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Alström, Per, ProfessorORCID iD iconorcid.org/0000-0001-7182-2763
Publications (10 of 25) Show all publications
Oliveros, C. H., Field, D. J., Ksepka, D. T., Barker, F. K., Aleixo, A., Andersen, M. J., . . . Faircloth, B. C. (2019). Earth history and the passerine superradiation. Proceedings of the National Academy of Sciences of the United States of America, 116(16), 7916-7925
Open this publication in new window or tab >>Earth history and the passerine superradiation
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2019 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 116, no 16, p. 7916-7925Article in journal (Refereed) Published
Abstract [en]

Avian diversification has been influenced by global climate change, plate tectonic movements, and mass extinction events. However, the impact of these factors on the diversification of the hyper-diverse perching birds (passerines) is unclear because family level relationships are unresolved and the timing of splitting events among lineages is uncertain. We analyzed DNA data from 4,060 nuclear loci and 137 passerine families using concatenation and coalescent approaches to infer a comprehensive phylogenetic hypothesis that clarifies relationships among all passerine families. Then, we calibrated this phylogeny using 13 fossils to examine the effects of different events in Earth history on the timing and rate of passerine diversification. Our analyses reconcile passerine diversification with the fossil and geological records; suggest that passerines originated on the Australian landmass ∼47 Ma; and show that subsequent dispersal and diversification of passerines was affected by a number of climatological and geological events, such as Oligocene glaciation and inundation of the New Zealand landmass. Although passerine diversification rates fluctuated throughout the Cenozoic, we find no link between the rate of passerine diversification and Cenozoic global temperature, and our analyses show that the increases in passerine diversification rate we observe are disconnected from the colonization of new continents. Taken together, these results suggest more complex mechanisms than temperature change or ecological opportunity have controlled macroscale patterns of passerine speciation.

Keywords
Passeriformes, diversification, macroevolution, climate, biogeography
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-382842 (URN)10.1073/pnas.1813206116 (DOI)000464767500051 ()30936315 (PubMedID)
Funder
Swedish Research Council, 2015-04402
Available from: 2019-05-21 Created: 2019-05-21 Last updated: 2019-05-21Bibliographically approved
He, X., Wang, X., DuBay, S., Reeve, A. H., Alström, P., Ran, J., . . . Wu, Y. (2019). Elevational patterns of bird species richness on the eastern slope of Mt. Gongga, Sichuan Province, China. Avian Research, 10, Article ID 1.
Open this publication in new window or tab >>Elevational patterns of bird species richness on the eastern slope of Mt. Gongga, Sichuan Province, China
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2019 (English)In: Avian Research, ISSN 0005-2175, E-ISSN 2053-7166, Vol. 10, article id 1Article in journal (Refereed) Published
Abstract [en]

Background: In biological systems, biological diversity often displays a rapid turn-over across elevations. This defining feature has made mountains classic systems for studying the spatial variation in diversity. Because patterns of elevational diversity can vary among lineages and mountain systems it remains difficult to extrapolate findings from one montane region to another, or among lineages. In this study, we assessed patterns and drivers of avian diversity along an elevational gradient on the eastern slope of Mt. Gongga, the highest peak in the Hengduan Mountain Range in central China, and a mountain where comprehensive studies of avian diversity are still lacking.

Methods: We surveyed bird species in eight 400-m elevational bands from 1200 to 4400m a.s.l. between 2012 and 2017. To test the relationship between bird species richness and environmental factors, we examined the relative importance of seven ecological variables on breeding season distribution patterns: land area (LA), mean daily temperature (MDT), seasonal temperature range (STR), the mid-domain effect (MDE), seasonal precipitation (SP), invertebrate biomass (IB) and enhanced vegetation index (EVI). Climate data were obtained from five local meteorological stations and three temperature/relative humidity smart sensors in 2016.

