Research Articles (Veterinary Genetics Laboratory)

Permanent URI for this collectionhttp://hdl.handle.net/2263/95117

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A highly divergent mitochondrial genome in extant Cape buffalo from Addo Elephant National Park, South Africa
(Wiley, 2025-01) De Jager, Deon; Moller, Marlo; Hoal, Eileen; Van Helden, Paul David; Glanzmann, Brigitte; Harper, Cindy Kim; Bloomer, Paulette; paulette.bloomer@up.ac.za
The reduced cost of next-generation sequencing (NGS) has allowed researchers to generate nuclear and mitochondrial genome data to gain deeper insights into the phylogeography, evolutionary history and biology of non-model species. While the Cape buffalo (Syncerus caffer caffer) has been well-studied across its range with traditional genetic markers over the last 25 years, researchers are building on this knowledge by generating whole genome, population-level data sets to improve understanding of the genetic composition and evolutionary history of the species. Using publicly available NGS data, we assembled 40 Cape buffalo mitochondrial genomes (mitogenomes) from four protected areas in South Africa, expanding the geographical range and almost doubling the number of mitogenomes available for this species. Coverage of the mitogenomes ranged from 154 to 1036X. Haplotype and nucleotide diversity for Kruger National Park (n = 15) and Mokala National Park (n = 5) were similar to diversity levels in southern and eastern Africa. Hluhluwe–iMfolozi Park (n = 15) had low levels of genetic diversity, with only four haplotypes detected, reflecting its past bottleneck. Addo Elephant National Park (n = 5) had the highest nucleotide diversity of all populations across Africa, which was unexpected, as it is known to have low nuclear diversity. This diversity was driven by a highly divergent mitogenome from one sample, which was subsequently identified in another sample via Sanger sequencing of the cytochrome b gene. Using a fossil-calibrated phylogenetic analysis, we estimated that this lineage diverged from all other Cape buffalo lineages approximately 2.51 million years ago. We discuss several potential sources of this mitogenome but propose that it most likely originated through introgressive hybridisation with an extinct buffalo species, either S. acoelotus or S. antiquus. We conclude by discussing the conservation consequences of this finding for the Addo Elephant National Park population, proposing careful genetic management to prevent inbreeding depression while maintaining this highly unique diversity.
Poaching forensics : animal victims in the courtroom
(Annual Reviews, 2023) Harper, Cindy Kim; cindy.harper@up.ac.za
Poaching and the international trade in wildlife are escalating problems driven by poverty and greed and coordinated by increasingly sophisticated criminal networks. Biodiversity loss, caused by habitat change, is exacerbated by poaching, and species globally are facing extinction. Forensic evidence underpins human and animal criminal investigations and is critical in criminal prosecution and conviction. The application of forensic tools, particularly forensic genetics, to animal case work continues to advance, providing the systems to confront the challenges of wildlife investigations. This article discusses some of these tools, their development, and implementations, as well as recent advances. Examples of cases are provided in which forensic evidence played a key role in obtaining convictions, thus laying the foundation for the future application of techniques to disrupt the criminal networks and safeguard biodiversity through species protection.
High diversity, inbreeding and a dynamic Pleistocene demographic history revealed by African buffalo genomes
(Nature Research, 2021) De Jager, Deon; Glanzmann, Brigitte; Möller, Marlo; Hoal, Eileen; Van Helden, Paul; Harper, Cindy Kim; Bloomer, Paulette
Genomes retain records of demographic changes and evolutionary forces that shape species and populations. Remnant populations of African bufalo (Syncerus cafer) in South Africa, with varied histories, provide an opportunity to investigate signatures left in their genomes by past events, both recent and ancient. Here, we produce 40 low coverage (7.14×) genome sequences of Cape bufalo (S. c. cafer) from four protected areas in South Africa. Genome-wide heterozygosity was the highest for any mammal for which these data are available, while diferences in individual inbreeding coefcients refected the severity of historical bottlenecks and current census sizes in each population. PSMC analysis revealed multiple changes in Ne between approximately one million and 20 thousand years ago, corresponding to paleoclimatic changes and Cape bufalo colonisation of southern Africa. The results of this study have implications for bufalo management and conservation, particularly in the context of the predicted increase in aridity and temperature in southern Africa over the next century as a result of climate change.
