{"entity": "label", "iuid": "211b36d229424a8380bc224de339495b", "timestamp": "2026-06-07T20:58:05.221Z", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/label/Jennifer%20James.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/label/Jennifer%20James"}}, "value": "Jennifer James", "created": "2024-10-17T10:58:29.157Z", "modified": "2024-10-17T10:58:29.164Z", "accounts": [{"entity": "account", "iuid": "3f3e8dbc15754fa8b4c92f9d97ca769d", "timestamp": "2026-06-07T20:58:05.221Z", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/account/jennifer.james%40icm.uu.se.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/account/jennifer.james%40icm.uu.se"}}, "email": "jennifer.james@icm.uu.se", "name": "Jennifer James", "orcid": "", "role": "curator", "status": "enabled", "login": "2024-11-27T09:14:20.251Z", "created": "2024-10-17T11:17:51.859Z", "modified": "2024-11-27T09:14:20.251Z"}, {"entity": "account", "iuid": "43d414f3d1d04ea19ac969a8df4ed4a6", "timestamp": "2026-06-07T20:58:05.221Z", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/account/sune.joubert%40scilifelab.uu.se.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/account/sune.joubert%40scilifelab.uu.se"}}, "email": "sune.joubert@scilifelab.uu.se", "name": "Sun\u00e9 Joubert", "orcid": "", "role": "curator", "status": "enabled", "login": "2025-10-31T11:15:30.148Z", "created": "2024-08-16T10:03:01.443Z", "modified": "2025-10-31T11:15:30.148Z"}, {"entity": "account", "iuid": "59d7e928268c4c5c9d866673716a8f2d", "timestamp": "2026-06-07T20:58:05.221Z", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/account/christopher.erdmann%40scilifelab.uu.se.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/account/christopher.erdmann%40scilifelab.uu.se"}}, "email": "christopher.erdmann@scilifelab.uu.se", "name": "Christopher Erdmann", "orcid": "", "role": "curator", "status": "enabled", "login": "2024-08-16T11:57:32.037Z", "created": "2024-08-16T10:02:45.342Z", "modified": "2024-10-17T11:21:28.034Z"}], "publications_count": 15, "publications": [{"entity": "publication", "iuid": "aa9f95b4639a44068ad80705aba1ec45", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/aa9f95b4639a44068ad80705aba1ec45.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/aa9f95b4639a44068ad80705aba1ec45"}}, "title": "The 'queen of the Andes' (Puya raimondii) is genetically fragile and fragmented: a consequence of long generation time and semelparity?", "authors": [{"family": "Liu", "given": "Lu", "initials": "L", "orcid": "0000-0001-7168-5017", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c659b1c306424989af636398dd57f975.json"}}, {"family": "James", "given": "Jennifer", "initials": "J", "orcid": "0000-0003-0518-6783", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4b807f7ab8f46f8a5e927e1b090d662.json"}}, {"family": "Zhang", "given": "Yu-Qu", "initials": "Y"}, {"family": "Wang", "given": "Zheng-Feng", "initials": "Z"}, {"family": "Arakaki", "given": "M\u00f3nica", "initials": "M", "orcid": "0000-0003-1081-2507", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b63566a5a85d4b75817fd1bb59b3f99a.json"}}, {"family": "Vadillo", "given": "Giovana", "initials": "G", "orcid": "0000-0002-0145-0367", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/29a2f91d2eab4066a098317b92075a8c.json"}}, {"family": "Zhou", "given": "Qiu-Jie", "initials": "Q", "orcid": "0000-0001-7351-2371", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/15244ffd4f4746ddb9ec39e4c038204e.json"}}, {"family": "Lascoux", "given": "Martin", "initials": "M", "orcid": "0000-0003-1699-9042", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0730d0f9c2524eb19383640612924701.json"}}, {"family": "Ge", "given": "Xue-Jun", "initials": "X", "orcid": "0000-0002-5008-9475", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ef81044779a4cf08dec7e2f062da88c.json"}}], "type": "journal article", "published": "2024-10-00", "journal": {"title": "New Phytol.", "issn": "1469-8137", "issn-l": "0028-646X", "volume": "244", "issue": "1", "pages": "277-291"}, "abstract": "Understanding how life history shapes genetic diversity is a fundamental issue in evolutionary biology, with important consequences for conservation. However, we still have an incomplete picture of the impact of life history on genome-wide patterns of diversity, especially in long-lived semelparous plants. Puya raimondii is a high-altitude semelparous species from the Andes that flowers at 40-100 years of age. We sequenced the whole genome and estimated the nucleotide diversity of 200 