Geostatistical genetic analysis for inferring the dispersal pattern of a partially clonal species: example of the chestnut blight fungus

Spatial genetic analyses can be used to infer dispersal processes in natural populations. For partially clonal species with alternating sexual and asexual reproduction, the repetition of genotypes must be taken into account in analyses. The methods currently employed to evaluate the relevance of the spatial scale used for the estimation of gene flow are not suitable for these species. We investigated recently developed methods for taking into account repeated genotypes and for determining whether the sampling scale is large enough to capture all the spatial genetic structure existing within a population. We applied these methods to a fungal plant pathogen species, Cryphonectria parasitica, which has caused the death of many American and European chestnut trees since its introduction from Asia at the beginning of the 20th century. These methods were found to be useful for unravelling the effects of clonality and historical gene flow on the spatial genetic structure, and indicated that dispersal processes have probably occurred over a larger spatial scale than previously assumed.     

EVALUATION OF THE PETRIFILMTM AND REDIGELTM AS RAPID METHODS TO THE STANDARD PLATE COUNT METHOD FOR THE ENUMERATION OF PROCESSED MEATS AND ENVIRONMENTAL SAMPLES

Aerobic plate counts (APC) are used by the food industry to help determine the sanitary state of equipment and bacterial load of finished product. Conventional aerobic count methods for processed meats require approximately 72 h incubation before results are available. Food processing plants with in-house analytical laboratories require methods that are simple, reliable and rapid. New test methods using Petrifilm^TM (PF) and Redigel^TM (RG) have been developed for determining APC. These methods are faster and easier than culturing in a standard agar medium. A variety of raw, cooked; cured and noncured meat products, cooling brine and environmental surface swabs were collected and analyzed for APC using PF, RG and plate count agar (PCA). Data analyses from over 200 samples indicated that the sensitivity of rapid testing methods for aerobic bacteria can vary depending on sample type.     

Long‐term changes in ground beetle (Coleoptera: Carabidae) assemblages in Scotland

1. One‐way, directional changes in both plant and animal associations are likely to be occurring as a result of changing climate. Current knowledge of long‐term cycles in insect communities is scarce, and therefore it is difficult to assess whether the observed changes in insect communities are the first part of a long‐term trend or parts of normal cycles. 2. In this study multivariate methods were used to describe the trends in ground beetle (Coleoptera: Carabidae) assemblages over an 18‐year (1994–2011) period at two Scottish sites. In order to have a deeper insight into the underlying processes, both environmental factors and the species driving the detected changes were investigated. 3. In four out of the six sample transects, insect community compositions showed trends rather than fluctuating patterns. Hierarchical cluster analysis also revealed a clear separation, after accounting for sampling location and broad habitat, between early and later years of sampling. Decreasing annual maximum temperatures and increasing precipitation were identified as the main environmental drivers. Although increased rainfall was expected to be beneficial for hygrophilous species, in the transects in this study generalist species increased in dominance. 4. The increasing importance of generalists, in the communities studied here, underlines the vulnerability of the specialist species and urges greater effort in their conservation. Assemblage changes along different trajectories at the sites in the present study could only be tracked using multivariate methods; commonly used diversity indices proved to be unsatisfactory. Therefore, the exclusive use of simple diversity indices should be discouraged and multivariate methods should be preferred in environmental assessments and conservation planning.     

A peninsula as an island: multiple forms of evidence for overwater colonization of Baja California by the gartersnake Thamnophis validus

The recent shift toward dispersal rather than vicariant explanations of disjunct distributions has been driven by the use of molecular data to estimate divergence dates between lineages. However, other kinds of evidence can also be critical in evaluating such biogeographic hypotheses. In the present study, we used a multifaceted approach employing diverse analyses of mitochondrial DNA sequences to assess explanations for the disjunct distribution of the gartersnake Thamnophis validus. The occurrence of this species in the Cape Region of the Baja California peninsula, isolated from mainland populations that occur along the west coast of Mexico, might be explained by: (1) separation of the peninsula from mainland Mexico through rifting 4–8 Mya (tectonic vicariance); (2) fragmentation of the range of this semi‐aquatic species because of post‐Pleistocene aridification (vicariance by aridification); (3) natural overwater dispersal across the Gulf of California; or (4) human introduction. Divergence dating indicates that peninsular and mainland T. validus separated from each other within the last 0.5 Myr, thus rejecting tectonic vicariance. In addition, the estimated closest mainland relatives of peninsular snakes are found farther north than expected under this hypothesis. Three findings argue against vicariance by aridification: (1) peninsular snakes and their closest mainland relatives are more genetically similar than predicted; (2) the location of closest mainland relatives is farther south than predicted; and (3) the species is absent from areas where one might expect to find relict populations. Taken together, refutation of the vicariance hypotheses and the fact that the estimated closest mainland relatives are found almost directly across the Gulf from the Cape Region supports some form of overwater colonization. Various additional arguments suggest that natural dispersal is more likely than human introduction. The present study emphasizes the need for multiple kinds of evidence, beyond divergence dates, to discriminate among hypotheses and to provide independent sources of corroboration or refutation in historical biogeography. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 95 , 409–424.     

Forticulcita glabra gen. et sp. n. (Digenea, Haploporidae) in a Red Sea Mullet

The genus Forticulcita was established solely for F. glabra sp. n. from Valamugil seheli (Forsskål) in the Gulf of Aqaba. Most closely related to Haploporus , it is diagnosed primarily by having a species with an acetabulum being conspicuously robust, prepharynx measuring shorter than the pharynx, ceca terminating at the testicular level, muscular hermaphroditic ejaculatory organ lacking accessory structures, and vitellarium consisting of a single mass.     

THE COMPOSITION AND STRUCTURE OF LOWER SILURIAN MARINE COMMUNITIES

Five benthic communities occupied the shelf regions of the British Isles, Norway, and North America in Upper Llandovery times. The communities are listed below in order of increasing distance from shore.

• 1 The Lingula Community is the least diverse; it has both infaunal elements, including a protobranch, and two lingulids, and epifaunal elements, including a rhynchonellid, a pterioid, and a cornulitid. A restricted and protected near-shore environment, such as a bay or estuary, is postulated.
• 2 The Eocoelia Community shares elements in common with the former community, but is more diverse and is dominated by epifaunal forms; the many small pedunculate brachiopods probably lived attached to the large leptostrophiid brachiopod.
• 3 The Pentamerus Community is dominated by this genus which lived free and upright on the bottom; smaller pedunculate brachiopods probably attached to this large neighbor.
• 4 The Costistricklandia Community was similar in structure to the former community with the many small pedunculate brachiopods being attached to the large Costistricklandia.
• 5 The Clorinda Community is the most diverse, with a great variety of small brachiopods which were probably able to attach to small objects in this quiet off-shore environment, or to some moderately sized brachiopods, such as Clorinda and Cyrtia, which apparently lived free on the bottom.

The brachiopod dominated communities of the Silurian clearly inhabited the ‘level bottom’, an area now occupied mainly by infaunal forms. The main attachment surfaces for the epifaunal elements of the Silurian communities were disarticulated, convex-upward shells.