Results: A total of 219 bird species were recorded in the field, of which 204 were recorded during the breeding season (April-August). Species richness curves (calculated separately for total species, large-ranged species, and small-ranged species) were all hump-shaped. Large-ranged species contributed more to the total species richness pattern than small-ranged species. EVI and IB were positively correlated with total species richness and small-ranged species richness. LA and MDT were positively correlated with small-ranged species richness, while STR and SP were negatively correlated with small-ranged species richness. MDE was positively correlated with large-ranged species richness. When we considered the combination of candidate factors using multiple regression models and model-averaging, total species richness and large-ranged species richness were correlated with STR (negative) and MDE (positive), while small-ranged species richness was correlated with STR (negative) and IB (positive).

Conclusions: Although no single key factor or suite of factors could explain patterns of diversity, we found that MDE, IB and STR play important but varying roles in shaping the elevational richness patterns of different bird species categories. Model-averaging indicates that small-ranged species appear to be mostly influenced by IB, as opposed to large-ranged species, which exhibit patterns more consistent with the MDE model. Our data also indicate that the species richness varied between seasons, offering a promising direction for future work.

Place, publisher, year, edition, pages
BMC, 2019
Keywords
Mt, Gongga, Elevational gradient, Environmental factors, Species richness, Stable microclimate
National Category
Ecology Physical Geography
Identifiers
urn:nbn:se:uu:diva-375226 (URN)10.1186/s40657-018-0140-7 (DOI)000455331100001 ()
Available from: 2019-01-29 Created: 2019-01-29 Last updated: 2019-01-29Bibliographically approved
Wei, C., Dong, L., Li, S.-H., Alström, P., Liu, Y., Xia, C., . . . Zhang, Y. (2019). From the Himalayas to a continental Island: Integrative species delimitation in the Brownish-flanked Bush Warbler Horornis fortipes complex. Molecular Phylogenetics and Evolution, 131, 219-227
Open this publication in new window or tab >>From the Himalayas to a continental Island: Integrative species delimitation in the Brownish-flanked Bush Warbler Horornis fortipes complex
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2019 (English)In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 131, p. 219-227Article in journal (Refereed) Published
Abstract [en]

As species serve as basic units of study in many fields of biology, assessments of species limits are fundamental for such studies. Here, we used a multilocus dataset and different coalescent-based methods to analyze species delimitation and phylogenetic relationships in the Brownish-flanked Bush Warbler Horornis fortipes complex, which is widespread in the Sino-Himalayan region. We also examined the vocal and morphometric divergence within this complex. Our genetic results suggested that Horornis fortipes is composed of at least three independently evolving lineages, which diverged 1.1-1.8 million years ago. However, these lineages have hardly diverged in song or morphometrics and only very slightly in plumage. Our result indicate that there are three incipient species in Horonis fortipes complex diverged in central Himalayas and Hengduan Mountains, but not between the continent and Taiwan island.

Place, publisher, year, edition, pages
ACADEMIC PRESS INC ELSEVIER SCIENCE, 2019
Keywords
Incipient species, Multispecies coalescent, Coalescent-based species delimitation, Horornis fortipes
National Category
Biological Systematics Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-376720 (URN)10.1016/j.ympev.2018.10.009 (DOI)000456387900022 ()30316948 (PubMedID)
Funder
Swedish Research Council, 2015-04402
Available from: 2019-02-11 Created: 2019-02-11 Last updated: 2019-02-11Bibliographically approved
Fuchs, J., Alström, P., Yosef, R. & Olsson, U. (2019). Miocene diversification of an open-habitat predatorial passerine radiation, the shrikes (Aves: Passeriformes: Laniidae). Zoologica Scripta, 48(5), 571-588
Open this publication in new window or tab >>Miocene diversification of an open-habitat predatorial passerine radiation, the shrikes (Aves: Passeriformes: Laniidae)
2019 (English)In: Zoologica Scripta, ISSN 0300-3256, E-ISSN 1463-6409, Vol. 48, no 5, p. 571-588Article in journal (Refereed) Published
Abstract [en]