individuals sampled from nine populations. Coalescent-based approaches were then used to infer past population dynamics. Finally, these results were compared with results obtained for the iteroparous species, Puya macrura. The nine populations of P. raimondii were highly divergent, highly inbred, and carried an exceptionally high genetic load. They are genetically depauperate, although, locally in the genome, balancing selection contributed to the maintenance of genetic polymorphism. While both P. raimondii and P. macrura went through a severe bottleneck during the Pleistocene, P. raimondii did not recover from it and continuously declined, while P. macrura managed to bounce back. Our results demonstrate the importance of life history, in particular generation time and reproductive strategy, in affecting population dynamics and genomic variation, and illustrate the genetic fragility of long-lived semelparous plants.", "doi": "10.1111/nph.20036", "pmid": "39135394", "labels": {"Jennifer James": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2024-11-27T09:19:02.046Z", "modified": "2024-11-29T09:33:59.308Z"}, {"entity": "publication", "iuid": "c848f64abd814890b0e81b905eea5401", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c848f64abd814890b0e81b905eea5401.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c848f64abd814890b0e81b905eea5401"}}, "title": "The protein domains of vertebrate species in which selection is more effective have greater intrinsic structural disorder", "authors": [{"family": "Weibel", "given": "Catherine A", "initials": "CA", "orcid": "0000-0003-1837-5209", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/54d6dc2af7084fc58d9ab18aa72423e7.json"}}, {"family": "Wheeler", "given": "Andrew L", "initials": "AL", "orcid": "0000-0002-5347-5419", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d5be19398f37475282b6d184b7e77cfe.json"}}, {"family": "James", "given": "Jennifer E", "initials": "JE", "orcid": "0000-0003-0518-6783", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4b807f7ab8f46f8a5e927e1b090d662.json"}}, {"family": "Willis", "given": "Sara M", "initials": "SM", "orcid": "0000-0002-1605-6426", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6316b06885844b32a451c3b8ab502060.json"}}, {"family": "McShea", "given": "Hanon", "initials": "H", "orcid": "0000-0002-9341-4899", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/04a9138ad6834af4be9e2d3c255cc1c9.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": "2024-09-06", "journal": {"title": "Elife", "issn": "2050-084X", "issn-l": "2050-084X", "volume": "12", "issue": null, "pages": null}, "abstract": null, "doi": "10.7554/elife.87335.3", "pmid": null, "labels": {"Jennifer James": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2024-11-27T09:19:34.636Z", "modified": "2024-11-29T09:34:08.559Z"}, {"entity": "publication", "iuid": "cd29ce0f417e4e118befac4bc3d0e76c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/cd29ce0f417e4e118befac4bc3d0e76c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/cd29ce0f417e4e118befac4bc3d0e76c"}}, "title": "Complex Polyploids: Origins, Genomic Composition, and Role of Introgressed Alleles.", "authors": [{"family": "Leal", "given": "J Luis", "initials": "JL", "orcid": "0000-0003-0731-7329", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5c8ad8376a7f483ebe91ed2d15d9147a.json"}}, {"family": "Milesi", "given": "Pascal", "initials": "P"}, {"family": "Hodkov\u00e1", "given": "Eva", "initials": "E"}, {"family": "Zhou", "given": "Qiujie", "initials": "Q", "orcid": "0000-0001-7351-2371", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/15244ffd4f4746ddb9ec39e4c038204e.json"}}, {"family": "James", "given": "Jennifer", "initials": "J", "orcid": "0000-0003-0518-6783", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4b807f7ab8f46f8a5e927e1b090d662.json"}}, {"family": "Eklund", "given": "D Magnus", "initials": "DM"}, {"family": "Pyh\u00e4j\u00e4rvi", "given": "Tanja", "initials": "T", "orcid": "0000-0001-6958-5172", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7256c4910788401f873272cf29fedf91.json"}}, {"family": "Saloj\u00e4rvi", "given": "Jarkko", "initials": "J"}, {"family": "Lascoux", "given": "Martin", "initials": "M", "orcid": "0000-0003-1699-9042", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0730d0f9c2524eb19383640612924701.json"}}], "type": "journal article", "published": "2024-07-27", "journal": {"title": "Syst. Biol.", "issn": "1076-836X", "issn-l": "1063-5157", "volume": "73", "issue": "2", "pages": "392-418"}, "abstract": "Introgression