Phylogeny and divergence times of suckers (Cypriniformes: Catostomidae) inferred from Bayesian total-evidence analyses of molecules, morphology, and fossils

Marine and freshwater fishes of Alabama: a revised checklist and discussion of taxonomic issues

Checklists are fundamental and important tools for organizing information about biodiversity that provide a basis for conservation and additional scientific research. While Alabama is recognized as an aquatic biodiversity hotspot with the highest native freshwater fish diversity in the contiguous United States, we currently lack an up-to-date list of the states fishes. In particular, much has changed over the past ~20 years regarding our knowledge of fishes from Alabama and the Mobile River Basin, rendering past comprehensive treatments by Mettee et al. (1996) and Boschung and Mayden (2004) out of date. Here, we provide a revised checklist of marine and freshwater fishes known from the coastal and inland waters of Alabama that includes 463 species (335 primarily freshwater fishes, and 128 marine or diadromous fishes) in 35 orders, 78 families, and 176 genera. Extant, extirpated, and extinct species are included, as are putative candidate species. The checklist is based on prior work, searches of the literature and online sources, as well as parsing a large compilation of >140,000 fish records for Alabama and the Mobile River Basin from 37 data providers in the global Fishnet2 database (www.fishnet2.net) and >4000 marine survey records from the SEAMAP database (https://www.gsmfc.org/seamap.php). After editing and quality control checks, the final combined database contained 144,215 collection records, ~95% of which were georeferenced. We discuss the species descriptions, nomenclatural changes, and updates to marine species that account for changes to the state list, and we close with a discussion of ~13 candidate species forms that remain undescribed, which represent outstanding taxonomic issues in need of further research attention.

Nearctic Dactylogyrus species (Platyhelminthes, Monogenea) parasitizing cypriniform fishes in the context of morphology and phylogeny, with descriptions of seven new species

Ribosomal DNA sequences are currently available for 32 morphologically recognized species of Dactylogyrus parasitizing Nearctic cypriniforms, but only 16 of them are assigned to nominal species. Herein, morphological data on 28 of the 32 species are provided, together with comments on their phylogenetic relationships in the context of the morphology of taxonomically important structures. Seven new species of Dactylogyrus are described from five species of leuciscids and one species of catostomids, as follows: D. aduncus n. sp. from Campostoma spadiceum, D. cloutmani n. sp. from Luxilus chrysocephalus isolepis, D. cornifrons n. sp. from Cyprinella venusta, D. fimbratus n. sp. from Rhinichthys cataractae, D. mcallisteri n. sp. from Semotilus atromaculatus, and D. chieni n. sp. and D. haneki n. sp. from Hypentelium nigricans. Four previously described species of Dactylogyrus, D. atromaculatus from S. atromaculatus, D. eos from C. neogaeus, D. parvicirrus from Notemigonus crysoleucas and D. perlus from L. c. isolepis, are redescribed and/or figured. As for the remaining 17 species, only the male copulatory organs (MCOs) taken from the respective hologenophores are illustrated. On the basis of phylogenetic analyses, two main clades of Nearctic Dactylogyrus were recognized and supported by the different morphology of the MCO. The first one included 22 strictly Nearctic species sharing the same MCO type with Dactylogyrus spp. parasitizing cyprinids likely of Asian origin. The second clade encompassed Dactylogyrus spp. with diverse MCO morphology and was placed in the sister position to Dactylogyrus spp. parasitizing European leuciscids and North-West African cyprinids.

Complete mitochondrial genomes of June sucker and Utah sucker (Chasmistes liorus and Catostomus ardens)

The relationship between June sucker (Chasmistes liorus, Jordan, 1878) and Utah sucker (Catostomus ardens, Jordan & Gilbert, 1881) has been a matter of controversy since the mid 1900s. Chasmistes liorus is endemic to Utah Lake, UT and has a subterminal mouth adapted for pelagic feeding. Catostomus ardens is widely distributed throughout the Bonneville Basin and Upper Snake River Basin and has a ventral mouth adapted for benthic feeding. Chasmistes has been recognized as a separate ancient genus. Despite being morphologically distinct, no study has successfully identified residual genetic markers that separate these species. Of these studies, several have used a subset of mitochondrial genes, but no study has analyzed the complete mitochondrial genomes (mitogenomes) of these suckers (Pisces: Catostomidae). To further explore the genetic relationships between these species, we report the complete mitogenomes of Chasmistes liorus and Catostomus ardens. DNA was sequenced using an Illumina HiSeq 2500 system and mitogenomes were assembled and annotated using Geneious v. 2021.2 and MitoAnnotator, respectively. The mitogenomes of Chasmistes liorus and Catostomus ardens are both 16,623 bp and are ∼0.072% divergent. We examine the phylogenetic relationship between Chasmistes liorus and Catostomus ardens using 33 mitogenomes, representing 16 species, from Catostomidae. Our data suggest that Chasmistes liorus is sister to Catostomus ardens. Additional samples from multiple localities and/or cohorts of these species will allow us to better resolve the complicated phylogenetic relationships between these species.

