{"entity": "journal", "iuid": "8bfb866f0ee547d0b404f550ee17109f", "timestamp": "2026-06-15T14:15:26.608Z", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/journal/Mol.%20Biol.%20Evol..json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/journal/Mol.%20Biol.%20Evol."}}, "title": "Mol. Biol. Evol.", "issn": "1537-1719", "issn-l": "0737-4038", "publications_count": 30, "publications": [{"entity": "publication", "iuid": "88fc94697e8f4ea2adceb6767b20da34", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/88fc94697e8f4ea2adceb6767b20da34.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/88fc94697e8f4ea2adceb6767b20da34"}}, "title": "Between but Not Within-Species Variation in the Distribution of Fitness Effects.", "authors": [{"family": "James", "given": "Jennifer", "initials": "J", "orcid": "0000-0003-0518-6783", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4b807f7ab8f46f8a5e927e1b090d662.json"}}, {"family": "Kastally", "given": "Chedly", "initials": "C", "orcid": "0000-0002-1820-4752", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f074636c47854f66a0287fb7382a1462.json"}}, {"family": "Budde", "given": "Katharina B", "initials": "KB", "orcid": "0000-0002-5361-2815", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb5427d15ddc46b0a0afaed44aea0cf0.json"}}, {"family": "Gonz\u00e1lez-Mart\u00ednez", "given": "Santiago C", "initials": "SC", "orcid": "0000-0002-4534-3766", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/eac16e91ca6a49c18fb4206b5349cfff.json"}}, {"family": "Milesi", "given": "Pascal", "initials": "P"}, {"family": "Pyh\u00e4j\u00e4rvi", "given": "Tanja", "initials": "T", "orcid": "0000-0001-6958-5172", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7256c4910788401f873272cf29fedf91.json"}}, {"family": "Lascoux", "given": "Martin", "initials": "M", "orcid": "0000-0003-1699-9042", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0730d0f9c2524eb19383640612924701.json"}}, {"family": "Consortium", "given": "GenTree", "initials": "G"}, {"family": ",", "given": "", "initials": ""}], "type": "journal article", "published": "2023-11-03", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "issn-l": "0737-4038", "volume": "40", "issue": "11", "pages": null}, "abstract": "New mutations provide the raw material for evolution and adaptation. The distribution of fitness effects (DFE) describes the spectrum of effects of new mutations that can occur along a genome, and is, therefore, of vital interest in evolutionary biology. Recent work has uncovered striking similarities in the DFE between closely related species, prompting us to ask whether there is variation in the DFE among populations of the same species, or among species with different degrees of divergence, that is whether there is variation in the DFE at different levels of evolution. Using exome capture data from six tree species sampled across Europe we characterized the DFE for multiple species, and for each species, multiple populations, and investigated the factors potentially influencing the DFE, such as demography, population divergence, and genetic background. We find statistical support for the presence of variation in the DFE at the species level, even among relatively closely related species. However, we find very little difference at the population level, suggesting that differences in the DFE are primarily driven by deep features of species biology, and those evolutionarily recent events, such as demographic changes and local adaptation, have little impact.", "doi": "10.1093/molbev/msad228", "pmid": "37832225", "labels": {"Pascal Milesi": null, "SciLifeLab Fellow": null, "Jennifer James": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC10630145"}, {"db": "pii", "key": "7313554"}], "notes": [], "created": "2023-12-04T08:37:18.774Z", "modified": "2025-04-11T07:24:26.148Z"}, {"entity": "publication", "iuid": "5ee01ddf5e5944ec80351b70a0ebf8c1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5ee01ddf5e5944ec80351b70a0ebf8c1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5ee01ddf5e5944ec80351b70a0ebf8c1"}}, "title": "Differential Retention of Pfam Domains Contributes to Long-term Evolutionary Trends.", "authors": [{"family": "James", "given": "Jennifer E", "initials": "JE", "orcid": "0000-0003-0518-6783", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4b807f7ab8f46f8a5e927e1b090d662.json"}}, {"family": "Nelson", "given": "Paul G", "initials": "PG", "orcid": "0000-0003-4453-9895", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/90045bdb5a234df4b5448db1ed4a5ff3.json"}}, {"family": "Masel", "given": "Joanna", "initials": "J", "orcid": "0000-0002-7398-2127", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/eed69f257e574f4aa53f59349c3ff384.json"}}], "type": "journal article", "published": "2023-04-04", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "issn-l": "0737-4038", "volume": "40", "issue": "4", "pages": null}, "abstract": "Protein domains that emerged more recently in evolution have a higher structural disorder and greater clustering of hydrophobic residues along the primary sequence. It is hard to explain how selection acting via descent with modification could act so slowly as not to saturate over the extraordinarily long timescales over which these trends persist. Here, we hypothesize that the trends were created by a higher level of selection that differentially affects the retention probabilities of protein domains with different properties. This hypothesis predicts that loss rates should depend on disorder and clustering trait values. To test this, we inferred loss rates via maximum likelihood for animal Pfam domains, after first performing a set of stringent quality control methods to reduce annotation errors. Intermediate trait values, matching those of ancient domains, are associated with the lowest loss rates, making our results difficult to explain with reference to previously described homology detection biases. Simulations confirm that effect sizes are of the right magnitude to produce the observed long-term trends. Our results support the hypothesis that differential domain loss slowly weeds out those protein domains that have nonoptimal levels of disorder and clustering. The same preferences also shape the differential diversification of Pfam domains, thereby further impacting proteome composition.", "doi": "10.1093/molbev/msad073", "pmid": "36947137", "labels": {"Jennifer James": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC10089649"}, {"db": "pii", "key": "7083726"}], "notes": [], "created": "2024-11-27T09:25:33.221Z", "modified": "2024-11-29T09:36:28.003Z"}, {"entity": "publication", "iuid": "115c550062bd43f0acdc5afb6c4d91a1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/115c550062bd43f0acdc5afb6c4d91a1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/115c550062bd43f0acdc5afb6c4d91a1"}}, "title": "Genomic Signatures of Sexual Selection on Pollen-Expressed Genes in Arabis alpina.", "authors": [{"family": "Guti\u00e9rrez-Valencia", "given": "Juanita", "initials": "J"}, {"family": "Fracassetti", "given": "Marco", "initials": "M"}, {"family": "Horvath", "given": "Robert", "initials": "R", "orcid": "0000-0002-3221-8835", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f810a2383e7045008002495ef4574adf.json"}}, {"family": "Laenen", "given": "Benjamin", "initials": "B"}, {"family": "D\u00e9samore", "given": "Aur\u00e9lie", "initials": "A"}, {"family": "Drouzas", "given": "Andreas D", "initials": "AD"}, {"family": "Friberg", "given": "Magne", "initials": "M"}, {"family": "Kol\u00e1\u0159", "given": "Filip", "initials": "F"}, {"family": "Slotte", "given": "Tanja", "initials": "T", "orcid": "0000-0001-6020-5102", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3daf6b63a930473b9a609949a3882b06.json"}}], "type": "journal article", "published": "2021-12-08", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "issn-l": "0737-4038", "volume": null, "issue": null, "pages": null}, "abstract": "Fertilization in angiosperms involves the germination of pollen on the stigma, followed by the extrusion of a pollen tube that elongates through the style and delivers two sperm cells to the embryo sac. Sexual selection could occur throughout this process when male gametophytes compete for fertilization. The strength of sexual selection during pollen competition should be affected by the number of genotypes deposited on the stigma. As increased self-fertilization reduces the number of mating partners, and the genetic diversity and heterozygosity of populations, it should thereby reduce the intensity of sexual selection during pollen competition. Despite the prevalence of mating system shifts, few studies have directly compared the molecular signatures of sexual selection during pollen competition in populations with different mating systems. Here we analyzed whole-genome sequences from natural populations of Arabis alpina, a species showing mating system variation across its distribution, to test whether shifts from cross- to self-fertilization result in molecular signatures consistent with sexual selection on genes involved in pollen competition. We found evidence for efficient purifying selection on genes expressed in vegetative pollen, and overall weaker selection on sperm-expressed genes. This pattern was robust when controlling for gene expression level and specificity. In agreement with the expectation that sexual selection intensifies under cross-fertilization, we found that the efficacy of purifying selection on male gametophyte-expressed genes was significantly stronger in genetically more diverse and outbred populations. Our results show that intra-sexual competition shapes the evolution of pollen-expressed genes, and that its strength fades with increasing self-fertilization rates.", "doi": "10.1093/molbev/msab349", "pmid": "34878144", "labels": {"Tanja Slotte": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "6456311"}], "notes": [], "created": "2021-12-04T09:21:53.138Z", "modified": "2022-11-04T11:32:12.167Z"}, {"entity": "publication", "iuid": "c6102e8d1468457bbe1d45499dd63de3", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c6102e8d1468457bbe1d45499dd63de3.