Trends analysis of precipitation data over the tropical South-West Indian Ocean (SWIO) basin using the Ensemble Empirical Mode Decomposition (EEMD) method

In this paper, we propose the use of the Ensemble Empirical Mode Decomposition (EEMD) method in the analysis of trends in climate data. As compared to existing traditional methods, EEMD is simple, fast and reliable. It works by decomposing the time-series data into intrinsic mode functions until a residual component is obtained which represents the trend in the data. The dataset considered consists of satellite precipitation estimates (SPE) obtained from the Tropical Rainfall Measuring Mission (TRMM) for the tropical South-West Indian Ocean (SWIO) basin recorded during the periods January 1998 to December 2013. The SWIO basin spans from the latitudes 5° S to 35° S and the longitudes 30° E to 70° E and comprises of part of the east coast of Africa and some small island developing states (SIDS) such as Comoros, Madagascar, Mauritius and Reunion Island. The EEMD analysis is carried out for summer, winter and yearly time series of the SPE data. The results from the study are presented in terms of intrinsic mode functions (IMFs) and the trends. The analysis reveals that in summer, there is a tendency to have an increase in the amount of rainfall, whereas in winter, from 1998 to 2004 there has been an initial increase of 0.0022 mm/hr/year and from there onwards till 2013 a decrease of 0.00052 mm/hr/year was noted.

Population Structure of the South West Indian Ocean Islands: Implications for Precision Medicine

Precision medicine has brought new hopes for patients around the world with the applications of novel technologies for understanding genetics of complex diseases and their translation into clinical services. Such applications however require a foundation of skills, knowledge and infrastructure to translate genetics for health care. The crucial element is no doubt the availability of genomics data for the target populations, which is seriously lacking for most parts of Africa. We discuss here why it is vital to prioritize genomics data for the South West Indian Ocean region where a mosaic of ethnicities co-exist. The islands of the SWIO, which comprise Madagascar, La Reunion, Mauritius, Seychelles and Comoros, have been the scene for major explorations and trade since the 17th century being on the route to Asia. This part of the world has lived through active passage of slaves from East Africa to Arabia and further. Today’s demography of the islands is a diverse mix of ancestries including European, African and Asian. The extent of admixtures has yet to be resolved. Except for a few studies in Madagascar, there is very little published data on human genetics for these countries. Isolation and small population sizes have likely resulted in reduced genetic variation and possible founder effects. There is a significant prevalence of diabetes, particularly in individuals of Indian descent, while breast and prostate cancers are on the rise. The island of La Reunion is a French overseas territory with a high standard of health care and close ties to Mauritius. Its demography is comparable to that of Mauritius but with a predominantly mixed population and a smaller proportion of people of Indian descent. On the other hand, Madagascar’s African descendants inhabit mostly the lower coastal zones of the West and South regions, while the upper highlands are occupied by peoples of mixed African-Indonesian ancestries. Historical records confirm the Austronesian contribution to the Madagascar genomes. With the rapid progress in genomic medicine, there is a growing demand for sequencing services in the clinical settings to explore the incidence of variants in candidate disease genes and other markers. Genome sequence data has become a priority in order to understand the population sub-structures and to identify specific pathogenic variants among the different groups of inhabitants on the islands. Genomic data is increasingly being used to advise families at risk and propose diagnostic screening measures to enhance the success of therapies. This paper discusses the complexity of the islands’ populations and argues for the needs for genotyping and understanding the genetic factors associated with disease risks. The benefits to patients and improvement in health services through a concerted regional effort are depicted. Some private patients are having recourse to external facilities for molecular profiling with no return of data for research. Evidence of disease variants through sequencing represents a valuable source of medical data that can guide policy decisions at the national level. There are presently no such records for future implementation of strategies for genomic medicine.

Population characteristics and exploitation of yellowfin tuna (Thunnus albacares Bonnaterre, 1788) in the coastal waters of Kenya

Yellowfin tuna, Thunnus albacares (Bonnaterre, 1788) is a highly migratory and important commercial fishery species. Data on length-frequency, growth parameters and mortality rates of yellowfin tuna in the coastal waters of Kenya is limited. We assessed Catch Per Unit Effort (CPUE), size distribution, growth parameters and mortality rates based on length-frequency and catch data collected from August 2015 to December 2016 at five fish landing sites along the Kenyan coast. The sample comprised of 1281 individuals of yellowfin tuna weighing 12,671 kg. Highest CPUE was recorded in October 2015 (10.8 kg·Fisher-1Trip-1) and lowest CPUE, 2.6 kg·Fisher-1Trip-1 in December 2016. Yellowfin tuna was more abundant in the South-East Monsoon (SEM), from May to October, with an average CPUE of 7.3 kg Fisher-1Trip-1 compared to North East Monsoon (NEM), from November to April, with a CPUE of 7.0 kg Fisher-1Trip-1. Spatial variation of CPUE was evident. Old Town recorded the highest CPUE of 54.2 kgTrip-1, while Mnarani the lowest of 19.4 kgTrip-1. At least 91 % of the fish sampled were < 100 cm FL and hence not yet mature. The asymptotic Length (L∞) was found to be 195 cm FL, the Von Bertalanffy growth constant (K) 0.43 year-1, t0 - 0.82 and the Growth Performance Index (f) 4.21. The total mortality coefficient (Z) was 2.59 year-1 , Natural Mortality (M) 0.59 year-1, Fishing Mortality (F) 2.00 year-1 and Exploitation Rate (E) 0.77 year-1. Results show that mortality and exploitation rates were above the optimal, indicating high fishing pressure on coastal yellowfin tuna. The information generated by this study provides some further insights on the scientific knowledge of the coastal yellowfin tuna to inform policy for sustainable management and development of this fishery in Kenya and the entire South West Indian Ocean (SWIO) region.

