Abstract:
:The plastid trnL-F region has proved useful in molecular phylogenetic studies addressing diverse evolutionary questions from biogeographic history to character evolution in a broad range of plant groups. An important assumption for phylogenetic reconstruction is that data used in combined analyses contain the same phylogenetic signal. The trnL-F region is often used in combined analyses of multiple chloroplast markers. These markers are assumed to contain congruent phylogenetic signal due to lack of recombination. Here we show that trnL-F sequences display a phylogenetic signal conflicting with that of other chloroplast markers in Annonaceae, and we demonstrate that this conflict results from ancient paralogy. TrnL-F copy 2 diverged from trnL-F copy 1 (as used in family-wide phylogenetic analyses) in a direct ancestor of the Annonaceae. Although this divergence dates back 88 million years or more, the exons of both copies appear to be intact. In this case, assuming that (putative) chloroplast markers contain the same phylogenetic signal results in an incorrect topology and an incorrect estimate of ages. Our study demonstrates that researchers should be cautious when interpreting gene phylogenies, irrespective of the genome from which they are presumed to have been sampled.
journal_name
Am J Botjournal_title
American journal of botanyauthors
Pirie MD,Vargas MP,Botermans M,Bakker FT,Chatrou LWdoi
10.3732/ajb.94.6.1003subject
Has Abstractpub_date
2007-06-01 00:00:00pages
1003-16issue
6eissn
0002-9122issn
1537-2197pii
94/6/1003journal_volume
94pub_type
杂志文章abstract:UNLABELLED:• PREMISE OF THE STUDY:Flower color is one of the best-studied floral traits in terms of its genetic basis and ecological significance, yet few studies have examined the processes that shape its evolution across deep timescales. Advances in comparative methods along with larger phylogenies for floral radiat...
journal_title:American journal of botany
pub_type: 杂志文章
doi:10.3732/ajb.1500163
更新日期:2015-07-01 00:00:00
abstract::Many plant species are characterized by a life cycle with a long-lived, subterranean phase that is completely dependent on mycorrhizal fungal symbionts for fixed carbon. This type of life cycle is both phylogenetically and ecologically widespread and is found in diverse vascular plant lineages from the tropics to suba...
journal_title:American journal of botany
pub_type: 杂志文章
doi:10.3732/ajb.94.7.1248
更新日期:2007-07-01 00:00:00
abstract::In turnip mitochondria the cox2 gene is partially contained within a 2-kb (kilobase) direct repeat that is the site of homologous recombination events that generate subgenomic molecules. Because of its partial presence within the direct repeat, the turnip cox2 gene exists in four genomic contexts, two on the master ch...
journal_title:American journal of botany
pub_type: 杂志文章
doi:
更新日期:1998-02-01 00:00:00
abstract::Phylogenetic relationships and biogeography of the genus Cerastium were studied using sequences of three noncoding plastid DNA regions (trnL intron, trnL-trnF spacer, and psbA-trnH spacer). A total of 57 Cerastium taxa was analyzed using two species of the putative sister genus Stellaria as outgroups. Maximum parsimon...
journal_title:American journal of botany
pub_type: 杂志文章
doi:10.3732/ajb.91.6.943
更新日期:2004-06-01 00:00:00
abstract::The selective maintenance of gynodioecy depends on the relative fitness of the male-sterile (female) and hermaphroditic morphs. Females may compensate for their loss of male fitness by reallocating resources from male function (pollen production and pollinator attraction) to female function (seeds and fruits), thus in...
journal_title:American journal of botany
pub_type: 杂志文章
doi:
更新日期:2000-05-01 00:00:00
abstract:PREMISE:Outcomes of species interactions, especially mutualisms, are notoriously dependent on environmental context, and environments are changing rapidly. Studies have investigated how mutualisms respond to or ameliorate anthropogenic environmental changes, but most have focused on nutrient pollution or climate change...
journal_title:American journal of botany
pub_type: 杂志文章
doi:10.1002/ajb2.1404
更新日期:2020-02-01 00:00:00
abstract::Many plant species contain populations with more than one polyploid cytotype, but little is known of the mechanisms maintaining several cytotypes in a population. Andropogon gerardii cytotypes were compared to evaluate different models of autopolyploid cytotype coexistence. The enneaploid (90 chromosome, 9x) cytotype ...
journal_title:American journal of botany
pub_type: 杂志文章
doi:
更新日期:1999-07-01 00:00:00
abstract:PREMISE OF THE STUDY:The evolutionary shift from radial to bilateral symmetry in flowers is generally associated with the evolution of low flower-size variation. This phenomenon supports the hypothesis that the lower size variation in bilateral flowers can be attributed to low pollinator diversity. In this study, we pr...
