164 research outputs found
Phylogeny and historical biogeography of Lauraceae
Phylogenetic relationships among 122 species of Lauraceae representing 44 of the 55 currently recognized genera are inferred from sequence variation in the chloroplast and nuclear genomes. The trnL-trnF, trnT-trnL, psbA-trnH, and rpll6 regions of cpDNA, and the 5' end of 26S rDNA resolved major lineages, while the ITS/5.8S region of rDNA resolved a large terminal lade. The phylogenetic estimate is used to assess morphology-based views of relationships and, with a temporal dimension added, to reconstruct the biogeographic history of the family. Results suggest Lauraceae radiated when trans-Tethyean migration was relatively easy, and basal lineages are established on either Gondwanan or Laurasian terrains by the Late Cretaceous. Most genera with Gondwanan histories place in Cryptocaryeae, but a small group of South American genera, the Chlorocardium-Mezilauruls lade, represent a separate Gondwanan lineage. Caryodaphnopsis and Neocinnamomum may be the only extant representatives of the ancient Lauraceae flora docu- mented in Mid- to Late Cretaceous Laurasian strata. Remaining genera place in a terminal Perseeae-Laureae lade that radiated in Early Eocene Laurasia. Therein, non-cupulate genera associate as the Persea group, and cupuliferous genera sort to Laureae of most classifications or Cinnamomeae sensu Kostermans. Laureae are Laurasian relicts in Asia. The Persea group and Cinnamomum group (of Cinnamomeae) show tropical amphi-Pacific disjunctions here credited to disruption of boreotropical ranges by Eocene-Oligocene climatic cooling. The Ocotea complex accommodates re- maining Cinnamomeae and shows a trans-Atlantic disjunction possibly derived from a Madrean-Tethyan ancestral distribution. These findings support Laurasian ancestry for most extant Lauraceae, with their considerable neotropical representation primarily derived from Early Miocene radiation of the Ocotea complex upon reaching South America
What is the relationship among Hernandiaceae, Lauraceae, and Monimiaceae, and why is this question so difficult to answer?
Indian indenture in the Straits Settlements, 1872-1910 : policy and practice in Province Wellesley
The Introduction to this thesis provides a brief
survey of Indian indentured immigration into selected
colonies, and presents some of the conflicting interpretations
of Indian indenture. It also states the main object of
this study.
Chapter I discusses the factors that gave rise to
large-scale sugar cultivation by Europeans in Province
Wellesley, and examines the reasons why the local Malays
and the Javanese and Chinese immigrants were not adequately
responsive to the demand for indentured labour, and why the
planters continued to rely on the Tamils of Madras Presidency,
despite their reluctance to emigrate overseas permanently.
Chapter III attempts to establish the commencement
date of unregulated Indian indentured emigration to the
Straits, and provides some glimpses of the nature of the
early traffic. It goes on to trace the events that led to
the embargo on labour migration from India to the Straits,
and examines the negotiations that eventually brought about
the establishment of regulated indenture.
The measures taken to satisfy the planters’ labour
needs and the reasons why indentured recruitment, competing
with "free” recruitment for Ceylon and Burma, failed to yield
the number of labourers required are discussed in Chapter IV.
Chapter V examines the conditions in which the
emigrants were housed and otherwise looked after at the depot
at Negapatam. It establishes that bona fide indentured
recruits were substituted, and that frequent illegal use was made of Karikal as a port of departure. It also examines
whether the emigrants' treatment during the voyage to Penang
conformed with the legal requirements.
An account of the betrayal by two planters of
Governor Ord's promise to the government of India, which
involved the scandalous ill-treatment and neglect of a large
number of labourers is provided in Chapter VI. It also
discusses the punishment of the offenders, the headmen's
exploitation and chastisement of the labourers, and why it
was difficult for them to obtain redress.
