Showing papers by "Damon P. Little published in 2010"
TL;DR: The timing of specific key events and a morphological and anatomical description of important features of S. apoda such as habit, stem, rhizophores, roots, leaves, ligules, strobili, sporangia, spores, and gametophytes are presented.
Abstract: Selaginella apoda is an appropriate model species because of its short life cycle and ease of cultivation. To work effectively with a model species, it is important to understand its morphology, anatomy, and life cycle in detail. We present the timing of specific key events (e.g., opening of the megaspore, development of the archegonium, fertilization, first branching) and a morphological and anatomical description of important features of S. apoda such as habit, stem, rhizophores, roots, leaves, ligules, strobili, sporangia, spores, and gametophytes, with many features newly described for Selaginella in general and for S. apoda in particular. Development and growth patterns indicate that each segment is an independent module consisting of a section of the stem, leaves, rhizophores, and roots. A comparison of different leaf types (dorsal and ventral leaves, dorsal and ventral sporophylls) shows similar stomata and papillae distributions but type‐specific forms and sizes. In the transition from vegetative ...
37 citations
TL;DR: This work provides a general method for detecting genes or groups of genes that may be under selection in directions that are in agreement with the phylogenetic pattern and shows that identifying partitions or genes in this way provides a platform to explain some of the more interesting organismal differences among species, and in particular, in the evolution of plants.
Abstract: We use measures of congruence on a combined expressed sequenced tag genome phylogeny to identify proteins that have potential significance in the evolution of seed plants. Relevant proteins are identified based on the direction of partitioned branch and hidden support on the hypothesis obtained on a 16-species tree, constructed from 2,557 concatenated orthologous genes. We provide a general method for detecting genes or groups of genes that may be under selection in directions that are in agreement with the phylogenetic pattern. Gene partitioning methods and estimates of the degree and direction of support of individual gene partitions to the overall data set are used. Using this approach, we correlate positive branch support of specific genes for key branches in the seed plant phylogeny. In addition to basic metabolic functions, such as photosynthesis or hormones, genes involved in posttranscriptional regulation by small RNAs were significantly overrepresented in key nodes of the phylogeny of seed plants. Two genes in our matrix are of critical importance as they are involved in RNA-dependent regulation, essential during embryo and leaf development. These are Argonaute and the RNA-dependent RNA polymerase 6 found to be overrepresented in the angiosperm clade. We use these genes as examples of our phylogenomics approach and show that identifying partitions or genes in this way provides a platform to explain some of the more interesting organismal differences among species, and in particular, in the evolution of plants.
29 citations
TL;DR: Re-analysis of published data demonstrates the utility of B, a novel, unified measure of sequence quality and contig overlap tailored to the needs of DNA barcoding.
Abstract: Summary: Barcode quality index (B) is a novel, unified measure of sequence quality and contig overlap tailored to the needs of DNA barcoding. Re-analysis of published data demonstrates the utility of B.
Availability and Implementation: A GPL PERL script is available for download ( http://www.nybg.org/files/scientists/dlittle/B.html).
Contact: dlittle@nybg.org
17 citations
TL;DR: Selaginella apoda has many advantages as a model species, including a short life cycle, and can be easily transplanted to soil and treated with 0.15% Previcur®N prevents most fungal contaminations.
Abstract: Selaginella apoda has many advantages as a model species, including a short life cycle. In order to work effectively with a lycophyte model species, it is important to be able to grow the gametophytes and sporophytes quickly. In the case of S. apoda, the gametophytes grow quickly and have high fertilization success in warm nutrient enriched water. Sporophytes at the three root stage can be easily transplanted to soil. They grow well in moist containers at a wide range of temperatures. Treatment with 0.15% Previcur®N prevents most fungal contaminations.
3 citations