Phylogenetic perspective on the relationships and evolutionary history of the Acipenseriformes

Metabolomics in sturgeon research: a mini-review

Sturgeons are ancient fish, with 27 species distributed in the Northern Hemisphere. This review first touches upon the significance of sturgeons in the context of their biological, ecological, and economic importance, highlighting their status as "living fossils" and the challenges they face in genomic research due to their diverse chromosome numbers. This review then discusses how omics technologies (genomics, transcriptomics, proteomics, and metabolomics) have been used in sturgeon research, which so far has only been done on Acipenser species. It focuses on metabolomics as a way to better understand how sturgeons work and how they react to their environment. Specific studies in sturgeon metabolomics are cited, showing how metabolomics has been used to investigate various aspects of sturgeon biology, such as growth, reproduction, stress responses, and nutrition. These studies demonstrate the potential of metabolomics in improving sturgeon aquaculture practices and conservation efforts. Overall, the review suggests that metabolomics, as a relatively new scientific tool, has the potential to enhance our understanding of sturgeon biology and aid in their conservation and sustainable aquaculture, contributing to global food security efforts.

True grit? Comparative anatomy and evolution of gizzards in fishes

Gut morphology frequently reflects the food organisms digest. Gizzards are organs of the gut found in archosaurs and fishes that mechanically reduce food to aid digestion. Gizzards are thought to compensate for edentulism and/or provide an advantage when consuming small, tough food items (e.g., phytoplankton and algae). It is unknown how widespread gizzards are in fishes and how similar these structures are among different lineages. Here, we investigate the distribution of gizzards across bony fishes to (1) survey different fishes for gizzard presence, (2) compare the histological structure of gizzards in three species, (3) estimate how often gizzards have evolved in fishes, and (4) explore whether anatomical and ecological traits like edentulism and microphagy predict gizzard presence. According to our analyses, gizzards are rare across bony fishes, evolving only six times in a broad taxonomic sampling of 51 species, and gizzard presence is not clearly correlated with factors like gut length or dentition. We find that gizzard morphology varies among the lineages where one is present, both macroscopically (presence of a crop) and microscopically (varying tissue types). We conclude that gizzards likely aid in the mechanical reduction of food in fishes that have lost an oral dentition in their evolutionary past; however, the relative scarcity of gizzards suggests they are just one of many possible solutions for processing tough, nutrient-poor food items. Gizzards have long been present in the evolutionary history of fishes, can be found in a wide variety of marine and freshwater clades, and likely have been overlooked in many taxa.

Distribution of gamma-aminobutyric acid immunoreactivity in the brain of the Siberian sturgeon (Acipenser baeri): Comparison with other fishes

Gamma-aminobutyric acid (GABA) is the main inhibitory neurotransmitter in the central nervous system (CNS) of vertebrates. Immunohistochemical techniques with specific antibodies against GABA or against its synthesizing enzyme, glutamic acid decarboxylase (GAD) allowed characterizing GABAergic neurons and fibers in the CNS. However, studies on the CNS distribution of GABAergic neurons and fibers of bony fishes are scant and were done in teleost species. With the aim of understanding the early evolution of this system in bony vertebrates, we analyzed the distribution of GABA-immunoreactive (-ir) and GAD-ir neurons and fibers in the CNS of a basal ray-finned fish, the Siberian sturgeon (Chondrostei, Acipenseriformes), using immunohistochemical techniques. Our results revealed the presence and distribution of GABA/GAD-ir cells in different regions of the CNS such as olfactory bulbs, pallium and subpallium, hypothalamus, thalamus, pretectum, optic tectum, tegmentum, cerebellum, central grey, octavolateralis area, vagal lobe, rhombencephalic reticular areas, and the spinal cord. Abundant GABAergic innervation was observed in most brain regions, and GABAergic fibers were very abundant in the hypothalamic floor along the hypothalamo-hypophyseal tract and neurohypophysis. In addition, GABA-ir cerebrospinal fluid-contacting cells were observed in the alar and basal hypothalamus, saccus vasculosus, and spinal cord central canal. The distribution of GABAergic systems in the sturgeon brain shows numerous similarities to that observed in lampreys, but also to those of teleosts and tetrapods.

