| 1. |
- Clark, M. S., et al.
(författare)
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Multi-omics for studying and understanding polar life
- 2023
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Ingår i: Nature Communications. - : NATURE PORTFOLIO. - 2041-1723. ; 14
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Tidskriftsartikel (refereegranskat)abstract
- Polar ecosystems are experiencing amongst the most rapid rates of regional warming on Earth. Here, we discuss ‘omics’ approaches to investigate polar biodiversity, including the current state of the art, future perspectives and recommendations. We propose a community road map to generate and more fully exploit multi-omics data from polar organisms. These data are needed for the comprehensive evaluation of polar biodiversity and to reveal how life evolved and adapted to permanently cold environments with extreme seasonality. We argue that concerted action is required to mitigate the impact of warming on polar ecosystems via conservation efforts, to sustainably manage these unique habitats and their ecosystem services, and for the sustainable bioprospecting of novel genes and compounds for societal gain.
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| 2. |
- Erséus, Christer, 1951, et al.
(författare)
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Phylogenomic analyses reveal a Palaeozoic radiation and support a freshwater origin for clitellate annelids
- 2020
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Ingår i: Zoologica Scripta. - : Wiley. - 0300-3256 .- 1463-6409. ; 49:5, s. 614-640
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Tidskriftsartikel (refereegranskat)abstract
- Clitellata is a major clade of Annelida comprising nearly all freshwater and terrestrial annelids as well as several marine species. We investigated clitellate phylogenetic relationships using transcriptomes sampled from 74 taxa (64 clitellates and 10 polychaetes), including multiple representatives of nearly all major clitellate higher taxa (Branchiobdellida, Capilloventridae, Crassiclitellata, Enchytraeidae, Haplotaxidae, Hirudinida, Lumbriculida, Moniligastridae, Naididae, Parvidrilidae, Phreodrilidae, Propappidae and Randiellidae). We used a number of filtered data matrices and phylogenetic analyses to examine the effects of data partitioning, missing data and compositional and branch-length heterogeneity and used the resulting phylogenies for divergence time estimation and ancestral habitat reconstructions. All analyses and filtering methods produced a consistent, strongly supported topology in which (a) Enchytraeidae, Hirudinida, Hirudinea (here, Branchiobdellida plus Hirudinida), Lumbriculida, Lumbriculata (Lumbriculida plus Hirudinea), Phreodrilidae and Naididae are monophyletic, (b) a Parvidrilidae + Randiellidae clade is sister to the rest of Clitellata, (c) Phreodrilidae is sister to Naididae, (d) Haplotaxidae is non-monophyletic, with some haplotaxids grouping with Crassiclitellata + Moniligastridae, (e) the Phreodrilidae + Naididae clade is sister to all other clitellates except Parvidrilidae + Randiellidae and Capilloventridae, and (f) Lumbriculata is sister to the Crassiclitellata + Moniligastridae + Haplotaxidae (in part) clade. Ancestral habitat reconstructions and divergence time analysis suggested that the most recent common ancestor of Clitellata lived in freshwater during the Devonian (419-359 million years ago) and that all major extant clitellate lineages arose over the next similar to 150 million years, with multiple lineages subsequently returning to marine habitats or invading land. This study provides a phylogenetic framework for further investigation of the geological, environmental and biotic forces and genomic changes that may have impacted clitellate evolution and enabled several major habitat transitions within this group.
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| 3. |
- Horn, K. M., et al.
(författare)
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Na + /K + -ATPase gene duplications in clitellate annelids are associated with freshwater colonization
- 2019
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Ingår i: Journal of Evolutionary Biology. - : Wiley. - 1010-061X .- 1420-9101. ; 32:6, s. 580-591
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Tidskriftsartikel (refereegranskat)abstract
- Major habitat transitions, such as those from marine to freshwater habitats or from aquatic to terrestrial habitats, have occurred infrequently in animal evolution and may represent a barrier to diversification. Identifying genomic events associated with these transitions can help us better understand mechanisms that allow animals to cross these barriers and diversify in new habitats. Study of the Capitella telata and Helobdella robusta genomes allows examination of one such habitat transition (marine to freshwater) in Annelida. Initial examination of these genomes indicated that the freshwater leech H.robusta contains many more copies (12) of the sodium–potassium pump alpha-subunit (Na + /K + -ATPase) gene than does the marine polychaete C.telata (2). The sodium–potassium pump plays a key role in maintenance of cellular ionic balance and osmoregulation, and Na + /K + -ATPase duplications may have helped annelids invade and diversify in freshwater habitats. To assess whether the timing of Na + /K + -ATPase duplications coincided with the marine-to-freshwater transition in Clitellata, we used transcriptomic data from 18 annelid taxa, along with the two genomes, to infer a species phylogeny and identified Na + /K + -ATPase gene transcripts in order to infer the timing of gene duplication events using tree-based methods. The inferred timing of Na + /K + -ATPase duplication events is consistent with the timing of the initial marine-to-freshwater transition early in the history of clitellate annelids, supporting the hypothesis that gene duplications may have played a role in the annelid diversification into freshwater habitats. © 2019 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2019 European Society For Evolutionary Biology
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| 4. |
- Anderson, F. E., et al.
