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opencc-by-4.0Aug 2024View details →

Dataset - "An Adaptive Multi-Seasonal ARIMA Approach for Domestic Hot Water Load Forecasting: A Pilot Study"

The description of the data is in README.txt.

opencc-by-4.0Nov 2024View details →

100 Years of Penaeids Domestication and Meta-analysis of Breeding Traits

Additional files Additional file 1 Table S1 Format: csv file Title: Quantitative genetic publications for penaeids genetic improvement programs from 1997 to 2024. Additional file 2 Table S2 Format: csv file Title: Summary of heritability estimates on breeding traits in penaeids selective breeding programs. Additional file 3 Table S3 Format: csv file Title: Analysis of heritability estimates in penaeids selective breeding programs for disaese resistance, feeding efficiency, growth traits, morphological traits, quality traits, reproductive traits, stress tolerance and survival.

opencc-zeroDec 2019View details →

Data from: The laboratory domestication of zebrafish: from diverse populations to inbred substrains

We know from human genetic studies that practically all aspects of biology are strongly influenced by the genetic background, as reflected in the advent of 'personalized medicine'. Yet, with few exceptions, this is not taken into account when using laboratory populations as animal model systems for research in these fields. Laboratory strains of zebrafish (Danio rerio) are widely used for research in vertebrate developmental biology, behaviour and physiology, for modelling diseases, and for testing pharmaceutic compounds in vivo. However, all of these strains are derived from artificial bottleneck events and therefore are likely to represent only a fraction of the genetic diversity present within the species. Here we use Restriction site-Associated DNA sequencing (RAD-seq) to genetically characterize wild populations of zebrafish from India, Nepal and Bangladesh, and to compare them to previously published data on four common laboratory strains. We measured nucleotide diversity, heterozygosity and allele frequency spectra, and find that wild zebrafish are much more diverse than laboratory strains. Further, in wild zebrafish there is a clear signal of GC-biased gene conversion that is missing in laboratory strains. We also find that zebrafish populations in Nepal and Bangladesh are most distinct from all other strains studied, making them an attractive subject for future studies of zebrafish population genetics and molecular ecology. Finally, isolates of the same strains kept in different laboratories show a pattern of ongoing differentiation into genetically distinct substrains. Together, our findings broaden the basis for future genetic, physiological, pharmaceutic and evolutionary studies in Danio rerio.

opencc-zeroJul 2021View details →

Cooperative communication with humans evolved to emerge early in domestic dogs

While we know that dogs evolved from wolves, it remains unclear how domestication affected dog cognition. One hypothesis suggests dog domestication altered social maturation by a process of selecting for an attraction to humans. Under this account, dogs became more flexible in using inherited skills to cooperatively-communicate with a new social partner that was previously feared and expressed these unusual social skills early in development. Here we tested dog (N=44) and wolf (N=37) puppies, 5-18 weeks old, on a battery of temperament and cognition tasks. We found that dog puppies were more attracted to humans, read human gestures more skillfully, and made more eye contact with humans than wolf puppies. The two species were similarly attracted to objects and performed similarly on nonsocial measures of memory and inhibitory control. These results are consistent with the idea that domestication enhanced the cooperative-communicative abilities of dogs as selection for attraction to humans altered social maturation.

opencc-by-4.0Jul 2021View details →

Effects of laboratory domestication on the rodent gut microbiome

Metagenome-assembled genomes generated from a collection of public and newly sequenced metagenomes derived from the rodent gut.

opencc-zeroJul 2021View details →

Contributions of wild and provisioned foods to the diets of domestic cats that depredate wild animals

Predation of wildlife by domestic cats Felis catus presents a threat to biodiversity conservation in some ecological contexts. The proportions of wild prey captured and eaten by domestic cats and thus the contributions of wild prey to cat diets are hard to quantify. This limits understanding of any impacts of cats may have on wild animal populations and confounds analyses of the effects of interventions aimed at reducing wildlife killing. We used stable isotope analyses to quantify the relative contributions of wild and provisioned foods to the diets of domestic cats kept as companion animals and which frequently captured wild prey. We tested the effects of treatments aimed at reducing killing upon stable isotope ratios of cat whiskers and, where treatments had significant effects, we estimated variation in the contributions of wild prey to cats' diets before and during treatment. We evaluated bells, Birdsbesafe collar covers, provision of food in a 'puzzle feeder', provision of food in which meat was the principal source of protein, object play and a control group. As expected, cat diets consisted primarily of provisioned foods, though the contribution of wild animals to the diets of these cats, all of which regularly caught wild animals, was low (cat food ~96%, wild animals ~3–4%). Compared to the pre-treatment period and control group, cats with a Birdsbesafe collar cover, exhibited significant reduction in nitrogen stable isotope ratios in their whiskers and consumed less wild prey, most likely attributable to effective inhibition of hunting, particularly for birds. Fitting cats with a Birdsbesafe collar cover, therefore, reduced both returns of wild birds and consumption of wild prey. While multiple interventions can significantly affect the numbers of wild animals that cats capture and return home, the remarkably small dietary contributions made by wild animal prey mean dietary change is harder to discern. Domestic cats rely almost exclusively on food provided by people even when they frequently kill wild animals. This suggests that the hunting behavior of domestic cats may be driven by behavioral motivations, or by a need to address micronutrient requirements, but is unlikely to alter macronutrient intake.

