Impact of Phylogenetic Tree Completeness and Mis-specification of Sampling Fractions on Trait Dependent Diversification Models.

Understanding the origins of diversity and the factors that drive some clades to be more diverse than others are important issues in evolutionary biology. Sophisticated SSE (state-dependent speciation and extinction) models provide insights into the association between diversification rates and the evolution of a trait. The empirical data used in SSE models and other methods is normally imperfect, yet little is known about how this can affect these models. Here, we evaluate the impact of common phylogenetic issues on inferences drawn from SSE models. Using simulated phylogenetic trees and trait information, we fitted SSE models to determine the effects of sampling fraction (phylogenetic tree completeness) and sampling fraction mis-specification on model selection and parameter estimation (speciation, extinction, and transition rates) under two sampling regimes (random and taxonomically biased). As expected, we found that both model selection and parameter estimate accuracies are reduced at lower sampling fractions (i.e., low tree completeness). Furthermore, when sampling of the tree is imbalanced across sub-clades and tree completeness is ≤ 60%, rates of false positives increase and parameter estimates are less accurate, compared to when sampling is random. Thus, when applying SSE methods to empirical datasets, there are increased risks of false inferences of trait dependent diversification when some sub-clades are heavily under-sampled. Mis-specifying the sampling fraction severely affected the accuracy of parameter estimates: parameter values were over-estimated when the sampling fraction was specified as lower than its true value, and under-estimated when the sampling fraction was specified as higher than its true value. Our results suggest that it is better to cautiously under-estimate sampling efforts, as false positives increased when the sampling fraction was over-estimated. We encourage SSE studies where the sampling fraction can be reasonably estimated and provide recommended best practices for SSE modeling. [Trait dependent diversification; SSE models; phylogenetic tree completeness; sampling fraction.].

Oxidative Processes in Muscle Systems and Fresh Meat: Sources, Markers, and Remedies.

Oxidation of meat occurs under postmortem conditions and is inevitable. This oxidation includes the biochemical changes in meat leading to changes in color pigments and lipids. As a consequence, color deteriorates, and undesirable flavors and rancidity develop in meat thereby impacting on consumer appeal and satisfaction. Across carcasses, there is variation in the rate at which muscle undergoes chemical reactions under postmortem conditions that reflect inherent variation at the biochemical level. It is expected that this underlying biochemical variation will be reflected in living muscle through oxidative processes. The oxidative process of muscle tissues will vary according to an animal's immunity status, temperament, and ability to cope with stress, with all these affected by nutrition, genetics, management practices, and environmental conditions (hot and cold seasons). Identification of biomarkers that indicate the oxidative status levels of animals or muscle tissues in vivo could provide insight as to how the muscle will respond to the anoxic conditions that produce undesirable results in meat. This review outlines the potential use of 1 group of biomarkers, the isoprostanes, in the context of complex biochemical reactions relating to oxidative processes that take place in the biological systems of live animals (in vivo) and subsequently in meat (in vitro).

Nano-chromium picolinate and heat stress enhance insulin sensitivity in cross-bred sheep.

This study evaluated the effects of heat stress (HS) and dietary nano chromium picolinate (nCrPic) on metabolic responses of sheep to an intravenous glucose tolerance test (IVGTT), an intravenous insulin tolerance test (ITT) and an intramuscular adrenocorticotropin hormone (ACTH) challenge in sheep. Thirty-six sheep housed in metabolic cages were randomly allocated within 3 dietary groups (0, 400 and 800 µg/kg supplemental nCrPic) to either thermoneutral (22 °C) or cyclic HS (22 to 40 °C) conditions for 3 wk. Basal plasma glucose tended to be increased during HS (P = 0.052) and decreased by dietary nCrPic (P = 0.013) while plasma non-esterified fatty acid concentrations were decreased (P = 0.010) by HS. Dietary nCrPic reduced the plasma glucose area under the curve (P = 0.012) while there were no significant effects of HS on plasma glucose area under the curve in response to the IVGTT. The plasma insulin response over the first 60 min after the IVGTT was decreased by HS (P = 0.013) and dietary nCrPic (P = 0.022) with the effects being additive. In response to the ITT plasma glucose reached a nadir sooner (P = 0.005) in sheep exposed to HS, although there was no effect on the depth of the nadir. Dietary nCrPic decreased (P = 0.007) the plasma glucose nadir after ITT. Over the duration of the ITT plasma insulin concentrations were lower in sheep exposed to HS (P = 0.013) whereas there was no significant effect of supplemental nCrPic. There was no effect of either HS or nCrPic on cortisol response to ACTH. Dietary nCrPic supplementation decreased (P = 0.013) mitogen-activated protein kinase-8 (JNK) and increased (P = 0.050) carnitine palmitoyltransferase 1B (CPT1B) mRNA expression in skeletal muscle. Results of this experiment demonstrated that animals under HS and supplemented with nCrPic had greater insulin sensitivity.