Diversification of avifaunas associated with savannah and steppes appears to correlate with open habitats becoming available, starting in the Miocene. Few comparative analyses exist for families for which all species are predominantly adapted to these habitats. One such group is Laniidae (Passeriformes), which are small- to medium-sized predatory passerines known for their distinctive behaviour of impaling prey. We used multispecies coalescent-based and concatenation methods to provide the first complete species-level phylogeny for this group, as well as an estimate of the timing of diversification. Our analyses indicate that Laniidae as currently delimited is not monophyletic, as the genus Eurocephalus is not closely related to the remaining species. The two species currently assigned to the monotypic genera Urolestes and Corvinella are part of the same clade as the Lanius species, and we propose that they are included in the genus Lanius, making Laniidae monogeneric. The initial diversification of the clade is inferred to have occurred very rapidly, starting about 7.2-9.1 million years ago, timing depending on calibration method, but in either case coinciding with the expansion of C4 grasses. An African origin is inferred in the biogeographic analysis. In the redefined Laniidae, cooperative breeding is inferred to be restricted to a single clade, characterized by gregarious behaviour and rallying. Migratory behaviour evolved multiple times within the family.

Place, publisher, year, edition, pages
WILEY, 2019
Keywords
biogeography, gregarious behaviour, Lanius, migratory behaviour, molecular phylogeny, radiation
National Category
Evolutionary Biology Biological Systematics
Identifiers
urn:nbn:se:uu:diva-396113 (URN)10.1111/zsc.12363 (DOI)000481121100001 ()
Funder
Swedish Research Council, 2015-04402
Available from: 2019-10-31 Created: 2019-10-31 Last updated: 2019-10-31Bibliographically approved
Cai, T., Cibois, A., Alström, P., Moyle, R., Kennedy, J., Shao, S., . . . Fjeldsa, J. (2019). Near-complete phylogeny and taxonomic revision of the world's babblers (Aves: Passeriformes). Molecular Phylogenetics and Evolution, 130, 346-356
Open this publication in new window or tab >>Near-complete phylogeny and taxonomic revision of the world's babblers (Aves: Passeriformes)
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2019 (English)In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 130, p. 346-356Article in journal (Refereed) Published
Abstract [en]

The babblers are a diverse group of passerine birds comprising 452 species. The group was long regarded as a "scrap basket" in taxonomic classification schemes. Although several studies have assessed the phylogenetic relationships for subsets of babblers during the past two decades, a comprehensive phylogeny of this group has been lacking. In this study, we used five mitochondrial and seven nuclear loci to generate a dated phylogeny for babblers. This phylogeny includes 402 species (ca. 89% of the overall clade) from 75 genera (97%) and all five currently recognized families, providing a robust basis for taxonomic revision. Our phylogeny supports seven major clades and reveals several non-monophyletic genera. Divergence time estimates indicate that the seven major clades diverged around the same time (18-20 million years ago, Ma) in the early Miocene. We use the phylogeny in a consistent way to propose a new taxonomy, with seven families and 64 genera of babblers, and a new linear sequence of names.

Keywords
Babblers, Passeriformes, Phylogeny, Supertree, Taxonomy, Rogue taxa, Temporal banding
National Category
Biological Systematics
Identifiers
urn:nbn:se:uu:diva-374117 (URN)10.1016/j.ympev.2018.10.010 (DOI)000452963200031 ()30321696 (PubMedID)
Funder
Swedish Research Council, 2015-04402Swedish Research Council, 621-2014-5113Swedish Research Council, 621-2013-5161
Available from: 2019-01-22 Created: 2019-01-22 Last updated: 2019-01-22Bibliographically approved
Alström, P., Rheindt, F. E., Zhang, R., Zhao, M., Wang, J., Zhu, X., . . . Olsson, U. (2018). Complete species-level phylogeny of the leaf warbler (Aves: Phylloscopidae) radiation. Molecular Phylogenetics and Evolution, 126, 141-152
Open this publication in new window or tab >>Complete species-level phylogeny of the leaf warbler (Aves: Phylloscopidae) radiation
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2018 (English)In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 126, p. 141-152Article in journal (Refereed) Published
Abstract [en]

