Similarities and differences between western cultures: Toddler temperament and parent-child interactions in the United States (US) and Germany.

Parents play a critical role in shaping social-emotional development, particularly in early childhood; however, children's influence on their own development is equally important. Parent-child interactions, fundamental to secure attachment and social schemes, represent a critical area of social-emotional development subject to child effects associated with temperament. The present study explores these effects through a cross-cultural lens via comparisons of dyads from the United States (US) and Germany. Specifically, cross-cultural differences in toddler temperament were evaluated via the Early Childhood Behavior Questionnaire (ECBQ; Putnam et al., 2006), with cross-cultural variability in parent-child interactions examined as well, along with differences in child temperament effects on the quality of these interactions. Ratings of temperament were generally similar between the two cultures; however, US toddlers were rated higher in attention shifting, whereas German children were rated higher on soothability and perceptual sensitivity. Additionally, dyadic interactions in the US were rated as more stimulating and demonstrating greater partner engagement than those in Germany. Differential contributions of temperament to interaction quality and complexity were also observed. Higher ratings of toddler discomfort and perceptual sensitivity predicted more stimulating interactions overall in the US but not Germany. In contrast, higher ratings of toddler low-intensity pleasure predicted more stimulating interactions in Germany but not the US. Overall, the present study identifies many similarities between US and German toddlers and supports theories describing children as active agents in shaping their own development, in what appears to be a different manner across cultures.

Metabarcoding by capture using a single COI probe (MCSP) to identify and quantify fish species in ichthyoplankton swarms.

The ability to determine the composition and relative frequencies of fish species in large ichthyoplankton swarms could have extremely important ecological applications However, this task is currently hampered by methodological limitations. We proposed a new method for Amazonian species based on hybridization capture of the COI gene DNA from a distant species (Danio rerio), absent from our study area (the Amazon basin). The COI sequence of this species is approximately equidistant from all COI of Amazonian species available. By using this sequence as probe we successfully facilitated the simultaneous identification of fish larvae belonging to the order Siluriformes and to the Characiformes represented in our ichthyoplankton samples. Species relative frequencies, estimated by the number of reads, showed almost perfect correlations with true frequencies estimated by a Sanger approach, allowing the development of a quantitative approach. We also proposed a further improvement to a previous protocol, which enables lowering the sequencing effort by 40 times. This new Metabarcoding by Capture using a Single Probe (MCSP) methodology could have important implications for ecology, fisheries management and conservation in fish biodiversity hotspots worldwide. Our approach could easily be extended to other plant and animal taxa.

DNA Metabarcoding of Amazonian Ichthyoplankton Swarms.

Tropical rainforests harbor extraordinary biodiversity. The Amazon basin is thought to hold 30% of all river fish species in the world. Information about the ecology, reproduction, and recruitment of most species is still lacking, thus hampering fisheries management and successful conservation strategies. One of the key understudied issues in the study of population dynamics is recruitment. Fish larval ecology in tropical biomes is still in its infancy owing to identification difficulties. Molecular techniques are very promising tools for the identification of larvae at the species level. However, one of their limits is obtaining individual sequences with large samples of larvae. To facilitate this task, we developed a new method based on the massive parallel sequencing capability of next generation sequencing (NGS) coupled with hybridization capture. We focused on the mitochondrial marker cytochrome oxidase I (COI). The results obtained using the new method were compared with individual larval sequencing. We validated the ability of the method to identify Amazonian catfish larvae at the species level and to estimate the relative abundance of species in batches of larvae. Finally, we applied the method and provided evidence for strong temporal variation in reproductive activity of catfish species in the Ucayalí River in the Peruvian Amazon. This new time and cost effective method enables the acquisition of large datasets, paving the way for a finer understanding of reproductive dynamics and recruitment patterns of tropical fish species, with major implications for fisheries management and conservation.

Genome-wide nucleotide diversity of hatchery-reared Atlantic and Mediterranean strains of brown trout Salmo trutta compared to wild Mediterranean populations.

A genome-wide assessment of diversity is provided for wild Mediterranean brown trout Salmo trutta populations from headwater tributaries of the Orb River and from Atlantic and Mediterranean hatchery-reared strains that have been used for stocking. Double-digest restriction-site-associated DNA sequencing (dd-RADseq) was performed and the efficiency of de novo and reference-mapping approaches to obtain individual genotypes was compared. Large numbers of single nucleotide polymorphism (SNP) markers with similar genome-wide distributions were discovered using both approaches (196 639 v. 121 016 SNPs, respectively), with c. 80% of the loci detected de novo being also found with reference mapping, using the Atlantic salmon Salmo salar genome as a reference. Lower mapping density but larger nucleotide diversity (π) was generally observed near extremities of linkage groups, consistent with regions of residual tetrasomic inheritance observed in salmonids. Genome-wide diversity estimates revealed reduced polymorphism in hatchery strains (π = 0·0040 and π = 0·0029 in Atlantic and Mediterranean strains, respectively) compared to wild populations (π = 0·0049), a pattern that was congruent with allelic richness estimated from microsatellite markers. Finally, pronounced heterozygote deficiency was found in hatchery strains (Atlantic FIS = 0·18; Mediterranean FIS = 0·42), indicating that stocking practices may affect the genetic diversity in wild populations. These new genomic resources will provide important tools to define better conservation strategies in S. trutta.

