Whole mitochondrial genomes unveil the impact of domestication on goat matrilineal variability.

BACKGROUND: The current extensive use of the domestic goat (Capra hircus) is the result of its medium size and high adaptability as multiple breeds. The extent to which its genetic variability was influenced by early domestication practices is largely unknown. A common standard by which to analyze maternally-inherited variability of livestock species is through complete sequencing of the entire mitogenome (mitochondrial DNA, mtDNA). RESULTS: We present the first extensive survey of goat mitogenomic variability based on 84 complete sequences selected from an initial collection of 758 samples that represent 60 different breeds of C. hircus, as well as its wild sister species, bezoar (Capra aegagrus) from Iran. Our phylogenetic analyses dated the most recent common ancestor of C. hircus to ~460,000 years (ka) ago and identified five distinctive domestic haplogroups (A, B1, C1a, D1 and G). More than 90 % of goats examined were in haplogroup A. These domestic lineages are predominantly nested within C. aegagrus branches, diverged concomitantly at the interface between the Epipaleolithic and early Neolithic periods, and underwent a dramatic expansion starting from ~12-10 ka ago. CONCLUSIONS: Domestic goat mitogenomes descended from a small number of founding haplotypes that underwent domestication after surviving the last glacial maximum in the Near Eastern refuges. All modern haplotypes A probably descended from a single (or at most a few closely related) female C. aegagrus. Zooarchaelogical data indicate that domestication first occurred in Southeastern Anatolia. Goats accompanying the first Neolithic migration waves into the Mediterranean were already characterized by two ancestral A and C variants. The ancient separation of the C branch (~130 ka ago) suggests a genetically distinct population that could have been involved in a second event of domestication. The novel diagnostic mutational motifs defined here, which distinguish wild and domestic haplogroups, could be used to understand phylogenetic relationships among modern breeds and ancient remains and to evaluate whether selection differentially affected mitochondrial genome variants during the development of economically important breeds.

Adaptations to climate-mediated selective pressures in sheep.

Following domestication, sheep (Ovis aries) have become essential farmed animals across the world through adaptation to a diverse range of environments and varied production systems. Climate-mediated selective pressure has shaped phenotypic variation and has left genetic "footprints" in the genome of breeds raised in different agroecological zones. Unlike numerous studies that have searched for evidence of selection using only population genetics data, here, we conducted an integrated coanalysis of environmental data with single nucleotide polymorphism (SNP) variation. By examining 49,034 SNPs from 32 old, autochthonous sheep breeds that are adapted to a spectrum of different regional climates, we identified 230 SNPs with evidence for selection that is likely due to climate-mediated pressure. Among them, 189 (82%) showed significant correlation (P ≤ 0.05) between allele frequency and climatic variables in a larger set of native populations from a worldwide range of geographic areas and climates. Gene ontology analysis of genes colocated with significant SNPs identified 17 candidates related to GTPase regulator and peptide receptor activities in the biological processes of energy metabolism and endocrine and autoimmune regulation. We also observed high linkage disequilibrium and significant extended haplotype homozygosity for the core haplotype TBC1D12-CH1 of TBC1D12. The global frequency distribution of the core haplotype and allele OAR22_18929579-A showed an apparent geographic pattern and significant (P ≤ 0.05) correlations with climatic variation. Our results imply that adaptations to local climates have shaped the spatial distribution of some variants that are candidates to underpin adaptive variation in sheep.

A case report of inadequately treated acute deep venous thrombus and venous stasis.

