Find research datasets worth reusing

opencc-by-4.0Oct 2023View details →

Genetic variability among and within domestic Old and New World Camels at the α-lactalbumin gene (LALBA) reveals new alleles and polymorphisms responsible for differential expression

Supplementary Figure 1. Schematic representation of the LALBA gene in camelids. Boxes indicate the exons (black for the un-translated, white for the signal peptide and grey for the translated). The line shows introns, 5’- and 3’-flanking regions. Supplementary Figure 2. Alignment of the α-LA calcium-binding site (red rectangle) of 23 terrestrial species available in the UniProt database (<a href="http://www.uniprot.org/uniprot/">http://www.uniprot.org/uniprot/</a>). The calcium-binding site in the Camelus dromedarius is indicated by a yellow rectangle.

opencc-by-nc-1.0Jan 2020View details →

Marble domestic fountain, Tarraco, Tarragona

Marble domestic fountain from the site of Tarraco (Tarragona, Spain), dated in the first half of the 2nd century AD. Domestic marble fountain replicating a nymphaeum of wich half is preserved. It would have decorated the peristyle or garden of a domus in the residential area of Tarraco. 2078 photos completely processed in Reality Capture. The project was done with the support of the National Archaeological Museum of Tarragona and the Agència Catalana del Patrimoni Cultural. Catalog No. MNAT 375. Museu Nacional Arqueològic de Tarragona (2019): Tarraco: Exposición de síntesis. Generalitat de Catalunya Publicacions. Source: Objaverse 1.0 / Sketchfab

opencc-by-4.0Mar 2024View details →

Phased T2T reference genome and pangenome reveal expanded resistance gene analogs in apple domestication

Phased T2T reference genome and pangenome reveal expanded resistance gene analogs in apple domestication The data contains two files, namely genome file and genome annotation file: 1. Genome: This file contains 12 genomes for 5 species (cultivar), namely: Malus domestica cv. ‘Golden Delicious’ (GD), Malus domestica cv. ‘Gala’ (Gala), Malus domestica cv. ‘Honeycrisp’ (HC), Malus domestica cv. ‘HFTH1’ (HFTH1), Malus baccata (Mba), Malus sieversii (Msi), and Malus sylvestris (Msy) 2. Genome annotation: Corresponding to the genome file. Note: Hap1 and hap2 represent two haplotypes of a species (cultivar), all data used for the construction of pan-genomes and comparative genomics analysis.

opencc-by-4.0Feb 2024View details →

Muller's Ratchet in Action: The Erosion of Sexual Reproduction Genes in Domesticated Cassava (Manihot esculenta)

Data Files for research study on Cassava gene evolutionary selection.

opencc-by-4.0Sep 2024View details →

Job Displacement, Unemployment Benefits and Domestic Violence

This is the replication package for the empirical analysis in  Sonia Bhalotra, Diogo Britto, Paolo Pinotti and Breno Sampaio "Job Displacement, Unemployment Benefits and Domestic Violence" to be published in the Review of Economic Studies. All instruction for the package can be found in the doc file Readme.docx.

Subspecies and Distribution. B. j. javanicus d'Alton, 1823 — Java, perhaps Bali. B. j. birmanicus Lydekker, 1898 — Asian mainland including Myanmar, S China (S Yunnan, current presence uncertain), Laos, Vietnam, Thailand, Cambodia, and N Peninsular Malaysia. B. j. low: Lydekker, 1912 — Borneo. The domestic form of the Banteng has been introduced, and is now feral, in N Australia, New Guinea, and on various islands of Indonesia (Bali, Sangihe, Sulawesi, Sumbawa, Sumba, and Enggano) and occurs in domestication throughout the islands of SE Asia. in Bovidae

Subspecies and Distribution. B. j. javanicus d'Alton, 1823 — Java, perhaps Bali. B. j. birmanicus Lydekker, 1898 — Asian mainland including Myanmar, S China (S Yunnan, current presence uncertain), Laos, Vietnam, Thailand, Cambodia, and N Peninsular Malaysia. B. j. low: Lydekker, 1912 — Borneo. The domestic form of the Banteng has been introduced, and is now feral, in N Australia, New Guinea, and on various islands of Indonesia (Bali, Sangihe, Sulawesi, Sumbawa, Sumba, and Enggano) and occurs in domestication throughout the islands of SE Asia.

