Population structure in the catfish Trichogenes longipinnis: drift offset by asymmetrical migration in a tiny geographic range

Based on population genetic theory and empirical studies of small populations, we expect that species with very small ranges (narrow endemics) will exhibit reduced genetic diversity, increasing their susceptibility to the negative effects of genetic homogeneity. Although this pattern of reduced diversity applies to most narrow endemics, conservation biologists have yet to identify a general pattern for the degree of spatial population genetic structure expected in species with very small ranges. In part, this is because the degree of population structure within narrow endemics will be highly variable depending on the equilibrium between the homogenizing effects of dispersal and the diversifying effects of drift and local selection in small populations, thus precluding general predictions about the relative importance of small range, small population sizes, and habitat patchiness for maintaining genetic diversity in narrowly-distributed species. We document a striking example of high population structure in the tiny geographic range of a stream-dwelling catfish, Trichogenes longipinnis , endemic to the Atlantic Forest of Brazil. The maintenance of this diversity results from a combination of asymmetrical and limited dispersal, and drift in small populations. Our results highlight the need to understand population structure, and not only overall genetic diversity, of narrowly-distributed species for their conservation planning.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 97 , 259–274.     

Microsatellite DNA markers for population genetic studies in the dinoflagellate Karenia brevis

Nine nuclear‐encoded microsatellites from an enriched genomic DNA library of the HAB (harmful algal bloom) dinoflagellate Karenia brevis were isolated and characterized. The microsatellites include five perfect (three dinucleotide and two trinucleotide) and four imperfect (two dinucleotide and two trinucleotide) repeat motifs. Gene (haplotype) diversity ranged from 0.153 to 0.750 among a sample of 13 isolates; the number of alleles among the isolates ranged from two to six and pairwise tests of genotypic disequilibria were nonsignificant. The microsatellites developed in this study will provide insight into the genetic diversity of this HAB species and tools that may prove useful in predicting source populations and physiological parameters of individual K. brevis blooms.     

Shed skin as a source of DNA for genotyping seals

Obtaining a sufficient number of DNA samples from ice‐breeding marine phocids, in a noninvasive manner, has proven difficult and has limited the ability to use molecular genetics on these species. We evaluate the ability to genotype ringed seals using a novel source of DNA, skin cells shed by the seal as it moults on sea ice. We found that shed skin samples yielded a lower quantity and purity of DNA compared to tissue samples. Nevertheless, the shed skin cells were a viable source of DNA for microsatellite analysis; we found no significant difference in allelic diversity or heterozygosities between tissue samples and shed skin cells. This source of DNA should allow the rapid collection of a large number of noninvasively collected DNA samples in ice‐breeding phocids.     

USE OF POLYMYXIN B IN A CAPTURE ENZYME IMMUNOASSAY FOR DETECTION OF SALMONELLAE SPP. LIPOPOLYSACCHARIDE

A capture enzyme immunoassay for detection of salmonellae sp. lipopolysaccharide was developed. The assay made use of polymyxin B sulfate, passively attached to a polystyrene matrix, to capture lipopolysaccharide. Bound lipopolysaccharride was then detected with a monoclonal antibody, specific for salmonellae spp. followed by goat antimouse antibody conjugated with horseradish peroxidase.
The analytical sensitivity of the assay was approximately 1 ng/ml of lipopolysaccharide. The results are comparable to those obtained with a competitive enzyme immunoassay previously developed. The sensitivity of the polymyxin B assay decreased to 4–5 ng/ml when the salmonellae spp. lipopolysaccharide was mixed with 1–100 μg/ml of Escherichia coli lipopolysaccharide, while this level of heterogeneous lipopolysaccharide, did not decrease the sensitivity of the competitive enzyme immunoassay.
The polymyxin B capture assay was advantageous in that polymyxin B is a standardized reagent that is relatively inexpensive and does not require extensive preparation or containment facilities. The assay is robust; however, because of the light sensitivity of polymyxin B, its stickiness to other reagents and interference by other lipopolysaccharides, this assay requires careful attention to detail and may therefore be an unsuitable assay for field use.     

