An ecological consideration of the significance of cation-exchange capacity of roots of some Utah range plants

Summary Root cation-exchange capacities (CEC) are related to tissue nutrient content of several native Utah range plants. The root CEC values for dicotyledonous species were found to be significantly larger than for monocotyledonous species (grasses). The relative amounts of monovalent and divalent cations taken up are strongly correlated with root CEC. Dicot species tend to take up divalent ions more efficiently than monocots, but monocots take up relatively more monovalent cations than dicots. The relationship of root CEC to cation uptake helps explain differential distribution of grass lands and shrublands in common climatic zones and has important implications for range revegetation programs.     

Hidden diversity in diatoms of Kenyan Lake Naivasha: a genetic approach detects temporal variation

This study provides insights into the morphological and genetic diversity in diatoms occurring in core sediments from tropical lakes in Kenya. We developed a genetic survey technique specific for diatoms utilizing a short region (76-67 bp) of the ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) gene as genetic barcode. Our analyses (i) validated the use of rbcL as a barcoding marker for diatoms, applied to sediment samples, (ii) showed a significant correlation between the results obtained by morphological and molecular data and (iii) indicated temporal variation in diatom assemblages on the inter- and intra-specific level. Diatom assemblages from a short core from Lake Naivasha show a drastic shift over the last 200 years, as littoral species (e.g. Navicula) are replaced by more planktonic ones (e.g. Aulacoseira). Within that same period, we detected periodic changes in the respective frequencies of distinct haplotype groups of Navicula, which coincide with wet and dry periods of Lake Naivasha between 1820 and 1938 AD. Our genetic analyses on historical lake sediments revealed inter- and intra-specific variation in diatoms, which is partially hidden behind single morphotypes. The occurrence of particular genetic lineages is probably correlated with environmental factors.     

Using the ratio of means as the effect size measure in combining results of microarray experiments

Background  

Development of efficient analytic methodologies for combining microarray results is a major challenge in gene expression analysis. The widely used effect size models are thought to provide an efficient modeling framework for this purpose, where the measures of association for each study and each gene are combined, weighted by the standard errors. A significant disadvantage of this strategy is that the quality of different data sets may be highly variable, but this information is usually neglected during the integration. Moreover, it is widely known that the estimated standard deviations are probably unstable in the commonly used effect size measures (such as standardized mean difference) when sample sizes in each group are small.     

Detection and characterization of gamete-specific molecules in Mytilus edulis using selective antibody production

The mussel Mytilus edulis can be used as model to study the molecular basis of reproductive isolation because this species maintains its species integrity, despite of hybridizing in zones of contact with the closely related species M. trossulus or M. galloprovincialis. This study uses selective antibody production by means of hybridoma technology to identify molecules which are involved in sperm function of M. edulis. Fragmented sperm were injected into mice and 25 hybridoma cell clones were established to obtain monoclonal antibodies (mAb). Five clones were identified producing mAb targeting molecules putatively involved in sperm function based on enzyme immunoassays, dot and Western blotting as well as immunostaining of tissue sections. Specific localization of these mAb targets on sperm and partly also in somatic tissue suggests that all five antibodies bind to different molecules. The targets of the mAb obtained from clone G26-AG8 were identified using mass spectrometry (nano-LC-ESI-MS/MS) as M6 and M7 lysin. These acrosomal proteins have egg vitelline lyses function and are highly similar (76%) which explains the cross reactivity of mAb G26-AG8. Furthermore, M7 lysin was recently shown to be under strong positive selection suggesting a role in interspecific reproductive isolation. This study shows that M6 and M7 lysin are not only found in the sperm acrosome but also in male somatic tissue of the mantle and the posterior adductor muscle, while being completely absent in females. The monoclonal antibody G26-AG8 described here will allow elucidating M7/M6 lysin function in somatic and gonad tissue of adult and developing animals.     

mtDNA indicates profound population structure in Indian tiger (Panthera tigris tigris)

We analyzed mtDNA polymorphisms (parts of control region, ND5, ND2, Cytb, 12S, together 902 bp) in 59 scat and 18 tissue samples from 13 Indian populations of the critically endangered Indian tiger (Panthera tigris tigris), along with zoo animals as reference. Northern tiger populations exhibit two unique haplotypes suggesting genetic isolation. Western populations from Sariska (extinct in 2004) and Ranthambore are genetically similar, such that Ranthambore could serve as a source for reintroduction in Sariska. Zoo populations maintain mitochondrial lineages that are rare or absent in the wild.     

