Why is Everyone on a Diet?
Have you ever wondered why some animals only eat meat? or plants? Imagine only eating salads, or raw antelope meat, for the rest of your life! The explanation for why animals have acquired particular diets is simple: evolution.
A recent study conducted by Nikolai Hecker, Virag Sharma and Michael Hiller has uncovered more supporting evidence for Darwin’s Theory of Evolution. Their paper, Convergent gene losses illuminate metabolic and physiological changes in herbivores and carnivores, sought to determine the molecular causes for diet specification in mammals. Darwin’s third postulate states, “Some individuals are more successful at surviving and reproducing than others” (Freeman et al. 77, 2014). Convergent evolution of certain traits can be explained by this postulate and the trends are consistent with the Theory of Evolution by Natural Selection. The acquired gene losses observed, and the respective specialized diets paint a picture of how repeated evolution of diets and other seemingly unrelated adaptations came to rise.
A number of species in recent news have been discovered to have convergently lost certain genes depending on their dietary habits. Gene loss can provide novel insights into the explanation for the observed phenotypic differences. These gene loss events often occur as a result of relaxed selection following adaptation, and thus serve as a mechanism which contributes to adaptive evolution.
Key insight into the role of gene loss events as a mechanism for adaptation and as a “predictable consequence of phenotypic evolution” were previously acknowledged by Dr. Virag Sharma. Sharma and his team conducted an inquiry of the importance of gene losses for mammalian adaptations using genomics and comparative physiology. What they found presented thought provoking evidence for how adaptations arise (Sharma et al., 2018).
Although the mechanism for adaptive gene loss is relatively straightforward, gene loss often creates irreversible mutations. Sharma offers an example of a bat (Fig. 1.) with gene losses which cause dietary specification and limit their ability to return to previous generalist diets by inducing mutations throughout other areas of the body. This irreversibility implies that the diversity of gene functionality “is preferentially preserved in generalist species and that gene loss could influence macroevolutionary trajectories by hampering phenotypic reversal in highly adapted specialists” (Sharma et al., 2018).
Fig. 1. Renal and Metabolic Adaptations in frugivorous bats. Multiple renal transporter genes (left, red) are shown to be lost which represents a capacity to efficiently excrete excess dietary water by reducing urine osmolarity. Losses of metabolic genes (right, red) indicate an adaptive efficiency of processing sugar-rich fruit juices. Blue genes represent consequential gene losses as a result of the acquired frugivorous diet (Sharma et al., 2018).
The use of comparative digestive physiology has many implications for science. William H. Karasov used comparative digestive physiology to examine a variety of species. One significant example of his many findings is the examination of House Sparrows. These sparrows have the ability to upregulate their carbohydrase activity as juveniles with a high carbohydrate diet, but lose this ability in adulthood. While inconclusive, his findings are representative of the fact that not all physiological responses of animals to their diets are simply to increase fitness or maximize energy gain, but they can instead be more complex (Karasov, 2013).
Karasov’s data also suggests that the microbial diversity hosted within each animal is key to understanding each individual’s phenotypic characteristics. And because each individual fosters a unique gut flora composition (Fig. 2.), differences in species dietary needs and habits arise (Karasov, 2013).
Fig. 2. Variation in bacterial communities of mammals differentiated by diet, and analyzed by principal components analysis. Each of the three categories of mammalian diets show consistent biome composition between each of the species labeled within (Karasov, 2013).
An examination into the gut microbes was conducted by Dr. Ruth E. Ley and a team of other scientists. Her published findings of mammalian gut microbes and their implications of co-evolution with their host further detail the significance of gut microbiotas. “Mammals are metagenomic in that they are composed not only of their own gene complements, but also those of all of their associated microbes” (Ley, 2018).The microbes co-evolve with their host. Gene sequence analysis confirms that the bacteria hosted within each individual were highly adapted to their host (Fig. 3.)and differed significantly from lineages found elsewhere (Ley, 2018).
The vertical transmission of the parental gut communities to their offspring is therefore highly advantageous. Newborn animals are gifted with a full flora of microbes containing previously adapted traits from the parent as a part of their innate immunity. This adapted flora thus, can also account for the heritable dietary preferences (Ley, 2018).
