{"entity": "journal", "iuid": "8d4963aeee094be4a73a0e67f15b5021", "timestamp": "2026-06-09T03:04:10.851Z", "links": {"self": {"href": "https://publications.scilifelab.se/journal/Syst.%20Biol..json"}, "display": {"href": "https://publications.scilifelab.se/journal/Syst.%20Biol."}}, "title": "Syst. Biol.", "issn": "1076-836X", "issn-l": "1063-5157", "publications_count": 9, "publications": [{"entity": "publication", "iuid": "f92276fcc0404b76b42475aafb471f44", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f92276fcc0404b76b42475aafb471f44.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f92276fcc0404b76b42475aafb471f44"}}, "title": "A Phylogenomic Backbone for Acoelomorpha Inferred From Transcriptomic Data.", "authors": [{"family": "Abalde", "given": "Samuel", "initials": "S", "orcid": "0000-0001-7790-0603", "researcher": {"href": "https://publications.scilifelab.se/researcher/8ca4ab7834dc493daaa1eb96b5d980c2.json"}}, {"family": "Jondelius", "given": "Ulf", "initials": "U", "orcid": "0000-0003-2847-2192", "researcher": {"href": "https://publications.scilifelab.se/researcher/6582e2e560474080a7d89240a3d43edd.json"}}], "type": "journal article", "published": "2025-02-10", "journal": {"title": "Syst. Biol.", "issn": "1076-836X", "volume": "74", "issue": "1", "pages": "70-85", "issn-l": "1063-5157"}, "abstract": "Xenacoelomorpha are mostly microscopic, morphologically simple worms, lacking many structures typical of other bilaterians. Xenacoelomorphs-which include three main groups, namely Acoela, Nemertodermatida, and Xenoturbella-have been proposed to be an early diverging Bilateria, sister to protostomes and deuterostomes, but other phylogenomic analyses have recovered this clade nested within the deuterostomes, as sister to Ambulacraria. The position of Xenacoelomorpha within the metazoan tree has understandably attracted a lot of attention, overshadowing the study of phylogenetic relationships within this group. Given that Xenoturbella includes only six species whose relationships are well understood, we decided to focus on the most speciose Acoelomorpha (Acoela + Nemertodermatida). Here, we have sequenced 29 transcriptomes, doubling the number of sequenced species, to infer a backbone tree for Acoelomorpha based on genomic data. The recovered topology is mostly congruent with previous studies. The most important difference is the recovery of Paratomella as the first off-shoot within Acoela, dramatically changing the reconstruction of the ancestral acoel. Besides, we have detected incongruence between the gene trees and the species tree, likely linked to incomplete lineage sorting, and some signal of introgression between the families Dakuidae and Mecynostomidae, which hampers inferring the correct placement of this family and, particularly, of the genus Notocelis. We have also used this dataset to infer for the first time diversification times within Acoelomorpha, which coincide with known bilaterian diversification and extinction events. Given the importance of morphological data in acoelomorph phylogenetics, we tested several partitions and models. Although morphological data failed to recover a robust phylogeny, phylogenetic placement has proven to be a suitable alternative when a reference phylogeny is available.", "doi": "10.1093/sysbio/syae057", "pmid": "39451056", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11809588"}, {"db": "pii", "key": "7841810"}], "notes": [], "created": "2024-10-31T12:39:22.128Z", "modified": "2025-11-28T10:50:09.314Z"}, {"entity": "publication", "iuid": "d392ed58887449ec845d08831ec8b3c2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d392ed58887449ec845d08831ec8b3c2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d392ed58887449ec845d08831ec8b3c2"}}, "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.scilifelab.se/researcher/22b1c077dfa040d0b65494d9b944cf7d.json"}}, {"family": "Milesi", "given": "Pascal", "initials": "P"}, {"family": "Hodkov\u00e1", "given": "Eva", "initials": "E"}, {"family": "Zhou", "given": "Qiujie", "initials": "Q"}, {"family": "James", "given": "Jennifer", "initials": "J", "orcid": "0000-0003-0518-6783", "researcher": {"href": "https://publications.scilifelab.se/researcher/627b7b16c94a440b9f5ba11b6aee12fc.