{"entity": "researcher", "timestamp": "2026-08-13T18:05:46.946Z", "family": "Sicheritz-Ponten", "given": "Thomas", "initials": "T", "orcid": "0000-0001-6615-1141", "affiliations": ["Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark"], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/0da5029f417945a790fbb57b5120dceb.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/0da5029f417945a790fbb57b5120dceb"}}, "publications": [{"entity": "publication", "iuid": "7013590bb16742499cb4ab2faf44231d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7013590bb16742499cb4ab2faf44231d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7013590bb16742499cb4ab2faf44231d"}}, "title": "Evolutionary history of the extinct Sardinian dhole", "authors": [{"family": "Ciucani", "given": "Marta Maria", "initials": "MM"}, {"family": "Jensen", "given": "Julie Kragmose", "initials": "JK", "orcid": "0000-0002-7882-0450", "researcher": {"href": "https://publications.scilifelab.se/researcher/aefb3d21ea1f433284b5cac0ce2deca0.json"}}, {"family": "Sinding", "given": "Mikkel Holger S", "initials": "MHS", "orcid": "0000-0003-1371-219X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c37b07e1cb9643279b8801c45dde9dbe.json"}}, {"family": "Smith", "given": "Oliver", "initials": "O", "orcid": "0000-0002-0146-9244", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ebee38f7617407897c80da437018a2f.json"}}, {"family": "Lucenti", "given": "Saverio Bartolini", "initials": "SB", "orcid": "0000-0003-1280-5378", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f6d5f7a65184e2d97c6e0ebf571c02d.json"}}, {"family": "Rosengren", "given": "Erika", "initials": "E", "orcid": "0000-0002-9658-2134", "researcher": {"href": "https://publications.scilifelab.se/researcher/0bea6444beec43f4a24bf1b8d04202aa.json"}}, {"family": "Rook", "given": "Lorenzo", "initials": "L"}, {"family": "Tuveri", "given": "Caterinella", "initials": "C"}, {"family": "Arca", "given": "Marisa", "initials": "M"}, {"family": "Cappellini", "given": "Enrico", "initials": "E"}, {"family": "Galaverni", "given": "Marco", "initials": "M"}, {"family": "Randi", "given": "Ettore", "initials": "E"}, {"family": "Guo", "given": "Chunxue", "initials": "C"}, {"family": "Zhang", "given": "Guojie", "initials": "G"}, {"family": "Sicheritz-Pont\u00e9n", "given": "Thomas", "initials": "T", "orcid": "0000-0001-6615-1141", "researcher": {"href": "https://publications.scilifelab.se/researcher/0da5029f417945a790fbb57b5120dceb.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Gilbert", "given": "M Thomas P", "initials": "MTP", "orcid": "0000-0002-5805-7195", "researcher": {"href": "https://publications.scilifelab.se/researcher/873e2383b99a43d7848bf387264cf0e8.json"}}, {"family": "Gopalakrishnan", "given": "Shyam", "initials": "S", "orcid": "0000-0002-2004-6810", "researcher": {"href": "https://publications.scilifelab.se/researcher/637bc46cf8094999aad02a3d646e82fd.json"}}], "type": "journal-article", "published": "2021-12-00", "journal": {"title": "Current Biology", "issn": "0960-9822", "volume": "31", "issue": "24", "pages": "5571-5579.e6", "issn-l": "0960-9822"}, "abstract": "The Sardinian dhole (Cynotherium sardous)1 was an iconic and unique canid species that was endemic to Sardinia and Corsica until it became extinct at the end of the Late Pleistocene.2-5 Given its peculiar dental morphology, small body size, and high level of endemism, several extant canids have been proposed as possible relatives of the Sardinian dhole, including the Asian dhole and African hunting dog ancestor.3,6-9 Morphometric analyses3,6,8-12 have failed to clarify the evolutionary relationship with other canids.We sequenced the genome of a ca-21,100-year-old Sardinian dhole in order to understand its genomic history and clarify its phylogenetic position. We found that it represents a separate taxon from all other living canids from