| 31. |
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| 32. |
- Liu, B. Y., et al.
(author)
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Explosive radiation and spatial expansion across the cold environments of the Old World in an avian family
- 2017
-
In: Ecology and Evolution. - : Wiley. - 2045-7758. ; 7:16, s. 6346-6357
-
Journal article (peer-reviewed)abstract
- Our objective was to elucidate the biogeography and speciation patterns in an entire avian family, which shows a complex pattern of overlapping and nonoverlapping geographical distributions, and much variation in plumage, but less in size and structure. We estimated the phylogeny and divergence times for all of the world's species of Prunella based on multiple genetic loci, and analyzed morphometric divergence and biogeographical history. The common ancestor of Prunella was present in the Sino-Himalayan Mountains or these mountains and Central Asia-Mongolia more than 9 million years ago (mya), but a burst of speciations took place during the mid-Pliocene to early Pleistocene. The relationships among the six primary lineages resulting from that differentiation are unresolved, probably because of the rapid radiation. A general increase in sympatry with increasing time since divergence is evident. With one exception, species in clades younger than c. 3.7 my are allopatric. Species that are widely sympatric, including the most recently diverged (2.4 mya) sympatric sisters, are generally more divergent in size/structure than allo-/parapatric close relatives. The distributional pattern and inferred ages suggest divergence in allopatry and substantial waiting time until secondary contact, likely due to competitive exclusion. All sympatrically breeding species are ecologically segregated, as suggested by differences in size/structure and habitat. Colonizations of new areas were facilitated during glacialperiods, followed by fragmentation during interglacials-contrary to the usual view that glacial periods resulted mainly in fragmentations.
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| 33. |
- Alström, Per, et al.
(author)
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Discovery of a relict lineage and monotypic family of passerine birds.
- 2014
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In: Biology Letters. - : The Royal Society. - 1744-9561 .- 1744-957X. ; 10:3
-
Journal article (peer-reviewed)abstract
- Analysis of one of the most comprehensive datasets to date of the largest passerine bird clade, Passerida, identified 10 primary well-supported lineages corresponding to Sylvioidea, Muscicapoidea, Certhioidea, Passeroidea, the ‘bombycillids’ (here proposed to be recognized as Bombycilloidea), Paridae/Remizidae (proposed to be recognized as Paroidea), Stenostiridae, Hyliotidae, Regulidae (proposed to be recognized as Reguloidea) and spotted wren-babbler Spelaeornis formosus. The latter was found on a single branch in a strongly supported clade with Muscicapoidea, Certhioidea and Bombycilloidea, although the relationships among these were unresolved. We conclude that the spotted wren-babbler represents a relict basal lineage within Passerida with no close extant relatives, and we support the already used name Elachura formosa and propose the new family name Elachuridae for this single species.
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| 34. |
- Alström, Per, et al.
(author)
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New insights into family relationships within the avian superfamily Sylvioidea (Passeriformes) based on seven molecular markers
- 2012
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In: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 12, s. 1-12
-
Journal article (peer-reviewed)abstract
- Background: The circumscription of the avian superfamily Sylvioidea is a matter of long ongoing debate. While the overall inclusiveness has now been mostly agreed on and 20 families recognised, the phylogenetic relationships among the families are largely unknown. We here present a phylogenetic hypothesis for Sylvioidea based on one mitochondrial and six nuclear markers, in total ~6.3 kbp, for 79 ingroup species representing all currently recognised families and some species with uncertain affinities, making this the most comprehensive analysis of this taxon. Results: The resolution, especially of the deeper nodes, is much improved compared to previous studies. However, many relationships among families remain uncertain and are in need of verification. Most families themselves are very well supported based on the total data set and also by indels. Our data do not support the inclusion of Hylia in Cettiidae, but do not strongly reject a close relationship with Cettiidae either. The genera Scotocerca and Erythrocercus are closely related to Cettiidae, but separated by relatively long internodes. The families Paridae, Remizidae and Stenostiridae clustered among the outgroup taxa and not within Sylvioidea. Conclusions: Although the phylogenetic position of Hylia is uncertain, we tentatively support the recognition of the family Hyliidae Bannerman, 1923 for this genus and Pholidornis. We propose new family names for the genera Scotocerca and Erythrocercus, Scotocercidae and Erythrocercidae, respectively, rather than including these in Cettiidae, and we formally propose the name Macrosphenidae, which has been in informal use for some time. We recommend that Paridae, Remizidae and Stenostiridae are not included in Sylvioidea. We also briefly discuss the problems of providing a morphological diagnosis when proposing a new family-group name (or genus-group name) based on a clade.
