DNA barcoding is a technique for identifying organisms based on a short, standardized fragment of genomic DNA. The standardized sequence region is called a DNA barcode because it is like a barcode ...tag for each taxon. Since the proposition of this concept and the launch of a large project named the Barcode of Life, this simple technique has attracted attention from taxonomists, ecologists, conservation biologists, agriculturists, plant‐quarantine officers and others, and the number of studies using the DNA barcode has rapidly increased. The extreme diversity of insects and their economical, epidemiological and agricultural importance have made this group a major target of DNA barcoding. However, there is some controversy about the utility of DNA barcoding. In this review, we present an overview of DNA barcoding and its application to entomology. We also introduce current advances and future implications of this promising technique.
Aim
Although the evolution of island endemic plants has long been investigated, the majority of such studies have focused on species with remarkable levels of morphological variation and on islands ...substantially far from the mainland. Endemic plants on nearshore oceanic islands have received less attention. We investigate the population genetic structure and dynamics in plants endemic to nearshore and recently formed oceanic islands and examined the possibility of multiple colonizations onto the islands.
Location
Japanese mainland Honshu and the adjacent Izu Islands.
Taxon
Solidago virgaurea (Asteraceae).
Methods
Sixteen and nine populations of S. virgaurea complex were sampled from the mainland and islands respectively; phylogeographical and population genetics analyses, including Bayesian Phylogeographic and Ecological Clustering (BPEC) analysis and Discrete Phylogeographic Approach (DPA) to trace the history of colonization events onto the islands, were performed using plastid DNA and nuclear microsatellite DNA variations.
Results
Phylogenetically close plastid DNA haplotypes were shared between the mainland and islands, although the populations of S. virgaurea from different islands tended to exhibit phylogenetically distinct haplotypes. Admixture analyses based on nuclear DNA variations revealed distinct genetic structures between the mainland and island populations. Gene flow among islands is restricted but may partially offset genetic drift on each island.
Main conclusions
The genetic structure observed in this study may not have originated from a single dispersal event and successive expansion but rather from at least three colonization events and subsequent gene flow among island populations. Based on the nuclear DNA variations, the Izu Island populations of S. virgaurea are genetically distinct from the mainland ones. Repeated colonization events may have provided sufficient genetic diversity, which would generally be susceptible to founder effects and exert a driving force for evolutionary adaptation, to these oceanic island populations.
DNA barcoding is expected to be an effective identification tool for organisms with heteromorphic generations such as pteridophytes, which possess a morphologically simple gametophyte generation. ...Although a reference data set including complete coverage of the target local flora/fauna is necessary for accurate identification, DNA barcode studies including such rich taxonomic sampling on a countrywide scale are lacking.
The Japanese pteridophyte flora (733 taxa including subspecies and varieties) was used to test the utility of two plastid DNA barcode regions (rbcL and trnH-psbA) with the intention of developing an identification system for native gametophytes. DNA sequences were obtained from each of 689 (94.0%) taxa for rbcL and 617 (84.2%) taxa for trnH-psbA. Mean interspecific divergence values across all taxon pairs (K2P genetic distances) did not reveal a significant difference in rate between trnH-psbA and rbcL, but mean K2P distances of each genus showed significant heterogeneity according to systematic position. The minimum fail rate of taxon discrimination in an identification test using BLAST (12.52%) was obtained when rbcL and trnH-psbA were combined, and became lower in datasets excluding infraspecific taxa or apogamous taxa, or including sexual diploids only.