Genetic structure in the Amazonian catfish Brachyplatystoma rousseauxii: influence of life history strategies.

The Dorado or Plateado (Gilded catfish) Brachyplatystoma rousseauxii (Pimelodidae, Siluriformes) is a commercially valuable migratory catfish performing the largest migration in freshwaters: from the Amazonian headwaters in the Andean foothills (breeding area) to the Amazon estuary (nursery area). In spite of its importance to inform management and conservation efforts, the genetic variability of this species has only recently begun to be studied. The aim of the present work was to determine the population genetic structure of B. rousseauxii in two regions: the Upper Madera Basin (five locations in the Bolivian Amazon) and the Western Amazon Basin (one regional sample from the Uyucalí-Napo-Marañon-Amazon basin, Peru). Length polymorphism at nine microsatellite loci (284 individuals) was used to determine genetic variability and to identify the most probable panmictic units (using a Bayesian approach), after a significant departure from Hardy-Weinberg equilibrium was observed in the overall dataset (Western Amazon + Upper Madera). Bayesian analyses revealed at least three clusters in admixture in the five locations sampled in the Bolivian Amazon, whereas only two of these clusters were observed in the Western Amazon. Considering the migratory behaviour of B. rousseauxii, different life history strategies, including homing, are proposed to explain the cluster distribution. Our results are discussed in the light of the numerous threats to the species survival in the Madera basin, in particular dam and reservoir construction.

Evolution of the structure and composition of house mouse satellite DNA sequences in the subgenus Mus (Rodentia: Muridea): a cytogenomic approach.

The composition and orientation of the house mouse satellite DNA sequences (minor, major, TLC) were investigated by a FISH and CO-FISH approach in 11 taxa belonging to three clades of the subgenus Mus. Using a phylogenetic framework, our results highlighted two distribution patterns. The TLC satellite, the most recently discovered satellite, was present in all clades but varied quantitatively among species. This distribution supported its appearance in the ancestor of the subgenus followed by independent evolution in species of each clade. In contrast, the minor and major satellites occurred in only two clades of the subgenus indicating the simultaneous and recent amplification of these sequences. In addition, although qualitative differences in the composition and orientation of the satellite sequences were observed among the taxa, none of the features studied were unique to the house mouse and could account for the extensive chromosomal plasticity evidenced in Mus musculus domesticus.

Disseminated Histoplasma capsulatum infection presenting with panniculitis and focal myositis in rheumatoid arthritis treated with etanercept.

We report the case of a patient with rheumatoid arthritis (RA) on etanercept who presented with panniculitis and focal myositis as manifestations of disseminated histoplasmosis. Systematic search of the literature showed 11 additional case reports of disseminated histoplasmosis with tumour necrosis factor-alpha (TNFalpha) blockade therapy (infliximab, n = 8; etanercept, n = 3). Although disseminated histoplasmosis may manifest with classical symptoms of fever and respiratory complaints, it may also present atypically, such as with panniculitis and focal myositis. This review illustrates and emphasizes the importance of being highly suspicious for infection, including by opportunistic organisms, and to exclude such process in patients treated with a TNFalpha inhibitor when faced with unusual complications, even when an alternative aetiology appears plausible.

Mouse biodiversity in the genomic era.

Comparative genomics has developed by comparison of distantly related genomes, for which the link between the reported evolutionary changes and species development/physiology/ecology is not obvious. It is argued that the mouse (genus Mus) is an optimal model for microevolutionary genomics in vertebrates. This is because the mouse genome sequence, physical and genetic map have been completed, because mouse genetics, morpho-anatomy, pathology, behavior and ecology are well-studied, and because the Mus genus is a diverse, well- documented taxon, allowing comparative studies at the level of individual, population, subspecies, and species. The potential of the interaction between mouse genome and mouse biodiversity is illustrated by recent studies of speciation in the house mouse Mus musculus, and studies about the evolution of isochores, the peculiar pattern of GC-content variation across mammalian genomes.

Molecular evolution of plant haemoglobin: two haemoglobin genes in Nymphaeaceae Euryale ferox.