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| 35. |
- Bourlat, Sarah, et al.
(author)
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Feeding ecology of Xenoturbella bocki (phylum Xenoturbellida) revealed by genetic barcoding
- 2008
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In: Molecular Ecology Resources. - 1755-098X. ; 8, s. 18-22
-
Journal article (peer-reviewed)abstract
- The benthic marine worm Xenoturbella is frequently contaminated with molluscan DNA, which had earlier caused confusion resulting in a suggested bivalve relationship. In order to find the source of the contaminant, we have used molluscan sequences derived from Xenoturbella and compared them to barcodes obtained from several individuals of the nonmicroscopic molluscs sharing the same environment as Xenoturbella. Using cytochrome oxidase 1, we found the contaminating sequences to be 98% similar to the bivalve Ennucula tenuis. Using the highly variable D1-D2 region of the large ribosomal subunit in Xenoturbella, we found three distinct species of contaminating molluscs, one of which is 99% similar to the bivalve Abra nitida, one of the most abundant bivalves in the Gullmarsfjord where Xenoturbella was found, and another 99% similar to the bivalve Nucula sulcata. These data clearly show that Xenoturbella only contains molluscan DNA originating from bivalves living in the same environment, refuting former hypotheses of a bivalve relationship. In addition, these data suggest that Xenoturbella feeds specifically on bivalve prey from multiple species, possibly in the form of eggs and larvae.
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| 36. |
- Green, Leon, et al.
(author)
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Ancestral Sperm Ecotypes Reveal Multiple Invasions of a Non-Native Fish in Northern Europe
- 2021
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In: Cells. - : MDPI AG. - 2073-4409. ; 10:7
-
Journal article (peer-reviewed)abstract
- For externally fertilising organisms in the aquatic environment, the abiotic fertilisation medium can be a strong selecting force. Among bony fishes, sperm are adapted to function in a narrow salinity range. A notable exception is the family Gobiidae, where several species reproduce across a wide salinity range. The family also contains several wide-spread invasive species. To better understand how these fishes tolerate such varying conditions, we measured sperm performance in relation to salinity from a freshwater and a brackish population within their ancestral Ponto-Caspian region of the round goby, Neogobius melanostomus. These two ancestral populations were then compared to nine additional invaded sites across northern Europe, both in terms of their sperm traits and by using genomic SNP markers. Our results show clear patterns of ancestral adaptations to freshwater and brackish salinities in their sperm performance. Population genomic analyses show that the ancestral ecotypes have generally established themselves in environments that fit their sperm adaptations. Sites close to ports with intense shipping show that both outbreeding and admixture can affect the sperm performance of a population in a given salinity. Rapid adaptation to local conditions is also supported at some sites. Historical and contemporary evolution in the traits of the round goby sperm cells is tightly linked to the population and seascape genomics as well as biogeographic processes in these invasive fishes. Since the risk of a population establishing in an area is related to the genotype by environment match, port connectivity and the ancestry of the round goby population can likely be useful for predicting the species spread.
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| 37. |
- Olsson, Urban, 1954, et al.
(author)
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Molecular evidence suggests that the enigmatic Sulawesi endemic Geomalia heinrichi belongs in the genus Zoothera (Turdidae, Aves).
- 2013
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In: Chinese Birds. - : Chinese Birds (Press). - 1674-7674. ; 4:2, s. 155-160
-
Journal article (peer-reviewed)abstract
- The taxonomic status of the Sulawesi endemic Geomalia heinrichi has long been debated, and it has variously been treated as a babbler (Timaliidae) or a turdid (Turdidae). We estimated the phylogeny of 43 taxa in the family Turdidae based on the mitochondrial cytochrome b gene and the nuclear myoglobin intron 2 and ornithine decarboxylase introns 6–7. Geomalia heinrichi was shown to be part of the Zoothera clade with high support. We propose that Geomalia is transferred to Zoothera under the name Zoothera heinrichi.
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| 38. |
- Olsson, Urban, 1954, et al.