Polygamous farmed Nile crocodiles (Crocodylus niloticus) : foetal membranes tell the story
(AOSIS Open Journals, 2020-11-06) Nothling, Johan Oliviette; Nöthling, Johan Antowan; Myburgh, Jan G.; Harper, Cindy Kim; johan.nothling@up.ac.za
Multiple paternity in crocodilian broods would increase effective population size and slow down the loss of genetic variation due to inbreeding and random genetic drift in real populations. Multiple paternity may also explain variation among offspring of the same brood with respect to characteristics of commercial interest to crocodile farmers. Foetal membranes may provide a non-invasive source of DNA from which to determine the genotypes of Nile crocodile (Crocodylus niloticus) hatchlings. The aims of this study were to determine the effectiveness of using the foetal membranes remaining inside the hatched eggs to determine the genotypes of Nile crocodile hatchlings, and to determine whether a brood (the hatchlings from a clutch of eggs) from a communal breeding pond on a commercial farm may have more than one sire. DNA profiles were determined on 4–6 (mean 4.4) foetal membrane specimens (FMSs) from each of 25 broods from the same breeding pond on a commercial Nile crocodile farm. Eleven microsatellite loci were used. DNA amplification occurred at all 11 loci in 95 of the 110 genotyped individuals, at 1–10 loci in 13 and at no locus in two. Three to 20 alleles were found per locus. Single-locus assessment showed that 13 broods had at least two sires. A multilocus programme (Colony) inferred that 19 broods had at least two sires, with polyandry and polygyny being common. Further research is necessary to determine the utility of foetal membranes as a source of DNA from nests in the wild and, using more FMSs per brood, to more precisely determine the extent of polyandry and polygyny in farmed and wild Nile crocodiles.
Genetic diversity, relatedness and inbreeding of ranched and fragmented Cape buffalo populations in southern Africa
(Public Library of Science, 2020-08-14) De Jager, G.J. (Deon); Harper, Cindy Kim; Bloomer, Paulette
Wildlife ranching, although not considered a conventional conservation system, provides a sustainable model for wildlife utilization and could be a source of valuable genetic material. However, increased fragmentation and intensive management may threaten the evolutionary potential and conservation value of species. Disease-free Cape buffalo (Syncerus caffer caffer) in southern Africa exist in populations with a variety of histories and management practices. We compared the genetic diversity of buffalo in national parks to private ranches and found that, except for Addo Elephant National Park, genetic diversity was high and statistically equivalent. We found that relatedness and inbreeding levels were not substantially different between ranched populations and those in national parks, indicating that breeding practices likely did not yet influence genetic diversity of buffalo on private ranches in this study. High genetic differentiation between South African protected areas highlighted their fragmented nature. Structure analysis revealed private ranches comprised three gene pools, with origins from Addo Elephant National Park, Kruger National Park and a third, unsampled gene pool. Based on these results, we recommend the Addo population be supplemented with disease-free Graspan and Mokala buffalo (of Kruger origin). We highlight the need for more research to characterize the genetic diversity and composition of ranched wildlife species, in conjunction with wildlife ranchers and conservation authorities, in order to evaluate the implications for management and conservation of these species across different systems.
