Distributional and Ecological Notes on the Halfbeaks of Eastern Gulf of Mexico, with a Provisional Key for Their Identification

Several fishes of the halfbeak genus Hyporhamphus occurring in the Mexican Gulf of Mexico and Caribbean Sea have been misidentified or confused in the literature. Most of it has centered around the taxonomic status of H. unifasciatus (including its synonym H. roberti), which is shown to comprise a complex of three species, H. unifasciatus, the recently described H. meeki, from the western Atlantic region, and an undescribed species from the eastern Pacific Ocean. Another eastern Mexico halfbeak is the freshwater form H. mexicanus. Using Banford and Collette (1993), we examined specimens from collections at UANL, UNAM, IPN, and ECOCH and have clarified the Mexican distribution of these species. We here report additional Mexican records of H. meeki, previously known only from United States waters and from the coast of Yucatán, clarify the distribution of H. unifasciatus, and provide the first marine record of the freshwater species H. mexicanus. A distribution map and keys for identification of the eastern Mexican species are provided

The Effects of Interactions on the Structure and Morphology of Elliptical/Lenticular galaxies in Pairs

We present a photometric and structural analysis of 42 E/S0 galaxies in (E/S0 + S) pairs observed in the BVRI color bands. We empirically determine the effects of interactions on their morphology, structure and stellar populations as seen from the light concentration (C), asymmetry (A), and clumpiness (S) parameters. We further compare these values to a control sample of 67 mostly isolated, non-interacting E/S0 galaxies. The paired E/S0 galaxies occupy a more scattered loci in CAS space than non-interacting E/S0's, and the structural effects of interactions on E/S0's are minor, in contrast to disk galaxies involved in interactions. This suggests that observational methods for recognizing interactions at high z, such the CAS methodology, would hardly detect E/S0's involved in interactions (related to early phases of the so called `dry-mergers'). We however find statistical differences in A when comparing isolated and interacting E/S0s. In the mean, paired E/S0 galaxies have A values 2.96+-0.72 times larger than the ones of non-interacting E/S0's. For the subset of presumably strongly interacting E/S0's, A and S can be several times larger than the typical values of the isolated E/S0's. We show that the asymmetries are consistent with several internal and external morphological distortions. We conclude that the interacting E/S0s in pairs should be dense, gas poor galaxies in systems spaning a wide range of interaction stages, with typical merging timescales >~ 0.1-0.5 Gyr. We use the observed phenomenology of these galaxies to predict the approximate loci of `dry pre-mergers' in the CAS space.(Abridged)Comment: 23 pages, 9 figures included. To appear in The Astronomical Journa

Complex evolutionary history of the Mexican stoneroller Campostoma ornatum Girard, 1856 (Actinopterygii: Cyprinidae)

<p>Abstract</p> <p>Background</p> <p>Studies of the phylogeography of Mexican species are steadily revealing genetic patterns shared by different species, which will help to unravel the complex biogeographic history of the region. <it>Campostoma ornatum </it>is a freshwater fish endemic to montane and semiarid regions in northwest Mexico and southern Arizona. Its wide range of distribution and the previously observed morphological differentiation between populations in different watersheds make this species a useful model to investigate the biogeographic role of the Sierra Madre Occidental and to disentangle the actions of Pliocene tecto-volcanic processes <it>vs </it>Quaternary climatic change. Our phylogeographic study was based on DNA sequences from one mitochondrial gene (<it>cytb</it>, 1110 bp, n = 285) and two nuclear gene regions (S7 and RAG1, 1822 bp in total, n = 56 and 43, respectively) obtained from 18 to 29 localities, in addition to a morphological survey covering the entire distribution area. Such a dataset allowed us to assess whether any of the populations/lineages sampled deserve to be categorised as an evolutionarily significant unit.</p> <p>Results</p> <p>We found two morphologically and genetically well-differentiated groups within <it>C. ornatum</it>. One is located in the northern river drainages (Yaqui, Mayo, Fuerte, Sonora, Casas Grandes, Santa Clara and Conchos) and another one is found in the southern drainages (Nazas, Aguanaval and Piaxtla). The split between these two lineages took place about 3.9 Mya (CI = 2.1-5.9). Within the northern lineage, there was strong and significant inter-basin genetic differentiation and also several secondary dispersal episodes whit gene homogenization between drainages. Interestingly, three divergent mitochondrial lineages were found in sympatry in two northern localities from the Yaqui river basin.</p> <p>Conclusions</p> <p>Our results indicate that there was isolation between the northern and southern phylogroups since the Pliocene, which was related to the formation of the ancient Nazas River paleosystem, where the southern group originated. Within groups, a complex reticulate biogeographic history for <it>C. ornatum </it>populations emerges, following the taxon pulse theory and mainly related with Pliocene tecto-volcanic processes. In the northern group, several events of vicariance promoted by river or drainage isolation episodes were found, but within both groups, the phylogeographic patterns suggest the occurrence of several events of river capture and fauna interchange. The Yaqui River supports the most diverse populations of <it>C. ornatum</it>, with several events of dispersal and isolation within the basin. Based on our genetic results, we defined three ESUs within <it>C. ornatum </it>as a first attempt to promote the conservation of the evolutionary processes determining the genetic diversity of this species. They will likely be revealed as a valuable tool for freshwater conservation policies in northwest Mexico, where many environmental problems concerning the use of water have rapidly arisen in recent decades.</p

Freshwater fishes and water status in Mexico: A country-wide appraisal.

