A Comparative Survey of the Frequency and Distribution of Polymorphism in the Genome of Xenopus tropicalis

Naturally occurring DNA sequence variation within a species underlies evolutionary adaptation and can give rise to phenotypic changes that provide novel insight into biological questions. This variation exists in laboratory populations just as in wild populations and, in addition to being a source of useful alleles for genetic studies, can impact efforts to identify induced mutations in sequence-based genetic screens. The Western clawed frog Xenopus tropicalis (X. tropicalis) has been adopted as a model system for studying the genetic control of embryonic development and a variety of other areas of research. Its diploid genome has been extensively sequenced and efforts are underway to isolate mutants by phenotype- and genotype-based approaches. Here, we describe a study of genetic polymorphism in laboratory strains of X. tropicalis. Polymorphism was detected in the coding and non-coding regions of developmental genes distributed widely across the genome. Laboratory strains exhibit unexpectedly high frequencies of genetic polymorphism, with alleles carrying a variety of synonymous and non-synonymous codon substitutions and nucleotide insertions/deletions. Inter-strain comparisons of polymorphism uncover a high proportion of shared alleles between Nigerian and Ivory Coast strains, in spite of their distinct geographical origins. These observations will likely influence the design of future sequence-based mutation screens, particularly those using DNA mismatch-based detection methods which can be disrupted by the presence of naturally occurring sequence variants. The existence of a significant reservoir of alleles also suggests that existing laboratory stocks may be a useful source of novel alleles for mapping and functional studies

A Poorly Known High-Latitude Parasitoid Wasp Community: Unexpected Diversity and Dramatic Changes through Time

Climate change will have profound and unanticipated effects on species distributions. The pace and nature of this change is largely unstudied, especially for the most diverse elements of terrestrial communities – the arthropods – here we have only limited knowledge concerning the taxonomy and the ecology of these groups. Because Arctic ecosystems have already experienced significant increases in temperature over the past half century, shifts in community structure may already be in progress. Here we utilise collections of a particularly hyperdiverse insect group – parasitoid wasps (Hymenoptera; Braconidae; Microgastrinae) – at Churchill, Manitoba, Canada in the early and mid-twentieth century to compare the composition of the contemporary community to that present 50–70 years ago. Morphological and DNA barcoding results revealed the presence of 79 species of microgastrine wasps in collections from Churchill, but we estimate that 20% of the local fauna awaits detection. Species composition and diversity between the two time periods differ significantly; species that were most common in historic collections were not found in contemporary collections and vice versa. Using barcodes we compared these collections to others from across North America; contemporary Churchill species are most affiliated with more south-western collections, while historic collections were more affiliated with eastern collections. The past five decades has clearly seen a dramatic change of species composition within the area studied coincident with rising temperature

Sound Finder: a new software approach for localizing animals recorded with a microphone array

Acoustic localization is a powerful technique for monitoring the positions, movements and behaviours of terrestrial animals. However, its prevalence in biological studies has been constrained by hardware and software that are custom-built, expensive and difficult to use. We recently helped to relieve the hardware constraint by describing a microphone array that is affordable, portable, easy to use and commercially available. Here, we help to relieve the software constraint by developing an acoustic localization program called “Sound Finder”, which is easy to use, freely available and accurate for a variety of animals and recording conditions. It runs in the free software environment R, and in spreadsheet programs such as Microsoft Excel and the open-source software LibreOffice. In this study, we describe how Sound Finder functions, and then test its accuracy by localizing natural sounds that were broadcast through loudspeakers and re-recorded with microphone arrays. We quantify Sound Finder's accuracy by comparing its location estimates with known loudspeaker locations and with output from other localization approaches. We show that Sound Finder generates accurate location estimates for a variety of animal sounds, microphone array configurations and environmental conditions. Furthermore, Sound Finder generates an error value that allows the user to assess its accuracy. In conclusion, Sound Finder provides accurate estimates of a vocalizing animal's location. It is easy to use, requires only widespread and affordable software and is freely available in a standard form as Supplementary material to this article