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.scilifelab.se/researcher/87ba3d35a88442848f22835c85fadbce.json"}}, {"family": "Saloj\u00e4rvi", "given": "Jarkko", "initials": "J"}, {"family": "Lascoux", "given": "Martin", "initials": "M", "orcid": "0000-0003-1699-9042", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ad3fadfb69448f397ad3bf55b2d2cb3.json"}}], "type": "journal article", "published": "2024-07-27", "journal": {"title": "Syst. Biol.", "issn": "1076-836X", "volume": "73", "issue": "2", "pages": "392-418", "issn-l": "1063-5157"}, "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": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11282369"}, {"db": "pii", "key": "7645150"}], "notes": [], "created": "2024-11-25T10:25:56.877Z", "modified": "2025-02-28T14:19:27.018Z"}, {"entity": "publication", "iuid": "838e0b3db3344e009deafc5bec93347c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/838e0b3db3344e009deafc5bec93347c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/838e0b3db3344e009deafc5bec93347c"}}, "title": "Introgression underlies phylogenetic uncertainty but not parallel plumage evolution in a recent songbird radiation.", "authors": [{"family": "Rancilhac", "given": "Lo\u00efs", "initials": "L", "orcid": "0000-0002-9859-1448", "researcher": {"href": "https://publications.scilifelab.se/researcher/c3a53ef0421c4c0990fbf9ef20f6bd3b.json"}}, {"family": "Enbody", "given": "Erik D", "initials": "ED"}, {"family": "Harris", "given": "Rebecca", "initials": "R"}, {"family": "Saitoh", "given": "Takema", "initials": "T"}, {"family": "Irestedt", "given": "Martin", "initials": "M"}, {"family": "Liu", "given": "Yang", "initials": "Y", "orcid": "0000-0003-4580-5518", "researcher": {"href": "https://publications.scilifelab.se/researcher/abd2de623f33467b89b1cf800db4b3f5.json"}}, {"family": "Lei", "given": "Fumin", "initials": "F"}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}, {"family": "Alstr\u00f6m", "given": "Per", "initials": "P", "orcid": "0000-0001-7182-2763", "researcher": {"href": "https://publications.scilifelab.se/researcher/f426ea7151c546939b707d5ed71e7d04.json"}}], "type": "journal article", "published": "2023-10-06", "journal": {"title": "Syst. Biol.", "issn": "1076-836X", "issn-l": "1063-5157", "volume": null, "issue": null, "pages": null}, "abstract": "Instances of parallel phenotypic evolution offer great opportunities to understand the evolutionary processes underlying phenotypic changes. However, confirming parallel phenotypic evolution and studying its causes requires a robust phylogenetic framework. One such example is the \"black-and-white wagtails\", a group of five species in the songbird genus Motacilla: one species, Motacilla alba, shows wide intra-specific plumage variation, while the four others form two pairs of very similar-looking species (M. aguimp + M. samveasnae and M. grandis + M. maderaspatensis, respectively). However, the two species in each of these pairs were not recovered as sisters in previous phylogenetic inferences. Their relationships varied depending on the markers used, suggesting that gene tree heterogeneity might have hampered accurate phylogenetic inference. Here, we use whole genome resequencing data to explore the phylogenetic relationships within this group, with a special emphasis on characterizing the extent of gene tree heterogeneity and its underlying causes. We first used multispecies coalescent methods to generate a \"complete evidence\" phylogenetic hypothesis based on genome-wide variants, while accounting for incomplete lineage sorting (ILS) and introgression. We then investigated the variation in phylogenetic signal across the genome, to quantify the extent of discordance across genomic regions, and test its underlying causes. We found that wagtail genomes are mosaics of regions supporting variable genealogies, because of ILS and inter-specific introgression. The most common topology across the genome, supporting M. alba and M. aguimp as sister species, appears to be influenced by ancient introgression. Additionally, we inferred another ancient introgression event, between M. alba and M. grandis. By combining results from multiple analyses, we propose a phylogenetic network for the black-and-white wagtails that confirms that similar phenotypes evolved in non-sister lineages, supporting parallel plumage evolution. Furthermore, the inferred reticulations do not connect species with similar plumage coloration, suggesting that introgression does not underlie parallel plumage evolution in this group. Our results demonstrate the importance of investigation of genome-wide patterns of gene tree heterogeneity to help understanding the mechanisms underlying phenotypic evolution.", "doi": "10.1093/sysbio/syad062", "pmid": "37801684", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "7294611"}], "notes": [], "created": "2023-10-19T13:54:24.722Z", "modified": "2024-01-16T13:48:32.004Z"}, {"entity": "publication", "iuid": "e8b81b926177401db8fe06fc1273b8cc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e8b81b926177401db8fe06fc1273b8cc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e8b81b926177401db8fe06fc1273b8cc"}}, "title": "Conflict