Mexico is the southernmost country in North America, and extends into Central America, south of the Isthmus of Tehuantepec. The northern half of M´exico is located on the Temperate belt and is arid in character (Nearctic), while the rest is within the Tropical belt (Neotropical). Climate varies from extremely temperate desert in the north, to tropical humid in the south.M´exico has more than 500 freshwater fish species, about 271 of them country endemics, and approximately 48 endemics from binational basins. There are still some 30–40 fish species not yet described. There are 563 fish species colonizing coastal flood plain species. In addition to the numbers of colonizing fishes, the burden of introduced exotics has also been growing. In 1904, only 4 species were recognized as exotics; by 1997 the number had increased to 94, and by 2008 to 11

Analysis of CpG methylation sites and CGI among human papillomavirus DNA genomes

<p>Abstract</p> <p>Background</p> <p>The Human Papillomavirus (HPV) genome is divided into early and late coding sequences, including 8 open reading frames (ORFs) and a regulatory region (LCR). Viral gene expression may be regulated through epigenetic mechanisms, including cytosine methylation at CpG dinucleotides. We have analyzed the distribution of CpG sites and CpG islands/clusters (CGI) among 92 different HPV genomes grouped in function of their preferential tropism: cutaneous or mucosal. We calculated the proportion of CpG sites (PCS) for each ORF and calculated the expected CpG values for each viral type.</p> <p>Results</p> <p>CpGs are underrepresented in viral genomes. We found a positive correlation between CpG observed and expected values, with mucosal high-risk (HR) virus types showing the smallest O/E ratios. The ranges of the PCS were similar for most genomic regions except <it>E4</it>, where the majority of CpGs are found within islands/clusters. At least one CGI belongs to each <it>E2/E4 </it>region. We found positive correlations between PCS for each viral ORF when compared with the others, except for the LCR against four ORFs and <it>E6 </it>against three other ORFs. The distribution of CpG islands/clusters among HPV groups is heterogeneous and mucosal HR-HPV types exhibit both lower number and shorter island sizes compared to cutaneous and mucosal Low-risk (LR) HPVs (all of them significantly different).</p> <p>Conclusions</p> <p>There is a difference between viral and cellular CpG underrepresentation. There are significant correlations between complete genome PCS and a lack of correlations between several genomic region pairs, especially those involving LCR and <it>E6</it>. <it>L2 </it>and <it>L1 </it>ORF behavior is opposite to that of oncogenes <it>E6 </it>and <it>E7</it>. The first pair possesses relatively low numbers of CpG sites clustered in CGIs while the oncogenes possess a relatively high number of CpG sites not associated to CGIs. In all HPVs, <it>E2/E4 </it>is the only region with at least one CGI and shows a higher content of CpG sites in every HPV type with an identified <it>E4</it>. The mucosal HR-HPVs show either the shortest CGI size, followed by the mucosal LR-HPVs and lastly by the cutaneous viral subgroup, and a trend to the lowest CGI number, followed by the cutaneous viral subgroup and lastly by the mucosal LR-HPVs.</p

Overview of the interactive task in BioCreative V

Fully automated text mining (TM) systems promote efficient literature searching, retrieval, and review but are not sufficient to produce ready-to-consume curated documents. These systems are not meant to replace biocurators, but instead to assist them in one or more literature curation steps. To do so, the user interface is an important aspect that needs to be considered for tool adoption. The BioCreative Interactive task (IAT) is a track designed for exploring user-system interactions, promoting development of useful TM tools, and providing a communication channel between the biocuration and the TM communities. In BioCreative V, the IAT track followed a format similar to previous interactive tracks, where the utility and usability of TM tools, as well as the generation of use cases, have been the focal points. The proposed curation tasks are user-centric and formally evaluated by biocurators. In BioCreative V IAT, seven TM systems and 43 biocurators participated. Two levels of user participation were offered to broaden curator involvement and obtain more feedback on usability aspects. The full level participation involved training on the system, curation of a set of documents with and without TM assistance, tracking of time-on-task, and completion of a user survey. The partial level participation was designed to focus on usability aspects of the interface and not the performance per se. In this case, biocurators navigated the system by performing pre-designed tasks and then were asked whether they were able to achieve the task and the level of difficulty in completing the task. In this manuscript, we describe the development of the interactive task, from planning to execution and discuss major findings for the systems tested

Fish biodiversity changes in the Lower Rio Grande/Rio Bravo, 1953–1996

Clearly defined changes in the fishesof the Lower Rio Grande/Rio Bravo, Texas andMexico, have been documented since 1953. Morerecent surveys show that the originalfreshwater fish fauna has been retreating fromthe lower reaches and is being replaced bybrackish and marine invaders. A total of 13localities between Colombia (Nuevo León,México) and the delta (580 km) weresurveyed, with a total fish fauna of 142species, which include native, exotic, andintruding species. Changes were analysed bylocality. These changes show a loss of themajority of freshwater species, replacement oflow to higher salinity forms. This shift isvery clear in marine invaders, with somespecies penetrating the whole areainvestigated. Those changes are morenoticeable in the lower-most localities, anddiminish upstream. Data suggest that thechanges in the basin, reflecting shifts inwhole-basin ecology, include elevatedtemperature, salinity, turbidity, and lowerrunoff levels. There are indications of higherlevels of pollution as well. Informationobtained in this study is being incorporated inan Index of Biological Integrity to appearelsewhere