| 1. |
- Escudero, Marcial, et al.
(author)
-
Karyotypic Changes through Dysploidy Persist Longer over Evolutionary Time than Polyploid Changes
- 2014
-
In: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 9:1, s. e85266-
-
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.
|
|
| 2. |
- Fiz-Palacios, Omar, et al.
(author)
-
Old Lineages in a New Ecosystem : Diversification of Arcellinid Amoebae (Amoebozoa) and Peatland Mosses
- 2014
-
In: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 9:4, s. e95238-
-
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.
|
|
| 3. |
- He, Ding, et al.
(author)
-
An Alternative Root for the Eukaryote Tree of Life
- 2014
-
In: Current Biology. - : Elsevier BV. - 0960-9822 .- 1879-0445. ; 24:4, s. 465-470
-
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.
|
|
| 4. |
- Pettersson, John H.-O., et al.
(author)
-
Dating the origin of the genus Flavivirus in the light of Beringian biogeography
- 2014
-
In: Journal of General Virology. - : Microbiology Society. - 0022-1317 .- 1465-2099. ; 95, s. 1969-1982
-
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.
|
|
| 5. |
- Valcarcel, Virginia, et al.
(author)
-
The origin of the early differentiation of Ivies (Hedera L.) and the radiation of the Asian Palmate group (Araliaceae)
- 2014
-
In: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903 .- 1095-9513. ; 70, s. 492-503
-
Journal article (peer-reviewed)abstract
- The Asian Palmate group is one of the four major clades of the family Araliaceae that is formed by 18 genera, including ivies (Hedera L.). The Mediterranean diversity centre and temperate affinity of ivies contrast with the inferred Asian centre of diversity of the primarily tropical and subtropical Asian Palmate group. We herein investigated the sister-group relationships of Hedera to reconstruct the evolutionary context for its origin and early diversification. Seven nuclear and plastid DNA regions were analyzed in 61 Araliaceae samples including all the 18 Asian Palmate genera. Maximum Parsimony, Maximum Likelihood and Bayesian Inference were run together with a battery of topology testing analyses constraining the expected Hedera's sister-group relationships. Additionally. Bayesian polytomy resolvability and divergence time analyses were also conducted. Genome incongruence and hard nuclear and plastid basal polytomies are detected for the Asian Palmate group where the lineage of Hedera is placed. Topology testing analyses do not allow rejecting any of the tentative sisters of Hedera. An early radiation with inter-lineage hybridization and genome doubling is suggested for the Asian Palmate group where all the seven temperate genera, including Hedera, seem to have played an important role. The radiation took placed during the Upper Cretaceous in Asia under a general cooling and the eastern Asian mountain uplift that produced new temperate environments and promoted lineage connections. This allows us to hypothesize that the origin of the Hedera lineage may fit in a temperate niche conservatism scenario where the combination of the radiation with lineage admixtures prevents us from discovering its sister-group.
|
|
