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1.
Aralia sect. Aralia (Araliaceae) consists of approximately eight species disjunctly distributed in Asia and North America. Phylogenetic and biogeographic analyses were conducted using sequences of the internal transcribed spacer regions of the nuclear ribosomal DNA. Aralia racemosa from eastern North America was sister to A. californica from western North America. Aralia cordata from eastern Asia did not form a species-pair relationship with the eastern North American A. racemosa. The two subspecies of A. racemosa formed a monophyletic group. Biogeographic analyses showed a close area relationship between eastern North America and western North America. The Himalayas were cladistically basal and eastern Asia was placed between the Himalayas and North America. The biogeographic analysis supported the origin of the eastern Asian and eastern North American disjunct pattern in Aralia sect. Aralia via the Bering land bridges. Comparisons with results of phylogenetic analyses of other genera suggested that (1) the floristic connection between eastern North America and western North America may be stronger than previously thought; and (2) the biogeographic patterns in the Northern Hemisphere are complex. Furthermore, a lack of correlation between sequence divergence values and phylogenetic positions was observed, suggesting the importance of a phylogenetic framework in biogeographic analyses. 相似文献
2.
AJ Harris Ping‐Ting Chen Xin‐Wei Xu Jian‐Qiang Zhang Xue Yang Jun Wen 《植物分类学报：英文版》2017,55(2):124-141
3.
Traditional phylogenies based on analysis of multiple genes have failed to obtain a well‐resolved evolutionary history for the backbone of the Asian Palmate group of Araliaceae, the largest clade of the family. In this study, we applied the genome skimming approach of next‐generation sequencing to address whether the lack of resolution at the base of the Asian Palmate tree is due to molecular sampling error or the footprint of ancient radiation. Twenty‐nine complete plastid genomes of Araliaceae (17 newly sequenced) were analyzed (RAxML, Beast, Lagrange, and BioGeoBears) to provide the first phylogenomic reconstruction of the group (95% of genera included). As a result, the early divergences of the Asian Palmate group have been clarified but the backbone of its core is not totally resolved, with short internal branches pointing to an ancient radiation scenario. East Asia is inferred as the most likely ancestral area for the Asian Palmate group (from late Paleocene to Eocene) from which early colonization of the Neotropics is inferred during the Eocene. The radiation of the core Palmate group took place during the late Eocene, most likely in the context of the Boreotropical hypothesis. Recurrent episodes of southward migration (to the tropics) coupled with northern latitude local extinctions (promoting geographic isolation of lineages) followed by northward expansion (promoting contact of lineages that erased the trace of preceding geographic isolation) are hypothesized to have linked to the alternation of the cold and warm periods of the Eocene. 相似文献
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Julia M. Richardson David J. Finnegan Malcolm D. Walkinshaw 《Acta Crystallographica. Section F, Structural Biology Communications》2007,63(5):434-437
A complex formed between Mos1 transposase and its inverted‐repeat DNA has been crystallized. The crystals diffract to 3.25 Å resolution and exhibit monoclinic (P21) symmetry, with unit‐cell parameters a = 120.8, b = 85.1, c = 131.6 Å, β = 99.3°. The X‐ray diffraction data display noncrystallographic twofold symmetry and characteristic dsDNA diffraction at ∼3.3 Å. Biochemical analyses confirmed the presence of DNA and full‐length protein in the crystals. The relationship between the axis of noncrystallographic symmetry, the unit‐cell axes and the DNA diffraction pattern are discussed. The data are consistent with the previously proposed model of the paired‐ends complex containing a dimer of the transposase. 相似文献
6.
