Diet and the evolution of ADH7 across seven orders of mammals.

Dietary variation within and across species drives the eco-evolutionary responsiveness of genes necessary to metabolize nutrients and other components. Recent evidence from humans and other mammals suggests that sugar-rich diets of floral nectar and ripe fruit have favoured mutations in, and functional preservation of, the ADH7 gene, which encodes the ADH class 4 enzyme responsible for metabolizing ethanol. Here we interrogate a large, comparative dataset of ADH7 gene sequence variation, including that underlying the amino acid residue located at the key site (294) that regulates the affinity of ADH7 for ethanol. Our analyses span 171 mammal species, including 59 newly sequenced. We report extensive variation, especially among frugivorous and nectarivorous bats, with potential for functional impact. We also report widespread variation in the retention and probable pseudogenization of ADH7. However, we find little statistical evidence of an overarching impact of dietary behaviour on putative ADH7 function or presence of derived alleles at site 294 across mammals, which suggests that the evolution of ADH7 is shaped by complex factors. Our study reports extensive new diversity in a gene of longstanding ecological interest, offers new sources of variation to be explored in functional assays in future study, and advances our understanding of the processes of molecular evolution.

Successional Changes of Microbial Communities and Host-Microbiota Interactions Contribute to Dietary Adaptation in Allodiploid Hybrid Fish.

Host-microbiota interactions play critical roles in host development, immunity, metabolism, and behavior. However, information regarding host-microbiota interactions is limited in fishes due to their complex living environment. In the present study, an allodiploid hybrid fish derived from herbivorous Megalobrama amblycephala (♀) × carnivorous Culter alburnus (♂) was used to investigate the successional changes of the microbial communities and host-microbiota interactions during herbivorous and carnivorous dietary adaptations. The growth level was not significantly different in any developmental stage between the two diet groups of fish. The diversity and composition of the dominant microbial communities showed similar successional patterns in the early developmental stages, but significantly changed during the two dietary adaptations. A large number of bacterial communities coexisted in all developmental stages, whereas the abundance of some genera associated with metabolism, including Acinetobacter, Gemmobacter, Microbacterium, Vibrio, and Aeromonas, was higher in either diet groups of fish. Moreover, the abundance of phylum Firmicutes, Actinobacteria, and Chloroflexi was positively correlated with the host growth level. In addition, Spearman's correlation analysis revealed that the differentially expressed homologous genes in the intestine associated with cell growth, immunity, and metabolism were related to the dominant gut microbiota. Our results present evidence that host genetics-gut microbiota interactions contribute to dietary adaptation in hybrid fish, which also provides basic data for understanding the diversity of dietary adaptations and evolution in fish.

An amateur gut microbial configuration formed in giant panda for striving to digest cellulose in bamboo: Systematic evidence from intestinal digestive enzymes, functional genes and microbial structures.

The giant panda has been considered to maximize nutritional intake including protein and soluble carbohydrates in bamboo, but it has spent almost entire life with the high-cellulose diet. Whether giant panda is still helpless about digesting bamboo cellulose or not is always contentious among many researchers around the world. The work has systematically clarified this issue from the perspectives of digestive enzymes, functional genes, and microbial structures in giant panda gut. The intestinal cellulase activities of panda increase with bamboo consumption, performing that the endoglucanase activity of adults reaches 10-fold that of pandas first consuming bamboo. More abundance and types of microbial endoglucanase genes occur in bamboo-diet giant panda gut, and the corresponding GH5 gene cluster is still efficiently transcribed. Gut microbes possessing cellulose-degrading genes, belong to the phylum Firmicutes and some Bacteroidetes, but their structural and functional configurations are insufficient to completely degrade cellulose. Therefore, giant panda is striving to digest cellulose in bamboo, but this adaptation is incomplete. This is probably related to the short straight carnivore-like gut structure of the giant panda, preventing the colonization of some efficient functional but anaerobic-preferred flora.

Host Species Influence the Gut Microbiota of Endemic Cold-Water Fish in Upper Yangtze River.

