| 1. |
- Baldauf, Sandra L., et al.
(author)
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A Deep Hidden Diversity of Dictyostelia
- 2018
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In: Protist. - : Elsevier BV. - 1434-4610 .- 1618-0941. ; 169:1, s. 64-78
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Journal article (peer-reviewed)abstract
- Dictyostelia is a monophyletic group of transiently multicellular (sorocarpic) amoebae, whose study is currently limited to laboratory culture. This tends to favour faster growing species with robust sorocarps, while species with smaller more delicate sorocarps constitute most of the group’s taxonomic breadth. The number of known species is also small (∼150) given Dictyostelia’s molecular depth and apparent antiquity (>600 myr). Nonetheless, dictyostelid sequences are rarely recovered in culture independent sampling (ciPCR) surveys. We developed ciPCR primers to specifically target dictyostelid small subunit (SSU or 18S) rDNA and tested them on total DNAs extracted from a wide range of soils from five continents. The resulting clone libraries show mostly dictyostelid sequences (∼90%), and phylogenetic analyses of these sequences indicate novel lineages in all four dictyostelid families and most genera. This is especially true for the species-rich Heterostelium and Dictyosteliaceae but also the less species-rich Raperosteliaceae. However, the most novel deep branches are found in two very species-poor taxa, including the deepest branch yet seen in the highly divergent Cavenderiaceae. These results confirm a deep hidden diversity of Dictyostelia, potentially including novel morphologies and developmental schemes. The primers and protocols presented here should also enable more comprehensive studies of dictyostelid ecology.
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| 2. |
- Escudero, Marcial, et al.
(author)
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Karyotypic Changes through Dysploidy Persist Longer over Evolutionary Time than Polyploid Changes
- 2014
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In: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 9:1, s. e85266-
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Journal article (peer-reviewed)abstract
- Chromosome evolution has been demonstrated to have profound effects on diversification rates and speciation in angiosperms. While polyploidy has predated some major radiations in plants, it has also been related to decreased diversification rates. There has been comparatively little attention to the evolutionary role of gains and losses of single chromosomes, which may or not entail changes in the DNA content (then called aneuploidy or dysploidy, respectively). In this study we investigate the role of chromosome number transitions and of possible associated genome size changes in angiosperm evolution. We model the tempo and mode of chromosome number evolution and its possible correlation with patterns of cladogenesis in 15 angiosperm clades. Inferred polyploid transitions are distributed more frequently towards recent times than single chromosome gains and losses. This is likely because the latter events do not entail changes in DNA content and are probably due to fission or fusion events (dysploidy), as revealed by an analysis of the relationship between genome size and chromosome number. Our results support the general pattern that recently originated polyploids fail to persist, and suggest that dysploidy may have comparatively longer-term persistence than polyploidy. Changes in chromosome number associated with dysploidy were typically observed across the phylogenies based on a chi-square analysis, consistent with these changes being neutral with respect to diversification.
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| 3. |
- Fiz-Palacios, Omar, et al.
(author)
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Did terrestrial diversification of amoebas (Amoebozoa) occur in synchrony with land plants?
- 2013
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In: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 8:9, s. e74374-
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Journal article (peer-reviewed)abstract
- Evolution of lineage diversification through time is an active area of research where much progress has been made in the last decade. Contrary to the situation in animals and plants little is known about how diversification rates have evolved in most major groups of protist. This is mainly due to uncertainty about phylogenetic relationships, scarcity of the protist fossil record and the unknown diversity within these lineages. We have analyzed the evolutionary history of the supergroup Amoebozoa over the last 1000 million years using molecular dating and species number estimates. After an origin in the marine environment we have dated the colonization of terrestrial habitats by three distinct lineages of Amoebozoa: Dictyostelia, Myxogastria and Arcellinida. The common ancestor of the two sister taxa, Dictyostelia and Myxogastria, appears to have existed before the colonization of land by plants. In contrast Arcellinida seems to have diversify in synchrony with land plant radiation, and more specifically with that of mosses. Detection of acceleration of diversification rates in Myxogastria and Arcellinida points to a co-evolution within the terrestrial habitats, where land plants and the amoebozoans may have interacted during the evolution of these new ecosystems.
