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Maddock S.T.,Natural History Museum in London | Maddock S.T.,University College London | Maddock S.T.,Reaseheath College | Briscoe A.G.,Natural History Museum in London | And 8 more authors.
PLoS ONE | Year: 2016

Mitochondrial genome (mitogenome) sequences are being generated with increasing speed due to the advances of next-generation sequencing (NGS) technology and associated analytical tools. However, detailed comparisons to explore the utility of alternative NGS approaches applied to the same taxa have not been undertaken. We compared a 'traditional' Sanger sequencing method with two NGS approaches (shotgun sequencing and non-indexed, multiplex amplicon sequencing) on four different sequencing platforms (Illumina's HiSeq and MiSeq, Roche's 454 GS FLX, and Life Technologies' Ion Torrent) to produce seven (near-) complete mitogenomes from six species that form a small radiation of caecilian amphibians from the Seychelles. The fastest, most accurate method of obtaining mitogenome sequences that we tested was direct sequencing of genomic DNA (shotgun sequencing) using the MiSeq platform. Bayesian inference and maximum likelihood analyses using seven different partitioning strategies were unable to resolve compellingly all phylogenetic relationships among the Seychelles caecilian species, indicating the need for additional data in this case. © 2016 Maddock et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Source


Charlton G.L.,Harper Adams University College | Charlton G.L.,Reaseheath College | Rutter S.M.,Harper Adams University College | East M.,Reaseheath College | Sinclair L.A.,Harper Adams University College
Journal of Dairy Science | Year: 2011

Grazing is considered a normal behavior for dairy cattle, although they may not be able to meet their nutritional requirements from grazing alone, and so to sustain higher yields requires access to a total mixed ration (TMR). The study aim was to provide dairy cows with access to TMR indoors and on pasture to establish influence on behavior and preference for each location. The study took place from August to November, 2009, using 36 late-lactation Holstein-Friesian dairy cows. The cows were allocated to 1 of 3 26-d study periods (n = 12. ×. 3). Within each period the cows were further divided into a control (n = 6) or treatment (n = 6) group using a crossover design, where the cows were changed between the control and treatment group after 13 d. Treatment cows had access to TMR indoors and on pasture, whereas control cows only had access to TMR indoors. Following a.m. and p.m. milkings the cows were taken to a point equidistant between indoors and pasture and given the choice of going to pasture (1.5 ha) or to a freestall barn. Between milkings the cows had free access between the locations. Initial choice was recorded and a video camera was used to record time spent in each location. Behavior observations were recorded to establish how the cows spent their time during the day. To determine what factors influenced preference, weather conditions, milk yield, body condition score, and lameness were recorded. Initially, the cows chose indoors following milking (96.4. ±. 0.80%). Overall, the cows expressed a partial preference for pasture (71.1. ±. 1.82%), which was different from 100, 50, and 0%. Study period influenced preference with cows spending less time on pasture as the season progressed (86.7 vs. 68.3 vs. 58.3% for study periods 1, 2, and 3, respectively). Providing the cows with TMR outdoors did not affect pasture use, but resulted in an increase in TMR intake of 2.2. ±. 0.41 kg of dry matter/d. The cows spent more time on pasture as the temperature-humidity index indoors (55.6. ±. 0.92) and outdoors (54.6. ±. 0.82) increased, but rainfall and milk yield did not influence preference. Cows with lameness score >1.5 spent more time indoors (35.4. ±. 4.52 vs. 25.2. ±. 2.64% for cows with >1.5 vs. ≤1.5 lameness score, respectively). In conclusion, the cows expressed a partial preference for pasture, which was not influenced by providing TMR on pasture. © 2011 American Dairy Science Association. Source


Charlton G.L.,Harper Adams University College | Charlton G.L.,Reaseheath College | Rutter S.M.,Harper Adams University College | East M.,Reaseheath College | Sinclair L.A.,Reaseheath College
Applied Animal Behaviour Science | Year: 2011

