{"entity": "researcher", "timestamp": "2026-09-23T14:46:22.060Z", "family": "Irestedt", "given": "Martin", "initials": "M", "orcid": "0000-0003-1680-6861", "affiliations": ["Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/8127e476558945a5b511757c8c22755b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/8127e476558945a5b511757c8c22755b"}}, "publications": [{"entity": "publication", "iuid": "4dc2cb7352d041dcb5f8df24457e3c18", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/4dc2cb7352d041dcb5f8df24457e3c18.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/4dc2cb7352d041dcb5f8df24457e3c18"}}, "title": "Ephemeral Speciation in a New Guinean Honeyeater Complex (Aves: Melidectes).", "authors": [{"family": "M\u00fcller", "given": "Ingo A", "initials": "IA", "orcid": "0000-0002-8812-9313", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/11e4184046d244f89bfb028be7058bac.json"}}, {"family": "Th\u00f6rn", "given": "Filip", "initials": "F", "orcid": "0000-0002-8173-7877", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3117c8710fe24703bae11e39a68744d6.json"}}, {"family": "Rajan", "given": "Samyuktha", "initials": "S"}, {"family": "Olsen", "given": "Remi-Andr\u00e9", "initials": "RA"}, {"family": "Ericson", "given": "Per G P", "initials": "PGP", "orcid": "0000-0002-4143-9998", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9c3585c6349947258d5650330b76b065.json"}}, {"family": "Peona", "given": "Valentina", "initials": "V"}, {"family": "Smith", "given": "Brian Tilston", "initials": "BT"}, {"family": "Maiah", "given": "Gibson", "initials": "G"}, {"family": "Koane", "given": "Bonny", "initials": "B"}, {"family": "Iova", "given": "Bulisa", "initials": "B"}, {"family": "Blom", "given": "Mozes P K", "initials": "MPK", "orcid": "0000-0002-6304-9827", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e9724c5da52749409138c4c647cb7f83.json"}}, {"family": "Irestedt", "given": "Martin", "initials": "M", "orcid": "0000-0003-1680-6861", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8127e476558945a5b511757c8c22755b.json"}}, {"family": "J\u00f8nsson", "given": "Knud A", "initials": "KA", "orcid": "0000-0002-1875-9504", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/03ce5c1eb142421fad86f21ef5156069.json"}}], "type": "journal article", "published": "2025-11-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "volume": "34", "issue": "21", "pages": "e17760", "issn-l": "0962-1083"}, "abstract": "Speciation is a fundamental concept in evolutionary biology, and understanding the mechanisms driving speciation remains the foremost research topic within this field. Hybridisation is often involved in speciation and can influence its rates, potentially accelerating, decelerating or even reversing the process. This study investigates the evolutionary history of the New Guinean bird genus Melidectes, consisting of six species that inhabit various montane regions at different elevations. While most Melidectes species have allopatric distributions, two species overlap in the central mountain range and hybridise. However, plumage differences and elevational adaptations are assumed to maintain the species' boundaries. Utilising specimens from natural history collections and comprehensive genomic analyses, including a de novo genome assembly, we characterise allopatric speciation patterns within the genus and highlight how future speciation could potentially be driven by climate change. Contrary to previous hypotheses, our findings suggest that in the two distributionally overlapping species, phenotypic differences do not prevent gene flow. We find limited acoustic differentiation and extensive admixture across most of their distributions. Divergence and admixture levels conform poorly to the current taxonomy and follow a geographical pattern in which the most isolated populations at the ends of the distributions are most divergent and show least admixture. However, in contrast, their mitochondrial genomes do group in accordance with species identity, namely, into two deeply divergent lineages. We propose that this system demonstrates the ephemeral nature of speciation, in which two incipient species have started mixing extensively as they came into secondary contact, resulting in nearly complete fusion into a single lineage.", "doi": "10.1111/mec.17760", "pmid": "40219608", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC12573753"}], "notes": [], "created": "2026-09-23T13:37:11.389Z", "modified": "2026-09-23T13:37:11.508Z"}, {"entity": "publication", "iuid": "c420a32c381d449ab65fde983d407fe5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c420a32c381d449ab65fde983d407fe5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c420a32c381d449ab65fde983d407fe5"}}, "title": "Reticulate and Hybrid Speciation is Promoted by Environmental Instability in an