Mitochondrial DNA suggests multiple colonizations of central Philippine islands (Boracay,Negros) by the sedentary Philippine bulbul Hypsipetes philippinus guimarasensis (Aves)

In this study, we have used fragments of three mitochondrial genes (Control Region, CR; transfer RNA for methionine, tRNA‐Met; NADH dehydrogenase subunit 2, ND2 for a total of 1066 bp) to reconstruct the phylogeographic history of the endemic Philippine bulbul (Hypsipetes philippinus) at the scale of the central area of the Philippine archipelago. The study includes two of the five recognized subspecies (guimarasensis and mindorensis), 7 populations and 58 individuals. Multiple phylogenetic and network analyses support the existence of two reciprocally monophyletic maternal lineages corresponding to the two named subspecies. Molecular clock estimates indicate that the split between the two subspecies is consistent with the Pleistocene geological history of the archipelago. Patterns of relationships within guimarasensis are biogeographically less clear. Here, a combination of vicariance and dispersal needs to be invoked to reconcile the molecular data with the geographical origin of samples. In particular, the two islands Boracay and Negros host mitochondrial lineages that do not form monophyletic clusters. Our genetic data suggest multiple independent colonization events for these locations.     

MHC class I and MHC class II DRB gene variability in wild and captive Bengal tigers (Panthera tigris tigris)

Bengal tigers are highly endangered and knowledge on adaptive genetic variation can be essential for efficient conservation and management. Here we present the first assessment of allelic variation in major histocompatibility complex (MHC) class I and MHC class II DRB genes for wild and captive tigers from India. We amplified, cloned, and sequenced alpha-1 and alpha-2 domain of MHC class I and beta-1 domain of MHC class II DRB genes in 16 tiger specimens of different geographic origin. We detected high variability in peptide-binding sites, presumably resulting from positive selection. Tigers exhibit a low number of MHC DRB alleles, similar to other endangered big cats. Our initial assessment—admittedly with limited geographic coverage and sample size—did not reveal significant differences between captive and wild tigers with regard to MHC variability. In addition, we successfully amplified MHC DRB alleles from scat samples. Our characterization of tiger MHC alleles forms a basis for further in-depth analyses of MHC variability in this illustrative threatened mammal.     

Genetic and morphological divergence among Gravel Bank Grasshoppers, <Emphasis Type="BoldItalic">Chorthippus pullus</Emphasis> (Acrididae), from contrasting environments

Gravel Bank Grasshopper (Chorthippus pullus) populations inhabit two contrasting environments, pebbly gravel banks with scarce vegetation cover in mountainous areas along the Alps and lowland grasslands dominated by Common Heather (Calluna vulgaris). Heath populations of C. pullus have been rediscovered only recently, and show a distribution scattered across Central Europe. The wings are reduced in this species; thus, it has low potential for long-distance dispersal. We used sequence data on a newly developed non-coding nuclear marker from three gravel-bank and four heath populations to test whether grasshoppers from the two environments represent distinct lineages. Gravel-bank populations were studied in southern Germany (Bavaria), heath populations in eastern Germany (Brandenburg and Saxony) and Ukraine. We compared those genetic data with an analysis of variation in a suite of morphometric traits. Finally, we combined genetic and morphometric data to reconstruct a plausible scenario for the ecological shift observed in C. pullus. Our newly developed marker did not sort populations from contrasting environments in two monophyletic lineages. Nevertheless, we found a general lack of gene flow between the gravel-bank and heath populations. There was pronounced variation among populations in morphometric traits. That variation was partially partitioned by habitat type, and populations from the same habitat tended to be more similar than those from different habitats. Our data suggest that heath populations originated through northward expansion from multiple southern European refugia, and that the gravel-bank populations represent one of these sources. Patterns of genetic and morphometric divergence suggest that gravel-bank and heath populations may be in the process of incipient speciation.