Density responses of lesser-studied carnivores to habitat and management strategies in southern Tanzania's Ruaha-Rungwa landscape

Compared to emblematic large carnivores, most species of the order Carnivora receive little conservation attention despite increasing anthropogenic pressure and poor understanding of their status across much of their range. We employed systematic camera trapping and spatially explicit capture-recapture modelling to estimate variation in population density of serval, striped hyaena and aardwolf across the mixed-use Ruaha-Rungwa landscape in southern Tanzania. We selected three sites representative of different habitat types, management strategies, and levels of anthropogenic pressure: Ruaha National Park’s core tourist area, dominated by Acacia-Commiphora bushlands and thickets; the Park’s miombo woodland; and the neighbouring community-run MBOMIPA Wildlife Management Area, also covered in Acacia-Commiphora. The Park’s miombo woodlands supported a higher serval density (5.56 [Standard Error = ±2.45] individuals per 100 km2) than either the core tourist area (3.45 [±1.04] individuals per 100 km2) or the Wildlife Management Area (2.08 [±0.74] individuals per 100 km2). Taken together, precipitation, the abundance of apex predators, and the level of anthropogenic pressure likely drive such variation. Striped hyaena were detected only in the Wildlife Management Area and at low density (1.36 [±0.50] individuals per 100 km2), potentially due to the location of the surveyed sites at the edge of the species’ global range, high densities of sympatric competitors, and anthropogenic edge effects. Finally, aardwolf were captured in both the Park’s core tourist area and the Wildlife Management Area, with a higher density in the Wildlife Management Area (13.25 [±2.48] versus 9.19 [±1.66] individuals per 100 km2), possibly as a result of lower intraguild predation and late fire outbreaks in the area surveyed. By shedding light on three understudied African carnivore species, this study highlights the importance of miombo woodland conservation and community-managed conservation, as well as the value of by-catch camera trap data to improve ecological knowledge of lesser-studied carnivores

Camera trapping and spatially explicit capture-recapture for the monitoring and conservation management of lions: Insights from a globally important population in Tanzania

Accurate and precise estimates of population status are required to inform and evaluate conservation management and policy interventions. Although the lion (Panthera leo) is a charismatic species receiving increased conservation attention, robust status estimates are lacking for most populations. While for many large carnivores population density is often estimated through spatially explicit capture–recapture (SECR) applied to camera trap data, the lack of pelage patterns in lions has limited the application of this technique to the species. Here, we present one of the first applications of this methodology to lion, in Tanzania's Ruaha-Rungwa landscape, a stronghold for the species for which no empirical estimates of status are available. We deployed four camera trap grids across habitat and land management types, and we identified individual lions through whisker spots, scars and marks, and multiple additional features. Double-blind identification revealed low inter-observer variation in photo identification (92% agreement), due to the use of xenon-flash cameras and consistent framing and angles of photographs. Lion occurred at highest densities in a prey-rich area of Ruaha National Park (6.12 ± SE 0.94 per 100 km2), and at relatively high densities (4.06 ± SE 1.03 per 100 km2) in a community-managed area of similar riparian-grassland habitat. Miombo woodland in both photographic and trophy hunting areas sustained intermediate lion densities (1.75 ± SE 0.62 and 2.25 ± SE 0.52 per 100 km2, respectively). These are the first spatially explicit density estimates for lion in Tanzania, including the first for a trophy hunting and a community-managed area, and also provide some of the first insights into lion status in understudied miombo habitats. We discuss in detail the methodology employed, the potential for scaling-up over larger areas, and its limitations. We suggest that the method can be an important tool for lion monitoring and explore the implications of our findings for lion management

Anthropogenic risk increases night-time activities and associations in African elephants (Loxodonta africana) in the Ruaha-Rungwa ecosystem, Tanzania

Elephants face diverse threats from human activities and use temporal and social strategies to reduce human-induced mortality risk. We used data from camera trap surveys in 2018–2019 (n= 1625 independent detection events from 11,751 sampling days) to investigate elephant responses to anthropogenic risk in the Ruaha-Rungwa ecosystem, Tanzania. The study was conducted in one low- risk and three high- risk sites using 26–40 paired camera trap stations per site. Risk influenced the active pe-riods, use of roads and water sources, social associations and behaviour of elephants. Elephants demonstrated significantly more night-time and reduced daytime activ-ity in the high- risk sites relative to the low- risk site. This higher night-time activity in the high- risk sites was observed for both males and females, though it was more pronounced for cow–calf groups than lone males. Foraging events and use of water sources were more frequent at night in the high- risk sites. Elephants used roads as movement routes in the low- risk site but avoided roads in the high- risk sites. Males were significantly more likely to associate with other males and cow–calf groups in the high- risk sites. Fewer occurrences of relaxed behaviours were observed in the high- risk sites compared to the low- risk site. We discuss the potential implications of our findings for elephant survival and reproduction.Output Status: Forthcoming/Available Onlin

