Fig 3
Relaxed molecular clock estimates for ages of extant holocephalans ; Bayesian inference of phylogeny (using BEAST 1.4.8) with three partitions corresponding to three mitochondrial DNA fragments, 10,000,000 generations, relaxed lognormal clock, tree prior 0 yule process (speciation); horizontal bars indicate credible intervals (95%)
Source publication
Much attention has been paid to the molecular
phylogeny of holocephalan fishes during recent years, but
sampling was very low and not all genera were examined.
This study offers an extended sampling of species from all
known genera to clarify their phylogeny and to provide an
estimate of the time of origin of extant holocephalan taxa.
Three mitocho...
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... it is important to mention that this is the first contribution of COI sequences in GenBank for this species. in fact, nucleotide sequences of the genus Hydrolagus in public databases are scarce, and only a few authors have reported the use of mitochondrial genes like 12S, 16S, coi and naDh (Ward et al., 2008;inoue et al., 2010;licht et al., 2012). in particular, for H. melanophasma, the mtDna 16S and 12S gene sequences have been reported for molecular identification and phylogenetic studies (De la cruz-agüero et al., 2012). ...
... thus, Finucci et al. (2018), synonymized these two species and placed them in the genus Chimaera under the original combination C. ogilbyi. Several authors have mentioned that the genera Hydrolagus and Chimaera are paralogous (Ward et al., 2008;De la cruz-agüero et al., 2012;licht et al., 2012;Violi et al., 2018) and highlighted the need for more studies to clarify the evolutionary relationships between chimaeridae species. Similarly, regarding the genus, further analysis to clarify some discrepancies observed among other species are needed. ...
Hydrolagus melanophasma James, Ebert, Long & Didier, 2009 is a widely distributed species in the eastern Pacific. It is regularly reported in fisheries such as the Patagonian toothfish fishery operating along west- ern South America. However, studies on chimaeras in Peru are scarce. In this study, new data on the distribution,
morphology (32 measurements), biology (reproductive) and molecular (mtDNA genes) analysis of H. melanophasma on the central and southern coast of Peru are presented. Its diagnosis was based, among other characteristics, on the absence of the anal fin, a blunt snout and a large, slightly curved dorsal spine extending beyond the apex of the first dorsal fin, as well as a long second dorsal fin of uniform height. The species dimensions, head shape, colouration and reproductive aspects are also described and compared. Phylogenetic analyses based on the mitochondrial genes cytochrome oxidase subunit 1 (COI) and 16S rRNA clearly discriminate H. melanophasma from its congeners. The sequences in this study clustered closely with two other 16S sequences of the same species reported from Mexico. While no previous COI sequences were available, this study is the first record of COI sequences for the species in a public database. Hydrolagus melanophasma is currently classified as Least Concern by the IUCN. However, data on catch volumes in Peru are almost non-existent and, given the fragility of chondrichthyan populations, a detailed study of their catches is warranted to assess their conservation status in a more documented manner
... As TNT requires that only one terminal be designated as an outgroup in which to root, it was not possible to constrain the monophyly of Chimaeriformes, which was thus recovered as paraphyletic. Nevertheless, it is important to stress that the monophyly of this group is not under dispute and it has been corroborated by several phylogenetic analyses (Didier, 1995;Inoue et al., 2010;Licht et al., 2012). As proposed in previous studies (Mirande, 2017(Mirande, , 2019Vanegas-R ıos et al., 2020), the analysis was also performed under extended implied weighting, using the command "xpiwe (*", to handle missing information for molecular characters (Goloboff, 2014). ...
The morphology of paired fins is commonly overlooked in morphological studies, particularly the pelvic girdle and fins. Consequently, previous phylogenetic studies incorporating morphological data used few skeletal characters from this complex. In this paper, the phylogenetic significance of pelvic articular characters for elasmobranchs is discussed in light of the morphological variation observed in 130 species, the most comprehensive study exploring the morphology of the pelvic girdle done so far. The 10 morphological characters proposed herein for the pelvic articulation were incorporated into a molecular matrix of NADH2 sequences and submitted to an analysis of maximum parsimony employing extended implied weighting. The most stable tree was selected based on the distortion coefficients, SPR distances (subtree pruning and regrafting) and fit values. Some of the striking synapomorphies recovered within elasmobranchs include the presence of an articular surface for the first enlarged pelvic radial supporting Elasmobranchii and the pelvic articular region for the basipterygium extending from the posterolatral margin of the pelvic girdle over its lateral surface in Echinorhinus + Hexanchiformes. Additionally, the proposed characters and their distributions are discussed considering the relationships recovered and also compared with previous morphological and molecular phylogenetic hypotheses.
