Predictive modelling of tree species distributions on the Iberian Peninsula during the Last Glacial Maximum and Mid-Holocene

This paper reports a bioclimatic envelope model study of the potential distribution of 19 tree species in the Iberian Peninsula during the Last Glacial Maximum (LGM; 21 000 yr BP) and the Mid-Holocene (6000 yr BP). Current patterns of tree species richness and distributions are believed to have been strongly influenced by the climate during these periods. The modelling employed novel machine learning techniques, and its accuracy was evaluated using a threshold-independent method. Two atmospheric general circulation models, UGAMP and ECHAM3 (generated by the Palaeoclimate Modelling Intercomparison Project, PMIP), were used to provide climate scenarios under which the distributions of the 19 tree species were modelled. The results obtained for these scenarios were assessed by agreement measure analysis; they differed significantly for the LGM, but were more similar for the Mid-Holocene.
The results for the LGM support the inferred importance of pines in the Iberian Peninsula at this time, and the presence of evergreen Quercus in the south. Important differences in the altitude at which the modelled species grew were also predicted. During the LGM, some normally higher mountain species potentially became re-established in the foothills of the Pyrenees. The warm Mid-Holocene climate is clearly reflected in the predicted expansion of broad-leaved forests during this period, including the colonization of the northern part of the Iberian Peninsula by evergreen Quercus species.     

Mutations of the coat protein gene of bacteriophage λ that overcome the necessity for the FI gene; the EFi domain

The functions of most of the 10 genes involved in phage λ capsid morphogenesis are well understood. The function of the FI gene is one of the exceptions. Mutants in FI fail to mature and package DNA. The gene product (gpFI) seems to act as a catalyst for the formation of an intermediate in capsid assembly called complex II, which contains a procapsid (an empty capsid precursor), terminase (the enzyme that cleaves the DNA precursor and packages it into the procapsid) and DNA. The mechanism for this stimulation remains unknown. It has also been reported that gpFI appeared to stimulate terminase-mediated cos cleavage, in the absence of procapsids, by increasing enzyme turnover. In comparison with other head-gene mutants, FI mutants are leaky, producing approx. 0.1 phage per infected cell. Some second-site revertants of FI ^? phages, called ‘fin’, that bypass the necessity for gpFI, have been isolated and found to harbour a mutation in the genes that code for the two subunits of terminase. In the course of mapping additional fin mutants, it was discovered that some mapped outside the terminase genes. To localize the mutations, restriction fragments of fin mutant DNAs were subcloned into plasmids and their ability to contribute to fin function was determined by marker-rescue analysis. The location of the fin mutation was further delineated by deletion analysis of a plasmid that was positive for fin. This showed that some fin mutations mapped to a region comprising genes E, D and a portion of C. The sequencing of this entire region in several fin isolates showed that the fin mutations are clustered in a small region of gene E corresponding to a portion of 26 amino acid residues of the coat protein (gpE). We have called this region of the protein the EFi domain. All the mutations result in an increase in positive charge relative to the wild-type protein. These results suggest that DNA maturation and packaging are in part controlled by an interaction between gpFI and capsid gpE.     

Lethal effect of lambda DNA terminase in recombination deficient Escherichia coli