Postprandial heat production in skeletal muscle is associated with altered mitochondrial function and altered futile calcium cycling.

This study aimed to determine whether postprandial temperature excursions in skeletal muscle are consistent with thermogenesis or altered blood flow. Temperature probes were implanted into the vastus lateralis muscle of ovariectomized ewes, and blood flow was assessed using laser-Doppler flowmetry (tissue flow) and transit-time ultrasound flowmetry (femoral artery flow). The animals were program-fed between 1100 and 1600, and temperature and blood flow were measured during intravenous administration of either isoprenaline or phenylephrine and during feeding and meal anticipation. In addition, muscle biopsies were collected prefeeding and postfeeding to measure uncoupling protein (UCP) expression and mitochondrial function, as well as indices of calcium cycling (ryanodine 1 receptor: RyR1 and sarcoendoplasmic calcium-dependent ATPases SERCA1/ SERCA2a). Isoprenaline increased femoral artery blood flow, whereas phenylephrine reduced blood flow. At high doses only, isoprenaline treatment increased heat production in muscle. Phenylephrine treatment did not alter muscle temperature. Meal anticipation was evoked in fasted animals (previously program-fed) that were housed beside animals that were fed. Increases in muscle temperature were elicited by feeding and meal anticipation, without changes in blood flow during either paradigm. Analyses of respiration in isolated mitochondria indicated that the postprandial increase in heat production was associated with an increase in state 4 respiration, without increased UCP1, UCP2, or UCP3 expression. Feeding increased the expression of RyR1 and SERCA2a. We conclude that excursions in muscle temperature may occur independent of blood flow, suggesting that postprandial heat production is driven by altered mitochondrial function and changes in calcium cycling.

Functional divergence of the pigmentation gene melanocortin-1 receptor (MC1R) in six endemic Macaca species on Sulawesi Island.

Coat color is often highly variable within and between animal taxa. Among hundreds of pigmentation-related genes, melanocortin-1 receptor (MC1R) plays key roles in regulating the synthesis of the dark eumelanin and the red-yellow pheomelanin. The six species of macaques that inhabit Sulawesi Island diverged rapidly from their common ancestor, M. nemestrina. Unlike most macaques, Sulawesi macaques commonly have a dark coat color, with divergence in shade and color pattern. To clarify the genetic and evolutionary basis for coat color in Sulawesi macaques, we investigated the MC1R sequences and functional properties, including basal cAMP production and α-MSH-induced activity in vitro. We found fixed non-synonymous substitutions in MC1R in each species. Furthermore, we found that six species-specific variants corresponded with variation in agonist-induced and basal activity of MC1R. Inconsistent with the dark coat color, four substitutions independently caused decreases in the basal activity of MC1R in M. hecki, M. nigra, M. tonkeana, and M. ochreata. Selective analysis suggested MC1R of M. nigra and M. nigrescens underwent purifying selection. Overall, our results suggest that fixed differences in MC1R resulted in different functional characteristics and might contribute to divergence in color among the six Sulawesi macaque species.

Dietary nano chromium picolinate can ameliorate some of the impacts of heat stress in cross-bred sheep.