The leaf warbler radiation (Aves: Phylloscopidae) has undergone a c. 50% increase in the number of recognised species over the last three decades, mainly as a result of analyses of vocalisations and DNA. Using a multilocus dataset for all of the species in this family, and multispecies coalescent-based as well as concatenation methods, we provide the first complete species-level phylogeny for this important group, as well as an estimate of the timing of diversification. The most recent common ancestor for the family was dated at 11.7 million years ago (mya) (95% highest posterior density 9.8-13.7 mya), and divergence times between sister species ranged from 0.5 mya (0.3-0.8 mya) to 6.1 mya (4.8-7.5 mya). Based on our results, we support synonymising Seicercus with Phylloscopus, which results in a monogeneric Phylloscopidae. We discuss the pros and cons of this treatment, and we argue against proliferation of taxonomic names, and conclude that a large monogeneric Phylloscopidae leads to the fewest taxonomic changes compared to traditional classifications. We briefly discuss morphological evolution in the light of the phylogeny. The time calibrated phylogeny is a major improvement compared to previous studies based on a smaller number of species and loci and can provide a basis for future studies of other aspects of phylloscopid evolution.

Place, publisher, year, edition, pages
ACADEMIC PRESS INC ELSEVIER SCIENCE, 2018
Keywords
Species tree, Concatenation, Taxonomic revision
National Category
Biological Systematics
Identifiers
urn:nbn:se:uu:diva-361026 (URN)10.1016/j.ympev.2018.03.031 (DOI)000437663900013 ()29631054 (PubMedID)
Funder
Swedish Research Council, 2015-04402Swedish Research Council, 2013-5161Swedish Research Council, 2015-04651
Available from: 2018-09-20 Created: 2018-09-20 Last updated: 2018-09-20Bibliographically approved
Song, G., Zhang, R., Alström, P., Irestedt, M., Cai, T., Qu, Y., . . . Lei, F. (2018). Complete taxon sampling of the avian genus Pica (magpies) reveals ancient relictual populations and synchronous Late-Pleistocene demographic expansion across the Northern Hemisphere. Journal of Avian Biology, 49(2), Article ID UNSP e01612.
Open this publication in new window or tab >>Complete taxon sampling of the avian genus Pica (magpies) reveals ancient relictual populations and synchronous Late-Pleistocene demographic expansion across the Northern Hemisphere
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2018 (English)In: Journal of Avian Biology, ISSN 0908-8857, E-ISSN 1600-048X, Vol. 49, no 2, article id UNSP e01612Article in journal (Refereed) Published
Abstract [en]

Previous studies have suggested that bird populations in east Asia were less affected by Pleistocene climatic fluctuations than those in Europe and North America. However, this is mainly based on comparisons among species. It would be more relevant to analyse geographical populations of widespread species or species complexes. We analyzed two mitochondrial genes and two nuclear introns for all taxa of Pica to investigate 1) which Earth history factors have shaped the lineage divergence, and 2) whether different geographical populations were differently affected by the Pleistocene climatic changes. Our mitochondrial tree recovered three widespread lineages, 1) in east Asia, 2) across north Eurasia, and 3) in North America, respectively, with three isolated lineages in northwest Africa, Arabia and the Qinghai‐Tibet Plateau, respectively. Divergences among lineages took place 1.4–3.1 million yr ago. The northwest African population was sister to the others, which formed two main clades. In one of these, Arabia was sister to Qinghai‐Tibet, and these formed the sister clade to the east Asia clade. The other main clade comprised the North American and north Eurasian clades. There was no or very slight structure within these six geographical clades, including a lack of differentiation between the two North American species black‐billed magpie P. hudsonia and yellow‐billed magpie P. nutalli. Demographic expansion was recorded in the three most widespread lineages after 0.06 Ma. Asymmetric gene flow was recorded in the north Eurasian clade from southwestern Europe eastward, whereas the east Asian clade was rooted in south central China. Our results indicate that the fragmentation of the six clades of Pica was related to climatic cooling and aridification during periods of the Pliocene–Pleistocene. Populations on both sides of the Eurasian continent were similarly influenced by the Pleistocene climate changes and expanded concomitantly with the expansion of steppes. Based on results we also propose a revised taxonomy recognising seven species of Pica.