Anthropogenic movement results in hybridisation in impala in southern Africa
(Springer, 2020-08) Miller, Susan M.; Moeller, Carl-Heinz; Harper, Cindy Kim; Bloomer, Paulette
Hybridisation caused by anthropogenic movements of animals is a conservation concern. Black-faced impala (Aepyceros melampus petersi) are endemic to north-western Namibia and south-western Angola and are geographically isolated from common impala (A. m. melampus). Common impala have been translocated into the black-faced impala range creating a hybridisation risk. We validated 13 microsatellite markers for the detection of recent hybridisation events. We used these markers to assess the genetic variation and differentiation among impala within Etosha National Park (NP), Southern Cross Private Game Reserve (SCPGR), Namibia, and private game ranches across South Africa. We confirmed that “black-nosed” impala in South Africa were A. m. melampus, thus providing more evidence that the black blaze on the face cannot be used to distinguish between the two subspecies. We detected four hybrids and one common impala on SCPGR. These five individuals were removed from SCPGR at time of sampling. We found two potential hybrids in southern Etosha NP. Further sampling of animals within Etosha NP is recommended to determine the extent of hybridisation within the park. The Namibian Ministry of the Environment & Tourism is developing a management plan for black-faced impala across Namibia that includes genetic testing for hybrids.
Genetic rescue of an isolated African lion population
(Springer, 2020-02) Miller, Susan M.; Druce, Dave J.; Dalton, Desire L.; Harper, Cindy Kim; Kotze, Antoinette; Packer, Craig; Slotow, Rob; Bloomer, Paulette
Fragmented wildlife populations are challenged by limited gene flow that can lead to significant inbreeding. The lion (Panthera leo) population in South Africa’s Hluhluwe-iMfolozi Park (HiP) started from a small founder population of one adult male (1958), one adult female, followed by two lionesses and three cubs (two females and one male; 1965; unrelated to the male). A genetic rescue effort was launched after signs of inbreeding were observed in the 1990s. Sixteen lions (13 females and three males) were translocated into the HiP population from Pilanesberg National Park and Madikwe Game Reserve. We assessed the genetic consequences 10 to 15 years post translocation (n = 91), using microsatellite markers. Structure analysis revealed integration of the translocated animals and evidence of a unique post-translocation genetic cluster. Allelic richness increased from 2.26 to 3.88, and heterozygosity from 0.40 to 0.65. However, overall relatedness within (0.19) and among (0.15) existing prides remained higher than in an open system, and both allelic richness and heterozygosity were declining in later post-translocation generations. Thus, although genetic rescue is a valuable tool for the recovery of inbred, isolated populations, genetic augmentation should be performed at regular intervals to ensure continued population viability.
Robust forensic matching of confiscated horns to individual poached African rhinoceros
(Elsevier (Cell Press), 2018) Harper, Cindy Kim; Ludwig, Anette; Clarke, Amy B.; Makgopela, Kagiso; Yurchenko, Andrey; Guthrie, Alan John; Dobrynin, Pavel; Tamazian, Gaik; Emslie, Richard; Van Heerden, Marile; Hofmeyr, Markus; Potter, Roderick; Roets, Johannes; Beytell, Piet; Otiende, Moses; Kariuki, Linus; Du Toit, Raoul; Anderson, Natasha; Okori, Joseph; Antonik, Alexey; Koepfli, Klaus-Peter; Thompson, P.N. (Peter N.); O’Brien, Stephen J.; cindy.harper@up.ac.za
Black and white rhinoceros (Diceros bicornis and Ceratotherium simum) are iconic African species that are classified by the International Union for the Conservation of Nature (IUCN) as Critically Endangered and Near Threatened (http://www.iucnredlist. org/), respectively. At the end of the 19th century, Southern white rhinoceros (Ceratotherium simum simum) numbers had declined to fewer than 50 animals in the Hluhluwe-iMfolozi region of the KwaZulu-Natal (KZN) province of South Africa, mainly due to uncontrolled hunting. Efforts by the Natal Parks Board facilitated an increase in population to over 20,000 in 2015 through aggressive conservation management. Black rhinoceros (Diceros bicornis) populations declined from several hundred thousand in the early 19th century to ~65,000 in 1970 and to ~2,400 by 1995 with subsequent genetic reduction, also due to hunting, land clearances and later poaching. In South Africa, rhinoceros poaching incidents have increased from 13 in 2007 to 1,215 in 2014. This has occurred despite strict trade bans on rhinoceros products and strict enforcement in recent years.
