A short critical history of the application of genomics to animal breeding

Two scientific schools have been in coexistence from the beginning of genetics, one of them searching for factors of inheritance and the other one applying biometrical models to study the relationships between relatives. With the development of molecular genetics, the possibilities of detecting genes having a noticeable effect in traits augmented. Some genes with large or medium effects were localized in animals, although the most common result was to detect markers linked to these genes, allowing the possibility of assisting selection programs with markers. When a large amount of simple and inexpensive markers were available, the SNPs, new possibilities were opened since they did not need the presence of genes of large or medium effect controlling a trait, because the whole genome was scanned. Using a large amount of SNPs permits having a prediction of the breeding value at birth accurate enough to be used in some cases, like dairy cattle, to halve its generation interval. In other animal breeding programs, the implementation of genomic selection is less clear and the way in which it can be useful should be carefully studied. The need for large populations for associating phenotypic data and markers, plus the need for repeating the process continuously, complicates its application in some cases. The implementation of the information provided by the SNPs in current genetic programs has led to the development of complex statistical tools, joining the efforts of the two schools, factorial and biometrical, that nowadays work closely related.

VIDA: a virus database system for the organization of animal virus genome open reading frames

VIDA is a new virus database that organizes open reading frames (ORFs) from partial and complete genomic sequences from animal viruses. Currently VIDA includes all sequences from GenBank for Herpesviridae, Coronaviridae and Arteriviridae. The ORFs are organized into homologous protein families, which are identified on the basis of sequence similarity relationships. Conserved sequence regions of potential functional importance are identified and can be retrieved as sequence alignments. We use a controlled taxonomical and functional classification for all the proteins and protein families in the database. When available, protein structures that are related to the families have also been included. The database is available for online search and sequence information retrieval at http://www.biochem.ucl.ac.uk/bsm/virus_database/VIDA.html.

Abyssal community analysis from replicate box cores in the central North Pacific

A 0.25 m**2 United States Naval Electronics Laboratory box corer was used to take replicate samples from an oligotrophic bottom under the North Pacific Central Water Mass (~28°N, 155°W). The bottom is a red clay with manganese nodules at a depth of 5500-5800 m. Macrofaunal density ranges from 84 to 160 individuals per m**2 and is therefore much the same as in Northwest Atlantic Gyre waters. Of the macrofaunal taxa, polychaetes dominate (55 %), followed by tanaids (18 %), bivalves (7 %), and isopods (6 %). Meiofaunal taxa were only partially retained by the 297 µm screen used in washing. Even then, they are 1.5-3.9 times as abundant as the macrofaunal taxa, with nematodes being numerically dominant by far. Foraminifera seem to comprise an important portion of the community, but could not be assessed accurately because of the inability to discriminate living and dead tests. Remains of what are probably xenophyophoridans are also very important, but offer the same problem. Faunal diversity is extremely high, with deposit feeders comprising the overwhelming majority. Most species are rare, being encountered only once. The distributions of only three species show any significant deviation from randomness. The polychaete fauna from box cores collected from 90 miles to the north was not significantly different from that of the principal study locality. Concordance appeared at several taxonomic levels, from species through macrofaunal/meiofaunal relationships. As a result, the variation in total animal abundance shows aggregation among cores. We discuss Sokolova's concept of a deep-sea oligotrophic zone dominated by suspension feeders, and reconcile it with our present findings. The high diversity of the fauna combined with the low food level contradict theories that relate diversity directly with productivity.

(Table 1) Age determination of sediment core SO147_106KL

Here we present a high-resolution marine sediment record from the El Niño region off the coast of Peru spanning the last 20,000 years. Sea surface temperature, photosynthetic pigments, and a lithic proxy for El Niño flood events on the continent are used as paleo-El Niño-Southern Oscillation proxy data. The onset of stronger El Niño activity in Peru started around 17,000 calibrated years before the present, which is later than modeling experiments show but contemporaneous with the Heinrich event 1. Maximum El Niño activity occurred during the early and late Holocene, especially during the second and third millennium B.P. The recurrence period of very strong El Niño events is 60-80 years. El Niño events were weak before and during the beginning of the Younger Dryas, during the middle of the Holocene, and during medieval times. The strength of El Niño flood events during the last millennium has positive and negative relationships to global and Northern Hemisphere temperature reconstructions.