Separating host-tree and environmental determinants of honeydew production by Ultracoelostoma scale insects in a Nothofagus forest

Abstract 1. Sugar‐rich honeydew excreted (‘produced’) by insects feeding on phloem sap is a key energy flow in a range of temperate and tropical ecosystems. The present study measured honeydew produced by Ultracoelostoma sp. (Homoptera: Coelostomidiidae) scale insects feeding on Nothofagus solandri var. solandri (Hook f.) Oerst. trees in a temperate evergreen forest in New Zealand. Simultaneous measurements of environmental variables and canopy photosynthesis were conducted to allow separation of host‐tree and environmental determinants of honeydew production. These relationships were further examined in experiments where canopy photosynthesis was manipulated by shading or plant nitrogen levels increased by foliar spray. 2. Rates of honeydew production varied nine‐fold from a maximum (± 1 SE) of 64.4 ± 15.2 mg dry mass m⁻² bark h⁻¹ in early summer (December) to a minimum of 7.4 ± 4.2 mg m⁻² h⁻¹ in winter (August). Rates of production measured 1.4 m from the base of the trees’ stems varied significantly with stem diameter, and were higher on medium‐sized (18 cm diameter) than small or large stems. 3. Rates of production were significantly related to environmental conditions over the hours preceding measurement (air temperature and air saturation deficit averaged over the preceding 24 and 12 h respectively). There was no evidence that rates of production were directly related to short‐term changes in the supply of carbohydrates from the canopy (either when compared with measurements of unmanipulated photosynthetic rate, or after sugar levels were manipulated by shading 80% of host‐trees’ leaf area), or to changes in phloem nitrogen content. 4. The results show that there is no clear effect of host‐tree carbon supply on honeydew production; if production is related to photosynthesis, the effect of this is much less important that the large and significant direct effect of environmental conditions on honeydew production.     

The role of the kinase OXI1 in cadmium‐ and copper‐induced molecular responses in Arabidopsis thaliana

The hypothesis that mitogen‐activated protein kinase (MAPK) signalling is important in plant defences against metal stress has become accepted in recent years. To test the role of oxidative signal‐inducible kinase (OXI1) in metal‐induced oxidative signalling, the responses of oxi1 knockout lines to environmentally realistic cadmium (Cd) and copper (Cu) concentrations were compared with those of wild‐type plants. A relationship between OXI1 and the activation of lipoxygenases and other initiators of oxylipin production was observed under these stress conditions, suggesting that lipoxygenase‐1 may be a downstream component of OXI1 signalling. Metal‐specific differences in OXI1 action were observed. For example, OXI1 was required for the up‐regulation of antioxidative defences such as catalase in leaves and Fe‐superoxide dismutase in roots, following exposure to Cu, processes that may involve the MEKK1‐MKK2‐WRKY25 cascade. Moreover, the induction of Cu/Zn superoxide dismutases in Cu‐exposed leaves was regulated by OXI1 in a manner that involves fluctuations in the expression of miRNA398. These observations contrast markedly with the responses to Cd exposure, which also involves OXI1‐independent pathways but rather involves changes in components mediating intracellular communication.     

When phylogenetic assumptions are violated: base compositional heterogeneity and among‐site rate variation in beetle mitochondrial phylogenomics

The ability to generate large molecular datasets for phylogenetic studies benefits biologists, but such data expansion introduces numerous analytical problems. A typical molecular phylogenetic study implicitly assumes that sequences evolve under stationary, reversible and homogeneous conditions, but this assumption is often violated in real datasets. When an analysis of large molecular datasets results in unexpected relationships, it often reflects violation of phylogenetic assumptions, rather than a correct phylogeny. Molecular evolutionary phenomena such as base compositional heterogeneity and among‐site rate variation are known to affect phylogenetic inference, resulting in incorrect phylogenetic relationships. The ability of methods to overcome such bias has not been measured on real and complex datasets. We investigated how base compositional heterogeneity and among‐site rate variation affect phylogenetic inference in the context of a mitochondrial genome phylogeny of the insect order Coleoptera. We show statistically that our dataset is affected by base compositional heterogeneity regardless of how the data are partitioned or recoded. Among‐site rate variation is shown by comparing topologies generated using models of evolution with and without a rate variation parameter in a Bayesian framework. When compared for their effectiveness in dealing with systematic bias, standard phylogenetic methods tend to perform poorly, and parsimony without any data transformation performs worst. Two methods designed specifically to overcome systematic bias, LogDet and a Bayesian method implementing variable composition vectors, can overcome some level of base compositional heterogeneity, but are still affected by among‐site rate variation. A large degree of variation in both noise and phylogenetic signal among all three codon positions is observed. We caution and argue that more data exploration is imperative, especially when many genes are included in an analysis.