over the eukaryote root resides in strong outliers, mosaics and missing data sensitivity of site-specific (CAT) mixture models.", "authors": [{"family": "Al Jewari", "given": "Caesar", "initials": "C", "orcid": "0000-0002-0868-0384", "researcher": {"href": "https://publications.scilifelab.se/researcher/350dc181d4d341fea9a9afae15453259.json"}}, {"family": "Baldauf", "given": "Sandra L", "initials": "SL", "orcid": "0000-0003-4485-6671", "researcher": {"href": "https://publications.scilifelab.se/researcher/bc40313ded12460288d0f33b9614bbec.json"}}], "type": "journal article", "published": "2022-04-12", "journal": {"title": "Syst. Biol.", "issn": "1076-836X", "issn-l": "1063-5157"}, "abstract": "Phylogenetic reconstruction using concatenated loci (\"phylogenomics\" or \"supermatrix phylogeny\") is a powerful tool for solving evolutionary splits that are poorly resolved in single gene/protein trees (SGTs). However, recent phylogenomic attempts to resolve the eukaryote root have yielded conflicting results, along with claims of various artefacts hidden in the data. We have investigated these conflicts using two new methods for assessing phylogenetic conflict. ConJak uses whole marker (gene or protein) jackknifing to assess deviation from a central mean for each individual sequence, while ConWin uses a sliding window to screen for incongruent protein fragments (mosaics). Both methods allow selective masking of individual sequences or sequence fragments in order to minimize missing data, an important consideration for resolving deep splits with limited data. Analyses focused on a set of 76 eukaryotic proteins of bacterial-ancestry previously used in various combinations to assess the branching order among the three major divisions of eukaryotes: Amorphea (mainly animals, fungi and Amoebozoa), Diaphoretickes (most other well-known eukaryotes and nearly all algae) and Excavata, represented here by Discoba (Jakobida, Heterolobosea, and Euglenozoa). ConJak analyses found strong outliers to be concentrated in under-sampled lineages, while ConWin analyses of Discoba, the most under-sampled of the major lineages, detected potentially incongruent fragments scattered throughout. Phylogenetic analyses of the full data using an LG-gamma model support a Discoba sister scenario (neozoan-excavate root), which rises to 99-100% bootstrap support with data masked according to either protocol. However, analyses with two site-specific (CAT) mixture models yielded widely inconsistent results and a striking sensitivity to missing data. The neozoan-excavate root places Amorphea and Diaphoretickes as more closely related to each other than either is to Discoba, a fundamental relationship that should remain unaffected by additional taxa.", "doi": "10.1093/sysbio/syac029", "pmid": "35412616", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "6567365"}], "notes": [], "created": "2022-11-09T15:38:24.625Z", "modified": "2024-01-16T13:48:37.059Z"}, {"entity": "publication", "iuid": "89662d49b5714d43b2d4ee811777dd15", "links": {"self": {"href": "https://publications.scilifelab.se/publication/89662d49b5714d43b2d4ee811777dd15.json"}, "display": {"href": "https://publications.scilifelab.se/publication/89662d49b5714d43b2d4ee811777dd15"}}, "title": "Parallel Evolution of Bower-Building Behavior in Two Groups of Bowerbirds Suggested by Phylogenomics.", "authors": [{"family": "Ericson", "given": "Per G P", "initials": "PGP"}, {"family": "Irestedt", "given": "Martin", "initials": "M"}, {"family": "Nylander", "given": "Johan A A", "initials": "JAA"}, {"family": "Christidis", "given": "Les", "initials": "L"}, {"family": "Joseph", "given": "Leo", "initials": "L"}, {"family": "Qu", "given": "Yanhua", "initials": "Y"}], "type": "journal article", "published": "2020-09-01", "journal": {"title": "Syst. Biol.", "issn": "1076-836X", "volume": "69", "issue": "5", "pages": "820-829", "issn-l": "1063-5157"}, "abstract": "The bowerbirds in New Guinea and Australia include species that build the largest and perhaps most elaborately decorated constructions outside of humans. The males use these courtship bowers, along with their displays, to attract females. In these species, the mating system is polygynous and the females alone incubate and feed the nestlings. The bowerbirds also include 10 species of the socially monogamous catbirds in which the male participates in most aspects of raising the young. How the bower-building behavior evolved has remained poorly understood, as no comprehensive phylogeny exists for the family. It has been assumed that the monogamous catbird clade is sister to all polygynous species. We here test this hypothesis using a newly developed