Generalized mathematical representation of the soft tissue artefact

While reconstructing skeletal movement using stereophotogrammetry, the relative movement between a skin marker and the underlying bone is regarded as an artefact (soft tissue artefact: STA). Similarly, the consequent pose, size and shape variations that affect a cluster of markers associated with a bony segment, or any arbitrary change of configuration in the marker local positions as representative of the skin envelope shape variation, may also be looked upon as an STA. Bone pose estimators able to compensate for these artefacts must embed relevant a priori knowledge in the form of an STA mathematical model. Prior to tackling this modeling exercise, an appropriate definition and mathematical representation of the STA time histories must be accomplished. Relevant appropriateness is based on the degree of approximation of the STA reconstruction and on the number of parameters involved.     

Structural variation of mitochondrial genomes sheds light on evolutionary history of soybeans

The architecture and genetic diversity of mitogenome (mtDNA) are largely unknown in cultivated soybean (Glycine max), which is domesticated from the wild progenitor, Glycine soja, 5000 years ago. Here, we de novo assembled the mitogenome of the cultivar ‘Williams 82’ (Wm82_mtDNA) with Illumina PE300 deep sequencing data, and verified it with polymerase chain reaction (PCR) and Southern blot analyses. Wm82_mtDNA maps as two autonomous circular chromosomes (370 871-bp Chr-m1 and 62 661-bp Chr-m2). Its structure is extensively divergent from that of the mono-chromosomal mitogenome reported in the landrace ‘Aiganhuang’ (AGH_mtDNA). Synteny analysis showed that the structural variations (SVs) between two genomes are mainly attributed to ectopic and illegitimate recombination. Moreover, Wm82_mtDNA and AGH_mtDNA each possess six and four specific regions, which are absent in their counterparts and likely result from differential sequence-loss events. Mitogenome SV was further studied in 39 wild and 182 cultivated soybean accessions distributed world-widely with PCR/Southern analyses or a comparable in silico analysis. The results classified both wild and cultivated soybeans into five cytoplasmic groups, named as GSa–GSe and G1–G5; ‘Williams 82’ and ‘Aiganhuang’ belong to G1 and G5, respectively. Notably, except for members in GSe and G5, all accessions carry a bi-chromosomal mitogenome with a common Chr-m2. Phylogenetic analyses based on mtDNA structures and chloroplast gene sequences both inferred that G1–G3, representing >90% of cultigens, likely inherited cytoplasm from the ancestor of domestic soybean, while G4 and G5 likely inherited cytoplasm from wild soybeans carrying GSa- and GSe-like cytoplasm through interspecific hybridization, offering new insights into soybean cultivation history.     

No consistent effects of humans on animal genetic diversity worldwide

Human impacts on genetic diversity are poorly understood yet critical to biodiversity conservation. We used 175 247 COI sequences collected between 1980 and 2016 to assess the global effects of land use and human density on the intraspecific genetic diversity of 17 082 species of birds, fishes, insects and mammals. Human impacts on mtDNA diversity were taxon and scale‐dependent, and were generally weak or non‐significant. Spatial analyses identified weak latitudinal diversity gradients as well as negative effects of human density on insect diversity, and negative effects of intensive land use on fish diversity. The observed effects were predominantly associated with species turnover. Time series analyses found nearly an equal number of positive and negative temporal trends in diversity, resulting in no net monotonic trend in diversity over this time period. Our analyses reveal critical data and theory gaps and call for increased efforts to monitor global genetic diversity.     

Unravelling plant diversification: Intraspecific genetic differentiation in hybridizing Anacyclus species in the western Mediterranean Basin

Premise

The interfertile species Anacyclus clavatus, A. homogamos, and A. valentinus represent a plant complex coexisting in large anthropic areas of the western Mediterranean Basin with phenotypically mixed populations exhibiting a great floral variation. The goal of this study was to estimate the genetic identity of each species, to infer the role of hybridization in the observed phenotypic diversity, and to explore the effect of climate on the geographic distribution of species and genetic clusters.

Methods

We used eight nuclear microsatellites to genotype 585 individuals from 31 populations of three Anacyclus species for population genetic analyses by using clustering algorithms based on Bayesian models and ordination methods. In addition, we used ecological niche models and niche overlap analyses for both the species and genetic clusters. We used an expanded data set, including 721 individuals from 129 populations for ecological niche models of the genetic clusters.

Results

We found a clear correspondence between species and genetic clusters, except for A. clavatus that included up to three genetic clusters. We detected individuals with admixed genetic ancestry in A. clavatus and in mixed populations. Ecological niche models predicted similar distributions for species and genetic clusters. For the two specific genetic clusters of A. clavatus, ecological niche models predicted remarkably different areas.

Conclusions

Gene flow between Anacyclus species likely explains phenotypic diversity in contact areas. In addition, we suggest that introgression could be involved in the origin of one of the two A. clavatus genetic clusters, which also showed ecological differentiation.     

Coding of intraspecific nucleotide polymorphisms: A tool to resolve reticulate evolutionary relationships in the ITS of beech trees (Fagus L., Fagaceae)

The internal transcribed spacers ITS1 and ITS2 of the nuclear ribosomal DNA (rDNA) have recently been found to display remarkable intraspecific polymorphism, a feature suggested as limiting their value for phylogenetic reconstructions. A comparative study of oligonucleotide motives and intraindividual nucleotide variability across all species of the tree genus Fagus (beech) shows, however, that this intraspecific ITS polymorphism follows a particular pattern, which can be used to detect reticulation and ancient polymorphism within the genus. Coding ITS polymorphisms as phylogenetically informative characters, moreover, resulted in better‐resolved phylogenies than traditional ‘base‐per‐base’ maximum parsimony and maximum likelihood analyses.     

Giving‐up densities and ideal pre‐emptive patch use in a predatory benthic stream fish

1. We used observational and experimental field studies together with an individual‐based simulation model to demonstrate that behaviours of mottled sculpin (Cottus bairdi) were broadly consistent with the expectations of Giving‐Up Density theory and an Ideal Pre‐emptive Distribution habitat selection model. 2. Specifically we found that: (i) adult mottled sculpin established territories within patches characterised by significantly higher prey densities and prey renewal rates than patches occupied by juveniles or randomly selected patches; (ii) patches abandoned by adult sculpin possessed significantly lower prey densities than newly occupied patches, although this was not true for juveniles; (iii) the observed giving‐up density (GUD) for adult sculpin (i.e. average prey density in patches recently abandoned) increased linearly with increasing fish size up to the average prey density measured in randomly selected patches (i.e. 350 prey items per 0.1 m²) and decreased with increasing sculpin density and (iv) juveniles rapidly shifted their distribution towards the highest quality patches following removal of competitively dominant adult sculpin. 3. These results provide the first evidence of the applicability of GUD theory to a stream‐dwelling organism, and they elucidate the underlying factors influencing juvenile and adult sculpin habitat selection and movement behaviours. Furthermore, optimal patch use, ideal pre‐emptive habitat selection and juvenile ‘floating’ provide behavioural mechanisms linking environmental heterogeneity in the stream benthos to density‐dependent regulation of mottled sculpin populations in this system.