opencc-zeroAug 2021View details →

Reservoir dynamics of rabies in Southeast Tanzania and the roles of cross-species transmission and domestic dog vaccination

Understanding the role of different species in the transmission of multi-host pathogens, such as rabies virus, is vital for effective control strategies. Across most of sub-Saharan Africa domestic dogs (Canis familiaris) are considered the reservoir for rabies, but the role of wildlife has been long debated. Here we explore the multi-host transmission dynamics of rabies across southeast Tanzania. Between January 2011 and July 2019 data on probable rabies cases were collected in the regions of Lindi and Mtwara. Hospital records of animal-bite patients presenting to healthcare facilities were used as sentinels for animal contact tracing. The timing, location and species of probable rabid animals was used to reconstruct transmission trees to infer who infected whom and the relative frequencies of within- and between-species transmission. During the study, 688 probable human rabies exposures were identified, resulting in 47 deaths. Of these exposures, 389 were from domestic dogs (56.5%) and 262 from jackals (38.1%). Over the same period 549 probable animal rabies cases were traced: 303 in domestic dogs (55.2%) and 221 in jackals (40.3%). Although dog-to-dog transmission was most commonly inferred (40.5% of transmission events), a third of inferred events involved wildlife-to-wildlife transmission (32.6%) and evidence suggested some sustained transmission chains within jackal populations. A steady decline in probable rabies cases in both humans and animals coincided with the implementation of widespread domestic dog vaccination during the first six years of the study. Following the lapse of this programme dog rabies cases began to increase in one of the northernmost districts. Synthesis and applications: In southeast Tanzania, despite a relatively high incidence of rabies in wildlife and evidence of wildlife-to-wildlife transmission, domestic dogs remain essential to the reservoir of infection. Continued dog vaccination alongside improved surveillance would allow a fuller understanding of the role of wildlife in maintaining transmission in this area. Nonetheless, dog vaccination clearly suppressed rabies in both domestic dog and wildlife populations, reducing both public health and conservation risks and, if sustained, has potential to eliminate rabies from this region.

opencc-zeroSep 2021View details →

Data from: Larval development in the Pacific oyster and the impacts of ocean acidification: differential genetic effects in wild and domesticated stocks

The adaptive capacity of marine calcifiers to ocean acidification (OA) is a topic of great interest to evolutionary biologists and ecologists. Previous studies have provided evidence to suggest that larval resilience to high pCO2 seawater for these species is a trait with a genetic basis and variability in natural populations. To date, however, it remains unclear how the selective effects of OA occur within the context of complex genetic interactions underpinning larval development in many of the most vulnerable taxa. Here we evaluated phenotypic and genetic changes during larval development of Pacific oysters (Crassostrea gigas) reared in ambient (~ 400 µatm) and high (~ 1600 µatm) pCO2 conditions, both in domesticated and naturalized 'wild' oysters from the Pacific Northwest, USA. Using pooled DNA samples, we determined changes in allele frequencies across larval development, from early "D-stage" larvae to metamorphosed juveniles (spat), in both groups and environments. Domesticated larvae had ~ 26% fewer loci with changing allele frequencies across developmental stages and < 50% as many loci affected by acidified culture conditions, compared to larvae from wild brood stock. Functional enrichment analyses of genetic markers with significant changes in allele frequency revealed that the structure and function of cellular membranes were disproportionately affected by high pCO2 conditions in both groups. These results indicate the potential for a rapid adaptive response of oyster populations to OA conditions; however, underlying genetic changes associated with larval development differ between these wild and domesticated oyster stocks and influence their adaptive responses to OA conditions.

opencc-by-4.0Oct 2022View details →

Compare Analysis with a High-quality Genome of Weedy Rice Reveals the Evolutionary Game of De-domestication

