Morphological and molecular descriptions of Moniliformis saudi sp. n. (Acanthocephala: Moniliformidae) from the desert hedgehog, Paraechinus aethiopicus (Ehrenberg) in Saudi Arabia, with a key to species and notes on histopathology.

A new acanthocepohalan species, Moniliformis saudi sp. n. is described from the desert hedgehog, Paraechinus aethiopicus (Ehrenberg), in central Saudi Arabia. Fourteen other valid species of Moniliformis Travassos, 1915 are recognised. The new species of Moniliformis is distinguished by having a small proboscis (315-520 µm long and 130-208 µm wide) with two apical pores, 14 rows of 8 hooks each and small hooks, thre largest being 25-31 µm long anteriorly. Distinguishing features are incorporated in a dichotomous key to the species of Moniliformis. The description is augmented by scanning electron microscopical (SEM) observation and DNA analysis of nuclear (18S rRNA) and mitochondrial (cytochrome oxidase subunit 1; cox1) gene sequences. Attached worms cause extensive damage to the immediate area of attachment in the host intestine. This includes tissue necrosis and blood loss due to damage to capillary beds. Worms also obstruct essential absorbing surfaces.

Morphological and molecular description of Tenuisentis niloticus (Meyer, 1932) (Acanthocephala: Tenuisentidae) from Heterotis niloticus (Cuvier) (Actinopterygii: Arapaimidae), in Burkina Faso, with emendation of the family diagnosis and notes on new features, cryptic genetic diversity and histopathology.

Specimens described as Rhadinorhynchus niloticus Meyer, 1932 (Rhadinorhynchidae) from two male specimens collected from Heterotis niloticus (Cuvier) in the Egyptian Nile were later redescribed in the genus Tenuisentis Van Cleave, 1936 (Tenuisentidae) based on 12 specimens collected from the same host species in the White Nile. That redescription basically distinguished the two genera based on five traits but did not actually provide a formal description. His account left out information about cerebral ganglion, lemnisci, some reproductive structures, eggs, proboscis hook dissymmetry and roots, size of trunk and a few other structures. We provide (i) the first complete description of this species enhanced by SEM, molecular, and histo-pathological studies; (ii) expand the existing descriptions; (iii) correct questionable accounts advanced by Van Cleave on the cement gland and the hypodermal giant nuclei; and (iv) add descriptions of new features such as the para-receptacle structure which we also report from Paratenuisentis Bullock & Samuel, 1975, the only other genus in Tenuisentidae Van Cleave, 1936. The subsequent description of a few more specimens from the same host collected in Mali was more informative yet incomplete and at variance with our specimens from Burkina Faso. Genetic divergence and phylogenetic analyses of mitochondrial (cytochrome oxidase c subunit I; COI) and nuclear (18S ribosomal RNA) gene relationships uncovered a cryptic species complex containing two lineages. Based on our studies, the family diagnosis is emended. The acanthocephalan causes damage to the host intestine as depicted in histopathological sections. The invading worm can extend from the mucosal layer to the muscularis externa of the host with subsequent tissue necrosis, villi compression, haemorrhaging and blood loss.

Climate oscillations, glacial refugia, and dispersal ability: factors influencing the genetic structure of the least salmonfly, Pteronarcella badia (Plecoptera), in Western North America.

BACKGROUND: Phylogeographic studies of aquatic insects provide valuable insights into mechanisms that shape the genetic structure of communities, yet studies that include broad geographic areas are uncommon for this group. We conducted a broad scale phylogeographic analysis of the least salmonfly Pteronarcella badia (Plecoptera) across western North America. We tested hypotheses related to mode of dispersal and the influence of historic climate oscillations on population genetic structure. In order to generate a larger mitochondrial data set, we used 454 sequencing to reconstruct the complete mitochondrial genome in the early stages of the project. RESULTS: Our analysis revealed high levels of population structure with several deeply divergent clades present across the sample area. Evidence from five mitochondrial genes and one nuclear locus identified a potentially cryptic lineage in the Pacific Northwest. Gene flow estimates and geographic clade distributions suggest that overland flight during the winged adult stage is an important dispersal mechanism for this taxon. We found evidence of multiple glacial refugia across the species distribution and signs of secondary contact within and among major clades. CONCLUSIONS: This study provides a basis for future studies of aquatic insect phylogeography at the inter-basin scale in western North America. Our findings add to an understanding of the role of historical climate isolations in shaping assemblages of aquatic insects in this region. We identified several geographic areas that may have historical importance for other aquatic organisms with similar distributions and dispersal strategies as P. badia. This work adds to the ever-growing list of studies that highlight the potential of next-generation DNA sequencing in a phylogenetic context to improve molecular data sets from understudied groups.