This study demonstrates the overall effectiveness of DNA barcodes for species identification in the Japanese pteridophyte flora. Although this flora is characterized by a high occurrence of apogamous taxa that pose a serious challenge to identification using DNA barcodes, such taxa are limited to a small number of genera, and only minimally detract from the overall success rate. In the case that a query sequence is matched to a known apogamous genus, routine species identification may not be possible. Otherwise, DNA barcoding is a practical tool for identification of most Japanese pteridophytes, and is especially anticipated to be helpful for identification of non-hybridizing gametophytes.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Stem cells are formed at particular times and positions during the development of multicellular organisms. Whereas flowering plants form stem cells only in the sporophyte generation, non-seed plants ...form stem cells in both the sporophyte and gametophyte generations. Although the molecular mechanisms underlying stem cell formation in the sporophyte generation have been extensively studied, only a few transcription factors involved in the regulation of gametophyte stem cell formation have been reported. The moss Physcomitrella patens forms a hypha-like body (protonema) and a shoot-like body (gametophore) from a protonema apical cell and a gametophore apical cell, respectively. These apical cells have stem cell characteristics and are formed as side branches of differentiated protonema cells. Here, we show that four AP2-type transcription factors orthologous to Arabidopsis thaliana AINTEGUMENTA, PLETHORA and BABY BOOM (APB) are indispensable for the formation of gametophore apical cells from protonema cells. Quadruple disruption of all APB genes blocked gametophore formation, even in the presence of cytokinin, which enhances gametophore apical cell formation in the wild type. All APB genes were expressed in emerging gametophore apical cells, but not in protonema apical cells. Heat-shock induction of an APB4 transgene driven by a heat-shock promoter increased the number of gametophores. Expression of all APB genes was induced by auxin but not by cytokinin. Thus, the APB genes function synergistically with cytokinin signaling to determine the identity of the two types of stem cells.
Hymenophyllum subg. Mecodium (Hymenophyllaceae) is represented by ca. 35 epiphytic species. Past reports suggest that Hymenophyllum polyanthos (Sw.) Sw., a pantropical species, does not represent a ...monophyletic grouping as it is recognized today. This research focuses on the H. polyanthos species complex, while comparing it to other species of subg. Mecodium using molecular and morphological traits. Here, chloroplast gene sequences of the atpB, atpB–rbcL–accD, rps4–trnS, and matK regions of 132 samples are compared under phylogenetic analyses and the resulting trees are discussed according to distributional and morphological differences. As a result, two big clades can be observed within Mecodium: one represented by plants distributed through Malesia, Australia, Pacific islands, Indian Ocean, and southern South America, and the other represented by plants occurring in Central and South America, Africa, and Asia. Hymenophyllum polyanthos samples appear interspersed in the phylogeny, evidencing its polyphyletic status. Main lineages identified here as H. polyanthos include: (1) plants from the Neotropics, closely related to species like H. myriocarpum Hook. and H. undulatum Sw., and probably representative of the type lineage for the species; (2) several independent lineages within the Asian samples; and (3) two distinct lineages distributed from Malesia and Pacific regions to South and Central America. The combination of distributional patterns and a morphological analysis of seven leaf traits suggests that these lineages are mostly sympatric and show a morphological variation that overlaps with each other.
Ecological speciation is an important factor in the diversification of plants. The distribution of the woody species Rhododendron indicum, which grows along rivers and is able to withstand water flow ...when rivers flood (i.e. it is a rheophyte), is disjunct, in contrast to the widespread distribution of its relative, Rhododendron kaempferi. This study aimed to elucidate the phylogenetic relationships between R. indicum and R. kaempferi and the evolutionary processes that gave rise to them. The sequences of three non-coding chloroplast DNA regions (total length 1977 bp) were obtained from 21 populations covering the ranges of the two species. In addition, genome-wide SNPs were genotyped from 20 populations using a genotyping by sequencing method. Leaf morphologies were measured for eight representative populations. Two chloroplast DNA haplotypes, which were detected in R. indicum, were shared between the two species. Genome-wide SNPs identified two lineages in R. indicum and these lineages did not constitute a monophyletic group. Each of these two lineages was related to geographically close populations of R. kaempferi. Leaf morphology, which is a characteristic feature in rheophytes, was not differentiated between the two lineages in R. indicum. The morphological similarity between the two heterogeneous lineages may be a result of parallel evolution from R. kaempferi or of introgressive hybridization between the species due to strong selective pressure imposed by flooding.
