{"entity": "journal", "iuid": "17d0c9c17e0c48eda88261731e9b9c7e", "timestamp": "2026-07-20T22:16:12.135Z", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/journal/Mol.%20Phylogenet.%20Evol..json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/journal/Mol.%20Phylogenet.%20Evol."}}, "title": "Mol. Phylogenet. Evol.", "issn": "1095-9513", "issn-l": "1055-7903", "publications_count": 6, "publications": [{"entity": "publication", "iuid": "2721b972cb2e40c5b6f64f2285aec738", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/2721b972cb2e40c5b6f64f2285aec738.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/2721b972cb2e40c5b6f64f2285aec738"}}, "title": "The last of their kind: Is the genus Scutiger (Anura: Megophryidae) a relict element of the paleo-Transhimalaya biota?", "authors": [{"family": "Hofmann", "given": "Sylvia", "initials": "S", "orcid": "0000-0003-0621-9049", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5e89cec6cf1d4923a3e8c142c15040c9.json"}}, {"family": "Podsiadlowski", "given": "Lars", "initials": "L"}, {"family": "Andermann", "given": "Tobias", "initials": "T", "orcid": "0000-0002-0932-1623", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dfff478dfcfc43ddbd40bb1bafbcb0a7.json"}}, {"family": "Matschiner", "given": "Michael", "initials": "M", "orcid": "0000-0003-4741-3884", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2afde3b4ccad4b0d91d9330781efb8be.json"}}, {"family": "Baniya", "given": "Chitra B", "initials": "CB"}, {"family": "Litvinchuk", "given": "Spartak N", "initials": "SN"}, {"family": "Martin", "given": "Sebastian", "initials": "S", "orcid": "0000-0002-0747-7456", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/68ae66fad62c4ebdb028816ec56a4283.json"}}, {"family": "Masroor", "given": "Rafaqat", "initials": "R"}, {"family": "Yang", "given": "Jianhuan", "initials": "J", "orcid": "0000-0002-4497-9615", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/813a309f6b5c46ff9bff0ac129512c48.json"}}, {"family": "Zheng", "given": "Yuchi", "initials": "Y"}, {"family": "Jablonski", "given": "Daniel", "initials": "D"}, {"family": "Schmidt", "given": "Joachim", "initials": "J"}], "type": "journal article", "published": "2024-12-00", "journal": {"title": "Mol. Phylogenet. Evol.", "issn": "1095-9513", "volume": "201", "pages": "108166", "issn-l": "1055-7903"}, "abstract": "The orographic evolution of the Himalaya-Tibet Mountain system continues to be a subject of controversy, leading to considerable uncertainty regarding the environment and surface elevation of the Tibetan Plateau during the Cenozoic era. As many geoscientific (but not paleontological) studies suggest, elevations close to modern heights exist in vast areas of Tibet since at least the late Paleogene, implicating the presence of large-scale alpine environments for more than 30 million years. To explore a recently proposed alternative model that assumes a warm temperate environment across paleo-Tibet, we carried out a phylogeographic survey using genomic analyses of samples covering the range of endemic lazy toads (Scutiger) across the Himalaya-Tibet orogen. We identified two main clades, with several, geographically distinct subclades. The long temporal gap between the stem and crown age of Scutiger may suggest high extinction rates. Diversification within the crown group, depending on the calibration, occurred either from the Mid-Miocene or Late-Miocene and continued until the Holocene. The present-day Himalayan Scutiger fauna could have evolved from lineages that existed on the southern edges of the paleo-Tibetan area (the Transhimalaya = Gangdese Shan), while extant species living on the eastern edge of the Plateau originated probably from the eastern edges of northern parts of the ancestral Tibetan area (Hoh Xil, Tanggula Shan). Based on the Mid-Miocene divergence time estimation and ancestral area reconstruction, we propose that uplift-associated aridification of a warm temperate Miocene-Tibet, coupled with high extirpation rates of ancestral populations, and species range shifts along drainage systems and epigenetic transverse valleys of the rising mountains, is a plausible scenario explaining the phylogenetic structure of Scutiger. This hypothesis aligns with the fossil record but conflicts with geoscientific concepts of high elevated Tibetan Plateau since the late Paleogene. Considering a Late-Miocene/Pliocene divergence time, an alternative scenario of dispersal from SE Asia into the East, Central, and West Himalaya cannot be excluded, although essential evolutionary and biogeographic