Species can be defined as populations that are diagnosably distinct, reproductively isolated, cohesive, or exclusive groups of organisms. Boundaries between species in sympatry are maintained by intrinsic barriers to gene exchange; these boundaries may not be uniform in space, in time, or across the genome. Here, we explore the nature of the species boundary, defined as the phenotypes/genes/genome regions that remain differentiated in the face of potential hybridization and introgression. We emphasize that species boundaries are semipermeable, with permeability (gene exchange) being a function of genome region. The early evidence for semipermeable species boundaries came from data on differential introgression in hybrid zones. This "genic view" of species was common in the hybrid zone literature even when few molecular markers were available to characterize genome-wide patterns of variation. Now, molecular tools allow detailed characterization of differentiation between diverging lineages and patterns of variation across natural hybrid zones, but the questions being asked by evolutionary biologists have remained much the same. Recent data (from DNA sequences and genotypes) reinforce earlier conclusions about the semipermeable nature of most species boundaries. However, debate persists over the nature and extent of genome divergence that accompanies speciation.
Insects and their arthropod relatives including mites, spiders, and crustaceans play major roles in the world's terrestrial, aquatic, and marine ecosystems. Arthropods compete with humans for food and transmit devastating diseases. They also comprise the most diverse and successful branch of metazoan evolution, with millions of extant species. Here, we describe an international effort to guide arthropod genomic efforts, from species prioritization to methodology and informatics. The 5000 arthropod genomes initiative (i5K) community met formally in 2012 to discuss a roadmap for sequencing and analyzing 5000 high-priority arthropods and is continuing this effort via pilot projects, the development of standard operating procedures, and training of students and career scientists, With university, governmental, and industry support, the i5K Consortium aspires to deliver sequences and analytical tools for each of the arthropod branches and each of the species having beneficial and negative effects on humankind.
Testing for Hardy-Weinberg proportions (HWP) is routine in almost all genetic studies of natural populations, but many researchers do not demonstrate a full understanding of the purposes of these tests or how to interpret the results. Common problems include a lack of understanding of statistical power and the difference between statistical significance and biological significance, how to interpret results of multiple tests, and how to distinguish between various factors that can cause statistically significant departures. In this perspective, which focuses on analysis of genetic data for nonmodel species, I 1) review factors that can cause departures from HWP at individual loci and linkage disequilibrium (LD) at pairs of loci; 2) discuss commonly used tests for HWP and LD, with an emphasis on multiple-testing issues; 3) show how to distinguish among possible causes of departures from HWP; and 4) outline some simple steps to follow when significant test results are found. Finally, I 5) identify some issues that merit particular attention as we move into an era in which analysis of genomics-scale datasets for nonmodel species is commonplace.
Feed and energy intake of ruminant animals can change dramatically in response to changes in diet composition or metabolic state, and such changes are poorly predicted by traditional models of feed intake regulation. Recent work suggests that temporal patterns of fuel absorption, mobilization, and metabolism affect feed intake in ruminants by altering meal size and frequency. Research with nonruminants suggests that meals can be terminated by signals carried from the liver to the brain via afferents in the vagus nerve and that these signals are affected by hepatic oxidation of fuels and generation of ATP. We find these results consistent with the effects of diet on feed intake of ruminants. Of fuels metabolized by the ruminant liver, propionate is likely a primary satiety signal because its flux to the liver increases greatly during meals. Propionate is utilized for gluconeogenesis or oxidized in the liver and stimulates oxidation of acetyl CoA. Although propionate is extensively metabolized by the ruminant liver, there is little net metabolism of acetate or glucose, which may explain why these fuels do not consistently induce hypophagia in ruminants. Lactate is metabolized in the liver but has less effect on satiety, probably because of greater latency for reaching the liver within meals and because of less hepatic extraction compared with propionate. Hypophagic effects of fatty acid oxidation in the liver are likely from delaying hunger rather than promoting satiety because beta-oxidation is inhibited during meals by propionate. A shortage of glucose precursors and increased fatty acid oxidation in the liver for early lactation cows lead to a lack of tricarboxylic acid (TCA) cycle intermediates, resulting in a buildup of the intracellular acetyl-CoA pool and export of ketone bodies. In this situation, hypophagic effects of propionate are likely enhanced because propionate entry into the liver provides TCA cycle intermediates that allow oxidation of acetyl-CoA. Oxidizing the pool of acetyl-CoA rather than exporting it increases ATP production and likely causes satiety despite the use of propionate for glucose synthesis. A better understanding of metabolic regulation of feed intake will allow diets to be formulated to increase the health and productivity of ruminants.
