotidae, Echinometridae, and Toxopneustidae). A relaxed molecular‐clock time calibration suggests a split between the three key Odontophore MT lineages occurred during the late Eocene/Oligocene. Major global oceanographic changes have been inferred during this time frame, potentially driving species diversification through environmental selection pressures. To test for signatures of selection acting on the mitochondria, the historical rate of gene evolution of individual MT genes was assessed through a branch‐site comparison of nonsynonymous to synonymous substitution ratios (ω). Models of positive selection and neutral evolution, as compared via a likelihood ratio test, show no evidence of strong historical positive selection on mitochondrial genes at the genesis of the Odontophora. However, while pairwise ω comparison revealed signatures of strong negative selection, relatively elevated ω values were observed within the Strongylocentrotus genus.

Characterization of the complete mitochondrial genome of Parabreviscolex niepini Xi et al., 2018 (Cestoda, Caryophyllidea)

“…The null model and alternative model were compared via a likelihood ratio test ( LRT ), and positive selection was confirmed when P<0.05. Comparing MA to MAnull can estimate positive selection, while comparing MA to M1a can identify instances of relaxation of selective constraints as well as positive selection ( Láruson 2017 ). The posterior probabilities value (≥ 95%) of Bayes Empirical Bayes ( BEB ) method was used to identify for positively selected sites (Yang 2005).…”

Trans-Species Polymorphism in Mitochondrial Genome of Camarodont Sea Urchins

“…The topology of the tree is in congruence with the recent most comprehensive morphological and phylogenetic analyses (e.g., [38,39,40,41,42,43,44] and references therein). The ND6 L and S variants (indicated by the corresponding letters, Figure 2, right) are shared among the sea urchins of the order Camarodonta, including mostly the members of the superfamily Odontophora [8,38,43]. Outside Odontophora, the L variant is found in Mespilia globulus (infraorder Temnopleuridea) only (Figure 2).…”

“…It is unlikely that the ND6 length polymorphism can be explained by a sequencing problem associated with sea urchins, because identical results were obtained by different authors investigating different sea urchin species (see Table S1). The pattern can represent an example of trans-species polymorphism (TSP), persisting at least since the time of the Odontophora sea urchin diversification at the Eocene/Oligocene boundary (approximately 34 MYA) [8,38,43]. TSP refers to the occurrence of identical or similar alleles maintained by the balancing selection in related species, except for the instances where similarity arose through convergence or introgression [49,50,51].…”

“…The species represent two major clades ( Strongylocentrotus and Mesocentrotus ) of the strongylocentrotid sea urchins (order Camarodonta, family Strongylocentrotidae) identified by genetic studies [4,5,6]. The estimated time of divergence between the Strongylocentrotus and Mesocentrotus clades is around 8.5–19 million years ago (MYA) [6,7,8]. Interspecies crosses between S. intermedius and M. nudus have been successfully performed in a laboratory [9,10], which is not unusual for sea urchins (review in [11]).…”

Gene expression across tissues, sex, and life stages in the sea urchin Tripneustes gratilla [Toxopneustidae, Odontophora, Camarodonta]

“…As such, T. gratilla is currently the object of a large-scale aquaculture and outplanting effort by the state of Hawai i as a biocontrol agent against invasive algae such as Acanthophoraspicifera, Gracilaria salicornia, Eucheuma denticulatum and Kappaphycus clade B (Westbrook et al 2014). A member of the family Toxopneustidae (Troschel 1872), a sister family to the Strongylocentrotidae, (Láruson 2017), T. gratilla is a confamilial of the highly venomous sea urchin, Toxopneustes pileolus (Lamark 1816). The increased collection and cultivation of T. gratilla has spawned increased interest in understanding the population structure of this broadly distributed urchin (Cyrus et al 2014, Westbrook et al 2015.…”