The fish gut microbiome plays an important role in nutrition absorption and energy metabolism. Studying the gut microbes of cold-water fish is important to understand the dietary adaptation strategies in extreme environments. In this study, the gut samples of Schizothorax wangchiachii (SW, herbivorous), Schizothorax kozlovi (SK, omnivorous), and Percocypris pingi (PP, carnivorous) in the upper Yangtze River were collected, and we sequenced 16S rRNA amplicon to study the potential relationship between gut microbes and host species. The results showed that gut microbial composition and diversity were significantly different between the three cold-water fishes. These fishes had different key taxa in their gut microbes, including bacteria involved in the breakdown of food (e.g., Cetobacterium, Aeromonas, and Clostridium sensu stricto 10). The highest alpha diversity indices (e.g., Chao 1 index) were identified in the herbivore (SW), followed by the carnivore (PP), and the lowest in the omnivore (SK). Non-metric multidimensional scaling (NMDS) results revealed that the gut microbial community of these species was different between host species. The neutral community model (NCM) showed that the microbial community structure of SW was shaped by stochastic processes, and the highest species dispersal was found in SW, followed by PP, and the lowest in SK. The results of niche breadth agreed with these findings. Our results demonstrated that host species influenced the gut microbiome composition, diversity, and microbial community assembly processes of the three cold-water fishes. These findings implied that the variation of gut microbiome composition and function plays a key role in digesting and absorbing nutrients from different foods in cold-water fish.

Food preference of nine-banded armadillo (Dasypus novemcinctus, Linnaeus, 1758) under human care.

This study aims to evaluate the food preference of nine banded armadillos kept in captivity, exposed to four different diets: Diet 1 (D1) - dry dog food and ground beef; Diet 2 (D2) - dry dog food, ground beef, and chicken eggs; Diet 3 (D3) - dog food, ground beef, bananas, and papaya; Diet 4 (D4) - dog food, ground beef, chicken eggs, banana, and papaya. To this end, an experiment was carried out for five weeks, the first four of which were for preliminary management and the fifth week for data collection. Frequency of consumption, total intake for each diet, and intake ratio were evaluated. The dietary preference was higher for the diets with a higher protein percentage (D1 and D2), mainly D2, which presented increased demand and intake starting on the fourth day of observation. In second day of observation, D1 presented the higher intake ratio, but D2 gradually replaced it. The diet containing the lowest protein rate (D3) was the least favored on all observation days and evaluations. In conclusion, the food preference of ex-situ armadillos seems to be related to the inclusion of greater amounts of protein, particularly that of animal origin, with eggs being the most appreciated ingredient in this study.

Trio-binned genomes of the woodrats Neotoma bryanti and Neotoma lepida reveal novel gene islands and rapid copy number evolution of xenobiotic metabolizing genes.

The genomic architecture underlying the origins and maintenance of biodiversity is an increasingly accessible feature of species, due in large part to third-generation sequencing and novel analytical toolsets. Applying these techniques to woodrats (Neotoma spp.) provides a unique opportunity to study how herbivores respond to environmental change. Neotoma bryanti and N. lepida independently achieved a major dietary feat in the aftermath of a natural climate change event: switching to the novel, toxic food source creosote bush (Larrea tridentata). To better understand the genetic mechanisms underlying this ability, we employed a trio binning sequencing approach with a N. bryanti × N. lepida F1 hybrid, allowing the simultaneous assembly of genomes representing each parental species. The resulting phased, chromosome-level, highly complete haploid references enabled us to explore the genomic architecture of several gene families-cytochromes P450, UDP-glucuronosyltransferases (UGTs), and ATP-binding cassette (ABC) transporters-known to play key roles in the metabolism of naturally occurring toxic dietary compounds. In addition to duplication events in the ABCG and UGT2B subfamilies, we found expansions in three P450 gene families (2A, 2B, 3A), including the evolution of multiple novel gene islands within the 2B and 3A subfamilies, which may have provided the crucial substrate for dietary adaptation. Our assemblies demonstrate that trio binning from an F1 hybrid rodent effectively recovers parental genomes from species that diverged more than a million years ago.