Summary DNA terminase is the enzyme that catalyses the cleavage of DNA concatemers into genome-size molecules and packages them into the capsid. The cleavage (DNA maturation) takes place in a specific site in the phage DNA called cos. Either one of two Escherichia coli proteins, integration host factor (IHF) and terminase host factor (THF), is required, in addition to terminase, for maturation of wild-type DNA in vitro. In vivo, at least some cos cleavage is known to occur in mutants that are unable to synthesize active IHF. No THF-defective mutants have yet been isolated. In order to determine if IHF, THF or any other host protein is involved in DNA maturation in vivo, I devised a selection for host mutants that are unable to support cos cleavage. The selection is based on the assumption that DNA terminase will kill cells by cleaving chromosomally located cos sites. I found that DNA terminase will indeed kill cells provided that they contain a chromosomal cos site and provided also that they are defective in the host recA or recB genes. These two genes are required for certain pathways of genetic recombination and repair of damaged DNA, and I suggest that they prevent terminase-induced killing by repairing broken chromosomes. Interstingly, mutation in a related host gene, recD, did not render cells susceptible to terminase killing. recD and recB both encode subunits of exonuclease V, but recD mutants, unlike recB, remain proficient in genetic recombination and repair. I found mutants that survived the lethal effect of terminase in cos-containing E. coli recA at a frequency of about 5×10^-5. About 90% of these survivors were defective in terminase synthesis, and the rest were defective in IHF function. This result suggests that in the absence of IHF in vivo cos cleavage decreases to a level that permits repair of the damage, and therefore survival, even in recombination deficient cells. The absence of mutations in any other host gene suggests that IHF is the major accessory factor in DNA maturation in vivo. Alternatively, or in addition, mutations in other accessory factors are lethal.Abbreviations gp gene product: e.g. gpA, product of gene A - () prophage state - [] plasmid-carrier state     

Rarity and threat relationships in the conservation planning of Iberian flora

We analysed the threatened flora of Iberia (including the Balearic Islands) in order to define and explain factors related to levels of rarity and threat. Conservation measures were derived from the relationships observed. We used a random sample of 59 narrowly distributed plant species from the pool (588 species) of potentially endangered flora. Twelve variables were used to classify species into groups based on a multivariate technique: non-parametric principal component analysis. Our results do not indicate a single management model driven by a single mechanism of rarity. Four classes of rare plants were produced from the statistical algorithm: agamospermic species, plants associated with water, endemics, and range-margin (geographical-limit) plants. Some specific strategies for each of these groups are proposed, allowing further discussion and assessment. The overall pattern in conservation practice of threatened Iberian plants seems to be defined by three of the variables in use: ecological specificity, geographical rarity and rate of threat. None of the biological variables in the sample show particularly strong trends in the data.     

Forest composition in Mediterranean mountains is projected to shift along the entire elevational gradient under climate change

Aim Species distribution models have been used frequently to assess the effects of climate change on mountain biodiversity. However, the value and accuracy of these assessments have been hampered by the use of low‐resolution data for species distributions and climatic conditions. Herein we assess potential changes in the distribution and community composition of tree species in two mountainous regions of Spain under specific scenarios of climate change using data with a high spatial resolution. We also describe potential changes in species distributions and tree communities along the entire elevational gradient. Location Two mountain ranges in southern Europe: the Central Mountain Range (central west of the Iberian Peninsula), and the Iberian Mountain Range (central east). Methods We modelled current and future distributions of 15 tree species (Eurosiberian, sub‐Mediterranean and Mediterranean species) as functions of climate, lithology and availability of soil water using generalized linear models (logistic regression) and machine learning models (gradient boosting). Using multivariate ordination of a matrix of presence/absence of tree species obtained under two Intergovernmental Panel on Climate Change (IPCC) scenarios (A2 and B2) for two different periods in the future (2041–70 and 2071–2100), we assessed the predicted changes in the composition of tree communities. Results The models predicted an upward migration of communities of Mediterranean trees to higher elevations and an associated decline in communities of temperate or cold‐adapted trees during the 21st century. It was predicted that 80–99% of the area that shows a climate suitable for cold–wet‐optimum Eurosiberian coniferous and broad‐leaved species will be lost. The largest overall changes were predicted for Mediterranean species found currently at low elevations, such as Pinus halepensis, Pinus pinaster, Quercus ilex ssp. ballota and Juniperus oxycedrus, with sharp increases in their range of 350%. Main conclusions It is likely that areas with climatic conditions suitable for cold‐adapted species will decrease significantly under climate warming. Large changes in species ranges and forest communities might occur, not only at high elevations within Mediterranean mountains but also along the entire elevational gradient throughout this region, particularly at low and mid‐elevations. Mediterranean mountains might lose their key role as refugia for cold‐adapted species and thus an important part of their genetic heritage.     

