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Digestion is driven by digestive enzymes and digestive enzyme gene copy number can provide insights on the genomic underpinnings of dietary specialization. The “Adaptive Modulation Hypothesis” (AMH) proposes that digestive enzyme activity, which increases with increased gene copy number, should correlate with substrate quantity in the diet. To test the AMH and reveal some of the genetics of herbivory vs carnivory, we sequenced, assembled, and annotated the genome ofAnoplarchus purpurescens, a carnivorous prickleback fish in the family Stichaeidae, and compared the gene copy number for key digestive enzymes to that ofCebidichthys violaceus, a herbivorous fish from the same family. A highly contiguous genome assembly of high quality (N50 = 10.6 Mb) was produced forA. purpurescens, using combined long-read and short-read technology, with an estimated 33,842 protein-coding genes. The digestive enzymes that we examined include pancreatic α-amylase, carboxyl ester lipase, alanyl aminopeptidase, trypsin, and chymotrypsin.Anoplarchus purpurescenshad fewer copies of pancreatic α-amylase (carbohydrate digestion) thanC. violaceus(1 vs. 3 copies). Moreover, A. purpurescenshad one fewer copy of carboxyl ester lipase (plant lipid digestion) thanC. violaceus(4 vs. 5). We observed an expansion in copy number for several protein digestion genes inA. purpurescenscompared toC. violaceus, including trypsin (5 vs. 3) and total aminopeptidases (6 vs. 5). Collectively, these genomic differences coincide with measured digestive enzyme activities (phenotypes) in the two species and they support the AMH. Moreover, this genomic resource is now available to better understand fish biology and dietary specialization.

 

Beyond a few obvious examples (e.g., gut length, amylase activity), digestive and metabolic specializations towards diet remain elusive in fishes. Thus, we compared gut length, δ¹³C and δ¹⁵N signatures of the liver, and expressed genes in the intestine and liver of wild-caught individuals of four closely-related, sympatric prickleback species (family Stichaeidae) with different diets:Xiphister mucosus(herbivore), its sister taxonX. atropurpureus(omnivore),Phytichthys chirus(omnivore) and the carnivorousAnoplarchus purpurescens. We also measured the same parameters after feeding them carnivore or omnivore diets in the laboratory for 4 weeks. Growth and isotopic signatures showed assimilation of the laboratory diets, and gut length was significantly longer inX. mucosusin comparison to the other fishes, whether in the wild, or in the lab consuming the different diets. Dozens of genes relating to digestion and metabolism were observed to be under selection in the various species, butP. chirusstood out with some genes in the liver showing strong positive selection, and these genes correlating with differing isotopic incorporation of the laboratory carnivore diet in this species. Although the intestine showed variation in the expression of hundreds of genes in response to the laboratory diets, the liver exhibited species-specific gene expression patterns that changed very little (generally <40 genes changing expression, withP. chirusproviding an exception). Overall, our results suggest that the intestine is plastic in function, but the liver may be where specialization manifests since this tissue shows species-specific gene expression patterns that match with natural diet.

 

Looking to nature for inspiration has led to many diverse technological advances. The spiral valve intestine of sharks has provided the opportunity to observe the efficiency of different valve systems. It is supposed that the spiral intestine present in sharks, skates and rays slows the transit rate of digesta through the gut and provides increased surface area for the absorption of nutrients. In this investigation, we use a novel technique—creating three-dimensional reconstructions from CT scans of spiral intestines—to describe the morphology of the spiral intestine of at least one species from 22 different shark families. We discuss the morphological data in an evolutionary, dietary and functional context. The evolutionary analyses suggest that the columnar morphology is the ancestral form of the spiral intestine. Dietary analyses reveal no correlation between diet type and spiral intestine morphology. Flow rate was slowed significantly more when the two funnel-shaped spiral intestines were subjected to flow in the posterior to anterior direction, indicating their success at producing unidirectional flow, similar to a Tesla valve. These data are available to generate additional three-dimensional morphometrics, create computational models of the intestine, as well as to further explore the function of the gastrointestinal tract of sharks in structural and physiological contexts. 

Neotropical wood‐eating catfishes (family Loricariidae) can occur in diverse assemblages with multiple genera and species feeding on the same woody detritus. As such, they present an intriguing system in which to examine the influence of host species identity on the vertebrate gut microbiome as well as to determine the potential role of gut bacteria in wood digestion. We characterized the gut microbiome of two co‐occurring catfish genera and four species: Panaqolus albomaculatus , Panaqolus gnomus , Panaqolus nocturnus, and Panaque bathyphilus , as well as that of submerged wood on which they feed. The gut bacterial community did not significantly vary across three gut regions (proximal, mid, distal) for any catfish species, although interspecific variation in the gut microbiome was significant, with magnitude of interspecific difference generally reflecting host phylogenetic proximity. Further, the gut microbiome of each species was significantly different to that present on the submerged wood. Inferring the genomic potential of the gut microbiome revealed that the majority of wood digesting pathways were at best equivalent to and more often depleted or nonexistent within the catfish gut compared to the submerged wood, suggesting a minimal role for the gut microbiome in wood digestion. Rather, these fishes are more likely reliant on fiber degradation performed by microbes in the environment, with their gut microbiome determined more by host identity and phylogenetic history. 

The herbivorous fishCatostomus santaanaeis a federally “threatened” freshwater fish species endemic to southern California and is the centre of legal battles over water use. Because little is known about the nutritional ecology of this species, we investigated the nutritional physiology ofC. santaanaeto better understand their dietary and energetic needs with the goal of generating data useful in conservation efforts. Individuals ofC. santaanaewere raised for six weeks on an algal diet in the laboratory. They digested approximately 45%, 55% and 80% of protein, soluble carbohydrate and lipid, respectively, from the algal diet. Their metabolic rate (~0.0024 mg O₂min⁻¹ g⁻¹) suggested they would need to eat more than their body mass per day of an algal diet to thrive. Digestive enzyme activities of the laboratory‐reared and wild‐caught fish showed patterns typical of a “plug‐flow reactor” gut with high intake and rapid gut transit. However, lipase activities remained elevated throughout the gut, and this result, coupled with the lipid digestibility data, and evidence of feeding selectivity on specific diatom taxa in nature, suggests thatC. santaanaetargets diatoms as it grazes and that diatom lipid may be crucial to their survival. Our data set provides parameters that can be used in conservation modelling efforts towards habitat restoration.

 

Apparent egg cannibalism was investigated in the beach‐spawning California grunionLeuresthes tenuis. Three hypotheses were tested to determine whetherL. tenuisregularly consumes and efficiently digests conspecific eggs. First, examination of the gut contents of adults collected at four spawning sites over two seasons showed that the intestines of most fish from all the sites (57–87%,n≥ 30, each site) containedL. tenuiseggs. The two other hypotheses focused on digestion of the eggs. First, the force required to crush cannibalized eggs was significantly less than that for uncannibalized eggs (fertilized or unfertilized), indicating that ingestion weakens the egg chorions. Second, conspecific eggs fed to fish held in the laboratory visibly degraded as they passed through the gut. The eggs lostc. half of their protein content and about two‐thirds of their lipid content as they passed from proximal to distal regions of the gut, indicating that digestion occurred. Digestive enzyme activities of the gut further confirmed thatL. tenuiscan break down the contents of ingested eggs. Trypsin activity decreased and aminopeptidase activity increased posteriorly along the gut, whereas amylase and lipase activities exhibited less clear patterns by gut region. As far as is known, this study is the first to show thatL. tenuisis an egg cannibal.