{"entity": "researcher", "timestamp": "2026-06-09T02:42:29.009Z", "family": "M\u00fcller", "given": "Ingo A", "initials": "IA", "orcid": "0000-0002-8812-9313", "affiliations": ["Department of Zoology, Division of Systematics and Evolution, Stockholm University, Stockholm, Sweden.", "Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.", "Leibniz Institut f\u00fcr Evolutions- und Biodiversit\u00e4tsforschung, Museum f\u00fcr Naturkunde, Berlin, Germany."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/5a64e79dc2214694b6fe09447161d115.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/5a64e79dc2214694b6fe09447161d115"}}, "publications": [{"entity": "publication", "iuid": "f48f131387f44524b2e0db88864b0c45", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f48f131387f44524b2e0db88864b0c45.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f48f131387f44524b2e0db88864b0c45"}}, "title": "Using Historic and Contemporary Genomes to Assess the Genetic Consequences of a Population Decline in an Endangered Tern Population.", "authors": [{"family": "Schnelle", "given": "Anna", "initials": "A", "orcid": "0000-0002-5403-8421", "researcher": {"href": "https://publications.scilifelab.se/researcher/a7a663ebd957425293ede7c37c1a2a34.json"}}, {"family": "Rollins", "given": "Robert E", "initials": "RE", "orcid": "0000-0002-5779-7001", "researcher": {"href": "https://publications.scilifelab.se/researcher/ceba437696254c37b039fa4631200a74.json"}}, {"family": "M\u00fcller", "given": "Ingo A", "initials": "IA", "orcid": "0000-0002-8812-9313", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a64e79dc2214694b6fe09447161d115.json"}}, {"family": "Irestedt", "given": "Martin", "initials": "M", "orcid": "0000-0003-1680-6861", "researcher": {"href": "https://publications.scilifelab.se/researcher/f390f09c31994a01a88d8e0d82c01ce6.json"}}, {"family": "Cecere", "given": "Jacopo G", "initials": "JG"}, {"family": "Serra", "given": "Lorenzo", "initials": "L", "orcid": "0000-0002-8911-8050", "researcher": {"href": "https://publications.scilifelab.se/researcher/de52abed5b814b7c82d985c448cafa7e.json"}}, {"family": "Guti\u00e9rrez", "given": "Jorge S", "initials": "JS"}, {"family": "Masero", "given": "Jose A", "initials": "JA"}, {"family": "Risch", "given": "Markus", "initials": "M"}, {"family": "Bouwhuis", "given": "Sandra", "initials": "S", "orcid": "0000-0003-4023-1578", "researcher": {"href": "https://publications.scilifelab.se/researcher/01f1fb8d7e1e4b0a94aac306ba67006a.json"}}, {"family": "Liedvogel", "given": "Miriam", "initials": "M"}], "type": "journal article", "published": "2026-01-00", "journal": {"title": "Evol Appl", "issn": "1752-4571", "volume": "19", "issue": "1", "pages": "e70192", "issn-l": "1752-4571"}, "abstract": "Many migratory species have experienced severe population declines, but the genetic consequences of such declines are still rarely assessed. The last Central European population of gull-billed terns (Gelochelidon nilotica) has declined from 500 breeding pairs in the 1940s to 52 in 2025, whereas Mediterranean populations of this migratory waterbird still thrive. Here, we compare whole-genome sequencing (WGS) data among the declining population, two thriving populations and the ancestors of the declining population. We find comparable nucleotide diversity, but lower observed heterozygosity in the Central European population compared to the Mediterranean populations. The contemporary samples show some population structure as well, although admixture analyses and low genetic differentiation (F ST) still suggest potential population connectivity. Museum specimens from the historic population reveal an increased level of genetic diversity compared to the contemporary population, with effective population size estimates suggesting two past population declines. While inbreeding coefficients (F ROH) in the current Central European population are significantly higher than in the historic population, they are similar to those in the Mediterranean populations. These results suggest that population structure may be emerging, and that although inbreeding is not yet at worrisome levels in the last Central European population of gull-billed terns, it may be on the rise. If this endangered population remains small and isolation manifests, the effects of inbreeding depression may become more pronounced over time, potentially reducing fitness and increasing the risk of extinction.", "doi": "10.1111/eva.70192", "pmid": "41488439", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12759046"}, {"db": "pii", "key": "EVA70192"}], "notes": [], "created": "2026-01-07T10:52:49.278Z", "modified": "2026-01-07T10:52:49.806Z"}, {"entity": "publication", "iuid": "0577c5369a1d4893bc7f6fb121420f6f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0577c5369a1d4893bc7f6fb121420f6f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0577c5369a1d4893bc7f6fb121420f6f"}}, "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.scilifelab.se/researcher/5a64e79dc2214694b6fe09447161d115.json"}}, {"family": "Th\u00f6rn", "given": "Filip", "initials": "F", "orcid": "0000-0002-8173-7877", "researcher": {"href": "https://publications.scilifelab.se/researcher/e272339ca04d4daf935b708b04c5c53e.json"}}, {"family": "Rajan", "given": "Samyuktha", "initials": "S"}, {"family": "Olsen", "given": "Remi-Andr\u00e9", "initials": "R"}, {"family": "Ericson", "given": "Per G P", "initials": "PGP", "orcid": "0000-0002-4143-9998", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c2c08919d6f4ad9a54dce2481f47cbc.