Subspecies and Distribution. S. s. scrofa Linnaeus, 1758 — W Europe, from Denmark, Germany, Poland, and Czech Republic to N Italy and N Iberian Peninsula; possibly also Albania. The taxonomic status of animals in Austria, Switzerland, Slovenia, and Slovakia is unclear but presumably these populations are included in scrofa, as are the populations of Sweden, Finland, and the Baltic states. However, restocking of once depleted populations, for example in Italy, has likely involved the introduction and mixing of this subspecies with other subspecies, such as attila. S. s. affinis Gray, 1847 — S India and Sri Lanka. S. s. algirus Loche, 1867 — Tunisia, Algeria, and Morocco, on the coastal side of the mountains or in the low montane areas. S. s. attila Thomas, 1912 — Hungary, Ukraine, C & S Belarus, Romania, Moldova, and S Russia towards the N flank of the Caucasus, but not including the Transcaucasian countries of Georgia, Armenia, and Azerbaijan. The range possibly extends as far S as the Mesopotamian Delta in Iraq, in which case it would likely include W & SW Iran, and possibly E Turkey and Syria, where it borders with lybicus. Such a range could not be easily reconciled with a statement by Groves that "the difference between pigs from N and S of the Caucasus is quite striking; Transcaucasian boars are certainly not attila." This subspecies may also extend into C Asia and include Kazakhstan, Uzbekistan, and Turkmenistan, but no data exist to support this. S. s. baeticus Thomas, 1912 — originally described from Coto Donana, S Spain, and later merged with meridionalis; also S Portugal. Unless evidence is found that these Italian and Iberian populations are the relics of a much larger formerly contiguous range, this subspecies should be kept as distinct. S. s. coreanus Heude, 1897 — Korean Peninsula. S. s. eristatus Wagner, 1839 — Himalayas S to C India and E to Indochina (N of the Kra Isthmus). S. s. davidi Groves, 1981 — the arid zone from E Iran to Gujarat, including Pakistan and NW India, and perhaps N to Tajikistan. S. s. leucomystax Temminck, 1842 — main Is ofJapan (Honshu, Shikoku, Kyushu, Nakadori, Hiburijima, Tojima, Kushima, and other smaller Is). S. s. lybicus Gray, 1868 — Bulgaria, Greece, Turkey, Syria, Jordan, Israel, Palestine, in the past also in Lybia, and Egypt. The former Yugoslavia was included in its range, which would suggest that now Slovenia, Serbia, Croatia, Bosnia and Herzegovina, Montenegro, and Kosovo are within the range of this subspecies, although the exact boundaries are unclear. Pigs from Albania have been assigned to S. s. scrofa. S. s. majori De Beaux & Festa, 1927 — C & S Italian Peninsula. S. s. menidionalis Forsyth Major, 1882 — Corsica and Sardinia, with the proviso that the two populations are very likely to be introduced or feral. S. s. moupinensis Milne-Edwards, 1871 — China, S to Vietnam and W to Sichuan. S. s. nigripes Blanford, 1875 — the flanks of the Tianshan mountains in Kyrgyzstan and NW China (Xinjiang). An animal photographed in NE Iran (Golestan) looked like this subspecies. S. s. nukiuanus Kuroda, 1924 — Iriomote, Ishigaki, Okinawa, Tokunoshima, Amamioshima, and Kakerome Is in the Ryukyu chain in extreme S Japan, though some of these populations have hybridized with introduced domesticates. S. s. sibiricus Staffe, 1922 — Mongolia and Transbaikal (S & E of Lake Baikal). S. s. tawvanus Swinhoe, 1863 — Taiwan. S. s. ussuricus Heude, 1888 — far E Russia and the Manchurian region (China). Korean populations were previously included in this subspecies, but based on new evidence, the Korean taxon seems more similar to moupinensis. S. s. vittatus Boie, 1828 — Malay Peninsula, S of the Isthmus of Kra, the offshore islands of Terutai and Langkawi, Sumatra, Riau Archipelago, Java, Bali, and a range of smaller islands around these, including Babi, Bakong, Batam, Bawean, Bengkalis, Bintan, Bulan, Bunguran, Cuyo, Deli, Durian, Enggano, Galang, Jambongan, Karimon (Riau Is), Kundur, Lagong, Laut, Lingga, Lingung, Mapor, Moro Kecil, North Pagai, Nias, Panaitan, Payong, Penang, Pinie, Rupat, Siantan, Siberut, Simeulue, Singkep, Sugi, Sugi Bawa, Telibon, Tinggi, Tuangku, and the Tambelan Is. This species was originally present from the British Is in the extreme W, through Eurasia from S Scandinavia to S Siberia, extending as far E as Korea and Japan, and SE into some of the Sunda Is and Taiwan. In the S the species ranged along the Nile Valley to Khartoum, and N of the Sahara in Africa, more orless following the continental coasts of S, E, and SE Asia. Within this range it was absent only from extremely dry deserts, e.g. the driest regions of Mongolia and in China W of Sichuan; and alpine zones, such as the high altitudes of Pamir and Tien Shan. In recent centuries, the range of S. scrofa has changed dramatically because of hunting and changes in available habitat. The species disappeared from the British Is in the 17" century, from Denmark in the 19" century, and was greatly reduced in range and numbers in the 20" century from areas as distant as Tunisia, Sudan, Germany, and Russia. Following these severe declines, there were some slight population recoveries in Russia, Italy, Spain, and Germany in the mid-20™ century, and natural and assisted range expansions in Denmark and Sweden. The species has also been inadvertently reintroduced in various locations in the Great Britain via escapees of mixed origin from commercial farming enterprises. Ex-S. scrofa stocks also occur as introduced feral populations in various other parts of the world, including Australia, New Zealand, the eastern Malay Archipelago, and in North, Central, and South America. In all of these areas they are now generally recognized as a major pest. in Suidae