... They represent an ancient lineage with a high degree of evolutionary divergence between the two subclasses and different orders (refer to Figure 1 for taxonomic relationships). It is estimated the class diverged roughly 473 million years ago (MYA) from other Gnathostomes (jawed vertebrates), with the two subclasses, Holocephali (chimeras) and Elasmobranchii (sharks, rays, and skates), diverging roughly 399 MYA (Hedges and Kumar, 2009;Inoue et al., 2010;Chen et al., 2012;Licht et al., 2012;Betancur-R et al., 2015). Chondrichthyans are a very distinct class as they are the only vertebrate clade to possess a cartilaginous skeleton, rather than bone (Boisvert et al., 2019). ...
Chondrichthyan species (sharks, rays, skates, and chimeras) are a class of high ecological, economic, and cultural significance, and yet they are the most threatened taxa in the marine environment. The creation of reference chromosome-length genome assemblies allows for conservation genomics methods, such as population and ecological genomics, to be utilized. Despite being greatly threatened and of great importance in maintaining ecosystem function, chondrichthyan species have been repeatedly absent from conservation-based genome sequencing projects. Less than 1% of these species have a genome sequence, despite their almost 50% either threatened or Data Deficient conservation status. Most notably, there are seven orders within this class without any genome representation. In this review, we identify gaps in chondrichthyan genomic resources and demonstrate how the lack of genomic resources for this major taxonomic class is limiting the conservation of these already difficult to conserve species. We highlight other applications for chondrichthyans genomics, such as evolutionary and developmental biology. Likely, the mismatching sampling protocols and limited computational skills and communication between fields have been preventing the integration of marine and molecular sciences. Here, we propose that this field is in dire need to move forward quickly to increase protection for marine species and ecosystems through improved collaboration between marine, molecular, and computer sciences.
... The increase to 106 chondrichthyan species in this study is the result of including recently identified species such as the spadenose guitarfish (Rutledge 2019) and the taxonomic verification of documented records of several sharks, including the sharpnose sevengill shark Heptranchias perlo (Bonnaterre, 1788) (Castro-Aguirre and Balart (1996) (Castro-Aguirre 1965); the presence of this species in the GC was confirmed through records of fish collections and distribution databases. As results of this updated diversity of Chondrichthyes in the GC, the chondrichthyans of this ecosystem represent between 53.9 and 93.7% of the total of cartilaginous fish species reported for Mexico (Espinosa- (74) 90 (81) 106 (87) In parenthesis are present the species-richness formerly reported by The comparative analysis of the taxonomic composition of the Chondrichthyes class in the GC presented here permitted the identification of a low species richness (four species = 3.8%) for the subclass Holocephali (Table 2), which is a small deep-water group widely distributed in the World Ocean but with some species restricted to the southern hemisphere as the family Callorhinchidae (Licht et al. 2012;Ebert et al. 2017). A single order containing all the extant taxa known in the world (Kriwet and Gaździcki 2003;Didier et al. 2012), Chimaeriformes, is represented in the GC by 2 families. ...
... The chimaeroids species richness in the GC represents twice that reported for all of Mexico and 80% of that for the MP (Espinosa-Pérez 2014; Ehemann et al. 2018) as well as 66.6%, 33.3%, and between 7.1 and 8.1% of the total families, genera, and species recognized worldwide, respectively (Weigmann 2016;Ebert et al. 2017). As in other regions of the world, the diversity of holocephalans in the GC is low; their bathydemersal habits hinder their capture by local fisheries relative to other more easily accessible cartilaginous fish species (Licht et al. 2012) as deep fishing methods are not common in the region. Thus, the low species record of chimaeroids in the GC (mostly derived from vagrants or For comparison, the species richness of the Euselachii subclass (the most diverse group of Chondrichthyes worldwide) in the GC is greater than that of its holocephalan counterpart, comprising 96.2% of the GC's total cartilaginous fish species (Table 3). ...