We define the geographical distributions of mitochondrial DNA (mtDNA) lineages embedded within a broadly distributed, arid-dwelling toad, Bufo punctatus. These patterns were evaluated as they relate to hypothesized vicariant events leading to the formation of desert biotas within western North America. We assessed mtDNA sequence variation among 191 samples from 82 sites located throughout much of the species' range. Parsimony-based haplotype networks of major identified lineages were used in nested clade analysis (NCA) to further elucidate and evaluate shallow phylogeographic patterns potentially associated with Quaternary (Pleistocene-Holocene) vicariance and dispersal. Phylogenetic analyses provided strong support for three monophyletic lineages (clades) within B. punctatus. The geographical distributions of the clades showed little overlap and corresponded to the general boundaries of the Peninsular Desert, and two continental desert regions, Eastern (Chihuahuan Desert-Colorado Plateau) and Western (Mojave-Sonoran deserts), geographically separated along the Rocky Mountains and Sierra Madre Occidental. The observed divergence levels and congruence with postulated events in earth history implicate a late Neogene (latest Miocene-early Pliocene) time frame for separation of the major mtDNA lineages. Evaluation of nucleotide and haplotype diversity and interpretations from NCA reveal that populations on the Colorado Plateau resulted from a recent, likely post-Pleistocene, range expansion from the Chihuahuan Desert. Dispersal across historical barriers separating major continental clades appear to be recent, resulting in secondary contacts in at least two areas. Given the observed contact between major clades, we speculated as to why the observed deep phylogeographic structure has not been eroded during the multiple previous interglacials of the Pleistocene. 相似文献
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Rgine Janel‐Bintz Lauriane Kuhn Philippe Frit Johana Chicher Jrme Wagner Lajos Haracska Philippe Hammann Agns M Cordonnier 《Proteomics》2020,20(3-4)
It is established that short inverted repeats trigger base substitution mutagenesis in human cells. However, how the replication machinery deals with structured DNA is unknown. It has been previously reported that in human cell‐free extracts, DNA primer extension using a structured single‐stranded template is transiently blocked at DNA hairpins. Here, the proteomic analysis of proteins bound to the DNA template is reported and evidence that the DNA‐PK complex (DNA‐PKcs and the Ku heterodimer) recognizes, and is activated by, structured single‐stranded DNA is provided. Hijacking the DNA‐PK complex by double‐stranded oligonucleotides results in a large removal of the pausing sites and an elevated DNA extension efficiency. Conversely, DNA‐PKcs inhibition results in its stabilization on the template, along with other proteins acting downstream in the Non‐Homologous End‐Joining (NHEJ) pathway, especially the XRCC4‐DNA ligase 4 complex and the cofactor PAXX. Retention of NHEJ factors to the DNA in the absence of DNA‐PKcs activity correlates with additional halts of primer extension, suggesting that these proteins hinder the progression of the DNA synthesis at these sites. Overall these results raise the possibility that, upon binding to hairpins formed onto ssDNA during fork progression, the DNA‐PK complex interferes with replication fork dynamics in vivo. 相似文献
9.
Previous molecular phylogenetic studies of Fabaceae indicated that species of Wisteria, an intercontinental disjunct genus between eastern Asia and eastern North America, formed a clade derived from within Callerya. However, interspecific relationships were not well resolved or supported. In this study, we used sequences of the nuclear ribosomal DNA internal transcribed spacer region and the chloroplast gene matK to examine interspecific relationships and explore implications of the phylogeny for the systematics and biogeography of Wisteria. Our results showed that Wisteria with deciduous leaves and racemose inflorescences formed a strongly supported clade derived from within the paraphyletic Callerya. Afgekia was also found to be included within Callerya. Therefore, our data support the merger ofAfgekia, Callerya, and Wisteria. The phylogenetic pattern suggested that the deciduousness in Wisteria may be a derived trait likely in response to temperate climate, and the racemose inflorescences in the Afgekia–Callerya–Wisteria clade may have evolved from panicles. Our study also provided strong support for the sister relationship of the North American and eastern Asian species of Wisteria. In the Asian clade, Wisteria brachybotrys Siebold & Zucc. of Japan was sister to the clade containing W. floribunda (Willd.) DC of Japan and Korea, and W. sinensis (Sims) Sweet of China. However, our data offered weak support for the sister relationship ofW. floribunda and W. sinensis. Our divergence time and biogeographic analyses suggested that the eastern Asian–North American disjunction in Wisteria may have occurred through a dispersal event in the middle Miocene (13.4 Mya) from the Old World to the New World across the Bering land bridge followed by vicariance in the late Miocene (6.8 Mya). This study added another example to the “out of Asia” migration for the eastern Asian–eastern North American disjunction. 相似文献
10.
