BackgroundThere are three main dietary groups in mammals: carnivores, omnivores, and herbivores. Currently, there is limited comparative genomics insight into the evolution of dietary specializations in mammals. Due to recent advances in sequencing technologies, we were able to perform in-depth whole genome analyses of representatives of these three dietary groups.ResultsWe investigated the evolution of carnivory by comparing 18 representative genomes from across Mammalia with carnivorous, omnivorous, and herbivorous dietary specializations, focusing on Felidae (domestic cat, tiger, lion, cheetah, and leopard), Hominidae, and Bovidae genomes. We generated a new high-quality leopard genome assembly, as well as two wild Amur leopard whole genomes. In addition to a clear contraction in gene families for starch and sucrose metabolism, the carnivore genomes showed evidence of shared evolutionary adaptations in genes associated with diet, muscle strength, agility, and other traits responsible for successful hunting and meat consumption. Additionally, an analysis of highly conserved regions at the family level revealed molecular signatures of dietary adaptation in each of Felidae, Hominidae, and Bovidae. However, unlike carnivores, omnivores and herbivores showed fewer shared adaptive signatures, indicating that carnivores are under strong selective pressure related to diet. Finally, felids showed recent reductions in genetic diversity associated with decreased population sizes, which may be due to the inflexible nature of their strict diet, highlighting their vulnerability and critical conservation status.ConclusionsOur study provides a large-scale family level comparative genomic analysis to address genomic changes associated with dietary specialization. Our genomic analyses also provide useful resources for diet-related genetic and health research.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-016-1071-4) contains supplementary material, which is available to authorized users.
BackgroundPrevious meta‐analyses on meat intake and risk of stroke did not report the effect of white meat (poultry meat, excluding fish) and did not examine stroke incidence and mortality separately. We aimed to investigate the relationship of total (red and processed meat), red (unprocessed or fresh red meat), and processed (processed red meat) consumption along with white meat on risk of stroke incidence and mortality.Methods and ResultsArticles were identified from databases and reference lists of relevant studies up to October 28, 2016. We selected prospective cohort studies on meat consumption specified by types of meat and stroke incidence and mortality reporting relative risks and 95% confidence intervals. The pooled relative risk was estimated using the random‐effects model. Based on the inclusion criteria, 10 articles containing 15 studies (5 articles with 7 studies including 9522 cases of stroke incidence and 254 742 participants and 5 articles with 8 studies containing 12 999 cases of stroke mortality and 487 150 participants) were selected for quantitative synthesis. The pooled relative risks (95% confidence intervals) for total, red, processed and white meat consumption and total stroke incidence were 1.18 (1.09–1.28), 1.11 (1.03–1.20), 1.17 (1.08–1.25), and 0.87 (0.78–0.97), respectively. Total meat consumption (0.97 [0.85–1.11]) and red meat consumption 0.87 (0.64–1.18) were not significantly associated with stroke‐related death.ConclusionsThe relationship between meat intake and risk of stroke may differ by type of meat. Recommendations for replacing proportions of red and processed meats to white meat for the prevention of stroke may be considered in clinical practice.
BackgroundThe cinereous vulture, Aegypius monachus, is the largest bird of prey and plays a key role in the ecosystem by removing carcasses, thus preventing the spread of diseases. Its feeding habits force it to cope with constant exposure to pathogens, making this species an interesting target for discovering functionally selected genetic variants. Furthermore, the presence of two independently evolved vulture groups, Old World and New World vultures, provides a natural experiment in which to investigate convergent evolution due to obligate scavenging.ResultsWe sequenced the genome of a cinereous vulture, and mapped it to the bald eagle reference genome, a close relative with a divergence time of 18 million years. By comparing the cinereous vulture to other avian genomes, we find positively selected genetic variations in this species associated with respiration, likely linked to their ability of immune defense responses and gastric acid secretion, consistent with their ability to digest carcasses. Comparisons between the Old World and New World vulture groups suggest convergent gene evolution. We assemble the cinereous vulture blood transcriptome from a second individual, and annotate genes. Finally, we infer the demographic history of the cinereous vulture which shows marked fluctuations in effective population size during the late Pleistocene.ConclusionsWe present the first genome and transcriptome analyses of the cinereous vulture compared to other avian genomes and transcriptomes, revealing genetic signatures of dietary and environmental adaptations accompanied by possible convergent evolution between the Old World and New World vultures.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-015-0780-4) contains supplementary material, which is available to authorized users.
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