Sediment microstructures of ODP Leg 105 holes

Possible genetic relationships between syn- and post-depositional processes and sediment microstructure were investigated. Samples from cores at Sites 646 and 647 of Ocean Drilling Program (ODP) Leg 105 included examples of bottom current deposition (contourites), turbidity current deposition, consolidation, and diagenesis. Examination of nearly 200 micrographs of 14 samples from Site 646 and 13 samples from Site 647 leads to the conclusion that sedimentation processes do not appear to have an obvious influence on fabric. The effects of post-depositional processes, such as bioturbation, coring disturbance, and even remolding, appear to be less significant than one might expect as a result of the relatively coarse grain size of the sediments studied. Consolidation resulting from increased overburden stress results in increased particle alignment and compression of fabric elements with depth. The transition from open, random fabric in shallow samples to preferred orientation at depth represents the only change in these sediments that can be ascribed directly to a specific depositional or post-depositional process. Mineralogical variations, owing to changes in weathering processes and growth of authigenic/diagenetic minerals, also have a pronounced effect on sediment fabric.

(Table 1) Calculated sea surface temperature of sediment core RC11-210

Proxy indicators of sea surface temperature and equatorial divergence based on radiolarian assemblage data, and of trade wind intensity based on eolian grain size data show similar aspects of variability during the late Pleistocene: All indicators fluctuate at higher frequencies than the 100,000-year glacial-interglacial cycle, display reduced amplitude variations since 300,000 years ago, exhibit a change in the record character at about 300,000 years ago (the mid-Brunhes climatic event), and have higher amplitude variations in sediments 300,000-850,000 years old. Time series analyses were conducted to determine the spectral character of each record (delta18O of planktonic foraminifer, sea surface temperature values, equatorial divergence indicators, and wind intensity indicators) and to quantify interrecord coherence and phase relationships. The record was divided at the 300,000-year clear change in climatic variability (nonstationarity). The delta18O-based time scale is better lower in the core so our spectral analyses concentrated on the interval from 402,000-774,000 years. The delta18O spectra show 100,000- and 41,000-year power in the younger portion, 0-300,000 years, and 100,000-, 41,000- and 23,000-year power in the older interval, all highly coherent and in phase with the SPECMAP average stacked isotope record. Unlike the isotope record the dominant period in both the eolian grain size and equatorial divergence indicators is 31,000 years. This period is also important in the sea surface temperature signal where the dominant spectral peak is 100,000 years. The 31,000-year spectral component is coherent and in phase between the eolian and divergence records, confirming the link between atmospheric and ocean surface circulation for the first time in the paleoclimate record. Since the 31,000-year power appears in independent data sets within this core and also appears in other equatorial records [J. Imbrie personal communication, 1987], we assume it to be real and representative of both a nonlinear response to orbital forcing, possibly a combination of orbital tilt and eccentricity, and some resonance phenomenon required to amplify the response at this period so that it appears as a dominant frequency component. The mid-Brunhes climatic event is an important aspect of these records, but its cause remains unknown.

(Table 2) Dinoflagellate cysts in surface sediment samples of METEOR cruises M20/2, M23/1, M34/2 and M34/2

The organic walled cyst content of 41 surface sediment samples from the south-eastern South Atlantic Ocean have been studied to create a dataset that can be used for palaeoceanographic reconstructions. In order to obtain insight into which environmental factors influence the distribution of individual cyst species, the cyst associations have been compared with oceanographic characteristics of the overlying water masses, i.e. temperature, salinity, density and stratification gradients. The associations and relationships have been established by visual examination of the dataset and the multivariate ordination techniques, Detrended Correspondence Analysis and Canonical Correspondence Analysis. Special attention has been given to the factors of transport and preservation of the cysts. Five associations have been recognised as being characteristic of (1) areas influenced by coastal upwelling and/or river outflow, (2) open ocean, (3) Agulhas Current and southern Benguela Current, (4) Benguela Current and (5) Walvis Bay, shelf break area. The factors dominant in influencing either directly or indirectly the cyst distributions appear to be the stratification in the upper 50 m of the water column, nutrient concentration and seasonality. Variations in sea surface temperatures and salinities have only minor effect on cyst distribution.

