Peter Arctander

A plea for DNA taxonomy.

Abstract Taxonomy underpins all biological research, with implications for many basic scientific and applied fields. Insights into the stability or change of animal and plant guilds require species identification on a broad scale and biodiversity questions have become a major public issue. But this comes at a time when taxonomy is facing a crisis, because ever fewer specialists are available. Here, we explore the possibility of using DNA-based methodology to overcome these problems. The utility of DNA sequences for taxonomic purposes is well established. However, all current taxonomic approaches intend to use DNA, at best, as an auxiliary criterion for identifying a species or a taxon, but have not given it a central role. We propose a scheme in which DNA would be the scaffold of a taxonomic reference system, whilst maintaining the importance of the morphological information associated with whole specimens.

ISIS, the intron information system, reveals the high frequency of alternative splicing in the human genome

ISIS, the intron information system, reveals the high frequency of alternative splicing in the human genome

Comparison of a mitochondrial gene and a corresponding nuclear pseudogene

Nuclear copies of mitochondrial genes have been reported several times. Presented here is a direct comparison of a fragment of the mitochondrial gene coding for Cytochrome b and its assumed nuclear pseudogene in a phylogenetic context. By studying eight such sets of genes a direct measurement of relative rates of several types of substitutions were made. As expected mitochondrial third position transitions are the fastest accumulating substitutions, here indicated to be at least up to 39 times faster than corresponding positions in the supposed nuclear pseudogene. Translocated mitochondrial genes, evolving much slower than their functional ‘counterpart’, reflect the ancestral-pre-translocated form of the gene. A warning is given against unwanted inclusion of paralogous sequences in phylogenetic analysis and against the use of versatile primers that can promote such incidents.

SIMPLICITY-CORRELATED SIZE GROWTH OF THE NUCLEAR 28S RIBOSOMAL RNA D3 EXPANSION SEGMENT IN THE CRUSTACEAN ORDER ISOPODA

The expansion segments within the eukaryote nuclear 23S-like ribosomal RNA molecule are now well characterized in many diverse organisms. A different base compositional bias, a higher propensity for size variability, and an increased evolutionary rate distinguish these regions from the universally conserved “core” regions of the molecule. In addition, some expansion segments of higher eukaryotes exhibit significant sequence simplicity which is hypothesized to occur by slippage-mediated mutational processes. We describe the discovery of extreme size variation of the D3 expansion segment in the crustacean order Isopoda. Among 11 species D3 varies in size from 180 to 518 nucleotides but maintains a homologous secondary structure. The D3 size is significantly positively correlated to relative simplicity factor (RSF), indicating that growth is most likely by insertion of simple sequences. D3 size and RSF correlate approximately with a morphology-based phylogeny, and within oniscideans RSF increases as more recent divergences occur. The D3 ofArmadillidium vulgare, with an RSF of 1.87, is the highest value recorded for any known expansion segment. Regions of high sequence simplicity in nuclear ribosomal RNA were previously only known from the higher vertebrate lineage. Here we demonstrate that this phenomenon occurs in a more extreme condition within a monophyletic invertebrate lineage. The extreme size changes identified could indicate that expansion segments are an extraneous element in the functioning ribosome.

Identification of miRNA targets with stable isotope labeling by amino acids in cell culture

miRNAs are small noncoding RNAs that regulate gene expression. We have used stable isotope labeling by amino acids in cell culture (SILAC) to investigate the effect of miRNA-1 on the HeLa cell proteome. Expression of 12 out of 504 investigated proteins was repressed by miRNA-1 transfection. This repressed set of genes significantly overlaps with miRNA-1 regulated genes that have been identified with DNA array technology and are predicted by computational methods. Moreover, we find that the 3′-untranslated region for the repressed set are enriched in miRNA-1 complementary sites. Our findings demonstrate that SILAC can be used for miRNA target identification and that one highly expressed miRNA can regulate the levels of many different proteins.

Population genetics of the roan antelope (Hippotragus equinus) with suggestions for conservation

The roan antelope (Hippotragus equinus) is the second largest African antelope, distributed throughout the continent in sub‐Saharan savannah habitat. Mitochondrial DNA (mtDNA) control region sequencing (401 bp, n = 137) and microsatellite genotyping (eight loci, n = 137) were used to quantify the genetic variability within and among 18 populations of this species. The within‐population diversity was low to moderate with an average mtDNA nucleotide diversity of 1.9% and average expected heterozygosity with the microsatellites of 46%, but significant differences were found among populations with both the mtDNA and microsatellite data. Different levels of genetic resolution were found using the two marker sets, but both lent strong support for the separation of West African populations (samples from Benin, Senegal and Ghana) from the remainder of the populations studied across the African continent. Mismatch distribution analyses revealed possible past refugia for roan in the west and east of Africa. The West African populations could be recognized together as an evolutionarily significant unit (ESU), referable to the subspecies H. e. koba. Samples from the rest of the continent constituted a geographically more diverse assemblage with genetic associations not strictly corresponding to the other recognized subspecies.