Food preference of nine-banded armadillo (Dasypus novemcinctus, Linnaeus, 1758) under human care

This study aims to evaluate the food preference of nine banded armadillos kept in captivity, exposed to four different diets: Diet 1 (D1) - dry dog food and ground beef; Diet 2 (D2) - dry dog food, ground beef, and chicken eggs; Diet 3 (D3) - dog food, ground beef, bananas, and papaya; Diet 4 (D4) - dog food, ground beef, chicken eggs, banana, and papaya. To this end, an experiment was carried out for five weeks, the first four of which were for preliminary management and the fifth week for data collection. Frequency of consumption, total intake for each diet, and intake ratio were evaluated. The dietary preference was higher for the diets with a higher protein percentage (D1 and D2), mainly D2, which presented increased demand and intake starting on the fourth day of observation. In second day of observation, D1 presented the higher intake ratio, but D2 gradually replaced it. The diet containing the lowest protein rate (D3) was the least favored on all observation days and evaluations. In conclusion, the food preference of ex-situ armadillos seems to be related to the inclusion of greater amounts of protein, particularly that of animal origin, with eggs being the most appreciated ingredient in this study.

Larvae of the Clothing Moth Tineola bisselliella Maintain Gut Bacteria that Secrete Enzyme Cocktails to Facilitate the Digestion of Keratin.

The evolutionary success of insects is promoted by their association with beneficial microbes that enable the utilization of unusual diets. The synanthropic clothing moth Tineola bisselliella provides an intriguing example of this phenomenon. The caterpillars of this species have adapted to feed on keratin-rich diets such as feathers and wool, which cannot be digested by most other animals and are resistant to common digestive enzymes. Inspired by the hypothesis that this ability may be conferred by symbiotic microbes, we utilized a simple assay to detect keratinase activity and a method to screen gut bacteria for candidate enzymes, which were isolated from feather-fed larvae. The isolation of DNA from keratin-degrading bacterial strains followed by de novo genome sequencing resulted in the identification of a novel bacterial strain related to Bacillus sp. FDAARGOS_235. Genome annotation identified 20 genes with keratinase domains. Proteomic analysis of the culture supernatant from this gut bacterium grown in non-nutrient buffer supplemented with feathers revealed several candidate enzymes potentially responsible for keratin degradation, including a thiol-disulfide oxidoreductase and multiple proteases. Our results suggest that the unusual diet of T. bisselliella larvae promotes their association with keratinolytic microorganisms and that the ability of larvae to feed on keratin can at least partially be attributed to bacteria that produce a cocktail of keratin-degrading enzymes.

TAS2R20 variants confer dietary adaptation to high-quercitrin bamboo leaves in Qinling giant pandas.

Sensitivity to bitter tastes provides animals with an important means of interacting with their environment and thus, influences their dietary preferences. Genetic variants encoding functionally distinct receptor types contribute to variation in bitter taste sensitivity. Our previous study showed that two nonsynonymous sites, A52V and Q296H, in the TAS2R20 gene are directionally selected in giant pandas from the Qinling Mountains, which are speculated to be the causative base-pair changes of Qinling pandas for the higher preference for bamboo leaves in comparison with other pandas. Here, we used functional expression in engineered cells to identify agonists of pTAS2R20 (i.e., giant panda's TAS2R20) and interrogated the differences in perception in the in vitro responses of pTAS2R20 variants to the agonists. Our results show that pTAS2R20 is specifically activated by quercitrin and that pTAS2R20 variants exhibit differences in the sensitivity of their response to the agonist. Compared with pTAS2R20 in pandas from other areas, the receptor variant with A52V and Q296H, which is most commonly found in Qinling pandas, confers a significantly decreased sensitivity to quercitrin. We subsequently quantified the quercitrin content of the leaves of bamboo distributed in the Qinling Mountains, which was found to be significantly higher than that of the leaves of bamboo from panda habitats in other areas. Our results suggest that the decreased sensitivity to quercitrin in Qinling pandas results in higher-quercitrin-containing bamboo leaves to be tasting less bitter to them and thus, influences their dietary preference. This study illustrates the genetic adaptation of Qinling pandas to their environments and provides a fine example of the functional effects of directional selection in the giant panda.