Cattle are grazing animals so it is generally assumed that pasture is a welfare friendly system as it is natural and allows the expression of normal behaviour, which may be restricted indoors. However, high yielding dairy cows may not be able to fulfil their nutritional demands from grass alone resulting in them becoming hungry, compromising their welfare. As indoor housing and pasture may both have positive and negative effects on the welfare of dairy cattle a study was conducted to determine the preference of high genetic merit Holstein dairy cows (n = 32) in mid to late lactation to be indoors or on pasture and to establish the factors that influenced their decision. Twice a day, after milking, cows were taken to a choice point equidistant (48. m) from indoor housing and pasture, where cows chose whether to go indoors or to pasture. After their initial choice, cows could then move between indoors and pasture until the next milking. Indoors, a total mixed ration (TMR) was available ad libitum. At pasture, sward dry matter (DM) was maintained between 1800 and 3000. kg DM/ha. Decision at the choice point and time spent in each location were recorded. To determine what influenced the cow's decision, behaviour, weather conditions, milk yield, lameness, body condition score (BCS) and liveweight were recorded. From the choice point cows chose to go indoors almost twice as often as to pasture (66.2 ± 5.02% vs. 33.8 ± 5.02%, respectively) which was significantly different from 100% (P< 0.001), 50% (P = 0.004) and 0% (P< 0.001), and spent more time indoors compared to pasture (91.9 ± 2.33% vs. 8.1 ± 2.33%, respectively) which was significantly different from 100% (P = 0.001), 50% (P< 0.001) and 0% (P< 0.001). Milk yield affected preference (P = 0.005) with high yielding cows (>26.9. kg/day; n = 12) spending more time indoors than low yielding dairy cows (≤26.9. kg/day; n = 12), and there was a tendency for cows with a higher BCS (>2.7; n = 12) to spend more time at pasture (P = 0.058). Of the weather conditions rainfall influenced preference (P = 0.015) with cows spending more time indoors on days when it rained. Indoor and outdoor temperature-humidity index (THI), lameness and liveweight had no effect on preference. The results indicate that the cows in this study had a partial preference to be indoors which is likely to be influenced by the TMR, allowing high yielding cows to meet their nutritional demands. However, this partial preference does not mean that pasture is not important for the welfare of dairy cows. © 2010 Elsevier B.V. Source


Charlton G.L.,Harper Adams University College | Charlton G.L.,Reaseheath College | Rutter S.,Harper Adams University College | East M.,Reaseheath College | Sinclair L.A.,Harper Adams University College
Journal of Dairy Science | Year: 2013

Several factors influence whether dairy cattle prefer to be indoors or at pasture, including weather conditions and milk yield, but it is unclear how motivated cows are for access to pasture. One way to measure motivation is to require the animal to work (e.g., walk different distances) for access to a resource. This study investigated whether pasture access located 60, 140, or 260m from the indoor housing would affect the proportion of time dairy cows spent at pasture. Thirty-two Holstein-Friesian dairy cows were used during the study, which took place in the United Kingdom from May to July 2010. The experiment consisted of four 18-d experimental periods, with 8 cows in each period, which were further divided into 2 groups of 4 cows. Following a training period, the cows were randomly allocated to distances of 60, 140, or 260m to pasture over three 4-d measurement periods. A video camera was used to record time spent indoors and outdoors 24h/d, and manual behavior observations (0700 to 2200h) took place 6 times during each period to record how the cows spent their time in each location. The video data showed that cows spent, on average, 57.8% (±3.44) of their time outside (either at pasture or on the track). One-sample t-tests revealed that this value was different from 0% (t=16.80), 50% (t=2.26), and 100% (t=-12.28). Analysis of the percentage time spent outside revealed that distance did not influence nighttime pasture use (2100 to 0430h; F2,8=0.16; 81.0% vs. 81.0% vs. 76.7%, for 60m vs. 140m vs. 260m, respectively). In contrast, during the day (0700 to 2100h; from behavior observations), time spent at pasture declined as distance increased; that is, cows spent more time at pasture when they had to walk 60m (F2,80=10.09) than when they had to walk 140 or 260m (45.3% vs. 27.4% vs. 21.2%, respectively). Time spent at pasture decreased on rainy days (y=-1.0672x + 59.646, R2=0.09, n=48d), but the indoor temperature-humidity index (THI), the outdoor THI, and body condition score did not influence time spent outside. Under the climatic conditions of the current study in the United Kingdom, cows had a partial preference for pasture, which was influenced by distance to pasture during daytime but not at night. This shows that dairy cows were more motivated to access pasture at night compared with during the day. © 2013 American Dairy Science Association. Source

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