The Lycaeides butterfly species complex in North America consists of two nominal, morphologically defined species. These butterflies are ecologically diverse and appear to be distributed as a geographically complex mosaic of locally differentiated populations that may be undergoing adaptive radiation. We asked whether patterns of molecular genetic variation within the species complex are congruent with currently recognized morphological species and whether the distribution of molecular variation is consistent with the hypothesis that Pleistocene climate changes contributed to the process of differentiation within the genus. Variation in the form of the genitalia from 726 males from 59 populations clearly distinguishes both species with only six populations containing morphologically intermediate or ambiguous individuals. However, partitioning of molecular variance in a 236 bp section of the mitochondrial AT-rich region from 628 individuals (57 populations) surveyed using single strand conformation polymorphism analysis (SSCP) indicates that only 26% of the total genetic variation is distributed along nominal species boundaries as defined by morphology. Instead, three phylogeographical groups were detected, represented by three major haplotype clades, which account for 90% of the total genetic variance. Pleistocene glaciations appear to have fostered divergence during glacial maxima, while post-glacial range expansions created opportunities for gene exchange and reticulation along suture zones between geographical groups. Data presented here allow us to make inferences about the history of the species complex. However, evidence of ancestral polymorphism and reticulation limit our ability to define species boundaries based on mitochondrial DNA sequence variation. 相似文献
11.
Leho Tedersoo Lauri Laanisto Saleh Rahimlou Aurèle Toussaint Tiit Hallikma Meelis Pärtel 《植被学杂志》2018,29(3):560-568
Plants associated with symbiotic N‐fixing bacteria play important roles in early successional, riparian and semi‐dry ecosystems. These so‐called N‐fixing plants are widely used for reclamation of disturbed vegetation and improvement of soil fertility in agroforestry. Yet, available information about plants that are capable of establishing nodulation is fragmented and somewhat outdated. This article introduces the NodDB database of N‐fixing plants based on morphological and phylogenetic evidence (available at https://doi.org/10.15156/bio/587469 ) and discusses plant groups with conflicting reports and interpretation, such as certain legume clades and the Zygophyllaceae family. During angiosperm evolution, N‐fixing plants became common in the fabid rather than in the ‘nitrogen‐fixing’ clade. The global GBIF plant species distribution data indicated that N‐fixing plants tend to be relatively more diverse in savanna and semi‐desert biomes. The compiled and re‐interpreted information about N‐fixing plants enables accurate analyses of biogeography and community ecology of biological N fixation. 相似文献
12.
The eastern Asian (EA)–eastern North American (ENA) floristic disjunction represents a major pattern of phytogeography of the Northern Hemisphere. Despite 20 years of studies dedicated to identification of taxa that display this disjunct pattern, its origin and evolution remain an open question, especially regarding post‐isolation evolution. The blue‐ or white‐fruited dogwoods (BW) are the most species‐rich among the four major clades of Cornus L., consisting of ~35 species divided into three subgenera (subg. Yinquania, subg. Mesomora, and subg. Kraniopsis). The BW group provides an excellent example of the EA–ENA floristic disjunction for biogeographic study due to its diversity distribution centered in eastern Asia and eastern North America, yet its species relationships and delineation have remained poorly understood. In this study, we combined genome‐wide markers from RAD‐seq, morphology, fossils, and climate data to understand species relationships, biogeographic history, and ecological niche and morphological evolution. Our phylogenomic analyses with RAxML and MrBayes recovered a strongly supported and well‐resolved phylogeny of the BW group with three intercontinental disjunct clades in EA and ENA or Eurasia and North America, of which two are newly identified within subg. Kraniopsis. These analyses also recovered a potential new species but failed to resolve relationships within the C. hemsleyi–C. schindleri complex. In an effort to develop an approach to reduce computation time, analysis of different nodal age settings in treePL suggests setting a node's minimum age constraint to the lower bound of a fossil's age range to obtain similar ages to that of BEAST. Divergence time analyses with BEAST and treePL dated the BW stem back to the very Late Cretaceous and the divergence of the three subgenera in the Paleogene. By integrating fossil ages and morphology, a total evidence‐based dating approach was used in conjunction with time‐slice probabilities of dispersal under a DEC model to resolve ancestral ranges of each disjunct in the Miocene: Eurasia and ENA (disjunct 1), EA and western North America (disjunct 2), and EA (disjunct 3). The dated biogeographic history supports dispersal via the North Atlantic Land Bridge in the late Paleogene in disjunct 1 and dispersal via the Bering Land Bridge in the Miocene for disjuncts 2 and 3. Character mapping with a stochastic model in phytools and comparison of ecological niche, morphospace, and rate of evolution indicated differential divergence patterns in morphology, ecological niche, and molecules between disjunct sisters. Although morphological stasis was observed in most of the characters, evolutionary changes in growth habit and some features of leaf, flower, and fruit morphology occurred in one or both sister clades. A significant differentiation of ecological habitats in temperature, precipitation, and elevation between disjunct sisters was observed, suggesting a role of niche divergence in morphological evolution post‐isolation. The patterns of evolutionary rate between morphology and molecules varied among disjunct clades and were not always congruent between morphology and molecules, suggesting cases of non‐neutral morphological evolution driven by ecological selection. Our phylogenetic evidence and comparisons of evolutionary rate among disjunct lineages lend new insights into the formation of the diversity anomaly between EA and ENA, with particular support of an early diversification in EA. These findings, in conjunction with previous studies, again suggest that the EA–ENA disjunct floras are an assembly of lineages descended from the Mesophytic Forests that evolved from the early Paleogene “boreotropical flora” through varied evolutionary pathways across lineages. 相似文献
13.