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.scilifelab.se/researcher/4ef542c596b64379941d3984dd73de63.json"}}, {"family": "Irestedt", "given": "Martin", "initials": "M", "orcid": "0000-0003-1680-6861", "researcher": {"href": "https://publications.scilifelab.se/researcher/f390f09c31994a01a88d8e0d82c01ce6.json"}}, {"family": "J\u00f8nsson", "given": "Knud A", "initials": "KA", "orcid": "0000-0002-1875-9504", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca007307f40c49d2baa3420c3fc61d02.json"}}], "type": "journal article", "published": "2025-11-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "issn-l": "0962-1083", "volume": "34", "issue": "21", "pages": "e17760"}, "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": {"Bioinformatics (NBIS)": "Service", "Bioinformatics Long-term Support WABI": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "NGI Other": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12573753"}], "notes": [], "created": "2025-11-19T08:27:00.806Z", "modified": "2025-11-19T09:18:52.732Z"}, {"entity": "publication", "iuid": "fdfce138b5554e72a4f6cf82097b08e2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fdfce138b5554e72a4f6cf82097b08e2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fdfce138b5554e72a4f6cf82097b08e2"}}, "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.scilifelab.se/researcher/f390f09c31994a01a88d8e0d82c01ce6.json"}}, {"family": "M\u00fcller", "given": "Ingo A", "initials": "IA", "orcid": "0000-0002-8812-9313", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a64e79dc2214694b6fe09447161d115.json"}}, {"family": "Th\u00f6rn", "given": "Filip", "initials": "F", "orcid": "0000-0002-8173-7877", "researcher": {"href": "https://publications.scilifelab.se/researcher/e272339ca04d4daf935b708b04c5c53e.json"}}, {"family": "Joseph", "given": "Leo", "initials": "L", "orcid": "0000-0001-7564-1978", "researcher": {"href": "https://publications.scilifelab.se/researcher/e5a0b6c400914ba9aaca4a51587d1893.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.scilifelab.se/researcher/ca007307f40c49d2baa3420c3fc61d02.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": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12573736"}], "notes": [], "created": "2025-11-19T08:33:24.398Z", "modified": "2025-11-19T08:33:24.490Z"}, {"entity": "publication", "iuid": "dbbacfc5e2734fc19c98ec14dd081705", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dbbacfc5e2734fc19c98ec14dd081705.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dbbacfc5e2734fc19c98ec14dd081705"}}, "title": "Frequent Hybridisation Between Parapatric Lekking Bird-of-Paradise Species.", "authors": [{"family": "Th\u00f6rn", "given": "Filip", "initials": "F", "orcid": "0000-0002-8173-7877", "researcher": {"href": "https://publications.scilifelab.se/researcher/e272339ca04d4daf935b708b04c5c53e.json"}}, {"family": "M\u00fcller", "given": "Ingo A", "initials": "IA", "orcid": "0000-0002-8812-9313", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a64e79dc2214694b6fe09447161d115.json"}}, {"family": "Soares", "given": "Andr\u00e9 E R", "initials": "AER"}, {"family": "Nagombi", "given": "Elizah", "initials": "E"}, {"family": "J\u00f8nsson", "given": "Knud A", "initials": "KA", "orcid": "0000-0002-1875-9504", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca007307f40c49d2baa3420c3fc61d02.json"}}, {"family": "Blom", "given": "Mozes P K", "initials": "MPK", "orcid": "0000-0002-6304-9827", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ef542c596b64379941d3984dd73de63.json"}}, {"family": "Irestedt", "given": "Martin", "initials": "M", "orcid": "0000-0003-1680-6861", "researcher": {"href": "https://publications.scilifelab.se/researcher/f390f09c31994a01a88d8e0d82c01ce6.json"}}], "type": "journal article", "published": "2025-06-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "volume": "34", "issue": "11", "pages": "e17780", "issn-l": "0962-1083"}, "abstract": "Hybridisation is known to occur between a wide range of taxa, including species for which strong sexual selection has led to markedly different sexual phenotypes and lek-mating behaviours. To what extent occasional hybridisation can overcome the reproductive barriers in such systems and, for example, lead to the establishment of hybrid zones is poorly known. In this study, we address this