This updated checklist of chondrichthyans from the Gulf of California (GC) with notes on zoogeography, conservation status, and commercial value includes 2 subclasses, 14 orders, 31 families, 55 genera, and 106 species. Euselachii (Batomorphi 44.3% and Selachii 51.8%) is the most diverse subclass (13 orders, 29 families, 53 genera, and 102 species). The order Carcharhiniformes (4 families, 16 genera, and 36 species) and Myliobatiformes (6 families, 11 genera, and 24 species) represent 56.6% of the total cartilaginous fish diversity in the GC. Based on the analysis of biogeographic affinities, most species include their ranges of distribution into the “Sinus-Californian” (55.7%), Mexican (41.5%), and Panamic (36.8%) provinces; 29 species are circumtropical, 7 amphipacific, 5 amphiamerican, and 4 endemic. Based on the IUCN Red List, 1 species is “Critically Endangered,” 2 are “Endangered,” 14 are “Vulnerable,” 23 are “Near Threatened,” 26 are of “Least Concern,” 3 “Not Evaluated,” and 36 are “Data Deficient.” Mexican laws fully protect 9 species classified as “Threatened,” at “Risk of Extinction,” or under “Special Protection,” whereas the rest are protected from fishing at least during 3 months of the year. Thirty-seven species (35%) are of commercial value; another 30 (28%) rare species of low commercial importance have been reported in the catches of artisanal and semi-industrial fisheries during the last 2 decades. Sørensen's coefficient of similarity and cluster analysis between major faunal divisions in the GC suggest the existence of 2 large chondrichthyan assemblages for this region ([NGC-CGC] + [SGC]). This study increases to 106 the species richness of Chondrichthyes known in the GC and serves as the baseline for formulating and implementing of conservation programs for this group of cartilaginous fish.
... Methylol adducts, in addition to other blocking lesions, inhibit techniques that employ amplification of DNA, including PCR, and consequently almost all currently available DNA sequencing techniques (Gilbert et al., 2007). Therefore, DNA extraction and sequencing from formaldehyde fixed animal samples has proven to be difficult and has a high failure rate (Gilbert et al., 2007;Licht et al., 2012;Tang, 2006;Wu, Patten, Yamashiro & Chui, 2002). An exception to this rule is formalin fixed and paraffin embedded (FFPE) clinical human samples, successfully analysed in multiple studies (e.g., Einaga, Yoshida, Yoga et al., 2017;Lin, Kennedy, Svarowski et al., 2009;Paireder, Werner, Bailer et al., 2013;Snow, Stance, Pruessner et al., 2014) even recovering whole genomes (e.g., Munchel, Hoang, Zao et al., 2015;Robbe, Popitsch, Knight et al., 2018;Zar, Smith, Smith et al., 2019). ...
Millions of scientific specimens are housed in museum collections, a large part of which are fluid preserved. The use of formaldehyde as fixative and subsequent storage in ethanol is especially common in ichthyology and herpetology. This type of preservation damages DNA and reduces the chance of successful retrieval of genetic data. We applied ancient DNA extraction and single stranded library construction protocols to a variety of vertebrate samples obtained from wet collections and of different ages. Our results show that almost all samples tested yielded endogenous DNA. Archival DNA extraction was successful across different tissue types as well as using small amounts of tissue. Conversion of archival DNA fragments into single‐stranded libraries resulted in usable data even for samples with initially undetectable DNA amounts. Subsequent target capture approaches for mitochondrial DNA using home‐made baits on a subset of 30 samples resulted in almost complete mitochondrial genome sequences in several instances. Thus, application of ancient DNA methodology makes wet collection specimens, including type material as well as rare, old or extinct species, accessible for genetic and genomic analyses. Our results, accompanied by detailed step‐by‐step protocols, are a large step forward to open the DNA archive of museum wet collections for scientific studies.