allows polyploid species to acquire new genomic content from diploid progenitors or from other unrelated diploid or polyploid lineages, contributing to genetic diversity and facilitating adaptive allele discovery. In some cases, high levels of introgression elicit the replacement of large numbers of alleles inherited from the polyploid's ancestral species, profoundly reshaping the polyploid's genomic composition. In such complex polyploids, it is often difficult to determine which taxa were the progenitor species and which taxa provided additional introgressive blocks through subsequent hybridization. Here, we use population-level genomic data to reconstruct the phylogenetic history of Betula pubescens (downy birch), a tetraploid species often assumed to be of allopolyploid origin and which is known to hybridize with at least four other birch species. This was achieved by modeling polyploidization and introgression events under the multispecies coalescent and then using an approximate Bayesian computation rejection algorithm to evaluate and compare competing polyploidization models. We provide evidence that B. pubescens is the outcome of an autoploid genome doubling event in the common ancestor of B. pendula and its extant sister species, B. platyphylla, that took place approximately 178,000-188,000 generations ago. Extensive hybridization with B. pendula, B. nana, and B. humilis followed in the aftermath of autopolyploidization, with the relative contribution of each of these species to the B. pubescens genome varying markedly across the species' range. Functional analysis of B. pubescens loci containing alleles introgressed from B. nana identified multiple genes involved in climate adaptation, while loci containing alleles derived from B. humilis revealed several genes involved in the regulation of meiotic stability and pollen viability in plant species.", "doi": "10.1093/sysbio/syae012", "pmid": "38613229", "labels": {"SciLifeLab Fellow": null, "Pascal Milesi": null, "Jennifer James": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC11282369"}, {"db": "pii", "key": "7645150"}], "notes": [], "created": "2024-11-26T09:22:05.553Z", "modified": "2025-04-08T06:08:08.863Z"}, {"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": "15bee8eb34a0438a9b7c764bc2631381", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/15bee8eb34a0438a9b7c764bc2631381.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/15bee8eb34a0438a9b7c764bc2631381"}}, "title": "A new codon adaptation metric predicts vertebrate body size and tendency to protein disorder", "authors": [{"family": "Weibel", "given": "Catherine A", "initials": "CA", "orcid": "0000-0003-1837-5209", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/54d6dc2af7084fc58d9ab18aa72423e7.json"}}, {"family": "Wheeler", "given": "Andrew L", "initials": "AL", "orcid": "0000-0002-5347-5419", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d5be19398f37475282b6d184b7e77cfe.json"}}, {"family": "James", "given": "Jennifer E", "initials": "JE", "orcid": "0000-0003-0518-6783", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4b807f7ab8f46f8a5e927e1b090d662.json"}}, {"family": "Willis", "given": "Sara M", "initials": "SM", "orcid": "0000-0002-1605-6426", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6316b06885844b32a451c3b8ab502060.json"}}, {"family": "Masel", "given": "Joanna", "initials": "J", "orcid": "0000-0002-7398-2127", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/eed69f257e574f4aa53f59349c3ff384.json"}}], "type": "posted-content", "published": "2023-07-26", "journal": {"title": null, "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.7554/elife.87335.1", "pmid": null, "labels": {"Jennifer James": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2024-11-27T09:25:31.199Z", "modified": "2024-11-29T09:34:33.892Z"}, {"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": "6494c4cad1f14a19a28472a8355a7586", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/6494c4cad1f14a19a28472a8355a7586.