Eurasia, Africa, and North America, and that the Sardinian dhole lineage diverged from the Asian dhole ca 885 ka. We additionally detected historical gene flow between the Sardinian and Asian dhole lineages, which ended approximately 500-300 ka, when the land bridge between Sardinia and mainland Italy was already broken, severing their population connectivity. Our sample showed low genome-wide diversity compared to other extant canids-probably a result of the long-term isolation-that could have contributed to the subsequent extinction of the Sardinian dhole.", "doi": "10.1016/j.cub.2021.09.059", "pmid": "34655517", "labels": {"NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "S0960-9822(21)01315-4"}], "notes": [], "created": "2021-12-06T13:49:17.223Z", "modified": "2023-06-19T11:38:27.891Z"}, {"entity": "publication", "iuid": "0cd1833de8764e41812f14260f5961b5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0cd1833de8764e41812f14260f5961b5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0cd1833de8764e41812f14260f5961b5"}}, "title": "Dense sampling of bird diversity increases power of comparative genomics.", "authors": [{"family": "Feng", "given": "Shaohong", 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"researcher": {"href": "https://publications.scilifelab.se/researcher/8c77b745d8b044d4aed9478d056be226.json"}}, {"family": "Haussler", "given": "David", "initials": "D", "orcid": "0000-0003-1533-4575", "researcher": {"href": "https://publications.scilifelab.se/researcher/de140026a4f24291be768e713e4881bb.json"}}, {"family": "Li", "given": "Qiye", "initials": "Q", "orcid": "0000-0002-5993-0312", "researcher": {"href": "https://publications.scilifelab.se/researcher/d807a3a13669425c9b00e4a2b7db672a.json"}}, {"family": "Yang", "given": "Huanming", "initials": "H"}, {"family": "Wang", "given": "Jian", "initials": "J"}, {"family": "Lei", "given": "Fumin", "initials": "F"}, {"family": "Rahbek", "given": "Carsten", "initials": "C"}, {"family": "Gilbert", "given": "M Thomas P", "initials": "MTP", "orcid": "0000-0002-5805-7195", "researcher": {"href": "https://publications.scilifelab.se/researcher/873e2383b99a43d7848bf387264cf0e8.json"}}, {"family": "Graves", "given": "Gary R", "initials": "GR", "orcid": "0000-0003-1406-5246", "researcher": {"href": "https://publications.scilifelab.se/researcher/bc3b9edee185456d971f5b596c3086fe.json"}}, {"family": "Jarvis", "given": "Erich D", "initials": "ED", "orcid": "0000-0001-8931-5049", "researcher": {"href": "https://publications.scilifelab.se/researcher/d565d5e1788e484d9d2da61af12f2120.json"}}, {"family": "Paten", "given": "Benedict", "initials": "B", "orcid": "0000-0001-8863-3539", "researcher": {"href": "https://publications.scilifelab.se/researcher/956ebe9c0b6e43d7ac2a568519f43431.json"}}, {"family": "Zhang", "given": "Guojie", "initials": "G", "orcid": "0000-0001-6860-1521", "researcher": {"href": "https://publications.scilifelab.se/researcher/62f3c7981a1c43909817e72519232ff8.json"}}], "type": "journal article", "published": "2020-11-00", "journal": {"title": "Nature", "issn": "1476-4687", "volume": "587", "issue": "7833", "pages": "252-257", "issn-l": "0028-0836"}, "abstract": "Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1-4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species.", "doi": "10.1038/s41586-020-2873-9", "pmid": "33177665", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41586-020-2873-9"}, {"db": "pmc", "key": "PMC7759463"}], "notes": [], "created": "2020-12-07T16:36:44.079Z", "modified": "2021-11-10T12:45:51.851Z"}, {"entity": "publication", "iuid": "04d609a90c47487388785c1d3bb89419", "links": {"self": {"href": "https://publications.scilifelab.se/publication/04d609a90c47487388785c1d3bb89419.json"}, "display": {"href": "https://publications.scilifelab.se/publication/04d609a90c47487388785c1d3bb89419"}}, "title": "Mitochondrial genome