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c6102e8d1468457bbe1d45499dd63de3"}}, "title": "Inferring Genome-Wide Correlations of Mutation Fitness Effects between Populations.", "authors": [{"family": "Huang", "given": "Xin", "initials": "X", "orcid": "0000-0002-9918-9602", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/27a6d482c13b437a8ba45a652135aef7.json"}}, {"family": "Fortier", "given": "Alyssa Lyn", "initials": "AL", "orcid": "0000-0001-5964-2540", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/11d3d037ce724d80b7d2ea2164df1c5d.json"}}, {"family": "Coffman", "given": "Alec J", "initials": "AJ"}, {"family": "Struck", "given": "Travis J", "initials": "TJ", "orcid": "0000-0001-7161-5107", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7b3ae2b67f30416cad05239492693184.json"}}, {"family": "Irby", "given": "Megan N", "initials": "MN"}, {"family": "James", "given": "Jennifer E", "initials": "JE", "orcid": "0000-0003-0518-6783", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4b807f7ab8f46f8a5e927e1b090d662.json"}}, {"family": "Le\u00f3n-Burguete", "given": "Jos\u00e9 E", "initials": "JE"}, {"family": "Ragsdale", "given": "Aaron P", "initials": "AP", "orcid": "0000-0003-0715-3432", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6cfa150360d54232b73bed31a8f6fa44.json"}}, {"family": "Gutenkunst", "given": "Ryan N", "initials": "RN", "orcid": "0000-0002-8659-0579", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9a32f8c1377947e0bc6185bd9c645a7e.json"}}], "type": "journal article", "published": "2021-09-27", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "issn-l": "0737-4038", "volume": "38", "issue": "10", "pages": "4588-4602"}, "abstract": "The effect of a mutation on fitness may differ between populations depending on environmental and genetic context, but little is known about the factors that underlie such differences. To quantify genome-wide correlations in mutation fitness effects, we developed a novel concept called a joint distribution of fitness effects (DFE) between populations. We then proposed a new statistic w to measure the DFE correlation between populations. Using simulation, we showed that inferring the DFE correlation from the joint allele frequency spectrum is statistically precise and robust. Using population genomic data, we inferred DFE correlations of populations in humans, Drosophila melanogaster, and wild tomatoes. In these species, we found that the overall correlation of the joint DFE was inversely related to genetic differentiation. In humans and D. melanogaster, deleterious mutations had a lower DFE correlation than tolerated mutations, indicating a complex joint DFE. Altogether, the DFE correlation can be reliably inferred, and it offers extensive insight into the genetics of population divergence.", "doi": "10.1093/molbev/msab162", "pmid": "34043790", "labels": {"Jennifer James": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC8476148"}, {"db": "pii", "key": "6287068"}], "notes": [], "created": "2024-11-27T09:25:37.774Z", "modified": "2024-11-29T09:36:38.141Z"}, {"entity": "publication", "iuid": "69cfdf6a53f74d0487f883c49054d9fa", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/69cfdf6a53f74d0487f883c49054d9fa.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/69cfdf6a53f74d0487f883c49054d9fa"}}, "title": "Selection on accessible chromatin regions in Capsella grandiflora.", "authors": [{"family": "Horvath", "given": "Robert", "initials": "R"}, {"family": "Josephs", "given": "Emily B", "initials": "EB"}, {"family": "Pesquet", "given": "Edouard", "initials": "E"}, {"family": "Stinchcombe", "given": "John R", "initials": "JR"}, {"family": "Wright", "given": "Stephen I", "initials": "SI"}, {"family": "Scofield", "given": "Douglas", "initials": "D"}, {"family": "Slotte", "given": "Tanja", "initials": "T"}], "type": "journal article", "published": "2021-09-08", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "issn-l": "0737-4038"}, "abstract": "Accurate estimates of genome-wide rates and fitness effects of new mutations are essential for an improved understanding of molecular evolutionary processes. Although eukaryotic genomes generally contain a large non-coding fraction, functional non-coding regions and fitness effects of mutations in such regions are still incompletely characterized. A promising approach to characterize functional non-coding regions relies on identifying accessible chromatin regions (ACRs) tightly associated with regulatory DNA. Here, we applied this approach to identify and estimate selection on ACRs in Capsella grandiflora, a crucifer species ideal for population genomic quantification of selection due to its favourable population demography. We describe a population-wide ACR distribution based on ATAC-seq data for leaf samples of 16 individuals from a natural population. We use population genomic methods to estimate fitness effects and proportions of positively selected fixations (\u03b1) in ACRs and find that intergenic ACRs harbor a considerable fraction of weakly deleterious new mutations, as well as a significantly higher proportion of strongly deleterious mutations than comparable inaccessible intergenic regions. ACRs are enriched for expression quantitative trait loci (eQTL) and depleted of transposable element (TE) insertions, as expected if intergenic ACRs are under selection because they harbor regulatory regions. By integrating empirical identification of intergenic ACRs with analyses of eQTL and population genomic analyses of selection, we demonstrate that intergenic regulatory regions are an important source of nearly neutral mutations. These results improve our understanding of selection on non-coding regions and the role of nearly neutral mutations for evolutionary processes in outcrossing Brassicaceae species.", "doi": "10.1093/molbev/msab270", "pmid": "34498072", "labels": {"Tanja Slotte": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "6366554"}], "notes": [], "created": "2021-12-04T09:16:32.926Z", "modified": "2022-11-04T11:32:12.546Z"}, {"entity": "publication", "iuid": "d28374fd05704cff82446954b9d1a5ed", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d28374fd05704cff82446954b9d1a5ed.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d28374fd05704cff82446954b9d1a5ed"}}, "title": "New Phylogenomic Analysis of the Enigmatic Phylum Telonemia Further Resolves the Eukaryote Tree of Life.", "authors": [{"family": "Strassert", "given": "J\u00fcrgen F H", "initials": "JFH"}, {"family": "Jamy", "given": "Mahwash", "initials": "M"}, {"family": "Mylnikov", "given": "Alexander P", "initials": "AP"}, {"family": "Tikhonenkov", "given": "Denis V", "initials": "DV"}, {"family": "Burki", "given": "Fabien", "initials": "F"}], "type": "journal article", "published": "2019-04-01", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "issn-l": "0737-4038", "volume": "36", "issue": "4", "pages": "757-765"}, "abstract": "The resolution of the broad-scale tree of eukaryotes is constantly improving, but the evolutionary origin of several major groups remains unknown. Resolving the phylogenetic position of these \"orphan\" groups is important, especially those that originated early in evolution, because they represent missing evolutionary links between established groups. Telonemia is one such orphan taxon for which little is known. The group is composed of molecularly diverse biflagellated protists, often prevalent although not abundant in aquatic environments. Telonemia has been hypothesized to represent a deeply diverging eukaryotic phylum but no consensus exists as to where it is placed in the tree. Here, we established cultures and report the phylogenomic analyses of three new transcriptome data sets for divergent telonemid lineages. All our phylogenetic reconstructions, based on 248 genes and using site-heterogeneous mixture models, robustly resolve the evolutionary origin of Telonemia as sister to the Sar supergroup. This grouping remains well supported when as few as 60% of the genes are randomly subsampled, thus is not sensitive to the sets of genes used but requires a minimal alignment length to recover enough phylogenetic signal. Telonemia occupies a crucial position in the tree to examine the origin of Sar, one of the most lineage-rich eukaryote supergroups. We propose the moniker \"TSAR\" to accommodate this new mega-assemblage in the phylogeny of eukaryotes.", "doi": "10.1093/molbev/msz012", "pmid": "30668767", "labels": {"Fabien Burki": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "5298736"}, {"db": "pmc", "key": "PMC6844682"}, {"db": "SRA", "key": "SRP150904"}], "notes": [], "created": "2020-09-28T11:59:15.625Z", "modified": "2022-11-04T11:32:16.604Z"}, {"entity": "publication", "iuid": "5ae36a17bb2340a6b98f6c186a6cce57", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5ae36a17bb2340a6b98f6c186a6cce57.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5ae36a17bb2340a6b98f6c186a6cce57"}}, "title": "Structural Patching Fosters Divergence of Mitochondrial Ribosomes.", "authors": [{"family": "Petrov", "given": "Anton S", "initials": "AS"}, {"family": "Wood", "given": "Elizabeth C", "initials": "EC"}, {"family": "Bernier", "given": "Chad R", "initials": "CR"}, {"family": "Norris", "given": "Ashlyn M", "initials": "AM"}, {"family": "Brown", "given": "Alan", "initials": "A"}, {"family": "Amunts", "given": "Alexey", "initials": "A"}], "type": "comparative study", "published": "2019-02-01", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "issn-l": "0737-4038", "volume": "36", "issue": "2", "pages": "207-219"}, "abstract": "Mitochondrial ribosomes (mitoribosomes) are essential components of all mitochondria that synthesize proteins encoded by the mitochondrial genome. Unlike other ribosomes, mitoribosomes are highly variable across species. The basis for this diversity is not known. Here, we examine the composition and evolutionary history of mitoribosomes across the phylogenetic tree by combining three-dimensional structural information with a comparative analysis of the secondary structures of mitochondrial rRNAs (mt-rRNAs) and available proteomic data. We generate a map of the acquisition of structural variation and reconstruct the fundamental stages that shaped the evolution of the mitoribosomal large subunit and led to this diversity. Our analysis suggests a critical role for ablation and expansion of rapidly evolving mt-rRNA. These changes cause structural instabilities that are \"patched\" by the acquisition of pre-existing compensatory elements, thus providing opportunities for rapid evolution. This mechanism underlies the incorporation of mt-tRNA into the central protuberance of the mammalian mitoribosome, and the altered path of the polypeptide exit tunnel of the yeast mitoribosome. We propose that since the toolkits of elements utilized for structural patching differ between mitochondria of different species, it fosters the growing divergence of mitoribosomes.", "doi": "10.1093/molbev/msy221", "pmid": "30517740", "labels": {"Alexey Amunts": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "5229934"}, {"db": "pmc", "key": "PMC6367999"}], "notes": [], "created": "2020-09-25T14:20:50.793Z", "modified": "2022-11-04T11:32:16.809Z"}, {"entity": "publication", "iuid": "e289c31695bc4702b2276fddfdf81eed", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e289c31695bc4702b2276fddfdf81eed.