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/6494c4cad1f14a19a28472a8355a7586"}}, "title": "nQMaker: Estimating Time Nonreversible Amino Acid Substitution Models.", "authors": [{"family": "Dang", "given": "Cuong Cao", "initials": "CC"}, {"family": "Minh", "given": "Bui Quang", "initials": "BQ", "orcid": "0000-0002-5535-6560", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e410aeb274c244cebec7c2aac20a4050.json"}}, {"family": "McShea", "given": "Hanon", "initials": "H"}, {"family": "Masel", "given": "Joanna", "initials": "J", "orcid": "0000-0002-7398-2127", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/eed69f257e574f4aa53f59349c3ff384.json"}}, {"family": "James", "given": "Jennifer Eleanor", "initials": "JE"}, {"family": "Vinh", "given": "Le Sy", "initials": "LS"}, {"family": "Lanfear", "given": "Robert", "initials": "R"}], "type": "journal article", "published": "2022-08-10", "journal": {"title": "Syst. Biol.", "issn": "1076-836X", "issn-l": "1063-5157", "volume": "71", "issue": "5", "pages": "1110-1123"}, "abstract": "Amino acid substitution models are a key component in phylogenetic analyses of protein sequences. All commonly used amino acid models available to date are time-reversible, an assumption designed for computational convenience but not for biological reality. Another significant downside to time-reversible models is that they do not allow inference of rooted trees without outgroups. In this article, we introduce a maximum likelihood approach nQMaker, an extension of the recently published QMaker method, that allows the estimation of time nonreversible amino acid substitution models and rooted phylogenetic trees from a set of protein sequence alignments. We show that the nonreversible models estimated with nQMaker are a much better fit to empirical alignments than pre-existing reversible models, across a wide range of data sets including mammals, birds, plants, fungi, and other taxa, and that the improvements in model fit scale with the size of the data set. Notably, for the recently published plant and bird trees, these nonreversible models correctly recovered the commonly estimated root placements with very high-statistical support without the need to use an outgroup. We provide nQMaker as an easy-to-use feature in the IQ-TREE software (http://www.iqtree.org), allowing users to estimate nonreversible models and rooted phylogenies from their own protein data sets. The data sets and scripts used in this article are available at https://doi.org/10.5061/dryad.3tx95x6hx. [amino acid sequence analyses; amino acid substitution models; maximum likelihood model estimation; nonreversible models; phylogenetic inference; reversible models.].", "doi": "10.1093/sysbio/syac007", "pmid": "35139203", "labels": {"Jennifer James": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC9366462"}, {"db": "pii", "key": "6525257"}, {"db": "Dryad", "key": "10.5061/dryad.3tx95x6hx"}], "notes": [], "created": "2024-11-27T09:25:35.329Z", "modified": "2024-11-29T10:50:48.619Z"}, {"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": "95fff65f500243b9810ad4c680a34ddf", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/95fff65f500243b9810ad4c680a34ddf.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/95fff65f500243b9810ad4c680a34ddf"}}, "title": "Universal and taxon-specific trends in protein sequences as a function of age.", "authors": [{"family": "James", "given": "Jennifer E", "initials": "JE", "orcid": "0000-0003-0518-6783", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4b807f7ab8f46f8a5e927e1b090d662.json"}}, {"family": "Willis", "given": "Sara M", "initials": "SM", "orcid": "0000-0002-1605-6426", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6316b06885844b32a451c3b8ab502060.json"}}, {"family": "Nelson", "given": "Paul G", "initials": "PG", "orcid": "0000-0003-4453-9895", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/90045bdb5a234df4b5448db1ed4a5ff3.json"}}, {"family": "Weibel", "given": "Catherine", "initials": "C", "orcid": "0000-0003-1837-5209", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/54d6dc2af7084fc58d9ab18aa72423e7.json"}}, {"family": "Kosinski", "given": "Luke J", "initials": "LJ", "orcid": "0000-0002-8146-5955", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2347dd3dc6ca4693ba3684c0dfc2cb8c.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": "2021-01-08", "journal": {"title": "Elife", "issn": "2050-084X", "issn-l": "2050-084X", "volume": "10", "issue": null, "pages": null}, "abstract": "Extant protein-coding sequences span a huge range of ages, from those that emerged only recently to those present in the last universal common ancestor. Because evolution has had less time to act on young sequences, there might be 'phylostratigraphy' trends in any properties that evolve slowly with age. A long-term reduction in hydrophobicity and hydrophobic clustering was found in previous, taxonomically restricted studies. Here we perform integrated phylostratigraphy across 