Friends and family : a software program for identification of unrelated individuals from molecular marker data
(Wiley, 2017-11) De Jager, G.J. (Deon); Swarts, Petrus; Harper, Cindy Kim; Bloomer, Paulette
The identification of related and unrelated individuals from molecular marker data is often difficult, particularly when no pedigree information is available and the data set is large. High levels of relatedness or inbreeding can influence genotype frequencies and thus genetic marker evaluation, as well as the accurate inference of hidden genetic structure. Identification of related and unrelated individuals is also important in breeding programmes, to inform decisions about breeding pairs and translocations. We present Friends and Family, a Windows executable program with a graphical user interface that identifies unrelated individuals from a pairwise relatedness matrix or table generated in programs such as coancestry and genalex. Friends and Family outputs a list of samples that are all unrelated to each other, based on a user‐defined relatedness cut‐off value. This unrelated data set can be used in downstream analyses, such as marker evaluation or inference of genetic structure. The results can be compared to that of the full data set to determine the effect related individuals have on the analyses. We demonstrate one of the applications of the program: how the removal of related individuals altered the Hardy–Weinberg equilibrium test outcome for microsatellite markers in an empirical data set.
Specifying and sustaining pigmentation patterns in domestic and wild cats
(American Association for the Advancement of Science, 2012-09) Kaelin, Christopher B.; Xu, Xiao; Hong, Lewis Z.; David, Victor A.; McGowan, Kelly A.; Schmidt-Küntzel, Anne; Roelke, Melody E.; Pino, Javier; Pontius, Joan; Cooper, Gregory M.; Manuel, Hermogenes; Swanson, William F.; Marker, Laurie; Harper, Cindy Kim; Van Dyk, Ann; Yue, Bisong; Mullikin, James C.; Warren, Wesley C.; Eizirik, Eduardo; Kos, Lidia; O’Brien, Stephen J.; Barsh, Gregory S.; Menotti-Raymond, Marilyn
Color markings among felid species display both a remarkable diversity and a common underlying periodicity. A similar range of patterns within domestic cats suggests a conserved mechanism whose appearance can be altered by selection. We identify the gene responsible for tabby pattern variation in domestic cats as Transmembrane aminopeptidase Q (Taqpep), which encodes a membrane-bound metalloprotease. Analyzing 31 other felid species we identify Taqpep as the cause of the rare king cheetah phenotype, in which spots coalesce into blotches and stripes. Histologic, genomic expression, and transgenic mouse studies indicate that paracrine expression of Endothelin3 (Edn3) coordinates localized color differences. We propose a two-stage model in which Taqpep helps to establish a periodic pre-pattern during skin development that is later implemented by differential expression of Edn3.
Missense mutation in the ligand-binding domain of the horse androgen receptor gene in a thoroughbred family with inherited 64,XY (SRY+) disorder of sex development
(Karger, 2016) Bolzon, Colin; Joone, C.J. (Carolynne); Schulman, M.L. (Martin); Harper, Cindy Kim; Villagómez, Daniel A.F.; King, W. Allan; Révay, Tamas
Disorders of sex development (DSD) have long been documented in domestic animal species including horses. However, there is only a single report of an androgen receptor mutation causative of such a DSD syndrome in a horse pedigree. Here, we present a new familial AR mutation in horses. A missense mutation (c.2042G>C) at AR exon 4 explains the segregation of the DSD in a Thoroughbred horse pedigree. The mutation, expected to affect the ligand-binding domain of the androgen receptor protein, led to complete androgen insensitivity of XY SRY+, testicular DSD individuals. Additionally, design of a PCR-RFLP technique provided an accurate molecular test for identification of horses carrying the mutation.
Single base-pair deletion in ASIP exon 3 associated with recessive black phenotype in impala (Aepyceros melampus)
(Wiley, 2016-08) Miller, Susan M.; Guthrie, Alan John; Harper, Cindy Kim
No abstract is available.