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e289c31695bc4702b2276fddfdf81eed"}}, "title": "Nearly Neutral Evolution across the Drosophila melanogaster Genome.", "authors": [{"family": "Castellano", "given": "David", "initials": "D"}, {"family": "James", "given": "Jennifer", "initials": "J", "orcid": "0000-0003-0518-6783", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4b807f7ab8f46f8a5e927e1b090d662.json"}}, {"family": "Eyre-Walker", "given": "Adam", "initials": "A", "orcid": "0000-0001-5527-8729", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/710750d73a5c4e1483168d45dfd0e93f.json"}}], "type": "journal article", "published": "2018-11-01", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "issn-l": "0737-4038", "volume": "35", "issue": "11", "pages": "2685-2694"}, "abstract": "Under the nearly neutral theory of molecular evolution, the proportion of effectively neutral mutations is expected to depend upon the effective population size (Ne). Here, we investigate whether this is the case across the genome of Drosophila melanogaster using polymorphism data from North American and African lines. We show that the ratio of the number of nonsynonymous and synonymous polymorphisms is negatively correlated to the number of synonymous polymorphisms, even when the nonindependence is accounted for. The relationship is such that the proportion of effectively neutral nonsynonymous mutations increases by \u223c45% as Ne is halved. However, we also show that this relationship is steeper than expected from an independent estimate of the distribution of fitness effects from the site frequency spectrum. We investigate a number of potential explanations for this and show, using simulation, that this is consistent with a model of genetic hitchhiking: Genetic hitchhiking depresses diversity at neutral and weakly selected sites, but has little effect on the diversity of strongly selected sites.", "doi": "10.1093/molbev/msy164", "pmid": "30418639", "labels": {"Jennifer James": null, "DDLS Fellow": null}, "xrefs": [{"db": "pii", "key": "5078937"}], "notes": [], "created": "2024-11-27T09:29:05.759Z", "modified": "2025-11-30T11:19:13.619Z"}, {"entity": "publication", "iuid": "04bc41c13061470593d3350733352538", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/04bc41c13061470593d3350733352538.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/04bc41c13061470593d3350733352538"}}, "title": "Origin and Evolution of the Bartonella Gene Transfer Agent.", "authors": [{"family": "Tamarit", "given": "Daniel", "initials": "D"}, {"family": "Neuvonen", "given": "Minna-Maria", "initials": "MM"}, {"family": "Engel", "given": "Philipp", "initials": "P"}, {"family": "Guy", "given": "Lionel", "initials": "L"}, {"family": "Andersson", "given": "Siv G E", "initials": "SGE"}], "type": "journal article", "published": "2018-02-01", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "volume": "35", "issue": "2", "pages": "451-464", "issn-l": "0737-4038"}, "abstract": "Gene transfer agents (GTAs) are domesticated bacteriophages that have evolved into molecular machines for the transfer of bacterial DNA. Despite their widespread nature and their biological implications, the mechanisms and selective forces that drive the emergence of GTAs are still poorly understood. Two GTAs have been identified in the Alphaproteobacteria: the RcGTA, which is widely distributed in a broad range of species; and the BaGTA, which has a restricted host range that includes vector-borne intracellular bacteria of the genus Bartonella. The RcGTA packages chromosomal DNA randomly, whereas the BaGTA particles contain a relatively higher fraction of genes for host interaction factors that are amplified from a nearby phage-derived origin of replication. In this study, we compare the BaGTA genes with homologous bacteriophage genes identified in the genomes of Bartonella species and close relatives. Unlike the BaGTA, the prophage genes are neither present in all species, nor inserted into homologous genomic sites. Phylogenetic inferences and substitution frequency analyses confirm codivergence of the BaGTA with the host genome, as opposed to multiple integration and recombination events in the prophages. Furthermore, the organization of segments flanking the BaGTA differs from that of the prophages by a few rearrangement events, which have abolished the normal coordination between phage genome replication and phage gene expression. Based on the results of our comparative analysis, we propose a model for how a prophage may be transformed into a GTA that transfers amplified bacterial DNA segments.", "doi": "10.1093/molbev/msx299", "pmid": "29161442", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pii", "key": "4638576"}], "notes": [], "created": "2018-12-05T12:24:13.124Z", "modified": "2018-12-05T12:24:13.144Z"}, {"entity": "publication", "iuid": "056d562b703345669c5f4081896d506a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/056d562b703345669c5f4081896d506a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/056d562b703345669c5f4081896d506a"}}, "title": "Gene Duplication Leads to Altered Membrane Topology of a Cytochrome P450 Enzyme in Seed Plants.", "authors": [{"family": "Renault", "given": "Hugues", "initials": "H"}, {"family": "De Marothy", "given": "Minttu", "initials": "M"}, {"family": "Jonasson", "given": "Gabriella", "initials": "G"}, {"family": "Lara", "given": "Patricia", "initials": "P"}, {"family": "Nelson", "given": "David R", "initials": "DR"}, {"family": "Nilsson", "given": "IngMarie", "initials": "I"}, {"family": "Andr\u00e9", "given": "Fran\u00e7ois", "initials": "F"}, {"family": "von Heijne", "given": "Gunnar", "initials": "G"}, {"family": "Werck-Reichhart", "given": "Dani\u00e8le", "initials": "D"}], "type": "journal article", "published": "2017-08-01", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "volume": "34", "issue": "8", "pages": "2041-2056", "issn-l": "0737-4038"}, "abstract": "Evolution of the phenolic metabolism was critical for the transition of plants from water to land. A cytochrome P450, CYP73, with cinnamate 4-hydroxylase (C4H) activity, catalyzes the first plant-specific and rate-limiting step in this pathway. The CYP73 gene is absent from green algae, and first detected in bryophytes. A CYP73 duplication occurred in the ancestor of seed plants and was retained in Taxaceae and most angiosperms. In spite of a clear divergence in primary sequence, both paralogs can fulfill comparable cinnamate hydroxylase roles both in vitro and in vivo. One of them seems dedicated to the biosynthesis of lignin precursors. Its N-terminus forms a single membrane spanning helix and its properties and length are highly constrained. The second is characterized by an elongated and variable N-terminus, reminiscent of ancestral CYP73s. Using as proxies the Brachypodium distachyon proteins, we show that the elongation of the N-terminus does not result in an altered subcellular localization, but in a distinct membrane topology. Insertion in the membrane of endoplasmic reticulum via a double-spanning open hairpin structure allows reorientation to the lumen of the catalytic domain of the protein. In agreement with participation to a different functional unit and supramolecular organization, the protein displays modified heme proximal surface. These data suggest the evolution of divergent C4H enzymes feeding different branches of the phenolic network in seed plants. It shows that specialization required for retention of gene duplicates may result from altered protein topology rather than change in enzyme activity.", "doi": "10.1093/molbev/msx160", "pmid": "28505373", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pii", "key": "3827453"}, {"db": "pmc", "key": "PMC5850782"}], "notes": [], "created": "2018-12-05T12:57:26.061Z", "modified": "2018-12-05T12:57:26.086Z"}, {"entity": "publication", "iuid": "a4a06848ff64489496e10ea5bc88c797", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a4a06848ff64489496e10ea5bc88c797.