Diet-MEF2 interactions shape lipid droplet diversification in muscle to influence Drosophila lifespan.

The number, size, and composition of lipid droplets can be influenced by dietary changes that shift energy substrate availability. This diversification of lipid droplets can promote metabolic flexibility and shape cellular stress responses in unique tissues with distinctive metabolic roles. Using Drosophila, we uncovered a role for myocyte enhancer factor 2 (MEF2) in modulating diet-dependent lipid droplet diversification within adult striated muscle, impacting mortality rates. Muscle-specific attenuation of MEF2, whose chronic activation maintains glucose and mitochondrial homeostasis, leads to the accumulation of large, cholesterol ester-enriched intramuscular lipid droplets in response to high calorie, carbohydrate-sufficient diets. The diet-dependent accumulation of these lipid droplets also correlates with both enhanced stress protection in muscle and increases in organismal lifespan. Furthermore, MEF2 attenuation releases an antagonistic regulation of cell cycle gene expression programs, and up-regulation of Cyclin E is required for diet- and MEF2-dependent diversification of intramuscular lipid droplets. The integration of MEF2-regulated gene expression networks with dietary responses thus plays a critical role in shaping muscle metabolism and function, further influencing organismal lifespan. Together, these results highlight a potential protective role for intramuscular lipid droplets during dietary adaptation.

Genetic evidence of widespread variation in ethanol metabolism among mammals: revisiting the 'myth' of natural intoxication.

Humans have a long evolutionary relationship with ethanol, pre-dating anthropogenic sources, and possess unusually efficient ethanol metabolism, through a mutation that evolved in our last common ancestor with African great apes. Increased exposure to dietary ethanol through fermenting fruits and nectars is hypothesized to have selected for this in our lineage. Yet, other mammals have frugivorous and nectarivorous diets, raising the possibility of natural ethanol exposure and adaptation in other taxa. We conduct a comparative genetic analysis of alcohol dehydrogenase class IV (ADH IV) across mammals to provide insight into their evolutionary history with ethanol. We find genetic variation and multiple pseudogenization events in ADH IV, indicating the ability to metabolize ethanol is variable. We suggest that ADH enzymes are evolutionarily plastic and show promise for revealing dietary adaptation. We further highlight the derived condition of humans and draw attention to problems with modelling the physiological responses of other mammals on them, a practice that has led to potentially erroneous conclusions about the likelihood of natural intoxication in wild animals. It is a fallacy to assume that other animals share our metabolic adaptations, rather than taking into consideration each species' unique physiology.

Giant Pandas Are Macronutritional Carnivores.

Giant pandas are unusual in belonging to a primarily carnivorous clade and yet being extremely specialized herbivores that feed almost exclusively on highly fibrous bamboo [1]. Paradoxically, they appear inconsistently adapted to their plant diet, bearing a mix of herbivore and carnivore traits. Herbivore traits include a skull, jaw musculature, and dentition that are adapted for fibrous diets and a specialized "pseudo-thumb" used for handling bamboo [2, 3]. They have lost functional versions of the T1R1 gene codes for umami taste receptors, which are often associated with meat eating [3]. They also have an herbivore-like subcellular distribution of the metabolic enzyme alanine: glyoxylate aminotransferase [4]. But meanwhile, giant pandas have a digestive tract [5], digestive enzymes [6], and a gut microbiota composition that resemble those of carnivores and not of herbivores [6, 7]. We draw on recent developments in multi-dimensional niche theory [8] to examine this apparent paradox. We show that the pandas' diet clustered in a macronutrient space among carnivores and was distinct from that of herbivores. The similarity with carnivore diets applied not only to the ingested diet but also to the absorbed diet, with the absorbed macronutrient ratios similar to those of the ingested foods. Comparison of the macronutrient composition of pandas' milk with those of other species shows that the carnivore-like dietary macronutrient composition extends across the life cycle. These results cast new light on the seemingly incongruous constellation of dietary adaptations in pandas, suggesting that the transition from carnivorous and omnivorous ancestry to specialized herbivory might be less abrupt than it might otherwise appear.

Maximum Bony Gape in Primates.