journal_title:American journal of botany
pub_type: 杂志文章
doi:10.3732/ajb.1500371
更新日期:2015-12-01 00:00:00
abstract::Molecular studies of apomictic plant species often detect more genotypic variation than predicted from their assumed reproductive mode. The two most commonly invoked mechanisms to explain these high levels of variation are recombination, via facultative sexuality, and mutation. The potential for sexual reproduction in...
journal_title:American journal of botany
pub_type: 杂志文章
doi:10.3732/ajb.91.1.37
更新日期:2004-01-01 00:00:00
abstract::Nuclear DNA contents (4C) were estimated by Feulgen microdensitometry in 27 species of slipper orchids. These data and recent information concerning the molecular systematics of Cypripedioideae allow an interesting re-evaluation of karyotype and genome size variation among slipper orchids in a phylogenetic context. DN...
journal_title:American journal of botany
pub_type: 杂志文章
doi:
更新日期:1998-05-01 00:00:00
abstract:PREMISE OF THE STUDY:A key question in evolutionary biology is why some clades are more successful by being widespread geographically, biome diverse, or species-rich. To extend understanding of how shifts in area, biomes, and pollinators impact diversification in plants, we examined the relationships of these shifts to...
journal_title:American journal of botany
pub_type: 杂志文章
doi:10.1002/ajb2.1268
更新日期:2019-04-01 00:00:00
abstract::We present here the first molecular phylogeny of tribe Diseae (Orchidoideae: Orchidaceae). Nuclear ribosomal ITS1, 5.8S rDNA, and ITS2 sequences were compared for 30 Diseae, 20 Orchideae, and four Cranichideae and Diurideae outgroups. ITS - rDNA sequences exhibited a transition:transversion ratio of 1.3 and extensive ...
journal_title:American journal of botany
pub_type: 杂志文章
doi:
更新日期:1999-06-01 00:00:00
abstract::Phylogenetic relationships of eight species of Saintpaulia H. Wendl., 19 species of Streptocarpus Lindl. (representing all major growth forms within the genus), and two outgroups (Haberlea rhodopensis Friv., Chirita spadiciformis W. T. Wang) were examined using comparative nucleotide sequences from the two internal tr...
journal_title:American journal of botany
pub_type: 杂志文章
doi:
更新日期:1997-07-01 00:00:00
abstract::Propagule banks are assumed to be able to store considerable genetic variability. Bryophyte populations are expected to rely more heavily on stored propagules than those of seed plants due to the vulnerability of the haploid gametophyte. This reliance has important implications for the genetic structure and evolutiona...
journal_title:American journal of botany
pub_type: 杂志文章
doi:10.3732/ajb.2007283
更新日期:2008-05-01 00:00:00
abstract::Welwitschiaceae, a family in the Gnetales, is known today from only one extant species, Welwitschia mirabilis. This species is distributed in the Namibian desert, along the western coast of southern Africa, about 10 km inland from the coast. Very little is known about the fossil record of this family. Lower Cretaceous...
journal_title:American journal of botany
pub_type: 杂志文章
doi:10.3732/ajb.92.8.1294
更新日期:2005-08-01 00:00:00
abstract:PREMISE OF THE STUDY:Microsatellite markers were isolated and characterized from Dacryodes edulis (Burseraceae), a tropical rainforests fruit tree of central Africa. METHODS AND RESULTS:Using an enrichment protocol, six microsatellites loci were developed from Dacryodes edulis. We investigated polymorphism using 45 tr...
journal_title:American journal of botany
pub_type: 杂志文章
doi:10.3732/ajb.1000463
更新日期:2011-04-01 00:00:00
abstract::Fluorescence in situ hybridization (FISH) of a large-insert genomic clone, BAC 22B2, previously suggested that Sorghum bicolor (2n = 20) has the tetraploid architecture A(b)A(b)B(b)B(b). Here, we report on BAC 22B2 subclone pCEN38 (1047-bp insert) as related to sorghum and sugarcane. Mitotic FISH of six different subc...
journal_title:American journal of botany
pub_type: 杂志文章
doi:
更新日期:2000-12-01 00:00:00
abstract:PREMISE OF THE STUDY:Phylogenetic incongruence between "gene trees" and "species trees" has been widely acknowledged in phylogenetic research. Conflicts may emerge from several processes including paralogy, hybridization, and incomplete lineage sorting. Although phylogenetic incongruence appears common, its impact on m...
journal_title:American journal of botany
pub_type: 杂志文章
doi:10.3732/ajb.1400527
更新日期:2015-04-01 00:00:00
abstract:UNLABELLED: PREMISE OF THE STUDY:Microsatellite markers were isolated and characterized in Mimulus ringens (Phrymaceae), a herbaceous wetland perennial, to facilitate studies of mating patterns and population genetic structure. • METHODS AND RESULTS:A total of 42 polymorphic loci were identified from a sample of 24 i...