Place, publisher, year, edition, pages
WILEY, 2018
Keywords
lineage divergence, Palearctic, population expansion
National Category
Evolutionary Biology Biological Systematics
Identifiers
urn:nbn:se:uu:diva-351111 (URN)10.1111/jav.01612 (DOI)000427922600005 ()
Funder
Swedish Research Council, 2013-5161]Swedish Research Council, 2014-5113]Swedish Research Council, 2015-04402]
Available from: 2018-05-25 Created: 2018-05-25 Last updated: 2018-05-25Bibliographically approved
Alström, P., Cibois, A., Irestedt, M., Zuccon, D., Gelang, M., Fjeldsa, J., . . . Olsson, U. (2018). Comprehensive molecular phylogeny of the grassbirds and allies (Locustellidae) reveals extensive non-monophyly of traditional genera, and a proposal for a new classification. Molecular Phylogenetics and Evolution, 127, 367-375
Open this publication in new window or tab >>Comprehensive molecular phylogeny of the grassbirds and allies (Locustellidae) reveals extensive non-monophyly of traditional genera, and a proposal for a new classification
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2018 (English)In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 127, p. 367-375Article in journal (Refereed) Published
Abstract [en]

The widespread Old World avian family Locustellidae ('grassbirds and allies') comprises 62 extant species in 11 genera. In the present study, we used one mitochondrial and, for most species, four nuclear loci to infer the phylogeny of this family. We analysed 59 species, including the five previously unsampled genera plus two genera that had not before been analysed in a densely sampled dataset. This study revealed extensive disagreement with current taxonomy; the genera Bradypterus, Locustella, Megalurus, Megalurulus and Schoenicola were all found to be non-monophyletic. Non-monophyly was particularly pronounced for Megalurus, which was widely scattered across the tree. Three of the five monotypic genera (Amphilais, Buettikoferella and Malia) were nested within other genera; one monotypic genus (Chaetornis) formed a Glade with one of the two species of Schoenicola; whereas the position of the fifth monotypic genus (Elaphrornis) was unresolved. Robsonius was confirmed as sister to the other genera. We propose a phylogenetically informed revision of genus-level taxonomy, including one new generic name. Finally, we highlight several non-monophyletic species complexes and deep intra-species divergences that point to conflict in taxonomy and suggest an underestimation of current species diversity in this group.

Place, publisher, year, edition, pages
ACADEMIC PRESS INC ELSEVIER SCIENCE, 2018
Keywords
Systematics, Taxonomy, Incongruence, Species diversity, New genus
National Category
Zoology
Identifiers
urn:nbn:se:uu:diva-371839 (URN)10.1016/j.ympev.2018.03.029 (DOI)000446021300031 ()29625229 (PubMedID)
Funder
Swedish Research Council, 2015-04402Swedish Research Council, 621-2014-5113
Available from: 2019-01-02 Created: 2019-01-02 Last updated: 2019-01-07Bibliographically approved
Cibois, A., Gelang, M., Alström, P., Pasquet, E., Fjeldsa, J., Ericson, P. G. P. & Olsson, U. (2018). Comprehensive phylogeny of the laughingthrushes and allies (Aves, Leiothrichidae) and a proposal for a revised taxonomy. Zoologica Scripta, 47(4), 428-440
Open this publication in new window or tab >>Comprehensive phylogeny of the laughingthrushes and allies (Aves, Leiothrichidae) and a proposal for a revised taxonomy
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2018 (English)In: Zoologica Scripta, ISSN 0300-3256, E-ISSN 1463-6409, Vol. 47, no 4, p. 428-440Article in journal (Refereed) Published
Abstract [en]

DNA phylogenies have gradually shed light on the phylogenetic relationships of the large babbler group. We focus in this study on the family Leiothrichidae (laughingthrushes and song babblers), which represents the largest clade of babblers in terms of species diversity. Our phylogeny includes all genera and 82% of the recognized species, using mitochondrial and nuclear loci. The sister group to Leiothrichidae is composed of the Pellorneidae (jungle babblers) plus the genus Alcippe. Within Leiothrichidae, four strongly supported primary clades (A-D) are recovered. Clade A includes Grammatoptila, Laniellus and Cutia. Clade B includes a large group of laughingthrushes, all of them classified in Trochalopteron. In Clade C, the two laughingthrushes endemic to southern India, T.fairbanki and T.cachinnans, which have recently been proposed to be placed in the newly erected genus Montecincla, form a sister clade to the group comprising the song babblers (Lioptila, Leiothrix, Heterophasia, Minla, Liocichla, Actinodura, Chrysominla, Siva, and Sibia). Clade D includes the African babblers (Turdoides, Phyllanthus, Kupeornis), Asian relatives (Argya, Acanthoptila, Chatarrhaea) and all remaining laughingthrushes (Garrulax). The time estimates suggest that the early diversification of the Leiothrichidae occurred in the mid-Miocene, a period that corresponds to the diversification of many passerine groups in Asia. A revised taxonomic classification of the family is proposed in the light of these results.