Geranium soboliferum
var.
kiusianum
and var.
hakusanense
(Geraniaceae) are believed to be relict plants that migrated southward from the Eurasian continent to the Japanese archipelago during the last ...glacial period.
G. soboliferum
var.
kiusianum
individuals and populations, which occur in wetlands in the Aso-Kuju region of Kyushu Island, are declining as a result of the deteriorating quality of the microhabitat, a process that is associated with the decrease in semi-natural grasslands. Using 10 polymorphic microsatellite markers, we evaluated the genetic diversity and population structure of the
G. soboliferum
complex, with the aim of understanding the species’ genetic characteristics to facilitate efficient conservation. Genetic demographic analysis suggested that Japanese
G. soboliferum
populations branched off from the Eurasian continental
G. soboliferum
var.
soboliferum
during the last glacial period and that, thereafter, the Japanese populations of the plant diverged into two lineages at the beginning of the Holocene epoch. The genetic diversity of
G. soboliferum
var.
kiusianum
was significantly lower than that of var.
hakusanense
, which is more widely distributed in central Honshu Island (mean
Ar
= 3.288 vs. 3.830 and
H
e
= 0.366 vs. 0.546). Genetic differentiation among populations was significantly higher (mean
F
ST
= 0.368 vs. 0.184) in var.
kiusianum
populations and, notably, exhibited non-significant patterns of isolation by distance, indicating that the populations underwent strong genetic drift independent of adjacent populations. Our findings suggested that the population’s isolation, and its associated habitat specialization and limited inter-population gene flow, would have accelerated genetic differentiation in var.
kiusianum
. Overall,
G. soboliferum
var.
kiusianum
, which is genetically unique to wetland habitats in the Aso-Kuju region, merits conservation, and appropriate human intervention and management are critical to maintaining its remaining habitats in semi-natural grasslands.
Eleven native
Geranium
species have been reported in Japan, several of which include infraspecific taxa. Although phylogenetic analyses have been conducted using conventional methods (i.e., ...chloroplast fragment and ribosomal DNA sequencing), relationships at the infraspecific level have not been elucidated due to a lack of genetic polymorphisms. We collected specimens of 22
Geranium
taxa from Japan and peripheral areas (e.g., mainland China, South Korea, Russia, and Taiwan), and performed detailed phylogenetic analyses using chloroplast genome sequencing and genome-wide single-nucleotide polymorphisms. Some discrepancies were observed between the current taxonomy and the phylogenetic relationships elucidated in our analyses. The
Geranium tripartitum
complex was found to be paraphyletic, and
Geranium onoei
f.
yezoense
, which is synonym of
Geranium reinii
, was found to be more closely related to
Geranium erianthum
than to
G. reinii
. In particular,
G. tripartitum
var.
hastatum
located at intermediate position between
Geranium thunbergii
and
Geranium wilfordii
in the network analysis. Therefore, we suggest that
G. tripartitum
var.
hastatum
should be treated as an independent species, and that
G. onoei
f.
yezoense
should be transferred to
G. erianthum
.
Early stages of ecological speciation can create populations with an ecology and reproduction timing distinct from those of related populations. Landscape genetic models incorporating environmental ...heterogeneity and population-specific reproductive traits enable the processes of population genetic differentiation to be inferred.
We investigated genome-wide genetic variation in ecotypic populations of Solidago virgaurea sensu lato, a herbaceous plant inhabiting a wide range of habitats (woodlands, serpentine barrens and alpine grasslands) and displaying remarkable variation in flowering time.
Simultaneous evaluation of environmental factors revealed an overwhelming effect of soil type differences on neutral genetic differentiation, compared with elevational differences. This result probably reflects the abrupt environmental changes generated by geological boundaries, whereas mountain slopes exhibit clinal changes, facilitating gene exchange between neighbouring populations. Temporal isolation was positively associated with genetic differentiation, with some early-flowering serpentine populations having allele frequencies distinct from adjacent nonserpentine populations.
Overall, this study highlights the importance of ecological processes and of evolution of flowering time to promote genetic differentiation of S. virgaurea populations in a complex landscape.
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