Article
Microbiology
Charlene Clarke, Tanya J. Kerr, Robin M. Warren, Leanie Kleynhans, Michele A. Miller, Wynand J. Goosen
Summary: This study investigated the diversity of nontuberculous mycobacteria (NTMs) in African buffalo respiratory secretions and tissue samples using novel molecular tools. The results revealed a high diversity of NTMs in buffaloes and further research is needed to determine their role in confounding bovine tuberculosis diagnosis in this species.
Article
Multidisciplinary Sciences
Charlene Clarke, David Cooper, Michele A. Miller, Wynand J. Goosen
Summary: This study aimed to investigate the detection of MTBC DNA in oronasal secretions of M. bovis infected buffaloes using a molecular transport media and a rapid qPCR assay. Further research is needed to validate the utility of this method.
SCIENTIFIC REPORTS
(2022)
Article
Veterinary Sciences
Eva Perez-Martin, Brianna Beechler, Fuquan Zhang, Katherine Scott, Lin-Mari De Klerk-Lorist, Georgina Limon, Brian Dugovich, Simon Gubbins, Arista Botha, Robyn Hetem, Louis van Schalkwyk, Nicholas Juleff, Francois F. Maree, Anna Jolles, Bryan Charleston
Summary: This study revealed for the first time that African buffalo are systemically affected by foot-and-mouth disease (FMD) virus and the clinical characteristics of FMD in buffalo include transient pyrexia. Despite the lack of lesions, African buffalo infection is characterized by high viral loads in blood and oropharynx, rapid and strong host innate and adaptive immune responses, and high transmissibility.
VETERINARY RESEARCH
(2022)
Article
Microbiology
Charlene Clarke, Netanya Bernitz, Wynand J. Goosen, Michele A. Miller
Summary: In this study, a high-specificity diagnostic algorithm utilizing serial test interpretation with IGRA and IPRA was developed, which can effectively screen buffalo herds with no previous history of M. bovis infection.
Article
Infectious Diseases
Hilary Ann Lakin, Hannah Tavalire, Kaori Sakamoto, Peter Buss, Michele Miller, Sarah A. Budischak, Kristina Raum, Vanessa O. Ezenwa, Brianna Beechler, Anna Jolles
Summary: The progression of bovine tuberculosis in African buffalo resembles that in experimental cattle models, providing insight into the disease and its interaction with the host in a natural environment.
PLOS NEGLECTED TROPICAL DISEASES
(2022)
Article
Ecology
Andreia Malpica, Clementina Gonzalez
Summary: This study examines the influence of landscape features on the genetic connectivity of Thryophilus sinaloa, a common bird species associated with tropical dry forests. The results show that open-areas resistance surface and geographic distance reduce genetic connectivity, indicating that protected areas are partially isolated from other non-protected areas.
Article
Environmental Sciences
Brittany L. McCall, Brook L. Fluker
Summary: The paleback darter populations show low genetic diversity and minimal gene flow, with distinct populations from the Caddo and Ouachita rivers. Phylogeographical analyses revealed three distinct clades originating from different river drainages. Population genetic diversity is relatively low but comparable to closely related species, indicating conservation implications for the vulnerable paleback darter populations.
AQUATIC CONSERVATION-MARINE AND FRESHWATER ECOSYSTEMS
(2021)
Article
Ecology
Caroline K. Glidden, Courtney A. C. Coon, Brianna R. Beechler, Chase McNulty, Vanessa O. Ezenwa, Anna E. Jolles
Summary: The dynamics of directly transmitted pathogens in natural populations are influenced by host traits, pathogen biology, and interactions among pathogens within a host. This study on wild African buffalo reveals that pathogen associations play a key role in determining infection risk, while host traits and season also impact pathogen dynamics.
JOURNAL OF ANIMAL ECOLOGY
(2021)
Article
Plant Sciences
Na Yuan, Shujing Wei, Hans Peter Comes, Sisheng Luo, Ruisen Lu, Yingxiong Qiu
Summary: The genetic effects of habitat fragmentation are complex and influenced by species traits and landscape features. This study compared the genetic diversity and population structure of a herb species in two contrasting island systems in China. The results showed significant differences in genetic diversity between the two island systems, but no significant genetic differences between island and mainland populations. A certain level of population substructure was found in one island system, and the level of gene flow was lower in this island system compared to the other system.
Article
Chemistry, Multidisciplinary
Kang Yang, Haotian Yu, Xinru Cao, Juan Guan, Siyu Cai, Zexin Yang, Wei Huang, Bin Wang, Nannan Qin, Zihong Wu, Wenhan Tian, Shihong Zhang, Robert O. Ritchie
Summary: This study reveals the microstructure characteristics of the Syncerus caffer horn sheath and demonstrates its high tensile strength and fracture energy. The curved corrugated lamellae play a key role in determining the mechanical properties of the horn sheath. The ridge region of the sheath exhibits more disulfide cross linking, indicating a purposeful evolution of its heterogeneous composition.