of the North African Sahara Honeybee, Apis mellifera sahariensis (Hymenoptera: Apidae).", "authors": [{"family": "Haddad", "given": "Nizar", "initials": "N", "orcid": "0000-0003-0250-5291", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ff610b5673c4050a4e4377c48b2a372.json"}}, {"family": "Adjlane", "given": "Noureddine", "initials": "N"}, {"family": "Loucif-Ayad", "given": "Wahida", "initials": "W"}, {"family": "Dash", "given": "Abhinandita", "initials": "A"}, {"family": "S", "given": "Naganeeswaran", "initials": "N"}, {"family": "Rajashekar", "given": "Balaji", "initials": "B"}, {"family": "Al-Nakeeb", "given": "Kosai", "initials": "K", "orcid": "0000-0003-3432-3628", "researcher": {"href": "https://publications.scilifelab.se/researcher/91d87f93200b4f0ba3480a0f975e9cd9.json"}}, {"family": "Sicheritz-Ponten", "given": "Thomas", "initials": "T", "orcid": "0000-0001-6615-1141", "researcher": {"href": "https://publications.scilifelab.se/researcher/0da5029f417945a790fbb57b5120dceb.json"}}], "type": "journal article", "published": "2017-08-22", "journal": {"volume": "2", "issn": "2380-2359", "issue": "2", "pages": "548-549", "title": "Mitochondrial DNA Part B", "issn-l": "2380-2359"}, "abstract": "We present the complete mitochondrial genome of honey bee subspecies, Apis mellifera sahariensis (Apidae) belonging to the African lineage. The assembled circular genome has a length of 16,569 bp which comprises 13 protein coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and AT rich region.", "doi": "10.1080/23802359.2017.1365647", "pmid": "33473895", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "1365647"}, {"db": "pmc", "key": "PMC7800622"}], "notes": [], "created": "2017-11-03T15:53:39.359Z", "modified": "2021-06-21T15:45:29.250Z"}, {"entity": "publication", "iuid": "7c8cc7a768524b84be600507b658f4b9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7c8cc7a768524b84be600507b658f4b9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7c8cc7a768524b84be600507b658f4b9"}}, "title": "The wolf reference genome sequence (Canis lupus lupus) and its implications for Canis spp. population genomics.", "authors": [{"family": "Gopalakrishnan", "given": "Shyam", "initials": "S"}, {"family": "Samaniego Castruita", "given": "Jose A", "initials": "JA"}, {"family": "Sinding", "given": "Mikkel-Holger S", "initials": "MS"}, {"family": "Kuderna", "given": "Lukas F K", "initials": "LFK"}, {"family": "R\u00e4ikk\u00f6nen", "given": "Jannikke", "initials": "J"}, {"family": "Petersen", "given": "Bent", "initials": "B"}, {"family": "Sicheritz-Ponten", "given": "Thomas", "initials": "T", "orcid": "0000-0001-6615-1141", "researcher": {"href": "https://publications.scilifelab.se/researcher/0da5029f417945a790fbb57b5120dceb.json"}}, {"family": "Larson", "given": "Greger", "initials": "G"}, {"family": "Orlando", "given": "Ludovic", "initials": "L"}, {"family": "Marques-Bonet", "given": "Tomas", "initials": "T"}, {"family": "Hansen", "given": "Anders J", "initials": "AJ"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Gilbert", "given": "M Thomas P", "initials": "MTP"}], "type": "journal article", "published": "2017-06-29", "journal": {"volume": "18", "issn": "1471-2164", "issue": "1", "pages": "495", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "An increasing number of studies are addressing the evolutionary genomics of dog domestication, principally through resequencing dog, wolf and related canid genomes. There is, however, only one de novo assembled canid genome currently available against which to map such data - that of a boxer dog (Canis lupus familiaris). We generated the first de novo wolf genome (Canis lupus lupus) as an additional choice of reference, and explored what implications may arise when previously published dog and wolf resequencing data are remapped to this reference.