Maximum jaw gape has important functional implications for behavior and feeding habits in primates. It has been suggested that gape is correlated to canine height and ingested food size. Extending these correlations to the fossil record would provide insights about the diets and/or social behavior of extinct primates. However, this can be problematic due to uncertainty about size and location of musculature, and it depends on reliability and repeatability of maximum gape estimation using only skeletal elements. In this study, maximum bony gape (MBG) was estimated using reliable landmarks and repeatable methods. The cranium was fixed in position and then the mandible was rotated and translated to the point immediately prior to loss of condyle-glenoid contact. Then it was photographed in a steady position using an adjustable wooden frame. This protocol allowed for photographs and linear measurements to be obtained for many museum specimens in a short time. The sample included 203 individuals, representing 42 species of primates. When scaled for body size, linear MBG correlates with maximum anesthetized gape (Hylander: Am J Phys Anthropol 150 (2013) 247-259), ingested food size (Perry and Hartstone-Rose: Am J Phys Anthropol 142 (2010) 625-635), and canine length but not condylar height. Anat Rec, 302:215-225, 2019. © 2018 Wiley Periodicals, Inc.

Lineage-specific evolution of bitter taste receptor genes in the giant and red pandas implies dietary adaptation.

Taste 2 receptors (TAS2R) mediate bitterness perception in mammals, thus are called bitter taste receptors. It is believed that these genes evolved in response to species-specific diets. The giant panda (Ailuropoda melanoleuca) and red panda (Ailurus fulgens styani) in the order Carnivora are specialized herbivores with an almost exclusive bamboo diet (>90% bamboo). Because bamboo is full of bitter tasting compounds, we hypothesized that adaptive evolution has occurred at TAS2R genes in giant and red pandas throughout the course of their dietary shift. Here, we characterized 195 TAS2R genes in 9 Carnivora species and examined selective pressures on these genes. We found that both pandas harbor more putative functional TAS2R genes than other carnivores, and pseudogenized TAS2R genes in the giant panda are different from the red panda. The purifying selection on TAS2R1, TAS2R9 and TAS2R38 in the giant panda, and TAS2R62 in the red panda, has been strengthened throughout the course of adaptation to bamboo diet, while selective constraint on TAS2R4 and TAS2R38 in the red panda is relaxed. Remarkably, a few positively selected sites on TAS2R42 have been specifically detected in the giant panda. These results suggest an adaptive response in both pandas to a dietary shift from carnivory to herbivory, and TAS2R genes evolved independently in the 2 pandas. Our findings provide new insight into the molecular basis of mammalian sensory evolution and the process of adaptation to new ecological niches.

Further morphological evidence on South African earliest Homo lower postcanine dentition: Enamel thickness and enamel dentine junction.

The appearance of the earliest members of the genus Homo in South Africa represents a key event in human evolution. Although enamel thickness and enamel dentine junction (EDJ) morphology preserve important information about hominin systematics and dietary adaptation, these features have not been sufficiently studied with regard to early Homo. We used micro-CT to compare enamel thickness and EDJ morphology among the mandibular postcanine dentitions of South African early hominins (N = 30) and extant Homo sapiens (N = 26), with special reference to early members of the genus Homo. We found that South African early Homo shows a similar enamel thickness distribution pattern to modern humans, although three-dimensional average and relative enamel thicknesses do not distinguish australopiths, early Homo, and modern humans particularly well. Based on enamel thickness distributions, our study suggests that a dietary shift occurred between australopiths and the origin of the Homo lineage. We also observed that South African early Homo postcanine EDJ combined primitive traits seen in australopith molars with derived features observed in modern human premolars. Our results confirm that some dental morphological patterns in later Homo actually occurred early in the Homo lineage, and highlight the taxonomic value of premolar EDJ morphology in hominin species.

Long-term feeding a plant-based diet devoid of marine ingredients strongly affects certain key metabolic enzymes in the rainbow trout liver.