Samuel E. Munoz David J. Mladenoff Sissel Schroeder John W. Williams 《Journal of Biogeography》2014,41(12):2195-2210
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Xiang QY Zhang WH Ricklefs RE Qian H Chen ZD Wen J Hua JL 《Evolution; international journal of organic evolution》2004,58(10):2175-2184
The eastern Asian (EAS)-eastern North American (ENA) floristic disjunction is one of the best-known biogeographic patterns in the Northern Hemisphere. Recent paleontological and molecular analyses have illuminated the origins of the biogeographic pattern, but subsequent diversification and evolution of the disjunct floras in each of the two continents after isolation remains poorly understood. Although similar in climate and floristic composition, EAS has twice as many species as ENA in genera occurring in both regions. Explaining such differences in species diversity between regions with similar environmental conditions (diversity anomalies) is an important goal of the study of the global patterns of biodiversity. We used a phylogenetic approach to compare rates of net speciation and molecular evolution between the two regions. We first identified EAS-ENA disjunct sister clades from ten genera (Asarum, Buckleya, Carpinus, Carya, Cornus, Hamamelis, Illicium, Panax, Stewartia, and Styrax) that represent diverse angiosperm lineages using phylogenetic analyses of ITS (internal transcribed spacer of nuclear ribosomal DNA) sequence data. Species richness and substitution rate of ITS between sister clades were compared. The results revealed a pattern of greater species diversity in the EAS counterparts. A positive relationship between species diversity and ITS substitution rate was also documented. These results suggest greater net speciation and accelerated molecular evolution in EAS. The data support the idea that a regional difference in net speciation rate related to topographic heterogeneity contributes to the diversity anomaly between EAS and ENA. The close relationship between rates of ITS evolution and species richness further suggests that species production may be directly linked to rate of nucleotide substitution. 相似文献
16.
Mapped cpDNA restriction site characters were analyzed cladistically and the resulting phylogenetic hypotheses were used to test monophyly and relationships of the infrageneric classification of Lathyrus (Fabaceae) proposed by Kupicha (1983, Notes from the Royal Botanic Garden Edinburgh 41: 209-244). The validity of previously proposed classification systems and questions presented by these classification schemes were explored. Two cpDNA regions, rpoC (rpoC1, its intron, part of rpoC2, and their intergenic spacer) and IR- (psbA, trnH-GUG, part of ndhF, and their intergenic spacers), were analyzed for 42 Lathyrus and two Vicia species. PCR (polymerase chain reaction) amplified rpoC and IR- products digested with 31 and 27 restriction endonucleases, respectively, resulted in 109 potentially informative characters. The strict consensus tree suggests that several of Kupicha's sections may be combined in order to constitute clades. The widespread section Orobus and the South American section Notolathyrus should be combined. Section Lathyrus, characterized by a twisted style, should either include sections Orobon and Orobastrum or be redefined as three sections, one of which is characterized by a 100 base pair deletion in the IR- region. Finally, a weighted parsimony analysis positions sections Clymenum (excluding L. gloeospermus) and Nissolia, both with phyllodic leaves, as sister sections. The affiliation of Lathyrus gloeospermus (section Clymenum) remains problematic. 相似文献
17.
