Genome-wide scan for runs of homozygosity in South American Camelids

BACKGROUND

Alpaca (Vicugna pacos), llama (Lama glama), vicugna (Vicugna vicugna) and guanaco (Lama guanicoe), are the camelid species distributed over the Andean high-altitude grasslands, the Altiplano, and the Patagonian arid steppes. Despite the wide interest on these animals, most of the loci under selection are still unknown. Using whole-genome sequencing (WGS) data we investigated the occurrence and the distribution of Runs Of Homozygosity (ROHs) across the South American Camelids (SACs) genome to identify the genetic relationship between the four species and the potential signatures of selection.

RESULTS

A total of 37 WGS samples covering the four species was included in the final analysis. The multi-dimensional scaling approach showed a clear separation between the four species; however, admixture analysis suggested a strong genetic introgression from vicugna and llama to alpaca. Conversely, very low genetic admixture of the guanaco with the other SACs was found. The four species did not show significant differences in the number, length of ROHs (100-500 kb) and genomic inbreeding values. Longer ROHs (> 500 kb) were found almost exclusively in alpaca. Seven overlapping ROHs were shared by alpacas, encompassing nine loci (FGF5, LOC107034918, PRDM8, ANTXR2, LOC102534792, BSN, LOC116284892, DAG1 and RIC8B) while nine overlapping ROHs were found in llama with twenty-five loci annotated (ERC2, FZD9, BAZ1B, BCL7B, LOC116284208, TBL2, MLXIPL, PHF20, TRNAD-AUC, LOC116284365, RBM39, ARFGEF2, DCAF5, EXD2, HSPB11, LRRC42, LDLRAD1, TMEM59, LOC107033213, TCEANC2, LOC102545169, LOC116278408, SMIM15, NDUFAF2 and RCOR1). Four overlapping ROHs, with three annotated loci (DLG1, KAT6B and PDE4D) and three overlapping ROHs, with seven annotated genes (ATP6V1E1, BCL2L13, LOC116276952, BID, KAT6B, LOC116282667 and LOC107034552), were detected for vicugna and guanaco, respectively.

CONCLUSIONS

The signatures of selection revealed genomic areas potentially selected for production traits as well as for natural adaptation to harsh environment. Alpaca and llama hint a selection driven by environment as well as by farming purpose while vicugna and guanaco showed selection signals for adaptation to harsh environment. Interesting, signatures of selection on KAT6B gene were identified for both vicugna and guanaco, suggesting a positive effect on wild populations fitness. Such information may be of interest to further ecological and animal production studies.

Sociability strongly affects the behavioural responses of wild guanacos to drones

Drones are being increasingly used in research and recreation but without an adequate assessment of their potential impacts on wildlife. Particularly, the effect of sociability on behavioural responses to drone-associated disturbance remains largely unknown. Using an ungulate with complex social behaviour, we (1) assessed how social aggregation and offspring presence, along with flight plan characteristics, influence the probability of behavioural reaction and the flight distance of wild guanacos (Lama guanicoe) to the drone's approach, and (2) estimated reaction thresholds and flight heights that minimise disturbance. Sociability significantly affected behavioural responses. Large groups showed higher reaction probability and greater flight distances than smaller groups and solitary individuals, regardless of the presence of offspring. This suggests greater detection abilities in large groups, but we cannot rule out the influence of other features inherent to each social unit (e.g., territoriality) that might be working simultaneously. Low flight heights increased the probability of reaction, although the effect of drone speed was less clear. Reaction thresholds ranged from 154 m (solitary individuals) to 344 m (mixed groups), revealing that the responsiveness of this guanaco population to the drone is the most dramatic reported so far for a wild species.

Clinical and pathological findings in a Dwarf Red Brocket Mazama rufina (Mammalia: Cetartiodactyla: Cervidae) attacked by dogs

Capture myopathy is a common fatal syndrome in wild ungulates resulting from anthropogenic stressful events such as the capture or transport of specimens.  There are, however, few published data on this issue due to predator attacks.  The present report describes for the first time the capture myopathy syndrome in a Dwarf Red Brocket Mazama rufina following dog Canis familiaris attack.  Clinical signs included pale mucous with increase capillary refill time, tachycardia, tachypnea, hypertension, hypothermia, hypoglycemia, and red brown urine.  Muscle tremors, ataxia, prostration, paralysis, and opisthotonus were progressively observed.  Laboratory tests showed increased levels of cortisol, creatinine, creatine kinase, lactate dehydrogenase, and potassium; decreased blood urea nitrogen-creatinine ratio; and myoglobinuria.  The animal died 72 hours after hospital admission.  At necropsy, findings included injuries on both hindlimbs with edema, emphysema, and soft-friable texture in affected muscles, dark kidneys and brown urine in bladder.  Histopathological exams were indicative of skeletal-cardiac muscle degenerative lesions and myoglobinuric nephrosis.  Immuno-histochemistry revealed myoglobin depletion in degenerate muscles and myoglobin accumulation in renal tissues.  We strongly recommend that treatment for capture myopathy be initiated when a wild ungulate is admitted with history of predator attack, since the syndrome may have already established.  This report adds to the instances of negative impacts caused by domestic dogs on threatened wildlife species.   

