A new study shows that Vanilla species are unique among orchids for having evolved a multimodal mechanism of seed and fruit dispersal. Bees inadvertently transport seeds externally while collecting ...fragrance or nest material from dehiscent fruits. Rodents and marsupials consume and disperse aromatic fleshy fruits and the crustose seeds within.
DNA barcode for land plants Hollingsworth, Peter M; Forrest, Laura L; Spouge, John L ...
Proceedings of the National Academy of Sciences - PNAS,
08/2009, Letnik:
106, Številka:
31
Journal Article
Recenzirano
Odprti dostop
DNA barcoding involves sequencing a standard region of DNA as a tool for species identification. However, there has been no agreement on which region(s) should be used for barcoding land plants. To ...provide a community recommendation on a standard plant barcode, we have compared the performance of 7 leading candidate plastid DNA regions (atpF-atpH spacer, matK gene, rbcL gene, rpoB gene, rpoC1 gene, psbK-psbI spacer, and trnH-psbA spacer). Based on assessments of recoverability, sequence quality, and levels of species discrimination, we recommend the 2-locus combination of rbcL+matK as the plant barcode. This core 2-locus barcode will provide a universal framework for the routine use of DNA sequence data to identify specimens and contribute toward the discovery of overlooked species of land plants.
(Myricaceae), also known as Chinese bayberry, is an economically important, subtropical, evergreen fruit tree. The phylogenetic placement of Myricaceae within Fagales and the origin of Chinese ...bayberry's domestication are still unresolved. In this study, we report the chloroplast (cp) genome of
and take advantage of several previously reported chloroplast genomes from related taxa to examine patterns of evolution in Fagales. The cp genomes of three
individuals were 159,478, 159,568, and 159.586 bp in length, respectively, comprising a pair of inverted repeat (IR) regions (26,014-26,069 bp) separated by a large single-copy (LSC) region (88,683-88,809 bp) and a small single-copy (SSC) region (18,676-18,767 bp). Each cp genome encodes the same 111 unique genes, consisting of 77 different protein-coding genes, 30 transfer RNA genes and four ribosomal RNA genes, with 18 duplicated in the IRs. Comparative analysis of chloroplast genomes from four representative Fagales families revealed the loss of
A and the pseudogenization of
15 in all analyzed species, and
22 has been pseudogenized in
and
, but not in
or
. The genome size variations are detected mainly due to the length of intergenic spacers rather than gene loss, gene pseudogenization, IR expansion or contraction. The phylogenetic relationships yielded by the complete genome sequences strongly support the placement of Myricaceae as sister to Juglandaceae. Furthermore, seven cpDNA markers (
H-
A,
A-
K,
2-
C2,
4-
A,
D-
A,
E-
G, and
A intron) with relatively high levels of variation and variable cpSSR loci were identified within
, which will be useful in future research characterizing the population genetics of
and investigating the origin of domesticated Chinese bayberry.