(author)
-
Systematic revision of the avian family Cisticolidae based on a multi-locus phylogeny of all genera
- 2013
-
In: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903 .- 1095-9513. ; 66:3, s. 790-799
-
Journal article (peer-reviewed)abstract
- The avian taxon Cisticolidae includes c. 110 species which are distributed throughout the tropical and subtropical parts of the Old World. We estimated the phylogeny of 47 species representing all genera assumed to be part of Cisticolidae based on sequence data from two mitochondrial and two nuclear markers, in total 3495 bp. Bayesian inference and maximum likelihood analyses resulted in a generally well-supported phylogeny which clarified the position of several previously poorly known taxa. The placement of Drymocichla, Malcorus, Micromacronus, Oreophilais, Phragmacia, Phyllolais, Poliolais and Urorhipis in Cisticolidae is corroborated, whereas Rhopophilus and Scotocerca are removed from Cisticolidae. Urorhipis and Heliolais are placed in the genus Prinia whereas Prinia burnesii is shown to be part of Timaliidae, and is placed in the genus Laticilla. Although not recovered by all single loci independently, four major clades were identified within Cisticolidae, and one of these is here described as a new taxon (Neomixinae).
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| 39. |
- Tedersoo, Leho, et al.
(author)
-
EUKARYOME: the rRNA gene reference database for identification of all eukaryotes
- 2024
-
In: Database. - 1758-0463. ; 2024
-
Journal article (peer-reviewed)abstract
- Molecular identification of micro- and macroorganisms based on nuclear markers has revolutionized our understanding of their taxonomy, phylogeny and ecology. Today, research on the diversity of eukaryotes in global ecosystems heavily relies on nuclear ribosomal RNA (rRNA) markers. Here, we present the research community-curated reference database EUKARYOME for nuclear ribosomal 18S rRNA, internal transcribed spacer (ITS) and 28S rRNA markers for all eukaryotes, including metazoans (animals), protists, fungi and plants. It is particularly useful for the identification of arbuscular mycorrhizal fungi as it bridges the four commonly used molecular markers - ITS1, ITS2, 18S V4-V5 and 28S D1-D2 subregions. The key benefits of this database over other annotated reference sequence databases are that it is not restricted to certain taxonomic groups and it includes all rRNA markers. EUKARYOME also offers a number of reference long-read sequences that are derived from (meta)genomic and (meta)barcoding - a unique feature that can be used for taxonomic identification and chimera control of third-generation, long-read, high-throughput sequencing data. Taxonomic assignments of rRNA genes in the database are verified based on phylogenetic approaches. The reference datasets are available in multiple formats from the project homepage, http://www.eukaryome.org.
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| 40. |
- Alström, Per, et al.
(author)
-
Integrative taxonomy of the Russet Bush Warbler Locustella mandelli complex reveals a new species from central China
- 2015
-
In: Avian Research. - : Elsevier BV. - 2053-7166. ; 6:9
-
Journal article (peer-reviewed)abstract
- Background: The Russet Bush Warbler Locustella (previously Bradypterus) mandelli complex occurs in mountains in the eastern Himalayas, southern China, Vietnam, the Philippines, and Indonesia. The taxonomy has been debated, with one (L. seebohmi) to four (L. seebohmi, L. mandelli, L. montis and L. timorensis) species having been recognised. Methods: We used an integrative approach, incorporating analyses of morphology, vocalizations and a molecular marker, to re-evaluate species limits in the L. mandelli complex. Results: We found that central Chinese L. mandelli differed from those from India through northern Southeast Asia to southeast China in plumage, morphometrics and song. All were easily classified by song, and (wing + culmen)/tail ratio overlapped only marginally. Both groups were reciprocally monophyletic in a mitochondrial cytochrome b (cytb) gene tree, with a mean divergence of 1.0 +/- 0.2%. They were sympatric and mostly altitudinally segregated in the breeding season in southern Sichuan province. We found that the Mt Victoria (western Myanmar) population differed vocally from other L. mandelli, but no specimens are available. Taiwan Bush Warbler L. alishanensis was sister to the L. mandelli complex, with the most divergent song. Plumage, vocal and cytb evidence supported the distinctness of the south Vietnamese L. mandelli idonea. The Timor Bush Warbler L. timorensis, Javan Bush Warbler L. montis and Benguet Bush Warbler L. seebohmi differed distinctly in plumage, but among-population song variation in L. montis exceeded the differences between some populations of these taxa, and mean pairwise cytb divergences were only 0.5-0.9%. We also found that some L. montis populations differed morphologically. Conclusions: We conclude that the central Chinese population of Russet Bush Warbler represents a new species, which we describe herein, breeding at mid elevations in Sichuan, Shaanxi, Hubei, Hunan and Guizhou provinces. The taxonomic status of the other allopatric populations is less clear. However, as they differ to a degree comparable with that of the sympatric L. mandelli and the new species, we elevate L. idonea to species status, and retain L. seebohmi and L. montis as separate species, the latter with timorensis as a subspecies. Further research should focus on different populations of L. montis and the Mt Victoria population of L. mandelli.
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