A predictive model to diagnose pregnancy in guanacos (Lama guanicoe) using non-invasive methods

Pregnancy status is usually not included in ecological studies because it is difficult to evaluate. The use of non-invasive methods to determine pregnancy, without physically restraining individuals, would enable pregnancy to be included in population studies. In this study, we evaluated sex steroid hormones in plasma and fecal samples from pregnant and non-pregnant females to develop a pregnancy predictive model for guanacos (Lama guanicoe (Müller, 1776)). Samples were obtained during live-shearing management (i.e., capture, shear, and release) of guanacos. Enzyme immunoassays were used to evaluate progesterone (P4) and estradiol (E2) concentrations in plasma and pregnanediol glucuronides (PdG) and conjugated estrogens (EC) in feces. Mean hormonal and fecal metabolite concentrations were significantly higher in pregnant females than in non-pregnant females. A linear relationship was found between each hormone and its fecal metabolite. Finally, hormonal data were combined with an independent source of pregnancy diagnosis such as abdominal ballottement to develop a logistic regression model to diagnose pregnancy in non-handled individuals. The use of predictive models and non-invasive methods might be suitable to incorporate pregnancy information in large-scale population studies on guanaco and other free-ranging ungulates.

Physiological and behavioral indices of short-term stress in wild vicuñas (Vicugna vicugna) in Jujuy Province, Argentina

The management of wild vicuñas can trigger a stress response that may compromise welfare. In Santa Catalina, Jujuy Province, Argentina, indices of short-term stress associated with capture, handling, and shearing were studied in 105 wild vicuñas (Vicugna vicugna). The study included 2 groups (n = 59 and n = 46) of wild vicuñas captured in 2 consecutive days. Independent variables analyzed included sex, restraint time, and groups. Cortisol, creatine kinase, glucose, white blood cells, temperature, heart rate, and respiratory frequency were higher than published values. Respiratory rate increased during handling and correlated with holding time and group size, while heart rate decreased. Packed cell volume was higher in females. Cortisol concentrations differed between restraint groups and sex and inversely correlated with agonistic behavior. The most common behavior was increased vigilance. Sternal recumbency increased over holding time. During handling procedures, frequency of sudden movements like kicking and attempts to stand increased as restraint time increased. Females vocalized more than males. In conclusion, the methods used triggered measurable changes suggestive of short-term stress that appeared to be physiologically tolerated by the vicuñas.

Clinical parameters and adrenocortical activity to assess stress responses of alpacas using different methods of restraint either alone or with shearing

Shearing of alpacas is stressful and is undertaken by restraint in the standing position, cast on the floor or on a tilt table. The objectives of the study were to evaluate and compare the stress responses between different methods. The study consisted of two parts. In part one, 15 animals were restrained applying all three methods but without shearing. In part two, 45 animals in three groups of 15 were shorn using one of the three procedures. Body temperature, heart rate, respiratory rate, salivary cortisol and faecal cortisol metabolites (FCM) were measured. Part 1: restraint in a standing position was less stressful than other procedures. Part 2: the classic clinical parameters changed significantly over time but without significant differences between the methods. The number of injuries did not differ. Saliva cortisol and FCM concentrations varied in wide ranges between animals. An increase in FCM concentrations occurred in all groups but saliva cortisol concentration increased only after shearing on the ground. The recommendations of the study are to shear calm alpacas in the standing position but animals showing severe defence reactions should be shorn either cast on the ground or on a table to decrease the risk of injuries.

Effects of live-shearing on population parameters and movement in sedentary and migratory populations of guanacos Lama guanicoe

Live-shearing of wild guanacos Lama guanicoe may affect their reproductive success and population resilience, and therefore it is important to assess the biological sustainability of obtaining their wool. We evaluated effects of capture and shearing on survival and reproduction, population parameters, daily movements, ranging behaviour and spatial distribution in sedentary and migratory populations. We assessed population variables by radio-telemetry and line-transect surveys before and after capture. We estimated high post-shearing survival rates in both populations and similar yearling production in shorn and non-shorn females in the migratory population. We did not find significant variations in density and population structure before and after shearing in the sedentary population, whereas in the migratory population density decreased and the population structure changed significantly after assembly of the capture structure, returning to pre-assembly levels 1 month later. The mean daily distance moved by radio-collared guanacos during the first 2 days after shearing was three times longer than during the following 30 days. There was a 25% decrease in the mean home-range size of shorn guanacos between the first and second month after shearing but this decline appeared to be associated with a seasonal change in movement, because a similar reduction occurred during the same period the following year, when the guanacos were not shorn. Live-shearing modified the spatial distribution pattern in the sedentary population but did not have a significant effect on the migratory population. Management of guanacos may contribute towards developing a biologically sustainable economic activity that promotes conservation of wildlife and habitats.

Do cortisol and corticosterone play the same role in coping with stressors? Measuring glucocorticoid serum in free-ranging guanacos (Lama guanicoe)

Habitat can constrain and shape successful ecological and physiological strategies, thus providing the context for the evolution of life-history traits. However, unpredictable challenges, such as storms, natural disasters, and human activities can also have great effects on stress. Glucocorticoids (GCs) are adrenal steroid hormones that play an important role in how vertebrates cope with these predictable and unpredictable environmental challenges. Although assessing GCs levels can have many applications in the study of wildlife and/or captive animals, with or without capturing individuals, it requires a species-specific complete validation (analytical and biological) before its use. In this work, our aim was to: (a) validate a radioimmunoassay (RIA) for measuring GCs levels in L. guanicoe serum; (b) assess cortisol and corticosterone levels (if present) in serum of wild L. guanicoe individuals; and (c) compare the response to acute stressors (handling, shearing, and release). Our results successfully: (a) validated RIA for asses GCs levels in wild ungulates; (b) confirmed the presence for cortisol and corticosterone and showed that both GCs are differently affected by environmental stimuli in L. guanicoe; and (c) showed that GCs exhibit different patterns in the field and in response to acute stressors, making these camelids an interesting endocrinological model when seeking the adaptive functions of a given variation and further emphasizing the complexity of GC physiology in wild mammals.