Host-Specific Parasites Reveal the History and Biogeographical Contacts of Their Hosts: The Monogenea of Nearctic Cyprinoid Fishes

Simple Summary

Parasites exhibiting close associations with their hosts may represent a useful tool when investigating historical biogeography, especially in the case of hosts associated with a once contiguous landmass. Host-specific gill parasites (Monogenea) were applied as a supplementary tool to reveal the historical biogeographical contacts between freshwater fish from North America and Europe and their contemporary contacts in North America. Cyprinoidei is the most species-rich lineage of cypriniform fish with Leuciscidae exhibiting a Holarctic distribution. Monogenean parasites of the genus Dactylogyrus are mostly restricted to this freshwater fish group, and the high species diversity of Dactylogyrus follows the high diversity of their cyprinoid fish hosts. Using a phylogenetic approach, two Nearctic clades of Dactylogyrus spp. with different origins were revealed indicating two different historical routes of cyprinoid dispersion to the North American continent. Our study showed that the historical contacts between European and North American leuciscids were accompanied by the host switching of gill monogeneans. The phylogenetic relationships among North American Dactylogyrus spp. indicated numerous colonizations of cypriniform fish resulting from ancient paleogeographic events and contemporary drainage reorganization, thereby, facilitating contacts among phylogenetically distant fish species.

Abstract

Host-specific parasites exhibit close co-evolutionary associations with their hosts. In the case of fragmented/disjunct host distribution, host-specific parasites may reflect the biogeographical history of regions and/or the role played by contacts of hosts. The present study was focused on Dactylogyrus (Monogenea) species almost exclusively parasitizing cyprinoid fishes. We investigated the phylogenetic relationships between Dactylogyrus parasites of Nearctic cyprinoids (Leuciscidae) and Dactylogyrus parasites of Palearctic cyprinoids and used Dactylogyrus phylogeny to explore the biogeography of fish hosts in Europe and North America. Phylogenetic analyses revealed that two Nearctic clades of Dactylogyrus spp. have different origins. Historical contacts between European and North American leuciscids were accompanied by the host switching of Dactylogyrus species. In the Nearctic region, Dactylogyrus parasites also colonized non-leuciscid fishes. Dactylogyrus spp. of three Nearctic leuciscid clades were included in the phylogenetic reconstruction; only Dactylogyrus spp. of the Plagopterinae had a common origin. Dactylogyrus species did not reflect the phylogenetic relationships among leuciscid clades, suggesting that past co-diversification was overshadowed by colonization events mediated by paleogeographic and climatological changes and extensive drainage reorganization. Host-specific monogeneans serve as a supplementary tool to reveal the historical biogeographical contacts between freshwater fish from the North America and Europe and also contemporary contacts of leuciscids in North America.

Chromosome-Level Genome Assembly of Chinese Sucker (Myxocyprinus asiaticus) Reveals Strongly Conserved Synteny Following a Catostomid-Specific Whole-Genome Duplication

Fishes of the family Catostomidae (“suckers”; Teleostei: Cypriniformes) are hypothesized to have undergone an allopolyploidy event approximately 60 Ma. However, genomic evidence has previously been unavailable to assess this hypothesis. We sequenced and assembled the first chromosome-level catostomid genome, Chinese sucker (Myxocyprinus asiaticus), and present clear evidence of a catostomid-specific whole-genome duplication (WGD) event (“Cat-4R”). Our results reveal remarkably strong, conserved synteny since this duplication event, as well as between Myxocyprinus and an unduplicated outgroup, zebrafish (Danio rerio). Gene content and repetitive elements are also approximately evenly distributed across homeologous chromosomes, suggesting that both subgenomes retain some function, with no obvious bias in gene fractionation or subgenome dominance. The Cat-4R duplication provides another independent example of genome evolution following WGD in animals, in this case at the extreme end of conserved genome architecture over at least 25.2 Myr since the duplication. The M. asiaticus genome is a useful resource for researchers interested in understanding genome evolution following WGD in animals.

Disentangling taxonomy of Biacetabulum (Cestoda, Caryophyllidea), parasites of catostomid fishes in North America: proposal of Megancestus gen. n. to accommodate B. carpiodi

A new genus, Megancestus n. gen., is proposed to accommodate the caryophyllidean tapeworm Biacetabulum carpiodi Mackiewicz, 1969 from carpsuckers and quillback (Carpiodes spp.) in North America. This species is not closely related to other species of Biacetabulum Hunter, 1927 and is transferred to a newly erected genus. This new genus is typified by the possession of a small body (total length of 3.1-7.5 mm) with a scolex that bears a pair of large acetabulum-like loculi, two pairs of shallow lateral loculi, and a slightly convex apical disc, testes arranged in one or two layers, oval, thick-walled cirrus-sac, well-developed external seminal vesicle, separate gonopores, H-shaped ovary, few median vitelline follicles, and the uterus extending by a single loop anterior to the cirrus-sac. Megancestus differs from all Nearctic caryophyllidean genera (family Capingentidae), including Biacetabulum, by vitelline follicles dorsal to the ovary that connect the preovarian and postovarian vitelline fields. The most closely related Hunterella Mackiewicz et McCrae, 1962 differs by shape of the scolex (tholate, i.e., devoid of any loculi), dumbbell-shaped ovary and the uterus not extending anterior to the cirrus-sac. Megancestus carpiodi (Mackiewicz, 1969) n. comb. is the only species of the genus and it is a stenoxenous parasite, which has been found only in the river carpsucker (Carpiodes carpio-type host), quillback (Carpiodes cyprinus) and highfin carpsucker (Carpiodes velifer) (Catostomidae: Ictiobinae) in the lower and middle Mississippi basin.