question by focusing on one of the most well-known avian radiations in which sexual selection has resulted in an extraordinary assemblage of phenotypic diversity and lek-mating behaviours: the birds-of-paradise (Paradisaeidae). We quantify the genome-wide distribution of introgression and find multiple signals of recent and historical gene flow between and within two genera of birds-of-paradise, Astrapia and Paradigalla. In addition, we present the first empirical genomic indication of a putative hybrid zone between two lekking bird-of-paradise species that differ substantially in their sexually selected traits and behaviours. Our findings are consistent with the idea that behavioural and phenotypic traits may constitute weaker pre- and post-zygotic barriers to gene flow than generally thought in lek-mating species.", "doi": "10.1111/mec.17780", "pmid": "40298045", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12100584"}], "notes": [], "created": "2025-05-26T07:50:33.961Z", "modified": "2025-11-28T10:51:32.111Z"}, {"entity": "publication", "iuid": "af19706f7c38424598b494c199cfa069", "links": {"self": {"href": "https://publications.scilifelab.se/publication/af19706f7c38424598b494c199cfa069.json"}, "display": {"href": "https://publications.scilifelab.se/publication/af19706f7c38424598b494c199cfa069"}}, "title": "Species-specific dynamics may cause deviations from general biogeographical predictions - evidence from a population genomics study of a New Guinean endemic passerine bird family (Melampittidae).", "authors": [{"family": "M\u00fcller", "given": "Ingo A", "initials": "IA", "orcid": "0000-0002-8812-9313", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a64e79dc2214694b6fe09447161d115.json"}}, {"family": "Th\u00f6rn", "given": "Filip", "initials": "F", "orcid": "0000-0002-8173-7877", "researcher": {"href": "https://publications.scilifelab.se/researcher/e272339ca04d4daf935b708b04c5c53e.json"}}, {"family": "Rajan", "given": "Samyuktha", "initials": "S"}, {"family": "Ericson", "given": "Per G P", "initials": "PGP", "orcid": "0000-0002-4143-9998", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c2c08919d6f4ad9a54dce2481f47cbc.json"}}, {"family": "Dumbacher", "given": "John P", "initials": "JP", "orcid": "0000-0001-8942-1554", "researcher": {"href": "https://publications.scilifelab.se/researcher/6221be035944462989353d66f126a5c5.json"}}, {"family": "Maiah", "given": "Gibson", "initials": "G"}, {"family": "Blom", "given": "Mozes P K", "initials": "MPK"}, {"family": "J\u00f8nsson", "given": "Knud A", "initials": "KA"}, {"family": "Irestedt", "given": "Martin", "initials": "M"}], "type": "journal article", "published": "2024-05-23", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "19", "issue": "5", "pages": "e0293715", "issn-l": "1932-6203"}, "abstract": "The family Melampittidae is endemic to New Guinea and consists of two monotypic genera: Melampitta lugubris (Lesser Melampitta) and Megalampitta gigantea (Greater Melampitta). Both Melampitta species have scattered and disconnected distributions across New Guinea in the central mountain range and in some of the outlying ranges. While M. lugubris is common and found in most montane regions of the island, M. gigantaea is elusive and known from only six localities in isolated pockets on New Guinea with very specific habitats of limestone and sinkholes. In this project, we apply museomics to determine the population structure and demographic history of these two species. We re-sequenced the genomes of all seven known M. gigantaea samples housed in museum collections as well as 24 M. lugubris samples from across its distribution. By comparing population structure between the two species, we investigate to what extent habitat dependence, such as in M. gigantaea, may affect population connectivity. Phylogenetic and population genomic analyses, as well as acoustic variation revealed that M. gigantaea consists of a single population in contrast to M. lugubris that shows much stronger population structure across the island. We suggest a recent collapse of M. gigantaea into its fragmented habitats as an explanation to its unexpected low diversity and lack of population structure. The deep genetic divergences between the M. lugubris populations on the Vogelkop region, in the western central range and the eastern central range, respectively, suggests that these three populations should be elevated to full species level. This work sheds new light on the mechanisms that have shaped the intriguing distribution of the two species within this family and is a prime example of the importance of museum collections for genomic studies of poorly known and rare species.", "doi": "10.1371/journal.pone.0293715", "pmid": "38781204", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11115331"}, {"db": "pii", "key": "PONE-D-23-33496"}], "notes": [], "created": "2024-06-03T08:57:15.775Z", "modified": "2024-11-25T10:31:56.366Z"}]}