aspects remain unresolved within this model.", "doi": "10.1016/j.ympev.2024.108166", "pmid": "39127262", "labels": {"Tobias Andermann": null, "DDLS Fellow": null}, "xrefs": [{"db": "pii", "key": "S1055-7903(24)00158-1"}], "notes": [], "created": "2025-03-18T16:05:23.392Z", "modified": "2025-04-07T06:59:26.098Z"}, {"entity": "publication", "iuid": "aad9dc6f82fa4fb6a1c5398b184fc96c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/aad9dc6f82fa4fb6a1c5398b184fc96c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/aad9dc6f82fa4fb6a1c5398b184fc96c"}}, "title": "Target sequence capture of Barnadesioideae (Compositae) demonstrates the utility of low coverage loci in phylogenomic analyses.", "authors": [{"family": "Ferreira", "given": "Paola de Lima", "initials": "PL"}, {"family": "Batista", "given": "Romina", "initials": "R"}, {"family": "Andermann", "given": "Tobias", "initials": "T"}, {"family": "Groppo", "given": "Milton", "initials": "M"}, {"family": "Bacon", "given": "Christine D", "initials": "CD"}, {"family": "Antonelli", "given": "Alexandre", "initials": "A"}], "type": "journal article", "published": "2022-04-00", "journal": {"title": "Mol. Phylogenet. Evol.", "issn": "1095-9513", "volume": "169", "pages": "107432", "issn-l": "1055-7903"}, "abstract": "Target sequence capture has emerged as a powerful method to sequence hundreds or thousands of genomic regions in a cost- and time-efficient approach. In most cases, however, targeted regions lack full sequence information for certain samples, due to taxonomic, laboratory, or stochastic factors. Loci lacking molecular data for a large number of samples are commonly excluded from downstream analyses, even though they may still contain valuable information. On the other hand, including data-poor loci may bias phylogenetic analyses. Here we use a target sequence capture dataset of an ecologically and taxonomically diverse group of spiny sunflowers (Asteraceae, or Compositae: Barnadesioideae) to test how the inclusion or exclusion of such data-poor loci affects phylogenetic inference. We investigate the sensitivity of concatenation and coalescent approaches to missing data with matrices of varying taxonomic completeness by filtering loci with different proportions of missing samples prior to data analysis. We find that missing data affect both the topology and branch support of the resulting phylogenies. The matrix containing all loci yielded the overall highest node support values, independently of the amount of missing nucleotides. These results provide empirical support to earlier suggestions based on single genes and data simulations that taxa with high amounts of missing data should not be readily dismissed as they can provide essential information for phylogenomic reconstruction.", "doi": "10.1016/j.ympev.2022.107432", "pmid": "35131421", "labels": {"Tobias Andermann": null, "DDLS Fellow": null}, "xrefs": [{"db": "pii", "key": "S1055-7903(22)00045-8"}], "notes": [], "created": "2022-11-11T09:10:44.671Z", "modified": "2022-11-11T09:10:44.701Z"}, {"entity": "publication", "iuid": "9ea60a3f14d349e7a8846c74154e29b8", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9ea60a3f14d349e7a8846c74154e29b8.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9ea60a3f14d349e7a8846c74154e29b8"}}, "title": "Predatory colponemids are the sister group to all other alveolates.", "authors": [{"family": "Tikhonenkov", "given": "Denis V", "initials": "DV"}, {"family": "Strassert", "given": "J\u00fcrgen F H", "initials": "JFH"}, {"family": "Janou\u0161kovec", "given": "Jan", "initials": "J"}, {"family": "Mylnikov", "given": "Alexander P", "initials": "AP"}, {"family": "Aleoshin", "given": "Vladimir V", "initials": "VV"}, {"family": "Burki", "given": "Fabien", "initials": "F"}, {"family": "Keeling", "given": "Patrick J", "initials": "PJ"}], "type": "journal article", "published": "2020-08-00", "journal": {"title": "Mol. Phylogenet. Evol.", "issn": "1095-9513", "issn-l": "1055-7903", "volume": "149", "issue": null, "pages": "106839"}, "abstract": "Alveolates are a major supergroup of eukaryotes encompassing more than ten thousand free-living and parasitic species, including medically, ecologically, and economically important apicomplexans, dinoflagellates, and ciliates. These three groups are among the most widespread eukaryotes on Earth, and their environmental success can be linked to unique innovations that emerged early in each group. Understanding the emergence of these well-studied and diverse groups and their innovations has relied heavily on the discovery