Indo-Pacific Species Complex of Whistlers (Aves: Pachycephala).", "authors": [{"family": "Irestedt", "given": "Martin", "initials": "M", "orcid": "0000-0003-1680-6861", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8127e476558945a5b511757c8c22755b.json"}}, {"family": "M\u00fcller", "given": "Ingo A", "initials": "IA", "orcid": "0000-0002-8812-9313", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/11e4184046d244f89bfb028be7058bac.json"}}, {"family": "Th\u00f6rn", "given": "Filip", "initials": "F", "orcid": "0000-0002-8173-7877", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3117c8710fe24703bae11e39a68744d6.json"}}, {"family": "Joseph", "given": "Leo", "initials": "L", "orcid": "0000-0001-7564-1978", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/41af7ce3fd7e4f19b4f9e1654bf6ff67.json"}}, {"family": "Nylander", "given": "Johan A A", "initials": "JAA"}, {"family": "Guinet", "given": "Benjamin", "initials": "B"}, {"family": "van der Valk", "given": "Tom", "initials": "T"}, {"family": "J\u00f8nsson", "given": "Knud Andreas", "initials": "KA", "orcid": "0000-0002-1875-9504", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/03ce5c1eb142421fad86f21ef5156069.json"}}], "type": "journal article", "published": "2025-11-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "volume": "34", "issue": "21", "pages": "e70018", "issn-l": "0962-1083"}, "abstract": "Genomic studies have revealed introgressive hybridisation as a common phenomenon across the tree of life, particularly among young radiations. As incipient speciation tends to be induced by vicariance events, it is assumed that introgressive hybridisation is more frequent in young radiations in which allopatrically distributed species have a high probability of coming into secondary contact. In this study, we use whole genomic data to investigate spatio-temporal introgression patterns in a songbird radiation that has colonised a highly dynamic island region in the Indo-Pacific. Some taxa within this radiation have colonised remote oceanic islands whereas others occur on landmasses and islands in the Sahul region that were periodically connected during Pleistocene periods of lower sea levels. Our results show that introgressive hybridisation has been pervasive within this young radiation, despite prominent plumage differences between taxa. Geographical proximity has been an important factor for hybridisation and we further find that species occupying islands in the environmentally unstable Sahul region exhibit particularly high signatures of introgressive hybridisation. Yet, one species appears to have been shielded from hybridisation, perhaps due to specific ecological specialisations. Finally, we identify a hybrid species on an island where two oceanic radiations meet. Our results also caution against relying solely on analyses that only detect asymmetric introgression when examining systems with complex introgression histories. Collectively, our results support a growing body of literature that suggests that reticulate speciation is more common than previously thought. This has implications for our understanding of species formation and their persistence through time.", "doi": "10.1111/mec.70018", "pmid": "40650490", "labels": {"DDLS Fellow": "", "Tom van der Valk": ""}, "xrefs": [{"db": "pmc", "key": "PMC12573736"}], "notes": [], "created": "2026-09-23T13:19:05.878Z", "modified": "2026-09-23T13:19:06.019Z"}, {"entity": "publication", "iuid": "c0ed2251f40c4a9dbafc8e4596efa6de", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c0ed2251f40c4a9dbafc8e4596efa6de.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c0ed2251f40c4a9dbafc8e4596efa6de"}}, "title": "Satellite DNA evolution in Corvoidea inferred from short and long reads.", "authors": [{"family": "Peona", "given": "Valentina", "initials": "V", "orcid": "0000-0001-5119-1837", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/12d645d316a64a54ad02fb915cf9b2d6.json"}}, {"family": "Kutschera", "given": "Verena E", "initials": "VE", "orcid": "0000-0002-8930-534X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c7185df2f7d44872960d604e9c70c551.json"}}, {"family": "Blom", "given": "Mozes P K", "initials": "MPK", "orcid": "0000-0002-6304-9827", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e9724c5da52749409138c4c647cb7f83.json"}}, {"family": "Irestedt", "given": "Martin", "initials": "M", "orcid": "0000-0003-1680-6861", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8127e476558945a5b511757c8c22755b.json"}}, {"family": "Suh", "given": "Alexander", "initials": "A", "orcid": "0000-0002-8979-9992", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e1790a31477c4376957d8c328299db1c.json"}}], "type": "journal article", "published": "2023-03-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "volume": "32", "issue": "6", "pages": "1288-1305", "issn-l": "0962-1083"}, "abstract": "Satellite