CELL REPORTS PHYSICAL SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
C. H. Frere, G. D. O'Reilly, K. Strickland, A. Schultz, K. Hohwieler, J. Hanger, D. de Villiers, R. Cristescu, D. Powell, W. Sherwin
Summary: The genetic consequences of population subdivision in human-impacted landscapes are significant for long-term evolution. This study analyzes the effects of population subdivision on genetic diversity using koala population data and proposes a method to evaluate mitigation measures.
Article
Ornithology
Shi Li, Dan Li, Lishi Zhang, Weiping Shang, Bo Qin, Yunlei Jiang
Summary: The Rufous-backed Bunting in Inner Mongolia exhibits high genetic diversity but shows high levels of gene flow and minimal genetic structuring among fragmented breeding populations. Despite the overall genetic diversity, local populations remain at risk of extinction due to habitat loss, with a high risk of inbreeding within the population. Conservation efforts in Inner Mongolia should focus on protecting breeding habitats and preventing over-grazing to preserve the genetic diversity of this endangered species.
Article
Ecology
Elodie Wielgus, Alexandre Caron, Emily Bennitt, Michel De Garine-Wichatitsky, Bradley Cain, Herve Fritz, Eve Miguel, Daniel Cornelis, Simon Chamaille-Jammes
Summary: The study compared contact patterns between neighboring groups of Cape buffalo in different environments. It found that neighboring groups were spatially segregated in both dry and rainy seasons, and that contact patterns were influenced by season and habitat, with dry season water availability playing a crucial role.
JOURNAL OF WILDLIFE MANAGEMENT
(2021)
Article
Multidisciplinary Sciences
Anna Jolles, Erin Gorsich, Simon Gubbins, Brianna Beechler, Peter Buss, Nick Juleff, Lin-Mari de Klerk-Lorist, Francois Maree, Eva Perez-Martin, O. L. van Schalkwyk, Katherine Scott, Fuquan Zhang, Jan Medlock, Bryan Charleston
Summary: Understanding the mechanisms enabling persistence of highly contagious pathogens in host populations is crucial, with occasional transmission from persistently infected carriers playing a key role in preventing fade-out of the most infectious viral strains. Additional mechanisms such as antigenic shift, loss of immunity, or spillover among host populations may be required for less transmissible strains to persist.
Article
Microbiology
Wynand Goosen, Mark Hamish Moseley, Tanya Jane Kerr, Andrew Potts, Michele Miller
Summary: The study found that free-ranging African buffaloes are exposed to Leptospira spp. infections, with seropositivity almost exclusively limited to serovar Tarassovi. There was no evidence of seropositivity in unweaned calves, and the study demonstrated temporal- or herd-specific variations in exposure risk, as well as an increased probability of seropositivity in female buffaloes.
Article
Biochemistry & Molecular Biology
Casia Nursyifa, Anna Bruniche-Olsen, Genis Garcia-Erill, Rasmus Heller, Anders Albrechtsen
Summary: The SATC method is proposed to assign sex to samples and identify sex-linked scaffolds from NGS data, working for species with a homogametic/heterogametic sex determination system. It uses scaffold depth distribution and PCA to achieve sex assignment and sex-linked scaffold identification, without prior knowledge of sample sex, using WGS data.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Genetics & Heredity
Roozbeh Manshaei, Sean DeLong, Veronica Andric, Esha Joshi, John B. A. Okello, Priya Dhir, Cherith Somerville, Kirsten M. Farncombe, Kelsey Kalbfleisch, Rebekah K. Jobling, Stephen W. Scherer, Raymond H. Kim, S. Mohsen Hosseini
Summary: GeneTerpret is a flexible platform that streamlines the variant interpretation process by integrating data from multiple databases and tools, applying phenotype-driven queries and validation criteria, and providing a prioritized list of potentially causal variants/genes. Comparisons with expert-curated databases and internal clinical datasets demonstrate high concordance and accuracy of GeneTerpret.
