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openCC (other)Jul 2020View details →

Annual Point Count Breeding Bird Survey at Pepperwood Preserve in the California Coast Ranges 2007-2019

The Dwight Center for Conservation Science at Pepperwood is an ecological institute dedicated to educating, engaging, and inspiring our community through habitat preservation, science-based conservation, leading-edge research, and interdisciplinary educational programs. Our mission is to steward the life and landscapes of the 3,200-acre Pepperwood Preserve and to advance science-based conservation of ecosystems throughout our region and beyond. The Pepperwood Breeding Bird Survey was initiated in the spring of 2007 with the goal of establishing a set of baseline bird community data that would be built upon for years to come. Four transects (totaling 38 points) are surveyed annually using standardized five-minute point count protocols outlined by the Point Reyes Bird Observatory (now called Point Blue Conservation Science; Ballard et al. 2003) and the Handbook of Field Methods for Monitoring Landbirds (Ralph et al. 1993). Surveys are conducted by experienced volunteers during the breeding season starting in late April and ending in June, with each transect surveyed a total of three times. The Rogers Creek and Martin Creek transects were established in 2007. The Weimar Flat and Pepperwood Road transects were established in 2008 and 2012, respectively, to ensure comprehensive coverage across the various habitats that occur at the preserve including Douglas-fir forest, mixed hardwood forest, oak woodland/forest, chaparral, and open grasslands. This dataset includes data collected between 2007-2019.

openCC (other)Jan 2020View details →

Autumn departure from breeding site (date and time) in Gambel's white crowned sparrows near Toolik Field Station, Alaska, summers 2014-2016

This data set contains information about an automated radio-telemetry study conducted near Toolik Field Station examining the date that adult male and female Gambel's white-crowned sparrows (Zonotrichia leucophrys gambelli) depart the breeding site relative to the timing of breeding and sunrise/ sunset. It was funded, in part, through ARC 0909133 (to John Wingfield) and ARC 1147289 (to Marilyn Ramenofsky). It is associated with publication: https://doi.org/10.1007/s10336-020-01754-z.

openCC (other)Jan 2025View details →

Cape Sable Seaside Sparrow (Ammospiza maritima mirabilis) breast feather total mercury concentrations from the Florida Everglades, Florida, USA: breeding seasons 2016 - 2018

This dataset was used to determine hydrologic parameters influencing Cape Sable Seaside Sparrow (CSSS) mercury exposure and potential mercury effects on their reproductive success in the Florida Everglades. We collected breast feathers for total mercury determination from juvenile and adult CSSS during (or shortly after) three breeding seasons (March 1 to July 31) and monitored the same individuals' breeding performance (mate status, number of nest attempts, number of successful nest attempts, total productivity of nests, clutch size, total count of eggs, and hatch success). Hydrologic parameters (average water depths, drought length, water recession rate, and hydroperiod) were estimated using the Everglades Depth Estimation Network and in situ depth measurements. Data collection is complete.

openCC0Apr 2023View details →

CBS06 Line transects surveys of breeding birds throughout Konza Prairie

Like CPB01 and PBG051, this dataset includes records of bird species based on line transect sampling. These surveys re-initiate most of the original KNZ transects surveyed from 1981-2009 (initiated by Zimmerma), continue the two focal 300-m transects conducted from 2011-2016 by Sandercock on watersheds C3A, C3B, C3C, C1A, and 1D, (but not the peripheral segments which have been dropped), and adds two new 300-m transects to additional watersheds with the goals of (i) replicating all surveyed treatments at the watershed level, (ii) adequately sampling the grassland habitats present on Konza as of 2017, (iii) capturing transitions in bird community in response to woody encroachment and fire reversal treatments. The goals are to document and quantify long-term changes in the population sizes of breeding birds at Konza prairie by obtaining a standardized measure of annual breeding bird abundance at the site level and individual watershed or treatment level.