435 fully sequenced species, using sensitive HMM methods to detect protein domain homology. We find that the reduction in hydrophobic clustering is universal across lineages. However, only young animal domains have a tendency to have higher structural disorder. Among ancient domains, trends in amino acid composition reflect the order of recruitment into the genetic code, suggesting that the composition of the contemporary descendants of ancient sequences reflects amino acid availability during the earliest stages of life, when these sequences first emerged.", "doi": "10.7554/eLife.57347", "pmid": "33416492", "labels": {"Jennifer James": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC7819706"}, {"db": "pii", "key": "57347"}, {"db": "figshare", "key": "10.6084/m9.figshare.12037281"}], "notes": [], "created": "2024-11-27T09:25:40.076Z", "modified": "2024-11-29T09:36:55.752Z"}, {"entity": "publication", "iuid": "2b906f9f91ae44ab8fcea3e1edd36dca", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/2b906f9f91ae44ab8fcea3e1edd36dca.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/2b906f9f91ae44ab8fcea3e1edd36dca"}}, "title": "Mitochondrial DNA Sequence Diversity in Mammals: A Correlation between the Effective and Census Population Sizes.", "authors": [{"family": "James", "given": "Jennifer", "initials": "J"}, {"family": "Eyre-Walker", "given": "Adam", "initials": "A"}], "type": "comparative study", "published": "2020-12-06", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "issn-l": "1759-6653", "volume": "12", "issue": "12", "pages": "2441-2449"}, "abstract": "What determines the level of genetic diversity of a species remains one of the enduring problems of population genetics. Because neutral diversity depends upon the product of the effective population size and mutation rate, there is an expectation that diversity should be correlated to measures of census population size. This correlation is often observed for nuclear but not for mitochondrial DNA. Here, we revisit the question of whether mitochondrial DNA sequence diversity is correlated to census population size by compiling the largest data set to date, using 639 mammalian species. In a multiple regression, we find that nucleotide diversity is significantly correlated to both range size and mass-specific metabolic rate, but not a variety of other factors. We also find that a measure of the effective population size, the ratio of nonsynonymous to synonymous diversity, is also significantly negatively correlated to both range size and mass-specific metabolic rate. These results together suggest that species with larger ranges have larger effective population sizes. The slope of the relationship between diversity and range is such that doubling the range increases diversity by 12-20%, providing one of the first quantifications of the relationship between diversity and the census population size.", "doi": "10.1093/gbe/evaa222", "pmid": "33095231", "labels": {"Jennifer James": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC7719226"}, {"db": "pii", "key": "5936529"}], "notes": [], "created": "2024-11-27T09:25:42.547Z", "modified": "2024-11-29T10:56:50.802Z"}, {"entity": "publication", "iuid": "bc2e0d95b2974e3893ee33215d183251", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/bc2e0d95b2974e3893ee33215d183251.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/bc2e0d95b2974e3893ee33215d183251"}}, "title": "Selective sweeps on novel and introgressed variation shape mimicry loci in a butterfly adaptive radiation.", "authors": [{"family": "Moest", "given": "Markus", "initials": "M", "orcid": "0000-0003-2370-2788", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/68ebb42ec8a04e78ac67b2002b361d83.json"}}, {"family": "Van Belleghem", "given": "Steven M", "initials": "SM", "orcid": "0000-0001-9399-1007", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ce786f23c8334751b73d3fd6b79aa8e8.json"}}, {"family": "James", "given": "Jennifer E", "initials": "JE", "orcid": "0000-0003-0518-6783", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4b807f7ab8f46f8a5e927e1b090d662.json"}}, {"family": "Salazar", "given": "Camilo", "initials": "C", "orcid": "0000-0001-9217-6588", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b1047fb6ca864cd08eb7876b190ebd8d.json"}}, {"family": "Martin", "given": "Simon H", "initials": "SH", "orcid": "0000-0002-0747-7456", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/68ae66fad62c4ebdb028816ec56a4283.json"}}, {"family": "Barker", "given": "Sarah