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323 results for “flock”
The genetic population structure of Lake Tanganyika's Lates species flock, an endemic radiation of pelagic top predators
<p>Data associated with the manuscript "The genetic population structure of Lake Tanganyika’s Lates species flock, an endemic radiation of pelagic top predators," where we investigate the genetic population structure of the four endemic <em>Lates </em>species in Lake Tanganyika.</p> <p><strong>Abstract</strong>: Life history traits are important in shaping gene flow within species and can thus determine whether a species exhibits genetic homogeneity or population structure across its range. Understanding genetic connectivity plays a crucial role in species conservation decisions, and genetic connectivity is an important component of modern fisheries management in fishes exploited for human consumption. In this study, we investigated the population genetics of four endemic <em>Lates</em> species of Lake Tanganyika (<em>Lates stappersii</em>, <em>L. microlepis</em>, <em>L. mariae</em> and <em>L. angustifrons</em>), using reduced-representation genomic sequencing methods. We find the four species to be strongly differentiated from one another, with no evidence for contemporary admixture. We also find evidence for high levels of genetic structure within <em>L. mariae</em>, with the majority of individuals from the most southern sampling site forming a genetic group distinct from the individuals at other sampling sites<em>.</em> We find evidence for much weaker structure within the other three species, <em>L. stappersii,</em> <em>L. microlepis</em>, and <em>L. angustifrons</em>, although small and unbalanced sample sizes and imprecise geographic sampling locations may hinder our ability to detect weak population structure. We call for further research into the origins of the genetic differentiation that we observe in these four species, particularly that of <em>L. mariae</em>, which may be important for the conservation and management of this species.</p> <p>Code associated with the analysis of these data can be found on GitHub at <a href="https://github.com/jessicarick/lates-popgen">https://github.com/jessicarick/lates-popgen</a>.</p>
Data from: Flock size and structure influence reproductive success in four species of flamingo in 540 captive populations worldwide
<p><strong>Summary</strong></p> <p>This dataset accompanies the publication "<strong>Flock size and structure influence reproductive success in four species of flamingo in 540 captive populations worldwide</strong>" published in Zoo Biology. It contains anonymised data from 540 captive flamingo populations, and includes the four species: <em>Phoeniconaias minor, Phoenicopterus chilensis, Phoenicopterus roseus</em> and<em> Phoenicopterus ruber</em>. Data were sourced from the Zoological Information Management System (ZIMS), operated by Species360 (https://www.species360.org/). ZIMS is the largest real-time database of comprehensive and standardized information spanning more than 1,200 zoological collections globally, and provides the number of institutions currently managing each flamingo species and both their current and historic population sizes. These data were used to investigate the relationship between reproductive success and both flock size, and structure, on a global scale.</p> <p>This dataset also contains climatic data provided by WorldClim, which were used to assess the influence of climatic variables on captive flamingo reproductive success globally. The WorldClim database averages 19 different climatic variables derived from monthly temperature and rainfall values at a 1 km spatial resolution for the period 1970-2000. Using geographic coordinates (latitude and longitude) we calculated several climatic metrics for each institution. </p> <p> </p> <p><strong>Description of the Dataset</strong></p> <p>One file is provided for each species (<em>P. minor, P. chilensis, P. roseus </em>and <em>P. ruber</em>) as a csv file. Each file contains the following 15 columns:</p> <ul> <li><strong>Institution Code: </strong>An anonymous code used to identify individual zoological institutions. </li> <li><strong>Country: </strong>The country where the institution is located.