Background: Venous stasis dermatitis is a common skin condition that typically affects the lower extremities and may occur secondarily to venous insufficiency which can lead to a pooling of fluid within the legs. The etiology of venous stasis dermatitis is largely related to medical conditions that affect the blood flow to the lower extremities. Chronic occlusion of the common iliac veins and femoral veins can cause a lack of proper blood flow to the lower extremities. When an inferior vena cava (IVC) filter becomes tilted, it can occlude the vessels distal to its placement. Definitive treatment of chronic venous insufficiency is not common and could be improved with a referral to an interventional radiologist. Case Description: Here, we present a case of a venous stasis that is presenting secondary to chronic occlusion of the left common iliac vein and femoral vein due to a tilted and irretrievable IVC filter that was placed more than 5 years prior to presentation. Upon presentation, the patient was unable to ambulate and was suffering from large lower leg ulcers and chronic venous insufficiency secondary to the occluded vessels. The patient was treated with a series of thrombectomies in an outpatient setting until the restoration of venous blood flow was achieved. The improved venous blood flow has reduced the painful leg ulcers both in number and severity-which greatly reduces the patient's likelihood of a secondary infection. Conclusions: This case emphasizes the importance of an interdisciplinary approach to patients who may present to an outpatient dermatology clinic with signs or symptoms of acute or chronic venous insufficiency for a more definitive treatment than the current standard of care.

A rare case report: chronic generalized idiopathic pruritus.

Background: Generalized chronic pruritus (CP) can be associated with seborrheic dermatitis and psoriasis but often can present without any noticeable diagnosis or obvious skin lesion. When not related to a clear diagnosis, CP can be characterized as idiopathic pruritus. CP is both a diagnostically and therapeutically challenging presentation due to the variety of systemic, dermatological, neurological, and psychogenic diseases that must be ruled out before diagnosing idiopathic pruritus. This presentation is often overlooked but can lead to a greatly diminished quality of life for patients who present with idiopathic generalized pruritus. The course of treatment will vary between providers and specialties, however, most dermatologists will attempt control with antihistamines, topical steroids, or oral steroids. The use of gabapentinoids for the treatment of CP is understudied. Gabapentin was initially developed as an antiepileptic that has since been approved to treat neuropathic pain and has a common off-label use in dermatology and can be used to effectively treat CP. Case Description: Here we present a case of a 56-year-old Caucasian male who presented to the outpatient dermatology clinic with new-onset, diffuse, and intense pruritic symptoms that gradually progressed over a period of seven weeks. This case study details a patient with Idiopathic generalized pruritus previously uncontrolled that was well-controlled with the use of gabapentin after trials of other common treatments failed. Conclusions: The understudied off-label use of gabapentin in the case of generalized chronic idiopathic pruritus should be explored and later implemented as a mainstay for patients suffering from uncontrolled CP as it was shown to completely eliminate pruritic symptoms and improve the quality of life for this patient.

Genetic Analysis of Novel Behaviour Traits in Pigs Derived from Social Network Analysis.

Social network analysis (SNA) has provided novel traits that describe the role of individual pigs in aggression. The objectives were to (1) estimate the genetic parameters for these SNA traits, (2) quantify the genetic association between SNA and skin lesion traits, and (3) investigate the possible response to selection for SNA traits on skin lesion traits. Pigs were video recorded for 24 h post-mixing. The observed fight and bullying behaviour of each animal was used as input for the SNA. Skin lesions were counted on different body parts at 24 h (SL24h) and 3 weeks (SL3wk) post-mixing. A Bayesian approach estimated the genetic parameters of SNA traits and their association with skin lesions. SNA traits were heritable (h2 = 0.09 to 0.26) and strongly genetically correlated (rg > 0.88). Positive genetic correlations were observed between all SNA traits and anterior SL24h, except for clustering coefficient. Our results suggest that selection for an index that combines the eigenvector centrality and clustering coefficient could potentially decrease SL24h and SL3wk compared to selection for each trait separately. This study provides a first step towards potential integration of SNA traits into a multi-trait selection index for improving pigs' welfare.

Genetic Associations of Novel Behaviour Traits Derived from Social Network Analysis with Growth, Feed Efficiency, and Carcass Characteristics in Pigs.

Reducing harmful aggressive behaviour remains a major challenge in pig production. Social network analysis (SNA) showed the potential in providing novel behavioural traits that describe the direct and indirect role of individual pigs in pen-level aggression. Our objectives were to (1) estimate the genetic parameters of these SNA traits, and (2) quantify the genetic associations between the SNA traits and commonly used performance measures: growth, feed intake, feed efficiency, and carcass traits. The animals were video recorded for 24 h post-mixing. The observed fighting behaviour of each animal was used as input for the SNA. A Bayesian approach was performed to estimate the genetic parameters of SNA traits and their association with the performance traits. The heritability estimates for all SNA traits ranged from 0.01 to 0.35. The genetic correlations between SNA and performance traits were non-significant, except for weighted degree with hot carcass weight, and for both betweenness and closeness centrality with test daily gain, final body weight, and hot carcass weight. Our results suggest that SNA traits are amenable for selective breeding. Integrating these traits with other behaviour and performance traits may potentially help in building up future strategies for simultaneously improving welfare and performance in commercial pig farms.

Social Network Analysis of Agonistic Behaviour and Its Association with Economically Important Traits in Pigs.

Aggression behaviour has several negative consequences on the performance and welfare of pigs. Here, the Social Network Analysis (SNA) approach was employed to (1) identify individual traits that describe the role of each animal in the aggression; (2) investigate the association of these traits with performance and feeding behaviour traits. The study was conducted on 326 Duroc pigs reared in 29 pens. Several individual centrality traits were identified and used to calculate the Social Rank Index. The Dominant, Subordinate, and Isolated animals represented 21.1%, 57.5% and 21.4%, respectively. No significant correlations were observed between out-degree (number of initiated agonistic behaviours) and growth traits, indicating the similarity of growth patterns for dominant and non-dominant animals. Furthermore, out-degree was correlated positively with average daily occupation time (time at the feeder/day) and average daily feeding frequency (number of visits to the feeder/day) but negatively with average daily feeding rate (gr/min). This may indicate the ability of non-dominant pigs to modify their behaviour to obtain their requirements. The Hamming distances between networks showed that there is no common behaviour pattern between pens. In conclusion, SNA showed the potential for extracting behaviour traits that could be used to improve pig performance and welfare.

Author Correction: The genetic ancestry of American Creole cattle inferred from uniparental and autosomal genetic markers.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

The genetic ancestry of American Creole cattle inferred from uniparental and autosomal genetic markers.

Cattle imported from the Iberian Peninsula spread throughout America in the early years of discovery and colonization to originate Creole breeds, which adapted to a wide diversity of environments and later received influences from other origins, including zebu cattle in more recent years. We analyzed uniparental genetic markers and autosomal microsatellites in DNA samples from 114 cattle breeds distributed worldwide, including 40 Creole breeds representing the whole American continent, and samples from the Iberian Peninsula, British islands, Continental Europe, Africa and American zebu. We show that Creole breeds differ considerably from each other, and most have their own identity or group with others from neighboring regions. Results with mtDNA indicate that T1c-lineages are rare in Iberia but common in Africa and are well represented in Creoles from Brazil and Colombia, lending support to a direct African influence on Creoles. This is reinforced by the sharing of a unique Y-haplotype between cattle from Mozambique and Creoles from Argentina. Autosomal microsatellites indicate that Creoles occupy an intermediate position between African and European breeds, and some Creoles show a clear Iberian signature. Our results confirm the mixed ancestry of American Creole cattle and the role that African cattle have played in their development.

Correlated responses to selection for intramuscular fat in several muscles in rabbits.

The aim of this study was to evaluate the effect of six generations of selection for intramuscular fat (IMF) in muscle Longissimus thoracis et lumborum (LTL) at 9 wk. in IMF and fatty acid (FA) composition of muscles with diverse metabolic profile in rabbits. Direct response to selection was 0.33 g of IMF/ 100 g of LTL, around 0.4 SD per generation. A positive correlated response was observed in IMF of Biceps femoris, Supraspinatus and Semimembranosus proprius muscles at 9 wk., representing around 0.2 SD of the trait per generation. Selection affected similarly the FA composition of all muscles at 9 wk., high-IMF line showing greater monounsaturated but lower polyunsaturated FA percentages than low-IMF line, whereas no differences were observed for saturated FA. Traits were also measured at 13 wk. and correlated responses were in the same direction. Our results suggest a common genetic background for IMF and FA composition in muscles with different metabolic profile in rabbits.

Mitogenomes from Egyptian Cattle Breeds: New Clues on the Origin of Haplogroup Q and the Early Spread of Bos taurus from the Near East.

BACKGROUND: Genetic studies support the scenario that Bos taurus domestication occurred in the Near East during the Neolithic transition about 10 thousand years (ky) ago, with the likely exception of a minor secondary event in Italy. However, despite the proven effectiveness of whole mitochondrial genome data in providing valuable information concerning the origin of taurine cattle, until now no population surveys have been carried out at the level of mitogenomes in local breeds from the Near East or surrounding areas. Egypt is in close geographic and cultural proximity to the Near East, in particular the Nile Delta region, and was one of the first neighboring areas to adopt the Neolithic package. Thus, a survey of mitogenome variation of autochthonous taurine breeds from the Nile Delta region might provide new insights on the early spread of cattle rearing outside the Near East. METHODOLOGY: Using Illumina high-throughput sequencing we characterized the mitogenomes from two cattle breeds, Menofi (N = 17) and Domiaty (N = 14), from the Nile Delta region. Phylogenetic and Bayesian analyses were subsequently performed. CONCLUSIONS: Phylogenetic analyses of the 31 mitogenomes confirmed the prevalence of haplogroup T1, similar to most African cattle breeds, but showed also high frequencies for haplogroups T2, T3 and Q1, and an extremely high haplotype diversity, while Bayesian skyline plots pointed to a main episode of population growth ~12.5 ky ago. Comparisons of Nile Delta mitogenomes with those from other geographic areas revealed that (i) most Egyptian mtDNAs are probably direct local derivatives from the founder domestic herds which first arrived from the Near East and the extent of gene flow from and towards the Nile Delta region was limited after the initial founding event(s); (ii) haplogroup Q1 was among these founders, thus proving that it underwent domestication in the Near East together with the founders of the T clades.

Origin and spread of Bos taurus: new clues from mitochondrial genomes belonging to haplogroup T1.

BACKGROUND: Most genetic studies on modern cattle have established a common origin for all taurine breeds in the Near East, during the Neolithic transition about 10 thousand years (ka) ago. Yet, the possibility of independent and/or secondary domestication events is still debated and is fostered by the finding of rare mitochondrial DNA (mtDNA) haplogroups like P, Q and R. Haplogroup T1, because of its geographic distribution, has been the subject of several investigations pointing to a possible independent domestication event in Africa and suggesting a genetic contribution of African cattle to the formation of Iberian and Creole cattle. Whole mitochondrial genome sequence analysis, with its proven effectiveness in improving the resolution of phylogeographic studies, is the most appropriate tool to investigate the origin and structure of haplogroup T1. METHODOLOGY: A survey of >2200 bovine mtDNA control regions representing 28 breeds (15 European, 10 African, 3 American) identified 281 subjects belonging to haplogroup T1. Fifty-four were selected for whole mtDNA genome sequencing, and combined with ten T1 complete sequences from previous studies into the most detailed T1 phylogenetic tree available to date. CONCLUSIONS: Phylogenetic analysis of the 64 T1 mitochondrial complete genomes revealed six distinct sub-haplogroups (T1a-T1f). Our data support the overall scenario of a Near Eastern origin of the T1 sub-haplogroups from as much as eight founding T1 haplotypes. However, the possibility that one sub-haplogroup (T1d) arose in North Africa, in domesticated stocks, shortly after their arrival from the Near East, can not be ruled out. Finally, the previously identified "African-derived American" (AA) haplotype turned out to be a sub-clade of T1c (T1c1a1). This haplotype was found here for the first time in Africa (Egypt), indicating that it probably originated in North Africa, reached the Iberian Peninsula and sailed to America, with the first European settlers.