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a4a06848ff64489496e10ea5bc88c797"}}, "title": "Genetic Diversity and the Efficacy of Purifying Selection across Plant and Animal Species.", "authors": [{"family": "Chen", "given": "Jun", "initials": "J"}, {"family": "Gl\u00e9min", "given": "Sylvain", "initials": "S"}, {"family": "Lascoux", "given": "Martin", "initials": "M"}], "type": "journal article", "published": "2017-06-01", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "volume": "34", "issue": "6", "pages": "1417-1428", "issn-l": "0737-4038"}, "abstract": "A central question in evolutionary biology is why some species have more genetic diversity than others and a no less important question is why selection efficacy varies among species. Although these questions have started to be tackled in animals, they have not been addressed to the same extent in plants. Here, we estimated nucleotide diversity at synonymous, \u03c0S, and nonsynonymous sites, \u03c0N, and a measure of the efficacy of selection, the ratio \u03c0N/\u03c0S, in 34 animal and 28 plant species using full genome data. We then evaluated the relationship of nucleotide diversity and selection efficacy with effective population size, the distribution of fitness effect and life history traits. In animals, our data confirm that longevity and propagule size are the variables that best explain the variation in \u03c0S among species. In plants longevity also plays a major role as well as mating system. As predicted by the nearly neutral theory of molecular evolution, the log of \u03c0N/\u03c0S decreased linearly with the log of \u03c0S but the slope was weaker in plants than in animals. This appears to be due to a higher mutation rate in long lived plants, and the difference disappears when \u03c0S is rescaled by the mutation rate. Differences in the distribution of fitness effect of new mutations also contributed to variation in \u03c0N/\u03c0S among species.", "doi": "10.1093/molbev/msx088", "pmid": "28333215", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pii", "key": "3049540"}], "notes": [], "created": "2018-12-05T11:26:15.471Z", "modified": "2018-12-05T11:26:15.490Z"}, {"entity": "publication", "iuid": "39eef356132344f98d4e84e88bf5e190", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/39eef356132344f98d4e84e88bf5e190.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/39eef356132344f98d4e84e88bf5e190"}}, "title": "Variation in Mutational Robustness between Different Proteins and the Predictability of Fitness Effects.", "authors": [{"family": "Lind", "given": "Peter A", "initials": "PA"}, {"family": "Arvidsson", "given": "Lars", "initials": "L"}, {"family": "Berg", "given": "Otto G", "initials": "OG"}, {"family": "Andersson", "given": "Dan I", "initials": "DI"}], "type": "journal article", "published": "2017-02-01", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "volume": "34", "issue": "2", "pages": "408-418", "issn-l": "0737-4038"}, "abstract": "Random mutations in genes from disparate protein classes may have different distributions of fitness effects (DFEs) depending on different structural, functional, and evolutionary constraints. We measured the fitness effects of 156 single mutations in the genes encoding AraC (transcription factor), AraD (enzyme), and AraE (transporter) used for bacterial growth on l-arabinose. Despite their different molecular functions these genes all had bimodal DFEs with most mutations either being neutral or strongly deleterious, providing a general expectation for the DFE. This contrasts with the unimodal DFEs previously obtained for ribosomal protein genes where most mutations were slightly deleterious. Based on theoretical considerations, we suggest that the 33-fold higher average mutational robustness of ribosomal proteins is due to stronger selection for reduced costs of translational and transcriptional errors. Whereas the large majority of synonymous mutations were deleterious for ribosomal proteins genes, no fitness effects could be detected for the AraCDE genes. Four mutations in AraC and AraE increased fitness, suggesting that slightly advantageous mutations make up a significant fraction of the DFE, but that they often escape detection due to the limited sensitivity of commonly used fitness assays. We show that the fitness effects of amino acid substitutions can be predicted based on evolutionary conservation, but those weakly deleterious mutations are less reliably detected. This suggests that large-effect mutations and the fraction of highly deleterious mutations can be computationally predicted, but that experiments are required to characterize the DFE close to neutrality, where many mutations ultimately fixed in a population will occur.", "doi": "10.1093/molbev/msw239", "pmid": "28025272", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pii", "key": "msw239"}], "notes": [], "created": "2018-12-05T11:58:54.269Z", "modified": "2018-12-05T11:58:54.288Z"}, {"entity": "publication", "iuid": "b7f9c130599d4974a5603fdc323e6c60", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b7f9c130599d4974a5603fdc323e6c60.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b7f9c130599d4974a5603fdc323e6c60"}}, "title": "Functional Relationship between a Dinoflagellate Host and Its Diatom Endosymbiont.", "authors": [{"family": "Hehenberger", "given": "Elisabeth", "initials": "E"}, {"family": "Burki", "given": "Fabien", "initials": "F"}, {"family": "Kolisko", "given": "Martin", "initials": "M"}, {"family": "Keeling", "given": "Patrick J", "initials": "PJ"}], "type": "journal article", "published": "2016-09-00", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "issn-l": "0737-4038", "volume": "33", "issue": "9", "pages": "2376-2390"}, "abstract": "While we know much about the evolutionary patterns of endosymbiotic organelle origins, we know less about how the actual process unfolded within each system. This is partly due to the massive changes endosymbiosis appears to trigger, and partly because most organelles evolved in the distant past. The dinotoms are dinoflagellates with diatom endosymbionts, and they represent a relatively recent but nevertheless obligate endosymbiotic association. We have carried out deep sequencing of both the host and endosymbiont transcriptomes from two dinotoms, Durinskia baltica and Glenodinium foliaceum, to examine how the nucleocytosolic compartments have functionally integrated. This analysis showed little or no functional reduction in either the endosymbiont or host, and no evidence for genetic integration. Rather, host and endosymbiont seem to be bound to each other via metabolites, such as photosynthate exported from the endosymbiont to the host as indicated by the presence of plastidic phosphate translocators in the host transcriptome. The host is able to synthesize starch, using plant-specific starch synthases, as a way to store imported photosynthate.", "doi": "10.1093/molbev/msw109", "pmid": "27297471", "labels": {"Affiliated researcher": null, "Fabien Burki": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "msw109"}], "notes": [], "created": "2018-12-03T14:40:55.775Z", "modified": "2022-11-04T11:32:19.299Z"}, {"entity": "publication", "iuid": "748104fa7e5c48e7b7882f8595bf1eb3", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/748104fa7e5c48e7b7882f8595bf1eb3.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/748104fa7e5c48e7b7882f8595bf1eb3"}}, "title": "Tracing the Archaeal Origins of Eukaryotic Membrane-Trafficking System Building Blocks.", "authors": [{"family": "Klinger", "given": "Christen M", "initials": "CM"}, {"family": "Spang", "given": "Anja", "initials": "A"}, {"family": "Dacks", "given": "Joel B", "initials": "JB"}, {"family": "Ettema", "given": "Thijs J G", "initials": "TJ"}], "type": "journal article", "published": "2016-06-00", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "volume": "33", "issue": "6", "pages": "1528-1541", "issn-l": "0737-4038"}, "abstract": "In contrast to prokaryotes, eukaryotic cells are characterized by a complex set of internal membrane-bound compartments. A subset of these, and the protein machineries that move material between them, define the membrane-trafficking system (MTS), the emergence of which represents a landmark in eukaryotic evolution. Unlike mitochondria and plastids, MTS organelles have autogenous origins. Much of the MTS machinery is composed of building blocks, including small GTPase, coiled-coil, beta-propeller\u2009+\u2009alpha-solenoid, and longin domains. Despite the identification of prokaryotic proteins containing these domains, only few represent direct orthologues, leaving the origins and early evolution of the MTS poorly understood. Here, we present an in-depth analysis of MTS building block homologues in the composite genome of Lokiarchaeum, the recently discovered archaeal sister clade of eukaryotes, yielding several key insights. We identify two previously unreported Eukaryotic Signature Proteins; orthologues of the Gtr/Rag family GTPases, involved in target of rapamycin complex signaling, and of the RLC7 dynein component. We could not identify golgin or SNARE (coiled-coil) or beta-propeller\u2009+\u2009alpha-solenoid orthologues, nor typical MTS domain fusions, suggesting that these either were lost from Lokiarchaeum or emerged later in eukaryotic evolution. Furthermore, our phylogenetic analyses of lokiarchaeal GTPases support a split into Ras-like and Arf-like superfamilies, with different prokaryotic antecedents, before the advent of eukaryotes. While no GTPase activating proteins or exchange factors were identified, we show that Lokiarchaeum encodes numerous roadblock domain proteins and putative longin domain proteins, confirming the latter's origin from Archaea. Altogether, our study provides new insights into the emergence and early evolution of the eukaryotic membrane-trafficking system.", "doi": "10.1093/molbev/msw034", "pmid": "26893300", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pii", "key": "msw034"}], "notes": [], "created": "2018-12-05T09:57:48.497Z", "modified": "2018-12-05T09:57:48.516Z"}, {"entity": "publication", "iuid": "ba824fa9c48c4536a870dc94f0558278", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ba824fa9c48c4536a870dc94f0558278.