pipeline for obtaining homologous alignments of thousands of exonic and intronic regions from genomic data to build a phylogeny. Our well-supported species tree shows that the polygynous, bower-building species are not monophyletic. The result suggests either that bower-building behavior is an ancestral condition in the family that was secondarily lost in the catbirds, or that it has arisen in parallel in two lineages of bowerbirds. We favor the latter hypothesis based on an ancestral character reconstruction showing that polygyny but not bower-building is ancestral in bowerbirds, and on the observation that Scenopoeetes dentirostris, the sister species to one of the bower-building clades, does not build a proper bower but constructs a court for male display. This species is also sexually monomorphic in plumage despite having a polygynous mating system. We argue that the relatively stable tropical and subtropical forest environment in combination with low predator pressure and rich food access (mostly fruit) facilitated the evolution of these unique life-history traits. [Adaptive radiation; bowerbirds; mating system, sexual selection; whole genome sequencing.].", "doi": "10.1093/sysbio/syaa040", "pmid": "32415976", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "5838197"}, {"db": "pmc", "key": "PMC7440736"}], "notes": [], "created": "2020-07-08T13:05:12.870Z", "modified": "2024-01-16T13:48:41.780Z"}, {"entity": "publication", "iuid": "0d5fa939ffd84f5eb9884fe38f94ad39", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0d5fa939ffd84f5eb9884fe38f94ad39.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0d5fa939ffd84f5eb9884fe38f94ad39"}}, "title": "SpeciesGeoCoder: Fast Categorization of Species Occurrences for Analyses of Biodiversity, Biogeography, Ecology, and Evolution.", "authors": [{"family": "T\u00f6pel", "given": "Mats", "initials": "M"}, {"family": "Zizka", "given": "Alexander", "initials": "A"}, {"family": "Cali\u00f3", "given": "Maria Fernanda", "initials": "MF"}, {"family": "Scharn", "given": "Ruud", "initials": "R"}, {"family": "Silvestro", "given": "Daniele", "initials": "D"}, {"family": "Antonelli", "given": "Alexandre", "initials": "A"}], "type": "journal article", "published": "2017-03-01", "journal": {"volume": "66", "issn": "1076-836X", "issue": "2", "pages": "145-151", "title": "Syst. Biol.", "issn-l": "1063-5157"}, "abstract": "Understanding the patterns and processes underlying the uneven distribution of biodiversity across space constitutes a major scientific challenge in systematic biology and biogeography, which largely relies on effectively mapping and making sense of rapidly increasing species occurrence data. There is thus an urgent need for making the process of coding species into spatial units faster, automated, transparent, and reproducible. Here we present SpeciesGeoCoder, an open-source software package written in Python and R, that allows for easy coding of species into user-defined operational units. These units may be of any size and be purely spatial (i.e., polygons) such as countries and states, conservation areas, biomes, islands, biodiversity hotspots, and areas of endemism, but may also include elevation ranges. This flexibility allows scoring species into complex categories, such as those encountered in topographically and ecologically heterogeneous landscapes. In addition, SpeciesGeoCoder can be used to facilitate sorting and cleaning of occurrence data obtained from online databases, and for testing the impact of incorrect identification of specimens on the spatial coding of species. The various outputs of SpeciesGeoCoder include quantitative biodiversity statistics, global and local distribution maps, and files that can be used directly in many phylogeny-based applications for ancestral range reconstruction, investigations of biome evolution, and other comparative methods. Our simulations indicate that even datasets containing hundreds of millions of records can be analyzed in relatively short time using a standard computer. We exemplify the use of SpeciesGeoCoder by inferring the historical dispersal of birds across the Isthmus of Panama, showing that lowland species crossed the Isthmus about twice as frequently as montane species with a marked increase in the number of dispersals during the last 10 million years. [ancestral area reconstruction; biodiversity patterns; ecology; evolution; point in polygon; species distribution data.].", "doi": "10.1093/sysbio/syw064", "pmid": "27486181", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "syw064"}, {"db": "pmc", "key": "PMC5410971"}, {"db": "Dryad", "key": "10.5061/dryad.tm32k"}], "notes": [], "created": "2019-01-14T19:02:47.673Z", "modified": "2021-06-21T15:56:01.806Z"}, {"entity": "publication", "iuid": "ecbaa43f8e1f4ee0accd6bafac629dce", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ecbaa43f8e1f4ee0accd6bafac629dce.