| 1. |
- Irestedt, Martin, et al.
(författare)
-
Systematic relationships and biogeography of the tracheophone suboscines (Aves: Passeriformes)
- 2002
-
Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier. - 1055-7903 .- 1095-9513. ; 23:3, s. 499-512
-
Tidskriftsartikel (refereegranskat)abstract
- Based on their highly specialized “tracheophone” syrinx, the avian families Furnariidae (ovenbirds), Dendrocolaptidae (woodcreepers), Formicariidae (ground antbirds), Thamnophilidae (typical antbirds), Rhinocryptidae (tapaculos), and Conopophagidae (gnateaters) have long been recognized to constitute a monophyletic group of suboscine passerines. However, the monophyly of these families have been contested and their interrelationships are poorly understood, and this constrains the possibilities for interpreting adaptive tendencies in this very diverse group. In this study we present a higher-level phylogeny and classification for the tracheophone birds based on phylogenetic analyses of sequence data obtained from 32 ingroup taxa. Both mitochondrial (cytochrome b) and nuclear genes (c-myc, RAG-1, and myoglobin) have been sequenced, and more than 3000 bp were subjected to parsimony and maximum-likelihood analyses. The phylogenetic signals in the mitochondrial and nuclear genes were compared and found to be very similar. The results from the analysis of the combined dataset (all genes, but with transitions at third codon positions in the cytochrome b excluded) partly corroborate previous phylogenetic hypotheses, but several novel arrangements were also suggested. Especially interesting is the result that the genus Melanopareia represents a basal branch within the tracheophone group, positioned in the phylogenetic tree well away from the typical tapaculos with which it has been supposed to group. Other novel results include the observation that the ground antbirds are paraphyletic and that Sclerurus is the sister taxon to an ovenbird–woodcreeper clade. Patterns of generic richness within each clade suggest that the early differentiation of feeble-winged forest groups took place south of the Amazon Basin, while the more recent diversification was near the equator and (in tapaculos and ovenbirds) in the south of the continent
|
|
| 2. |
- Aagaard, Sunniva M. D., 1977-, et al.
(författare)
-
Occurrence and evolutionary origins of polyploids in the club moss genus Diphasiastrum (Lycopodiaceae)
- 2009
-
Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903 .- 1095-9513. ; 52:3, s. 746-754
-
Tidskriftsartikel (refereegranskat)abstract
- Two polyploid taxa are commonly recognized in the genus Diphasiastrum, D. wightianum from Asia and D. zanclophyllum from South Africa and Madagascar. Here we present results from Feulgen DNA image densitometry analyses providing the first evidence for the polyploid origin of D. zanclophyllum. Reported for the first time is also data confirming that D. multispicatum and D. veitchii, representing putative parent lineages for D. wightianum, are diploids. Phylogenetic analyses of nuclear regions RPB2, LEAFY and LAMB4 reveal that putative tetraploid accessions are of allopolyploid origin. Diphasiastrum zanclophyllum shows close relationships to the North American taxon D. digitatum on the maternal side, but the paternal relationship is less clear. Two accessions from Asia, both found to be polyploid, have D. veitchii as maternal parent, whereas the paternal paralogs show relationships to D. multispicatum and D. tristachyum, respectively. None of these parental combinations have previously been hypothesized.
|
|
| 3. |
- Abalde, Samuel, et al.
(författare)
-
Hidden species diversity and mito-nuclear discordance within the Mediterranean cone snail, Lautoconus ventricosus
- 2023
-
Ingår i: Molecular Phylogenetics and Evolution. - 1055-7903 .- 1095-9513. ; 186, s. 107838-107838
-
Tidskriftsartikel (refereegranskat)abstract
- The Mediterranean cone snail, Lautoconus ventricosus, is currently considered a single species inhabiting the whole Mediterranean basin and the adjacent Atlantic coasts. Yet, no population genetic study has assessed its taxonomic status. Here, we collected 245 individuals from 75 localities throughout the Mediterranean Sea and used cox1 barcodes, complete mitochondrial genomes, and genome skims to test whether L. ventricosus represents a complex of cryptic species. The maximum likelihood phylogeny based on complete mitochondrial genomes recovered six main clades (hereby named blue, brown, green, orange, red, and violet) with sufficient sequence divergence to be considered putative species. On the other hand, phylogenomic analyses based on 437 nuclear genes only recovered four out of the six clades: blue and orange clades were thoroughly mixed and the brown one was not recovered. This mito-nuclear discordance revealed instances of incomplete lineage sorting and introgression, and may have caused important differences in the dating of main cladogenetic events. Species delimitation tests proposed the existence of at least three species: green, violet, and red + blue + orange (i.e., cyan). Green plus cyan (with sympatric distributions) and violet, had West and East Mediterranean distributions, respectively, mostly separated by the Siculo-Tunisian biogeographical barrier. Morphometric analyses of the shell using species hypotheses as factor and shell length as covariate showed that the discrimination power of the studied parameters was only 70.2%, reinforcing the cryptic nature of the uncovered species, and the importance of integrative taxonomic approaches considering morphology, ecology, biogeography, and mitochondrial and nuclear population genetic variation.
|
|
| 4. |
|
|
| 5. |
- Abraham, David, et al.