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ba824fa9c48c4536a870dc94f0558278"}}, "title": "Evolutionary Origins of Rhizarian Parasites.", "authors": [{"family": "Sierra", "given": "Roberto", "initials": "R"}, {"family": "Ca\u00f1as-Duarte", "given": "Silvia J", "initials": "SJ"}, {"family": "Burki", "given": "Fabien", "initials": "F"}, {"family": "Schwelm", "given": "Arne", "initials": "A"}, {"family": "Fogelqvist", "given": "Johan", "initials": "J"}, {"family": "Dixelius", "given": "Christina", "initials": "C"}, {"family": "Gonz\u00e1lez-Garc\u00eda", "given": "Laura N", "initials": "LN"}, {"family": "Gile", "given": "Gillian H", "initials": "GH"}, {"family": "Slamovits", "given": "Claudio H", "initials": "CH"}, {"family": "Klopp", "given": "Christophe", "initials": "C"}, {"family": "Restrepo", "given": "Silvia", "initials": "S"}, {"family": "Arzul", "given": "Isabelle", "initials": "I"}, {"family": "Pawlowski", "given": "Jan", "initials": "J"}], "type": "letter", "published": "2016-04-00", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "issn-l": "0737-4038", "volume": "33", "issue": "4", "pages": "980-983"}, "abstract": "The SAR group (Stramenopila, Alveolata, Rhizaria) is one of the largest clades in the tree of eukaryotes and includes a great number of parasitic lineages. Rhizarian parasites are obligate and have devastating effects on commercially important plants and animals but despite this fact, our knowledge of their biology and evolution is limited. Here, we present rhizarian transcriptomes from all major parasitic lineages in order to elucidate their evolutionary relationships using a phylogenomic approach. Our results suggest that Ascetosporea, parasites of marine invertebrates, are sister to the novel clade Apofilosa. The phytomyxean plant parasites branch sister to the vampyrellid algal ectoparasites in the novel clade Phytorhiza. They also show that Ascetosporea + Apofilosa + Retaria + Filosa + Phytorhiza form a monophyletic clade, although the branching pattern within this clade is difficult to resolve and appears to be model-dependent. Our study does not support the monophyly of the rhizarian parasitic lineages (Endomyxa), suggesting independent origins for rhizarian animal and plant parasites.", "doi": "10.1093/molbev/msv340", "pmid": "26681153", "labels": {"Fabien Burki": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "msv340"}], "notes": [], "created": "2018-12-03T14:40:04.497Z", "modified": "2022-11-04T11:32:19.521Z"}, {"entity": "publication", "iuid": "b94c5441bd534451bcbaa76af760d580", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b94c5441bd534451bcbaa76af760d580.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b94c5441bd534451bcbaa76af760d580"}}, "title": "Cis-Regulatory Changes Associated with a Recent Mating System Shift and Floral Adaptation in Capsella.", "authors": [{"family": "Steige", "given": "Kim A", "initials": "KA"}, {"family": "Reimeg\u00e5rd", "given": "Johan", "initials": "J"}, {"family": "Koenig", "given": "Daniel", "initials": "D"}, {"family": "Scofield", "given": "Douglas G", "initials": "DG"}, {"family": "Slotte", "given": "Tanja", "initials": "T"}], "type": "journal article", "published": "2015-10-00", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "issn-l": "0737-4038", "volume": "32", "issue": "10", "pages": "2501-2514"}, "abstract": "The selfing syndrome constitutes a suite of floral and reproductive trait changes that have evolved repeatedly across many evolutionary lineages in response to the shift to selfing. Convergent evolution of the selfing syndrome suggests that these changes are adaptive, yet our understanding of the detailed molecular genetic basis of the selfing syndrome remains limited. Here, we investigate the role of cis-regulatory changes during the recent evolution of the selfing syndrome in Capsella rubella, which split from the outcrosser Capsella grandiflora less than 200 ka. We assess allele-specific expression (ASE) in leaves and flower buds at a total of 18,452 genes in three interspecific F1 C. grandiflora x C. rubella hybrids. Using a hierarchical Bayesian approach that accounts for technical variation using genomic reads, we find evidence for extensive cis-regulatory changes. On average, 44% of the assayed genes show evidence of ASE; however, only 6% show strong allelic expression biases. Flower buds, but not leaves, show an enrichment of cis-regulatory changes in genomic regions responsible for floral and reproductive trait divergence between C. rubella and C. grandiflora. We further detected an excess of heterozygous transposable element (TE) insertions near genes with ASE, and TE insertions targeted by uniquely mapping 24-nt small RNAs were associated with reduced expression of nearby genes. Our results suggest that cis-regulatory changes have been important during the recent adaptive floral evolution in Capsella and that differences in TE dynamics between selfing and outcrossing species could be important for rapid regulatory divergence in association with mating system shifts.", "doi": "10.1093/molbev/msv169", "pmid": "26318184", "labels": {"Affiliated researcher": null, "Tanja Slotte": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "msv169"}, {"db": "pmc", "key": "PMC4576713"}], "notes": [], "created": "2018-12-03T14:38:17.563Z", "modified": "2022-11-04T11:32:19.821Z"}, {"entity": "publication", "iuid": "ed7a4c9578d14a38b905728a14150e99", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ed7a4c9578d14a38b905728a14150e99.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ed7a4c9578d14a38b905728a14150e99"}}, "title": "Quantitative Mass Spectrometry Reveals Partial Translational Regulation for Dosage Compensation in Chicken.", "authors": [{"family": "Uebbing", "given": "Severin", "initials": "S"}, {"family": "Konzer", "given": "Anne", "initials": "A"}, {"family": "Xu", "given": "Luohao", "initials": "L"}, {"family": "Backstr\u00f6m", "given": "Niclas", "initials": "N"}, {"family": "Brunstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Bergquist", "given": "Jonas", "initials": "J"}, {"family": "Ellegren", "given": "Hans", "initials": "H"}], "type": "journal article", "published": "2015-10-00", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "volume": "32", "issue": "10", "pages": "2716-2725", "issn-l": "0737-4038"}, "abstract": "There is increasing evidence that dosage compensation is not a ubiquitous feature following sex chromosome evolution, especially not in organisms where females are the heterogametic sex, like in birds. Even when it occurs, compensation can be incomplete and limited to dosage-sensitive genes. However, previous work has mainly studied transcriptional regulation of sex-linked genes, which may not reflect expression at the protein level. Here, we used liquid chromatography-tandem mass spectrometry to detect and quantify expressed levels of more than 2,400 proteins in ten different tissues of male and female chicken embryos. For comparison, transcriptome sequencing was performed in the same individuals, five of each sex. The proteomic analysis revealed that dosage compensation was incomplete, with a mean male-to-female (M:F) expression ratio of Z-linked genes of 1.32 across tissues, similar to that at the RNA level (1.29). The mean Z chromosome-to-autosome expression ratio was close to 1 in males and lower than 1 in females, consistent with partly reduced Z chromosome expression in females. Although our results exclude a general mechanism for chromosome-wide dosage compensation at translation, 30% of all proteins encoded from Z-linked genes showed a significant change in the M:F ratio compared with the corresponding ratio at the RNA level. This resulted in a pattern where some genes showed balanced expression between sexes and some close to 2-fold higher expression in males. This suggests that proteomic analyses will be necessary to reveal a more complete picture of gene regulation and sex chromosome evolution. ", "doi": "10.1093/molbev/msv147", "pmid": "26108680", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pii", "key": "msv147"}, {"db": "pmc", "key": "PMC4576709"}], "notes": [], "created": "2018-12-05T10:03:10.624Z", "modified": "2018-12-05T10:03:10.642Z"}, {"entity": "publication", "iuid": "684e75e56bd94ea6a172b58920b0699c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/684e75e56bd94ea6a172b58920b0699c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/684e75e56bd94ea6a172b58920b0699c"}}, "title": "Species Tree Inference Using a Mixture Model.", "authors": [{"family": "Ullah", "given": "Ikram", "initials": "I"}, {"family": "Parviainen", "given": "Pekka", "initials": "P"}, {"family": "Lagergren", "given": "Jens", "initials": "J"}], "type": "journal article", "published": "2015-09-00", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "volume": "32", "issue": "9", "pages": "2469-2482", "issn-l": "0737-4038"}, "abstract": "Species tree reconstruction has been a subject of substantial research due to its central role across biology and medicine. A species tree is often reconstructed using a set of gene trees or by directly using sequence data. In either of these cases, one of the main confounding phenomena is the discordance between a species tree and a gene tree due to evolutionary events such as duplications and losses. Probabilistic methods can resolve the discordance by coestimating gene trees and the species tree but this approach poses a scalability problem for larger data sets. We present MixTreEM-DLRS: A two-phase approach for reconstructing a species tree in the presence of gene duplications and losses. In the first phase, MixTreEM, a novel structural expectation maximization algorithm based on a mixture model is used to reconstruct a set of candidate species trees, given sequence data for monocopy gene families from the genomes under study. In the second phase, PrIME-DLRS, a method based on the DLRS model (\u00c5kerborg O, Sennblad B, Arvestad L, Lagergren J. 2009. Simultaneous Bayesian gene tree reconstruction and reconciliation analysis. Proc Natl Acad Sci U S A. 106(14):5714-5719), is used for selecting the best species tree. PrIME-DLRS can handle multicopy gene families since DLRS, apart from modeling sequence evolution, models gene duplication and loss using a gene evolution model (Arvestad L, Lagergren J, Sennblad B. 2009. The gene evolution model and computing its associated probabilities. J ACM. 56(2):1-44). We evaluate MixTreEM-DLRS using synthetic and biological data, and compare its performance with a recent genome-scale species tree reconstruction method PHYLDOG (Boussau B, Sz\u00f6ll\u0151si GJ, Duret L, Gouy M, Tannier E, Daubin V. 2013. Genome-scale coestimation of species and gene trees. Genome Res. 23(2):323-330) as well as with a fast parsimony-based algorithm Duptree (Wehe A, Bansal MS, Burleigh JG, Eulenstein O. 2008. Duptree: a program for large-scale phylogenetic analyses using gene tree parsimony. Bioinformatics 24(13):1540-1541). Our method is competitive with PHYLDOG in terms of accuracy and runs significantly faster and our method outperforms Duptree in accuracy. The analysis constituted by MixTreEM without DLRS may also be used for selecting the target species tree, yielding a fast and yet accurate algorithm for larger data sets. MixTreEM is freely available at