Globally, food-producing animals consume 70 to 90% of genetically engineered (GE) crop biomass. This review briefly summarizes the scientific literature on performance and health of animals consuming feed containing GE ingredients and composition of products derived from them. It also discusses the field experience of feeding GE feed sources to commercial livestock populations and summarizes the suppliers of GE and non-GE animal feed in global trade. Numerous experimental studies have consistently revealed that the performance and health of GE-fed animals are comparable with those fed isogenic non-GE crop lines. United States animal agriculture produces over 9 billion food-producing animals annually, and more than 95% of these animals consume feed containing GE ingredients. Data on livestock productivity and health were collated from publicly available sources from 1983, before the introduction of GE crops in 1996, and subsequently through 2011, a period with high levels of predominately GE animal feed. These field data sets, representing over 100 billion animals following the introduction of GE crops, did not reveal unfavorable or perturbed trends in livestock health and productivity. No study has revealed any differences in the nutritional profile of animal products derived from GE-fed animals. Because DNA and protein are normal components of the diet that are digested, there are no detectable or reliably quantifiable traces of GE components in milk, meat, and eggs following consumption of GE feed. Globally, countries that are cultivating GE corn and soy are the major livestock feed exporters. Asynchronous regulatory approvals (i.e., cultivation approvals of GE varieties in exporting countries occurring before food and feed approvals in importing countries) have resulted in trade disruptions. This is likely to be increasingly problematic in the future as there are a large number of "second generation" GE crops with altered output traits for improved livestock feed in the developmental and regulatory pipelines. Additionally, advanced techniques to affect targeted genome modifications are emerging, and it is not clear whether these will be encompassed by the current GE process-based trigger for regulatory oversight. There is a pressing need for international harmonization of both regulatory frameworks for GE crops and governance of advanced breeding techniques to prevent widespread disruptions in international trade of livestock feedstuffs in the future.
Acute heat stress (HS) and heat stroke can be detrimental to the health, well-being, and performance of mammals such as swine. Therefore, our objective was to chronologically characterize how a growing pig perceives and initially copes with a severe heat load. Crossbred gilts (n = 32; 63.8 +/- 2.9 kg) were subjected to HS conditions (37 degrees C and 40% humidity) with ad libitum intake for 0, 2, 4, or 6 h (n = 8/time point). Rectal temperature (T-r), respiration rates (RR), and feed intake were determined every 2 h. Pigs were euthanized at each time point and fresh ileum and colon samples were mounted into modified Ussing chambers to assess ex vivo intestinal integrity and function. Transepithelial electrical resistance (TER) and fluorescein isothiocyanate-labeled dextran (FD4) permeability were assessed. As expected, Tr increased linearly over time (P < 0.001) with the highest temperature observed at 6 h of HS. Compared to the 0-h thermal-neutral (TN) pigs, RR increased (230%; P < 0.001) in the first 2 h and remained elevated over the 6 h of HS (P < 0.05). Feed intake was dramatically reduced due to HS and this corresponded with significant changes in plasma glucose, ghrelin, and glucose-dependent insulinotropic peptide (P < 0.050). At as early as 2 h of HS, ileum TER linearly decreased (P < 0.01), while FD4 linearly increased with time (P < 0.05). Colon TER and FD4 changed due to HS in quadratic responses over time (P = 0.050) similar to the ileum but were less pronounced. In response to HS, ileum and colon heat shock protein (HSP) 70 mRNA and protein abundance increased linearly over time (P < 0.050). Altogether, these data indicated that a short duration of HS (2-6 h) compromised feed intake and intestinal integrity in growing pigs.