Cadmium-109 Internal Kinetics in Diamond Sturgeon Acipenser gueldenstaedtii are Strongly Influenced by Salinity, Exposure Pathway and History

Cadmium-109 whole-body and internal biokinetics were experimentally investigated in critically endangered diamond sturgeon Acipenser gueldenstaedtii after uptake from water or food, in fresh (FW) and brackish (BW; 9‰) salinities typical of the Caspian Sea. Whole-body rates of uptake of 109Cd from water and subsequent depuration were quantified over 14 and 28 days, respectively. Uptake was greater in FW than BW by a factor of 2.4, but depuration rates were similar in both salinities. In contrast, for the dietary (chironomid) exposure pathway 109Cd assimilation efficiencies (AEs) were higher in BW (13%) compared to FW (9.5%). Head (including gills) or digestive tract were major repositories of 109Cd following aqueous and dietary exposures, respectively, including both uptake and depuration phases. The point-of-entry of 109Cd into the body was also a major and persistent determiner of its subsequent internal distribution. For aqueous exposures, the internal distributions of 109Cd changed appreciably during depuration with increased activity concentrations in some body components, which again varied with salinity. Increased salinity appreciably enhanced the percentage distributions and activity concentrations of 109Cd in the liver, kidney and digestive tract, which are typically most pathologically altered by elevated Cd exposure. For dietary exposure, increased salinity also enhanced 109Cd activity concentrations in most body components. The results repeatedly indicate the important role of salinity in the whole-body and internal biokinetics of 109Cd in A. gueldenstaedtii, a representative of both a phylogenetically distinct and most endangered family of fishes.

Characterization of the mitochondrial Huso huso genome and new aspects of its organization in the presence of tandem repeats in 12S rRNA

BACKGROUND

The sturgeon group has been economically significant worldwide due to caviar production. Sturgeons consist of 27 species in the world. Mitogenome data could be used to infer genetic diversity and investigate the evolutionary history of sturgeons. A limited number of complete mitogenomes in this family were sequenced. Here, we annotated the mitochondrial Huso huso genome, which revealed new aspects of this species.

RESULTS

In this species, the mitochondrial genome consisted of 13 genes encoding proteins, 22tRNA and 2rRNA, and two non-coding regions that followed other vertebrates. In addition, H. huso had a pseudo-tRNA-Glu between ND6 and Cytb and a 52-nucleotide tandem repeat with two replications in 12S rRNA. This duplication event is probably related to the slipped strand during replication, which could remain in the strand due to mispairing during replication. Furthermore, an 82 bp repeat sequence with three replications was observed in the D-loop control region, which is usually visible in different species. Regulatory elements were also seen in the control region of the mitochondrial genome, which included termination sequences and conserved regulatory blocks. Genomic compounds showed the highest conservation in rRNA and tRNA, while protein-encoded genes and nonencoded regions had the highest divergence. The mitochondrial genome was phylogenetically assayed using 12 protein-encoding genes.

CONCLUSIONS

In H. huso sequencing, we identified a distinct genome organization relative to other species that have never been reported. In recent years, along with the advancement in sequencing identified more genome rearrangements. However, it is an essential aspect of researching the evolution of the mitochondrial genome that needs to be recognized.

Comparison of metabolic rate between two genetically distinct populations of lake sturgeon

Environmental temperatures differ across latitudes in the temperate zone, with relatively lower summer and fall temperatures in the north leading to a shorter growing season prior to winter. As an adaptive response, during early life stages, fish in northern latitudes may grow faster than their conspecifics in southern latitudes, which potentially manifests as different allometric relationships between body mass and metabolic rate. In the present study, we examined if population or year class had an effect on the variation of metabolic rate and metabolic scaling of age-0 lake sturgeon (Acipenser fulvescens) by examining these traits in both a northern (Nelson River) and a southern (Winnipeg River) population. We compiled 6 years of data that used intermittent flow respirometry to measure metabolic rate within the first year of life for developing sturgeon that were raised in the same environment at 16°C. We then used a Bayesian modeling approach to examine the impacts of population and year class on metabolic rate and mass-scaling of metabolic rate. Despite previous reports of genetic differences between populations, our results showed that there were no significant differences in standard metabolic rate, routine metabolic rate, maximum metabolic rate, and metabolic scaling between the two geographically separated populations at a temperature of 16°C. Our analysis implied that the lack of metabolic differences between populations could be due to family effects/parental contribution, or the rearing temperature used in the study. The present research provided insights for conservation and reintroduction strategies for these populations of lake sturgeon, which are endangered or threatened across most of their natural range.