L", "initials": "SL"}, {"family": "Moreira", "given": "Gilson R P", "initials": "GRP"}, {"family": "M\u00e9rot", "given": "Claire", "initials": "C", "orcid": "0000-0003-2607-7818", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4730b49cb0db4560baa7454d8044ae79.json"}}, {"family": "Joron", "given": "Mathieu", "initials": "M", "orcid": "0000-0003-1043-4147", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ee1b5386def34ee9aee4327a4991e69b.json"}}, {"family": "Nadeau", "given": "Nicola J", "initials": "NJ", "orcid": "0000-0002-9319-921X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a57ba1ad6be044079645609d75cd41d7.json"}}, {"family": "Steiner", "given": "Florian M", "initials": "FM"}, {"family": "Jiggins", "given": "Chris D", "initials": "CD", "orcid": "0000-0002-7809-062X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9bd55f1db6ab4e7daaa61e052886060b.json"}}], "type": "journal article", "published": "2020-02-00", "journal": {"title": "PLoS Biol.", "issn": "1545-7885", "issn-l": "1544-9173", "volume": "18", "issue": "2", "pages": "e3000597"}, "abstract": "Natural selection leaves distinct signatures in the genome that can reveal the targets and history of adaptive evolution. By analysing high-coverage genome sequence data from 4 major colour pattern loci sampled from nearly 600 individuals in 53 populations, we show pervasive selection on wing patterns in the Heliconius adaptive radiation. The strongest signatures correspond to loci with the greatest phenotypic effects, consistent with visual selection by predators, and are found in colour patterns with geographically restricted distributions. These recent sweeps are similar between co-mimics and indicate colour pattern turn-over events despite strong stabilising selection. Using simulations, we compare sweep signatures expected under classic hard sweeps with those resulting from adaptive introgression, an important aspect of mimicry evolution in Heliconius butterflies. Simulated recipient populations show a distinct 'volcano' pattern with peaks of increased genetic diversity around the selected target, characteristic of sweeps of introgressed variation and consistent with diversity patterns found in some populations. Our genomic data reveal a surprisingly dynamic history of colour pattern selection and co-evolution in this adaptive radiation.", "doi": "10.1371/journal.pbio.3000597", "pmid": "32027643", "labels": {"Jennifer James": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC7029882"}, {"db": "pii", "key": "PBIOLOGY-D-19-01905"}], "notes": [], "created": "2024-11-27T09:29:03.471Z", "modified": "2024-11-29T09:37:04.682Z"}, {"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": "e2c4f0ac955444da825fb678eeb35caf", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e2c4f0ac955444da825fb678eeb35caf.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e2c4f0ac955444da825fb678eeb35caf"}}, "title": "DNA sequence diversity and the efficiency of natural selection in animal mitochondrial DNA.", "authors": [{"family": "James", "given": "J", "initials": "J"}, {"family": "Castellano", "given": "D", "initials": "D"}, {"family": "Eyre-Walker", "given": "A", "initials": "A", "orcid": "0000-0001-5527-8729", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/710750d73a5c4e1483168d45dfd0e93f.json"}}], "type": "journal article", "published": "2017-01-00", "journal": {"title": "Heredity (Edinb)", "issn": "1365-2540", "volume": "118", "issue": "1", "pages": "88-95", "issn-l": "0018-067X"}, "abstract": "Selection is expected to be more efficient in species that are more diverse because both the efficiency of natural selection and DNA sequence diversity are expected to depend upon the effective population size. We explore this relationship across a data set of 751 mammal species for which we have mitochondrial polymorphism data. We introduce a method by which we can examine the relationship between our measure of the efficiency of natural selection, the nonsynonymous relative to the synonymous nucleotide site diversity (\u03c0N/\u03c0S), and synonymous nucleotide diversity (\u03c0S), avoiding the statistical non-independence between the two quantities. We show that these two variables are strongly negatively and linearly correlated on a log scale. The slope is such that as \u03c0S doubles, \u03c0N/\u03c0S is reduced by 34%. We show that the slope of this relationship differs between the two phylogenetic groups for which we have the most data, rodents and bats, and that it also differs between species with high and