http://prime.scilifelab.se/mixtreem/. ", "doi": "10.1093/molbev/msv115", "pmid": "25963975", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pii", "key": "msv115"}], "notes": [], "created": "2018-12-05T12:19:11.632Z", "modified": "2018-12-05T12:19:11.651Z"}, {"entity": "publication", "iuid": "b31bfa11859f4429b50d3758d9a9b2b1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b31bfa11859f4429b50d3758d9a9b2b1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b31bfa11859f4429b50d3758d9a9b2b1"}}, "title": "Human adaptation to arsenic-rich environments.", "authors": [{"family": "Schlebusch", "given": "Carina M", "initials": "CM"}, {"family": "Gattepaille", "given": "Lucie M", "initials": "LM"}, {"family": "Engstr\u00f6m", "given": "Karin", "initials": "K"}, {"family": "Vahter", "given": "Marie", "initials": "M"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M"}, {"family": "Broberg", "given": "Karin", "initials": "K"}], "type": "journal article", "published": "2015-06-00", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "volume": "32", "issue": "6", "pages": "1544-1555", "issn-l": "0737-4038"}, "abstract": "Adaptation drives genomic changes; however, evidence of specific adaptations in humans remains limited. We found that inhabitants of the northern Argentinean Andes, an arid region where elevated arsenic concentrations in available drinking water is common, have unique arsenic metabolism, with efficient methylation and excretion of the major metabolite dimethylated arsenic and a less excretion of the highly toxic monomethylated metabolite. We genotyped women from this population for 4,301,332 single nucleotide polymorphisms (SNPs) and found a strong association between the AS3MT (arsenic [+3 oxidation state] methyltransferase) gene and mono- and dimethylated arsenic in urine, suggesting that AS3MT functions as the major gene for arsenic metabolism in humans. We found strong genetic differentiation around AS3MT in the Argentinean Andes population, compared with a highly related Peruvian population (FST = 0.014) from a region with much less environmental arsenic. Also, 13 of the 100 SNPs with the highest genome-wide Locus-Specific Branch Length occurred near AS3MT. In addition, our examination of extended haplotype homozygosity indicated a selective sweep of the Argentinean Andes population, in contrast to Peruvian and Colombian populations. Our data show that adaptation to tolerate the environmental stressor arsenic has likely driven an increase in the frequencies of protective variants of AS3MT, providing the first evidence of human adaptation to a toxic chemical. ", "doi": "10.1093/molbev/msv046", "pmid": "25739736", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pii", "key": "msv046"}], "notes": [], "created": "2018-12-05T09:05:47.163Z", "modified": "2018-12-05T09:05:47.184Z"}, {"entity": "publication", "iuid": "3f8572871ba941da8d15ecc2944365da", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3f8572871ba941da8d15ecc2944365da.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3f8572871ba941da8d15ecc2944365da"}}, "title": "Evolutionary histories of transposable elements in the genome of the largest living marsupial carnivore, the Tasmanian devil.", "authors": [{"family": "Gallus", "given": "Susanne", "initials": "S"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "Kumar", "given": "Vikas", "initials": "V"}, {"family": "Dodt", "given": "William G", "initials": "WG"}, {"family": "Janke", "given": "Axel", "initials": "A"}, {"family": "Schumann", "given": "Gerald G", "initials": "GG"}, {"family": "Nilsson", "given": "Maria A", "initials": "MA"}], "type": "journal article", "published": "2015-05-00", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "volume": "32", "issue": "5", "pages": "1268-1283", "issn-l": "0737-4038"}, "abstract": "The largest living carnivorous marsupial, the Tasmanian devil (Sarcophilus harrisii), is the sole survivor of a lineage originating about 12 Ma. We set out to investigate the spectrum of transposable elements found in the Tasmanian devil genome, the first high-coverage genome of an Australian marsupial. Marsupial genomes have been shown to have the highest amount of transposable elements among vertebrates. We analyzed the horizontally transmitted DNA transposons OC1 and hAT-1_MEu in the Tasmanian devil genome. OC1 is present in all carnivorous marsupials, while having a very limited distribution among the remaining Australian marsupial orders. In contrast, hAT-1_MEu is present in all Australian marsupial orders, and has so far only been identified in a few placental mammals. We screened 158 introns for phylogenetically informative retrotransposons in the order Dasyuromorphia, and found that the youngest SINE (Short INterspersed Element), WSINE1, is no longer active in the subfamily Dasyuridae. The lack of detectable WSINE1 activity in this group may be due to a retrotransposon inactivation event approximately 30 Ma. We found that the Tasmanian devil genome contains a relatively low number of continuous full-length LINE-1 (Long INterspersed Element 1, L1) retrotransposons compared with the opossum genome. Furthermore, all L1 elements in the Tasmanian devil appeared to be nonfunctional. Hidden Markov Model approaches suggested that other potential sources of functional reverse transcriptase are absent from the genome. We discuss the issues associated with assembling long, highly similar L1 copies from short read Illumina data and describe how assembly artifacts can potentially lead to erroneous conclusions. ", "doi": "10.1093/molbev/msv017", "pmid": "25633377", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pii", "key": "msv017"}, {"db": "pmc", "key": "PMC4408412"}], "notes": [], "created": "2018-12-05T10:25:28.257Z", "modified": "2018-12-05T10:25:28.277Z"}, {"entity": "publication", "iuid": "c1e34b2b4f71463183cb8166673cd8f5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c1e34b2b4f71463183cb8166673cd8f5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c1e34b2b4f71463183cb8166673cd8f5"}}, "title": "Investigating population history using temporal genetic differentiation.", "authors": [{"family": "Skoglund", "given": "Pontus", "initials": "P"}, {"family": "Sj\u00f6din", "given": "Per", "initials": "P"}, {"family": "Skoglund", "given": "Tobias", "initials": "T"}, {"family": "Lascoux", "given": "Martin", "initials": "M"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M"}], "type": "journal article", "published": "2014-09-00", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "volume": "31", "issue": "9", "pages": "2516-2527", "issn-l": "0737-4038"}, "abstract": "The rapid advance of sequencing technology, coupled with improvements in molecular methods for obtaining genetic data from ancient sources, holds the promise of producing a wealth of genomic data from time-separated individuals. However, the population-genetic properties of time-structured samples have not been extensively explored. Here, we consider the implications of temporal sampling for analyses of genetic differentiation and use a temporal coalescent framework to show that complex historical events such as size reductions, population replacements, and transient genetic barriers between populations leave a footprint of genetic differentiation that can be traced through history using temporal samples. Our results emphasize explicit consideration of the temporal structure when making inferences and indicate that genomic data from ancient individuals will greatly increase our ability to reconstruct population history. ", "doi": "10.1093/molbev/msu192", "pmid": "24939468", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pii", "key": "msu192"}, {"db": "pmc", "key": "PMC4137715"}], "notes": [], "created": "2018-12-05T09:41:44.655Z", "modified": "2018-12-05T09:41:44.674Z"}, {"entity": "publication", "iuid": "2f3b3d41561e48bb816289e60dc9efe9", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/2f3b3d41561e48bb816289e60dc9efe9.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/2f3b3d41561e48bb816289e60dc9efe9"}}, "title": "Brown and polar bear Y chromosomes reveal extensive male-biased gene flow within brother lineages.", "authors": [{"family": "Bidon", "given": "Tobias", "initials": "T"}, {"family": "Janke", "given": "Axel", "initials": "A"}, {"family": "Fain", "given": "Steven R", "initials": "SR"}, {"family": "Eiken", "given": "Hans Geir", "initials": "HG"}, {"family": "Hagen", "given": "Snorre B", "initials": "SB"}, {"family": "Saarma", "given": "Urmas", "initials": "U"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "Lecomte", "given": "Nicolas", "initials": "N"}, {"family": "Hailer", "given": "Frank", "initials": "F"}], "type": "journal article", "published": "2014-06-00", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "volume": "31", "issue": "6", "pages": "1353-1363", "issn-l": "0737-4038"}, "abstract": "Brown and polar bears have become prominent examples in phylogeography, but previous phylogeographic studies relied largely on maternally inherited mitochondrial DNA (mtDNA) or were geographically restricted. The male-specific Y chromosome, a natural counterpart to mtDNA, has remained underexplored. Although this paternally inherited chromosome is indispensable for comprehensive analyses of phylogeographic patterns, technical difficulties and low variability have hampered its application in most mammals. We developed 13 novel Y-chromosomal sequence and microsatellite markers from the polar bear genome and screened these in a broad geographic sample of 130 brown and polar bears. We also analyzed a 390-kb-long Y-chromosomal scaffold using sequencing data from published male ursine genomes. Y chromosome evidence support the emerging understanding that brown and polar bears started to diverge no later than the Middle Pleistocene. Contrary to mtDNA patterns, we found 1) brown and polar bears to be reciprocally monophyletic sister (or rather brother) lineages, without signals of introgression, 2) male-biased gene flow across continents and on phylogeographic time scales, and 3) male dispersal that links the Alaskan ABC islands population to mainland brown bears. Due to female philopatry, mtDNA provides a highly structured estimate of population differentiation, while male-biased gene flow is a