A New Sturgeon Herpesvirus from Juvenile Lake Sturgeon Acipenser fulvescens Displaying Epithelial Skin Lesions

Herpesvirus infections of sturgeon pose a potential threat to sturgeon culture efforts worldwide. A new epitheliotropic herpesvirus named Acipenser herpesvirus 3 (AciHV-3) was detected in hatchery-reared Lake Sturgeon Acipenser fulvescens displaying skin lesions in central Canada. The growths were discovered in the fall, reached average prevalence levels of 0.2-40% and eventually regressed. No unusual mortality was observed. The cellular changes within the lesions included epithelial hyperplasia and were reminiscent of other herpesvirus infections. The virus was not evident in lesions examined by electron microscopy. Skin tissue homogenates from symptomatic sturgeon produced atypical cytopathic effects on a primary Lake Sturgeon cell line, and next-generation sequence analysis of the DNA samples revealed the presence of an alloherpesvirus. A new genotyping PCR assay targeting the major capsid protein sequence detected AciHV-3 in symptomatic Lake Sturgeon as well as other apparently healthy sturgeon species. Bayesian inference of phylogeny reconstructed with a concatenation of five alloherpesvirus core proteins revealed a new Alloherpesviridae lineage isomorphic with a new genus. The presence of AciHV-3 homologs in cell lines and sturgeon sequence datasets, low sequence divergence among these homologs and branching patterns within the genotyping phylogeny provide preliminary evidence of an endogenous virus lifestyle established in an ancestral sturgeon.

Tissue-specific transcriptomes reveal potential mechanisms of microbiome heterogeneity in an ancient fish

The lake sturgeon (Acipenser fulvescens) is an ancient, octoploid fish faced with conservation challenges across its range in North America, but a lack of genomic resources has hindered molecular research in the species. To support such research, we created a transcriptomic database from 13 tissues: brain, esophagus, gill, head kidney, heart, white muscle, liver, glandular stomach, muscular stomach, anterior intestine, pyloric cecum, spiral valve and rectum. The transcriptomes for each tissue were sequenced and assembled individually from a mean of 98.3 million (±38.9 million SD) reads each. In addition, an overall transcriptome was assembled and annotated with all data used for each tissue-specific transcriptome. All assembled transcriptomes and their annotations were made publicly available as a scientific resource. The non-gut transcriptomes provide important resources for many research avenues. However, we focused our analysis on messenger ribonucleic acid (mRNA) observations in the gut because the gut represents a compartmentalized organ system with compartmentalized functions, and seven of the sequenced tissues were from each of these portions. These gut-specific analyses were used to probe evidence of microbiome regulation by studying heterogeneity in microbial genes and genera identified from mRNA annotations. Gene set enrichment analyses were used to reveal the presence of photoperiod and circadian-related transcripts in the pyloric cecum, which may support periodicity in lake sturgeon digestion. Similar analyses were used to identify different types of innate immune regulation across the gut, while analyses of unique transcripts annotated to microbes revealed heterogeneous genera and genes among different gut tissues. The present results provide a scientific resource and information about the mechanisms of compartmentalized function across gut tissues in a phylogenetically ancient vertebrate. Database URL: https://figshare.com/projects/Lake_Sturgeon_Transcriptomes/133143.