A02.SV.vcf is the SV information between the A02 genome and Nipponbare genome. All.population.SV.vcf  is the data of the SV genotyping information based on the super pan-genome.

opencc-by-4.0Nov 2022View details →

Data for the article "Management of social behaviour of domestic yaks in Manang, Nepal: an etho-ethnographic study"

Data for the paper "Social behaviour of domestic yaks in Manang, Nepal: an etho-ethnographic study". ANimated GIFs, GPS data, activity data and proximity data. Herdsmen use different techniques, as per varying geographies and cultures, to keep the cohesion within herds and avoid animals getting lost or predated. However, there is no study on the social behaviour of yaks and on herdsmen management practices. Therefore, this ethology study was initiated by ethnographic inquiries. We collected data from two herds living at the same settlement (Yak kharka, 4,100 m altitude, Nepal) by equipping them with loggers. One of the herdsman used the tether rope while other did not. Moreover, the Thaku herd had a more proactive shepherd than the Phurba one. In each herd, 17 animals were equipped with one actigraph wgt3x-BT to measure activity using accelerometer and spatial associations using proximity recorder. One of the herds was equipped with GPS (N=11) as well. Using GPS locations and activity, we showed that the two herds were cohesive and synchronised their activities but the herd with the tether rope was more cohesive.

opencc-zeroNov 2022View details →

Rapid evolution of seed dormancy during sunflower de-domestication

Hybridization between crops and their wild relatives may promote the evolution of de-domesticated (feral) weeds. Wild sunflower (Helianthus annuus L.) is typically found in ruderal environments, but crop-wild hybridization may facilitate the evolution of weedy populations. Using one crop-specific mitochondrial marker (CMS-PET1) and 14 nuclear SSR markers, we studied the origin and genetic diversity of a recently discovered weedy population of sunflower (named BRW). Then, using a resurrection approach, we tested for rapid evolution of weedy traits (seed dormancy, herbicide resistance, and competitive ability) by sampling weedy and wild populations 10 years apart (2007 and 2017). All the weedy plants present the CMS-PET1 cytotype, confirming their feral origin. At the nuclear markers, BRW showed higher genetic diversity than the cultivated lines and low differentiation with one wild population, suggesting that wild hybridization increased their genetic diversity. We found support for rapid evolution towards higher seed dormancy, but not for higher competitive ability or herbicide resistance. Our results highlight the importance of seed dormancy during the earliest stages of adaptation and show that crop-wild hybrids can evolve quickly in agricultural environments.

opencc-by-4.0Dec 2022View details →

Describing and mapping of the main existing structures and systematic initiatives and academic activities for surveillance in the EU for zoonoses (transboundary, emerging and re-emerging) in domestic animals and wildlife

These annexes refer to a report which describes and maps the main existing structures and systematic initiatives and academic activities for surveillance in the EU for transboundary, emerging and re-emerging zoonoses in domestic animals, wildlife, and the environment, developed by the different sectors, namely human, domestic animal, wildlife and environmental, under One Health approach. This is essential to provide scientific and technical advice and improve future schemes of surveillance. A questionnaire was compiled by MSs and the information collected was complemented by literature reviews about (i) the main existing structures and systematic initiatives or activities, and (ii) academic activities for surveillance in the EU for zoonoses in domestic animals and wildlife. The annexes to the report are as follows: Annex 1. Questionnaire survey on official zoonotic disease surveillance activities in the EU and neighbouring countries. -          Sheet 1: PART 1 – Surveillance. This part explores the general organization of the surveillance plan -          Sheet 2: PART 2 – Pathogens. This part aims to identify target pathogen and species and methods for surveillance Annex 2. Characteristic of surveillance plans. -          Sheet “Pathogens”, where not primary but also a wide range of hosts are summarized. -          Sheet “active/passive surveillance” by country -          Sheet “origin of funding” (the proportion and number) of surveillance plans Annex 3. More detailed distribution of active and passive surveillance planaccording to countries and pathogen is presented in this Annex. Annex 4. Standardized data model (to extract key information to characterize the surveillance systems in the literature review on systematic surveillance. The data model was divided into two parts: -          Sheet 1: PART 1 – Surveillance system (explores the general organization) -          Sheet 2: PART 2 – Pathogens (identifies the target pathogen, species, and methods) Annex 5. Standardized data model used during the literature review to extract key information to characterize the surveillance performed by the academia

opencc-zeroFeb 2023View details →

Cuisine in transition? Organic residue analysis of domestic containers from 9th-14th century Sicily