Evaluation of microsatellites for common ungulates in the South African wildlife industry
(Springer, 2016-09) Miller, Susan M.; Clarke, Amy B.; Bloomer, Paulette; Guthrie, Alan John; Harper, Cindy Kim
Wildlife is a multi-million dollar industry in South Africa ranging from intensively farmed animals on small properties to free-roaming animals in large functional ecosystems. Specific concerns surrounding the conservation value of the intensively managed wildlife have been raised. Increasingly it is recognised that genetics must be considered when developing conservation policy and management practices. Minimal genetic data are available to assist with decisions within the industry. Microsatellite markers have been developed for some species and are currently used for individual identification, parentage assessment and to inform translocation decisions. However, validation for standardized application in wildlife management has not been completed. Common species for which conservation management decisions have to be made include: Cape buffalo (Syncerus caffer), blue wildebeest (Connochaetes taurinus taurinus), common impala (Aepyceros melampus) and sable antelope (Hippotragus niger). Using existing microsatellite markers for domestic and wild species, we have developed multiplex panels for use in these species. We discriminated between 751 buffalo (four pairs were not distinguishable), 1307 blue wildebeest (three pairs were not distinguishable), 580 impala and 493 sable antelope. We determined parentage in four case studies using a combination of microsatellite and demographic data. We also tested microsatellite markers on roan antelope (Hippotragus equinus), gemsbok (Oryx gazella) and eland (Tragelaphus oryx) and report preliminary data. Further research to improve this validation includes: extensive sampling from more diverse areas, targeted or full genome sequencing to identify additional microsatellite loci, development of sampling kits and training of veterinarians, as well as expansion of the species tested.
Fenced and fragmented : conservation value of managed metapopulations
(Public Library of Science, 2015-12-23) Miller, Susan M.; Harper, Cindy Kim; Bloomer, Paulette; Hofmeyr, Jennifer; Funston, Paul J.
Population fragmentation is threatening biodiversity worldwide. Species that once roamed vast areas are increasingly being conserved in small, isolated areas. Modern management approaches must adapt to ensure the continued survival and conservation value of these populations. In South Africa, a managed metapopulation approach has been adopted for several large carnivore species, all protected in isolated, relatively small, reserves that are fenced. As far as possible these approaches are based on natural metapopulation structures. In this network, over the past 25 years, African lions (Panthera leo) were reintroduced into 44 fenced reserves with little attention given to maintaining genetic diversity. To examine the situation, we investigated the current genetic provenance and diversity of these lions. We found that overall genetic diversity was similar to that in a large national park, and included a mixture of four different southern African evolutionarily significant units (ESUs). This mixing of ESUs, while not ideal, provides a unique opportunity to study the impact of mixing ESUs over the long term. We propose a strategic managed metapopulation plan to ensure the maintenance of genetic diversity and improve the long-term conservation value of these lions. This managed metapopulation approach could be applied to other species under similar ecological constraints around the globe.
The selection of a standard STR panel for DNA profiling of the African elephant (Loxodonta africana) in Kenya
(SpringerOpen Journal, 2015-06) Kinuthia, Julius; Harper, Cindy Kim; Muya, Shadrack; Kimwele, Charles; Alakonya, Amos; Muigai, Anne; Gakuya, Francis; Mwaniki, Mercy; Gatebe, Erastus
The African elephant (Loxodonta africana) population in Kenya is declining at an alarming rate due to habitat destruction, human-elephant conflicts and the current escalation of poaching for ivory. This study established a standard protocol for forensic analysis of L. africana and their products such as ivory. Three multiplex PCR panels consisting of 17 Short Tandem Repeat markers were selected from 40 markers using bioinformatics tools, amplification and polymorphism. Genotyping was successful and reproducible. This method is efficient, accurate and cost effective and has potential for application in conservation of L. africana.