This review integrates established and new information on the biological role of ovarian progesterone (P4) and interferon tau as well as conceptus-and endometrial-derived factors, PG and cortisol, in endometrial function and conceptus elongation during the periimplantation period of pregnancy in ruminants. Interferon tau is the maternal recognition of pregnancy signal that inhibits production of luteolytic pulses of PGF(2 alpha) by the endometrium to maintain corpora lutea and their production of P4, the unequivocal hormone of pregnancy. Conceptus-endometrial interactions in ruminants are complex and involve carefully orchestrated temporal and spatial alterations in endometrial gene expression during pregnancy. Available results from studies in sheep support the idea that the individual, interactive, and coordinated actions of P4, interferon tau, PG, and cortisol regulate expression of elongation- and implantation-related genes in the endometrial epithelia and that P4 and PG are essential regulators of conceptus elongation. The outcome of these gene expression changes is alterations in endometrial secretions that govern conceptus elongation via effects on trophectoderm proliferation, migration, attachment, and adhesion. An increased knowledge of conceptus-endometrial interactions during early pregnancy in ruminants is necessary to understand and elucidate the causes of recurrent pregnancy loss and to provide a basis for new strategies to improve pregnancy outcome and reproductive efficiency.
Approximately 600-bp sequences of mitochondrial DNA (mtDNA) have been designated as "DNA barcodes" and have become one of the most contentious and animated issues in the application of genetic information to global biodiversity assessment and species identification. Advocates of DNA barcodes have received extensive attention and promotion in many popular and refereed scientific publications. However, we suggest that the utility of barcodes is suspect and vulnerable to technical challenges that are particularly pertinent to mtDNA. We review the natural history of mtDNA and discuss problems for barcoding which are particularly associated with mtDNA and inheritance, including reduced effective population size, maternal inheritance, recombination, inconsistent mutation rate, heteroplasmy, and compounding evolutionary processes. The aforementioned could significantly limit the application and utility of mtDNA barcoding efforts. Furthermore, global use of barcodes will require application and acceptance of a barcode-based species concept that has not been evaluated in the context of the extensive literature concerning species designation. Implementation of mtDNA barcodes in spite of technical and practical shortcomings we discuss may degrade the longstanding synthesis of genetic and organism-based research and will not advance studies ranging from genomic evolution to biodiversity assessment.
The present study was undertaken to investigate the impact of heat (thermal) stress and dietary antioxidant supplementation on the oxidative and physiological status of sheep. Twenty-four Merino x Poll Dorset crossbred ewes were housed in 1 of 2 climatic chambers (thermoneutral or heat stress) and offered either a control (10 IU vitamin E/kg DM and 0.24 mg Se/kg DM) or high antioxidant (100 IU vitamin E/kg DM and 1.20 mg Se/kg DM) diet. The sheep were exposed to 2 thermal (temperature) treatments (thermoneutral [TN]: 18-21 C and 26-30% relative humidity; and heat stress [HS]: 28-40 C and 40-50% relative humidity) for 2 wk in a single reversal design. After 1 wk of dietary treatment, animals in 1 chamber were subjected to HS for 1 wk, with the temperature being increased to 40 degrees C between 0900 and 1700 h and then maintained at 28 degrees C overnight. Those sheep in the TN group were maintained at 18 to 21 C. Physiological parameters were recorded 4 times a day (0900, 1300, 1700, and 2100 h) and blood samples were collected on d 1 and 7 of heat treatment. Plasma samples and red blood cell lysates were assayed for oxidative stress biomarkers. The thermal treatments were then reversed and the above measures repeated. All measured physiological parameters were elevated (P < 0.001) by thermal treatment. Respiration rate was lower during HS in sheep supplemented with antioxidants as indicated by a diet x temperature x time interaction (P = 0.010). There was 13% decline (P = 0.014) in feed intake of the unsupplemented animals during HS whereas the same was maintained in sheep supplemented with high doses of antioxidants. Plasma reactive oxygen metabolites concentrations were reduced (114 vs. 85 units/dL; P < 0.005) while biological antioxidant potential tended to be increased (3,688 vs. 3,985 mol/L; P = 0.070) in heat stressed sheep supplemented with antioxidants. The oxidative stress index was 30% lower (P < 0.001) in supplemented sheep (2.16 similar to 0.06 arbitrary units) during HS than in unsupplemented sheep (3.12 similar to 0.08 arbitrary units). Plasma advanced oxidation protein products tended (P = 0.070) to decrease in antioxidant supplemented heat stressed sheep as compared to their unsupplemented counterparts. It was concluded that heat stress negatively affects the oxidative status of sheep along with the physiological responses and some of these affects can be ameliorated through dietary antioxidants supplementation at supranutritional concentrations.