From the 9th to 14th centuries AD, Sicily experienced a series of rapid and quite radical changes in political regime, but the impact of these regime changes on the lives of the people that experienced them remains largely elusive within the historical narrative. We use a multi-faceted lipid residue approach to give direct chemical evidence of the use of 248 everyday domestic ceramic containers from Islamic and post-Islamic contexts in western Sicily to aid our understanding of daily habits throughout this period of political change. A range of commodities was successfully identified, including animal fats, vegetable products, fruit products, (potentially including wine), and plant resins. The study highlights the complexity of residues in Early Medieval Mediterranean society, as in many cases mixtures of commodities were observed, reflecting sequential cooking events and/or the complex mixtures reflective of medieval recipes. However, overall there were no clear changes in the composition of the residues following the imposition of Norman control over the island and through subsequent periods, despite some differences between urban centres and rural sites. Thus, lending to the idea that post-Islamic populations largely flourished and benefited from the agricultural systems, resources, and recipes left by their predecessors.

opencc-by-4.0Apr 2023View details →

Data and code: Plants cultivated for ecosystem restoration can evolve towards a domestication syndrome

Data and code to the publication Conrady et al (2023): Plants cultivated for ecosystem restoration can evolve towards a domestication syndrome, PNAS.

opencc-zeroDec 2022View details →

Understanding the incidence and timing of rabies cases in domestic animals and wildlife in south-east Tanzania in the presence of widespread domestic dog vaccination campaigns

The "Zero by 30" strategic plan aims to eliminate human deaths from dog-mediated rabies by 2030, and domestic dog vaccination is a vital component of this strategic plan. In areas where domestic dog vaccination has been implemented, it is important to assess the impact of this intervention. Additionally, understanding temporal and seasonal trends in the incidence of animal rabies cases may assist in optimizing such interventions. Data on the incidence of probable rabies cases in domestic and wild animals were collected between January 2011 and December 2018 in thirteen districts of south-east Tanzania where jackals comprise over 40% of reported rabies cases. Vaccination coverage was estimated over this period, as five domestic dog vaccination campaigns took place in all thirteen districts between 2011 and 2016. Negative binomial generalized linear models were used to explore the impact of domestic dog vaccination on the annual incidence of animal rabies cases, whilst generalized additive models were used to investigate the presence of temporal and/or seasonal trends. Increases in domestic dog vaccination coverage were significantly associated with a decreased incidence of rabies cases in both domestic dogs and jackals. A 35% increase in vaccination coverage was associated with a reduction in the incidence of probable dog rabies cases of between 78.0 and 85.5% (95% confidence intervals ranged from 61.2 to 92.2%) and a reduction in the incidence of probable jackal rabies cases of between 75.3 and 91.2% (95% confidence intervals ranged from 53.0 to 96.1%). A statistically significant common seasonality was identified in the monthly incidence of probable rabies cases in both domestic dogs and jackals with the highest incidence from February to August and lowest incidence from September to January. These results align with evidence supporting the use of domestic dog vaccination as part of control strategies aimed at reducing animal rabies cases in both domestic dogs and jackals in this region. The presence of a common seasonal trend requires further investigation but may have implications for the timing of future vaccination campaigns.

MicroCT scan of the nasal airway of a domestic short hair cat

The peripheral structures of mammalian sensory organs often serve to support their functionality, such as alignment of hair cells to the mechanical properties of the inner ear. Here, we examined the structure-function relationship for mammalian olfaction by creating an anatomically accurate computational nasal model for the domestic cat (Felis catus) based on high resolution microCT and sequential histological sections. Our results showed a distinct separation of respiratory and olfactory flow regimes, featuring a high-speed dorsal medial stream that increases odor delivery speed and efficiency to the ethmoid olfactory region without compromising the filtration and conditioning purpose of the nose. These results corroborated previous findings in other mammalian species, which implicates a common theme to deal with the physical size limitation of the head that confines the nasal airway from increasing in length infinitely as a straight tube. We thus hypothesized that these ethmoid olfactory channels function as parallel coiled chromatograph channels, and further showed that the theoretical plate number, a widely-used indicator of gas chromatograph efficiency, is more than 100 times higher in the cat nose than an "amphibian-like" straight channel fitting the similar skull space, at restful breathing state. The parallel feature also reduces airflow speed within each coil, which is critical to achieving the high plate number, while feeding collectively from the high-speed dorsal medial stream so that total odor sampling speed is not sacrificed. The occurrence of ethmoid turbinates is an important step in the evolution of mammalian species that correlates to their expansive olfactory function and brain development. Our findings reveal novel mechanisms on how such structure may facilitate better olfactory performance, furthering our understanding of the successful adaptation of mammalian species, including F. catus, a popular pet, to diverse environments.