Two studies were conducted to evaluate the effect of nano chromium picolinate (nCrPic) during heat stress (HS) in sheep. In the initial study, 36 Merino × Poll cross-bred sheep were individually penned and allocated to 3 dietary treatments (0, 400 and 800 µg/kg nCrPic) for 8 wk. Body composition was determined at the beginning and end of the experiment using dual energy X-ray absorptiometry. The sheep remained in their dietary groups but were then placed in metabolic cages and randomly allocated within the dietary group to differing ambient temperature regimes, i.e., thermo-neutral (TN) (n = 18) and HS (n = 18), for 3 wk. Dietary nCrPic had no effect on growth performance and body composition during the initial study conducted under TN conditions. Heat stress decreased average daily feed intake (ADFI) (P = 0.002) whereas sheep under HS had reduced average daily gain (ADG) and indeed lost weight (P < 0.001). Dietary nCrPic increased both ADFI (P = 0.041) and ADG (P = 0.049) under both TH and HS conditions such that the performance of sheep receiving supplemental nCrPic and exposed to HS was similar to that of control sheep maintained under TN conditions. Heat stress increased rectal temperature (P < 0.001) and respiration rate (P < 0.001), particularly during the hottest parts of the day as indicated by interactions (P < 0.001) between time of day and thermal treatment. Rectal temperature was lower in sheep fed nCrPic (P = 0.050), particularly under peak HS conditions during the afternoon as indicated by the interactions between dietary nCrPic and time of day (P < 0.001) and dietary nCrPic, thermal treatment and time of day (P = 0.010). Similarly, respiration rate was lower in sheep fed nCrPic under peak HS conditions during the afternoon as indicated by the interactions between dietary nCrPic and thermal treatment (P < 0.001) and dietary nCrPic and time of day (P = 0.030). In conclusion, dietary nCrPic can partially ameliorate the negative effects of HS as indicated by the maintenance of ADFI and decreased physiological responses, such as elevations in rectal temperature and respiration rate.

Nano Chromium Picolinate Improves Gene Expression Associated with Insulin Signaling in Porcine Skeletal Muscle and Adipose Tissue.

The aim of this study was to investigate the interactive effects of dietary nano chromium picolinate (nCrPic) and dietary fat on genes involved in insulin signaling in skeletal muscle and subcutaneous adipose tissue of pigs. Forty-eight gilts were stratified on body weight into four blocks of four pens of three pigs and then within each block each pen was randomly allocated to four treatment groups in a 2 × 2 factorial design. The respective factors were dietary fat (22 or 57 g/kg) and dietary nCrPic (0 or 400 ppb nCrPic) fed for six weeks. Skeletal muscle samples were collected from the Longissimus thoracis and subcutaneous adipose tissue collected from above this muscle. Dietary nCrPic increased adiponectin, uncoupling protein 3 (UCP3) and serine/threonine protein kinase (AKT) mRNA expression, whereas dietary fat decreased adiponectin and increased leptin, tumor necrosis factor-α (TNF-α), peroxisome proliferator-activated receptors γ (PPARγ) and CCAAT/enhancer-binding protein α (C/EBPα) mRNA expression in adipose tissue. In skeletal muscle, dietary nCrPic increased phosphatidylinositol 3 kinase (PI3K), AKT, UCP3 and interleukin-15 (IL-15), as well as decreased suppressor of cytokine signaling 3 (SOCS3) mRNA expression. The improvement in insulin signaling and muscle mass and the reduction in carcass fatness by dietary nCrPic may be via decreased SOCS3 and increased UCP3 and IL-15 in skeletal muscle and increased adiponectin in subcutaneous adipose tissue.

Functional divergence of the bitter receptor TAS2R38 in Sulawesi macaques.

ABSTRACT: Bitter perception is mediated by G protein-coupled receptors TAS2Rs and plays an important role in avoiding the ingestion of toxins by inducing innate avoidance behavior in mammals. One of the best-studied TAS2Rs is TAS2R38, which mediates the perception of the bitterness of synthetic phenylthiocarbamide (PTC). Previous studies of TAS2R38 have suggested that geographical separation enabled the independent divergence of bitter taste perception. The functional divergence of TAS2R38 in allopatric species has not been evaluated. We characterized the function of TAS2R38 in four allopatric species of Sulawesi macaques on Sulawesi Island. We found variation in PTC taste perception both within and across species. In most cases, TAS2R38 was sensitive to PTC, with functional divergence among species. We observed different truncated TAS2R38s that were not responsive to PTC in each species of Macaca nigra and M. nigrescens due to premature stop codons. Some variants of intact TAS2R38 with an amino acid substitution showed low sensitivity to PTC in M. tonkeana. Similarly, this intact TAS2R38 with PTC-low sensitivity has also been found in humans. We detected a shared haplotype in all four Sulawesi macaques, which may be the ancestral haplotype of Sulawesi macaques. In addition to shared haplotypes among Sulawesi macaques, other TAS2R38 haplotypes were species-specific. These results implied that the variation in TAS2R38 might be shaped by geographical patterns and local adaptation. OPEN RESEARCH BADGES: This article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results. The data is available at https://doi.org/10.5061/dryad.908jf3r.

