Demography and adaptation promoting evolutionary transitions in a mammalian genus that diversified during the Pleistocene

Species that evolved in temperate regions during the Pleistocene experienced periods of extreme climatic transitions. Consequent population fragmentation and dynamics had the potential to generate small, isolated populations where the influence of genetic drift would be expected to be strong. We use comparative genomics to assess the evolutionary influence of historical demographics and natural selection through a series of transitions associated with the formation of the genus Capreolus, speciation within this genus during the Quaternary and during divergence among European roe deer (C. capreolus) populations. Our analyses were facilitated by the generation of a new high‐coverage reference genome for the Siberian roe deer (C. pygargus). We find progressive reductions in effective population size (N_e), despite very large census sizes in modern C. capreolus populations and show that low N_e has impacted the C. capreolus genome, reducing diversity and increasing linkage disequilibrium. Even so, we find evidence for natural selection shared among C. capreolus populations, including a historically documented founder population that has been through a severe bottleneck. During each phylogenetic transition there is evidence for selection (from dN/dS and nucleotide diversity tests), including at loci associated with diapause (delayed embryonic development), a phenotype restricted to this genus among the even‐toed ungulates. Together these data allow us to assess expectations for the origin and diversification of a mammalian genus during a period of extreme environmental change.     

Phylogeny and evolution of the South African genus Metalasia (Asteraceae–Gnaphalieae) inferred from molecular and morphological data

Metalasia is a genus in tribe Gnaphalieae (Asteraceae), endemic to South Africa and with its main distribution in the Cape Floristic Region. The genus comprises 57 species and, with a number of closely related genera, it constitutes the ‘Metalasia clade’. A species‐level phylogenetic analysis is presented, based on DNA sequences from two nuclear (internal and external transcribed spacer: ITS, ETS) and two plastid (psbA‐trnH, trnL‐trnF) regions together with morphological data. Analyses combining molecular and morphological data attempt not only to resolve species interrelationships, but also to detect patterns in character evolution. Phylogenetic analyses corroborate our earlier study and demonstrate that Metalasia is formed of two equally sized, well‐supported sister groups, one of which is characterized by papillose cypselas. The results differ greatly from earlier hypotheses based on morphology alone, as few morphological characters support the phylogenetic patterns obtained. The two clades of Metalasia do, however, appear to differ in distribution, corresponding to the different rainfall regimes of South Africa. Analyses show a few taxa to be problematic; one example is the widely distributed M. densa which appears to be an intricate species complex. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 174 , 173–198.     

Measuring Nitrogen and Phosphorus Uptake by Intact Roots of Mature Acer saccharum Marsh., Pinus resinosa Ait., and Picea abies (L.) Karst

A common method for measuring uptake by intact roots in situ is the depletion method, wherein intact fine roots are separated from soil and placed in nutrient solution. The difference between initial and final amounts of nutrient in solution is attributed to root uptake. Variations on this method include applying pretreatment solutions, training roots to grow into bags or trays, and varying concentrations of nutrient solution. We tested whether variations in methods affected measured net uptake rates of NH ₄ ⁺ , NO ₃ ⁻ , and PO ₄ ³⁻ . Intact roots of 60 year-old sugar maple (Acer saccharum Marsh.), red pine (Pinus resinosa Ait.), and Norway spruce (Picea abies (L.) Karst.) were given one of four treatments prior to measuring net uptake. “Trained” roots were grown in a sand-soil mixture. “Recovered” roots were excavated and allowed to recover in nutrient solution for two or four days (“two-day recovery” and “four-day recovery”, respectively). “No recovery” roots were excavated and used immediately in experiments. We exposed roots to three concentrations of nutrient solutions to observe the effects of initial nutrient solution concentration. Initial nutrient solution concentration was an important source of variation in measured uptake rates, and N uptake was stimulated by low antecedent concentrations. We found no significant differences in net uptake rates between pretreatments for any of the species studied, indicating that our pretreatments were not effective in improving measurement of uptake. Such pretreatments may not be necessary for measuring net uptake and may not hinder the comparison of rates measured using variations of the depletion method.     