Conservation Genetics of Lake Sturgeon (Acipenser fulvescens): Nuclear Phylogeography Drives Contemporary Patterns of Genetic Structure and Diversity

Sustainable management of exploited and endangered species is facilitated by knowledge of their geographic genetic structure. Lake sturgeon (Acipenser fulvescens) epitomizes both categories, but genetic information has largely been limited to the Laurentian Great Lakes basin. We assessed the hierarchical geographic genetic structure of lake sturgeon across their Canadian range using a variation at 14 microsatellite loci. Observed patterns showed evidence of two ancestral groups which originated from Mississippian and Missourian glacial refugia. Coalescent analysis indicates the two lineages most recently shared common ancestry during the late Pleistocene and were likely isolated by the late Wisconsinan ice advance, with subsequent interpopulation divergences within each lineage reflecting their reciprocal isolation as glacial meltwaters receded. Hierarchical patterns of genetic relationships among contemporary populations largely reflect colonization histories and connections within primary and secondary watersheds. Populations in western Canada showed strong similarities based on their shared Missourian origins and colonization from glacial Lake Agassiz. By contrast, populations in the Great Lakes–St. Lawrence River drainage were largely founded from a Mississippian source. Sturgeon populations in northern parts of Ontario and Quebec showed evidence of mixed ancestry from secondary contact between the two refugial groups through Holocene meltwater lakes. Within major watersheds, the strong similarity among geographically separate populations reflects their shared ancestry during postglacial colonization. The general lack of structure within major river systems highlights historically continuous habitat (connectivity) and gene flow rather than contemporary barriers (dams). These data highlight the importance of Quaternary and prehistoric events on patterns of genetic diversity and divergence within and among contemporary populations, as well as the importance of these populations for conserving the species’ evolutionary legacy.

Mitochondrial genomic characterization of two endemic Chinese freshwater crabs of the genus Sinopotamon (Brachyura: Potamidae) and implications for biogeography analysis of Potamidae

As an endemic freshwater crab group in China, the phylogenetic relationships within Sinopotamon are still controversial because of the limited taxon samples. In this study, the complete mitogenomes of Sinopotamon chishuiense with 17,311 bp and the nearly complete mitogenomes of S. wushanense with 16,785 bp were firstly sequenced and analyzed. Compared with other reported mitogenomes of Potamidae, some novel patterns of gene rearrangement were detected in these two Sinopotamon mitogenomes, which could be illuminated by the mechanisms of tandem duplication-random loss, recombination, and translocation. Phylogenetic analyses showed the nonmonophyly of the Sinopotamon and a sister group relationship with Tenuilapotamon. These crabs from the eastern and southern of the Yangtze River basin were more closely related while other crabs form the plateau areas formed a separate clade. Divergence time indicated that the Sinopotamon and its sister group Tenuilapotamon diverged from other potamiscine freshwater crabs approximately 42.65 Mya, which belongs to the recent main uplifts period of the Tibetan Plateau in the Late Miocene. Combined with the similar evolutionary rates and relatively stable habitat altitude of these Sinopotamon species, these results implied that the ecological environment may be relatively stable during the speciation. Overall, our study yielded worthy perceptions for the evolutionary and taxonomic relationship of Sinopotamon and will help to better clarify the gene rearrangement events of the invertebrate mitogenome and lay the foundation for further phylogenetic study of Sinopotamon. Overall, our study yielded valuable insights into the evolutionary history and taxonomic relationship of Sinopotamon and these results will help to better explain the gene rearrangement events of the invertebrate mitogenome and lay the foundation for further phylogenetic study of Sinopotamon.

Mitochondrial characteristics of Pseudohynobius flavomaculatus a protected salamander in China, and biogeographical implications for the family Hynobiidae (Amphibia, Caudata)

Pseudohynobius flavomaculatus a provincially-protected salamander species, inhabits mountainous areas of Chongqing and surrounding provinces in China. In the present study, the complete mitochondrial genome of P. flavomaculatus was sequenced and analyzed. The mitogenome is 16,401 bp in length and consisted of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a control region. We performed a novel phylogenetic analysis, which demonstrated a sister relationship between P. flavomaculatus and P. jinfo. The 95% confidence interval around our new divergence date estimate suggest that Hynobiidae originated at 101.62–119.84 (mean=110.87) Ma. Species within Hynobiidae diverged successively in the Cenozoic era, and hynobiid speciation coincides primarily with geologic events. Our biogeographical inference demonstrates that nearly all early hynobiids divergences correspond to geological estimates of orogeny, which may have contributed to the notably high dN/dS ratio in this clade. We conclude that orogeny is likely a primary, dynamic factor, which may have repeatedly initiated the process of speciation in the family Hynobiidae.