... For each character identified in our results, we built a character matrix and used phylogenetic relationships from Licht et al. (2012), Naylor et al. (2012), andLast et al. (2016). We reconstructed the ancestral state for each character (globular mineralization, fibrous mineralization, and lamellar mineralization: presence/absence; mineralization architecture: continuous/semi-discontinuous/discontinuous (tessellated or reduced) with Mesquite (v3.61) (Maddison and Maddison, 2019). ...
The diversity of skeletal tissues in extant vertebrates includes mineralized and unmineralized structures made of bone, cartilage, or tissues of intermediate nature. This variability, together with the diverse nature of skeletal tissues in fossil species question the origin of skeletonization in early vertebrates. In particular, the study of skeletal tissues in cartilaginous fishes is currently mostly restrained to tessellated cartilage, a derived form of mineralized cartilage that evolved at the origin of this group. In this work, we describe the architectural and histological diversity of neural arch mineralization in cartilaginous fishes. The observed variations in the architecture include tessellated cartilage, with or without more massive sites of mineralization, and continuously mineralized neural arches devoid of tesserae. The histology of these various architectures always includes globular mineralization that takes place in the cartilaginous matrix. In many instances, the mineralized structures also include a fibrous component that seems to emerge from the perichondrium and they may display intermediate features, ranging from partly cartilaginous to mostly fibrous matrix, similar to fibrocartilage. Among these perichondrial mineralized tissues is also found, in few species, a lamellar arrangement of the mineralized extracellular matrix. The evolution of the mineralized tissues in cartilaginous fishes is discussed in light of current knowledge of their phylogenetic relationships.
... The family Chimaeridae comprises only two genera, Chimaera and Hydrolagus, separated on the basis of the respective presence or absence of an anal fin. However, recent molecular inferences suggest paraphylies within the chimaerid genera that undermine the validity of the genus Hydrolagus (Didier et al. 2012;Licht et al. 2012;Finucci et al. 2018). Twenty species are currently recognised within Chimaera, most of them with regionally limited distributions (Table 1). ...
Chimaera compacta sp. nov., a new species of shortnose chimaera (Holocephali: Chimaeriformes: Chimaeridae), is described from a single specimen collected at 595–655 m depth, off Amsterdam Island, in the southern Indian Ocean. The species is easily distinguished from its congeners by the combination of the following characters: massive head with short snout; stocky and relatively long trunk 44% BDL, short tail with second dorsal fin base 72% BDL; long pelvic fin anterior margin 26% BDL. Caudal fin dorsal origin slightly posterior to caudal fin ventral origin. Firm, non-deciduous skin; brown color with yellow blotches. Chimaera compacta sp. nov. is morphologically close to Chimaera lignaria Didier 2002 from New Zealand and Chimaera willwatchi Clerkin, Ebert and Kemper 2017 from south western Indian Ocean. The new species can be distinguished from other Chimaera species based on DNA sequences divergence of the COI and NADH2 genes. This species has a nucleotide sequence divergence (uncorrected p distances) for the studied genes of 4.2 and 4.1%, respectively, with its closest relatives. Phylogenetically, Chimaera compacta sp. nov. is nested within a well-supported group including Chimaera carophila Kemper, Ebert, Naylor and Didier 2014, Chimaera didierae Clerkin, Ebert and Kemper 2017, C. lignaria, Chimaera macrospina Didier, Last and White 2008, Chimaera notafricana Kemper, Ebert, Compagno and Didier 2010, Chimaera opalescens Luchetti, Iglésias and Sellos 2011, and C. willwatchi. It is the first Chimaeridae described for the Territory of the French Southern and Antarctic Lands.
... Callorhinchus milii Bory de Saint-Vincent 1823, a holocephalan, and Scyliorhinus canicula Linnaeus 1758, an elasmobranch. C. milii is a callorhinchid, the sister group to all other holocephalans (Inoue et al., 2010;Licht et al., 2012), and historically one of the best known holocephalans due to its being one of only two species to inhabit shallow, nearshore waters (Didier, 1995). As a result, the musculature of the genus has been described several times (Edgeworth, 1935;Kesteven, 1933;Luther, 1909a;Ribbink, 1971;Shann, 1919), most recently with Didier (1995) providing a detailed overview of the anatomy and systematics of holocephalans, including Callorhinchus. ...