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| 4. |
- Fiz-Palacios, Omar, et al.
(author)
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Diversification of land plants : insights from a family-level phylogenetic analysis
- 2011
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In: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 11, s. 341-
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Journal article (peer-reviewed)abstract
- Background: Some of the evolutionary history of land plants has been documented based on the fossil record and a few broad-scale phylogenetic analyses, especially focusing on angiosperms and ferns. Here, we reconstructed phylogenetic relationships among all 706 families of land plants using molecular data. We dated the phylogeny using multiple fossils and a molecular clock technique. Applying various tests of diversification that take into account topology, branch length, numbers of extant species as well as extinction, we evaluated diversification rates through time. We also compared these diversification profiles against the distribution of the climate modes of the Phanerozoic. Results: We found evidence for the radiations of ferns and mosses in the shadow of angiosperms coinciding with the rather warm Cretaceous global climate. In contrast, gymnosperms and liverworts show a signature of declining diversification rates during geological time periods of cool global climate. Conclusions: This broad-scale phylogenetic analysis helps to reveal the successive waves of diversification that made up the diversity of land plants we see today. Both warm temperatures and wet climate may have been necessary for the rise of the diversity under a successive lineage replacement scenario.
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| 5. |
- Fiz-Palacios, Omar, et al.
(author)
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From Messinian crisis to Mediterranean climate : A temporal gap of diversification recovered from multiple plant phylogenies
- 2013
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In: Perspectives in plant ecology, evolution and systematics. - : Elsevier BV. - 1433-8319 .- 1618-0437. ; 15:2, s. 130-137
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Journal article (peer-reviewed)abstract
- Paleobotanical and molecular studies link diversification of plants in the Mediterranean Basin with the onset of the Mediterranean climate. Screening diversification before this period is needed in order to analyze whether the observed increase in diversification is a legitimate footprint denoting radiation or instead the biological signal of a previous mass extinction or rate stasis period. A shared post-Messinian temporal gap of cladogenesis has been previously observed in two Mediterranean sister genera. Based on this evidence we explored recently published molecular studies to recover lineages with similar diversification profiles exhibiting a cladogenesis gap. Using this criterion, we conducted a meta-analysis of 36 Mediterranean plant lineages with a post-Messinian temporal gap of cladogenesis, including a new molecular dating of Genista (Fabaceae). Whereas 39% of these lineages have not diversified since the Miocene, another 39% began to rediversify during the onset of the Mediterranean climate and the remaining 22% began diversifying again afterwards during the Quaternary. The pattern of Mediterranean diversification recovery after a temporal gap of cladogenesis was also obtained with phylogenetic tree simulations under birth and death processes when forcing one or two temporal shifts in diversification rates. The relative importance of the Mediterranean onset as a driving force promoting speciation or triggering extinction remains as an open question, since neither the mass extinction nor the rate stasis evolutionary scenarios can be rule out. The independent analysis of individual clades within phylogenies is also essential to detect clade-dependent patterns hidden by phylogeny-level ones. We disclose the importance of analyzing diversification patterns of Mediterranean lineages since the Miocene to understand the recent history of the Mediterranean biota.
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| 6. |
- Fiz-Palacios, Omar, et al.