Mind the Outgroup and Bare Branches in Total-Evidence Dating: a Case Study of Pimpliform Darwin Wasps (Hymenoptera, Ichneumonidae)

Taxon sampling is a central aspect of phylogenetic study design, but it has received limited attention in the context of total-evidence dating, a widely used dating approach that directly integrates molecular and morphological information from extant and fossil taxa. We here assess the impact of commonly employed outgroup sampling schemes and missing morphological data in extant taxa on age estimates in a total-evidence dating analysis under the uniform tree prior. Our study group is Pimpliformes, a highly diverse, rapidly radiating group of parasitoid wasps of the family Ichneumonidae. We analyze a data set comprising 201 extant and 79 fossil taxa, including the oldest fossils of the family from the Early Cretaceous and the first unequivocal representatives of extant subfamilies from the mid-Paleogene. Based on newly compiled molecular data from ten nuclear genes and a morphological matrix that includes 222 characters, we show that age estimates become both older and less precise with the inclusion of more distant and more poorly sampled outgroups. These outgroups not only lack morphological and temporal information but also sit on long terminal branches and considerably increase the evolutionary rate heterogeneity. In addition, we discover an artifact that might be detrimental for total-evidence dating: “bare-branch attraction,” namely high attachment probabilities of certain fossils to terminal branches for which morphological data are missing. Using computer simulations, we confirm the generality of this phenomenon and show that a large phylogenetic distance to any of the extant taxa, rather than just older age, increases the risk of a fossil being misplaced due to bare-branch attraction. After restricting outgroup sampling and adding morphological data for the previously attracting, bare branches, we recover a Jurassic origin for Pimpliformes and Ichneumonidae. This first age estimate for the group not only suggests an older origin than previously thought but also that diversification of the crown group happened well before the Cretaceous-Paleogene boundary. Our case study demonstrates that in order to obtain robust age estimates, total-evidence dating studies need to be based on a thorough and balanced sampling of both extant and fossil taxa, with the aim of minimizing evolutionary rate heterogeneity and missing morphological information. [Bare-branch attraction; ichneumonids; fossils; morphological matrix; phylogeny; RoguePlots.]

Genetic structure of endangered lake chubsucker Erimyzon sucetta in Canada reveals a differentiated population in a precarious habitat

We used mitochondrial DNA to assess the genetic structure of endangered lake chubsucker Erimyzon sucetta across its Canadian range. We found unique mitochondrial haplotypes in Lyons Creek, a tributary of the Niagara River that faces a strong potential for habitat deterioration. Lyons Creek may therefore serve as a reservoir of unique genetic diversity. The sensitivity of Lyons Creek, combined with the genetic uniqueness of its E. sucetta population, call for further investigation into whether this population should be considered a separate designatable unit for conservation purposes.

Total-Evidence Framework Reveals Complex Morphological Evolution in Nightbirds (Strisores)

Strisores is a clade of neoavian birds that include diurnal aerial specialists such as swifts and hummingbirds, as well as several predominantly nocturnal lineages such as nightjars and potoos. Despite the use of genome-scale molecular datasets, the phylogenetic interrelationships among major strisorean groups remain controversial. Given the availability of next-generation sequence data for Strisores and the clade’s rich fossil record, we reassessed the phylogeny of Strisores by incorporating a large-scale sequence dataset with anatomical data from living and fossil strisoreans within a Bayesian total-evidence framework. Combined analyses of molecular and morphological data resulted in a phylogenetic topology for Strisores that is congruent with the findings of two recent molecular phylogenomic studies, supporting nightjars (Caprimulgidae) as the extant sister group of the remainder of Strisores. This total-evidence framework allowed us to identify morphological synapomorphies for strisorean clades previously recovered using molecular-only datasets. However, a combined analysis of molecular and morphological data highlighted strong signal conflict between sequence and anatomical data in Strisores. Furthermore, simultaneous analysis of molecular and morphological data recovered differing placements for some fossil taxa compared with analyses of morphological data under a molecular scaffold, highlighting the importance of analytical decisions when conducting morphological phylogenetic analyses of taxa with molecular phylogenetic data. We suggest that multiple strisorean lineages have experienced convergent evolution across the skeleton, obfuscating the phylogenetic position of certain fossils, and that many distinctive specializations of strisorean subclades were acquired early in their evolutionary history. Despite this apparent complexity in the evolutionary history of Strisores, our results provide fossil support for aerial foraging as the ancestral ecological strategy of Strisores, as implied by recent phylogenetic topologies derived from molecular data.