opencc-by-4.0Jan 2020View details →

Developing a new genic SSR primer database for Vicia faba molecular breeding

Accelerating breeding programs require the use of efficient molecular tools and enhance the diversity of local faba bean cultivars. The aim of this study is to develop a new genetic database of available SSR primers, to classify these PCR primers according to the target genes and their respective cell processes, to assess the diversity and efficacy of the microsatellite markers applied to faba bean and to study the genetic structure of some selected faba bean cultivars. Approximately 75,605 and 148,196 previously published genomic and transcriptomic sequences were used to detect possible simple sequence repetitions in faba genomic content. The number of identified SSRs was 25502 and 12319, where the distribution to different repeat type classes shows that, the trinucleotide was the highest number of repeat counts followed by dinucleotide repeats. These genic SSR sequences were used to design 1091 PCR primers, out of which only 238 (21.8%) primers target genomic sequences and the other 853 PCR primers target transcriptomic sequences. The annotation of gene-targeted SSRs has shown that approximately 897 genes are targeted through our designed SSR primers. About 1890 gene ontology (GO) identification code has been obtained. The GOs keywords distributed between distinct cell molecular features, where the highest amount of redundant sentences is the technical word, domain and molecular feature phrases with 554, 196 and 160 GOs, respectively. These GOs belong to the general level of gene ontology, such as molecular function, cellular component and biological process with 544, 670 and 676 GOs, respectively. Twenty-seven SSR PCR primers were synthesized to genotype 12 Egyptian faba bean genotypes. About 11 SSR gave from 1 to 2 PCR bands, other gave only one sharp band with polymorphic band size. The number of polymorphic primers was 13 primers. The polymorphic mean polymorphism information content was 0.3 which implies moderate informativeness.

opencc-by-4.0Dec 2019View details →

Data for Bovine breed-specific augmented reference graphs facilitate accurate sequence read mapping and unbiased variant discovery

Description of the datasets Data are organized as folders and compressed with tar.gz. There are two compressed data folder: data which used for cattle genome graphs experiment and data_human which we used for human genome graphs experiment.  Cattle genome graphs experiments First you need to unzip the file using command tar -xvzf data.tar.gz. After unzipping, the data folder is organized as follows: <ul> <li>Utilities: contain bovine ARS-UCD 1.2 fasta reference with the accompanying index.</li> <li>Bin: contain the softwares used in the paper (vg, liftover, vcf2diploid)</li> <li>Part1: data for analysis in variant prioritization section, further subdivided into: <ul> <li>vcf_sim: variant files from four animal in each breed used to simulate reads</li> <li>reads_sim: simulated short reads used for read mapping</li> <li>vcf_freq: variants augmented to graphs filtered based on allele frequency</li> </ul> </li> <li>Part2: data used for analysis in the section of graph mapping with breeds-filtered variants, further subdivided into: <ul> <li>vcf_breed: variant files used to graphs construction.</li> </ul> </li> <li>Part3: data used for analysis in the section of consensus genome, further subdivided into: <ul> <li>read_sims: simulated reads as in the part1, but the coordinates are liftovered to the new consensus genomes.</li> <li>reference: contain the original reference and consensus references.</li> <li>vcf_consensus: contain major allele variants to construct consensus genomes.</li> </ul> </li> <li>Part4: data analysis in the section of whole genome graph construction and variant genotyping. <ul> <li>vcf_construct: variants from chromosome 1-29 from 82 Brown Swiss used to construct BSW whole genome graph.</li> <li>BSW_graph: whole genome Brown Swiss graph with the three accompanying indexes (xg,gcsa, and gbwt).</li> </ul> </li> </ul> Human genome graphs experiments First you need to unzip the data_human file using command tar -xvzf data_hum.tar.gz. After unzipping, the data folder is organized as follows: <ul> <li>reference: the g1k_v37 reference used as a graph backbone</li> <li>vcf_sim: variant files from four individuals in each population used to simulate reads</li> <li>reads_sim: simulated short reads used for read mapping</li> <li>vcf_freq: variants augmented to graphs filtered based on allele frequency</li> </ul>

opencc-by-4.0Jan 2014View details →

Figure 1 in Home range and foraging habitat selection by breeding lesser kestrels (Falco naumanni) in Greece

Figure 1. Minimum convex polygon home ranges (outer: 100%, interior: 95% of locations) of male (A) and female (B) lesser kestrels during the breeding season in central Greece, 2008.

opencc-zeroOct 2020View details →

Data from: First records of complete annual cycles in water rails Rallus aquaticus show evidence of itinerant breeding and a complex migration system