</li> <li><strong>Year: </strong>Current year (<em>t</em>).</li> <li><strong>Flock Size:</strong> Flock size in year <em>t.</em></li> <li><strong>Males: </strong>The number of males in the flock in year <em>t.</em> </li> <li><strong>Females:</strong> The number of females in the flock in year <em>t.</em></li> <li><strong>Unsexed:</strong> The number of unsexed individuals in the flock in year <em>t.</em></li> <li><strong>Proportion of Females: </strong>The proportion of the flock made up of female individuals in year <em>t</em>. </li> <li><strong>Proportion of Unsexed:</strong> The proportion of the flock made up of unsexed individuals in year <em>t.</em></li> <li><strong>Hatches:</strong> Number of birds hatched in year <em>t.</em></li> <li><strong>Proportion of Additions:</strong> The proportion of the flock in year <em>t</em> made up of additions from year <em>t-1</em> (not including new birds hatched into the flock).</li> <li><strong>MAP: </strong>Mean annual precipitation (mm).</li> <li><strong>MAT: </strong>Mean annual temperature (°C).</li> <li><strong>MAP Var: </strong>Mean annual variation in precipitation (MAP coefficient of variation).</li> <li><strong>MAT Var: </strong>Mean annual variation in temperature (MAT standard deviation).</li> </ul> <p>Note: Mean Annual Temperature (MAT) is provided by WorldClim as °C multiplied by 10, and similarly mean annual variation in temperature as MAT standard deviation multiplied by 100. In the corresponding publication, both were divided (by 10 and 100 respectively) prior to modelling to avoid confusion in the units used.</p> <p> </p> <p><strong>Acknowledgements</strong></p> <p>We acknowledge and thank all Species360 member institutions for their continued support and data input. The research which data refers to was funded by the Irish Research Council Laureate Awards 2017/2018 IRCLA/2017/60 to Y.M.B. Additionally, S.Q.S. received funding from the International Max Planck Research School for Organismal Biology. The Species360 Conservation Science Alliance would like to thank their sponsors: the World Association of Zoos and Aquariums, Wildlife Reserves of Singapore, and Copenhagen Zoo. </p> <p> </p> <p><strong>Disclaimer</strong></p> <p>Despite our best efforts at screening the data for errors and inconsistencies, some information could be erroneous. Similarly, data contained within ZIMS are based on submitted records from individual institutions, and are not subject to editorial verification, potentially permitting errors or failure to update species holdings etc. Despite this, ZIMS represents the only global database of zoo collection composition records, and as a result, is used by the IUCN, Convention on International Trade in Endangered Species (CITES), the Wildlife Trade Monitoring Network (TRAFFIC), United States Fish and Wildlife Service (USFWS) and Department for Environment, Food and Rural Affairs (DEFRA). </p> <p> </p> <p><strong>Credit</strong></p> <p>If you use this dataset, please cite the corresponding publication:</p> <p>Mooney, A., Teare, J. A., Staerk, J.,Smeele, S. Q., Rose, P., Edell, R. H., King, C. E., Conrad, L., & Buckley, Y. M. (2023). Flock size and structure influence reproductive success in four species of flamingo in 540 captive populations worldwide.<em> Zoo Biology</em>, 1–14. <a href="https://doi.org/10.1002/zoo.21753">https://doi.org/10.1002/zoo.21753</a></p> <p> </p> <p> </p>
Arbitrage equilibrium, invariance and the emergence of spontaneous order in the dynamics of birds flocking
<p>This is the dataset used to report the findings in the paper "Arbitrage equilibrium, invariance and the emergence of spontaneous order in the dynamics of birds flocking". </p>
Supplementary dataset to publication: "Genomic insight into Campylobacter jejuni isolated from commercial turkey flocks in Germany using whole-genome sequencing analysis"