Fig. 3. Network Based Analysis of fecal bacterial communities in select mammalian species. (a) simplified example of host-gut microbe network structure. (b-e) network diagrams for respective categories, color coded by diet (b), taxonomic order (c), and Provenance (d) (Ley, 2018).
The diets of herbivores and carnivores are composed of distinct nutritional compositions. Herbivores require the proper mechanisms to constantly digest cellulose and byproducts produced by plants, unlike the random and periodic feeding patterns of most carnivores whose diets are high in fat and protein. These specific patterns of feeding and accompanying physiological adaptations have evolved in species as a result of genetic mutations and relaxed selection, such as gene loss (Hecker, 2019).
How did Hecker’s team prove this? In order to detect the gene-inactivating mutations in each species a systematic screen was used to generate gene-loss data from the sequenced genomes. The gene-loss data was generated computationally based on sequence alignments. Common mutations which deactivate gene expression include premature stop codons, frameshift mutations, or the deletion of larger sequences. All of these scenarios were used to locate gene loss characters (Fig. 4)for further analysis (Hecker, 2019).
Fig. 4. Convergent gene losses identified in experimental carnivorous and herbivorous mammals. Both herbivorous and carnivorous diets in mammals independently evolved several times as shown by the collective genome sequences patterns (Hecker, 2019).
So what did scientists find? A number of mammalian species within each category of herbivore and carnivore showed patterns of repeated evolution of gene losses. Herbivores were noted to have lost a variety of genes, including the most notable PNLIPRP1 and SYCN inactivations. These two genes are responsible for production of a triglyceride lipase inhibitor and a pancreatic exocytosis factor. Other genes were found to be convergently lost in herbivores, but they were not directly related to dietary specialization (Hecker, 2019).
But why are the deactivated PNIPRP1 and SYCN genes important? Herbivores notoriously have diets rich in carbohydrates and plant derived xenobiotics. The pancreas is directly responsible for facilitating digestion by secreting both enzymes and bicarbonate into the small intestine from pancreatic acinar cells. The genomic screening methods identified repeated gene loss for both PNIPRP1 and SYCN, which directly affects the pancreas capabilities in these cells (Hecker, 2019).
The SYCN gene is responsible for aiding in the efficiency of compound exocytosis of zymogens from the pancreatic acinar cells into the small intestines. SYCN forms granules which contain the deactivated zymogens (inactivated enzymes) and fuses with the acinar cell membrane so that exocytosis may occur. The zymogens are only activated upon entry into the small intestine lumen. All of this is to say that without the production of SYCN, the pancreas can no longer efficiently secrete food digesting enzymes into the small intestines (Hecker, 2019).
The loss of function for pancreas enzyme secretion is likely related to the herbivorous feeding habits. Herbivores are generally grazers, constantly feeding every day. Thus, they require a constant rate of pancreatic secretion without exception. Unlike carnivores, herbivores have no need for an increased rate of pancreatic secretions mediated by compound exocytosis. Herbivores can therefore afford to lack SYCN expression (Hecker, 2019).
PNIPRP1 encodes for a triglyceride lipase inhibitor, producing the protein PLPR1. PLPR1 is a competitive inhibitor of the pancreatic triglyceride lipase (PTL). The presence of PLPR1 essentially inhibits triglyceride (fat) digestion, which encourages fat buildup within the body. Thus, the loss of the PNIPRP1 (inhibitor gene) results in an increase in dietary triglyceride digestion ability. An increased capacity for triglyceride digestion is paramount for herbivorous mammals whose diet generally lacks high amounts of fats (Hecker, 2019).
Fig. 5. Inactivating mutations in genes which are repeatedly lost in herbivorous and carnivorous mammals. Advantageous gene losses in herbivorous mammals observed in A and B, and carnivorous mammals in C-F. For space-saving purposes, only one representative inactivating mutation is shown. Herbivores are distinguished by blue font, separate from the carnivores in red font. The diagram above each box represents the exon-intron coding structure for each related gene (Hecker, 2019).