\n\nReassuringly, we find that regardless of the reference genome choice, most evolutionary genomic analyses yield qualitatively similar results, including those exploring the structure between the wolves and dogs using admixture and principal component analysis. However, we do observe differences in the genomic coverage of re-mapped samples, the number of variants discovered, and heterozygosity estimates of the samples.\n\nIn conclusion, the choice of reference is dictated by the aims of the study being undertaken; if the study focuses on the differences between the different dog breeds or the fine structure among dogs, then using the boxer reference genome is appropriate, but if the aim of the study is to look at the variation within wolves and their relationships to dogs, then there are clear benefits to using the de novo assembled wolf reference genome.", "doi": "10.1186/s12864-017-3883-3", "pmid": "28662691", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-017-3883-3"}, {"db": "pmc", "key": "PMC5492679"}], "notes": [], "created": "2017-11-03T16:21:39.181Z", "modified": "2021-07-07T20:31:10.838Z"}, {"entity": "publication", "iuid": "d76c5dadcc0f4b3a8c4a2839d6667beb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d76c5dadcc0f4b3a8c4a2839d6667beb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d76c5dadcc0f4b3a8c4a2839d6667beb"}}, "title": "Complete mitochondrial genome of the Oriental Hornet, Vespa orientalis F. (Hymenoptera: Vespidae).", "authors": [{"family": "Haddad", "given": "Nizar Jamal", "initials": "NJ", "orcid": "0000-0003-0250-5291", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ff610b5673c4050a4e4377c48b2a372.json"}}, {"family": "Al-Nakeeb", "given": "Kosai", "initials": "K", "orcid": "0000-0003-3432-3628", "researcher": {"href": "https://publications.scilifelab.se/researcher/91d87f93200b4f0ba3480a0f975e9cd9.json"}}, {"family": "Petersen", "given": "Bent", "initials": "B", "orcid": "0000-0002-2472-8317", "researcher": {"href": "https://publications.scilifelab.se/researcher/62045d9b6dc443be936d3346daa4e1b1.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Blom", "given": "Nikolaj", "initials": "N", "orcid": "0000-0001-8012-6380", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd245cd9d02443f4814e6fb1e949265d.json"}}, {"family": "Sicheritz-Pont\u00e9n", "given": "Thomas", "initials": "T", "orcid": "0000-0001-6615-1141", "researcher": {"href": "https://publications.scilifelab.se/researcher/0da5029f417945a790fbb57b5120dceb.json"}}], "type": "journal article", "published": "2017-03-01", "journal": {"volume": "2", "issn": "2380-2359", "issue": "1", "pages": "139-140", "title": "Mitochondrial DNA Part B", "issn-l": "2380-2359"}, "abstract": "The Oriental Hornet ( Vespa orientalis) is a social insect belonging to the Vespiade family (Wasps, Hornets, Yellowjackets), genus Vespa (true Hornets). The oriental hornet is a scavenger and an agricultural pest, especially to bee farmers, but is also recently described as a harvester of solar energy. Here, we report the mitochondrial genome sequence of the Oriental Hornet, Vespa orientalis F., which may play a vital role in understanding this wasp biology, light trapping and generation of electricity. The mitochondrial genome of this hornet is 16,099 bp in length, containing 13 protein-coding genes, 21 transfer RNA genes, and 2 ribosomal RNA genes. The overall base composition of the heavy-strand is 40.3% A, 5.9% C, 13.2% G, and 40.6% T, the percentages of A and T being higher than that of G and C. The mitochondrial genome of the Oriental Hornet, Vespa orientalis F. represents the first mitogenome of a solar energy harvesting insect.", "doi": "10.1080/23802359.2017.1292480", "pmid": "33473744", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "1292480"}, {"db": "pmc", "key": "PMC7800523"}], "notes": [], "created": "2017-11-03T15:53:38.192Z", "modified": "2021-06-21T15:47:32.461Z"}]}