Xiao‐Long Jiang Andrew L. Hipp Min Deng Tao Su Zhe‐Kun Zhou Meng‐Xiao Yan 《Journal of Biogeography》2019,46(10):2203-2214
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Matthew J. Clement James D. Nichols Jaime A. Collazo Adam J. Terando James E. Hines Steven G. Williams 《Ecology and evolution》2019,9(4):1985-2003
Understanding the relative impact of climate change and land cover change on changes in avian distribution has implications for the future course of avian distributions and appropriate management strategies. Due to the dynamic nature of climate change, our goal was to investigate the processes that shape species distributions, rather than the current distributional patterns. To this end, we analyzed changes in the distribution of Eastern Wood Pewees (Contopus virens) and Red‐eyed Vireos (Vireo olivaceus) from 1997 to 2012 using Breeding Bird Survey data and dynamic correlated‐detection occupancy models. We estimated the local colonization and extinction rates of these species in relation to changes in climate (hours of extreme temperature) and changes in land cover (amount of nesting habitat). We fit six nested models to partition the deviance explained by spatial and temporal components of land cover and climate. We isolated the temporal components of environmental variables because this is the essence of global change. For both species, model fit was significantly improved when we modeled vital rates as a function of spatial variation in climate and land cover. Model fit improved only marginally when we added temporal variation in climate and land cover to the model. Temporal variation in climate explained more deviance than temporal variation in land cover, although both combined only explained 20% (Eastern Wood Pewee) and 6% (Red‐eyed Vireo) of temporal variation in vital rates. Our results showing a significant correlation between initial occupancy and environmental covariates are consistent with biological expectation and previous studies. The weak correlation between vital rates and temporal changes in covariates indicated that we have yet to identify the most relevant components of global change influencing the distributions of these species and, more importantly, that spatially significant covariates are not necessarily driving temporal shifts in avian distributions. 相似文献
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Qiujia Chen Millie Georgiadis 《Acta Crystallographica. Section F, Structural Biology Communications》2016,72(9):713-719
Transposable elements have played a critical role in the creation of new genes in all higher eukaryotes, including humans. Although the chimeric fusion protein SETMAR is no longer active as a transposase, it contains both the DNA‐binding domain (DBD) and catalytic domain of the Hsmar1 transposase. The amino‐acid sequence of the DBD has been virtually unchanged in 50 million years and, as a consequence, SETMAR retains its sequence‐specific binding to the ancestral Hsmar1 terminal inverted repeat (TIR) sequence. Thus, the DNA‐binding activity of SETMAR is likely to have an important biological function. To determine the structural basis for the recognition of TIR DNA by SETMAR, the design of TIR‐containing oligonucleotides and SETMAR DBD variants, crystallization of DBD–DNA complexes, phasing strategies and initial phasing experiments are reported here. An unexpected finding was that oligonucleotides containing two BrdUs in place of thymidines produced better quality crystals in complex with SETMAR than their natural counterparts. 相似文献
20.
Yan Y Zhang Y Yang K Sun Z Fu Y Chen X Fang R 《The Plant journal : for cell and molecular biology》2011,65(5):820-828
Small silencing RNAs (sRNAs) are non-coding RNA regulators that negatively regulate gene expression by guiding mRNA degradation, translation repression or chromatin modification. Plant sRNAs play crucial roles in various developmental processes, hormone signaling, immune responses and adaptation to a variety of abiotic stresses. miR441 and miR446 were previously annotated as microRNAs (miRNAs) because their precursors can form typical stem-loop structures, but are not considered as real miRNAs because of inconsistency with some ancillary criteria of the recent guidelines for annotation of plant miRNAs. We tentatively rename them small interfering (si)R441 and siR446, respectively, in this study. It has recently been shown that the precursors of siR441 and siR446 might originate from the miniature inverted-repeat transposable element (MITE) Stowaway1. In this report, we show that, in contrast with Dicer-like (DCL)3- and RNA-dependent RNA polymerase (RDR)2-dependent MITE-derived ra-siRNAs, siR441 and siR446 are processed by OsDCL3a but independent of OsRDR2, indicating that siR441 and siR446 are generated from single-stranded stem-loop precursors. We also show that abscisic acid (ABA) and abiotic stresses downregulate the expression of siR441 and siR446 but, surprisingly, increase the accumulation of their precursors in rice plants, implying that processing of siRNA precursors is inhibited. We provide evidence to show that this defective processing is due to increased precursor accumulation per se, possibly by intermolecular self-pairing of the processing intermediate sequences, thus hindering their normal processing. Functional examinations indicate that siR441 and siR446 are positive regulators of rice ABA signaling and tolerance to abiotic stress, possibly by regulating MAIF1 expression. 相似文献