Identification of a BRCA2-Specific modifier locus at 6p24 related to breast cancer risk

Common genetic variants contribute to the observed variation in breast cancer risk for BRCA2 mutation carriers; those known to date have all been found through population-based genome-wide association studies (GWAS). To comprehensively identify breast cancer risk modifying loci for BRCA2 mutation carriers, we conducted a deep replication of an ongoing GWAS discovery study. Using the ranked P-values of the breast cancer associations with the imputed genotype of 1.4 M SNPs, 19,029 SNPs were selected and designed for inclusion on a custom Illumina array that included a total of 211,155 SNPs as part of a multi-consortial project. DNA samples from 3,881 breast cancer affected and 4,330 unaffected BRCA2 mutation carriers from 47 studies belonging to the Consortium of Investigators of Modifiers of BRCA1/2 were genotyped and available for analysis. We replicated previously reported breast cancer susceptibility alleles in these BRCA2 mutation carriers and for several regions (including FGFR2, MAP3K1, CDKN2A/B, and PTHLH) identified SNPs that have stronger evidence of association than those previously published. We also identified a novel susceptibility allele at 6p24 that was inversely associated with risk in BRCA2 mutation carriers (rs9348512; per allele HR = 0.85, 95% CI 0.80-0.90, P = 3.9×10−8). This SNP was not associated with breast cancer risk either in the general population or in BRCA1 mutation carriers. The locus lies within a region containing TFAP2A, which encodes a transcriptional activation protein that interacts with several tumor suppressor genes. This report identifies the first breast cancer risk locus specific to a BRCA2 mutation background. This comprehensive update of novel and previously reported breast cancer susceptibility loci contributes to the establishment of a panel of SNPs that modify breast cancer risk in BRCA2 mutation carriers. This panel may have clinical utility for women with BRCA2 mutations weighing options for medical prevention of breast cancer

An original phylogenetic approach identified mitochondrial haplogroup T1a1 as inversely associated with breast cancer risk in BRCA2 mutation carriers

Introduction: Individuals carrying pathogenic mutations in the BRCA1 and BRCA2 genes have a high lifetime risk of breast cancer. BRCA1 and BRCA2 are involved in DNA double-strand break repair, DNA alterations that can be caused by exposure to reactive oxygen species, a main source of which are mitochondria. Mitochondrial genome variations affect electron transport chain efficiency and reactive oxygen species production. Individuals with different mitochondrial haplogroups differ in their metabolism and sensitivity to oxidative stress. Variability in mitochondrial genetic background can alter reactive oxygen species production, leading to cancer risk. In the present study, we tested the hypothesis that mitochondrial haplogroups modify breast cancer risk in BRCA1/2 mutation carriers. Methods: We genotyped 22,214 (11,421 affected, 10,793 unaffected) mutation carriers belonging to the Consortium of Investigators of Modifiers of BRCA1/2 for 129 mitochondrial polymorphisms using the iCOGS array. Haplogroup inference and association detection were performed using a phylogenetic approach. ALTree was applied to explore the reference mitochondrial evolutionary tree and detect subclades enriched in affected or unaffected individuals. Results: We discovered that subclade T1a1 was depleted in affected BRCA2 mutation carriers compared with the rest of clade T (hazard ratio (HR) = 0.55; 95% confidence interval (CI), 0.34 to 0.88; P = 0.01). Compared with the most frequent haplogroup in the general population (that is, H and T clades), the T1a1 haplogroup has a HR of 0.62 (95% CI, 0.40 to 0.95; P = 0.03). We also identified three potential susceptibility loci, including G13708A/rs28359178, which has demonstrated an inverse association with familial breast cancer risk. Conclusions: This study illustrates how original approaches such as the phylogeny-based method we used can empower classical molecular epidemiological studies aimed at identifying association or risk modification effects.Peer reviewe

Genome-Wide Association Study in BRCA1 Mutation Carriers Identifies Novel Loci Associated with Breast and Ovarian Cancer Risk

BRCA1-associated breast and ovarian cancer risks can be modified by common genetic variants. To identify further cancer risk-modifying loci, we performed a multi-stage GWAS of 11,705 BRCA1 carriers (of whom 5,920 were diagnosed with breast and 1,839 were diagnosed with ovarian cancer), with a further replication in an additional sample of 2,646 BRCA1 carriers. We identified a novel breast cancer risk modifier locus at 1q32 for BRCA1 carriers (rs2290854, P = 2.7×10-8, HR = 1.14, 95% CI: 1.09-1.20). In addition, we identified two novel ovarian cancer risk modifier loci: 17q21.31 (rs17631303, P = 1.4×10-8, HR = 1.27, 95% CI: 1.17-1.38) and 4q32.3 (rs4691139, P = 3.4×10-8, HR = 1.20, 95% CI: 1.17-1.38). The 4q32.3 locus was not associated with ovarian cancer risk in the general population or BRCA2 carriers, suggesting a BRCA1-specific associat

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead