A Review of the Mitogenomic Phylogeny of the Chondrichthyes

Abstract

The phylogenetic analysis of the Chondrichthyes has been the subject of intense debate over the past two decades. The principal relationships within the group based on the analysis of morphological traits are inconsistent with the available molecular topologies, and the phylogeny of these animals is highly controversial, at all levels, ranging from superorders to families and even the genera within families. With the recent development of new generation sequencing (NGS), many phylogenies are now being inferred based on the complete genome of the species. In 2015 and 2016 alone, around 21 new elasmobranch genomes were made available in GenBank. In this context, the principal objective of the present study was to infer the phylogeny of the sharks and rays based on the complete mitochondrial genomes available in the literature. A total of 73 mitogenomes of chondrichthyan species were analyzed. The phylogenetic trees generated rejected the "Hypnosqualea" hypothesis and confirmed the monophyly of the Neoselachii and Batoidea as sister groups of the sharks. These mitogenomic analyses provided ampler and more complete insights into the relationships between the sharks and rays, in particular, the topologies obtained by the analyses revealed a number of incongruities in certain groups of sharks and rays, and the interrelationships between them.

Mineralization of the Callorhinchus Vertebral Column (Holocephali; Chondrichthyes)

“…From this perspective, the tesserae of C. milii most closely resemble the tesserae of the sevengill shark (Notorynchus cepedianus) in terms of their arrangement, being very tightly organized and separated by minimal uncalcified cartilage, while also lacking vital chondrocytes; however, they are not comparable in size, being ∼19-57% of the size (Seidel et al, 2016). This is notable, as the Hexanchiformes, to which N. cepedianus belongs, are considered one of the most primitive of modern selachian groups (Barnett et al, 2012;Tanaka et al, 2013;da Cunha et al, 2017). However, despite this resemblance, it is likely that this tissue organization does not represent a plesiomorphic trait given the morphology of the skeletal tissues of stem holocephalans such as Cobelodus (see section "Mineralised Tissue Development").…”

Unique osmoregulatory morphology in primitive sharks: an intermediate state between holocephalan and derived shark secretory morphology

“…Hexanchids and echinorhinids are often considered primitive, given their plesiomorphic characteristics and early origin in the fossil record (Barnett et al ., ; Crofts, ; da Cunha et al ., ; Daly‐Engel et al ., ). Echinorhinus brucus and the prickly shark Echinorhinus cookei Pietschmann 1928 are basal elasmobranchs with an estimated family radiation from other squaliform sharks roughly 148 M BP (Straube et al ., ).…”

“…Although we were able to determine that digitiform and lobulate rectal glands were characteristic of phylogenetic age and not depth, the origin of kidney‐bean rectal‐gland morphology in somniosids remains a mystery. Digitiform rectal glands observed in other phylogenetically older squaliform genera Squalus and Centrophorus (Kriwet & Klug 2009; Naylor et al ., ; Straube et al ., 2015; da Cunha et al ., ) suggests that this trait is not a relic of phylogenetic lineage. Depth is not a likely explanation for kidney‐bean rectal‐gland morphology in somniosids either given the homologous distribution of digitiform morphology through all other squaliform sharks despite depth preference.…”

“…Although we were able to determine that digitiform and lobulate rectal glands were characteristic of phylogenetic age and not depth, the origin of kidney-bean rectal-gland morphology in somniosids remains a mystery. Digitiform rectal glands observed in other phylogenetically older squaliform genera Squalus and Centrophorus(Kriwet & Klug 2009;Naylor et al, 2012;Straube et al, 2015;da Cunha et al, 2017) suggests that this…”

Mineralisation of theCallorhinchusvertebral column (Holocephali; Chondrichthyes)

“…From this perspective, the tesserae of C. milii most closely resemble the tesserae of the sevengill shark (Notorynchus cepedianus) in terms of their arrangement, being very tightly organised and separated by minimal uncalcified cartilage, while also lacking vital chondrocytes; however, they are not comparable in size, being ~19-57% of the size (Seidel et al, 2016). This is notable, as the Hexanchiformes, to which N. cepedianus belongs, are considered one of the most primitive of modern selachian groups (Barnett et al, 2012;Tanaka et al, 2013;da Cunha et al, 2017). However, despite this resemblance, it is likely that this tissue organisation does not represent a plesiomorphic trait given the morphology of the skeletal tissues of stem holocephalans such as Cobelodus (see section 4.2).…”