The carrier prevalence of severe combined immunodeficiency, lavender foal syndrome and cerebellar abiotrophy in Arabian horses in South Africa
(Wiley, 2014-07) Tarr, Carolynne Jane; Thompson, P.N. (Peter N.); Guthrie, Alan John; Harper, Cindy Kim; cindy.harper@up.ac.za
REASONS FOR PERFORMING STUDY : The carrier prevalence of severe combined immunodeficiency (SCID), lavender foal syndrome (LFS) and cerebellar abiotrophy (CA) in Arabian foals in South Africawas determined in order to quantify the potential impact of these conditions locally. Furthermore, the carrier prevalence of SCID prior to and following the introduction of a genetic test was compared to evaluate the effect of testing in the population. OBJECTIVES : To estimate the carrier prevalence of SCID, LFS and CA in registered purebred Arabians born in South Africa in the 2004/5 and 2009/10 foaling seasons and compare the changes in prevalence in these disorders between the 2 groups of foals. STUDY DESIGN : Cross-sectional survey. METHODS : Samples were collected from individuals randomly selected from 2 populations of purebred Arabian foals born during the 2004/5 and 2009/10 foaling seasons. Genetic testing for SCID, LFS and CA was performed on DNA extracts using specific polymerase chain reactions, with the products being analysed using fragment analysis on a genetic analyser. RESULTS : The carrier prevalence of LFS and CA for the 2009/10 season was 11.7% (95% confidence interval [CI] 7.6–17.0%) and 5.1% (95% CI 2.5–9.1%), respectively, with no statistically significant change in prevalence between the 2004/5 and 2009/10 foaling seasons. However, the carrier prevalence of SCID was found to have decreased significantly from 6.4% (95% CI 4.8–8.3%) in the 2004/5 foals to 3.4% (95% CI 2.2–5.1%) in the 2009/10 foals (P = 0.009). CONCLUSIONS: The results of this study indicate that genetic screening of Arabian horses for SCID may have played a role in significantly reducing the carrier prevalence within the breeding population and thereby reducing the birth of clinically affected individuals. This study provides an indication of the positive effect of genetic screening for specific conditions in horses.
Evaluation of microsatellite markers for populations studies and forensic identification of African lions (Panthera leo)
(Oxford University Press, 2014-11) Miller, Susan M.; Harper, Cindy Kim; Bloomer, Paulette; Hofmeyr, Jennifer; Funston, Paul J.
The South African lion (Panthera leo) population is highly fragmented. One third of its wild lions occur in small (<1000 km2) reserves. These lions were reintroduced from other areas of the species’ historical range. Management practices on these reserves have not prioritised genetic provenance or heterozygosity. These trends potentially constrain the conservation value of these lions. To ensure the best management and long-term survival of these subpopulations as a viable collective population, the provenance and current genetic diversity must be described. Concurrently, poaching of lions to supply a growing market for lion bones in Asia may become a serious conservation challenge in the future. Having a standardised, validated method for matching confiscated lion parts with carcasses will be a key tool in investigating these crimes. We evaluated 28 microsatellites in the African lion using samples from 18 small reserves and one captive facility in South Africa, two conservancies in Zimbabwe, and Kruger National and Kgalagadi Transfrontier Parks to determine the loci most suited for population management and forensic genetic applications. Twelve microsatellite loci with a match probability of 1.1 x 10- 5 between siblings were identified for forensics. A further ten could be added for population genetics studies.
Cyclic neutropenia in a basset hound
(BMJ Publishing Group, 2015) Koster, Liza Sally; Harper, Cindy Kim; Goddard, Amelia
A 6 month old, male basset hound was referred for intermittent malaise, and pyrexia that repeated every 10-11 days. Sequential blood counts and bone marrow aspirates demonstrated severe neutropaenia and increased myeloid precursor cells in the bone marrow from day two of each cycle. By day five the bone marrow had predominantly mature neutrophils and band cells, and by day 10 the myeloid precursors had decreased with a myeloid:erythroid of 0.4:1. During the same period the blood neutrophils had rebounded to normal counts by day five, and were declining by day 9 and 10. The monocytes and platelets were oscillating in an opposite phase to the neutrophils. The age of onset, regular cycle length, oscillation of neutrophil, platelet and monocyte counts and characteristic bone marrow cytology were diagnostic for cyclic neutropaenia. This syndrome has never before been described in any breed other than the grey collie. The grey collie gene mutation was not found in this dog. However, based on the clinical signs, and haematological and bone marrow results, it can be deduced that cyclic neutropaenia may develop as a result of other mutations in neutrophil elastase expression.
