Hsuan-Ching Ho

Evolutionary history of anglerfishes (Teleostei: Lophiiformes): a mitogenomic perspective

BackgroundThe teleost order Lophiiformes, commonly known as the anglerfishes, contains a diverse array of marine fishes, ranging from benthic shallow-water dwellers to highly modified deep-sea midwater species. They comprise 321 living species placed in 68 genera, 18 families and 5 suborders, but approximately half of the species diversity is occupied by deep-sea ceratioids distributed among 11 families. The evolutionary origins of such remarkable habitat and species diversity, however, remain elusive because of the lack of fresh material for a majority of the deep-sea ceratioids and incompleteness of the fossil record across all of the Lophiiformes. To obtain a comprehensive picture of the phylogeny and evolutionary history of the anglerfishes, we assembled whole mitochondrial genome (mitogenome) sequences from 39 lophiiforms (33 newly determined during this study) representing all five suborders and 17 of the 18 families. Sequences of 77 higher teleosts including the 39 lophiiform sequences were unambiguously aligned and subjected to phylogenetic analysis and divergence time estimation.ResultsPartitioned maximum likelihood analysis confidently recovered monophyly for all of the higher taxa (including the order itself) with the exception of the Thaumatichthyidae (Lasiognathus was deeply nested within the Oneirodidae). The mitogenomic trees strongly support the most basal and an apical position of the Lophioidei and a clade comprising Chaunacoidei + Ceratioidei, respectively, although alternative phylogenetic positions of the remaining two suborders (Antennarioidei and Ogcocephaloidei) with respect to the above two lineages are statistically indistinguishable. While morphology-based intra-subordinal relationships for relatively shallow, benthic dwellers (Lophioidei, Antennarioidei, Ogcocephaloidei, Chaunacoidei) are either congruent with or statistically indistinguishable from the present mitogenomic tree, those of the principally deep-sea midwater dwellers (Ceratioidei) cannot be reconciled with the molecular phylogeny. A relaxed molecular-clock Bayesian analysis of the divergence times suggests that all of the subordinal diversifications have occurred during a relatively short time period between 100 and 130 Myr ago (early to mid Cretaceous).ConclusionsThe mitogenomic analyses revealed previously unappreciated phylogenetic relationships among the lophiiform suborders and ceratioid familes. Although the latter relationships cannot be reconciled with the earlier hypotheses based on morphology, we found that simple exclusion of the reductive or simplified characters can alleviate some of the conflict. The acquisition of novel features, such as male dwarfism, bioluminescent lures, and unique reproductive modes allowed the deep-sea ceratioids to diversify rapidly in a largely unexploited, food-poor bathypelagic zone (200-2000 m depth) relative to the other lophiiforms occurring in shallow coastal areas.

Does counting species count as taxonomy? On misrepresenting systematics, yet again

Recent commentary by Costello and collaborators on the current state of the global taxonomic enterprise attempts to demonstrate that taxonomy is not in decline as feared by taxonomists, but rather is increasing by virtue of the rate at which new species are formally named. Having supported their views with data that clearly indicate as much, Costello et al. make recommendations to increase the rate of new species descriptions even more. However, their views appear to rely on the perception of species as static and numerically if not historically equivalent entities whose value lie in their roles as “metrics”. As such, their one‐dimensional portrayal of the discipline, as concerned solely with the creation of new species names, fails to take into account both the conceptual and epistemological foundations of systematics. We refute the end‐user view that taxonomy is on the rise simply because more new species are being described compared with earlier decades, and that, by implication, taxonomic practice is a formality whose pace can be streamlined without considerable resources, intellectual or otherwise. Rather, we defend the opposite viewpoint that professional taxonomy is in decline relative to the immediacy of the extinction crisis, and that this decline threatens not just the empirical science of phylogenetic systematics, but also the foundations of comparative biology on which other fields rely. The allocation of space in top‐ranked journals to propagate views such as those of Costello et al. lends superficial credence to the unsupportive mindset of many of those in charge of the institutional fate of taxonomy. We emphasize that taxonomy and the description of new species are dependent upon, and only make sense in light of, empirically based classifications that reflect evolutionary history; homology assessments are at the centre of these endeavours, such that the biological sciences cannot afford to have professional taxonomists sacrifice the comparative and historical depth of their hypotheses in order to accelerate new species descriptions.

The complete mitochondrial genome of the great white shark, Carcharodon carcharias (Chondrichthyes, Lamnidae)

Abstract The complete mitochondrial genome of the great white shark having 16,744 bp and including 13 protein-coding genes, 2 ribosomal RNA, 22 transfer RNA genes, 1 replication origin region and 1 control region. The mitochondrial gene arrangement of the great white shark is the same as the one observed in the most vertebrates. Base composition of the genome is A (30.6%), T (28.7%), C (26.9%) and G (13.9%).