Using de novo transcriptomes to decipher the relationships in cutthroat trout subspecies (Oncorhynchus clarkii).

For almost 200 years, the taxonomy of cutthroat trout (Oncorhynchus clarkii), a salmonid native to Western North America, has been in flux as ichthyologists and fisheries biologists have tried to describe the diversity within these fishes. Starting in the 1950s, Robert Behnke reexamined the cutthroat trout and identified 14 subspecies based on morphological traits, Pleistocene events, and modern geographic ranges. His designations became instrumental in recognizing and preserving the remaining diversity of cutthroat trout. Over time, molecular techniques (i.e. karyotypes, allozymes, mitochondrial DNA, SNPs, and microsatellite arrays) have largely reinforced Behnke's phylogenies, but have also revealed that some relationships are consistently weakly supported. To further resolve these relationships, we generated de novo transcriptomes for nine cutthroat subspecies, as well as a Bear River Bonneville form and two Colorado River lineages (blue and green). We present phylogenies of these subspecies generated from multiple sets of orthologous genes extracted from our transcriptomes. We confirm many of the relationships identified in previous morphological and molecular studies, as well as discuss the importance of significant differences apparent in our phylogenies from these studies within a geological perspective. Specific findings include three distinct clades: (1) Bear River Bonneville form and Yellowstone cutthroat trout; (2) Bonneville cutthroat trout (n = 2); and (3) Greenback and Rio Grande cutthroat trout. We also identify potential gene transfer between Bonneville cutthroat trout and a population of Colorado River green lineage cutthroat trout. Using these findings, it appears that additional groups warrant species-level consideration if other recent species elevations are retained.

Heterochronic shift in gene expression leads to ontogenetic morphological divergence between two closely related polyploid species.

Heterochrony-alteration to the rate or timing of development-is an important mechanism of trait differentiation associated with speciation. Heterochrony may explain the morphological divergence between two polyploid species, June sucker (Chasmistes liorus) and Utah sucker (Catostomus ardens). The larvae of both species have terminal mouths; however, as adults, June sucker and Utah sucker develop subterminal and ventral mouths, respectively. We document a difference in the timing of shape development and a corresponding change in the timing of gene expression, suggesting the distinctive mouth morphology in June suckers may result from paedomorphosis. Specifically, adult June suckers exhibit an intermediate mouth morphology between the larval (terminal) and ancestral (ventral) states. Endemic and sympatric Chasmistes/Catostomus pairs in two other lakes also are morphologically divergent, but genetically similar. These species pairs could have resulted from the differential expression of genes and corresponding divergence in trait development. Paedomorphosis may lead to adaptive diversification in Catostomids.

Single nucleotide polymorphism discovery in cutthroat trout subspecies using genome reduction, barcoding, and 454 pyro-sequencing.

BACKGROUND: Salmonids are popular sport fishes, and as such have been subjected to widespread stocking throughout western North America. Historically, stocking was done with little regard for genetic variation among populations and has resulted in genetic mixing among species and subspecies in many areas, thus putting the genetic integrity of native salmonid populations at risk and creating a need to assess the genetic constitution of native salmonid populations. Cutthroat trout is a salmonid species with pronounced geographic structure (there are 10 extant subspecies) and a recent history of hybridization with introduced rainbow trout in many populations. Genetic admixture has also occurred among cutthroat trout subspecies in areas where introductions have brought two or more subspecies into contact. Consequently, management agencies have increased their efforts to evaluate the genetic composition of cutthroat trout populations to identify populations that remain uncompromised and manage them accordingly, but additional genetic markers are needed to do so effectively. Here we used genome reduction, MID-barcoding, and 454-pyrosequencing to discover single nucleotide polymorphisms that differentiate cutthroat trout subspecies and can be used as a rapid, cost-effective method to characterize the genetic composition of cutthroat trout populations. RESULTS: Thirty cutthroat and six rainbow trout individuals were subjected to genome reduction and next-generation sequencing. A total of 1,499,670 reads averaging 379 base pairs in length were generated by 454-pyrosequencing, resulting in 569,060,077 total base pairs sequenced. A total of 43,558 putative SNPs were identified, and of those, 125 SNP primers were developed that successfully amplified 96 cutthroat trout and rainbow trout individuals. These SNP loci were able to differentiate most cutthroat trout subspecies using distance methods and Structure analyses. CONCLUSIONS: Genomic and bioinformatic protocols were successfully implemented to identify 125 nuclear SNPs that are capable of differentiating most subspecies of cutthroat trout from one another. The ability to use this suite of SNPs to identify individuals of unknown genetic background to subspecies can be a valuable tool for management agencies in their efforts to evaluate the genetic structure of cutthroat trout populations prior to constructing and implementing conservation plans.

