Does polyploidy lead to fewer and shorter microsatellites in Barbus (Teleostei: Cyprinidae)?

Screening of a hybrid Barbus barbus-B. meridionalis genome was performed for CA, GA, TAT, TCT, TAG, TGT, TATT, TACT, ATCT motifs, and simultaneously on another fish species, tilapia S. melanotheron . Sequences of positive clones were obtained for Barbus and revealed that repetitive structure significantly depends on the motif: most TAT and TATT repeats contain small numbers of repeats, and these repeats are highly heterogeneous, whereas other motifs (we mainly obtained CA and GATA repeats) form longer and much more homogeneous arrays. Polymorphism data from five loci in two different species of barbel show that perfectly repetitive loci are much more variable than imperfect loci (TAT and TATT). We compared the frequency of positive clones for different repeat motifs between barbel and tilapia. For dinucleotide repeats (CA and GA), the comparison was extended to additional fish species, trout and sea bass, which were screened in nearly identical conditions for these motifs. The most salient feature of these comparisons reveals that arrays of dinucleotide motifs are significantly under-represented and shorter in Barbus than in other fish species. We propose an explanation that can account for most features of microsatellites characterizing the genome of barbel. A bias toward deletion affecting slipped-strand mispairing events would lead to shortening and loss of microsatellite loci. Such a bias would represent an efficient way of eliminating useless DNA from polyploidized species with an excessive amount of DNA.     

Detection and normalization of biases present in spotted cDNA microarray data: a composite method addressing dye, intensity-dependent, spatially-dependent, and print-order biases.

Microarrays are often used to identify target genes that trigger specific diseases, to elucidate the mechanisms of drug effects, and to check SNPs. However, data from microarray experiments are well known to contain biases resulting from the experimental protocols. Therefore, in order to elucidate biological knowledge from the data, systematic biases arising from their protocols must be removed prior to any data analysis. To remove these biases, many normalization methods are used by researchers. However, not all biases are eliminated from the microarray data because not all types of errors from experimental protocols are known. In this paper, we report an effective way of removing various types of biases by treating each microarray dataset independently to detect biases present in the dataset. After the biases contained in each dataset were identified, a combination of normalization methods specifically made for each dataset was applied to remove biases one at a time.     

Genomics of speciation and introgression in Princess cichlid fishes from Lake Tanganyika

How variation in the genome translates into biological diversity and new species originate has endured as the mystery of mysteries in evolutionary biology. African cichlid fishes are prime model systems to address speciation‐related questions for their remarkable taxonomic and phenotypic diversity, and the possible role of gene flow in this process. Here, we capitalize on genome sequencing and phylogenomic analyses to address the relative impacts of incomplete lineage sorting, introgression and hybrid speciation in the Neolamprologus savoryi‐complex (the ‘Princess cichlids’) from Lake Tanganyika. We present a time‐calibrated species tree based on whole‐genome sequences and provide strong evidence for incomplete lineage sorting in the early phases of diversification and multiple introgression events affecting different stages. Importantly, we find that the Neolamprologus chromosomes show centre‐to‐periphery biases in nucleotide diversity, sequence divergence, GC content, incomplete lineage sorting and rates of introgression, which are likely modulated by recombination density and linked selection. The detection of heterogeneous genomic landscapes has strong implications on the genomic mechanisms involved in speciation. Collinear chromosomal regions can be protected from gene flow and harbour incompatibility genes if they reside in lowly recombining regions, and coupling can evolve between nonphysically linked genomic regions (chromosome centres in particular). Simultaneously, higher recombination towards chromosome peripheries makes these more dynamic, evolvable regions where adaptation polymorphisms have a fertile ground. Hence, differences in genome architecture could explain the levels of taxonomic and phenotypic diversity seen in taxa with collinear genomes and might have contributed to the spectacular cichlid diversity observed today.     

The good,the bad,and the ugly: which Australian terrestrial mammal species attract most research?