(författare)
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Phylogenomic analyses of Crassiclitellata support major Northern and Southern Hemisphere clades and a Pangaean origin for earthworms
- 2017
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Ingår i: Bmc Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 17
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Tidskriftsartikel (refereegranskat)abstract
- Background: Earthworms (Crassiclitellata) are a diverse group of annelids of substantial ecological and economic importance. Earthworms are primarily terrestrial infaunal animals, and as such are probably rather poor natural dispersers. Therefore, the near global distribution of earthworms reflects an old and likely complex evolutionary history. Despite a long-standing interest in Crassiclitellata, relationships among and within major clades remain unresolved. Methods: In this study, we evaluate crassiclitellate phylogenetic relationships using 38 new transcriptomes in combination with publicly available transcriptome data. Our data include representatives of nearly all extant earthworm families and a representative of Moniligastridae, another terrestrial annelid group thought to be closely related to Crassiclitellata. We use a series of differentially filtered data matrices and analyses to examine the effects of data partitioning, missing data, compositional and branch-length heterogeneity, and outgroup inclusion. Results and discussion: We recover a consistent, strongly supported ingroup topology irrespective of differences in methodology. The topology supports two major earthworm clades, each of which consists of a Northern Hemisphere subclade and a Southern Hemisphere subclade. Divergence time analysis results are concordant with the hypothesis that these north-south splits are the result of the breakup of the supercontinent Pangaea. Conclusions: These results support several recently proposed revisions to the classical understanding of earthworm phylogeny, reveal two major clades that seem to reflect Pangaean distributions, and raise new questions about earthworm evolutionary relationships.
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| 5. |
- Dahlgren, Thomas G., 1963, et al.
(författare)
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Molecular phylogeny of the model annelid Ophryotrocha
- 2001
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Ingår i: Biological Bulletin. - 0006-3185. ; 201:2, s. 193-203
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Tidskriftsartikel (refereegranskat)abstract
- Annelids of the genus Ophryotrocha are small opportunistic worms commonly found in polluted and nutrient-rich habitats such as harbors. Within this small group of about a, 40 described taxa a large variety of reproductive strategies are found, ranging from gonochoristic broadcast spawners to sequential hermaphroditic brooders. Many of the species have a short generation time and are easily maintained as laboratory cultures. Thus they have become a popular system for exploring a variety of biological questions including developmental genetics, ethology, and sexual selection. Despite considerable behavioral, reproductive, and karyological studies, a phylogenetic framework is lacking because most taxa are morphologically similar. In this study we use 16S mitochondrial gene sequence data to infer the phylogeny of Ophryotrocha strains commonly used in the laboratory. The resulting mtDNA topologies are generally well resolved and support a genetic split between hermaphroditic and gonochoristic species. Although the ancestral state could not be unambiguously identified, a change in reproductive strategy (i.e., hermaphroditism and gonochorism) occurred once within Ophryotrocha. Additionally, we show that sequential hermaphroditism evolved from a simultaneous hermaphroditic ancestor, and that characters previously used in phylogenetic reconstruction (i.e., jaw morphology and shape of egg mass) are homoplasic within the group.
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| 6. |
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| 7. |
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| 8. |
- Halanych, K. M., et al.
