Genomics of adaptation to multiple concurrent stresses: insights from comparative transcriptomics of a Cichlid fish from one of earth’s most extreme environments, the Hypersaline Soda Lake Magadi in Kenya, East Africa

The Magadi tilapia (Alcolapia grahami) is a cichlid fish that inhabits one of the Earth's most extreme aquatic environments, with high pH (~10), salinity (~60% of seawater), high temperatures (~40 °C), and fluctuating oxygen regimes. The Magadi tilapia evolved several unique behavioral, physiological, and anatomical adaptations, some of which are constituent and thus retained in freshwater conditions. We conducted a transcriptomic analysis on A. grahami to study the evolutionary basis of tolerance to multiple stressors. To identify the adaptive regulatory changes associated with stress responses, we massively sequenced gill transcriptomes (RNAseq) from wild and freshwater-acclimated specimens of A. grahami. As a control, corresponding transcriptome data from Oreochromis leucostictus, a closely related freshwater species, were generated. We found expression differences in a large number of genes with known functions related to osmoregulation, energy metabolism, ion transport, and chemical detoxification. Over-representation of metabolism-related gene ontology terms in wild individuals compared to laboratory-acclimated specimens suggested that freshwater conditions greatly decrease the metabolic requirements of this species. Twenty-five genes with diverse physiological functions related to responses to water stress showed signs of divergent natural selection between the Magadi tilapia and its freshwater relative, which shared a most recent common ancestor only about four million years ago. The complete set of genes responsible for urea excretion was identified in the gill transcriptome of A. grahami, making it the only fish species to have a functional ornithine-urea cycle pathway in the gills--a major innovation for increasing nitrogenous waste efficiency

The use of non-invasive molecular techniques to confirm the presence of mountain bongo Tragelaphus eurycerus isaaci populations in Kenya and preliminary inference of their mitochondrial genetic variation

The mountain bongo antelope Tragelaphus eurycerus isaaci has rapidly declined in recent decades, due to a combination of hunting, habitat degradation and disease. Endemic to Kenya, mountain bongo populations have shrunk to approximately 100 individuals now mainly confined to the Aberdares mountain ranges. Indirect observation of bongo signs (e. g. tracks, dung) can be misleading, thus methods to ensure reliable species identification, such as DNA-based techniques, are necessary to effectively study and monitor this species. We assessed bongo presence in four mountain habitats in Kenya (Mount Kenya National Park, Aberdare National Park, Eburu and Mau forests) and carried out a preliminary analysis of genetic variation by examining 466 bp of the first domain of the mtDNA control region using DNA extracted from faecal samples. Of the 201 dung samples collected in the field, 102 samples were molecularly identified as bongo, 97 as waterbuck, one as African buffalo and one as Aders\u27 duiker. Overall species-identification accuracy by experienced trackers was 64%, with very high error of commission when identifying bongo sign (37%), and high error of omission for waterbuck sign (82%), suggesting that the two species\u27 signs are easily confused. Despite high variation in the mtDNA control region in most antelope species, our results suggest low genetic variation in mountain bongo as only two haplotypes were detected in 102 samples analyzed. In contrast, the analysis of 63 waterbuck samples from the same sites revealed 21 haplotypes. Nevertheless, further examination using nuclear DNA markers (e. g. microsatellites) in a multi-locus approach is still required, especially because the use of mitochondrial DNA can result in population overestimation as distinct dung samples can potentially be originated from the same individual. © 2011 Springer Science+Business Media B.V

Erratum to: The use of non-invasive molecular techniques to confirm the presence of mountain bongo Tragelaphus eurycerus isaaci populations in Kenya and preliminary inference of their mitochondrial genetic variation

