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Background and Aims: Individuals with primary sclerosing cholangitis (PSC) have expressed a need for more dietary information. The aim of this study was to evaluate the dietary intake of individuals with PSC and compare it with Nordic nutrition recommendations 2023 (NNR2023)., Methods: A cross-sectional assessment of dietary intake was performed using a food-frequency questionnaire among 120 individuals with PSC from five regions across Sweden. Macro- and micronutrient intake was compared to NNR2023. Dietary quality was evaluated using an index developed by the National Food Agency in Sweden., Results: The median age was 47 years (IQR 18), and median body mass index (BMI) was 25.2 kg/m 2 (IQR 5.9). Eight percent had a BMI < 20, and 13% had a BMI > 30. The average fibre intake was 18 g (IQR 18). Median energy distribution included 36% from fat (15% saturated, 4.6% polyunsaturated), 17% from protein and 43% from carbohydrates, highlighting an imbalanced diet with low carbohydrate, fibre and polyunsaturated fat intake and high saturated fat consumption. More than half reported suboptimal intake of zinc, selenium and vitamins C, D and K and > 30% suboptimal intake of vitamins A, B6, E, niacin, folate, potassium, magnesium and iron. Forty percent had poor dietary quality. Longer PSC duration and previous colectomy were associated with a lower dietary quality., Conclusions: Many individuals with PSC do not reach the recommended levels of various micronutrients, especially fat-soluble vitamins and report a poor dietary quality. The results highlight the need for a comprehensive approach to nutritional management in this population., Trial Registration: ClinicalTrials.gov identifier: NCT04133792., (© 2024 The Author(s). Liver International published by John Wiley & Sons Ltd.)

Over the past 15 years, the D-statistic, a four-taxon test for organismal admixture (hybridization, or introgression) which incorporates single nucleotide polymorphism data with allelic patterns ABBA and BABA, has seen considerable use. This statistic seeks to discern significant deviation from either a given species tree assumption, or from the balanced incomplete lineage sorting that could otherwise defy this species tree. However, while the D-statistic can successfully discriminate admixture from incomplete lineage sorting, it is not a simple matter to determine the directionality of admixture using only four-leaf tree models. As such, methods have been developed that use five leaves to evaluate admixture. Among these, the DFOIL method ("FOIL", a mnemonic for "First-Outer-Inner-Last"), which tests allelic patterns on the "symmetric" tree S=(((1,2),(3,4)),5), succeeds in finding admixture direction for many five-taxon examples. However, DFOIL does not make full use of all symmetry, nor can DFOIL function properly when ancient samples are included because of the reliance on singleton patterns (such as BAAAA and ABAAA). Here, we take inspiration from DFOIL to develop a new and completely general family of five-leaf admixture tests, dubbed Δ-statistics, that can either incorporate or exclude the singleton allelic patterns depending on individual taxon and age sampling choices. We describe two new shapes that are also fully testable, namely the "asymmetric" tree A=((((1,2),3),4),5) and the "quasisymmetric" tree Q=(((1,2),3),(4,5)), which can considerably supplement the "symmetric" S=(((1,2),(3,4)),5) model used by DFOIL. We demonstrate the consistency of Δ-statistics under various simulated scenarios, and provide empirical examples using data from black, brown and polar bears, the latter also including two ancient polar bear samples from previous studies. Recently, DFOIL and one of these ancient samples was used to argue for a dominant polar bear → brown bear introgression direction. However, we find, using both this ancient polar bear and our own, that by far the strongest signal using both DFOIL and Δ-statistics on tree S is actually bidirectional gene flow of indistinguishable direction. Further experiments on trees A and Q instead highlight what were likely two phases of admixture: one with stronger brown bear → polar bear introgression in ancient times, and a more recent phase with predominant polar bear → brown bear directionality., Competing Interests: Conflict of Interest: The authors have no conflict of interest to declare., (© The Author(s) 2024. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)

Dietary fatty acids (FA) affect metabolic risk factors. The aim of this study was to explore if changes in dietary fat intake during energy restriction were associated with plasma FA composition. The study also investigated if these changes were associated with changes in liver fat, liver stiffness and plasma lipids among persons with non-alcoholic fatty liver disease. Dietary and plasma FA were investigated in patients with non-alcoholic fatty liver disease ( n 48) previously enrolled in a 12-week-long open-label randomised controlled trial comparing two energy-restricted diets: a low-carbohydrate high-fat diet and intermittent fasting diet (5:2), to a control group. Self-reported 3 d food diaries were used for FA intake, and plasma FA composition was analysed using GC. Liver fat content and stiffness were measured by MRI and transient elastography. Changes in intake of total FA ( r 0·41; P = 0·005), SFA ( r 0·38; P = 0·011) and MUFA ( r 0·42; P = 0·004) were associated with changes in liver stiffness. Changes in plasma SFA ( r 0·32; P = 0·032) and C16 : 1 n -7 ( r 0·33; P = 0·028) were positively associated with changes in liver fat, while total n -6 PUFA ( r -0·33; P = 0·028) and C20 : 4 n -6 ( r -0·42; P = 0·005) were inversely associated. Changes in dietary SFA, MUFA, cholesterol and C20:4 were positively associated with plasma total cholesterol and LDL-cholesterol. Modifying the composition of dietary fats during dietary interventions causes changes in the plasma FA profile in patients with non-alcoholic fatty liver disease. These changes are associated with changes in liver fat, stiffness, plasma cholesterol and TAG. Replacing SFA with PUFA may improve metabolic parameters in non-alcoholic fatty liver disease patients during weight loss treatment.

Island systems provide important contexts for studying processes underlying lineage migration, species diversification, and organismal extinction. The Hawaiian endemic mints (Lamiaceae family) are the second largest plant radiation on the isolated Hawaiian Islands. We generated a chromosome-scale reference genome for one Hawaiian species, Stenogyne calaminthoides, and resequenced 45 relatives, representing 34 species, to uncover the continental origins of this group and their subsequent diversification. We further resequenced 109 individuals of two Stenogyne species, and their purported hybrids, found high on the Mauna Kea volcano on the island of Hawai'i. The three distinct Hawaiian genera, Haplostachys, Phyllostegia, and Stenogyne, are nested inside a fourth genus, Stachys. We uncovered four independent polyploidy events within Stachys, including one allopolyploidy event underlying the Hawaiian mints and their direct western North American ancestors. While the Hawaiian taxa may have principally diversified by parapatry and drift in small and fragmented populations, localized admixture may have played an important role early in lineage diversification. Our genomic analyses provide a view into how organisms may have radiated on isolated island chains, settings that provided one of the principal natural laboratories for Darwin's thinking about the evolutionary process., (© 2024. The Author(s).)

With populations of threatened and endangered species declining worldwide, efforts are being made to generate high quality genomic records of these species before they are lost forever. Here, we demonstrate that data from single Oxford Nanopore Technologies (ONT) MinION flow cells can, even in the absence of highly accurate short DNA-read polishing, produce high quality de novo plant genome assemblies adequate for downstream analyses, such as synteny and ploidy evaluations, paleodemographic analyses, and phylogenomics. This study focuses on three North American ash tree species in the genus Fraxinus (Oleaceae) that were recently added to the International Union for Conservation of Nature (IUCN) Red List as critically endangered. Our results support a hexaploidy event at the base of the Oleaceae as well as a subsequent whole genome duplication shared by Syringa, Osmanthus, Olea, and Fraxinus. Finally, we demonstrate the use of ONT long-read sequencing data to reveal patterns in demographic history., (© 2024. The Author(s).)