Population structure of African buffalo inferred from mtDNA sequences and microsatellite loci : High variation but low differentiation

The African buffalo (Syncerus caffer) is widespread throughout sub‐Saharan Africa and is found in most major vegetation types, wherever permanent sources of water are available, making it physically able to disperse through a wide range of habitats. Despite this, the buffalo has been assumed to be strongly philopatric and to form large aggregations that remain within separate home ranges with little interchange between units, but the level of differentiation within the species is unknown. Genetic differences between populations were assessed using mitochondrial DNA (control region) sequence data and analysis of variation at six microsatellite loci among 11 localities in eastern and southern Africa. High levels of genetic variability were found, suggesting that reported severe population bottlenecks due to outbreak of rinderpest during the last century did not strongly reduce the genetic variability within the species. The high level of genetic variation within the species was found to be evenly distributed among populations and only at the continental level were we able to consistently detect significant differentiation, contrasting with the assumed philopatric behaviour of the buffalo. Results of mtDNA and microsatellite data were found to be congruent, disagreeing with the alleged male‐biased dispersal. We propose that the observed pattern of the distribution of genetic variation between buffalo populations at the regional level can be caused by fragmentation of a previous panmictic population due to human activity, and at the continental level, reflects an effect of geographical distance between populations.

Genetic diversity of the attachment (H) protein gene of current field isolates of canine distemper virus

To characterize the variability of recent field isolates of canine distemper virus (CDV) from different hosts and geographical areas, we conducted nucleotide sequence analysis of the gene encoding the haemagglutinin (H), the attachment protein of this virus. Pronounced differences between field isolates were revealed in comparison to the Convac and Onderstepoort vaccine strains. The diversity of CDV appeared to exceed that determined for measles virus. Phylogenetic analysis also separated the field isolates of CDV from the vaccine strains and provided evidence for the existence of different contemporary genotypes of CDV. Isolates from a Greenlandic sledge dog and a Siberian seal formed a distinct lineage. The remaining isolates formed a group. This group contained two European isolates from mink and ferret, a single lineage comprising three European dog isolates, and another separate lineage of North American isolates from dog, javelina, raccoon and captive leopards.

Beringian Paleoecology Inferred from Permafrost-Preserved Fungal DNA

ABSTRACT The diversity of fungi in permanently frozen soil from northeastern Siberia was studied by culture-independent PCR amplification of diverse environmental 18S rRNA genes. Elaborate protocols to avoid contamination during drilling, sampling, and amplification were used. A broad diversity of eukaryotic DNA sequences that were 510 bp long, including sequences of various fungi, plants, and invertebrates, could be obtained reproducibly from samples that were up to 300,000 to 400,000 years old. The sequences revealed that ancient fungal communities included a diversity of cold-adapted yeasts, dark-pigmented fungi, plant-parasitic fungi, and lichen mycobionts. DNA traces of tree-associated macrofungi in a modern tundra sample indicated that there was a shift in fungal diversity following the last ice age and supported recent results showing that there was a severe change in the plant composition in northeastern Siberia during this period. Interestingly, DNA sequences with high homology to sequences of coprophilic and keratinophilic fungi indicated that feces, hair, skin, and nails could have been sources of ancient megafauna DNA recently reported to be present in small amounts of Siberian permafrost sediments.

Population genetic structure of the African elephant in Uganda based on variation at mitochondrial and nuclear loci: evidence for male-biased gene flow

A drastic decline has occurred in the size of the Uganda elephant population in the last 40 years, exacerbated by two main factors; an increase in the size of the human population and poaching for ivory. One of the attendant consequences of such a decline is a reduction in the amount of genetic diversity in the surviving populations due to increased effects of random genetic drift. Information about the amount of genetic variation within and between the remaining populations is vital for their future conservation and management. The genetic structure of the African elephant in Uganda was examined using nucleotide variation of mitochondrial control region sequences and four nuclear microsatellite loci in 72 individuals from three localities. Eleven mitochondrial DNA (mtDNA) haplotypes were observed, nine of which were geographically localized. We found significant genetic differentiation between the three populations at the mitochondrial locus while three out of the four microsatellite loci differentiated KV and QE, one locus differentiated KV and MF and no loci differentiated MF and QE. Expected heterozygosity at the four loci varied between 0.51 and 0.84 while nucleotide diversity at the mitochondrial locus was 1.4%. Incongruent patterns of genetic variation within and between populations were revealed by the two genetic systems, and we have explained these in terms of the differences in the effective population sizes of the two genomes and male‐biased gene flow between populations.