(author)
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Imbalanced diversification of two Mediterranean sister genera (Bellis and Bellium, Asteraceae) within the same time frame
- 2011
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In: Plant Systematics and Evolution. - : Springer Science and Business Media LLC. - 0378-2697 .- 1615-6110. ; 295:1-4, s. 109-118
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Journal article (peer-reviewed)abstract
- The Daisies, Bellis and Bellium, form a monophyletic complex within the core Astereae (Asteraceae). Although most early diverging lineages show an African distribution, the core Astereae is today widespread on five continents with the Bellis/Bellium complex as the only representative in the Mediterranean basin. Molecular clock estimates placed the divergence of Astereae from its sister tribe Anthemideae in the Oligocene. Using a combination of three plastid genes, we estimated divergence times for different lineages of the tribe Astereae. This, together with temporal and biogeographical reconstructions using the nrITS region, allows placing and timing of the major lineages of the Bellis/Bellium complex. The age reconstruction places the divergence of the tribe Astereae in the late Miocene (18-19 million years ago), followed by an out-of-Africa dispersal into Asia where the worldwide expansion may have started. Our results suggest that the colonization of the Mediterranean basin by the Astereae started from Eurasia some 10 million years ago. A Messinian early divergence of the Bellis/Bellium complex in the Mediterranean was estimated. However, a parallel 4-million-year delay for the within-genera diversification was inferred, probably related to the establishment of the sclerophyllous Mediterranean forest. Despite a similar time frame for the within-genera diversification, today's species numbers differ considerably between Bellis (15 spp.) and Bellium (five spp.).
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| 7. |
- Fiz-Palacios, Omar, et al.
(author)
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Old Lineages in a New Ecosystem : Diversification of Arcellinid Amoebae (Amoebozoa) and Peatland Mosses
- 2014
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In: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 9:4, s. e95238-
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Journal article (peer-reviewed)abstract
- Arcellinid testate amoebae (Amoebozoa) form a group of free-living microbial eukaryotes with one of the oldest fossil records known, yet several aspects of their evolutionary history remain poorly understood. Arcellinids occur in a range of terrestrial, freshwater and even brackish habitats; however, many arcellinid morphospecies such as Hyalosphenia papilio are particularly abundant in Sphagnum-dominated peatlands, a relatively new ecosystem that appeared during the diversification of Sphagnum species in the Miocene (5-20 Myr ago). Here, we reconstruct divergence times in arcellinid testate amoebae after selecting several fossils for clock calibrations and then infer whether or not arcellinids followed a pattern of diversification that parallels the pattern described for Sphagnum. We found that the diversification of core arcellinids occurred during the Phanerozoic, which is congruent with most arcellinid fossils but not with the oldest known amoebozoan fossil (i.e. at ca. 662 or ca. 750 Myr). Overall, Sphagnum and the Hyalospheniidae exhibit different patterns of diversification. However, an extensive molecular phylogenetic analysis of distinct clades within H. papilio species complex demonstrated a correlation between the recent diversification of H. papilio, the recent diversification of Sphagnum mosses, and the establishment of peatlands.
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| 8. |
- Fiz-Palacios, Omar, et al.
(author)
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The uneven phylogeny and biogeography of Erodium (Geraniaceae) : radiations in the Mediterranean and recent recurrent intercontinental colonization
- 2010
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In: Annals of Botany. - : Oxford University Press (OUP). - 0305-7364 .- 1095-8290. ; 106:6, s. 871-884
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Journal article (peer-reviewed)abstract
- Background and Aims: The genus Erodium is a common feature of Mediterranean-type climates throughout the world, but the Mediterranean Basin has significantly higher diversity than other areas. The aim here is to reveal the biogeographical history of the genus and the causes behind the evolution of the uneven distribution. Methods Seventy-eight new nrITS sequences were incorporated with existing plastid data to explore the phylogenetic relationships and biogeography of Erodium using several reconstruction methods. Divergence times for major clades were calculated and contrasted with other previously published information. Furthermore, topological and temporal diversification rate shift analyses were employed using these data. Key Results Phylogenetic relationships among species are widely congruent with previous plastid reconstructions, which refute the classical taxonomical classification. Biogeographical reconstructions point to Asia as the ancestral area of Erodium, arising approx. 18 MYA. Four incidences of intercontinental dispersal from the Mediterranean Basin to similar climates are demonstrated. Increases in diversification were present in two independent Erodium lineages concurrently. Two bursts of diversification (3 MYA and 0·69 MYA) were detected only in the Mediterranean flora.Conclusions Two lineages diverged early in the evolution of the genus Erodium: (1) subgenus Erodium plus subgenus Barbata subsection Absinthioidea and (2) the remainder of subgenus Barbata. Dispersal across major water bodies, although uncommon, has had a major influence on the distribution of this genus and is likely to have played as significant role as in other, more easily dispersed, genera. Establishment of Mediterranean climates has facilitated the spread of the genus and been crucial in its diversification. Two, independent, rapid radiations in response to the onset of drought and glacial climate change indicate putative adaptive radiations in the genus.