Ablation of RIC8A Function in Mouse Neurons Leads to a Severe Neuromuscular Phenotype and Postnatal Death

Resistance to inhibitors of cholinesterase 8 (RIC8) is a guanine nucleotide exchange factor required for the intracellular regulation of G protein signalling. RIC8 activates different Gα subunits via non-canonical pathway, thereby amplifying and prolonging the G protein mediated signal. In order to circumvent the embryonic lethality associated with the absence of RIC8A and to study its role in the nervous system, we constructed Ric8a conditional knockout mice using Cre/loxP technology. Introduction of a synapsin I promoter driven Cre transgenic mouse strain (SynCre) into the floxed Ric8a (Ric8a ^F/F) background ablated RIC8A function in most differentiated neuron populations. Mutant SynCre ^+/- Ric8 ^lacZ/F mice were born at expected Mendelian ratio, but they died in early postnatal age (P4-P6). The mutants exhibited major developmental defects, like growth retardation and muscular weakness, impaired coordination and balance, muscular spasms and abnormal heart beat. Histological analysis revealed that the deficiency of RIC8A in neurons caused skeletal muscle atrophy and heart muscle hypoplasia, in addition, the sinoatrial node was misplaced and its size reduced. However, we did not observe gross morphological changes in brains of SynCre ^+/- Ric8a ^lacZ/F mutants. Our results demonstrate that in mice the activity of RIC8A in neurons is essential for survival and its deficiency causes a severe neuromuscular phenotype.     

Estimating nutrient uptake by mature tree roots under field conditions: challenges and opportunities

Nutrient uptake by roots of mature trees is difficult to measure accurately under field conditions using existing methods. In this review, we discuss current techniques for measuring uptake at the root surface including excised roots, isotopic tracers, autoradiography, depletion, and lysimeters. Although these methods have provided many insights, each has drawbacks. Estimates of uptake are affected by the sampling scheme, experimental conditions, whether roots are excised or not, concentrations of ions, and the rate of efflux of ions. Microbes and mycorrhizas can also affect estimates of uptake. A greater focus on methods development is critical to advancing our understanding of nutrient uptake of mature trees under conditions representative of those in the field.     

Sapwood estimates of pedunculate oak (Quercus robur L.) in eastern Baltic

Pedunculate oak (Quercus robur L.) is one of the widely used and dendrochronologically investigated species in Europe. Still, it is a problematical dating object if its outermost section is missing partly or totally. Thus, we need sapwood estimation of living trees. As sapwood amount varies geographically, numbers of sapwood rings have been published for different regions in Europe but no such estimation has been done for the Baltic States yet. Therefore, this paper deals with the estimation of pedunculate oak sapwood growing in the eastern Baltic region, i.e. in Finland, Estonia, Latvia, and Lithuania.In total, 668 oak core samples of living trees from 43 stands were investigated. Ring widths were measured and the number of sapwood rings was determined according to two criteria: difference of colour and absence of tyloses in earlywood vessels. The samples were divided into two sets, according to the t_H-values between site chronologies and the major geobotanical sub-provinces. Thus, the nine Finnish and western Estonian sites were attributed to the western region and the 34 eastern Estonian, Latvian and Lithuanian sites to the eastern region.As the result of a statistical analysis, we explain that the number of oak sapwood rings ranges from 4.09 to 20.85 and 6.45 to 18.02 within 95% confidence limits in the western and eastern regions, respectively. For the three Baltic countries and southern Finland in general, we recommend to consider a sapwood estimate of 6.18–18.71 rings. Regarding earlier studies, the general European trend of decreasing sapwood ring number towards the east was confirmed. A geographical pattern of eastward decrease of the median sapwood ring number was noticed in the Baltics as well. The chronology based upon 668 samples of living oak trees from all sites covered the period of 1631–2008.     

Heterotopic and Orthotopic Tracheal Transplantation in Mice used as Models to Study the Development of Obliterative Airway Disease

Obliterative airway disease (OAD) is the major complication after lung transplantations that limits long term survival (1-7).To study the pathophysiology, treatment and prevention of OAD, different animal models of tracheal transplantation in rodents have been developed (1-7). Here, we use two established models of trachea transplantation, the heterotopic and orthotopic model and demonstrate their advantages and limitations.For the heterotopic model, the donor trachea is wrapped into the greater omentum of the recipient, whereas the donor trachea is anastomosed by end-to-end anastomosis in the orthotopic model.In both models, the development of obliterative lesions histological similar to clinical OAD has been demonstrated (1-7).This video shows how to perform both, the heterotopic as well as the orthotopic tracheal transplantation technique in mice, and compares the time course of OAD development in both models using histology.Download video file.^{(54M, flv)}