People with HIV (PWH) are at increased risk for atherosclerotic cardiovascular disease (ASCVD). Proportions of vascular homing monocytes are enriched in PWH; however, little is known regarding ...monocyte-derived macrophages (MDMs) that may drive atherosclerosis in this population. We isolated PBMCs from people with and without HIV, and cultured these cells for 5 days in medium containing autologous serum to generate MDMs. Differential gene expression (DGE) analysis of MDMs from PWH identified broad alterations in innate immune signaling (IL-1β, TLR expression, PPAR βδ) and lipid processing (LXR/RXR, ACPP, SREBP1). Transcriptional changes aligned with the functional capabilities of these cells. Expression of activation markers and innate immune receptors (CD163, TLR4, and CD300e) was altered on MDMs from PWH, and these cells produced more TNFα, reactive oxygen species (ROS), and matrix metalloproteinases (MMPs) than did cells from people without HIV. MDMs from PWH also had greater lipid accumulation and uptake of oxidized LDL. PWH had increased serum levels of free fatty acids (FFAs) and ceramides, with enrichment of saturated FAs and a reduction in polyunsaturated FAs. Levels of lipid classes and species that are associated with CVD correlated with unique DGE signatures and altered metabolic pathway activation in MDMs from PWH. Here, we show that MDMs from PWH display a pro-atherogenic phenotype; they readily form foam cells, have altered transcriptional profiles, and produce mediators that likely contribute to accelerated ASCVD.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Aim: Orchidaceae is the most species-rich angiosperm family and has one of the broadest distributions. Until now, the lack of a well-resolved phylogeny has prevented analyses of orchid historical ...biogeography. In this study, we use such a phylogeny to estimate the geographical spread of orchids, evaluate the importance of different regions in their diversification and assess the role of long-distance dispersal (LDD) in generating orchid diversity. Location: Global. Methods: Analyses use a phylogeny including species representing all five orchid subfamilies and almost all tribes and subtribes, calibrated against 17 angiosperm fossils. We estimated historical biogeography and assessed the importance of different regions for rates of speciation, extinction and net species diversification. We evaluated the impact of particular LDD events on orchid diversity by asking how many species evolved in the new range subsequent to those events. Results: Orchids appear to have arisen in Australia 112 Ma (95% higher probability distribution: 102.0—120.0 Ma), then spread to the Neotropics via Antarctica by 90 Ma (HPD: 79.7—99.5 Ma), when all three continents were in close contact and apostasioids split from the ancestor of all other orchids. Ancestors of vanilloids, cypripedioids and orchidoids+ epidendroids appear to have originated in the Neotropics 84—64 Ma. Repeated long- and short-distance dispersal occurred through orchid history: stochastic mapping identified a mean total of 74 LDD events or 0.8 Ma⁻¹. Across orchid history, Southeast Asia was the most important source and maximally accelerated net diversification; across epidendroids, the Neotropics maximally accelerated diversification. Main conclusions: Our analysis provides the first biogeographical history of the orchids, implicating Australia, the Neotropics and Antarctica in their origin. LDD and life in the Neotropics — especially the Andes — had profound effects on their spread and diversification; > 97% of all orchid species are restricted to individual continents.
updated classification of Orchidaceae Chase, Mark W; Cameron, Kenneth M; Freudenstein, John V ...
Botanical journal of the Linnean Society,
February 2015, Letnik:
177, Številka:
2
Journal Article
Orchids are the most diverse family of angiosperms, with over 25 000 species, more than mammals, birds and reptiles combined. Tests of hypotheses to account for such diversity have been stymied by ...the lack of a fully resolved broad-scale phylogeny. Here, we provide such a phylogeny, based on 75 chloroplast genes for 39 species representing all orchid subfamilies and 16 of 17 tribes, time-calibrated against 17 angiosperm fossils. A supermatrix analysis places an additional 144 species based on three plastid genes. Orchids appear to have arisen roughly 112 million years ago (Mya); the subfamilies Orchidoideae and Epidendroideae diverged from each other at the end of the Cretaceous; and the eight tribes and three previously unplaced subtribes of the upper epidendroids diverged rapidly from each other between 37.9 and 30.8 Mya. Orchids appear to have undergone one significant acceleration of net species diversification in the orchidoids, and two accelerations and one deceleration in the upper epidendroids. Consistent with theory, such accelerations were correlated with the evolution of pollinia, the epiphytic habit, CAM photosynthesis, tropical distribution (especially in extensive cordilleras), and pollination via Lepidoptera or euglossine bees. Deceit pollination appears to have elevated the number of orchid species by one-half but not via acceleration of the rate of net diversification. The highest rate of net species diversification within the orchids (0.382 sp sp−1 My−1) is 6.8 times that at the Asparagales crown.
