The Trouble with Triplets in Biodiversity Informatics: A Data-Driven Case against Current Identifier Practices

The biodiversity informatics community has discussed aspirations and approaches for assigning globally unique identifiers (GUIDs) to biocollections for nearly a decade. During that time, and despite misgivings, the de facto standard identifier has become the “Darwin Core Triplet”, which is a concatenation of values for institution code, collection code, and catalog number associated with biocollections material. Our aim is not to rehash the challenging discussions regarding which GUID system in theory best supports the biodiversity informatics use case of discovering and linking digital data across the Internet, but how well we can link those data together at this moment, utilizing the current identifier schemes that have already been deployed. We gathered Darwin Core Triplets from a subset of VertNet records, along with vertebrate records from GenBank and the Barcode of Life Data System, in order to determine how Darwin Core Triplets are deployed “in the wild”. We asked if those triplets follow the recommended structure and whether they provide an easy and unambiguous means to track from specimen records to genetic sequence records. We show that Darwin Core Triplets are often riddled with semantic and syntactic errors when deployed and curated in practice, despite specifications about how to construct them. Our results strongly suggest that Darwin Core Triplets that have not been carefully curated are not currently serving a useful role for relinking data. We briefly consider needed next steps to overcome current limitations.     

奇特的海马

海马属脊索动物门、鱼纲、海龙科(Syngnathidae),全球约有海马354个种,其中有经济价值的有30多种,有的已被列入《濒危动物种红色名录》。我国海马共有6种,即为:冠海马(Hippocampus coronatus)分布于黄海、渤海。刺海马(H．histris)分布于南海、东海、台湾海峡,栖息于内湾海藻丛中。     

Constructing Level-2 Phylogenetic Networks from Triplets

Jansson and Sung showed that, given a dense set of input triplets T (representing hypotheses about the local evolutionary relationships of triplets of taxa), it is possible to determine in polynomial time whether there exists a level-1 network consistent with T, and if so, to construct such a network [24]. Here, we extend this work by showing that this problem is even polynomial time solvable for the construction of level-2 networks. This shows that, assuming density, it is tractable to construct plausible evolutionary histories from input triplets even when such histories are heavily nontree-like. This further strengthens the case for the use of triplet-based methods in the construction of phylogenetic networks. We also implemented the algorithm and applied it to yeast data.     

Metrics for Phylogenetic Networks II: Nodal and Triplets Metrics

The assessment of phylogenetic network reconstruction methods requires the ability to compare phylogenetic networks. This is the second in a series of papers devoted to the analysis and comparison of metrics for tree-child time consistent phylogenetic networks on the same set of taxa. In this paper, we generalize to phylogenetic networks two metrics that have already been introduced in the literature for phylogenetic trees: the nodal distance and the triplets distance. We prove that they are metrics on any class of tree-child time consistent phylogenetic networks on the same set of taxa, as well as some basic properties for them. To prove these results, we introduce a reduction/expansion procedure that can be used not only to establish properties of tree-child time consistent phylogenetic networks by induction, but also to generate all tree-child time consistent phylogenetic networks with a given number of leaves.     

Twins and Triplets in Pearl Millet: their Cytology and Origin

Multiple radicles and plumules were produced in high frequenciesin selfed seed of six plants in pearl millet (L.S. 326–3).Ninety-five of these survived to maturity. All were diploids,except in one twin where a trisomic (2n+1) was found. The occurrenceof albino twins in progenies of heterozygous plants, and normalhomozygotes in twins from translocation heterozygotes suggeststheir origin through sexual reproduction. The origin of theremaining twins and triplets is not known with certainty. Pennisetum americanum, twins, triplets, tertiary trisomy, translocation hybridity     

Peculiar Distribution of Fodrin in Fat-Storing Cells

Fat-storing cells (FSCs) show unique morphology containing many lipid droplets in the cytoplasm. In this study, we found that a membrane skeletal protein, fodrin, shows peculiar distribution in FSCs of rat liver. By immunofluorescence microscopy of FSCs in culture, intense labeling for fodrin was seen as coarse filaments in the cytoplasm. Especially in FSCs isolated from vitamin A-treated rats, the labeling was often seen as many small rings in the cytoplasm. In contrast, labeling for fodrin in human fibroblasts or rat adipocytes in culture was seen diffusely in the cell cortex. Distribution of actin, tubulin, vimentin, and desmin in FSCs was also examined, but none of them appeared correlated with fodrin. By immunoelectron microscopy using nanogold labeling with silver enhancement, positive labeling for fodrin was seen around some lipid droplets in FSCsin vivo.We assume that the peculiar distribution of fodrin may be related to the morphological characteristics of FSCs.     

On a Peculiar Mode of Germ-Layer Formation

In some planulae of the alcyonarian Gersemia rubiformis an interior structure was found in the entodermal cavity. It consisted of two layers separated by a basement membrane, the inner layer facing a central cavity. The outer layer was structurally identical with the inner “entomesoderm” of the body wall, while the inner layer of the “ball” was provided with numerous cilia and a brushborder. The development of the interior structure is described as appearing from the structural findings in different planulae. This development is very different from any other developmental process described so far.     

Peculiar ultraviolet absorbing moieties of human osteoarthritic cartilage

The ultraviolet absorbing components of human cartilage have been measured by microspectrophotometry. The characteristics of the chondrocytes appeared to be identical, irrespective of the pathology. However the matrix of osteoarthritis cartilage contained components that absorbed maximally in the region of 270 to 250 nm; such components were not found in the matrix of cartilage of non-arthritic joints. Substances that absorb maximally in this region of the ultraviolet could generate free radicals.