DNA (satDNA) is a fast-evolving portion of eukaryotic genomes. The homogeneous and repetitive nature of such satDNA causes problems during the assembly of genomes, and therefore it is still difficult to study it in detail in nonmodel organisms as well as across broad evolutionary timescales. Here, we combined the use of short- and long-read data to explore the diversity and evolution of satDNA between individuals of the same species and between genera of birds spanning ~40 millions of years of bird evolution using birds-of-paradise (Paradisaeidae) and crow (Corvus) species. These avian species highlighted the presence of a GC-rich Corvoidea satellitome composed of 61 satellite families and provided a set of candidate satDNA monomers for being centromeric on the basis of length, abundance, homogeneity and transcription. Surprisingly, we found that the satDNA of crow species rapidly diverged between closely related species while the satDNA appeared more similar between birds-of-paradise species belonging to different genera.", "doi": "10.1111/mec.16484", "pmid": "35488497", "labels": [], "xrefs": [], "notes": [], "created": "2026-09-23T08:44:06.632Z", "modified": "2026-09-23T08:44:06.738Z"}, {"entity": "publication", "iuid": "17b1a0c94588468ead80b474d9015001", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/17b1a0c94588468ead80b474d9015001.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/17b1a0c94588468ead80b474d9015001"}}, "title": "Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird-of-paradise.", "authors": [{"family": "Peona", "given": "Valentina", "initials": "V", "orcid": "0000-0001-5119-1837", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/12d645d316a64a54ad02fb915cf9b2d6.json"}}, {"family": "Blom", "given": "Mozes P K", "initials": "MPK", "orcid": "0000-0002-6304-9827", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e9724c5da52749409138c4c647cb7f83.json"}}, {"family": "Xu", "given": "Luohao", "initials": "L", "orcid": "0000-0002-3714-8047", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dd2890c2e19c4ab7b1564d04822892c1.json"}}, {"family": "Burri", "given": "Reto", "initials": "R"}, {"family": "Sullivan", "given": "Shawn", "initials": "S"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Liachko", "given": "Ivan", "initials": "I"}, {"family": "Haryoko", "given": "Tri", "initials": "T"}, {"family": "J\u00f8nsson", "given": "Knud A", "initials": "KA"}, {"family": "Zhou", "given": "Qi", "initials": "Q", "orcid": "0000-0002-7419-2047", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d865b275e2684383b0285d959977da6a.json"}}, {"family": "Irestedt", "given": "Martin", "initials": "M", "orcid": "0000-0003-1680-6861", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8127e476558945a5b511757c8c22755b.json"}}, {"family": "Suh", "given": "Alexander", "initials": "A", "orcid": "0000-0002-8979-9992", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e1790a31477c4376957d8c328299db1c.json"}}], "type": "journal article", "published": "2021-01-00", "journal": {"title": "Mol Ecol Resour", "issn": "1755-0998", "volume": "21", "issue": "1", "pages": "263-286", "issn-l": "1755-098X"}, "abstract": "Genome assemblies are currently being produced at an impressive rate by consortia and individual laboratories. The low costs and increasing efficiency of sequencing technologies now enable assembling genomes at unprecedented quality and contiguity. However, the difficulty in assembling repeat-rich and GC-rich regions (genomic \"dark matter\") limits insights into the evolution of genome structure and regulatory networks. Here, we compare the efficiency of currently available sequencing technologies (short/linked/long reads and proximity ligation maps) and combinations thereof in assembling genomic dark matter. By adopting different de novo assembly strategies, we compare individual draft assemblies to a curated multiplatform reference assembly and identify the genomic features that cause gaps within each assembly. We show that a multiplatform assembly implementing long-read, linked-read and proximity sequencing technologies performs best at recovering transposable elements, multicopy MHC genes, GC-rich microchromosomes and the repeat-rich W chromosome. Telomere-to-telomere assemblies are not a reality yet for most organisms, but by leveraging technology choice it is now possible to minimize genome assembly gaps for downstream analysis. We provide a roadmap to tailor sequencing projects for optimized completeness of both the coding and noncoding parts of nonmodel genomes.", "doi": "10.1111/1755-0998.13252", "pmid": "32937018", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC7757076"}], "notes": [], "created": "2026-09-23T06:47:56.312Z", "modified": "2026-09-23T06:47:56.533Z"}]}