Cichlid fish of the genus Oreochromis form the basis of the global tilapia aquaculture and fisheries industries. Broodstocks for aquaculture are often collected from wild populations, which in Africa ...may be from locations containing multiple Oreochromis species. However, many species are difficult to distinguish morphologically, hampering efforts to maintain good quality farmed strains. Additionally, non-native farmed tilapia populations are known to be widely distributed across Africa and to hybridize with native Oreochromis species, which themselves are important for capture fisheries. The morphological identification of these hybrids is particularly unreliable. Here, we describe the development of a single nucleotide polymorphism (SNP) genotyping panel from whole-genome resequencing data that enables targeted species identification in Tanzania. We demonstrate that an optimized panel of 96 genome-wide SNPs based on FST outliers performs comparably to whole genome resequencing in distinguishing species and identifying hybrids. We also show this panel outperforms microsatellite-based and phenotype-based classification methods. Case studies indicate several locations where introduced aquaculture species have become established in the wild, threatening native Oreochromis species. The novel SNP markers identified here represent an important resource for assessing broodstock purity in hatcheries and helping to conserve unique endemic biodiversity.
•We present a novel panel of 96 SNPs, which can be used to accurately distinguish species and hybrids of Oreochromis tilapias.•This SNP panel performs comparably to full-genome data, and is more reliable than microsatellite or morphological assignment.•This will enable assessment of broodstock for aquaculture, as well as hybridisation between invasive and native tilapia.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
The Nile tilapia (Oreochromis niloticus) is the third most important freshwater fish for aquaculture. Its success is directly linked to continuous breeding efforts focusing on production traits such ...as growth rate and weight. Among those elite strains, the Genetically Improved Farmed Tilapia (GIFT) programme initiated by WorldFish is now distributed worldwide. To accelerate the development of the GIFT strain through genomic selection, a high-quality reference genome is necessary.
Using a combination of short (10X Genomics) and long read (PacBio HiFi, PacBio CLR) sequencing and a genetic map for the GIFT strain, we generated a chromosome level genome assembly for the GIFT. Using genomes of two closely related species (O. mossambicus, O. aureus), we characterised the extent of introgression between these species and O. niloticus that has occurred during the breeding process. Over 11 Mb of O. mossambicus genomic material could be identified within the GIFT genome, including genes associated with immunity but also with traits of interest such as growth rate.
Because of the breeding history of elite strains, current reference genomes might not be the most suitable to support further studies into the GIFT strain. We generated a chromosome level assembly of the GIFT strain, characterising its mixed origins, and the potential contributions of introgressed regions to selected traits.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Challenges in semileptonic B decays Gambino, P.; Kronfeld, A. S.; Rotondo, M. ...
The European physical journal. C, Particles and fields,
10/2020, Volume:
80, Issue:
10
Journal Article
Peer reviewed
Open access
Two of the elements of the Cabibbo–Kobayashi–Maskawa quark mixing matrix,
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V
ub
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and
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V
cb
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, are extracted from semileptonic
B
decays. The results of the
B
factories, analysed in the light of ...the most recent theoretical calculations, remain puzzling, because for both
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V
ub
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and
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V
cb
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the exclusive and inclusive determinations are in clear tension. Further, measurements in the
τ
channels at Belle, Babar, and LHCb show discrepancies with the Standard Model predictions, pointing to a possible violation of lepton flavor universality. LHCb and Belle II have the potential to resolve these issues in the next few years. This article summarizes the discussions and results obtained at the MITP workshop held on April 9–13, 2018, in Mainz, Germany, with the goal to develop a medium-term strategy of analyses and calculations aimed at solving the puzzles. Lattice and continuum theorists working together with experimentalists have discussed how to reshape the semileptonic analyses in view of the much higher luminosity expected at Belle II, searching for ways to systematically validate the theoretical predictions in both exclusive and inclusive
B
decays, and to exploit the rich possibilities at LHCb.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
A
bstract
It is well known that in
b
-hadron decays with a single unreconstructible final state particle, the decay kinematics can be solved up to a quadratic ambiguity, without any knowledge of the
...b
-hadron momentum. We present a method to infer the momenta of
b
-hadrons produced in hadron collider experiments using information from their reconstructed flight vectors. Our method is strictly agnostic to the decay itself, which implies that it can be validated with control samples of topologically similar decays to fully reconstructible final states. A multivariate regression algorithm based on the flight information provides a
b
-hadron momentum estimate with a resolution of around 60% which is sufficient to select the correct solution to the quadratic equation in around 70% of cases. This will improve the ability of hadron collider experiments to make differential decay rate measurements with semileptonic
b
-hadron decays.