Three new "caecate" earthworm species from Sulawesi, Indonesia (Oligochaeta, Megascolecidae).

Three new earthworm species are described from Sulawesi, Indonesia. Two belong to the genus Pithemera Sims & Easton, 1972, namely P.suwastikai Fahri, Amaliah & Atmowidi, sp. n. and P.tadulako Fahri, Amaliah & Atmowidi, sp. n. The new species, P.suwastikai sp. n. is distinguished by a medium size (135-165 mm long, 4.5-6.5 mm diameter), four pairs of spermathecal pores in 5/6/7/8/9, 7-12 setae between male pores, no genital markings, holandry, and simple intestinal caeca. Pithemeratadulako sp. n. is recognized by a large size (217-340 mm long, 13-15 mm diameter), two pairs of spermathecal pores in 7/8/9, no setae between male pores, no genital markings, holandry, and simple intestinal caeca. Another new species, Metaphirerusydii Fahri, Amaliah & Nguyen, sp. n., is diagnosed by its large size (250-280 mm long,12-16 mm diameter), two pairs of spermathecal pores in 7/8/9, no setae between male porophores, presence of genital markings in the male region, holandry, and complex intestinal caeca. Additionally, an identification key to "caecate" species is provided to the Sulawesi's fauna.

Dietary lecithin improves feed efficiency without impacting meat quality in immunocastrated male pigs and gilts fed a summer ration containing added fat.

The aim of this study was to investigate the effects of sex and dietary lecithin on growth performance, meat quality, muscle collagen content and gene expression of key genes involved in collagen synthesis in finisher pigs. A total of 256 pigs (Large White × Landrace) were allotted to a 2 × 2 factorial arrangement involving sex (gilt or immunocastrated [IC] male) and dietary treatment (0 or 5 g/kg of dietary lecithin). All diets were formulated to contain 4.6% tallow with relatively high total fat of 6.3%. After 5 weeks of dietary treatment, pigs were slaughtered and Longissimus dorsi muscle was obtained for evaluation of meat quality and collagen content. Rectus abdominis muscle was analysed for gene expression of key genes involved in collagen synthesis namely, type I (α1) procollagen (COL1A1), type III (α1) procollagen (COL3A1), α-subunit of prolyl 4-hydroxylase (P4H), lysyl oxidase and metalloproteinase-1 (MMP-1). The results showed that lecithin improved feed efficiency of all pigs (P < 0.05) but it had no effect on feed intake, average daily gain and dressing percentage (P > 0.05). Lecithin also had no effect on meat compression, shear force, collagen content and gene expression (P > 0.05). Immunocastrated male had higher growth rate and increased COL1A1 expression than gilts. However, sex had no effect on fat depth at the P2 site (65 mm from the midline over the last rib), collagen content and expression of other genes (P > 0.05). In conclusion, lecithin improved feed efficiency in finishing pigs without impacting pork quality. Thus, inclusion of lecithin in diets containing high amount of tallow during the summer period could be beneficial.

Knockdown of a disintegrin A metalloprotease 12 (ADAM12) during adipogenesis reduces cell numbers, delays differentiation, and increases lipid accumulation in 3T3-L1 cells.

