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- Dunn, Casey W, et al.
(författare)
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Broad phylogenomic sampling improves resolution of the animal tree of life.
- 2008
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 452:7188, s. 745-9
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Tidskriftsartikel (refereegranskat)abstract
- Long-held ideas regarding the evolutionary relationships among animals have recently been upended by sometimes controversial hypotheses based largely on insights from molecular data. These new hypotheses include a clade of moulting animals (Ecdysozoa) and the close relationship of the lophophorates to molluscs and annelids (Lophotrochozoa). Many relationships remain disputed, including those that are required to polarize key features of character evolution, and support for deep nodes is often low. Phylogenomic approaches, which use data from many genes, have shown promise for resolving deep animal relationships, but are hindered by a lack of data from many important groups. Here we report a total of 39.9 Mb of expressed sequence tags from 29 animals belonging to 21 phyla, including 11 phyla previously lacking genomic or expressed-sequence-tag data. Analysed in combination with existing sequences, our data reinforce several previously identified clades that split deeply in the animal tree (including Protostomia, Ecdysozoa and Lophotrochozoa), unambiguously resolve multiple long-standing issues for which there was strong conflicting support in earlier studies with less data (such as velvet worms rather than tardigrades as the sister group of arthropods), and provide molecular support for the monophyly of molluscs, a group long recognized by morphologists. In addition, we find strong support for several new hypotheses. These include a clade that unites annelids (including sipunculans and echiurans) with nemerteans, phoronids and brachiopods, molluscs as sister to that assemblage, and the placement of ctenophores as the earliest diverging extant multicellular animals. A single origin of spiral cleavage (with subsequent losses) is inferred from well-supported nodes. Many relationships between a stable subset of taxa find strong support, and a diminishing number of lineages remain recalcitrant to placement on the tree.
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| 2. |
- Mapalo, Marc A., et al.
(författare)
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The Unique Antimicrobial Recognition and Signaling Pathways in Tardigrades with a Comparison Across Ecdysozoa
- 2020
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Ingår i: G3-GENES GENOMES GENETICS. - : Oxford University Press (OUP). - 2160-1836. ; 10:3, s. 1137-1148
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Tidskriftsartikel (refereegranskat)abstract
- Tardigrades are microscopic animals known to withstand unfavorable abiotic conditions. These animals are also constantly exposed to biotic stresses, including parasites and internal microbiomes. However, the tardigrade immune mechanisms against these biotic stresses are largely uncharacterized. Due to the contentious phylogenetic position of tardigrades, it is not intuitive whether they possess an immune system more similar to that of arthropods (e.g., Toll, Imd, and JNK pathways of the Drosophila melanogaster antimicrobial response) or to that of nematodes (e.g., the Tir-1/Nsy-1/Sek-1/Pmk-1/Atf-7 signaling cassette [called Tir-1 pathway here]) in Caenorhabditis elegans). In this study, comparative genomic analyses were conducted to mine homologs of canonical D. melanogaster and C. elegans immune pathway genes from eight tardigrades (Echiniscoides cf. sigismundi, Echiniscus testudo, Hypsibius exemplaris, Mesobiotus philippinicus, Milnesium tardigradum, Paramacrobiotus richtersi, Richtersius cf. coronifer, and Ramazzottius varieornatus) and four non-arthropod ecdysozoans (two onychophorans: Epiperipatus sp. and Opisthopatus kwazululandi; one nematomorph: Paragordius varius; and one priapulan: Priapulus caudatus) in order to provide insights into the tardigrade antimicrobial system. No homologs of the intracellular components of the Toll pathway were detected in any of the tardigrades examined. Likewise, no homologs of most of the Imd pathway genes were detected in any of the tardigrades or any of the other non-arthropod ecdysozoans. Both the JNK and Tir-1 pathways, on the other hand, were found to be conserved across ecdysozoans. Interestingly, tardigrades had no detectable homologs of NF-kappa B, the major activator of antimicrobial response gene expression. Instead, tardigrades appear to possess NF-kappa B distantly related NFAT homologs. Overall, our results show that tardigrades have a unique gene pathway repertoire that differs from that of other ecdysozoans. Our study also provides a framework for future studies on tardigrade immune responses.
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| 5. |
- Wallberg, Andreas
(författare)
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The Dawn of a New Age : Interrelationships of Acoela and Nemertodermatida and the Early Evolution of Bilateria
- 2009
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Deciphering the rapid emergence of bilaterian animals around the time of the Cambrian Explosion and reconstructing the interrelationships of animal groups have long been two of the most elusive problems in Zoology. This thesis concerns the phylogenetic interrelationships within and among Acoela and Nemertodermatida, two groups of small worms that are believed to be basal bilaterians and which may provide important clues for understanding the early evolution of animals. In addition to trying to resolve the phylogenetic positions of these groups, major focus is put on inferring how ancestral animals might have looked, given the phylogenetic hypotheses put forward. The data used to infer phylogenies include nuclear ribosomal DNA, the mitochondrial COI gene and microRNAs. Based on phylogenetic analyses of a large number of 18S SSU ribosomal DNA sequences, it is proposed that Cnidaria is the sister taxon to Bilateria. Poor taxon sampling is suggested to be one of the reasons for why earlier assessments of the interrelationships among the most basal animal groups have yielded many conflicting results using the same gene. Analyses of new 18S SSU rDNA and 28S LSU rDNA sequences from six of the nine known species of nemertodermatids corroborate earlier indications that Acoela and Nemertodermatida are not sister taxa, as once thought. Being separate basal bilaterian animal groups, it is suggested that the last common ancestor of all bilaterians shared much of their comparatively simple morphology. Many methods are deployed to assess whether the phylogenetic results are mainly due to long-branch attraction, but no indication of this artifact is detected. The first comprehensive phylogenetic framework of Acoela is reconstructed from the 18S SSU, 28S LSU and COI genes, in combination with morphological data. The ancestral acoel worm is reconstructed using Bayesian methods and morphological observations in extant species. Two indeces, posterior similarity and reconstruction signal, are implemented to assess how similar different species are to the last common ancestor of all acoels and illustrate how clearly different characters or nodes are reconstructed. It is suggested that the ancestral acoel looked much like extant species of Diopisthoporus. The phylogenetic positions of Acoela and Nemertodermatida are assessed using new data on microRNAs in the acoel Hofstenia miamia and the nemertodermatid Meara stichopi. Acoela and Nemertodermatida are again found to be basal bilaterians, in congruence with earlier results. Using the work-flow and indeces developed earlier, it is concluded that the bilaterian ancestral microRNA repertoire can not yet be reconstructed with high confidence. All papers stress the importance of inclusive taxon sampling for making generalized inferences about ancestral features in animals.
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