A physical map of the highly heterozygous Populus genome: integration with the genome sequence and genetic map and analysis of haplotype variation

As part of a larger project to sequence the Populus genome and generate genomic resources for this emerging model tree, we constructed a physical map of the Populus genome, representing one of the few such maps of an undomesticated, highly heterozygous plant species. The physical map, consisting of 2802 contigs, was constructed from fingerprinted bacterial artificial chromosome (BAC) clones. The map represents approximately 9.4-fold coverage of the Populus genome, which has been estimated from the genome sequence assembly to be 485 ± 10 Mb in size. BAC ends were sequenced to assist long-range assembly of whole-genome shotgun sequence scaffolds and to anchor the physical map to the genome sequence. Simple sequence repeat-based markers were derived from the end sequences and used to initiate integration of the BAC and genetic maps. A total of 2411 physical map contigs, representing 97% of all clones assigned to contigs, were aligned to the sequence assembly (JGI Populus trichocarpa , version 1.0). These alignments represent a total coverage of 384 Mb (79%) of the entire poplar sequence assembly and 295 Mb (96%) of linkage group sequence assemblies. A striking result of the physical map contig alignments to the sequence assembly was the co-localization of multiple contigs across numerous regions of the 19 linkage groups. Targeted sequencing of BAC clones and genetic analysis in a small number of representative regions showed that these co-aligning contigs represent distinct haplotypes in the heterozygous individual sequenced, and revealed the nature of these haplotype sequence differences.     

Patterns of lake occupancy by fish indicate different adaptations to life in a harsh Arctic environment

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Complete genome sequence of Polynucleobacter necessarius subsp. asymbioticus type strain (QLW-P1DMWA-1(T))

Polynucleobacter necessarius subsp. asymbioticus strain QLW-P1DMWA-1(T) is a planktonic freshwater bacterium affiliated with the family Burkholderiaceae (class Betaproteobacteria). This strain is of interest because it represents a subspecies with cosmopolitan and ubiquitous distribution in standing freshwater systems. The 16S-23S ITS genotype represented by the sequenced strain comprised on average more than 10% of bacterioplankton in its home habitat. While all strains of the subspecies P. necessarius asymbioticus are free-living freshwater bacteria, strains belonging to the only other subspecies, P. necessarius subsp. necessarius are obligate endosymbionts of the ciliate Euplotes aediculatus. The two subspecies of P. necessarius are the instances of two closely related subspecies that differ in their lifestyle (free-living vs. obligate endosymbiont), and they are the only members of the genus Polynucleobacter with completely sequenced genomes. Here we describe the features of P. necessarius subsp. asymbioticus, together with the complete genome sequence and annotation. The 2,159,490 bp long chromosome with a total of 2,088 protein-coding and 48 RNA genes is the first completed genome sequence of the genus Polynucleobacter to be published and was sequenced as part of the DOE Joint Genome Institute Community Sequencing Program 2006.     

Assessing the efficiency of connectivity measures with regard to the EU-Water Framework Directive in a Danube-tributary system

The effect of restoring connectivity for fish by the construction of 11 fish ladders in the Pielach and Melk rivers, both tributaries to the Danube in Austria, was monitored using electric fishing and fish traps between 1999 and 2004. In order to assess the efficiency of connectivity rehabilitation measures pre- and post-project data combining electric fishing and trap catch data were analyzed by means of three fish-based assessment methods: a MUlti-Level concept for a Fish-based, river-type-specific Assessment of ecological integrity (MULFA), the Fish Index Austria (FIA) and the European Fish Index (EFI). The effect of adding qualitative trap catch data to electric fishing data on metrics and indices was also tested and the magnitude of the effect was related to the distance of the sites from the river mouth. The results clearly demonstrated the significant contribution of connectivity rehabilitation measures to the ecological integrity of rivers like the River Pielach where morphological conditions are good, whereas remaining channelization still limits the success of connectivity measures in the River Melk. Trap catch data were found to represent an essential source of additional information to assess the efficiency of connectivity measures shortly after their implementation. The negative correlations of the magnitude of the effect of different indices and metrics with the distance of assessment sites from river mouths obviously underline the importance of the river Danube as a source for the re-colonization process. While the indices tested were found to have limited ability to reflect short-term response of fish assemblages to continuum rehabilitation, guild metrics were able to detect improvements of the ecological status shortly after the implementation of connectivity measures. Six metrics showed significant differences between pre and post-project data reflecting the expected increase of the ecological integrity: (1) Fish Region Index (FRI; FIA, MULFA), (2) number of subdominant species and (3) number of flow-guilds (FIA), (4) number of type specific species (MULFA), (5) number of benthic species and (6) number of potamodromous species (EFI); the FRI differences were only significant when trap catch data were added. The EFI indicated a decline of ecological integrity through increases in the density of omnivorous species and the relative number of tolerant species as well as a decrease in the relative number of intolerant species. Significantly decreasing responses with the distance from the river mouth were documented by the EFI and MULFA-index, the FRI (FIA, MULFA), total biomass and for the number of type specific species (MULFA). Guest editors: R. L. Welcomme & G. Marmulla Hydropower, Flood Control and Water Abstraction: Implications for Fish and Fisheries     

Association of an Agouti allele with fawn or sable coat color in domestic dogs

The type of pigment synthesized in mammalian hair, yellow–red pheomelanin or black–brown eumelanin, depends on the interaction between Agouti protein and the Melanocortin 1 receptor. Although the genetics of pigmentation is broadly conserved across most mammalian species, pigment type-switching in domestic dogs is unusual because a yellow–tan coat with variable amounts of dark hair is thought to be caused by an allele of the Agouti locus referred to as fawn or sable (a^y). In a large survey covering thirty seven breeds, we identified an Agouti allele with two missense alterations, A82S and R83H, which was present (heterozygous or homozygous) in 41 dogs (22 breeds) with a fawn or sable coat, but was absent from 16 dogs (8 breeds) with a black-and-tan or tricolor phenotype. In an additional 33 dogs (14 breeds) with a eumelanic coat, 8 (German Shepherd Dogs, Groenendaels, Schipperkes, or Shetland Sheepdogs) were homozygous for a previously reported mutation, non-agouti R96C; the remainder are likely to have carried dominant black, which is independent of and epistatic to Agouti. This work resolves some of the complexity in dog coat color genetics and provides diagnostic opportunities and practical guidelines for breeders.     

Changes in abundance and spatial distribution of geese molting near Teshekpuk Lake,Alaska: interspecific competition or ecological change?

Goose populations molting in the Teshekpuk Lake Special Area of the National Petroleum Reserve—Alaska have changed in size and distribution over the past 30 years. Black brant (Branta bernicla nigricans) are relatively stable in numbers but are shifting from large, inland lakes to salt marshes. Concurrently, populations of greater white-fronted geese (Anser albifrons frontalis) have increased seven fold. Populations of Canada geese (Branta canadensis and/or B. hutchinsii) are stable with little indication of distributional shifts. The lesser snow goose (Anser caerulescens caerulescens) population is proportionally small, but increasing rapidly. Coastline erosion of the Beaufort Sea has altered tundra habitats by allowing saltwater intrusion, which has resulted in shifts in composition of forage plant species. We propose two alternative hypotheses for the observed shift in black brant distribution. Ecological change may have altered optimal foraging habitats for molting birds, or alternatively, interspecific competition between black brant and greater white-fronted geese may be excluding black brant from preferred habitats. Regardless of the causative mechanism, the observed shifts in species distributions are an important consideration for future resource planning.