... Callorhinchus milii Bory de Saint-Vincent 1823, a holocephalan, and Scyliorhinus canicula Linnaeus 1758, an elasmobranch. C. milii is a callorhinchid, the sister group to all other holocephalans (Inoue et al., 2010;Licht et al., 2012), and historically one of the best known holocephalans due to its being one of only two species to inhabit shallow, nearshore waters (Didier, 1995). As a result, the musculature of the genus has been described several times (Edgeworth, 1935;Kesteven, 1933;Luther, 1909a;Ribbink, 1971;Shann, 1919), most recently with Didier (1995) providing a detailed overview of the anatomy and systematics of holocephalans, including Callorhinchus. ...
The anatomy of sharks, rays, and chimaeras (chondrichthyans) is crucial to understanding the evolution of the cranial system in vertebrates due to their position as the sister group to bony fishes (osteichthyans). Strikingly different arrangements of the head in the two constituent chondrichthyan groups—holocephalans and elasmobranchs—have played a pivotal role in the formation of evolutionary hypotheses targeting major cranial structures such as the jaws and pharynx. However, despite the advent of digital dissections as a means of easily visualizing and sharing the results of anatomical studies in three dimensions, information on the musculoskeletal systems of the chondrichthyan head remains largely limited to traditional accounts, many of which are at least a century old. Here, we use synchrotron tomographic data to carry out a digital dissection of a holocephalan and an elasmobranch widely used as model species: the elephantfish, Callorhinchus milii, and the small‐spotted catshark, Scyliorhinus canicula. We describe and figure the skeletal anatomy of the head, labial, mandibular, hyoid, and branchial cartilages in both taxa as well as the muscles of the head and pharynx. In Callorhinchus, we make several new observations regarding the branchial musculature, revealing several previously unreported or ambiguously characterized muscles, likely homologous to their counterparts in the elasmobranch pharynx. We also identify a previously unreported structure linking the pharyngohyal of Callorhinchus to the neurocranium. Finally, we review what is known about the evolution of chondrichthyan cranial muscles from their fossil record and discuss the implications for muscle homology and evolution, broadly concluding that the holocephalan pharynx is likely derived from a more elasmobranch‐like form which is plesiomorphic for the chondrichthyan crown group. This dataset has great potential as a resource, particularly for researchers using these model species for zoological research, functional morphologists requiring models of musculature and skeletons, as well as for palaeontologists seeking comparative models for extinct taxa.
... Dentitions are the most common and best-preserved remains, providing the basis for taxonomy and phylogenetic research. The geological history of Chimaeridae sensu lato is traced back to the mid-Cretaceous (Stahl, 1999), which is younger than the estimated time of divergence of the family obtained by using the molecular clock method: 107 Ma (Heinicke et al., 2009), 122 Ma (Inoue et al., 2010), or 159 Ma as calculated more recently by Licht et al. (2012). In the fossil record, the genus Chimaera, is known from the late Eocene to Pliocene and includes seven nominal species (Stahl, 1999). ...
A chimaeroid mandibular dental plate from the nearshore upper Oligocene Sooke Formation west of Victoria, Vancouver Island, British Columbia, is described here as a new genus of chimaerid fish (Holocephali, Chimaeridae), Canadodus suntoki, gen. et sp. nov. The new genus differs from mandibular plates of both Recent and Cenozoic Chimaeridae (Chimaera, Hydrolagus) in having a more robust plate with a massive symphyseal tritor filled by laminated whitlockin, the presence of a large compound median tritor and a small inner tritor, as well as the absence of solid whitlockin in the dental structure. The chimaerid individual is estimated to have measured nearly 1 m in total body length. This is a first record of a Paleogene chimaeroid fish in both British Columbia and Canada and only the second record from the Oligocene of the northern Pacific. In addition, the species Chimaera gosseleti Winkler, 1880, is transferred to the genus Harriotta, resulting in the new combination Harriotta gosseleti (Winkler, 1880).