(författare)
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Phylogeography of the horse mussel Modiolus modiolus
- 2013
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Ingår i: Journal of the Marine Biological Association of the United Kingdom. - : Cambridge University Press (CUP). - 0025-3154 .- 1469-7769. ; 93:7, s. 1857-1869
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Tidskriftsartikel (refereegranskat)abstract
- Phylogeographic inferences concerning marine species are largely based on intertidal species. In high latitudes, intertidal species have been affected by ice coverage and ice scour, and therefore show northern range limitations during glaciations. In this study, we use the subtidal horse mussel (Modiolus modiolus) to investigate whether generalizations about genetic structure of high latititude intertidal species, specifically in the North Atlantic, are representative of other near shore taxa. We analysed genetic diversity, molecular variance, and geographical patterns of genetic relatedness using data from the mtDNA CO1 gene. Although we do find little to no haplotype structure in the North Atlantic, our results show that north-eastern Pacific individuals represent a different haplotype network with no haplotypes in common with Atlantic individuals. Thus, M. modiolus in the Pacific may represent an unrecognized species. Genetic diversity and population expansion times suggest a Pacific origin is most likely, with subsequent dispersal to the Atlantic. The lack of genetic structure in the Atlantic suggests that a rapid range expansion occurred less than 50 KYA, rather than a stepping stone mode of dispersal.
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| 9. |
- Halanych, K. M., et al.
(författare)
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Unsegmented annelids? Possible origins of four lophotrochozoan worm taxa
- 2002
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Ingår i: Integrative and Comparative Biology. - 1540-7063. ; 42:3, s. 678-684
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Tidskriftsartikel (refereegranskat)abstract
- In traditional classification schemes, the Annelida consists of the Polychaeta and the Clitellata (the latter including the Oligochaeta and Hirudinida). However, recent analyses suggest that annelids are much more diverse than traditionally believed, and that polychaetes are paraphyletic. Specifically, some lesser-known taxa. (previously regarded as separate phyla) appear to fall within the annelid radiation. Abundant molecular, developmental, and morphological data show that the Siboglinidae, which includes the formerly recognized Pogonophora and Vestimentifera, are derived annelids; recent data from the Elongation Factor-1alpha (EF-1alpha) gene also suggest that echiurids are of annelid ancestry. Further, the phylogenetic origins of two other lesser-known groups of marine worms, the Myzostomida and Sipuncula, have recently been called into question. Whereas some authors advocate annelid affinities, others argue that these taxa do not fall within the annelid radiation. With advances in our understanding of annelid phylogeny, our perceptions of body plan evolution within the Metazoa are changing. The evolution of segmentation probably is more plastic than traditionally believed. However, as our understanding of organismal evolution is being revised, we are also forced to reconsider the specific characters being examined. Should segmentation be considered a developmental process or an ontological endpoint?
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| 10. |
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| 11. |
- Weinberg, J. R., et al.
(författare)
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Genetic differences within and between species of deep-sea crabs (Chaceon) from the North Atlantic Ocean
- 2003
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Ingår i: Biological Bulletin. - 0006-3185. ; 204:3, s. 318-326
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Tidskriftsartikel (refereegranskat)abstract
- The deep-sea red crab Chaceon quinquedens is a commercially important crustacean on the Atlantic continental shelf and slope of North America. To assess genetic subdivision in C quinquedens, we examined the nucleotide sequence of the mitochondrial 16S rDNA gene and the internal transcribed spacers (ITS) of the nuclear ribosomal repeat in samples from southern New England and the Gulf of Mexico. We compared those data to sequences from two congeners, a sympatric species from the Florida coast, C fenneri, and an allopatric eastern Atlantic species, C affinis. The 16S rDNA data consisted of 379 aligned nucleotides obtained from 37 individuals. The greatest genetic difference among geographical groups or nominal species was between C quinquedens from southern New England and C. quinquedens from the Gulf of Mexico. Haplotypes from these two groups had a minimum of 10 differences. All I I C fenneri samples matched the most common haplotype found in C quinquedens from the Gulf of Mexico, and this haplotype was not detected in C. quinquedens from southern New England. The three haplotypes of C. affinis were unique to that recognized species, but those haplotypes differed only slightly from those of C fenneri and C. quinquedens from the Gulf of Mexico. Based on 16S rDNA and ITS data, genetic differences between C. quinquedens from southern New England and the Gulf of Mexico are large enough to conclude that these are different fishery stocks. Our results also indicate that the designation of morphological species within the commercially important genus Chaceon is not congruent with evolutionary history. The genetic similarity of C. affinis from the eastern Atlantic and C. quinquedens from the Gulf of Mexico suggests these trans-Atlantic taxa share a more recent common history than the two populations of "C. quinquedens" that we examined.
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