journal_title:American journal of botany
pub_type: 杂志文章
doi:10.3732/ajb.1200180
更新日期:2012-12-01 00:00:00
abstract:PREMISE OF THE STUDY:The perennial feather moss Hylocomium splendens is one of the most widely distributed and common bryophytes in the Northern Hemisphere and has, because of its capacity to grow under a wide range of environmental conditions, been used as a biomonitor for atmospheric metal deposition in Europe. METH...
journal_title:American journal of botany
pub_type: 杂志文章
doi:10.3732/ajb.1200028
更新日期:2012-09-01 00:00:00
abstract:PREMISE OF THE STUDY:The phenotype of an individual can be modified by the environment experienced by its predecessors, a phenomenon called transgenerational or maternal effects. These effects are studied mostly across sexual generations and are thought to be mediated also by epigenetic variation. However, we do not kn...
journal_title:American journal of botany
pub_type: 杂志文章
doi:10.3732/ajb.1500526
更新日期:2016-09-01 00:00:00
abstract:PREMISE:The genus Arisaema (Araceae) has rapidly diversified in Japan, and multiple species often coexist in the field. Although Japanese Arisaema species hybridize from artificial crossing, hybrid individuals are rare in mixed populations; suggesting the presence of effective pre-pollination barriers. We examined the ...
journal_title:American journal of botany
pub_type: 杂志文章
doi:10.1002/ajb2.1389
更新日期:2019-12-01 00:00:00
abstract::This paper presents the first broad overview of three main features of microsporogenesis (male meiosis) in angiosperms: cytokinesis (cell division), intersporal wall formation, and tetrad form. A phylogenetic comparative approach was used to test for correlated evolution among these characters and to make hypotheses a...
journal_title:American journal of botany
pub_type: 杂志文章
doi:10.3732/ajb.0800110
更新日期:2008-11-01 00:00:00
abstract:PREMISE OF THE STUDY:Over one-third of the native flowering plant species in the Hawaiian Islands are listed as federally threatened or endangered. Lack of sufficient pollination could contribute to reductions in populations, reproduction, and genetic diversity among these species but has been little studied. METHODS:...
journal_title:American journal of botany
pub_type: 杂志文章
doi:10.1002/ajb2.1233
更新日期:2019-02-01 00:00:00
abstract::Six of 14 species of Triteleia were studied. All possess septal nectaries, raphides in the ovary wall, an anatropous and crassinucellate ovule with a micropyle formed by the inner integument only, and parietal cells. A short and thick nucellus, which is not penetrated by the embryo sac, has a one-layered apical epider...
journal_title:American journal of botany
pub_type: 杂志文章
doi:10.3732/ajb.90.6.937
更新日期:2003-06-01 00:00:00
abstract::Pinus baileyi from the Paleogene of Idaho was initially related to the bristlecone pine P. longaeva (subgen. Strobus, sect. Parrya, subsect. Balfourianae) from western North America. Unlike the centromucronate condition in P. longaeva, P. baileyi cones have raised umbos that are excentromucronate, i.e., the mucro posi...
journal_title:American journal of botany
pub_type: 杂志文章
doi:10.3732/ajb.93.2.197
更新日期:2006-02-01 00:00:00
abstract:PREMISE:Medullary bundles, i.e., vascular units in the pith, have evolved multiple times in vascular plants. However, no study has ever explored their anatomical diversity and evolution within a phylogenetic framework. Here, we investigated the development of the primary vascular system within Nyctaginaceae showing how...
journal_title:American journal of botany
pub_type: 杂志文章
doi:10.1002/ajb2.1471
更新日期:2020-05-01 00:00:00
abstract::Phylogenetic analyses of Meliaceae, including representatives of all four currently recognized subfamilies and all but two tribes (32 genera and 35 species, respectively), were carried out using DNA sequence data from three regions: plastid genes rbcL, matK (partial), and nuclear 26S rDNA (partial). Individual and com...
journal_title:American journal of botany
pub_type: 杂志文章
doi:10.3732/ajb.90.3.471
更新日期:2003-03-01 00:00:00
abstract::In a 3-yr study, we examined the pollinator guild and intersexual floral characteristics of the dioecious, perennial cloudberry (Rubus chamaemorus), which flowers in early spring. The findings contribute to our general understanding of pollination ecology at high latitudes and provide important information for the com...
journal_title:American journal of botany
pub_type: 杂志文章
doi:10.3732/ajb.0800102
更新日期:2009-06-01 00:00:00
abstract::Ontogenetic changes in architecture, carbohydrate reserves, and resource allocation can constrain the ability of plants to compensate for herbivore damage. To evaluate ontogenetic changes in compensation, saplings and reproductive individuals of the tropical tree Casearia nitida were subjected to three levels of defol...
journal_title:American journal of botany
pub_type: 杂志文章
doi:10.3732/ajb.92.10.1632
更新日期:2005-10-01 00:00:00