homogenizing force for nuclear genetic variation. Our findings highlight the importance of analyzing both maternally and paternally inherited loci for a comprehensive view of phylogeographic history, and that mtDNA-based phylogeographic studies of many mammals should be reevaluated. Recent advances in sequencing technology render the analysis of Y-chromosomal variation feasible, even in nonmodel organisms. ", "doi": "10.1093/molbev/msu109", "pmid": "24667925", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pii", "key": "msu109"}], "notes": [], "created": "2018-12-05T09:13:30.788Z", "modified": "2018-12-05T09:13:30.805Z"}, {"entity": "publication", "iuid": "e47681aa0dde40a18c863aadfb918a9e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e47681aa0dde40a18c863aadfb918a9e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e47681aa0dde40a18c863aadfb918a9e"}}, "title": "Assessing the maximum contribution from ancient populations.", "authors": [{"family": "Sj\u00f6din", "given": "Per", "initials": "P"}, {"family": "Skoglund", "given": "Pontus", "initials": "P"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M"}], "type": "historical article", "published": "2014-05-00", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "volume": "31", "issue": "5", "pages": "1248-1260", "issn-l": "0737-4038"}, "abstract": "Ancestral relationships between populations separated by time represent an often neglected dimension in population genetics, a field which historically has focused on analysis of spatially distributed samples from the same point in time. Models are usually straightforward when two time-separated populations are assumed to be completely isolated from all other populations. However, this is usually an unrealistically stringent assumption when there is gene flow with other populations. Here, we investigate continuity in the presence of gene flow from unknown populations. This setup allows a more nuanced treatment of questions regarding population continuity in terms of \"level of contribution\" from a particular ancient population to a more recent population. We propose a statistical framework which makes use of a biallelic marker sampled at two different points in time to assess population contribution, and present two different interpretations of the concept. We apply the approach to published data from a prehistoric human population in Scandinavia (Malmstr\u00f6m H, Gilbert MTP, Thomas MG, Brandstr\u00f6m M, Stor\u00e5 J, Molnar P, Andersen PK, Bendixen C, Holmlund G, G\u00f6therstr\u00f6m A, et al. 2009. Ancient DNA reveals lack of continuity between Neolithic hunter-gatherers and contemporary Scandinavians. Curr Biol. 19:1758-1762) and Pleistocene woolly mammoth (Barnes I, Shapiro B, Lister A, Kuznetsova T, Sher A, Guthrie D, Thomas MG. 2007. Genetic structure and extinction of the woolly mammoth, Mammuthus primigenius. Curr Biol. 17:1072-1075; Debruyne R, Chu G, King CE, Bos K, Kuch M, Schwarz C, Szpak P, Gr\u00f6cke DR, Matheus P, Zazula G, et al. 2008. Out of America: ancient DNA evidence for a new world origin of late quaternary woolly mammoths. Curr Biol. 18:1320-1326). ", "doi": "10.1093/molbev/msu059", "pmid": "24497031", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pii", "key": "msu059"}], "notes": [], "created": "2018-12-05T11:22:30.281Z", "modified": "2018-12-05T11:22:30.300Z"}, {"entity": "publication", "iuid": "a2b52866856f4e5fba9c772b3acff174", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a2b52866856f4e5fba9c772b3acff174.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a2b52866856f4e5fba9c772b3acff174"}}, "title": "Protein expansion is primarily due to indels in intrinsically disordered regions.", "authors": [{"family": "Light", "given": "Sara", "initials": "S"}, {"family": "Sagit", "given": "Rauan", "initials": "R"}, {"family": "Sachenkova", "given": "Oxana", "initials": "O"}, {"family": "Ekman", "given": "Diana", "initials": "D"}, {"family": "Elofsson", "given": "Arne", "initials": "A"}], "type": "journal article", "published": "2013-12-00", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "volume": "30", "issue": "12", "pages": "2645-2653", "issn-l": "0737-4038"}, "abstract": "Proteins evolve not only through point mutations but also by insertion and deletion events, which affect the length of the protein. It is well known that such indel events most frequently occur in surface-exposed loops. However, detailed analysis of indel events in distantly related and fast-evolving proteins is hampered by the difficulty involved in correctly aligning such sequences. Here, we circumvent this problem by first only analyzing homologous proteins based on length variation rather than pairwise alignments. Using this approach, we find a surprisingly strong relationship between difference in length and difference in the number of intrinsically disordered residues, where up to three quarters of the length variation can be explained by changes in the number of intrinsically disordered residues. Further, we find that disorder is common in both insertions and deletions. A more detailed analysis reveals that indel events do not induce disorder but rather that already disordered regions accrue indels, suggesting that there is a lowered selective pressure for indels to occur within intrinsically disordered regions. ", "doi": "10.1093/molbev/mst157", "pmid": "24037790", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pii", "key": "mst157"}], "notes": [], "created": "2018-12-05T09:12:07.979Z", "modified": "2018-12-05T09:12:07.996Z"}, {"entity": "publication", "iuid": "55b615aec7f544f981e89c7e4e2519ff", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/55b615aec7f544f981e89c7e4e2519ff.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/55b615aec7f544f981e89c7e4e2519ff"}}, "title": "Anisotropic isolation by distance: the main orientations of human genetic differentiation.", "authors": [{"family": "Jay", "given": "Flora", "initials": "F"}, {"family": "Sj\u00f6din", "given": "Per", "initials": "P"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M"}, {"family": "Blum", "given": "Michael G B", "initials": "MG"}], "type": "journal article", "published": "2013-03-00", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "volume": "30", "issue": "3", "pages": "513-525", "issn-l": "0737-4038"}, "abstract": "Genetic differentiation among human populations is greatly influenced by geography due to the accumulation of local allele frequency differences. However, little is known about the possibly different increment of genetic differentiation along the different geographical axes (north-south, east-west, etc.). Here, we provide new methods to examine the asymmetrical patterns of genetic differentiation. We analyzed genome-wide polymorphism data from populations in Africa (n = 29), Asia (n = 26), America (n = 9), and Europe (n = 38), and we found that the major orientations of genetic differentiation are north-south in Europe and Africa, and east-west in Asia, but no preferential orientation was found in the Americas. Additionally, we showed that the localization of the individual geographic origins based on single nucleotide polymorphism data was not equally precise along all orientations. Confirming our findings, we obtained that, in each continent, the orientation along which the precision is maximal corresponds to the orientation of maximum differentiation. Our results have implications for interpreting human genetic variation in terms of isolation by distance and spatial range expansion processes. In Europe, for instance, the precise northnorthwest-southsoutheast axis of main European differentiation cannot be explained by a simple Neolithic demic diffusion model without admixture with the local populations because in that case the orientation of greatest differentiation should be perpendicular to the direction of expansion. In addition to humans, anisotropic analyses can guide the description of genetic differentiation for other organisms and provide information on expansions of invasive species or the processes of plant dispersal.", "doi": "10.1093/molbev/mss259", "pmid": "23171862", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pii", "key": "mss259"}, {"db": "pmc", "key": "PMC3563970"}], "notes": [], "created": "2018-12-05T09:43:11.208Z", "modified": "2018-12-05T09:43:11.227Z"}, {"entity": "publication", "iuid": "ced2adea955b404eabf1c9ed0774382a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ced2adea955b404eabf1c9ed0774382a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ced2adea955b404eabf1c9ed0774382a"}}, "title": "Genome-wide analyses of recombination suggest that Giardia intestinalis assemblages represent different species.", "authors": [{"family": "Xu", "given": "Feifei", "initials": "F"}, {"family": "Jerlstr\u00f6m-Hultqvist", "given": "Jon", "initials": "J"}, {"family": "Andersson", "given": "Jan O", "initials": "JO"}], "type": "journal article", "published": "2012-10-00", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "volume": "29", "issue": "10", "pages": "2895-2898", "issn-l": "0737-4038"}, "abstract": "Giardia intestinalis is a major cause of waterborne enteric disease in humans. The species is divided into eight assemblages suggested to represent separate Giardia species based on host specificities and the genetic divergence of marker genes. We have investigated whether genome-wide recombination occurs between assemblages using the three available G. intestinalis genomes. First, the relative nonsynonymous substitution rates of the homologs were compared for 4,009 positional homologs. The vast majority of these comparisons indicate genetic isolation without interassemblage recombinations. Only a region of 6 kbp suggests genetic exchange between assemblages A and E, followed by gene conversion events. Second, recombination-detecting software fails to identify within-gene recombination between the different assemblages for most of the homologs. Our results indicate very low frequency of recombination between the syntenic core genes, suggesting that G. intestinalis assemblages are genetically isolated lineages and thus should be viewed as separated Giardia species.", "doi": "10.1093/molbev/mss107", "pmid": "22474166", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pii", "key": "mss107"}], "notes": [], "created": "2018-12-05T09:47:34.251Z", "modified": "2018-12-05T09:47:34.270Z"}, {"entity": "publication", "iuid": "0068f2bb3ff94f68a693eb87e4308e67", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0068f2bb3ff94f68a693eb87e4308e67.