Subspecies and Distribution. S. s. scrofa Linnaeus, 1758 — W Europe, from Denmark, Germany, Poland, and Czech Republic to N Italy and N Iberian Peninsula; possibly also Albania. The taxonomic status of animals in Austria, Switzerland, Slovenia, and Slovakia is unclear but presumably these populations are included in scrofa, as are the populations of Sweden, Finland, and the Baltic states. However, restocking of once depleted populations, for example in Italy, has likely involved the introduction and mixing of this subspecies with other subspecies, such as attila. S. s. affinis Gray, 1847 — S India and Sri Lanka. S. s. algirus Loche, 1867 — Tunisia, Algeria, and Morocco, on the coastal side of the mountains or in the low montane areas. S. s. attila Thomas, 1912 — Hungary, Ukraine, C & S Belarus, Romania, Moldova, and S Russia towards the N flank of the Caucasus, but not including the Transcaucasian countries of Georgia, Armenia, and Azerbaijan. The range possibly extends as far S as the Mesopotamian Delta in Iraq, in which case it would likely include W & SW Iran, and possibly E Turkey and Syria, where it borders with lybicus. Such a range could not be easily reconciled with a statement by Groves that "the difference between pigs from N and S of the Caucasus is quite striking; Transcaucasian boars are certainly not attila." This subspecies may also extend into C Asia and include Kazakhstan, Uzbekistan, and Turkmenistan, but no data exist to support this. S. s. baeticus Thomas, 1912 — originally described from Coto Donana, S Spain, and later merged with meridionalis; also S Portugal. Unless evidence is found that these Italian and Iberian populations are the relics of a much larger formerly contiguous range, this subspecies should be kept as distinct. S. s. coreanus Heude, 1897 — Korean Peninsula. S. s. eristatus Wagner, 1839 — Himalayas S to C India and E to Indochina (N of the Kra Isthmus). S. s. davidi Groves, 1981 — the arid zone from E Iran to Gujarat, including Pakistan and NW India, and perhaps N to Tajikistan. S. s. leucomystax Temminck, 1842 — main Is ofJapan (Honshu, Shikoku, Kyushu, Nakadori, Hiburijima, Tojima, Kushima, and other smaller Is). S. s. lybicus Gray, 1868 — Bulgaria, Greece, Turkey, Syria, Jordan, Israel, Palestine, in the past also in Lybia, and Egypt. The former Yugoslavia was included in its range, which would suggest that now Slovenia, Serbia, Croatia, Bosnia and Herzegovina, Montenegro, and Kosovo are within the range of this subspecies, although the exact boundaries are unclear. Pigs from Albania have been assigned to S. s. scrofa. S. s. majori De Beaux & Festa, 1927 — C & S Italian Peninsula. S. s. menidionalis Forsyth Major, 1882 — Corsica and Sardinia, with the proviso that the two populations are very likely to be introduced or feral. S. s. moupinensis Milne-Edwards, 1871 — China, S to Vietnam and W to Sichuan. S. s. nigripes Blanford, 1875 — the flanks of the Tianshan mountains in Kyrgyzstan and NW China (Xinjiang). An animal photographed in NE Iran (Golestan) looked like this subspecies. S. s. nukiuanus Kuroda, 1924 — Iriomote, Ishigaki, Okinawa, Tokunoshima, Amamioshima, and Kakerome Is in the Ryukyu chain in extreme S Japan, though some of these populations have hybridized with introduced domesticates. S. s. sibiricus Staffe, 1922 — Mongolia and Transbaikal (S & E of Lake Baikal). S. s. tawvanus Swinhoe, 1863 — Taiwan. S. s. ussuricus Heude, 1888 — far E Russia and the Manchurian region (China). Korean populations were previously included in this subspecies, but based on new evidence, the Korean taxon seems more similar to moupinensis. S. s. vittatus Boie, 1828 — Malay Peninsula, S of the Isthmus of Kra, the offshore islands of Terutai and Langkawi, Sumatra, Riau Archipelago, Java, Bali, and a range of smaller islands around these, including Babi, Bakong, Batam, Bawean, Bengkalis, Bintan, Bulan, Bunguran, Cuyo, Deli, Durian, Enggano, Galang, Jambongan, Karimon (Riau Is), Kundur, Lagong, Laut, Lingga, Lingung, Mapor, Moro Kecil, North Pagai, Nias, Panaitan, Payong, Penang, Pinie, Rupat, Siantan, Siberut, Simeulue, Singkep, Sugi, Sugi Bawa, Telibon, Tinggi, Tuangku, and the Tambelan Is. This species was originally present from the British Is in the extreme W, through Eurasia from S Scandinavia to S Siberia, extending as far E as Korea and Japan, and SE into some of the Sunda Is and Taiwan. In the S the species ranged along the Nile Valley to Khartoum, and N of the Sahara in Africa, more orless following the continental coasts of S, E, and SE Asia. Within this range it was absent only from extremely dry deserts, e.g. the driest regions of Mongolia and in China W of Sichuan; and alpine zones, such as the high altitudes of Pamir and Tien Shan. In recent centuries, the range of S. scrofa has changed dramatically because of hunting and changes in available habitat. The species disappeared from the British Is in the 17" century, from Denmark in the 19" century, and was greatly reduced in range and numbers in the 20" century from areas as distant as Tunisia, Sudan, Germany, and Russia. Following these severe declines, there were some slight population recoveries in Russia, Italy, Spain, and Germany in the mid-20™ century, and natural and assisted range expansions in Denmark and Sweden. The species has also been inadvertently reintroduced in various locations in the Great Britain via escapees of mixed origin from commercial farming enterprises. Ex-S. scrofa stocks also occur as introduced feral populations in various other parts of the world, including Australia, New Zealand, the eastern Malay Archipelago, and in North, Central, and South America. In all of these areas they are now generally recognized as a major pest.

Distribution. Sulawesi and adjacent Is (Buton, Kabaena, Muna, Peleng, Lembeh, and on some of the Togian Is); thought to be extinct on Selayar I. Pigs have been widely domesticated through the Indonesian archipelago and beyond. This primarily involved the Eurasian Wild Pig (S. scrofa), but also S. celebensis, the only other species of pig successfully domesticated. Mitochondrial DNA studies of the dispersion of these domesticated forms agree on three major dispersal events, two involving S. scrofa and one S. celebensis. Evidence supports an early human-mediated translocation of S. celebensis to Flores and Timor and two later, separate human-mediated dispersals of domestic pig through islands of SE Asia into Oceania. In addition to Flores and Timor, S. celebensis is also thought to occur in its domesticated form on Halmahera, Lendu, Roti, and Savur Is, and even on Simeulue and Nias Is to the W of Sumatra and far from its island of origin, Sulawesi. In the Moluccas, and possibly elsewhere in this region, introduced S. celebensis are thought to have hybridized with other introduced pigs of S. scrofa derivation, and apparent hybrids between these species are now reported to survive on a number of islands, including Salawatti, Great Kei, Dobu, Seram, Ambon, Bacan, Ternate, Morotai, and New Guinea. It is also reported that in the 19" century the sows of domestic pigs in Sulawesi frequently mated with wild animals, after which they returned to their villages. in Suidae

Distribution. Sulawesi and adjacent Is (Buton, Kabaena, Muna, Peleng, Lembeh, and on some of the Togian Is); thought to be extinct on Selayar I. Pigs have been widely domesticated through the Indonesian archipelago and beyond. This primarily involved the Eurasian Wild Pig (S. scrofa), but also S. celebensis, the only other species of pig successfully domesticated. Mitochondrial DNA studies of the dispersion of these domesticated forms agree on three major dispersal events, two involving S. scrofa and one S. celebensis. Evidence supports an early human-mediated translocation of S. celebensis to Flores and Timor and two later, separate human-mediated dispersals of domestic pig through islands of SE Asia into Oceania. In addition to Flores and Timor, S. celebensis is also thought to occur in its domesticated form on Halmahera, Lendu, Roti, and Savur Is, and even on Simeulue and Nias Is to the W of Sumatra and far from its island of origin, Sulawesi. In the Moluccas, and possibly elsewhere in this region, introduced S. celebensis are thought to have hybridized with other introduced pigs of S. scrofa derivation, and apparent hybrids between these species are now reported to survive on a number of islands, including Salawatti, Great Kei, Dobu, Seram, Ambon, Bacan, Ternate, Morotai, and New Guinea. It is also reported that in the 19" century the sows of domestic pigs in Sulawesi frequently mated with wild animals, after which they returned to their villages.

opencc-by-4.0Oct 2022View details →

Genetic basis of cytonuclear conflicts in citrus hybridization, domestication, and diversification

184.cp.variations.map.vcf.zip--the chloroplast variation map of 184 samples 184.mt.variations.map.vcf.zip----the mitochondrial variation map of 184 samples aligment1.fa-- the group of grapefruit, sweet orange and sour orange for mitochondrial heteroplasmy analysis aligment2.fa-- the group of lemon for mitochondrial heteroplasmy analysis coverage depth of 184 short reads samples.zip -- the coverage depth of BAMs in mitochondrial variation map in 184 samples Fortunella hindsii mitochondrial genome.gb -- the conservation proteins annotation of kumquat reference mitochondrial genome GWAS-118.samples.input.phenotype.for GWAS.txt -- the inputfiles for GWAS  GWAS-LD.linked.input.gwas.vcf.gz -- the LD linked variations for GWAS LD.purning.nuclear.variation.map.vcf.gz -- LD purning nuclear variations for demography analysis normalization.RNA-seqs.txt -- the nomarlization data of expression of mitochondrial genome nuclear.variation.map.vcf.gz -- the nuclaer variation map ORFs annotation based on Augustus.gtf -- the annotation gene structure using Augustus  pan-genome and aligned mitochondrial genomes.zip -- the pan-genome(.fa and .gfa) and aligned mitochondrial genomes scaffold-assemblies.zip -- the scaffolds of mitochondrial genomes

opencc-zeroJan 2022View details →

High pitch sounds small for domestic dogs dataset

Humans possess intuitive associations linking certain non-redundant features of stimuli – e.g., high-pitched sounds with small object-size (or similarly, low-pitched sounds with large object-size). This phenomenon, known as crossmodal correspondence, has been identified in humans across multiple different senses. There is some evidence that non-human animals also form crossmodal correspondences, but the known examples are mostly limited to the associations between the pitch of vocalisations and the size of callers. To investigate whether domestic dogs, like humans, show abstract pitch-size association, we first trained dogs to approach and touch an object after hearing a sound emanating from it. Subsequently, we repeated the task but presented dogs with two objects differing in size, only one of which was playing a sound. The sound was either high- or low-pitched, thereby creating trials that were either congruent (high-pitch from small object; low-pitch from large objects) or incongruent (the reverse). We found that dogs reacted faster on congruent versus incongruent trials. Moreover, their accuracy was at chance on incongruent trials, but significantly above chance for congruent trials. Our results suggest that non-human animals show abstract pitch-sound correspondences, indicating these correspondences may not be uniquely human but rather a sensory processing feature shared by other species.

opennotspecifiedJun 2006View details →

Figure 1 in Solanum Perlongistylum and S. Catilliflorum, New Endemic Peruvian Species of Solanum, Section Basarthrum, Are Close Relatives of the Domesticated Pepino, S. Muricatum

Figure 1. Photographs of Solanum perlongistylum (A–D) and S. catilliflorum (E–H). —A. Flowers. —B. Form. —C. Fruits. —D. Field habit. —E. Flowers. —F. Form. —G. Fruits. —H. Field habit. Scale as indicated, except for the fruits (C & G), where each square is 10 × 10 mm.

opencc-zeroMar 2022View details →

Phylogeny and disparate selection signatures suggest two genetically independent domestication events of pea (Pisum L.)

Domestication is considered a model of adaptation that can be used to draw conclusions about the modus operandi of selection in natural systems. Investigating domestication may give insights into how plants react to different intensities of human manipulation, which has direct implication for the continuing efforts of crop improvement. Therefore, scientists of various disciplines study domestication-related questions to understand the biological and cultural bases of the domestication process. We employed restriction site-associated DNA sequencing (RAD-seq) of 494 Pisum sativum (pea) samples from all wild and domesticated groups to analyze the genetic structure of the collection. Patterns of ancient admixture were investigated by analysis of admixture graphs. We used two complementary approaches, one diversity based and one based on differentiation, to detect the selection signatures putatively associated with domestication. An analysis of the subpopulation structure of wild P. sativum revealed five distinct groups with a notable geographic pattern. Pisum abyssinicum clustered unequivocally within the P. sativum complex, without any indication of hybrid origin. We detected 32 genomic regions putatively subjected to selection: 29 in P. sativum ssp. sativum and three in P. abyssinicum. The two domesticated groups did not share regions under selection and did not display similar haplotype patterns within those regions. Wild P. sativum is structured into well-diverged subgroups. Although Pisum sativum ssp. humile is not supported as a taxonomic entity, the so-called 'southern humile' is a genuine wild group. Introgression did not shape the variation observed within the sampled germplasm. The two domesticated pea groups display distinct genetic bases of domestication, suggesting two genetically independent domestication events.