Optimal average path of the instantaneous helical axis in planar motions with one functional degree of freedom

This paper presents a model for determining the path of the instantaneous helical axis (IHA) that optimally represents human planar motions with one functional degree of freedom (fDOF). A human movement is said to have one fDOF when all degrees of freedom (DOFs) are coordinated such that all the kinematic variables can be expressed, across movement repetitions, as functions of only one independent DOF, except for a small natural intercycle variability quantified as lower than a prespecified value. The concept of fDOF allows taking into account that, due to motor coordination, human movements are executed in a repeatable manner. Our method uses the measurement of several repetitions of a given movement to obtain the optimal average IHA path. The starting point is a change of variables, from time to a joint position magnitude (generally an angle). In this way, instead of operating with the time-dependent single-valued trajectory of the successive cycles, our model permits the representation of any motion variable (e.g. positions and their time derivatives) as a cloud of points dependent on the joint angle. This allows the averaging to be performed over the displacements and their derivatives before determining the mean IHA path. We thus avoid the nonlinear magnification of errors and variability inherent in the IHA computation. Moreover, the IHA path can be considered as a geometric attribute of the joint and the type of motion, rather than of each single movement execution. An experiment was performed that show the accuracy and usefulness of the method.     

Biological properties of the endemic and threatened shrub in Iberia Vella pseudocytisus subsp. paui Gómez Campo (Cruciferae) and implications for its conservation

We present new data about chorology, seed bank, dispersal, seedling biology and population structure of the threatened endemic shrub Vella pseudocytisus subsp. paui Gómez Campo in Spain. In addition, we investigate human activities that are linked with the fine-scale distribution of the taxon to offer conservation recommendations.Currently, the plant occurs in two populations close to the city of Teruel (East central Spain), growing in an open shrubby community on patches of gypsum substrate surrounded by agricultural landscape. The plant has disappeared from two reported locations dated from early 20th Century likely due to human activities.The seed bank seems to be poor. A ballistic dispersal mechanism appears to move seeds between 0 and 4 m. We did not find a clear seasonal pattern of seedlings emergence although spring cohorts are the largest. Also, this period was where leaf seedling growth was more prominent. During the 3 years of our survey, the cumulative mortality was 94.2% of all seedlings plants. Plants are estimated to remain in the seedling stage for approximately 5 years. The demographic structure of both populations shows no apparent gaps in the distribution of size classes. Adult plants greater than 200 dm³ represent the most important stage for seed production and persistence.We point out two key factors for conservation purposes, first the weakness of some of the plant biological properties for natural establishment and second its ability to colonise artificial environments. We propose a mitigation of clonal spread in those sites and the protection of juvenile stages in more natural locations.     

The maturation of coliphage lambda DNA in the absence of its packaging

In vivo, λ DNA cannot be cleaved at cos (matured) if proheads are not present; in vitro, however, cos cleavage readily takes place in the absence of proheads. In order to investigate this paradox, we have constructed plasmids that synthesize λ terminase in vivo upon induction. The plasmids also contain cos at the normal position, about 190 bp upstream of λ gene Nul. One of the plasmids, pFM3, produces levels of terminase comparable to those found after phage induction. If cells carrying pFM3 are thermoinduced, almost 100% of the intracellular plasmid DNA has a double-strand interruption at or near cos.

Since the only λ genes that pFM3 carries are Nul, A, W and B, this in vivo cleavage is occurring in the absence of proheads. Previous failure to observe 2 maturation with phages carrying prohead mutations may be due to exonucleolytic degradation of the unprotected DNA ends, a different DNA topology or compartmentalization, or terminase inhibition in the absence of prohead by the product of another λ gene that maps to the right of gene B.