Incorporation of a plant blend in the diet can affect growth parameters and metabolism in carnivorous fish. We studied for the first time the long-term (1 year) metabolic response of rainbow trout fed from first feeding with a plant-based diet totally devoid of marine ingredients. Hepatic enzymes were analyzed at enzymatic and molecular levels, at 3, 8 and 24 h after the last meal to study both the short-term effects of the last meal and long-term effects of the diet. The results were compared with those of fish fed a control diet of fish meal and fish oil. Growth, feed intake, feed efficiency and protein retention were lower in the group fed the plant-based diet. Glucokinase and pyruvate kinase activity were lower in the livers of trout fed the plant-based diet which the proportion of starch was lower than in the control diet. Glutamate dehydrogenase was induced by the plant-based diet, suggesting an imbalance of amino acids and a possible link with the lower protein retention observed. Gene expression of delta 6 desaturase was higher in fish fed the plant-based diet, probably linked to a high dietary level of linolenic acid and the absence of long-chain polyunsaturated fatty acids in vegetable oils. Hydroxymethylglutaryl-CoA synthase expression was also induced by plant-based diet because of the low rate of cholesterol in the diet. Changes in regulation mechanisms already identified through short-term nutritional experiments (<12 weeks) suggest that metabolic responses are implemented at short term and remain in the long term.

Form and function in the platyrrhine skull: a three-dimensional analysis of dental and TMJ morphology.

Cranial and temporomandibular joint (TMJ) form has been shown to reflect masticatory forces and mandibular range of motion, which vary in relation to feeding strategy. Similarly, the dentition, as the portion of the masticatory apparatus most directly involved in triturating food items, strongly reflects dietary profile. Fine control over condylar and mandibular movements guides the teeth into occlusion, while the topography and position of the dental arcade mediate mandibular movements. We hypothesize that masticatory, and particularly TMJ, morphology and dental form covary in predictable ways with one another and with diet. We employed three-dimensional geometric morphometric techniques to examine inter-specific variation in ten platyrrhine species. Landmarks were collected on six datasets describing the upper and lower molars, cranium, glenoid fossa, mandible, and mandibular condyle; two-block partial least squares analyses were performed to assess covariation between cranial morphology, dentition, and diet. Significant relationships were identified between the molars and the cranium, mandible, and glenoid fossa. Some of these shape complexes reflect feeding strategy; for example, higher crowned/cusped dentitions, as found in primates consuming larger quantities of structural carbohydrates (e.g., Alouatta and Saimiri), correspond to anteroposterior longer and deeper glenoid fossae. These results indicate strong covariance between dental and TMJ form, aspects of which are related to feeding behavior. However, other aspects of morphological variation display a strong phylogenetic signal; we must therefore examine further ways in which to control for phylogeny when examining covariation in interspecific masticatory form.

Short-term adaptation of the ruminal epithelium involves abrupt changes in sodium and short-chain fatty acid transport.

The objectives of this study were to determine the effect of an increase in diet fermentability on 1) the rate and extent to which short-chain fatty acid (SCFA) absorption pathways adapt relative to changes in Na(+) transport, 2) the epithelial surface area (SA), and 3) the barrier function of the bovine ruminal epithelium. Twenty-five Holstein steer calves were assigned to either the control diet (CON; 91.5% hay and 8.5% supplement) or a moderately fermentable diet (50% hay; 41.5% barley grain (G), and 8.5% supplement) fed for 3 (G3), 7 (G7), 14 (G14), or 21 days (G21). All calves were fed at 2.25% body weight at 0800. Calves were killed (at 1000), and ruminal tissue was collected to determine the rate and pathway of SCFA transport, Na(+) transport and barrier function in Ussing chambers. Tissue was also collected for SA measurement and gene expression. Mean reticular pH decreased from 6.90 for CON to 6.59 for G7 and then increased (quadratic P < 0.001). While effective SA of the ruminal epithelium was not affected (P > 0.10) by dietary treatment, the net Na(+) flux increased by 125% within 7 days (quadratic P = 0.016). Total acetate and butyrate flux increased from CON to G21, where passive diffusion was the primary SCFA absorption pathway affected. Increased mannitol flux, tissue conductance, and tendencies for increased expression of IL-1ß and TLR2 indicated reduced rumen epithelium barrier function. This study indicates that an increase in diet fermentability acutely increases Na(+) and SCFA absorption in the absence of increased SA, but reduces barrier function.