About the Origin of the Family Allocreadiidae (Trematoda: Plagiorchiida)

The phylogenetic relationships established in the family Allocreadiidae by genetic methods suggest that the center of origin, distribution, and divergence of the studied family is, apparently, eastern regions of Laurasia (the territory of the modern Southeast Asia), from where these trematodes penetrated through the Amur paleomicrocontinent and Beringia to North America and further through Central America to South, as well as through Transbaikalia and Yakutia to the western part of Eurasia.

Novel mitochondrial gene rearrangements pattern in the millipede Polydesmus sp. GZCS-2019 and phylogenetic analysis of the Myriapoda

The subphylum Myriapoda included four extant classes (Chilopoda, Symphyla, Diplopoda, and Pauropoda). Due to the limitation of taxon sampling, the phylogenetic relationships within Myriapoda remained contentious, especially for Diplopoda. Herein, we determined the complete mitochondrial genome of Polydesmus sp. GZCS-2019 (Myriapoda: Polydesmida) and the mitochondrial genomes are circular molecules of 15,036 bp, with all genes encoded on + strand. The A+T content is 66.1%, making the chain asymmetric, and exhibits negative AT-skew (-0.236). Several genes rearrangements were detected and we propose a new rearrangement model: "TD (N\R) L + C" based on the genome-scale duplication + (non-random/random) loss + recombination. Phylogenetic analyses demonstrated that Chilopoda and Symphyla both were monophyletic group, whereas Pauropoda was embedded in Diplopoda to form the Dignatha. Divergence time showed the first split of Myriapoda occurred between the Chilopoda and other classes (Wenlock period of Silurian). We combine phylogenetic analysis, divergence time, and gene arrangement to yield valuable insights into the evolutionary history and classification relationship of Myriapoda and these results support a monophyletic Progoneata and the relationship (Chilopoda + (Symphyla + (Diplopoda + Pauropoda))) within myriapod. Our results help to better explain the gene rearrangement events of the invertebrate mitogenome and lay the foundation for further phylogenetic study of Myriapoda.

Analysis of Islet-1, Nkx2.1, Pax6, and Orthopedia in the forebrain of the sturgeon Acipenser ruthenus identifies conserved prosomeric characteristics

The distribution patterns of a set of conserved brain developmental regulatory transcription factors were analyzed in the forebrain of the basal actinopterygian fish Acipenser ruthenus, consistent with the prosomeric model. In the telencephalon, the pallium was characterized by ventricular expression of Pax6. In the subpallium, the combined expression of Nkx2.1/Islet-1 (Isl1) allowed to propose ventral and dorsal areas, as the septo-pallidal (Nkx2.1/Isl1+) and striatal derivatives (Isl1+), respectively, and a dorsal portion of the striatal derivatives, ventricularly rich in Pax6 and devoid of Isl1 expression. Dispersed Orthopedia (Otp) cells were found in the supracommissural and posterior nuclei of the ventral telencephalon, related to the medial portion of the amygdaloid complex. The preoptic area was identified by the Nkx2.1/Isl1 expression. In the alar hypothalamus, an Otp-expressing territory, lacking Nkx2.1/Isl1, was identified as the paraventricular domain. The adjacent subparaventricular domain (Spa) was subdivided in a rostral territory expressing Nkx2.1 and an Isl1+ caudal one. In the basal hypothalamus, the tuberal region was defined by the Nkx2.1/Isl1 expression and a rostral Otp-expressing domain was identified. Moreover, the Otp/Nkx2.1 combination showed an additional zone lacking Isl1, tentatively identified as the mamillary area. In the diencephalon, both Pax6 and Isl1 defined the prethalamic domain, and within the basal prosomere 3, scattered Pax6- and Isl1-expressing cells were observed in the posterior tubercle. Finally, a small group of Pax6 cells was observed in the pretectal area. These results improve the understanding of the forebrain evolution and demonstrate that its basic bauplan is present very early in the vertebrate lineage.