(författare)
-
Molecular phylogeny of the subfamilies in Geometridae (Geometroidea: Lepidoptera)
- 2001
-
Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1095-9513 .- 1055-7903. ; 20:1, s. 65-77
-
Tidskriftsartikel (refereegranskat)abstract
- Molecular sequence data from three gene fragments were used to examine critically a provisional phylogenetic classification based on morphological characters of the Geometridae, one of the most species-rich families of moths. The sister group relationship between Geometridae and Drepanidae gained further support from the molecular analysis, which was based on the ND1 mitochondrial gene and the first and second expansion segments of the 28S ribosomal RNA gene. Although the alignment of the second expansion segment contained regions with many gaps, it provided the most resolution of the gene fragments. Parsimony analysis of the combined data resulted in a cladogram in which species belonging to Drepanidae, Larentiinae, and Sterrhinae formed monophyletic groups. The Ennominae did not form a monophyletic group but rather were contained within a broader monophyletic group including Archiearinae, Geometrinae, and Alsophilinae (represented by only one species per group in the present study). The molecular results were used to explore further the relationship between Sterrhinae and Larentiinae, the question as to whether Ennominae actually represent a monophyletic group, and the relationships between Ennominae and some of the other subfamilies.
|
|
| 6. |
- Abraham, D, et al.
(författare)
-
Molecular phylogeny of the subfamilies in geometridae (Geometroidea : Lepidoptera)
- 2001
-
Ingår i: MOLECULAR PHYLOGENETICS AND EVOLUTION. - : ACADEMIC PRESS INC. - 1055-7903. ; 20:1, s. 65-77
-
Tidskriftsartikel (refereegranskat)abstract
- Molecular sequence data from three gene fragments were used to examine critically a provisional phylogenetic classification based on morphological characters of the Geometridae, one of the most species-rich families of moths. The sister group relationship
|
|
| 7. |
- Ali, Raja Hashim, et al.
(författare)
-
Tracing the evolution of FERM domain of Kindlins
- 2014
-
Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier. - 1055-7903 .- 1095-9513. ; 80, s. 193-204
-
Tidskriftsartikel (refereegranskat)abstract
- Kindlin proteins represent a novel family of evolutionarily conserved FERM domain containing proteins (FDCPs) and are members of B4.1 superfamily. Kindlins consist of three conserved protein homologs in vertebrates: Kindlin-1, Kindlin-2 and Kindlin-3. All three homologs are associated with focal adhesions and are involved in Integrin activation. FERM domain of each Kindlin is bipartite and plays a key role in Integrin activation. A single ancestral Kindlin protein can be traced back to earliest metazoans, e.g., to Parazoa. This protein underwent multiple rounds of duplication in vertebrates, leading to the present Kindlin family. In this study, we trace phylogenetic and evolutionary history of Kindlin FERM domain with respect to FERM domain of other FDCPs. We show that FERM domain in Kindlin homologs is conserved among Kindlins but amount of conservation is less in comparison with FERM domain of other members in B4.1 superfamily. Furthermore, insertion of Pleckstrin Homology like domain in Kindlin FERM domain has important evolutionary and functional consequences. Important residues in Kindlins are traced and ranked according to their evolutionary significance. The structural and functional significance of high ranked residues is highlighted and validated by their known involvement in Kindlin associated diseases. In light of these findings, we hypothesize that FERM domain originated from a proto-Talin protein in unicellular or proto-multicellular organism and advent of multi-cellularity was accompanied by burst of FDCPs, which supported multi-cellularity functions required for complex organisms. This study helps in developing a better understanding of evolutionary history of FERM domain of FDCPs and the role of FERM domain in metazoan evolution.
|
|
| 8. |
- Aliabadian, Mansour, et al.
(författare)
-
Convergent evolution of morphological and ecological traits in the open-habitat chat complex (Aves, Muscicapidae : Saxicolinae).
- 2012
-
Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903 .- 1095-9513. ; 65:1, s. 35-45
-
Tidskriftsartikel (refereegranskat)abstract
- Open-habitat chats (genera Myrmecocichla, Cercomela, Oenanthe and relative) are a morphologically and ecologically cohesive group of genera with unclear phylogenetic relationships. They are distributed mostly in open, arid and/or rocky habitats of Africa and Eurasia. Here, we present the most comprehensive molecular phylogenetic analysis of this group to date, with a complete taxon sampling at the species level. The analysis, based on a multilocus dataset including three mitochondrial and three nuclear loci, allows us to elucidate the phylogenetic relationships and test the traditional generic limits. All genera are non-monophyletic, suggesting extensive convergence on similar plumage patterns in unrelated species. While the colour pattern appear to be a poor predictor of the phylogenetic relationships, some of the ecological and behavioural traits agree relatively well with the major clades. Following our results, we also propose a revised generic classification for the whole group.
|
|
| 9. |
|
|
| 10. |
- Alström, Per, et al.
(författare)
-
Complete species-level phylogeny of the leaf warbler (Aves: Phylloscopidae) radiation
- 2018
-
Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903 .- 1095-9513. ; 126, s. 141-152
-
Tidskriftsartikel (refereegranskat)abstract
- 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.
|
|