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ecbaa43f8e1f4ee0accd6bafac629dce"}}, "title": "Toward a Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa.", "authors": [{"family": "Antonelli", "given": "Alexandre", "initials": "A"}, {"family": "Hettling", "given": "Hannes", "initials": "H"}, {"family": "Condamine", "given": "Fabien L", "initials": "FL"}, {"family": "Vos", "given": "Karin", "initials": "K"}, {"family": "Nilsson", "given": "R Henrik", "initials": "RH"}, {"family": "Sanderson", "given": "Michael J", "initials": "MJ"}, {"family": "Sauquet", "given": "Herv\u00e9", "initials": "H"}, {"family": "Scharn", "given": "Ruud", "initials": "R"}, {"family": "Silvestro", "given": "Daniele", "initials": "D"}, {"family": "T\u00f6pel", "given": "Mats", "initials": "M"}, {"family": "Bacon", "given": "Christine D", "initials": "CD"}, {"family": "Oxelman", "given": "Bengt", "initials": "B"}, {"family": "Vos", "given": "Rutger A", "initials": "RA"}], "type": "journal article", "published": "2017-03-01", "journal": {"volume": "66", "issn": "1076-836X", "issue": "2", "pages": "152-166", "title": "Syst. Biol.", "issn-l": "1063-5157"}, "abstract": "Rapidly growing biological data-including molecular sequences and fossils-hold an unprecedented potential to reveal how evolutionary processes generate and maintain biodiversity. However, researchers often have to develop their own idiosyncratic workflows to integrate and analyze these data for reconstructing time-calibrated phylogenies. In addition, divergence times estimated under different methods and assumptions, and based on data of various quality and reliability, should not be combined without proper correction. Here we introduce a modular framework termed SUPERSMART (Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa), and provide a proof of concept for dealing with the moving targets of evolutionary and biogeographical research. This framework assembles comprehensive data sets of molecular and fossil data for any taxa and infers dated phylogenies using robust species tree methods, also allowing for the inclusion of genomic data produced through next-generation sequencing techniques. We exemplify the application of our method by presenting phylogenetic and dating analyses for the mammal order Primates and for the plant family Arecaceae (palms). We believe that this framework will provide a valuable tool for a wide range of hypothesis-driven research questions in systematics, biogeography, and evolution. SUPERSMART will also accelerate the inference of a \"Dated Tree of Life\" where all node ages are directly comparable. [Bayesian phylogenetics; data mining; divide-and-conquer methods; GenBank; multilocus multispecies coalescent; next-generation sequencing; palms; primates; tree calibration.].", "doi": "10.1093/sysbio/syw066", "pmid": "27616324", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "syw066"}, {"db": "pmc", "key": "PMC5410925"}, {"db": "Dryad", "key": "10.5061/dryad.sk81k"}], "notes": [], "created": "2019-01-14T19:03:30.954Z", "modified": "2021-06-21T15:55:31.210Z"}, {"entity": "publication", "iuid": "2acaefa3aa994d84bb23367986a3a7d9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2acaefa3aa994d84bb23367986a3a7d9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2acaefa3aa994d84bb23367986a3a7d9"}}, "title": "Resolving Evolutionary Relationships in Closely Related Species with Whole-Genome Sequencing Data.", "authors": [{"family": "Nater", "given": "Alexander", "initials": "A"}, {"family": "Burri", "given": "Reto", "initials": "R"}, {"family": "Kawakami", "given": "Takeshi", "initials": "T"}, {"family": "Smeds", "given": "Linn\u00e9a", "initials": "L"}, {"family": "Ellegren", "given": "Hans", "initials": "H"}], "type": "journal article", "published": "2015-11-00", "journal": {"volume": "64", "issn": "1076-836X", "issue": "6", "pages": "1000-1017", "title": "Syst. Biol.", "issn-l": "1063-5157"}, "abstract": "Using genetic data to resolve the evolutionary relationships of species is of major interest in evolutionary and systematic biology. However, reconstructing the sequence of speciation events, the so-called species tree, in closely related and potentially hybridizing species is very challenging. Processes such as incomplete lineage sorting and interspecific gene flow result in local gene genealogies that differ in their topology from the species tree, and analyses of few loci with a single sequence per species are likely to produce conflicting or even misleading results. To