The planters' illegal separation of the labourers
into first and second class gangs, the labourers' low earning
capacity and their inability to procure adequate food, and
the consequences that followed are discussed in Chapter VII.
Finally, Chapter VIII examines the quality of the
necessary provisions made for the labourers' accommodation and
medical treatment, and discusses the effects of the sexual
disproportion and of injuries on the labourers' health. The
discussion closes with an examination of the main causes of
the high mortality-rate among the labourers, which dealt
the coup de >?race to the system in 1910
Phylogeny and evolutionary history of glycogen synthase kinase 3/SHAGGY-like kinase genes in land plants
Background: GSK3 (glycogen synthase kinase 3) genes encode signal transduction proteins with roles in a variety of biological processes in eukaryotes. In contrast to the low copy numbers observed in animals, GSK3 genes have expanded into a multi-gene family in land plants (embryophytes), and have also evolved functions in diverse plant specific processes, including floral development in angiosperms. However, despite previous efforts, the phylogeny of land plant GSK3 genes is currently unclear. Here, we analyze genes from a representative sample of phylogenetically pivotal taxa, including basal angiosperms, gymnosperms, and monilophytes, to reconstruct the evolutionary history and functional diversification of the GSK3 gene family in land plants. Results: Maximum Likelihood phylogenetic analyses resolve a gene tree with four major gene duplication events that coincide with the emergence of novel land plant clades. The single GSK3 gene inherited from the ancestor of land plants was first duplicated along the ancestral branch to extant vascular plants, and three subsequent duplications produced three GSK3 loci in the ancestor of euphyllophytes, four in the ancestor of seed plants, and at least five in the ancestor of angiosperms. A single gene in the Amborella trichopoda genome may be the sole survivor of a sixth GSK3 locus that originated in the ancestor of extant angiosperms. Homologs of two Arabidopsis GSK3 genes with genetically confirmed roles in floral development, AtSK11 and AtSK12, exhibit floral preferential expression in several basal angiosperms, suggesting evolutionary conservation of their floral functions. Members of other gene lineages appear to have independently evolved roles in plant reproductive tissues in individual taxa. Conclusions: Our phylogenetic analyses provide the most detailed reconstruction of GSK3 gene evolution in land plants to date and offer new insights into the origins, relationships, and functions of family members. Notably, the diversity of this “green” branch of the gene family has increased in concert with the increasing morphological and physiological complexity of land plant life forms. Expression data for seed plants indicate that the functions of GSK3 genes have also diversified during evolutionary time
Comparison of next generation sequencing technologies for transcriptome characterization
<p>Abstract</p> <p>Background</p> <p>We have developed a simulation approach to help determine the optimal mixture of sequencing methods for most complete and cost effective transcriptome sequencing. We compared simulation results for traditional capillary sequencing with "Next Generation" (NG) ultra high-throughput technologies. The simulation model was parameterized using mappings of 130,000 cDNA sequence reads to the <it>Arabidopsis </it>genome (NCBI Accession SRA008180.19). We also generated 454-GS20 sequences and <it>de novo </it>assemblies for the basal eudicot California poppy (<it>Eschscholzia californica</it>) and the magnoliid avocado (<it>Persea americana</it>) using a variety of methods for cDNA synthesis.</p> <p>Results</p> <p>The <it>Arabidopsis </it>reads tagged more than 15,000 genes, including new splice variants and extended UTR regions. Of the total 134,791 reads (13.8 MB), 119,518 (88.7%) mapped exactly to known exons, while 1,117 (0.8%) mapped to introns, 11,524 (8.6%) spanned annotated intron/exon boundaries, and 3,066 (2.3%) extended beyond the end of annotated UTRs. Sequence-based inference of relative gene expression levels correlated significantly with microarray data. As expected, NG sequencing of normalized libraries tagged more genes than non-normalized libraries, although non-normalized libraries yielded more full-length cDNA sequences. The <it>Arabidopsis </it>data were used to simulate additional rounds of NG and traditional EST sequencing, and various combinations of each. Our simulations suggest a combination of FLX and Solexa sequencing for optimal transcriptome coverage at modest cost. We have also developed ESTcalc <url>http://fgp.huck.psu.edu/NG_Sims/ngsim.pl</url>, an online webtool, which allows users to explore the results of this study by specifying individualized costs and sequencing characteristics.