We isolated and sequenced two haemoglobin genes from the early-branching angiosperm Euryale ferox (Nymphaeaceae). The two genes belong to the two known classes of plant haemoglobin. Their existence in Nymphaeaceae supports the theory that class 1 haemoglobin was ancestrally present in all angiosperms, and is evidence for class 2 haemoglobin being widely distributed. These sequences allowed us to unambiguously root the angiosperm haemoglobin phylogeny, and to corroborate the hypothesis that the class 1/class 2 duplication event occurred before the divergence between monocots and eudicots. We addressed the molecular evolution of plant haemoglobin by comparing the synonymous and nonsynonymous substitution rates in various groups of genes. Class 2 haemoglobin genes of legumes (functionally involved in a symbiosis with nitrogen-fixing bacteria) show a higher nonsynonymous substitution rate than class 1 (nonsymbiotic) haemoglobin genes. This suggests that a change in the selective forces applying to plant haemoglobins has occurred during the evolutionary history of this gene family, potentially in relation with the evolution of symbiosis.

Combined mapping of DALP and AFLP markers in cultivated sunflower using F9 recombinant inbred lines.

A genetic map was constructed with specific PCRs, DALPs and AFLPs using F8-generation sunflower recombinant inbred lines. RI lines generated from a F2 population of one cross between the two cultivated inbred lines HA89 (maintainer for Pet1 CMS) and LR4 (restorer for Pet1 CMS) were used. A total of 305 markers were located using seven sPCR, 64 DALP and 301 AFLP loci. They were generated with one, seven and 14 primer pairs, respectively. The map construction consisted of a two-step strategy using 6 and 3.1 LOD scores revealed by a simulation file. Mapped markers were assembled into 18 linkage groups covering 2,168.6 cM with an average of 6.1 cM. The distribution of DALPs and AFLPs revealed that both markers tagged different regions to enable covering most of the sunflower genome. This leads to the longest map published so far for sunflower.

Polymerase chain reaction-single strand conformation polymorphism analyses of nuclear and chloroplast DNA provide evidence for recombination, multiple introductions and nascent speciation in the Caulerpa taxifolia complex.

Independent lines of evidence support an Australian origin for the Mediterranean populations of the tropical alga Caulerpa taxifolia. To complement previous biogeographical studies based on nuclear rDNA internal transcribed spacer (ITS), a new chloroplast marker was developed--the cp 16S rDNA intron-2. Sequence variability for both nuclear and chloroplast markers were assessed in 110 individuals using single strand conformation polymorphism. Comparison of intrapopulation genetic diversity between invasive Mediterranean and 'native' Australian populations revealed the occurrence of two divergent and widespread clades. The first clade grouped nontropical invasive populations with inshore-mainland populations from Australia, while the second clustered all offshore-island populations studied so far. Despite our finding of nine distinct nuclear and five distinct chloroplast profiles, a single nucleocytoplasmic combination was characteristic of the invasive populations and sexual reproduction was found to be very rare. C. taxifolia is clearly a complex of genetically and ecologically differentiated sibling species or subspecies.

Is the Octomacridae the sister family of the Diplozodae?

Diplozoidae and Octomacridae are usually considered as sister families. Essentially this is because they are the only polyopisthocotyleans parasitising primary freshwater teleosts. Because of the lack of phylogenetically informative morphological characters to explore the pattern of colonisation of the primary continental freshwater teleosts and in order to understand the appearance of the "natural parabiosis" of Diplozoidae, a molecular phylogeny was inferred by comparing newly obtained partial 28S and 18S rDNA gene sequences of Eudiplozoon nipponicum and Diplozoon homoion with other already available sequences. The phylogenetic analysis seems to show that Diplozoidae and Octomacridae are not sister groups. Thus, the colonisation of primary freshwater teleosts by these two families could be independent.

[Molecular characterization of Diplozoidae populations on 5 species of Cyprinidae: new data on parasite specificity]. / Caractérisation moléculaire des populations de Diplozoidae sur cinq espèces de Cyprinidae: nouvelles données sur la spécificité parasitaire.

The genus Diplozoon (Platyhelminth) exhibits one of the most striking modes of reproduction. Adults reproduce after the permanent fusion of two larval hermaphrodites, which play a symmetrical role. The Diplozoidae are also exceptional among the Monogenea Polyopisthocotylea for two other reasons. They represent the only group really diversified on continental freshwater fishes; however, this diversification is difficult to evaluate since few morphoanatomical criteria are available to distinguish species and their host specificity is atypically variable among the Monogenea. For the first time in the Diplozoidae, the problems of species definition and of host specificity are examined using molecular tools. Two ribosomal markers (ITS2 and 28S rDNA (D1)) have been sequenced in five Diplozoidae, interacting with five Cyprinidae host species: the corresponding parasite-host systems have been well characterised, revealing some contrasting situations in the relations between Diplozoidae and Cyprinidae. Some species are effectively strictly host specific, but Diplozoon scardinii initially considered as a specific species on Scardinius erythrophtalmus and D. homoion on Rutilus rutilus are proposed to be a single species on the basis of their identical ITS2 and 28S rDNA sequences. On the same basis we proposed that D. paradoxum is able to parasitize two fish species, Abramis brama and Blicca bjoerkna, despite the morphological differences observed between the two xenopopulations. Phylogenetic relationships among Diplozoidae species were estimated with ITS2 sequences while cytochrome b sequences were used for their fish hosts. Finally, the comparison between these two molecular phylogenies seems to exhibit the phenomenon of cospeciation.