In water rails Rallus aquaticus, northern and eastern populations are migratory while southern and western populations are sedentary. Few details are known about the annual cycle of this elusive species. We studied movements and breeding in water rails from southernmost Norway where the species occurs year-round. Colour-ringed wintering birds occurred only occasionally at the study site in summer, and vice versa. Geolocator tracks revealed that wintering birds (n = 10) migrated eastwards in spring to breed on both sides of the Baltic Sea, whereas a single breeding bird from the study site wintered in north Italy. Ambient light records of geolocator birds further indicated that all but one incubated 2–4 clutches per season. By combining information on incubation and movement, we found evidence for itinerant breeding in three individual birds: After a first breeding attempt (one did not incubate), all moved 129–721 km to breed again. This behaviour is rarely recorded in birds and was unexpected because the water rail is described as monogamous with both parents caring for eggs and chicks. The study greatly improves our knowledge about the annual cycle and reproduction in water rails. However, more studies are warranted to evaluate the generality of our findings and causes of breeding itinerancy.

opencc-zeroNov 2019View details →

H_GRONINGEN - Western marsh harriers (Circus aeruginosus, Accipitridae) breeding in Groningen (the Netherlands)

H_GRONINGEN - Western marsh harriers (Circus aeruginosus, Accipitridae) breeding in Groningen (the Netherlands) is a bird tracking dataset collected by the <a href="https://grauwekiekendief.nl/">Grauwe kiekendief - Kenniscentrum Akkervogels (GKA)</a> / Dutch Montagu's Harrier Foundation and published by the <a href="https://www.inbo.be/en">Research Institute for Nature and Forest (INBO)</a>. It contains animal tracking data collected for the project/study H_GRONINGEN, using trackers developed by the University of Amsterdam Bird Tracking System (UvA-BiTS, <a href="http://www.uva-bits.nl">http://www.uva-bits.nl</a>). The study was operational from 2012 until 2018. In total 4 individuals of western marsh harriers (Circus aeruginosus) have been tagged in their breeding area in the province Groningen (the Netherlands) close to the Netherlands-Germany border, mainly to study their habitat use and migration behaviour. Data are uploaded from the UvA-BiTS database to Movebank and from there archived on Zenodo (see <a href="https://github.com/inbo/bird-tracking">https://github.com/inbo/bird-tracking</a>). No new data are expected. See Milotic et al. (2020, <a href="https://doi.org/10.3897/zookeys.947.52570">https://doi.org/10.3897/zookeys.947.52570</a>) for a more detailed description of this dataset. <h2>Files</h2> Data in this package are exported from Movebank study <a href="https://www.movebank.org/cms/webapp?gwt_fragment=page=studies,path=study922263102">922263102</a>. Fields in the data follow the <a href="http://vocab.nerc.ac.uk/collection/MVB">Movebank Attribute Dictionary</a> and are described in <code>datapackage.json</code>. Files are structured as a <a href="https://specs.frictionlessdata.io/data-package/">Frictionless Data Package</a>. You can access all data in R via <code>https://zenodo.org/records/10053658/files/datapackage.json</code> using <a href="https://frictionlessdata.github.io/frictionless-r/">frictionless</a>. <ul> <li>datapackage.json: technical description of the data files.</li> <li>H_GRONINGEN-reference-data.csv: reference data about the animals, tags and deployments.</li> <li>H_GRONINGEN-gps-yyyy.csv.gz: GPS data recorded by the tags, grouped by year.</li> <li>H_GRONINGEN-acceleration-yyyy.csv.gz: acceleration data recorded by the tags, grouped by year.</li> </ul>