<p><em>Campylobacter jejuni </em>is a zoonotic bacterium of public health significance. The present investigation was designed to assess the epidemiology and genetic heterogeneity of <em>Campylobacter jejuni</em> recovered from commercial turkey farms in Germany using whole-genome sequencing. The Illumina MiSeq<sup>®</sup> technology was used to sequence 66 <em>Campylobacter jejuni </em>isolates obtained between 2010 and 2011 from commercial meat turkey flocks located in ten German federal states. Phenotypic antimicrobial resistance was determined. Phylogeny, resistome, plasmidome and virulome profiles were analyzed using whole-genome sequencing data. Genetic resistancemarkers were identified with bioinformatics tools (AMRFinder, ResFinder, NCBI and ABRicate) and compared with the phenotypic antimicrobial resistance.</p>
Data underlying the publication: "Effects of hatching system on chick quality, welfare and health of young breeder flock offspring"
<p>The aim of the current study was to evaluate effects of two alternative hatching systems (hatchery-feeding and on-farm hatching)<br> compared to conventional hatching systems with respect to chick quality, welfare and health of a young breeder flock.<br> To study the effect of treatments on the competence of the humoral immune response, blood titres after a live attenuated NCD<br> vaccination was assessed.<br> To study differences in disease resilience, the susceptibility to develop tracheal inflammation after infection with a<br> life attenuated infectious bronchitis vaccine virus was assessed by trachea lesion scoring and expression of genes related<br> to epithelial integrity and inflammatory responses.</p>
APHA/FSA monitoring programme for Campylobacter in broiler flocks and broiler carcases in the UK (2012-2017) (FS241051, FS101126)
<p><em>Campylobacter </em>counts from broiler caecal samples and broiler carcases samples in the United Kingdom.</p>
FIGURE 33 in The Hyalella species flock of Lake Titicaca (Crustacea: Amphipoda): perspectives and drawbacks of DNA-based identiFIcation
FIGURE 33 Hyalella nefrens González & Watling, 2003, male. A, inset of distal portion of right mandible; B, right pereiopod V, medial; C, left pereiopod VI, medial; D, left pereiopod VII, medial. Scale bars: 0.1 mm (A); 0.5 mm (B-D).
FIGURE 30 in The Hyalella species flock of Lake Titicaca (Crustacea: Amphipoda): perspectives and drawbacks of DNA-based identiFIcation
FIGURE 30 Hyalella nefrens González & Watling, 2003. A, male right gnathopod I, medial; B, inset of propodus+dactylus of left counterpart of latter, medial; C, inset of palm angle and armature along lateral side of palm margin of latter, medial; D, distal portion of female left gnathopod II, medial. Scale bars: 0.2 mm (A, C); 0.1 mm (B, D).
FIGURE 32 in The Hyalella species flock of Lake Titicaca (Crustacea: Amphipoda): perspectives and drawbacks of DNA-based identiFIcation
FIGURE 32 Hyalella nefrens González & Watling, 2003, male. A, left antennule, lateral; B, left antenna, lateral; C, right pereiopod III, medial; D, left pereiopod IV, medial; E, left uropod III, dorsal; F, telson, dorsal. Scale bars: 0.5 mm (A–D); 0.1 mm (E, F).
FIGURE 27 in The Hyalella species flock of Lake Titicaca (Crustacea: Amphipoda): perspectives and drawbacks of DNA-based identiFIcation
FIGURE 27 Hyalella nefrens González & Watling, 2003. Range of configurations of dorsal armature. A–B, specimens showing three posterodistal processes, one on each pereionite VII and pleonites I–II; C, specimen with only two processes developed, one on each pleonite I–II; D, specimen with only one process, on pleonite I; E, specimen with smooth dorsum.
FIGURE 19 in The Hyalella species flock of Lake Titicaca (Crustacea: Amphipoda): perspectives and drawbacks of DNA-based identiFIcation
FIGURE 19 Hyalella hirsuta Jaume sp. nov., male. A, right pereiopod V, lateral; B, left pereiopod VI, lateral; C, left pereiopod VII, medial.
FIGURE 15 in The Hyalella species flock of Lake Titicaca (Crustacea: Amphipoda): perspectives and drawbacks of DNA-based identiFIcation
FIGURE 15 Hyalella hirsuta Jaume sp. nov., male. A, maxillule; B, maxilla; C, right uropod III, dorsal; D, telson, dorsal.