Place, publisher, year, edition, pages
WILEY, 2018
Keywords
babblers, multilocus analysis, phylogeny, taxonomy
National Category
Biological Systematics Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-361113 (URN)10.1111/zsc.12296 (DOI)000437704400005 ()
Funder
Swedish Research Council, 621-2007-5280Swedish Research Council, 2015-04402
Available from: 2018-09-21 Created: 2018-09-21 Last updated: 2018-09-21Bibliographically approved
Harris, R. B., Alström, P., Ödeen, A. & Leache, A. D. (2018). Discordance between genomic divergence and phenotypic variation in a rapidly evolving avian genus (Motacilla). Molecular Phylogenetics and Evolution, 120, 183-195
Open this publication in new window or tab >>Discordance between genomic divergence and phenotypic variation in a rapidly evolving avian genus (Motacilla)
2018 (English)In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 120, p. 183-195Article in journal (Refereed) Published
Abstract [en]

Generally, genotypes and phenotypes are expected to be spatially congruent; however, in widespread species complexes with few barriers to dispersal, multiple contact zones, and limited reproductive isolation, discordance between phenotypes and phylogeographic groups is more probable. Wagtails (Motacilla) are a genus of birds with striking plumage pattern variation across the Old World. Up to 13 subspecies are recognized within a single species, yet previous studies using mitochondrial DNA have supported polyphyletic phylogeographic groups that are inconsistent with subspecies plumage characteristics. In this study, we investigate the link between phenotypes and genotype by taking a phylogenetic approach. We use genome-wide SNPs, nuclear introns, and mitochondrial DNA to estimate population structure, isolation by distance, and species relationships. Together, our genetic sampling includes complete species-level sampling and comprehensive coverage of the three most phenotypically diverse Palearctic species. Our study provides strong evidence for species-level patterns of differentiation, however population-level differentiation is less pronounced. SNPs provide a robust estimate of species-level relationships, which are mostly corroborated by a combined analysis of mtDNA and nuclear introns (the first time-calibrated species tree for the genus). However, the mtDNA tree is strongly incongruent and is considered to misrepresent the species phylogeny. The extant wagtail lineages originated during the Pliocene and the Eurasian lineage underwent rapid diversification during the Pleistocene. Three of four widespread Eurasian species exhibit an east-west divide that contradicts both subspecies taxonomy and phenotypic variation. Indeed, SNPs fail to distinguish between phenotypically distinct subspecies within the M. alba and M. flava complexes, and instead support geographical regions, each of which is home to two or more different looking subspecies. This is a major step towards our understanding of wagtail phylogeny compared to previous analyses of fewer species and considerably less sequence data.

Place, publisher, year, edition, pages
ACADEMIC PRESS INC ELSEVIER SCIENCE, 2018
Keywords
Phylogenetics, Genetic differentiation, Plumage divergence, Mito-nuclear discordance
National Category
Evolutionary Biology Biological Systematics
Identifiers
urn:nbn:se:uu:diva-350061 (URN)10.1016/j.ympev.2017.11.020 (DOI)000426199700017 ()29246816 (PubMedID)
Funder
NIH (National Institute of Health), S10RR029668NIH (National Institute of Health), S10RR027303Swedish Research Council, 2015-04402
Available from: 2018-05-04 Created: 2018-05-04 Last updated: 2018-05-04Bibliographically approved
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ORCID iD: ORCID iD iconorcid.org/0000-0001-7182-2763

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