Repeated morphological evolution through cis-regulatory changes in a pleiotropic gene

The independent evolution of morphological similarities is widespread. For simple traits, such as overall body colour, repeated transitions by means of mutations in the same gene may be common. However, for more complex traits, the possible genetic paths may be more numerous; the molecular mechanisms underlying their independent origins and the extent to which they are constrained to follow certain genetic paths are largely unknown. Here we show that a male wing pigmentation pattern involved in courtship display has been gained and lost multiple times in a Drosophila clade. Each of the cases we have analysed (two gains and two losses) involved regulatory changes at the pleiotropic pigmentation gene yellow. Losses involved the parallel inactivation of the same cis-regulatory element (CRE), with changes at a few nucleotides sufficient to account for the functional divergence of one element between two sibling species. Surprisingly, two independent gains of wing spots resulted from the co-option of distinct ancestral CREs. These results demonstrate how the functional diversification of the modular CREs of pleiotropic genes contributes to evolutionary novelty and the independent evolution of morphological similarities.     

PARAMAP vs. Isomap: A Comparison of Two Nonlinear Mapping Algorithms

Dimensionality reduction techniques are used for representing higher dimensional data by a more parsimonious and meaningful lower dimensional structure. In this paper we will study two such approaches, namely Carroll’s Parametric Mapping (abbreviated PARAMAP) (Shepard and Carroll, 1966) and Tenenbaum’s Isometric Mapping (abbreviated Isomap) (Tenenbaum, de Silva, and Langford, 2000). The former relies on iterative minimization of a cost function while the latter applies classical MDS after a preprocessing step involving the use of a shortest path algorithm to define approximate geodesic distances. We will develop a measure of congruence based on preservation of local structure between the input data and the mapped low dimensional embedding, and compare the different approaches on various sets of data, including points located on the surface of a sphere, some data called the "Swiss Roll data", and truncated spheres.     

A mathematical programming approach to fitting general graphs

We present an algorithm for fitting general graphs to proximity data. The algorithm utilizes a mathematical programming procedure based on a penalty function approach to impose additivity constraints upon parameters. For a user-specified number of links, the algorithm seeks to provide the connected network that gives the least-squares approximation to the proximity data with the specified number of links, allowing for linear transformations of the data. The network distance is the minimum-path-length metric for connected graphs. As a limiting case, the algorithm provides a tree where each node corresponds to an object, if the number of links is set equal to the number of objects minus one. A Monte Carlo investigation indicates that the resulting networks tend to fall within one percentage point of the least-squares solution in terms of the variance accounted for, but do not always attain this global optimum. The network model is discussed in relation to ordinal network representations (Klauer 1989) and NETSCAL (Hutchinson 1989), and applied to several well-known data sets.     

Least squares algorithms for constructing constrained ultrametric and additive tree representations of symmetric proximity data

A mathematical programming algorithm is developed for fitting ultrametric or additive trees to proximity data where external constraints are imposed on the topology of the tree. The two procedures minimize a least squares loss function. The method is illustrated on both synthetic and real data. A constrained ultrametric tree analysis was performed on similarities between 32 subjects based on preferences for ten odors, while a constrained additive tree analysis was carried out on some proximity data between kinship terms. Finally, some extensions of the methodology to other tree fitting procedures are mentioned.The first author is supported as Bevoegdverklaard Navorser of the Belgian Nationaal Fonds voor Wetenschappelijk Onderzoek.     

Host-parasite studies of Trichophrya infesting cutthroat trout ( Salmo clarki ) and longnose suckers ( Catostomus catostomus ) from Yellowstone Lake, Wyoming

Trichophrya sp. (Protozoa) on the gills of cutthroat trout ( Salmo clarki ) and longnose suckers ( Catostomus catostomus ) was studied using light and electron microscopy and tracer techniques. All cutthroat trout, 14 cm in total length and above, from Yellowstone Lake, Yellowstone National Park, Wyoming, were infested with the suctorian. No trichophryans were found on fry or fingerling cutthroat trout. Sixty percent of the examined longnose suckers from the same location were infested. Light microscopy disclosed extensive pathology of gill epithelium in longnose suckers infested with Trichophrya that was not observed for infested cutthroat trout. Electron micrographs show damage to immediate host gill cells by both parasites, depicted by a reduction and lack of mitochondria. Both parasites form attachment helices (0.52 × 0.04 μ m), which may originate in the protozoan cell membrane and function for maintenance of parasite position on the host cell. There was no uptake of 14 C, injected into host fish, via the attachment helices by the parasite that further substantiated the mechanical function for the spiral structure. Protozoan feeding on host tissue may be accomplished by use of necrotic gill tissue and mucus.        

History and status of the Franklin's Gull on Malheur National Wildlife Refuge, Oregon

Franklin's Gulls first arrived in southeast Oregon in 1943, but the first nest was not located until 1948. From 1949 to 1964 gull numbers showed annual fluctuations. An increase began in 1965 and continued through 1980. By 1980 an estimated 2500 Franklin's Gulls were nesting on Malheur National Wildlife Refuge, Harney County, Oregon. The species arrives in April and nesting begins by 1 June. Average nest and egg measurements were similar to those from other areas within the species range.     

A modified CANDECOMP method for fitting the extended INDSCAL model

A modified CANDECOMP algorithm is presented for fitting the metric version of the Extended INDSCAL model to three-way proximity data. The Extended INDSCAL model assumes, in addition to the common dimensions, a unique dimension for each object. The modified CANDECOMP algorithm fits the Extended INDSCAL model in a dimension-wise fashion and ensures that the subject weights for the common and the unique dimensions are nonnegative. A Monte Carlo study is reported to illustrate that the method is fairly insensitive to the choice of the initial parameter estimates. A second Monte Carlo study shows that the method is able to recover an underlying Extended INDSCAL structure if present in the data. Finally, the method is applied for illustrative purposes to some empirical data on pain relievers. In the final section, some other possible uses of the new method are discussed. Geert De Soete is supported as “Bevoegdverklaard Navorser” of the Belgian “Nationaal Fonds voor Wetenschappelijik Onderzoek”.