The Pacific bluefin tuna (Thunnus orientalis) is a regionally endothermic fish that maintains temperatures in their swimming musculature, eyes, brain and viscera above that of the ambient water. ...Within their skeletal muscle, a thermal gradient exists, with deep muscles, close to the backbone, operating at elevated temperatures compared to superficial muscles near the skin. Their heart, by contrast, operates at ambient temperature, which in bluefin tunas can range widely. Cardiac function in tunas reduces in cold waters, yet the heart must continue to supply blood for metabolically demanding endothermic tissues. Physiological studies indicate Pacific bluefin tuna have an elevated cardiac capacity and increased cold-tolerance compared to warm-water tuna species, primarily enabled by increased capacity for sarcoplasmic reticulum calcium cycling within the cardiac muscles.
Here, we compare tissue-specific gene-expression profiles of different cardiac and skeletal muscle tissues in Pacific bluefin tuna. There was little difference in the overall expression of calcium-cycling and cardiac contraction pathways between atrium and ventricle. However, expression of a key sarcoplasmic reticulum calcium-cycling gene, SERCA2b, which plays a key role maintaining intracellular calcium stores, was higher in atrium than ventricle. Expression of genes involved in aerobic metabolism and cardiac contraction were higher in the ventricle than atrium. The two morphologically distinct tissues that derive the ventricle, spongy and compact myocardium, had near-identical levels of gene expression. More genes had higher expression in the cool, superficial muscle than in the warm, deep muscle in both the aerobic red muscle (slow-twitch) and anaerobic white muscle (fast-twitch), suggesting thermal compensation.
We find evidence of widespread transcriptomic differences between the Pacific tuna ventricle and atrium, with potentially higher rates of calcium cycling in the atrium associated with the higher expression of SERCA2b compared to the ventricle. We find no evidence that genes associated with thermogenesis are upregulated in the deep, warm muscle compared to superficial, cool muscle. Heat generation may be enabled by by the high aerobic capacity of bluefin tuna red muscle.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Invasive freshwater fishes are known to readily hybridize with indigenous congeneric species, driving loss of unique and irreplaceable genetic resources. Here we reveal that newly discovered ...(2013–2016) evolutionarily significant populations of Korogwe tilapia (Oreochromis korogwe) from southern Tanzania are threatened by hybridization with the larger invasive Nile tilapia (Oreochromis niloticus). We use a combination of morphology, microsatellite allele frequencies and whole genome sequences to show that O. korogwe from southern lakes (Nambawala, Rutamba and Mitupa) are distinct from geographically disjunct populations in northern Tanzania (Zigi River and Mlingano Dam). We also provide genetic evidence of O. korogwe × niloticus hybrids in three southern lakes and demonstrate heterogeneity in the extent of admixture across the genome. Finally, using the least admixed genomic regions we estimate that the northern and southern O. korogwe populations most plausibly diverged ~140,000 years ago, suggesting that the geographical separation of the northern and southern groups is not a result of a recent translocation, and instead these populations represent independent evolutionarily significant units. We conclude that these newly discovered and phenotypically unique cichlid populations are already threatened by hybridization with an invasive species, and propose that these irreplaceable genetic resources would benefit from conservation interventions.
see also the Perspective by Iva Popovic and Louis Bernatchez.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
One of the key assumptions of the standard model of particle physics is that the interactions of the charged leptons, namely electrons, muons and taus, differ only because of their different masses. ...Whereas precision tests comparing processes involving electrons and muons have not revealed any definite violation of this assumption, recent studies of B-meson decays involving the higher-mass tau lepton have resulted in observations that challenge lepton universality at the level of four standard deviations. A confirmation of these results would point to new particles or interactions, and could have profound implications for our understanding of particle physics.
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IJS, KISLJ, NUK, SBMB, UL, UM, UPUK
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