and characterization of early-branching relatives, which allow ancestral states to be inferred with much greater confidence. Here we report the phylogenomic analyses of 313 eukaryote protein-coding genes from transcriptomes of three members of one such group, the colponemids (Colponemidia), which support their monophyly and position as the sister lineage to all other known alveolates. Colponemid-related sequences from environmental surveys and our microscopical observations show that colponemids are not common in nature, but they are diverse and widespread in freshwater habitats around the world. Studied colponemids possess two types of extrusive organelles (trichocysts or toxicysts) for active hunting of other unicellular eukaryotes and potentially play an important role in microbial food webs. Colponemids have generally plesiomorphic morphology and illustrate the ancestral state of Alveolata. We further discuss their importance in understanding the evolution of alveolates and the origin of myzocytosis and plastids.", "doi": "10.1016/j.ympev.2020.106839", "pmid": "32325195", "labels": {"Fabien Burki": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "S1055-7903(20)30111-1"}], "notes": [], "created": "2020-11-30T10:27:32.121Z", "modified": "2022-11-04T11:32:14.585Z"}, {"entity": "publication", "iuid": "7183af161c214228ad43cf08b7162aaa", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/7183af161c214228ad43cf08b7162aaa.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/7183af161c214228ad43cf08b7162aaa"}}, "title": "Phylogenomics supports the monophyly of the Cercozoa.", "authors": [{"family": "Irwin", "given": "Nicholas A T", "initials": "NAT"}, {"family": "Tikhonenkov", "given": "Denis V", "initials": "DV"}, {"family": "Hehenberger", "given": "Elisabeth", "initials": "E", "orcid": "0000-0002-2904-8214", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0528b2aef96b4c52a3a4c4fa0f2be43c.json"}}, {"family": "Mylnikov", "given": "Alexander P", "initials": "AP"}, {"family": "Burki", "given": "Fabien", "initials": "F"}, {"family": "Keeling", "given": "Patrick J", "initials": "PJ"}], "type": "journal article", "published": "2019-01-00", "journal": {"title": "Mol. Phylogenet. Evol.", "issn": "1095-9513", "issn-l": "1055-7903", "volume": "130", "issue": null, "pages": "416-423"}, "abstract": "The phylum Cercozoa consists of a diverse assemblage of amoeboid and flagellated protists that forms a major component of the supergroup, Rhizaria. However, despite its size and ubiquity, the phylogeny of the Cercozoa remains unclear as morphological variability between cercozoan species and ambiguity in molecular analyses, including phylogenomic approaches, have produced ambiguous results and raised doubts about the monophyly of the group. Here we sought to resolve these ambiguities using a 161-gene phylogenetic dataset with data from newly available genomes and deeply sequenced transcriptomes, including three new transcriptomes from Aurigamonas solis, Abollifer prolabens, and a novel species, Lapot gusevi n. gen. n. sp. Our phylogenomic analysis strongly supported a monophyletic Cercozoa, and approximately-unbiased tests rejected the paraphyletic topologies observed in previous studies. The transcriptome of L. gusevi represents the first transcriptomic data from the large and recently characterized Aquavolonidae-Treumulida-'Novel Clade 12' group, and phylogenomics supported its position as sister to the cercozoan subphylum, Endomyxa. These results provide insights into the phylogeny of the Cercozoa and the Rhizaria as a whole.", "doi": "10.1016/j.ympev.2018.09.004", "pmid": "30318266", "labels": {"Fabien Burki": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "S1055-7903(18)30474-3"}], "notes": [], "created": "2020-09-28T12:01:40.857Z", "modified": "2022-11-04T11:32:16.944Z"}, {"entity": "publication", "iuid": "fd6e264aa72d471989a7c509b0691361", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/fd6e264aa72d471989a7c509b0691361.