BACKGROUND AND AIMS: Most molecular phylogenetic studies of Orchidaceae have relied heavily on DNA sequences from the plastid genome. Nuclear and mitochondrial loci have only been superficially ...examined for their systematic value. Since 40% of the genera within Vanilloideae are achlorophyllous mycoheterotrophs, this is an ideal group of orchids in which to evaluate non-plastid gene sequences. METHODS: Phylogenetic reconstructions for Vanilloideae were produced using independent and combined data from the nuclear 18S, 5·8S and 26S rDNA genes and the mitochondrial atpA gene and nad1b-c intron. KEY RESULTS: These new data indicate placements for genera such as Lecanorchis and Galeola, for which plastid gene sequences have been mostly unavailable. Nuclear and mitochondrial parsimony jackknife trees are congruent with each other and previously published trees based solely on plastid data. Because of high rates of sequence divergence among vanilloid orchids, even the short 5·8S rDNA gene provides impressive levels of resolution and support. CONCLUSIONS: Orchid systematists are encouraged to sequence nuclear and mitochondrial gene regions along with the growing number of plastid loci available.
Premise
Numerous processes influence plant distributions and co‐occurrence patterns, including ecological sorting, limiting similarity, and stochastic effects. To discriminate among these processes ...and determine the spatial scales at which they operate, we investigated how functional traits and phylogenetic relatedness influence the distribution of temperate forest herbs.
Methods
We surveyed understory plant communities across 257 forest stands in Wisconsin and Michigan (USA) and applied Bayesian phylogenetic linear mixed‐effects models (PGLMMs) to quantify how functional traits and phylogenetic relatedness influence the environmental distribution of 139 herbaceous plant species along broad edaphic, climatic, and light gradients. These models also allowed us to test how functional and phylogenetic similarity affect species co‐occurrence within microsites.
Results
Leaf height, specific leaf area, and seed mass all influenced individualistic plant distributions along landscape‐scale gradients in soil texture, soil fertility, light availability, and climate. In contrast, phylogenetic relationships did not consistently predict species‐environment relationships. Neither functionally similar nor phylogenetically related herbs segregated among microsites within forest stands.
Conclusions
Trait‐mediated ecological sorting appears to drive temperate‐forest community assembly, generating individualistic plant distributions along regional environmental gradients. This finding links classic studies in plant ecology and prior research in plant physiological ecology to current trait‐based approaches in community ecology. However, our results fail to support the common assumption that limiting similarity governs local plant co‐occurrences. Strong ecological sorting among forest stands coupled with stochastic fine‐scale interactions among species appear to weaken deterministic, niche‐based assembly processes at local scales.
Phylogenomics have been widely used to resolve ambiguous and controversial evolutionary relationships among plant species and genera, and the identification of unique indels in plastomes may even ...help to understand the evolution of some plant families.
L. (Menispermaceae) consists of three species,
DC.,
L., and
Rose, which are disjuncly distributed among East Asia, Eastern North America and Mexico. Taxonomists continue to debate whether
is a distinct species, a variety of
, or simply a synonym of
. To date, no molecular systematics studies have included this doubtful species in phylogenetic analyses.
In this study, we examined phylogenomics and phylogeography of
across its entire range using 29 whole plastomes of Menispermaceae and 18 ITS1&ITS2 sequences of Menispermeae. We reconstructed interspecific relationships of
and explored plastome evolution in Menispermaceae, revealing several genomic hotspot regions for the family.
Phylogenetic and network analyses based on whole plastome and ITS1&ITS2 sequences show that
clusters into two clades with high support values, Clade A (
) and Clade B (
+
). However,
is nested within
and, as a result, we support that
is a synonym of
. We also identified important molecular variations in the plastomes of Menispermaceae. Several indels and consequently premature terminations of genes occur in Menispermaceae. A total of 54 regions were identified as the most highly variable plastome regions, with nucleotide diversity (
) values > 0.05, including two coding genes (
K,
1), four introns (
K intron,
intron,
16 intron,
A intron), and 48 intergenic spacer (IGS) regions. Of these, four informative hotspot regions (
H-
A,
F-
32,
K-
16, and
P-
J) should be especially useful for future studies of phylogeny, phylogeography and conservation genetics of Menispermaceae.
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