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| 9. |
- He, Ding, et al.
(author)
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An Alternative Root for the Eukaryote Tree of Life
- 2014
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In: Current Biology. - : Elsevier BV. - 0960-9822 .- 1879-0445. ; 24:4, s. 465-470
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Journal article (peer-reviewed)abstract
- The root of the eukaryote tree of life defines some of the most fundamental relationships among species. It is also critical for defining the last eukaryote common ancestor (LECA), the shared heritage of all extant species. The unikont-bikont root has been the reigning paradigm for eukaryotes for more than 10 years but is becoming increasingly controversial. We developed a carefully vetted data set, consisting of 37 nuclear-encoded proteins of close bacterial ancestry (euBacs) and their closest bacterial relatives, augmented by deep sequencing of the Acrasis kona (Heterolobosea, Discoba) transcriptome. Phylogenetic analysis of these data produces a highly robust, fully resolved global phy- logeny of eukaryotes. The tree sorts all examined eukaryotes into three megagroups and identifies the Discoba, and potentially its parent taxon Excavata, as the sister group to the bulk of known eukaryote diversity, the proposed Neozoa (Amorphea + Stramenopila+Alveolata+Rhizaria+ Plantae [SARP]). All major alternative hypotheses are rejected with as little as w50% of the data, and this resolu- tion is unaffected by the presence of fast-evolving alignment positions or distant outgroup sequences. This ‘‘neozoan- excavate’’ root revises hypotheses of early eukaryote evolution and highlights the importance of the poorly stud- ied Discoba for understanding the evolution of eukaryotic diversity and basic cellular processes.
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| 10. |
- Pettersson, John H.-O., et al.
(author)
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Dating the origin of the genus Flavivirus in the light of Beringian biogeography
- 2014
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In: Journal of General Virology. - : Microbiology Society. - 0022-1317 .- 1465-2099. ; 95, s. 1969-1982
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Journal article (peer-reviewed)abstract
- The genus Flavivirus includes some of the most important human viral pathogens, and itsmembers are found in all parts of the populated world. The temporal origin of diversification of thegenus has long been debated due to the inherent problems with dating deep RNA virus evolution.A generally accepted hypothesis suggests that Flavivirus emerged within the last 10 000 years.However, it has been argued that the tick-borne Powassan flavivirus was introduced into NorthAmerica some time between the opening and closing of the Beringian land bridge that connectedAsia and North America 15 000–11 000 years ago, indicating an even older origin for Flavivirus.To determine the temporal origin of Flavivirus, we performed Bayesian relaxed molecular clockdating on a dataset with high coverage of the presently available Flavivirus diversity by combiningtip date calibrations and internal node calibration, based on the Powassan virus and Beringianland bridge biogeographical event. Our analysis suggested that Flavivirus originated ~85 000(64 000–110 000) or 120 000 (87 000–159 000) years ago, depending on the circumscriptionof the genus. This is significantly older than estimated previously. In light of our results, wepropose that it is likely that modern humans came in contact with several members of the genusFlavivirus much earlier than suggested previously, and that it is possible that the spread of severalflaviviruses coincided with, and was facilitated by, the migration and population expansion ofmodern humans out of Africa.
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