The mountain bongo antelope Tragelaphus eurycerus isaaci has rapidly declined in recent decades, due to a combination of hunting, habitat degradation and disease. Endemic to Kenya, mountain bongo populations have shrunk to approximately 100 individuals now mainly confined to the Aberdares mountain ranges. Indirect observation of bongo signs (e. g. tracks, dung) can be misleading, thus methods to ensure reliable species identification, such as DNA-based techniques, are necessary to effectively study and monitor this species. We assessed bongo presence in four mountain habitats in Kenya (Mount Kenya National Park, Aberdare National Park, Eburu and Mau forests) and carried out a preliminary analysis of genetic variation by examining 466 bp of the first domain of the mtDNA control region using DNA extracted from faecal samples. Of the 201 dung samples collected in the field, 102 samples were molecularly identified as bongo, 97 as waterbuck, one as African buffalo and one as Aders\u27 duiker. Overall species-identification accuracy by experienced trackers was 64%, with very high error of commission when identifying bongo sign (37%), and high error of omission for waterbuck sign (82%), suggesting that the two species\u27 signs are easily confused. Despite high variation in the mtDNA control region in most antelope species, our results suggest low genetic variation in mountain bongo as only two haplotypes were detected in 102 samples analyzed. In contrast, the analysis of 63 waterbuck samples from the same sites revealed 21 haplotypes. Nevertheless, further examination using nuclear DNA markers (e. g. microsatellites) in a multi-locus approach is still required, especially because the use of mitochondrial DNA can result in population overestimation as distinct dung samples can potentially be originated from the same individual. © 2011 Springer Science+Business Media B.V

The use of non-invasive molecular techniques to confirm the presence of mountain bongo Tragelaphus eurycerus isaaci populations in Kenya and preliminary inference of their mitochondrial genetic variation

The mountain bongo antelope Tragelaphus eurycerus isaaci has rapidly declined in recent decades, due to a combination of hunting, habitat degradation and disease. Endemic to Kenya, mountain bongo populations have shrunk to approximately 100 individuals now mainly confined to the Aberdares mountain ranges. Indirect observation of bongo signs (e.g. tracks, dung) can be misleading, thus methods to ensure reliable species identification, such as DNA-based techniques, are necessary to effectively study and monitor this species. We assessed bongo presence in four mountain habitats in Kenya (Mount Kenya National Park, Aberdare National Park, Eburu and Mau forests) and carried out a preliminary analysis of genetic variation by examining 466 bp of the first domain of the mtDNA control region using DNA extracted from faecal samples. Of the 201 dung samples collected in the field, 102 samples were molecularly identified as bongo, 97 as waterbuck, one as African buffalo and one as Aders’ duiker. Overall species-identification accuracy by experienced trackers was 64%, with very high error of commission when identifying bongo sign (37%), and high error of omission for waterbuck sign (82%), suggesting that the two species’ signs are easily confused. Despite high variation in the mtDNA control region in most antelope species, our results suggest low genetic variation in mountain bongo as only two haplotypes were detected in 102 samples analyzed. In contrast, the analysis of 63 waterbuck samples from the same sites revealed 21 haplotypes. Nevertheless, further examination using nuclear DNA markers (e.g. microsatellites) in a multi-locus approach is still required, especially because the use of mitochondrial DNA can result in population overestimation as distinct dung samples can potentially be originated from the same individual

Morphological evaluation of spermatogenesis in Lake Magadi tilapia (Alcolapia grahami): a fish living on the edge

Spermatogenesis in Lake Magadi tilapia (Alcolapia grahami), a cichlid fish endemic to the highly alkaline and saline Lake Magadi in Kenya, was evaluated using light and transmission electron microscopy. Spermatogenesis, typified by its three major phases (spermatocytogenesis, meiosis and spermiogenesis), was demonstrated by the presence of maturational spermatogenic cells namely spermatogonia, spermatocytes, spermatids and spermatozoa. Primary spermatogonia, the largest of all the germ cells, underwent a series of mitotic divisions producing primary spermatocytes, which then entered two consecutive meiotic divisions to produce secondary spermatocytes and spermatids. Spermatids, in turn, passed through three structurally distinct developmental stages typical of type-I spermiogenesis to yield typical primitive anacrosomal spermatozoa of the externally fertilizing type (aquasperm). The spermatozoon of this fish exhibited a spheroidal head with the nucleus containing highly electron-dense chromatin globules, a midpiece containing ten ovoid mitochondria arranged in two rows and a flagellum formed by the typical 9 + 2 microtubule axoneme. In addition, the midpiece, with no cytoplasmic sheath, appeared to end blindly distally in a lobe-like pattern around the flagellum; a feature that was unique and considered adaptive for the spermatozoon of this species to the harsh external environment. These observations show that the testis of A. grahami often undergoes active spermatogenesis despite the harsh environmental conditions to which it is exposed on a daily basis within the lake. Further, the spermiogenic features and spermatozoal ultrastructure appear to be characteristic of Cichlidae and, therefore, may be of phylogenetic significance