Prediction of the optimal time for insemination using frozen-thawed semen in a multi-sire insemination trial in bitches
(Elsevier, 2013-11) Steckler, Daniela; Nothling, Johan Oliviette; Harper, Cindy Kim
The aims of the study were to determine which of Days 5, 6 or 7 after the blood plasma progesterone concentration (PPC) of bitches first reached 6–9 nmol/L (Day 0) yield the highest fertility and whether day of insemination affects the gender ratio of conceptuses. Six bitches were inseminated on Days 5 and 6 and 6 on Days 6 and 7. Ten million progressively motile frozen-thawed sperm from each of 5 dogs were pooled for the first insemination. The same number of sperm from 5 other dogs were pooled for the second insemination. Only one batch of semen from each dog was used on all bitches, which largely prevented any effect of male and semen. Twenty-three autosomal microsatellites and the amelogenin gene were used to determine the paternity and gender of the conceptuses. Pregnancy rate was 100%. Out of 103 ovulations 66 conceptuses were conceived (conception rate: 64%). The proportion of available oocytes fertilised was 0.11, 0.56, and 0.27 for Days 5, 6, and 7, respectively. The odds of fertilisation was 16.7 and 4.2 times higher from insemination on Day 6 compared to Day 5 (P < 0.001) and Day 7 (P = 0.013), respectively. The numbers of male- and female conceptuses were equal (33 each) and gender was independent of insemination day (P = 0.18). This study suggests that intrauterine insemination of bitches should best be done 6 days after PPC first reaches a value between 6 and 9 nmol/L with a second insemination one day later.
The tiger genome and comparative analysis with lion and snow leopard genomes
(Nature Publishing Group, 2013-09) Cho, Yun Sung; Hu, Li; Hou, Haolong; Lee, Hang; Xu, Jiaohui; Kwon, Soowhan; Oh, Sukhun; Kim, Hak-Min; Jho, Sungwoong; Kim, Sangsoo; Shin, Young-Ah; Kim, Byung Chul; Kim, Hyunmin; Kim, Chang-uk; Luo, Shu-Jin; Johnson, Warren E.; Koepfli, Klaus-Peter; Schmidt-Küntzel, Anne; Turner, Jason A.; Marker, Laurie; Harper, Cindy Kim; Miller, Susan M.; Jacobs, Wilhelm; Bertola, Laura D.; Kim, Tae Hyung; Lee, Sunghoon; Zhou, Qian; Jung, Hyun-Ju; Xu, Xiao; Gadhvi, Priyvrat; Xu, Pengwei; Xiong, Yingqi; Luo, Yadan; Pan, Shengkai; Gou, Caiyun; Chu, Xiuhui; Zhang, Jilin; Liu, Sanyang; He, Jing; Chen, Ying; Yang, Linfeng; Yang, Yulan; He, Jiaju; Liu, Sha; Wang, Junyi; Kim, Chul Hong; Kwak, Hwanjong; Kim, Jong-Soo; Hwang, Seungwoo; Ko, Junsu; Kim, Chang-Bae; Kim, Sangtae; Bayarlkhagva, Damdin; Paek, Woon Kee; Kim, Seong-Jin; O’Brien, Stephen J.; Wang, Jun; Bhak, Jong
Tigers and their close relatives (Panthera) are some of the world’s most endangered species. Here we report the de novo assembly of an Amur tiger whole-genome sequence as well as the genomic sequences of a white Bengal tiger, African lion, white African lion and snow leopard. Through comparative genetic analyses of these genomes, we find genetic signatures that may reflect molecular adaptations consistent with the big cats’ hypercarnivorous diet and muscle strength. We report a snow leopard-specific genetic determinant in EGLN1 (Met394Lys39), which is likely to be associated with adaptation to high altitude. We also detect a TYR260G4A mutation likely responsible for the white lion coat colour. Tiger and cat genomes show similar repeat composition and an appreciably conserved synteny. Genomic data from the five big cats provide an invaluable resource for resolving easily identifiable phenotypes evident in very close, but distinct, species.

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