opencc-zeroDec 2022View details →

Efficient genomics based 'end-to-end' selective tree breeding framework

Since their initiation in the 1950s, worldwide selective tree breeding programs followed the recurrent selection scheme of repeated cycles of selection, breeding (mating), and testing phases and essentially remained unchanged to accelerate this process or address environmental contingences and concerns. Here, we introduce an "end-to-end" selective tree breeding framework that: 1) leverages strategically preselected GWAS-based sequence data capturing trait architecture information, 2) generates unprecedented resolution of genealogical relationships among tested individuals, and 3) leads to the elimination of the breeding phase through the utilization of readily available wind-pollinated (OP) families. Individuals' breeding values generated from multi-trait multi-site analysis were also used in an optimum contribution selection protocol to effectively manage genetic gain/co-ancestry trade-offs and traits' correlated response to selection. The proof-of-concept study involved a 40-year-old spruce OP testing population growing on three sites in British Columbia, Canada, clearly demonstrating our method's superiority in capturing most of the available genetic gains in a substantially reduced timeline relative to the traditional approach. The proposed framework is expected to increase the efficiency of existing selective breeding programs, accelerate the start of new programs for ecologically and environmentally important tree species, and address climate-change caused biotic and abiotic stress concerns more effectively.

opencc-by-4.0Nov 2023View details →

Raw landmarks related to the paper, "Evolution under intensive industrial breeding: skull size and shape comparison between historic and modern pig lineages "

PLEASE NOTE: This dataset has been superseeded by an updated version which has the correct number of specimens as referred to in the below article. It can be accesssed at: https://doi.org/10.5281/zenodo.14262754     Raw coordinates (p x k = 82 x 3) of domestic and wild pig skulls that form the dataset for the paper, "Evolution under intensive industrial breeding: skull size and shape comparison between historic and modern pig lineages "

opencc-zeroNov 2023View details →

Black-legged kittiwake abundance and breeding productivity, OSPAR region II

This data set contains information on breeding abundance and breeding productivity of black-legged kittiwake (Rissa tridactyla) in OSPAR Region II (Greater North Sea). These data have been used to construct a demographic indicator of breeding productivity as part of OSPAR Quality Status Report 2023, and for reporting under the European Union's Marine Strategy Framework Directive.

opencc-zeroNov 2023View details →

Male song structure predicts offspring recruitment to the breeding population in a migratory bird

Bird song is a classic example of a sexually selected trait, but much of the work relating individual song components to fitness has not accounted for song typically being composed of multiple, often-correlated components, necessitating a multivariate approach. We explored the role of sexual selection in shaping complex male song of house wrens (Troglodytes aedon) by simultaneously relating its multiple components to fitness using multivariate selection analysis, which is widely used in insect and anuran studies but not in birds. The analysis revealed significant variation in the form and strength of selection acting on song across different selection episodes, from nest-site defense to recruitment of offspring to the breeding population. Males that sang more song typically employed in close communication sired more offspring that were subsequently recruited to the breeding population than those that sang far-communication song. However, this relationship was not consistent across earlier selection episodes, as evidenced by non-linear selection acting on these song components in other contexts. Collectively, our results present a complex picture of multivariate selection on male song structure that would not be evident using univariate approaches and suggest possible trade-offs within and among song components at different points of the breeding season.

Fig. 9 in Distribution, systematics and nomenclature of the three taxa of Common Stonechats (Aves, Passeriformes, Muscicapidae, Saxicola) that breed in the Caucasian region

Fig. 9. Main types of variations of tail colouration of males in Saxicola maura variegatus. A, 5 to 10 mm; B, 11 to 20 mm; C, 21 mm and more.

Fig. 8 in Distribution, systematics and nomenclature of the three taxa of Common Stonechats (Aves, Passeriformes, Muscicapidae, Saxicola) that breed in the Caucasian region

Fig. 8. Adult males in breeding plumage, ventral (A–C) and dorsal (D–E) view. A, D, Saxicola maurus armenicus, coll. No. 28292/109, Azerbaijan, Nakhichevan Autonomous Republic, Dzul'fa Distr., NW slopes of Ilan-Dag Mt., 39°08.78′ N, 45°40.47′ E, 1,160 m a.s.l., 12 June 1974, Yu.A. Volnenko leg. (NMNH); B, E, Saxicola maurus variegatus, coll. No. 28005/106, Azerbaijan, Ismailli Distr., vicinity of Ismailly, 40°46.99′ N, 48°06.73′ E, 540 m a.s.l., 2 July 1973, V.M. Loskot leg. (NMNH); C, F, S. m. variegatus, coll. No. 173387/208-2002, Russia, Rostov Prov., Don River Delta, floodplain at mouth of Aksay River, Starodon'e Lake, 47°17.00′ N, 40°15.10′ E, 1 m a.s.l., 2 May 1997, G.B. Bakhtadze leg. (ZIN).