study these phenomena on a full phylogenomic scale, we use whole-genome sequence data from 200 individuals of four black-and-white flycatcher species with so far unresolved phylogenetic relationships to infer gene tree topologies and visualize genome-wide patterns of gene tree incongruence. Using phylogenetic analysis in nonoverlapping 10-kb windows, we show that gene tree topologies are extremely diverse and change on a very small physical scale. Moreover, we find strong evidence for gene flow among flycatcher species, with distinct patterns of reduced introgression on the Z chromosome. To resolve species relationships on the background of widespread gene tree incongruence, we used four complementary coalescent-based methods for species tree reconstruction, including complex modeling approaches that incorporate post-divergence gene flow among species. This allowed us to infer the most likely species tree with high confidence. Based on this finding, we show that regions of reduced effective population size, which have been suggested as particularly useful for species tree inference, can produce positively misleading species tree topologies. Our findings disclose the pitfalls of using loci potentially under selection as phylogenetic markers and highlight the potential of modeling approaches to disentangle species relationships in systems with large effective population sizes and post-divergence gene flow.", "doi": "10.1093/sysbio/syv045", "pmid": "26187295", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "syv045"}, {"db": "pmc", "key": "PMC4604831"}], "notes": [], "created": "2017-05-02T12:58:08.693Z", "modified": "2020-01-21T13:56:01.227Z"}, {"entity": "publication", "iuid": "e0bf412e7b65470aa17c3e0bc106b686", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e0bf412e7b65470aa17c3e0bc106b686.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e0bf412e7b65470aa17c3e0bc106b686"}}, "title": "On the biogeography of Centipeda: a species-tree diffusion approach.", "authors": [{"family": "Nylinder", "given": "Stephan", "initials": "S"}, {"family": "Lemey", "given": "Philippe", "initials": "P"}, {"family": "De Bruyn", "given": "Mark", "initials": "M"}, {"family": "Suchard", "given": "Marc A", "initials": "MA"}, {"family": "Pfeil", "given": "Bernard E", "initials": "BE"}, {"family": "Walsh", "given": "Neville", "initials": "N"}, {"family": "Anderberg", "given": "Arne A", "initials": "AA"}], "type": "journal article", "published": "2014-03-00", "journal": {"volume": "63", "issn": "1076-836X", "issue": "2", "pages": "178-191", "title": "Syst. Biol.", "issn-l": "1063-5157"}, "abstract": "Reconstructing the biogeographic history of groups present in continuous arid landscapes is challenging due to the difficulties in defining discrete areas for analyses, and even more so when species largely overlap both in terms of geography and habitat preference. In this study, we use a novel approach to estimate ancestral areas for the small plant genus Centipeda. We apply continuous diffusion of geography by a relaxed random walk where each species is sampled from its extant distribution on an empirical distribution of time-calibrated species-trees. Using a distribution of previously published substitution rates of the internal transcribed spacer (ITS) for Asteraceae, we show how the evolution of Centipeda correlates with the temporal increase of aridity in the arid zone since the Pliocene. Geographic estimates of ancestral species show a consistent pattern of speciation of early lineages in the Lake Eyre region, with a division in more northerly and southerly groups since \u223c840 ka. Summarizing the geographic slices of species-trees at the time of the latest speciation event (\u223c20 ka), indicates no presence of the genus in Australia west of the combined desert belt of the Nullabor Plain, the Great Victoria Desert, the Gibson Desert, and the Great Sandy Desert, or beyond the main continental shelf of Australia. The result indicates all western occurrences of the genus to be a result of recent dispersal rather than ancient vicariance. This study contributes to our understanding of the spatiotemporal processes shaping the flora of the arid zone, and offers a significant improvement in inference of ancestral areas for any organismal group distributed where it remains difficult to describe geography in terms of discrete areas.", "doi": "10.1093/sysbio/syt102", "pmid": "24335493", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "syt102"}, {"db": "pmc", "key": "PMC3926304"}], "notes": [], "created": "2017-05-04T14:56:35.814Z", "modified": "2020-01-21T13:53:20.934Z"}], "created": "2017-05-09T09:12:22.425Z", "modified": "2020-11-27T13:14:00.900Z"}