BMC MEDICAL GENOMICS
(2022)
Article
Biochemistry & Molecular Biology
Xiaodong Liu, Suzanne Ronhoj Schjott, Sandra M. Granquist, Aqqalu Rosing-Asvid, Rune Dietz, Jonas Teilmann, Anders Galatius, Kristina Cammen, Greg O'Corry-Crowe, Karin Harding, Tero Harkonen, Ailsa Hall, Emma L. Carroll, Yumi Kobayashi, Mike Hammill, Garry Stenson, Anne Kirstine Frie, Christian Lydersen, Kit M. Kovacs, Liselotte W. Andersen, Joseph Hoffman, Simon J. Goodman, Filipe G. Vieira, Rasmus Heller, Ida Moltke, Morten Tange Olsen
Summary: This study reveals the origin, expansion, population structure, and genetic diversity of the harbour seal. It suggests that the harbour seal originated in the Northeast Pacific, colonized the North Atlantic via the Canadian Arctic, and expanded its range from North America to Europe. There is a deep divergence between modern North Pacific and North Atlantic harbour seals, with strong philopatry observed.
Article
Biochemistry & Molecular Biology
Ming Li, Congjiao Sun, Naiyi Xu, Peipei Bian, Xiaomeng Tian, Xihong Wang, Yuzhe Wang, Xinzheng Jia, Rasmus Heller, Mingshan Wang, Fei Wang, Xuelei Dai, Rongsong Luo, Yingwei Guo, Xiangnan Wang, Peng Yang, Dexiang Hu, Zhenyu Liu, Weiwei Fu, Shunjin Zhang, Xiaochang Li, Chaoliang Wen, Fangren Lan, Amam Zonaed Siddiki, Chatmongkon Suwannapoom, Xin Zhao, Qinghua Nie, Xiaoxiang Hu, Yu Jiang, Ning Yang
Summary: The gene numbers and evolutionary rates of birds are lower than those of mammals, but birds have a large species number and morphological diversity. To understand avian evolution, it is necessary to study the complete avian genome. A chicken pan-genome was constructed from 20 de novo assembled genomes, revealing novel protein-coding genes and long noncoding RNAs not found in previous databases. These hidden genes were found to be shared by all chicken genomes, including many housekeeping genes, and were enriched in immune pathways. Comparative genomics showed that these novel genes have higher substitution rates than known genes, updating our knowledge about evolutionary rates in birds. This study provides a framework for constructing a better chicken genome, contributing to the understanding of avian evolution and improvement of poultry breeding.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Joana L. Rocha, Pedro Vaz Pinto, Hans R. Siegismund, Matthias Meyer, Bettine Jansen van Vuuren, Luis Verissimo, Nuno Ferrand, Raquel Godinho
Summary: The study explores the factors driving the evolution of the sable antelope in southcentral Africa by analyzing complete mitogenomes. The results suggest that both climatic events and geomorphological barriers have shaped the species' patterns of diversification and vicariance. The use of comprehensive mitogenomic data sets contributes to a better understanding of environmental, geomorphological, and evolutionary patterns in Africa throughout the Quaternary.
Article
Biodiversity Conservation
Elisabetta Canteri, Stuart C. Brown, Niels Martin Schmidt, Rasmus Heller, David Nogues-Bravo, Damien A. Fordham
Summary: This study used multiple approaches including modern and fossil occurrence records, ancient DNA, spatiotemporal reconstructions of past climatic change, and species-specific population ecology to analyze the ecological mechanisms behind the decline and extinction of muskox in Eurasia and its expansion in North America. The results show that climatic change played a key role in driving muskox distribution shifts and demographic changes, with human activities also contributing to population declines. This research highlights the vulnerability of muskox to future warming and emphasizes the importance of using process-explicit macroecological models for the conservation and management of this iconic species in the Arctic.
GLOBAL CHANGE BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Genis Garcia-Erill, Christian H. F. Jorgensen, Vincent B. Muwanika, Xi Wang, Malthe S. Rasmussen, Yvonne A. de Jong, Philippe Gaubert, Ayodeji Olayemi, Jordi Salmona, Thomas M. Butynski, Laura D. Bertola, Hans R. Siegismund, Anders Albrechtsen, Rasmus Heller
Summary: African wild pigs, desert warthog and common warthog, have a contentious evolutionary history. Through whole-genome sequencing, it was found that the divergence between these two species occurred later than previously estimated, and the origin and range expansion of the common warthog were revealed. The study also identified the adaptively introgressed immune system-related genes in the common warthog, indicating the role of disease resistance in their evolution.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Genetics & Heredity
Qiliang Ding, Cherith Somerville, Roozbeh Manshaei, Brett Trost, Miriam S. Reuter, Kelsey Kalbfleisch, Kaitlin Stanley, John B. A. Okello, S. Mohsen Hosseini, Eriskay Liston, Meredith Curtis, Mehdi Zarrei, Edward J. Higginbotham, Ada J. S. Chan, Worrawat Engchuan, Bhooma Thiruvahindrapuram, Stephen W. Scherer, Raymond H. Kim, Rebekah K. Jobling
Summary: This study introduces SCIP, a software package that enables efficient and accurate clinical interpretation of CNVs, facilitating improved genetic diagnoses.