Slow rate of evolution in the mitochondrial control region of gulls (Aves: Laridae).

We sequenced part of the mitochondrial control region and the cytochrome b gene in 72 specimens from 32 gull species (Laridae, Larini) and 2 outgroup representatives (terns: Laridae, Sternini). Our control region segment spanned the conserved central domain II and the usually hypervariable 3' domain III. Apart from some heteroplasmy at the 3' end of the control region, domain III was not more variable than domain II or the cytochrome b gene. Furthermore, variation in the tempo of evolution of domain III was apparent between phyletic species groups. The lack of variation of the gull control region could not be explained by an increase in the proportion of conserved sequences in these birds, and the gull control region showed an organization similar to those of other avian control regions studied to date. A novel invariant direct repeat was identified in domain II of gulls, and in domain III, two to three inverted, sometimes imperfect, repeats are able to form a significantly stable stem-and-loop structure. These putative secondary structures have not been reported before, and a comparison between species groups showed that they are more stable in the group with the more conserved control region. The unusually slow rate of evolution of control region part III of the gulls could thus be partly explained by the existence of secondary structures in domain III of these species.

Derivation of a simple microsatellite locus from a compound ancestor in the genus Mus.

Many microsatellite loci contain more than a single repeat motif. These compound microsatellites are perhaps most easily explained as arising from simple ancestors. We have uncovered a contrary example in mice of the genus Mus. Sequence analysis of the locus D1MIT29 in most of the members of the genus Mus reveals that this locus is compound in all species except M. musculus, in which it is simple. Moreover, phylogenetic analyses of base substitutions in the non-repetitive flanking region gives trees which are consistent with the previously accepted phylogenetic hypothesis that M. musculus is nested within the subgenus Mus. This confirms that the history of this locus is similar to that of molecular markers previously used in phylogenetic studies of this group and, therefore, demonstrates that the simple state in this lineage is derived from a compound ancestor. We also demonstrate the utility of this type of nuclear sequence variation for phylogeographic studies in the genus Mus. Finally, our sequences reveal homoplasy for size, reemphasizing the danger of using microsatellite size variation alone when the individuals under study are not closely related.

Isolation and characterization by direct amplification of length polymorphisms (DALP) of codominant genetic markers with Mendelian inheritance in Neoseiulus californicus (Acari: Phytoseiidae).

We report the first application of a new method designed to isolate polymorphic loci in any organism, the direct amplification of length polymorphism. Five polymorphic loci were readily isolated in the predatory mite Neoseiulus californicus (Acari: Phytoseiidae). Two to five alleles were identified among 46 isofemale lines based on fragment size variation due to micro-deletions/insertions. Genotyping F1 and F2 progenies from controlled heterogametic crosses and backcrosses allowed to establish the Mendelian inheritance of these alleles, their codominance, and pairwise recombination rates. Nucleotidic sequence divergence due to single base substitution was also found in the flanking regions of the polymorphism. We discuss the usefulness of these markers in studies of reproductive systems as well as population genetics, in particular, in mite species where the amount of DNA or richness in microsatellites could be limiting factors in the isolation of polymorphic loci.

Direct amplification of length polymorphisms (DALP), or how to get and characterize new genetic markers in many species.

Direct amplification of length polymorphisms (DALP) uses an arbitrarily primed PCR (AP-PCR) to produce genomic fingerprints and to enable sequencing of DNA polymorphisms in virtually any species. Oligonucleotide pairs were designed to each produce a specific multi-banded pattern and all the fragments thus generated can be directly sequenced with the same two universal M13 sequencing primers. This strategy combines the advantages of a high resolution fingerprint technique and the possibility of characterizing the polymorphisms. The use of family members as templates in the multi-locus detection step allows a direct test of allele transmission, as well as early mapping of the markers or selection of loci associated with some traits or diseases. We used this method to detect micro-deletions/insertions and microsatellite DNA loci useful in population genetics studies, but it could be applied in many other fields of biology, such as genome mapping for definition of polymorphic sequence tagged sites, directly localized on a genetic map.

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.