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.
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.
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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Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
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 1 but is becoming increasingly controversial 2–4. 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 phylogeny of eukaryotes. The tree sorts all examined eukaryotes into three megagroups and identifies the Discoba, and potentially its parent taxon Excavata 5, as the sister group to the bulk of known eukaryote diversity, the proposed Neozoa (Amorphea + Stramenopila+Alveolata+Rhizaria+Plantae SARP 6). All major alternative hypotheses are rejected with as little as ∼50% of the data, and this resolution 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 studied Discoba for understanding the evolution of eukaryotic diversity and basic cellular processes.
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•A new 37-protein data set produces a robust and rooted eukaryote tree•All examined eukaryotes form three megagroups: Amorphea, SARP, and Excavata•A new neozoan-excavate root is proposed with strong statistical support•Discoba (Excavata) has a long, unique, and largely unknown evolutionary history
He et al. developed a novel data set of 37 eukaryotic proteins of bacterial ancestry (euBacs) to explore the major radiations of eukaryotes. A neozoan-excavate root is found, with the little-known Discoba (and potentially its parent taxon Excavata) identified as sister group to the bulk of known eukaryote diversity.
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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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The genus Flavivirus includes some of the most important human viral pathogens, and its members are found in all parts of the populated world. The temporal origin of diversification of the genus 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 North America some time between the opening and closing of the Beringian land bridge that connected Asia 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 clock dating on a dataset with high coverage of the presently available Flavivirus diversity by combining tip date calibrations and internal node calibration, based on the Powassan virus and Beringian land 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 circumscription of the genus. This is significantly older than estimated previously. In light of our results, we propose that it is likely that modern humans came in contact with several members of the genus Flavivirus much earlier than suggested previously, and that it is possible that the spread of several flaviviruses coincided with, and was facilitated by, the migration and population expansion of modern humans out of Africa.
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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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
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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Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Differences in plant annual/perennial habit are hypothesized to cause a generation time effect on divergence rates. Previous studies that compared rates of divergence for internal transcribed spacer ...(ITS1 and ITS2) sequences of nuclear ribosomal DNA (nrDNA) in angiosperms have reached contradictory conclusions about whether differences in generation times (or other life history features) are associated with divergence rate heterogeneity. We compared annual/perennial ITS divergence rates using published sequence data, employing sampling criteria to control for possible artifacts that might obscure any actual rate variation caused by annual/perennial differences.
Relative rate tests employing ITS sequences from 16 phylogenetically-independent annual/perennial species pairs rejected rate homogeneity in only a few comparisons, with annuals more frequently exhibiting faster substitution rates. Treating branch length differences categorically (annual faster or perennial faster regardless of magnitude) with a sign test often indicated an excess of annuals with faster substitution rates. Annuals showed an approximately 1.6-fold rate acceleration in nucleotide substitution models for ITS. Relative rates of three nuclear loci and two chloroplast regions for the annual Arabidopsis thaliana compared with two closely related Arabidopsis perennials indicated that divergence was faster for the annual. In contrast, A. thaliana ITS divergence rates were sometimes faster and sometimes slower than the perennial. In simulations, divergence rate differences of at least 3.5-fold were required to reject rate constancy in > 80 % of replicates using a nucleotide substitution model observed for the combination of ITS1 and ITS2. Simulations also showed that categorical treatment of branch length differences detected rate heterogeneity > 80% of the time with a 1.5-fold or greater rate difference.
Although rate homogeneity was not rejected in many comparisons, in cases of significant rate heterogeneity annuals frequently exhibited faster substitution rates. Our results suggest that annual taxa may exhibit a less than 2-fold rate acceleration at ITS. Since the rate difference is small and ITS lacks statistical power to reject rate homogeneity, further studies with greater power will be required to adequately test the hypothesis that annual and perennial plants have heterogeneous substitution rates. Arabidopsis sequence data suggest that relative rate tests based on multiple loci may be able to distinguish a weak acceleration in annual plants. The failure to detect rate heterogeneity with ITS in past studies may be largely a product of low statistical power.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
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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•nrITS and 6-gene plastid phylogenetic incongruence and hard basal polytomies.•Upper Cretaceous early radiation coupled with lineage admixture in the Asian Palmate group.•Temperate ...lineages involved in the early diversification of the mainly tropical Asian Palmate group.•No sister recovered for the temperate Hedera lineage as it diverged during the Asian Palmate early radiation.•24–39myr of lineage isolation predating the Miocene diversification of extant species of Hedera.
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.
A Deep Hidden Diversity of Dictyostelia Baldauf, Sandra L.; Romeralo, Maria; Fiz-Palacios, Omar ...
Protist,
02/2018, Letnik:
169, Številka:
1
Journal Article
Recenzirano
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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