Article
Biochemistry & Molecular Biology
Liam Quinn, Genis Garcia-Erill, Cindy Santander, Anna Bruniche-Olsen, Xiaodong Liu, Mikkel-Holger S. Sinding, Michael P. P. Heaton, Timothy P. L. Smith, Patricia Pecnerova, Laura D. D. Bertola, Kristian Hanghoj, Malthe Sebro Rasmussen, Deon de Jager, Hans R. R. Siegismund, Anders Albrechtsen, Rasmus Heller, Ida Moltke
Summary: The iconic Cape buffalo has experienced population declines attributed to multiple factors, including the rinderpest pandemic and recent human activity. This study analyzed whole genome sequencing data to assess genetic diversity in Cape buffalo populations. The results indicate that recent inbreeding and colonialism-associated events have significantly impacted the genetic diversity of the southernmost populations.
Article
Genetics & Heredity
Alida de Flamingh, Yasuko Ishida, Patricia Pecnerova, Sahara Vilchis, Hans R. Siegismund, Rudi J. van Aarde, Ripan S. Malhi, Alfred L. Roca
Summary: Non-invasive biological samples are valuable for studying rare, elusive, endangered, or dangerous species. By combining genomic techniques with computational approaches, we can improve wildlife conservation and management. In this study, we used non-invasive fecal DNA samples and easily accessible DNA preservation cards to generate genomic and metagenomic data, showcasing the utility of this approach for conservation science.
FRONTIERS IN GENETICS
(2023)
Article
Genetics & Heredity
Hong Cheng, Zhuangbiao Zhang, Jiayue Wen, Johannes A. Lenstra, Rasmus Heller, Yudong Cai, Yingwei Guo, Ming Li, Ran Li, Wenrong Li, Sangang He, Jintao Wang, Junjie Shao, Yuxuan Song, Lei Zhang, Masum Billah, Xihong Wang, Mingjun Liu, Yu Jiang
Summary: This study analyzed the whole-genome sequencing of 1,098 domestic sheep and 69 wild sheep, and found that introgression from wild sheep contributed to the morphological diversity of sheep breeds and individual variations within breeds. The frequency of introgressed fragments varied greatly among domestic breeds, indicating the role of selection and recombination in shaping genetic and phenotypic diversity.
Article
Biodiversity Conservation
Kathelijne Koops, Tatyana Humle, Peter Frandsen, Maegan Fitzgerald, Lucy D'Auvergne, Hazel A. Jackson, Claus Borsting, Hans R. Siegismund, Aly Gaspard Soumah, Christina Hvilsom
Summary: Guinea is a key habitat for western chimpanzees, but it also has high-grade iron-ore deposits. This study used genetic sampling to estimate the population size and characteristics of western chimpanzees in the Nimba Mountains, and recommended the use of genetic sampling and camera trapping for future conservation efforts.
CONSERVATION SCIENCE AND PRACTICE
(2023)
Article
Cardiac & Cardiovascular Systems
Cherith Somerville, Roozbeh Manshaei, Qiliang Ding, John B. A. Okello, Rachel Silver, David Chitayat, Varsha Thakur, Olivier Villemain, Rebekah Jobling
Summary: We report the case of a three-year-old male child with congenital valvular defects, right ventricular malformation, and initial developmental delay. Genome sequencing revealed rare deleterious biallelic missense variants in PLD1. In the second pregnancy of his parents, fetal echocardiography at 13 weeks gestation showed right-sided cardiac malformations similar to their first child. Targeted DNA analysis confirmed that the fetus carried the same biallelic PLD1 variants as their older sibling. This case helps expand our understanding of PLD1-related defects and highlights the importance of genome sequencing and early fetal echocardiography in establishing the phenotype of congenital heart disease.
CONGENITAL HEART DISEASE
(2023)
Article
Zoology
Yuan Yuan, Da-Ming Sun, Tao Qin, Sheng-Yong Mao, Wei-Yun Zhu, Yu-Yang Yin, Jie Huang, Rasmus Heller, Zhi-Peng Li, Jun-Hua Liu, Qiang Qiu
Summary: This study identified eight major cell types and captured dynamic changes in the rumen using single-cell transcriptomes. The cellular basis for rumen epithelium formation and the role of enriched stratum spinosum cells in metabolism and immune response were revealed. The study provides insights into the complexity of rumen development and its interactions with dietary metabolism.
ZOOLOGICAL RESEARCH
(2022)
Meeting Abstract
Genetics & Heredity
Genis Garcia-Erill, Kristian Hanghoj, Rasmus Heller, Anders Albrechtsen