Fig. 7 in Distribution, systematics and nomenclature of the three taxa of Common Stonechats (Aves, Passeriformes, Muscicapidae, Saxicola) that breed in the Caucasian region

Fig. 7. Subadult females in spring plumage, ventral (A, B) and dorsal (C, D) view. A, C, Saxicola maurus armenicus, coll. No. 136211, Iraq, Wasit Governorate, Bagsaya ruins, 32°53.73′ N, 46°27.60′ E, 95 m a.s.l., 17 March 1914, P.V. Nesterov leg. (ZIN); B, D, Saxicola maurus variegatus, coll. No. 136212, the same locality, collector and collection, 16 March 1914.

Fig. 4 in Distribution, systematics and nomenclature of the three taxa of Common Stonechats (Aves, Passeriformes, Muscicapidae, Saxicola) that breed in the Caucasian region

Fig. 4. First year male of Saxicola rubicola rubicola in fresh autumnal plumage. Holotype of Saxicola torquata amaliae Buturlin, 1929. ZMMU, coll. No. R-13488, Russia, Republic Severnaya Osetiya – Alaniya, vicinity of Vladikavkaz, 42°59.99′ N, 44°38.53′ E, 750 m a.s.l., 13 Oct. 1919, L.B. Beme leg. Ventral (A) and dorsal (B) view.

Fig. 5 in Distribution, systematics and nomenclature of the three taxa of Common Stonechats (Aves, Passeriformes, Muscicapidae, Saxicola) that breed in the Caucasian region

Fig. 5. Females in fresh autumnal plumage, ventral (A, B) and dorsal (C, D) view. A, C, Saxicola maurus armenicus, coll. No. 136219, Iran, West Azerbaijan Prov., Vezne River valley, 36°34.51′ N, 45°10.80′ E, 1,400 m a.s.l., 18 July 1914, ad., P.V. Nesterov leg. (ZIN); B, D, Saxicola maurus variegatus, coll. No. R-97651, Russia, Krasnodar Terr., vicinity of Krasnodar, 45°16.60′ N, 38°05.39′ E, 3 m a.s.l., 10 Aug. 1973, 1-st year, A.M. Peklo leg. (ZMMU).

Fig. 3 in Distribution, systematics and nomenclature of the three taxa of Common Stonechats (Aves, Passeriformes, Muscicapidae, Saxicola) that breed in the Caucasian region

Fig. 3. Males in fresh autumnal plumage, ventral (A–C) and dorsal (D–F) view. A, D, Saxicola maurus armenicus, coll. No. 136248, Iran, West Azerbaijan Prov., Vezne River valley, 36°34.51′ N, 45°10.80′ E, 1,400 m a.s.l., 22 July 1914, ad., P.V. Nesterov leg. (ZIN); B–F, Saxicola maurus variegatus, Georgia, Kakhetiya, vicinity of Lagodekhi, 41°48.28′ N, 46°16.56′ E, 380 m a.s.l., L.A. Portenko leg. (ZIN): coll. No. 163316/425- 974, 19 Sept. 1953, ad. (B, E) and coll. No. 163315/425-974, 21 Sept. 1953, 1-st year (C, F).

Fig. 2 in Distribution, systematics and nomenclature of the three taxa of Common Stonechats (Aves, Passeriformes, Muscicapidae, Saxicola) that breed in the Caucasian region

Fig. 2. Birds in nesting plumage. A, Saxicola maurus armenicus, coll. No. 28126/108, Azerbaijan, Nakhichevan Autonomous Republic, Dzul'fa Distr., NW slopes of Ilan-Dag Mt., 39°08.78′ N, 45°40.47′ E, 1,160 m a.s.l., 12 June 1974, female, Yu.A. Volnenko leg. (NMNH); B, Saxicola maurus variegatus, coll. No. 137879, Russia, Kabardino-Balkar Republic, Prokhladnyy (= Prokhladnaya Vill.), 43°45.11′ N, 44°05.79′ E, 180 m a.s.l., 2 July 1883, male, K.N. Rossikov leg. (ZIN).