The complete mitochondrial genome of the big-eye thresher shark, Alopias superciliosus (Chondrichthyes, Alopiidae)

Abstract The complete mitochondrial genome of the big-eye thresher shark was sequenced using a polymerase chain reaction (PCR)-based method. The total length of mitochondrial DNA is 16,719 bp and includes 13 protein-coding genes, 2 ribosomal RNA, 22 transfer RNA genes, 1 replication origin region and 1 control region. The mitochondrial gene arrangement of the big-eye thresher shark is the same as the one observed in the most vertebrates. Base composition of the genome is A (31.8%), T (28.9%), C (25.8%) and G (13.5%).

The complete mitochondrial genome of the shortfin mako, Isurus oxyrinchus (Chondrichthyes, Lamnidae)

Abstract The complete mitochondrial genome of the shortfin mako (Isurus oxyrinchus) was determined by using a PCR-based method. The total length of mitochondrial DNA is 16,701 bp and includes 13 protein-coding genes, 2 ribosomal RNA, 22 transfer RNA genes, 1 replication origin region, and 1 control region. The mitochondrial gene arrangement of the tiger tail seahorse is also matching the one observed in the most vertebrate creatures. Base composition of the genome is A (28.8%), T (28.0%), C (28.0%), and G (15.2%) with an A + T rich hallmark as that of other vertebrate mitochondrial genomes.

The complete mitochondrial genome of the tiger tail seahorse, Hippocampus comes (Teleostei, Syngnathidae)

The complete mitochondrial genome of the tiger tail seahorse was sequenced using a polymerase chain reaction-based method. The total length of mitochondrial DNA is 16,525 bp and includes 13 protein-coding genes, 2 ribosomal RNA, 22 transfer RNA genes, and a control region. The mitochondrial gene arrangement of the tiger tail seahorse is also matching the one observed in the most vertebrate creatures. Base composition of the genome is A (32.8%), T (29.8%), C (23.0%), and G (14.4%) with an A+T-rich hallmark as that of other vertebrate mitochondrial genomes.

New species of the snake eels Echelus and Ophichthus (Anguilliformes: Ophichthidae) from Taiwan

Three new species of ophichthid eels, subfamily Ophichthinae, are described and illustrated from specimens collected at fish markets in Taiwan. Included are: Echelus polyspondylus sp. nov., which is unique in its vertebral number (172-183), dorsal-fin origin (behind gill openings), and coloration (anal-fin membrane black posteriorly); Ophichthus bicolor sp. nov., which is unique in its mean vertebral formula (18-64-158), dorsal-fin origin (well behind gill openings), dentition (teeth large and conical), and contrasting coloration (tan dorsally, white ventrally); and O. shaoi sp. nov., which is unique in its mean vertebral formula (11-69-159), and prominent lip barbels. A key to Taiwanese species of Echelus and Ophichthus is provided.

Review of the Halieutichthys aculeatus species complex (Lophiiformes: Ogcocephalidae), with descriptions of two new species

The Halieutichthys aculeatus species complex is reviewed. Members of this clade are distinguished by the presence of tubercles on the tail and a reticulate dorsal pigmentation pattern. Three species are recognized, including two species new to science. A neotype is chosen for H. aculeatus. Halieutichthys bispinosus n. sp. is characterized by having relatively strong tubercles on the dorsal surface, a row of tubercles almost always present dorsal to the orbit, both sphenotic tubercles well developed and sharp, trifid principal tubercles on the disk margin with anterior spinelet enlarged, dense arrangement of tubercles on the tail and a comparatively large adult body size. Halieutichthys intermedius n. sp. can be distinguished from congeners by having both sphenotic tubercles strongly reduced, the tubercles almost always absent dorsal to the orbit, principal tubercles on the disk margin uniformly short and blunt tubercles, with all spinelets generally reduced.

Renaming of three recently described eels of the genus Neenchelys (Teleostei: Anguilliformes: Ophichthidae) from the western Pacific.

In our earlier paper (Ho et al., 2013), we described three new species of the eel genus Neenchelys Bamber, 1915. Unfortunately, the critical step of registering the work in ZooBank was omitted, thus rendering the names unavailable. In this paper, we present abbreviated descriptions of the new species in order to make these names available in accordance with the amended Article 8.5 of the International Code of Zoological Nomenclature.

Annotated checklist of eels (orders Anguilliformes and Saccopharyngiformes) from Taiwan

An annotated checklist of eels, orders Anguilliformes and Saccopharyngiformes, occurring in Taiwanese waters is presented. The checklist is the result of a series of systematic studies conducted by the authors in the past few years. The eel fauna of Taiwan is one of the richest in the world with a total of 206 species in 74 genera and 13 families in Anguilliformes and a single species in Saccopharyngiformes. The most species-rich families are the Muraenidae with 71 species, followed by the Ophichthidae with 60 species, the Congridae with 29 species, and the Synaphobranchidae with 17 species. Moreover, three genera and 42 species have been described based on at least one type specimen collected from Taiwan. Of these, 36 species are recognized as valid and 23 species are known only from Taiwanese waters at present. Historical records of all Taiwanese eel species are reviewed by examining the original descriptions and figures, vouchers, as well as the recently collected specimens, where available. This represents the first detailed checklist of eels from Taiwanese waters.