Fishes from Bassas Da India Atoll in the Mozambique Channel

Bassas da India is a remote, uninhabited coral atoll in the West Indian Ocean. Its inaccessibility had historically precluded study of its ichthyofauna until a small group of scientists from the Oceanographic Research Institute in South Africa undertook a two-week biodiversity survey in 1991. Since then, the discourse on climate change has taken on a higher relevance, calling for protection and study of biodiversity hotspots such as Bassas da India. The survey recorded 309 fish species, including a number of vulnerable teleosts and elasmobranchs. As the only published information on the biodiversity of this remote small island, it is intended that this dataset will contribute to increased relevance as an ecological baseline for detecting impacts relating to climate change in the South West Indian Ocean. Each species is listed in terms of its individual abundance, IUCN status as well as its museum and photographic record. Comparisons are made with survey results of other small coral islands in the region, notably Europa Island, revealing several distinct differences in fish diversity. There is evidence that giant groupers will replace sharks as apex predators when there is no local exploitation. A total of 86 species were photographed to confirm identity, and a further 84 species were provided to the South African Institute for Aquatic Biodiversity museum in Grahamstown and also to several international species experts.

Fishes from Bassas Da India Atoll in the Mozambique Channel

Bassas da India is a remote, uninhabited coral atoll in the West Indian Ocean. Its inaccessibility had historically precluded study of its ichthyofauna until a small group of scientists from the Oceanographic Research Institute in South Africa undertook a two-week biodiversity survey in 1991. Since then, the discourse on climate change has taken on a higher relevance, calling for protection and study of biodiversity hotspots such as Bassas da India. The survey recorded 309 fish species, including a number of vulnerable teleosts and elasmobranchs. As the only published information on the biodiversity of this remote small island, it is intended that this dataset will contribute to increased relevance as an ecological baseline for detecting impacts relating to climate change in the South West Indian Ocean. Each species is listed in terms of its individual abundance, IUCN status as well as its museum and photographic record. Comparisons are made with survey results of other small coral islands in the region, notably Europa Island, revealing several distinct differences in fish diversity. There is evidence that giant groupers will replace sharks as apex predators when there is no local exploitation. A total of 86 species were photographed to confirm identity, and a further 84 species were provided to the South African Institute for Aquatic Biodiversity museum in Grahamstown and also to several international species experts.

First historical genome of a crop bacterial pathogen from herbarium specimen: Insights into citrus canker emergence

Over the past decade, ancient genomics has been used in the study of various pathogens. In this context, herbarium specimens provide a precious source of dated and preserved DNA material, enabling a better understanding of plant disease emergences and pathogen evolutionary history. We report here the first historical genome of a crop bacterial pathogen, Xanthomonas citri pv. citri (Xci), obtained from an infected herbarium specimen dating back to 1937. Comparing the 1937 genome within a large set of modern genomes, we reconstructed their phylogenetic relationships and estimated evolutionary parameters using Bayesian tip-calibration inferences. The arrival of Xci in the South West Indian Ocean islands was dated to the 19th century, probably linked to human migrations following slavery abolishment. We also assessed the metagenomic community of the herbarium specimen, showed its authenticity using DNA damage patterns, and investigated its genomic features including functional SNPs and gene content, with a focus on virulence factors.

Variability of Ocean Features and their Impact on Cyclogenesis over Arabian Sea During Post Monsoon Season

Arabian Sea (AS), the western sector of North Indian Ocean (NIO) produce smaller number of tropical cyclones as compared to Bay of Bengal. Though limited in numbers, the cyclones over Arabian sea are catastrophic by character. This make west coast of Indian subcontinent vulnerable to these hazards. The post-monsoon cyclogenesis over this region is known to be modulated by both monsoon rainfall and the El-Niño accompanied with positive Indian Ocean Dipole events. No single phenomena, however, can fully explain the variability observed in AS region. In this study, it is observed that apart from several known atmospheric forcings, inter-annual variability of ocean heat content (OHC) influence the post-monsoon AS cyclogenesis. The OHC of this region is partially modulated by the changes in salinity. Heat exchanges between the South West Indian Ocean (SWIO) and AS also modulates the OHC over AS. This remote influence is facilitated largely by the variability in the equatorial currents. Further it is seen that the recent trend of increased OHC post-2011 matches with the enhanced sea surface carbon over AS.