Data from: Maintenance and expansion of genetic and trait variation following domestication in a clonal crop: Enset tGBS individual genotype data

Clonal propagation enables favourable crop genotypes to be rapidly selected and multiplied. However, the absence of sexual propagation can lead to low genetic diversity and accumulation of deleterious mutations, which may eventually render crops less resilient to pathogens or environmental change. To better understand this trade-off, we characterise the domestication and contemporary genetic diversity of Enset (Ensete ventricosum), an indigenous African relative of bananas (Musa) and principal starch staple for 20 million Ethiopians. Wild enset is strictly sexually outcrossing, but in cultivation is propagated clonally and associated with diversification and specialisation into hundreds of named landraces. We applied tGBS sequencing to generate genome-wide genotypes for 192 accessions from across enset's cultivated distribution, and surveyed 1340 farmers on enset agronomic traits. Overall, reduced heterozygosity in the domesticated lineage was consistent with a domestication bottleneck that retained 37% of wild diversity. However, an excess of putatively deleterious missense mutations at low frequency present as heterozygotes suggested accumulation of mutational load in clonal domesticated lineages. Our evidence indicates that the major domesticated lineages initially arose through historic sexual recombination associated with a domestication bottleneck, followed by amplification of favourable genotypes through an extended period of clonal propagation. Among domesticated lineages we found significant phylogenetic signal for multiple farmer-identified food, nutrition and disease resistance traits and little evidence of contemporary recombination. Development of future-climate adapted genotypes may require crop breeding, but outcrossing risks exposing deleterious alleles as homozygotes. This trade-off may partly explain the ubiquity and persistence of clonal propagation over recent centuries of comparative climate stability.

Amplicon sequence variants (ASV) of gut pathogens in hooded cranes and domestic geese

Driven by habitat loss from anthropogenic activities, wintering migratory birds forage together with poultry in paddy fields, and thus impose risks of cross transmitting pathogens. To date, there is little evidence for such risks of pathogen transmission between wild birds and poultry. Using the high-throughput sequencing, we report on detected potential pathogens of both wild hooded cranes Grus monacha and sympatric domestic geese Anser anser domesticus during the wintering period and infer the possibility of cross-species pathogen transmission. The results revealed that the number of shared amplicon sequence variants (ASVs) of potential pathogens between the gut microbiota of the two species was low during the early wintering stage (17.2%; 5 ASVs shared) but increased to 56.3% (18 ASVs shared) during the late wintering stage. That is, potential pathogens in the gut microbial communities of the two species became more similar through co-foraging in paddy fields, supporting cross-transmission of pathogens between hooded cranes and domestic geese during the wintering period. Importantly, transmission appeared to be largely from wild hooded cranes to domestic geese, although some potential pathogens may have become specialized to the domestic goose in late wintering stage. Humans are also facing the risks of contracting these potential pathogens from migratory birds through their frequent contact with domestic poultry. It is, therefore, necessary to closely monitor this pathway of pathogen transmission from wild birds to domestic animals and even to humans.

Axiom canine microarray data from Australian dingoes and domestic dogs for admixture and population structure analysis

Admixture between species is a cause for concern in wildlife management. Canids are particularly vulnerable to inter-specific hybridisation, and genetic admixture has shaped their evolutionary history. Microsatellite DNA testing, relying on a small number of genetic markers and geographically restricted reference populations, has identified extensive domestic dog admixture in Australian dingoes and driven conservation management policy. There has been concern that geographic variation in dingo genotypes could confound ancestry analyses that use a small number of genetic markers. Here we apply genome-wide single nucleotide polymorphism (SNP) genotyping to a set of 385 wild and captive dingoes from across Australia and then carry out comparisons to domestic dogs, and perform ancestry modelling and biogeographic analyses to characterize population structure in dingoes and investigate the extent of admixture between dingoes and dogs in different regions of the continent. We show that there are at least five distinct dingo populations across Australia. We observed limited evidence of dog admixture in wild dingoes, challenging previous reports regarding the occurrence and extent of dog admixture in dingoes, as our ancestry analyses show that previous assessments severely overestimate the degree of domestic dog admixture in dingo populations, particularly in southeastern Australia. These findings strongly support the use of genome-wide SNP genotyping as a refined method for wildlife managers and policy makers to assess and inform dingo management policy and legislation moving forwards.