</p> <p>Conclusion</p> <p>NG sequencing technologies are a highly flexible set of platforms that can be scaled to suit different project goals. In terms of sequence coverage alone, the NG sequencing is a dramatic advance over capillary-based sequencing, but NG sequencing also presents significant challenges in assembly and sequence accuracy due to short read lengths, method-specific sequencing errors, and the absence of physical clones. These problems may be overcome by hybrid sequencing strategies using a mixture of sequencing methodologies, by new assemblers, and by sequencing more deeply. Sequencing and microarray outcomes from multiple experiments suggest that our simulator will be useful for guiding NG transcriptome sequencing projects in a wide range of organisms.</p
A genome triplication associated with early diversification of the core eudicots
Background: Although it is agreed that a major polyploidy event, gamma, occurred within the eudicots, the phylogenetic placement of the event remains unclear. Results: To determine when this polyploidization occurred relative to speciation events in angiosperm history, we employed a phylogenomic approach to investigate the timing of gene set duplications located on syntenic gamma blocks. We populated 769 putative gene families with large sets of homologs obtained from public transcriptomes of basal angiosperms, magnoliids, asterids, and more than 91.8 gigabases of new next-generation transcriptome sequences of non-grass monocots and basal eudicots. The overwhelming majority (95%) of well-resolved gamma duplications was placed before the separation of rosids and asterids and after the split of monocots and eudicots, providing strong evidence that the gamma polyploidy event occurred early in eudicot evolution. Further, the majority of gene duplications was placed after the divergence of the Ranunculales and core eudicots, indicating that the gamma appears to be restricted to core eudicots. Molecular dating estimates indicate that the duplication events were intensely concentrated around 117 million years ago. Conclusions: The rapid radiation of core eudicot lineages that gave rise to nearly 75% of angiosperm species appears to have occurred coincidentally or shortly following the gamma triplication event. Reconciliation of gene trees with a species phylogeny can elucidate the timing of major events in genome evolution, even when genome sequences are only available for a subset of species represented in the gene trees. Comprehensive transcriptome datasets are valuable complements to genome sequences for high-resolution phylogenomic analysis
A physical map for the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structure
Background: Recent phylogenetic analyses have identified Amborella trichopoda, an understory tree species endemic to the forests of New Caledonia, as sister to a clade including all other known flowering plant species. The Amborella genome is a unique reference for understanding the evolution of angiosperm genomes because it can serve as an outgroup to root comparative analyses. A physical map, BAC end sequences and sample shotgun sequences provide a first view of the 870 Mbp Amborella genome.Results: Analysis of Amborella BAC ends sequenced from each contig suggests that the density of long terminal repeat retrotransposons is negatively correlated with that of protein coding genes. Syntenic, presumably ancestral, gene blocks were identified in comparisons of the Amborella BAC contigs and the sequenced Arabidopsis thaliana, Populus trichocarpa, Vitis vinifera and Oryza sativa genomes. Parsimony mapping of the loss of synteny corroborates previous analyses suggesting that the rate of structural change has been more rapid on lineages leading to Arabidopsis and Oryza compared with lineages leading to Populus and Vitis. The gamma paleohexiploidy event identified in the Arabidopsis, Populus and Vitis genomes is shown to have occurred after the divergence of all other known angiosperms from the lineage leading to Amborella.Conclusions: When placed in the context of a physical map, BAC end sequences representing just 5.4% of the Amborella genome have facilitated reconstruction of gene blocks that existed in the last common ancestor of all flowering plants. The Amborella genome is an invaluable reference for inferences concerning the ancestral angiosperm and subsequent genome evolution
Late Neogene history of the laurel tree (Laurus L., Lauraceae) based on phylogeographical analyses of Mediterranean and Macaronesian populations
Aim The post-glacial range dynamics of many European plant species have been
widely investigated, but information rapidly diminishes as one moves further
back in time. Here we infer the historical range shifts of Laurus, a paradigmatic
tree of the Tethyan flora that has covered southern Eurasia since the
Oligo-Miocene, by means of phylogenetic and phylogeographical analyses.