opencc-zeroApr 2022View details →

The assembly of caprine Y chromosome sequence reveals a unique paternal phylogenetic pattern and improves our understanding the origin of domestic goat

The mammalian Y chromosome offers a unique perspective on the male reproduction and paternal evolutionary histories. However, further understanding of the Y chromosome biology for most mammals is hindered by the lack of a Y chromosome assembly. This study presents an integrated in silico strategy for identifying and assembling the goat Y-linked scaffolds using existing data. A total of 11.5 Mb Y-linked sequences were clustered into 33 scaffolds, and 187 protein-coding genes were annotated. We also identified high abundance of repetitive elements. A 5.84 Mb subset was further ordered into an assembly with the evidence from the goat Radiation-Hybrid map (RH map). The existing whole-genome re-sequencing data of 96 goats (worldwide distribution) were utilized to exploit the paternal relationships among bezoars and domestic goats. Goat paternal lineages were clearly divided into two clades (Y1 and Y2), predating the goat domestication. Demographic history analyses indicated that maternal lineages experienced a bottleneck effect around 2,000 YBP (years before present), after which goats belonging to the A haplogroup spread worldwide from the Near East. As opposed to this, paternal lineages experienced a population decline around the 10,000 YBP. The evidence from the Y chromosome suggests that male goats were not affected by the A haplogroup worldwide transmission, which implies sexually unbalanced contribution to the goat trade and population expansion in post-Neolithic period.

Subspecies and Distribution. B.j.javanicusd'Alton,1823—Java,perhapsBali. B.j.birmanicusLydekker,1898—AsianmainlandincludingMyanmar,SChina(SYunnan,currentpresenceuncertain),Laos,Vietnam,Thailand,Cambodia,andNPeninsularMalaysia. B. j. low: Lydekker, 1912 — Borneo. The domestic form of the Banteng has been introduced, and is now feral, in N Australia, New Guinea, and on various islands of Indonesia (Bali, Sangihe, Sulawesi, Sumbawa, Sumba, and Enggano) and occurs in domestication throughout the islands of SE Asia. in Bovidae

Subspecies and Distribution. B.j.javanicusd'Alton,1823—Java,perhapsBali. B.j.birmanicusLydekker,1898—AsianmainlandincludingMyanmar,SChina(SYunnan,currentpresenceuncertain),Laos,Vietnam,Thailand,Cambodia,andNPeninsularMalaysia. B. j. low: Lydekker, 1912 — Borneo. The domestic form of the Banteng has been introduced, and is now feral, in N Australia, New Guinea, and on various islands of Indonesia (Bali, Sangihe, Sulawesi, Sumbawa, Sumba, and Enggano) and occurs in domestication throughout the islands of SE Asia.

opencc-zeroMay 2022View details →

Review and synthesis of the global literature on domestic cat impacts on wildlife

A vast global literature documents that free-roaming domestic cats (Felis catus) have substantial negative effects on wildlife, including through predation, fear, disease, and competition-related impacts that have contributed to numerous wildlife extinctions and population declines worldwide. However, no study has synthesized this literature on cat impacts on wildlife to evaluate its overarching biases and major gaps. To direct future research and conservation related to cat impacts on wildlife, we conducted a global literature review that entailed evaluation and synthesis of patterns and gaps in the literature related to the geographic context, methods, and types of impacts studied. Our systematic literature search compiled 2,245 publications. We extracted information from 332 of these meeting inclusion criteria designed to ensure the relevance of studies analyzed. This synthesis of research on cat impacts on wildlife highlights a focus on oceanic islands, Australia, Europe, and North America, and on rural areas, predation, impacts of unowned cats, and impacts at population and species levels. Key research advances needed to better understand and manage cat impacts include more studies in underrepresented, highly biodiverse regions (Africa, Asia, South America), on cat impacts other than predation, and on methods designed to reduce impacts on wildlife. The identified areas of needed research into cat impacts on wildlife will be critical to further clarifying the role of cats in global wildlife declines and to implementing science-driven policy and management that benefit conservation efforts.

opencc-by-4.0Dec 2021View details →

One million articles from five post socialist countries with extracted features: sentiment, basic emotions, LDA topics and presence of influential domestic politicians