FIGURE 23 Hyalella solida Chevreux, 1907. A, male left gnathopod II in The Hyalella species flock of Lake Titicaca (Crustacea: Amphipoda): perspectives and drawbacks of DNA-based identiFIcation
FIGURE 23 Hyalella solida Chevreux, 1907. A, male left gnathopod II, medial (armature along palm margin of propodus omitted); B, inset of palm margin of latter, medial; C, distal portion of left female gnathopod II, medial. Scale bars: 0.2 mm (A); 0.1 mm (B, C).
FIGURE 18 in The Hyalella species flock of Lake Titicaca (Crustacea: Amphipoda): perspectives and drawbacks of DNA-based identiFIcation
FIGURE 18 Hyalella hirsuta Jaume sp. nov., male. A, right mandible; B, right pereiopod III, lateral; C, left pereiopod IV, lateral; D, left uropod I, posterior; E, inset of distal portion of modified spine on endopod of latter. Scale bars: 0.1 mm (A, D); 0.4 mm (B, C).
FIGURE 12 in The Hyalella species flock of Lake Titicaca (Crustacea: Amphipoda): perspectives and drawbacks of DNA-based identiFIcation
FIGURE 12 Hyalella gonzalezi Jaume sp. nov., male. A, right pereiopod V, lateral; B, right pereiopod VI, lateral; C, left pereiopod VII, medial.
FIGURE 11 in The Hyalella species flock of Lake Titicaca (Crustacea: Amphipoda): perspectives and drawbacks of DNA-based identiFIcation
FIGURE 11 Hyalella gonzalezi Jaume sp. nov., male. A, left pereiopod III, medial (arrowheads pointing to teratological armature present on anterior margin of merus); B, left pereiopod IV, medial; C, left uropod I, lateral. Scale bars: 0.4 mm (A, B); 0.2 mm (C).
FIGURE 6 in The Hyalella species flock of Lake Titicaca (Crustacea: Amphipoda): perspectives and drawbacks of DNA-based identiFIcation
FIGURE 6 Hyalella krolli Jaume sp. nov., brooding female. A, left pereiopod V with ooöstegite and coxal gill detached, medial; B, left pereiopod VI, medial; C, right pereiopod VII, lateral; D, pair of sternal gills on sternite of pereionite VII, anterior.
FIGURE 8 in The Hyalella species flock of Lake Titicaca (Crustacea: Amphipoda): perspectives and drawbacks of DNA-based identiFIcation
FIGURE 8 Hyalella gonzalezi Jaume sp. nov., male. A, left mandible; B, inset of incisor of latter; C, maxillule; D, maxilla; E, left uropod II, lateral; F, right uropod III, dorsal; G, telson, dorsal. Scale bars: 0.1 mm (A–D, F, G); 0.2 mm (E).
FIGURE 3 in The Hyalella species flock of Lake Titicaca (Crustacea: Amphipoda): perspectives and drawbacks of DNA-based identiFIcation
FIGURE 3 Hyalella krolli Jaume sp. nov. A, brooding female left gnathopod I, medial; B, inset of distal portion of propodus of latter, medial; C, inset of dactylus, medial; D, left epimeral plates, lateral; E, right pleopod I, posterior; F, right uropod I, lateral; G, distal portion of male right gnathopod I, medial. Scale bars: 0.1 mm (B, C, F, G); 0.2 mm (A, D, E).
FIGURE 7 in The Hyalella species flock of Lake Titicaca (Crustacea: Amphipoda): perspectives and drawbacks of DNA-based identiFIcation
FIGURE 7 Hyalella gonzalezi Jaume sp. nov., male. A, head with left antennule and antenna, lateral; B, coxa and basis+basal endite of left maxilliped, anterior; C, ischium+ischial endite of latter, anterior; D, carpusdactylus of latter; E, left epimeral plates I–III, lateral. Scale bars: 0.5 mm (A, E); 0.1 mm (B-D).
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