What about carnivores? Carnivorous animals showed a different variety of repeated gene loss patterns. Carnivores were observed to have a loss of food intake regulation and glucose homeostasis regulating genes, the innate immunity gene NOX1, and detoxification genes. These gene losses likely are a result of the diet of carnivores, which obviously differs from that of the herbivorous diet in that it consists of a fat and protein- rich diet (Hecker, 2019).
INSL5 and RXFP4 work together as a hormone-receptor pair involved in regulating appetite and glucose homeostasis. The preferred loss of this pair in carnivores (Fig. 3) has lead to a lack of routine feeding, compared to the regular interval feeding patterns of herbivores. But INSL5 and RXFP4 have been further linked to glucose homeostasis. INSL5 is responsible for regulation of gluconeogenesis in the liver by its interaction with the RXFP4 receptor, indicating an involvement in the observed low carbohydrate content in the carnivore diet. With a significantly low carbohydrate intake, the need for gluconeogenesis regulation is obsolete, and constant gluconeogenesis is required (Hecker, 2019).
Fig. 6. Inactivating mutations of INSL5. Exons are shown as boxes, introns as horizontal lines. Both representations of exons and introns are proportional to their size. Each structure visualizes the orthologous gene mutations in carnivorous and herbivorous mammals. A red box indicates an exon deletion and a grey box missing genomic sequence. Vertical red lines represent frameshift deletions and blue lines indicate preserving insertions or deletions.The size of each deletion or insertion is labeled above. Black vertical line indicate premature stop codons and the triplet code is labeled above (Hecker, 2019).
Furthermore, Carnivores were marked by the loss of the NOX1 gene for innate immunity. The loss of this gene directly relates to the less-diverse gut flora influenced by the mammal’s innate immunity. Due to the lack of diversity in carnivorous guts, the antimicrobial defenses provided by the encoded reactive oxygen species (ROS) are not as necessary as they might be in herbivorous mammals with highly diverse gut flora (Hecker, 2019).
The NR1I3 gene loss in carnivores depicts the final convergent gene loss in representative mammalian species of this study. The NR1I3 gene is responsible for detoxifying plant xenobiotics. The receptor coded by this gene plays a large part in the intestinal xenobiotic detoxification pathway. For obvious reason, the carnivorous species show a loss of this gene’s expression most likely because of their low exposure to plant-derived xenobiotics in their diet (Hecker, 2019).
So who cares, right? The use of comparative genomics in analyzing changes in biological processes is key to further understanding how analogous dietary specializations evolved independently and repeatedly in mammals. The convergent gene loss trends discovered by Nikolai Hecker and the other scientists involved in these studies provide novel insights into the overlooked effects of an animal’s dietary needs and tendencies on the evolution of other physiological aspects which define current species.
Freeman, Scott, and Jon C. Herron. Evolutionary Analysis. Pearson Education, 2014.
Hecker, Nikolai, Virag Sharma, and Michael Hiller. 2019. “Convergent Gene Losses Illuminate Metabolic and Physiological Changes in Herbivores and Carnivores.” Proceedings of the National Academy of Sciences 116 (8):3036. https://doi.org/10.1073/pnas.1818504116.
Karasov, William H, and Angela E Douglas. 2013. “Comparative Digestive Physiology.” Comprehensive Physiology 3 (2):741–83. https://doi.org/10.1002/cphy.c110054.
Ley, Ruth E, Micah Hamady, Catherine Lozupone, Peter J Turnbaugh, Rob Roy Ramey, J Stephen Bircher, Michael L Schlegel, et al. 2008. “Evolution of Mammals and Their Gut Microbes.” Science (New York, N.Y.) 320 (5883):1647–51. https://doi.org/10.1126/science.1155725.
Sharma, Virag, Nikolai Hecker, Juliana G. Roscito, Leo Foerster, Bjoern E. Langer, and Michael Hiller. 2018. “A Genomics Approach Reveals Insights into the Importance of Gene Losses for Mammalian Adaptations.” Nature Communications 9 (1):1215. https://doi.org/10.1038/s41467-018-03667-1.