This is a replication data for my paper under blind review. This paper develops a new prediction model for media content presence on a website. It analyses a new corpus of one million articles from five countries: Poland, Russia, Belarus, Kazakhstan and Ukraine, in two languages, Polish and Russian. These articles were scraped daily from seventeen websites in 2017-2020 period. The research applies a wide range of natural language processing methods to automatically derive several properties of each article: its topic, sentiment, basic emotions, mentions of influential domestic politicians. The articles’ embeddings and their cosine similarity are used to calculate the news context, such as how an article differs from the daily issue main themes. These features are used to estimate a logistic regression assessing the likelihood that the same or slightly modified, as measured by cosine similarity, article will remain on the main web page the next day. The key, and somewhat unexpected result is that articles with negative sentiment polarity are less likely to be published for more than one day. This result holds for all countries analyzed. It means that the negative news bias documented in the literature is partly offset by their shorter life cycle. Data is in the Python pickle format. Should be read into Python using the pickle.load() function. Each element (row) is the data frames or list represents one news article. Each file has the same format. Loading a pickle file returns a list of four elements: 1. A dummy variable equal to 1 when the article was published the next day, with the text being identical 2. A dummy variable equal to 1 when the article was published the next day, but we allow for small text modifications (cosine similarity > 0.99) 3. Dataframe with extracted features, described below. 4. List with texts of articles in Polish or Russian Ad 3. The columns of the dataframe are as follows (we refer to row number i in description): - pandas index (may appear once or twice in the datafame) - maxcosine: maximum cosine similarity between art i and all articles published next day - cosine_diff: cosine similarity between article i and the elementwise average of embeddings of all articles in the current issue. Measure how similar is the article i to the core narrative of the current issue - cosine_std: std. dev. of cosine similarity measures between all pairs of articles in the current issue. Measures how focused or dispersed is the current issue news coverage - thirteen LDA topic groups: politics, legislation and legal affairs (POL); economy, finance, various sectors of the economy (ECO); military, war, protests, crime, security threats (MIL); international affairs, specific issues concerning foreign countries (INT); technology (TECH); family issues, culture, sport, education (FAM); regional issues and housing (REG); health issues and the Covid-19 pandemic (HEA); media (MED); accidents (ACC); religion (REL); the Soviet Union (USSR); and articles for which no topic could be determined (MISC). - rsent.c: relative sentiment that is dictionary based sentiment of articles i minus the average sentiment of the newspaper. This approach eliminates newspaper or country idiosyncratic sentiment factors. c stands for Covid, the sentiment lexicon was augmented with Covid related terms - dip_*: Variable measuring if influential domestic politicians are mentioned in article i, * represent a country acronym. If N is equal to the number of occurrences of the names of influential domestic politicians in the article i, dip_* = 0 if N=0, dip_* = 1+ log(N) if N>0. - three or four names of news portals from which the data was scraped. - names of six basic emotions and the article i emotion scores calculated using zero-shot learning and the large version of the XLM (Conneau et al., 2019) model from the huggingface transformers library available at https://huggingface.co/vicgalle/xlm-roberta-large-xnli-anli Names of the politicians used to calculate dip variables Russia "putin" "medvedev" "vaino" "shoigu" "bortnikov" "lavrov" "mishustin" "kirienko" "sechin" Ukraine "zelensky" "shmygal" "akhmetov" "avakov" "ermak" "poroshenko" "medvedchuk" "groisman" Kazakhstan "sagyntaev" "mamin" "tokayev" "nnazarbayev" "dnazarbayeva" "kulibayev" "masimov" Belarus "alukashenko" "vakulchik" "vlukashenko" "kobyakov" "makei" "myasnikovich"  "rumas" "golovchenko" Poland "kaczynski" "duda" "morawiecki" "ziobro" Data coverage Country, news portal, numbr of articles Russia iz.ru 43,782 Russia kommersant.ru 46,070 Russia novayagazeta.ru 29,357 Russia vedomosti.ru 27,797 Kazakhstan informburo.kz 29,375 Kazakhstan nur.kz 67,350 Kazakhstan tengrinews.kz 44,285 Kazakhstan zakon.kz 109,442 Belarus bdg.by 33,447 Belarus belgazeta.by 21,995 Belarus sb.by 83,685 Ukraine kp.ua 194,792 Ukraine segodnya.ua 45,835 Ukraine vesti.ua 90,559 Poland gazeta.pl 53,321 Poland rp.pl 49,587 Poland wpolityce.pl 76,625 In the provided dataframes the number of observations is smaller, because the issues for which there was no next day issue, were removed. Data was scraped daily between 2017 or 2018 (depending on the country) and January 2021.