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/fd6e264aa72d471989a7c509b0691361"}}, "title": "RAD-seq data point to a northern origin of the arctic-alpine genus Cassiope (Ericaceae).", "authors": [{"family": "Hou", "given": "Yan", "initials": "Y"}, {"family": "Nowak", "given": "Michael D", "initials": "MD"}, {"family": "Mirr\u00e9", "given": "Virginia", "initials": "V"}, {"family": "Bjor\u00e5", "given": "Charlotte Sletten", "initials": "CS"}, {"family": "Brochmann", "given": "Christian", "initials": "C"}, {"family": "Popp", "given": "Magnus", "initials": "M"}], "type": "journal article", "published": "2016-02-00", "journal": {"volume": "95", "issn": "1095-9513", "issue": null, "pages": "152-160", "title": "Mol. Phylogenet. Evol.", "issn-l": "1055-7903"}, "abstract": "Many arctic-alpine plants display a highly disjunct distribution between the Arctic/Boreal regions and the southern Asian mountains. Two main hypotheses have been proposed to explain the origin of this biogeographic pattern: (1) south-to-north migration in the late Pliocene/early Pleistocene, and (2) north-to-south migration during the Miocene. The genus Cassiope is disjunctly distributed between the Arctic/Boreal regions and the Himalayan-Hengduan Mountains (HHM) and was selected to test these hypotheses. We constructed a fossil-calibrated phylogeny of Ericaceae using two plastid regions to estimate the crown group age of Cassiope, and used sequence data from thousands of loci produced by restriction site associated DNA sequencing (RAD-seq) to reconstruct the phylogeny of Cassiope. We also performed Bayesian divergence time analysis and biogeographic analysis. The Cassiope crown group was estimated to have originated in the Miocene, which predates the onset of Northern hemisphere glaciation. All HHM species formed a clade together with one eastern Siberian species, and this clade was sister to all other Arctic/Boreal species. This topology implies a northern origin of Cassiope, which is confirmed by our biogeographic analysis. Our results thus suggest that the ancient north-to-south migration hypothesis is most consistent with the origin of Cassiope. ", "doi": "10.1016/j.ympev.2015.11.009", "pmid": "26691641", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pii", "key": "S1055-7903(15)00362-0"}], "notes": [], "created": "2018-12-05T12:36:17.567Z", "modified": "2018-12-05T15:16:43.455Z"}, {"entity": "publication", "iuid": "f7fa1d1c4f64479d8aa4daa1cf6ae391", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f7fa1d1c4f64479d8aa4daa1cf6ae391.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f7fa1d1c4f64479d8aa4daa1cf6ae391"}}, "title": "Tracing the evolution of FERM domain of Kindlins.", "authors": [{"family": "Ali", "given": "Raja Hashim", "initials": "RH"}, {"family": "Khan", "given": "Ammad Aslam", "initials": "AA"}], "type": "journal article", "published": "2014-11-00", "journal": {"title": "Mol. Phylogenet. Evol.", "issn": "1095-9513", "volume": "80", "issue": null, "pages": "193-204", "issn-l": "1055-7903"}, "abstract": "Kindlin proteins represent a novel family of evolutionarily conserved FERM domain containing proteins (FDCPs) and are members of B4.1 superfamily. Kindlins consist of three conserved protein homologs in vertebrates: Kindlin-1, Kindlin-2 and Kindlin-3. All three homologs are associated with focal adhesions and are involved in Integrin activation. FERM domain of each Kindlin is bipartite and plays a key role in Integrin activation. A single ancestral Kindlin protein can be traced back to earliest metazoans, e.g., to Parazoa. This protein underwent multiple rounds of duplication in vertebrates, leading to the present Kindlin family. In this study, we trace phylogenetic and evolutionary history of Kindlin FERM domain with respect to FERM domain of other FDCPs. We show that FERM domain in Kindlin homologs is conserved among Kindlins but amount of conservation is less in comparison with FERM domain of other members in B4.1 superfamily. Furthermore, insertion of Pleckstrin Homology like domain in Kindlin FERM domain has important evolutionary and functional consequences. Important residues in Kindlins are traced and ranked according to their evolutionary significance. The structural and functional significance of high ranked residues is highlighted and validated by their known involvement in Kindlin associated diseases. In light of these findings, we hypothesize that FERM domain originated from a proto-Talin protein in unicellular or proto-multicellular organism and advent of multi-cellularity was accompanied by burst of FDCPs, which supported multi-cellularity functions required for complex organisms. This study helps in developing a better understanding of evolutionary history of FERM domain of FDCPs and the role of FERM domain in metazoan evolution. ", "doi": "10.1016/j.ympev.2014.08.008", "pmid": "25150025", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pii", "key": "S1055-7903(14)00275-9"}], "notes": [], "created": "2018-12-05T11:02:02.067Z", "modified": "2018-12-05T11:02:02.099Z"}], "created": "2018-12-05T11:02:02.081Z", "modified": "2020-11-27T13:12:52.400Z"}