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.

Complete mitochondrial genomes of two rockfish: Sebastes maliger and Sebastes norvegicus (Scorpaenidae, Scorpaeniformes).

We report the complete mitochondrial genomes of two rockfish: Sebastes maliger and Sebastes norvegicus. The mitogenomes consist of 13 protein-coding regions, 22 tRNAs, two rRNAs, and one control region. Sebastes mitogenome control regions are highly variable due to the presence of repeat sequences. The mitogenomes for S. maliger and S. norvegicus are 16,403 and 16,401 bp, respectively. Using these two mitogenomes and 25 additional Sebastes mitogenomes from GenBank, we examine the phylogenetic relationships in Sebastes. Sebastes maliger is sister to a clade including S. rubrivinctus, S. nigrocinctus, S. umbrosus, and S. oculatus, while S. norvegicus is sister to S. fasciatus.

A description of Echinorhynchus baeri Kostylew, 1928 (Acanthocephala: Echinorhynchidae) from Salmo trutta in Turkey, with notes on synonymy, geographical origins, geological history, molecular profile, and X-ray microanalysis.

A population of Echinorhynchus baeri Kostylew, 1928 with 18-24 rows of 8-10 proboscis hooks each and long fusiform eggs measuring 95-110 × 18-22 µm collected from Salmo trutta (Salmonidae) in a branch of the Murat River in Turkey is described and specimens are designated as neotype. Specimens of two similar populations of E. baeri (E. baeri Kostylew, 1928 and E. sevani Dinnik, 1932) were previously described from Salmo ischchan in Lake Sevan, Armenia. Waters of Lake Sevan and the Murat River were previously joined during the Middle Miocene-Pliocene. The two populations from Lake Sevan and ours from Turkey had identical morphology and size eggs. The proboscis armature and eggs, among other features of our Turkish specimens, proved intermediate between E. baeri and E. sevani, thus eliminating the significance of the described differences between these two species and confirming their synonymy with priority to Echinorhynchus baeri (junior synonym: Echinorhynchus sevani Dinnik, 1932). Echinorhynchus baeri is apparently a highly variable species. The two descriptions from Lake Sevan did not include features or illustrations of females, except for references to trunk and egg size but the eggs were illustrated. Complete morphometric comparisons are made and females of the Turkish material are described for the first time. DNA sequencing (mitochondrial cytochrome oxidase subunit I gene; nuclear 18S rRNA gene) results from two available E. baeri individuals were equivocal. New features to the Acanthocephala include the presence of rootless uncalcified apical proboscis hooks studied with X-ray microanalysis.

Pluvial Drainage Patterns and Holocene Desiccation Influenced the Genetic Architecture of Relict Dace, Relictus solitarius (Teleostei: Cyprinidae).

Changing drainage patterns have played a significant role in the evolution of western North American aquatic taxa. Relict dace, Relictus solitarius, is a Great Basin endemic cyprinid with a native range that is restricted to four valleys in eastern Nevada. Relictus solitarius now occupies spring systems that are the remnants of Pleistocene-era pluvial lakes, although it may have occurred in the area for much longer. Here we use mitochondrial DNA sequence data to assess range-wide genetic diversity of R. solitarius, and to estimate divergence times to determine whether pluvial drainages played an important role in shaping intraspecific genetic diversity. Genetic diversification within R. solitarius began during the early to mid-Pleistocene, separating populations within two sets of valleys (Butte/Ruby and Goshute/Steptoe). Additional diversification in each of the two sets of valleys occurred more recently, in the mid- to late-Pleistocene. Holocene desiccation has further isolated populations, and each population sampled contains unique mtDNA haplotypes. Pluvial drainage patterns did contribute to the genetic structure observed within R. solitarius, but most of the intraspecific diversification does not appear to be associated with the Last Glacial Maximum. Holocene desiccation has also contributed to the observed genetic structure. The relict dace populations we sampled are all unique, and we recommend that future management efforts should strive to preserve as much of the genetic diversity as possible.

Across the great divide: genetic forensics reveals misidentification of endangered cutthroat trout populations.

Accurate assessment of species identity is fundamental for conservation biology. Using molecular markers from the mitochondrial and nuclear genomes, we discovered that many putatively native populations of greenback cutthroat trout (Oncorhynchus clarkii stomias) comprised another subspecies of cutthroat trout, Colorado River cutthroat trout (Oncorhynchus clarkii pleuriticus). The error can be explained by the introduction of Colorado River cutthroat trout throughout the native range of greenback cutthroat trout in the late 19th and early 20th centuries by fish stocking activities. Our results suggest greenback cutthroat trout within its native range is at a higher risk of extinction than ever before despite conservation activities spanning more than two decades.