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Enhancing Low‐Bias Performance of Hematite Photoanodes for Solar Water Splitting by Simultaneous Reduction of Bulk,Interface, and Surface Recombination Pathways

For a hematite (α‐Fe₂O₃) photoanode, multiple electron/hole recombination pathways occurring in the bulk, interfaces, and surfaces largely limit its low‐bias performance (low photocurrent density at low‐bias potential) for photoelectrochemical water splitting. Here, a facile and rapid three‐step approach is reported to simultaneously reduce these recombinations for hematite nanorods (NRs) array photoanode, leading to a greatly improved photocurrent density at low bias potential. First, flame‐doping enables high concentration of Ti doping without hampering the morphology and surface properties of the hematite NRs, which reduces both the bulk and surface recombinations effectively. Second, the addition of a dense‐layer between the hematite NRs and fluorine‐doped SnO₂ substrate effectively reduces the interfacial recombination by suppressing the electron back‐injection into electrolyte. Finally, the sequential oxalic acid etching and FeOOH deposition improves both the interface quality between FeOOH electrocatalyst and hematite NRs and the surface catalytic activity. Significantly, the combination of flame‐doping, dense‐layer deposition, surface etching, and electrocatalyst deposition effectively reduces the multiple electron/hole recombination pathways in a hematite NRs photoanode, which decreases the photocurrent onset potential from 1.02 V _RHE to 0.64 V_RHE, a reduction of 380 mV.     

Uncertainty in identifying local extinctions: the distribution of missing data and its effects on biodiversity measures

Identifying local extinctions is integral to estimating species richness and geographic range changes and informing extinction risk assessments. However, the species occurrence records underpinning these estimates are frequently compromised by a lack of recorded species absences making it impossible to distinguish between local extinction and lack of survey effort—for a rigorously compiled database of European and Asian Galliformes, approximately 40% of half-degree cells contain records from before but not after 1980. We investigate the distribution of these cells, finding differences between the Palaearctic (forests, low mean human influence index (HII), outside protected areas (PAs)) and Indo-Malaya (grassland, high mean HII, outside PAs). Such cells also occur more in less peaceful countries. We show that different interpretations of these cells can lead to large over/under-estimations of species richness and extent of occurrences, potentially misleading prioritization and extinction risk assessment schemes. To avoid mistakes, local extinctions inferred from sightings records need to account for the history of survey effort in a locality.     

Purification of (1→3)-β-glucan endohydrolase isoenzyme II from germinated barley and determination of its primary structure from a cDNA clone

A (13)--D-glucan 3-glucanonydrolase (EC 3.2.1.39) of apparent M _r 32 000, designated GII, has been purified from germinated barley grain and characterized. The isoenzyme is resolved from a previously purified isoenzyme (GI) on the basis of differences in their isoelectric points; (13)--glucanases GI and GII have pI values of 8.6 and 10.0, respectively. Comparison of the sequences of their 40 NH₂-terminal amino acids reveals 68% positional identity. A 1265 nucleotide pair cDNA encoding (13)--glucanase isoenzyme GII has been isolated from a library prepared with mRNA of 2-day germinated barley scutella. Nucleotide sequence analysis of the cDNA has enabled the complete primary structure of the 306 amino acid (13)--glucanase to be deduced, together with that of a putative NH₂-terminal signal peptide of 28 amino acid residues. The (13)--glucanase cDNA is characterized by a high (G+C) content, which reflects a strong bias for the use of G or C in the wobble base position of codons. The amino acid sequence of the (13)--glucanase shows highly conserved internal domains and 52% overall positional identity with barley (13, 14)--glucanase isoenzyme EII, an enzyme of related but quite distinct substrate specificity. Thus, the (13)--glucanases, which may provide a degree of protection against microbial invasion of germinated barley grain through their ability to degrade fungal cell wall polysaccharides, appear to share a common evolutionary origin with the (13, 14)--glucanases, which function to depolymerize endosperm cell walls in the germinated grain.     

Female-biased natal dispersal in the Siberian flying squirrel

Natal dispersal is usually sex biased in birds and mammals.Female-biased natal dispersal is the prevailing pattern in birdsbut is rare among mammals. Hypotheses explaining sex bias indispersal include the mate-defense mating hypothesis, whichpredicts male-biased dispersal, the resource-defense hypothesispredicting female-biased dispersal, and the competition hypothesis,which predicts that if dispersal is caused by competition forresources between sexes, then the subdominant sex will disperse.We studied natal dispersal of Siberian flying squirrels Pteromysvolans using radio telemetry in Southern Finland in 1996–2004.Of 86 juveniles that survived over the dispersal period, almostall young females dispersed from the natal site, whereas almost40% of males were philopatric. Dispersal was farther for femalesthan males. Females began dispersal on average 2 weeks earlierthan males and were lighter in mass at the onset of dispersalthan later dispersing males. No mate- or resource-defense matingsystem could be found among males, but females seemed to defendnest and apparently food resources, in contrast to the expectationof dispersal bias in resource-defense systems. Competition forresources between sexes does not explain female bias either:in the flying squirrel, the female seems to be the dominantsex. We propose that young females are subordinate to theirmothers and have to disperse to find a vacant, suitable sitefor reproduction.