Location Mediterranean Basin, Black Sea and Macaronesian archipelagos
(Azores, Madeira, Canary Islands).
Methods We analysed plastid DNA (cpDNA) sequence (trnK–matK, trnD–trnT)
variation in 57 populations of Laurus and three Lauraceae genera. Phylogenetic
methods (maximum parsimony and Bayesian inference) and statistical parsimony
networks were used to reconstruct relationships among haplotypes. These results
were contrasted with the fossil record and bioclimatic niche-based model
predictions of past distributions to infer the migration routes and location of
refugia.
Results The phylogenetic tree revealed monophyly for Laurus. Overall sequence
variability was low within Laurus, but six different haplotypes were distinguished
and a single network retrieved, portraying three lineages primarily related to
geography. A strongly divergent eastern lineage occupied Turkey and the Near
East, a second clade was located in the Aegean region and, lastly, a western clade
grouped all Macaronesian and central and western Mediterranean populations.
A close relationship was observed between the Macaronesian populations of
L. azorica and the western populations of L. nobilis.
Main conclusions The phylogeographical structure of Laurus preserves the
imprints of an ancient contraction and break-up of the range that resulted in the
evolution of separate cpDNA lineages in its western- and easternmost extremes.
Intense range dynamics in the western Mediterranean and multiple glacial refugia
contributed to the generation and long-term conservation of this phylogeographical
pattern, as shown by the fit between the haplotype ranges and
past suitable areas inferred from bioclimatic models. Finally, our results challenge
the taxonomic separation of Laurus into two distinct species
Recent advances in understanding the roles of whole genome duplications in evolution
Ancient whole-genome duplications (WGDs)—paleopolyploidy events—are key to solving Darwin’s ‘abominable mystery’ of how flowering plants evolved and radiated into a rich variety of species. The vertebrates also emerged from their invertebrate ancestors via two WGDs, and genomes of diverse gymnosperm trees, unicellular eukaryotes, invertebrates, fishes, amphibians and even a rodent carry evidence of lineage-specific WGDs. Modern polyploidy is common in eukaryotes, and it can be induced, enabling mechanisms and short-term cost-benefit assessments of polyploidy to be studied experimentally. However, the ancient WGDs can be reconstructed only by comparative genomics: these studies are difficult because the DNA duplicates have been through tens or hundreds of millions of years of gene losses, mutations, and chromosomal rearrangements that culminate in resolution of the polyploid genomes back into diploid ones (rediploidisation). Intriguing asymmetries in patterns of post-WGD gene loss and retention between duplicated sets of chromosomes have been discovered recently, and elaborations of signal transduction systems are lasting legacies from several WGDs. The data imply that simpler signalling pathways in the pre-WGD ancestors were converted via WGDs into multi-stranded parallelised networks. Genetic and biochemical studies in plants, yeasts and vertebrates suggest a paradigm in which different combinations of sister paralogues in the post-WGD regulatory networks are co-regulated under different conditions. In principle, such networks can respond to a wide array of environmental, sensory and hormonal stimuli and integrate them to generate phenotypic variety in cell types and behaviours. Patterns are also being discerned in how the post-WGD signalling networks are reconfigured in human cancers and neurological conditions. It is fascinating to unpick how ancient genomic events impact on complexity, variety and disease in modern life
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