Mouse models have shown that a disintegrin A metalloprotease 12 (ADAM12) is implicated during adipogenesis; the molecular pathways are not well understood. Stealth RNA interference was used to knock down ADAM12 in 3T3-L1 cells. Using gene profiling and metabolic enzymatic markers, we have identified signaling pathways ADAM12 impacts upon during proliferation, differentiation, and maturation of adipocytes. ADAM12 reduced cell numbers in proliferating preadipocytes, delayed differentiation of preadipocytes to adipocytes, and increased lipid accumulation in mature adipocytes. The pathway most affected by ADAM12 knockdown was regulation of insulin-like growth factor (IGF) activity by insulin-like growth factor binding proteins (IGFBPs); ADAM12 is known to cleave IGFBP3 and IGFBP5. The IGF/mTOR signaling pathway was down-regulated, supporting a role for ADAM12 in the IGFBP/IGF/mTOR-growth pathway. PPARγ signaling was also down-regulated by ADAM12 knockdown. Gene ontology (GO) analysis revealed that the extracellular matrix was the cellular compartment most impacted. Filtering for matrisome genes, connective tissue growth factor ( Ctgf) was up-regulated. CTGF and IGBP3 can interact with PPARγ to hinder its regulation. Increased expression of these molecules could have influenced PPARγ signaling reducing differentiation and an imbalance of lipids. We believe ADAM12 regulates cell proliferation of preadipocytes through IGFBP/IGF/mTOR signaling and delays differentiation through altered PPAR signaling to cause an imbalance of lipids within mature adipocytes.

Dietary Lecithin Decreases Skeletal Muscle COL1A1 and COL3A1 Gene Expression in Finisher Gilts.

The purpose of this study was to investigate the effect of dietary lecithin on skeletal muscle gene expression of collagen precursors and enzymes involved in collagen synthesis and degradation. Finisher gilts with an average start weight of 55.9 ± 2.22 kg were fed diets containing either 0, 4, 20 or 80 g/kg soybean lecithin prior to harvest for six weeks and the rectus abdominis muscle gene expression profile was analyzed by quantitative real-time PCR. Lecithin treatment down-regulated Type I (α1) procollagen (COL1A1) and Type III (α1) procollagen (COL3A1) mRNA expression ( p < 0.05, respectively), indicating a decrease in the precursors for collagen synthesis. The α-subunit of prolyl 4-hydroxylase (P4H) mRNA expression also tended to be down-regulated ( p = 0.056), indicating a decrease in collagen synthesis. Decreased matrix metalloproteinase-1 (MMP-1) mRNA expression may reflect a positive regulatory response to the reduced collagen synthesis in muscle from the pigs fed lecithin ( p = 0.035). Lecithin had no effect on tissue inhibitor metalloproteinase-1 (TIMP-1), matrix metalloproteinase-13 (MMP-13) and lysyl oxidase mRNA expression. In conclusion, lecithin down-regulated COL1A1 and COL3A1 as well as tended to down-regulate α-subunit P4H expression. However, determination of muscle collagen content and solubility are required to support the gene functions.

Forms of n-3 (ALA, C18:3n-3 or DHA, C22:6n-3) Fatty Acids Affect Carcass Yield, Blood Lipids, Muscle n-3 Fatty Acids and Liver Gene Expression in Lambs.

The effects of supplementing diets with n-3 alpha-linolenic acid (ALA) and docosahexaenoic acid (DHA) on plasma metabolites, carcass yield, muscle n-3 fatty acids and liver messenger RNA (mRNA) in lambs were investigated. Lambs (n = 120) were stratified to 12 groups based on body weight (35 ± 3.1 kg), and within groups randomly allocated to four dietary treatments: basal diet (BAS), BAS with 10.7 % flaxseed supplement (Flax), BAS with 1.8 % algae supplement (DHA), BAS with Flax and DHA (FlaxDHA). Lambs were fed for 56 days. Blood samples were collected on day 0 and day 56, and plasma analysed for insulin and lipids. Lambs were slaughtered, and carcass traits measured. At 30 min and 24 h, liver and muscle samples, respectively, were collected for determination of mRNA (FADS1, FADS2, CPT1A, ACOX1) and fatty acid composition. Lambs fed Flax had higher plasma triacylglycerol, body weight, body fat and carcass yield compared with the BAS group (P < 0.001). DHA supplementation increased carcass yield and muscle DHA while lowering plasma insulin compared with the BAS diet (P < 0.01). Flax treatment increased (P < 0.001) muscle ALA concentration, while DHA treatment increased (P < 0.001) muscle DHA concentration. Liver mRNA FADS2 was higher and CPT1A lower in the DHA group (P < 0.05). The FlaxDHA diet had additive effects, including higher FADS1 and ACOX1 mRNA than for the Flax or DHA diet. In summary, supplementation with ALA or DHA modulated plasma metabolites, muscle DHA, body fat and liver gene expression differently.