opennotspecifiedJul 2016View details →

Subspecies and Distribution. O.c.cuniculusLinnaeus,1758—N,NE&EIberianPeninsula(Spain). O.c.algirusLoche,1858—S,SW&WIberianPeninsula(Spain,Portugal),NMorocco,NAlgeria(includingHabibasI). O.c.brachyotusTrouessart,1917—SFrance. O.c.cnossiusBate,1906—CreteI. O.c.habetensisCabrera,1923—Tanger-Tetouan-AlHoceimaRegion(NMorocco). O. c. huxleyi Haeckel, 1874 — Mediterranean Is (Balearic Is, Corsica, Sardinia, Sicily and Macaronesia (Azores, Madeira, and Canary Is). Original distribution after last Ice Age restricted to Iberian Peninsula, W France, and N Africa. Ancient introductions of the nominate subspecies probably during the Ro- man period have spread it throughout Europe, and now it is present in most of W, C & E Europe and the Mediterranean and Macaronesian Is (these mostly old introductions are also shaded on the map). During the 20" century it has been released into the steppes of the Black Sea in Ukraine and Russia (N Caucasus); introduced into Australia in 1788 and again in 1859 where it is now widespread; it is found on many Pacific Is, islands off the coast of South Africa and Namibia, and in New Zealand; successfully introduced only since 1936 into South America, nowadays with a limited range in Chile, Argentina, and Falkland Is, it is also present in the Caribbean Is (all these modern introductions not shaded in the map). Worldwide as domesticated forms. in Leporidae

Subspecies and Distribution. O.c.cuniculusLinnaeus,1758—N,NE&EIberianPeninsula(Spain). O.c.algirusLoche,1858—S,SW&WIberianPeninsula(Spain,Portugal),NMorocco,NAlgeria(includingHabibasI). O.c.brachyotusTrouessart,1917—SFrance. O.c.cnossiusBate,1906—CreteI. O.c.habetensisCabrera,1923—Tanger-Tetouan-AlHoceimaRegion(NMorocco). O. c. huxleyi Haeckel, 1874 — Mediterranean Is (Balearic Is, Corsica, Sardinia, Sicily and Macaronesia (Azores, Madeira, and Canary Is). Original distribution after last Ice Age restricted to Iberian Peninsula, W France, and N Africa. Ancient introductions of the nominate subspecies probably during the Ro- man period have spread it throughout Europe, and now it is present in most of W, C & E Europe and the Mediterranean and Macaronesian Is (these mostly old introductions are also shaded on the map). During the 20" century it has been released into the steppes of the Black Sea in Ukraine and Russia (N Caucasus); introduced into Australia in 1788 and again in 1859 where it is now widespread; it is found on many Pacific Is, islands off the coast of South Africa and Namibia, and in New Zealand; successfully introduced only since 1936 into South America, nowadays with a limited range in Chile, Argentina, and Falkland Is, it is also present in the Caribbean Is (all these modern introductions not shaded in the map). Worldwide as domesticated forms.

opencc-zeroDec 2018View details →

Data from: The complex geography of domestication of the African rice Oryza glaberrima

While the domestication history of Asian rice has been extensively studied, details of the evolution of African rice remain elusive. The inner Niger delta has been suggested as the center of origin but molecular data to support this hypothesis is lacking. Here, we present a comprehensive analysis of the evolutionary and domestication history of African rice. By analyzing whole genome re-sequencing data from 282 individuals of domesticated African rice Oryza glaberrima and its progenitor O. barthii, we hypothesize a non-centric (i.e. multiregional) domestication origin for African rice. Our analyses showed genetic structure within O. glaberrima that has a geographical association. Furthermore, we have evidence that the previously hypothesized O. barthii progenitor populations in West Africa have evolutionary signatures similar to domesticated rice and carried causal domestication mutations, suggesting those progenitors were either mislabeled or may actually represent feral wild-domesticated hybrids. Phylogeographic analysis of genes involved in the core domestication process suggests that the origins of causal domestication mutations could be traced to wild progenitors in multiple different locations in West and Central Africa. In addition, measurements of panicle threshability, a key early domestication trait for seed shattering, were consistent with the gene phylogeographic results. We suggest seed non-shattering was selected from multiple genotypes, possibly arising from different geographical regions. Based on our evidence, O. glaberrima was not domesticated from a single centric location but was a result of diffuse process where multiple regions contributed key alleles for different domestication traits.

opencc-zeroJul 2022View details →

Rational domestication of a plant-based recombinant expression system expands its biosynthetic range

Plant molecular farming aims to provide a green, flexible, and rapid alternative to conventional recombinant expression systems, capable of producing complex biologics such as enzymes, vaccines, and antibodies. Historically, the recombinant expression of therapeutic peptides in plants has proven difficult, largely due to their small size and instability. However, some plant species harbour the capacity for peptide backbone cyclization, a feature inherent in stable therapeutic peptides. One obstacle to realizing the potential of plant-based therapeutic peptide production is the proteolysis of the precursor before it is matured into its final stabilized form. Here we demonstrate the rational domestication of Nicotiana benthamiana within two generations to endow this plant molecular farming host with an expanded repertoire of peptide sequence space. The in planta production of molecules including an insecticidal peptide, a prostate cancer therapeutic lead and an orally active analgesic are demonstrated.