Effects of suspended solids and sediment on reproduction and early life of warmwater fishes : a review /

Mode of access: Internet.

Relationships of Efficiency to Reproductive Disorders in Danish Milk Production: A Stochastic Frontier Analysis

Relationships of various reproductive disorders and milk production performance of Danish dairy farms were investigated. A stochastic frontier production function was estimated using data collected in 1998 from 514 Danish dairy farms. Measures of farm-level milk production efficiency relative to this production frontier were obtained, and relationships between milk production efficiency and the incidence risk of reproductive disorders were examined. There were moderate positive relationships between milk production efficiency and retained placenta, induction of estrus, uterine infections, ovarian cysts, and induction of birth. Inclusion of reproductive management variables showed that these moderate relationships disappeared, but directions of coefficients for almost all those variables remained the same. Dystocia showed a weak negative correlation with milk production efficiency. Farms that were mainly managed by young farmers had the highest average efficiency scores. The estimated milk losses due to inefficiency averaged 1142, 488, and 256 kg of energy-corrected milk per cow, respectively, for low-, medium-, and high-efficiency herds. It is concluded that the availability of younger cows, which enabled farmers to replace cows with reproductive disorders, contributed to high cow productivity in efficient farms. Thus, a high replacement rate more than compensates for the possible negative effect of reproductive disorders. The use of frontier production and efficiency/ inefficiency functions to analyze herd data may enable dairy advisors to identify inefficient herds and to simulate the effect of alternative management procedures on the individual herd's efficiency.

A theoretical exploration of catchment-scale sediment delivery

This paper proposes a theoretical explanation of the variations of the sediment delivery ratio (SDR) versus catchment area relationships and the complex patterns in the behavior of sediment transfer processes at catchment scale. Taking into account the effects of erosion source types, deposition, and hydrological controls, we propose a simple conceptual model that consists of two linear stores arranged in series: a hillslope store that addresses transport to the nearest streams and a channel store that addresses sediment routing in the channel network. The model identifies four dimensionless scaling factors, which enable us to analyze a variety of effects on SDR estimation, including (1) interacting processes of erosion sources and deposition, (2) different temporal averaging windows, and (3) catchment runoff response. We show that the interactions between storm duration and hillslope/channel travel times are the major controls of peak-value-based sediment delivery and its spatial variations. The interplay between depositional timescales and the travel/residence times determines the spatial variations of total-volume-based SDR. In practical terms this parsimonious, minimal complexity model could provide a sound physical basis for diagnosing catchment to catchment variability of sediment transport if the proposed scaling factors can be quantified using climatic and catchment properties.

Relationships of sauries and needlefishes (Teleostei : Scomberesocoidea) to the internally fertilizing halfbeaks (Zenarchopteridae) based on the pharyngeal jaw apparatus

The 40 life history, myological, and osteological characters that Tibbetts (1992) used in his study of the hemiramphids are evaluated for both saury genera (Cololabis and Scomberesox) to determine if the Scomberesocidae are more closely related to the Zenarchopteridae, to the needlefishes (Belonidae), or to the halfbeaks (Hemiramphidae) and flyingfishes (Exocoetidae). Data were analyzed using PAUP*, and eight equally parsimonious trees were found (70 steps, CI 0.814, RI 0.938). This analysis indicates that sauries are most closely related to needlefishes, supporting the historical concept of the superfamily Scomberesocoidea as a monophyletic assemblage. A caudal displacement of the origin of the retractor dorsalis muscle is a tentative additional synapomorphy for all four saury species. Zenarchopteridae is strongly supported as a valid family sister to the Scomberesocoidea (decay index = 19, bootstrap = 100). Resolution of the internal structure of the Belonidae and the Hemiramphidae requires the identification of additional characters and examination of a greater number of taxa.