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0068f2bb3ff94f68a693eb87e4308e67"}}, "title": "Intragenomic Spread of Plastid-Targeting Presequences in the Coccolithophore Emiliania huxleyi", "authors": [{"family": "Burki", "given": "Fabien", "initials": "F"}, {"family": "Hirakawa", "given": "Yoshihisa", "initials": "Y"}, {"family": "Keeling", "given": "Patrick J", "initials": "PJ"}], "type": "journal-article", "published": "2012-09-00", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "issn-l": "0737-4038", "volume": "29", "issue": "9", "pages": "2109-2112"}, "abstract": "Nucleus-encoded plastid-targeted proteins of photosynthetic organisms are generally equipped with an N-terminal presequence required for crossing the plastid membranes. The acquisition of these presequences played a fundamental role in the establishment of plastids. Here, we report a unique case of two non-homologous proteins possessing completely identical presequences consisting of a bipartite plastid-targeting signal in the coccolithophore Emiliania huxleyi. We further show that this presequence is highly conserved in five additional proteins that did not originally function in plastids, representing de novo plastid acquisitions. These are among the most recent cases of presequence spreading from gene to gene and shed light on important evolutionary processes that have been usually erased by the ancient history of plastid evolution. We propose a mechanism of acquisition involving genomic duplications and gene replacement through non-homologous recombination that may have played a more general role for equipping proteins with targeting information.", "doi": "10.1093/molbev/mss103", "pmid": "22466155", "labels": {"Fabien Burki": null, "SciLifeLab Fellow": null}, "xrefs": [], "notes": [], "created": "2018-12-03T14:29:28.607Z", "modified": "2023-06-02T06:07:30.069Z"}, {"entity": "publication", "iuid": "4bb27677c66a43c79651f27507405d13", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/4bb27677c66a43c79651f27507405d13.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/4bb27677c66a43c79651f27507405d13"}}, "title": "Resequencing data provide no evidence for a human bottleneck in Africa during the penultimate glacial period.", "authors": [{"family": "Sj\u00f6din", "given": "Per", "initials": "P"}, {"family": "E Sj\u00f6strand", "given": "Agn\u00e8s", "initials": "A"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M"}, {"family": "Blum", "given": "Michael G B", "initials": "MG"}], "type": "journal article", "published": "2012-07-00", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "volume": "29", "issue": "7", "pages": "1851-1860", "issn-l": "0737-4038"}, "abstract": "Based on the accumulation of genetic, climatic, and fossil evidence, a central theory in paleoanthropology stipulates that a demographic bottleneck coincided with the origin of our species Homo Sapiens. This theory proposes that anatomically modern humans--which were only present in Africa at the time--experienced a drastic bottleneck during the penultimate glacial age (130-190 kya) when a cold and dry climate prevailed. Two scenarios have been proposed to describe the bottleneck, which involve either a fragmentation of the range occupied by humans or the survival of one small group of humans. Here, we analyze DNA sequence data from 61 nuclear loci sequenced in three African populations using Approximate Bayesian Computation and numerical simulations. In contrast to the bottleneck theory, we show that a simple model without any bottleneck during the penultimate ice age has the greatest statistical support compared with bottleneck models. Although the proposed bottleneck is ancient, occurring at least 130 kya, we can discard the possibility that it did not leave detectable footprints in the DNA sequence data except if the bottleneck involves a less than a 3-fold reduction in population size. Finally, we confirm that a simple model without a bottleneck is able to reproduce the main features of the observed patterns of genetic variation. We conclude that models of Pleistocene refugium for modern human origins now require substantial revision.", "doi": "10.1093/molbev/mss061", "pmid": "22319141", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pii", "key": "mss061"}], "notes": [], "created": "2018-12-05T09:43:37.347Z", "modified": "2018-12-05T09:43:37.364Z"}, {"entity": "publication", "iuid": "3fb75c6a1f8349bfac1f6c771ccb9425", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3fb75c6a1f8349bfac1f6c771ccb9425.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3fb75c6a1f8349bfac1f6c771ccb9425"}}, "title": "Independent genome reduction and phylogenetic reclassification of the oceanic SAR11 clade.", "authors": [{"family": "Viklund", "given": "Johan", "initials": "J"}, {"family": "Ettema", "given": "Thijs J G", "initials": "TJ"}, {"family": "Andersson", "given": "Siv G E", "initials": "SG"}], "type": "journal article", "published": "2012-02-00", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "volume": "29", "issue": "2", "pages": "599-615", "issn-l": "0737-4038"}, "abstract": "The SAR11 clade, here represented by Candidatus Pelagibacter ubique, is the most successful group of bacteria in the upper surface waters of the oceans. In contrast to previous studies that have associated the 1.3 Mb genome of Ca. Pelagibacter ubique with the less than 1.5 Mb genomes of the Rickettsiales, our phylogenetic analysis suggests that Ca. Pelagibacter ubique is most closely related to soil and aquatic Alphaproteobacteria with large genomes. This implies that the SAR11 clade and the Rickettsiales have undergone genome reduction independently. A gene flux analysis of 46 representative alphaproteobacterial genomes indicates the loss of more than 800 genes in each of Ca. Pelagibacter ubique and the Rickettsiales. Consistent with their different phylogenetic affiliations, the pattern of gene loss differs with a higher loss of genes for repair and recombination processes in Ca. Pelagibacter ubique as compared with a more extensive loss of genes for biosynthetic functions in the Rickettsiales. Some of the lost genes in Ca. Pelagibacter ubique, such as mutLS, recFN, and ruvABC, are conserved in all other alphaproteobacterial genomes including the small genomes of the Rickettsiales. The mismatch repair genes mutLS are absent from all currently sequenced SAR11 genomes and also underrepresented in the global ocean metagenome data set. We hypothesize that the unique loss of genes involved in repair and recombination processes in Ca. Pelagibacter ubique has been driven by selection and that this helps explain many of the characteristics of the SAR11 population, such as the streamlined genomes, the long branch lengths, the high recombination frequencies, and the extensive sequence divergence within the population.", "doi": "10.1093/molbev/msr203", "pmid": "21900598", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pii", "key": "msr203"}], "notes": [], "created": "2018-12-05T08:51:58.402Z", "modified": "2018-12-05T08:51:58.434Z"}, {"entity": "publication", "iuid": "4a2131b2767a48819e7273a440b8dbae", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/4a2131b2767a48819e7273a440b8dbae.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/4a2131b2767a48819e7273a440b8dbae"}}, "title": "Polyploid speciation did not confer instant reproductive isolation in Capsella (Brassicaceae).", "authors": [{"family": "Slotte", "given": "Tanja", "initials": "T"}, {"family": "Huang", "given": "Huirun", "initials": "H"}, {"family": "Lascoux", "given": "Martin", "initials": "M"}, {"family": "Ceplitis", "given": "Alf", "initials": "A"}], "type": "journal article", "published": "2008-07-00", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "volume": "25", "issue": "7", "pages": "1472-1481", "issn-l": "0737-4038"}, "abstract": "Polyploid formation is a major mode of sympatric speciation in flowering plants. Unlike other speciation processes, polyploidization is often assumed to confer instant reproductive isolation. Shared polymorphism across ploidy levels has therefore often been attributed to multiple polyploid origins, whereas the alternative hypothesis of introgressive hybridization has rarely been rigorously tested. Here, we sequence 12 nuclear loci representing 6 genes duplicated by polyploidy in 92 accessions of the tetraploid Capsella bursa-pastoris together with the corresponding loci in 21 accessions of its close diploid relative Capsella rubella. In C. bursa-pastoris accessions from western Eurasia, where the 2 species occur in partial sympatry, we find higher levels of nucleotide diversity than in accessions from eastern Eurasia, where C. rubella does not grow. Furthermore, haplotypes are shared across ploidy levels at 4 loci in western but not in eastern Eurasia. We test whether haplotype sharing is due to retention of ancestral polymorphism or due to hybridization and introgression using a coalescent-based isolation-with-migration model. In western but not in eastern Eurasia, there is evidence for unidirectional gene flow from C. rubella to C. bursa-pastoris. An independent estimate of the timing of dispersal of C. bursa-pastoris to eastern Eurasia indicates that it probably predated introgression. Our results show that polyploid speciation need not result in immediate and complete reproductive isolation, that postpolyploidization hybridization and introgression can contribute significantly to genetic variation in a newly formed polyploid, and that divergence population genetic analysis constitutes a powerful way of testing hypotheses on polyploid speciation.", "doi": "10.1093/molbev/msn092", "pmid": "18417485", "labels": {"Tanja Slotte": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "msn092"}], "notes": [], "created": "2020-10-09T13:57:38.423Z", "modified": "2022-11-07T11:38:19.946Z"}], "created": "2018-12-05T08:51:58.415Z", "modified": "2020-11-27T13:12:55.237Z"}