low body mass, and between those with high and low mass-specific metabolic rate.", "doi": "10.1038/hdy.2016.108", "pmid": "27827387", "labels": {"Jennifer James": null}, "xrefs": [{"db": "pmc", "key": "PMC5176113"}, {"db": "pii", "key": "hdy2016108"}], "notes": [], "created": "2024-11-27T09:29:07.798Z", "modified": "2024-11-27T09:29:07.854Z"}, {"entity": "publication", "iuid": "f51bf9b567714a3da0ee16ca1c433d6c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f51bf9b567714a3da0ee16ca1c433d6c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f51bf9b567714a3da0ee16ca1c433d6c"}}, "title": "Molecular Evolutionary Consequences of Island Colonization.", "authors": [{"family": "James", "given": "Jennifer E", "initials": "JE"}, {"family": "Lanfear", "given": "Robert", "initials": "R"}, {"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": "2016-07-02", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "issn-l": "1759-6653", "volume": "8", "issue": "6", "pages": "1876-1888"}, "abstract": "Island endemics are expected to have low effective population sizes (Ne), first because some may experience population bottlenecks when they are founded, and second because they have restricted ranges. Therefore, we expect island species to have reduced genetic diversity, inefficient selection, and reduced adaptive potential compared with their mainland counterparts. We used both polymorphism and substitution data to address these predictions, improving on the approach of recent studies that only used substitution data. This allowed us to directly test the assumption that island species have small values of Ne We found that island species had significantly less genetic diversity than mainland species; however, this pattern could be attributed to a subset of island species that appeared to have undergone a recent population bottleneck. When these species were excluded from the analysis, island and mainland species had similar levels of genetic diversity, despite island species occupying considerably smaller areas than their mainland counterparts. We also found no overall difference between island and mainland species in terms of the effectiveness of selection or the mutation rate. Our evidence suggests that island colonization has no lasting impact on molecular evolution. This surprising result highlights gaps in our knowledge of the relationship between census and effective population size.", "doi": "10.1093/gbe/evw120", "pmid": "27358424", "labels": {"Jennifer James": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC4943191"}, {"db": "pii", "key": "evw120"}], "notes": [], "created": "2024-11-27T09:29:09.889Z", "modified": "2025-11-30T11:20:37.566Z"}, {"entity": "publication", "iuid": "f7fc10b81a7b416686c84dcc21001be0", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f7fc10b81a7b416686c84dcc21001be0.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f7fc10b81a7b416686c84dcc21001be0"}}, "title": "The rate of adaptive evolution in animal mitochondria.", "authors": [{"family": "James", "given": "Jennifer E", "initials": "JE"}, {"family": "Piganeau", "given": "Gwenael", "initials": "G"}, {"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": "2016-01-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "issn-l": "0962-1083", "volume": "25", "issue": "1", "pages": "67-78"}, "abstract": "We have investigated whether there is adaptive evolution in mitochondrial DNA, using an extensive data set containing over 500 animal species from a wide range of taxonomic groups. We apply a variety of McDonald-Kreitman style methods to the data. We find that the evolution of mitochondrial DNA is dominated by slightly deleterious mutations, a finding which is supported by a number of previous studies. However, when we control for the presence of deleterious mutations using a new method, we find that mitochondria undergo a significant amount of adaptive evolution, with an estimated 26% (95% confidence intervals: 5.7-45%) of nonsynonymous substitutions fixed by adaptive evolution. We further find some weak evidence that the rate of adaptive evolution is correlated to synonymous diversity. We interpret this as evidence that at least some adaptive evolution is limited by the supply of mutations.", "doi": "10.1111/mec.13475", "pmid": "26578312", "labels": {"Jennifer James": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC4737298"}, {"db": "figshare", "key": "10.6084/M9.FIGSHARE.1408490"}], "notes": [], "created": "2024-11-27T09:29:11.932Z", "modified": "2025-11-30T11:18:43.689Z"}]}