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The red fox (Vulpes vulpes) has a wide global distribution with many ecotypes, and has been bred in captivity for various traits, making it a useful evolutionary model system. The Y chromosome represents one of the most informative markers of phylogeography, yet it has not been well-studied in the red fox due to a lack of the necessary genomic resources. We used a target capture approach to sequence a portion of the red fox Y chromosome in a geographically diverse red fox sample, along with other canid species, to develop single nucleotide polymorphism (SNP) markers, 13 of which we validated for use in subsequent studies. Phylogenetic analyses of the Y chromosome sequences, including calibration to outgroups, confirmed previous estimates of the timing of two intercontinental exchanges of red foxes, the initial colonization of North America from Eurasia approximately half a million years ago and a subsequent continental exchange before the last Pleistocene glaciation (∼100,000 years ago). However, in contrast to mtDNA, which showed unidirectional transfer from Eurasia to North America prior to the last glaciation, the Y chromosome appears to have been transferred from North America to Eurasia during this period. Additional sampling is needed to confirm this pattern and to further clarify red fox Y chromosome phylogeography.

Lettuce downy mildew, caused by Bremia lactucae, is the most important foliar disease of lettuce in California. In recent years, there were apparent failures of fungicides containing fosetyl-aluminum (Aliette) to control downy mildew in commercial lettuce fields in California. Consequently, we characterized 134 isolates collected over 2 years from throughout the coastal growing areas of California for insensitivity to the fungicides fosetyl-aluminum and maneb, pathotype, and mating type. Tests using seedlings in controlled growth room conditions demonstrated the widespread occurrence of insensitivity to fosetyl-aluminum in California populations of B. lactucae. Fifty percent of the isolates assayed sporulated profusely in the presence of fosetyl-aluminum applied at rates twice the normal field dosage, and an additional 40% showed moderate sporulation at this rate. Fosetyl-aluminum-insensitive isolates were detected from all regions sampled. Insensitivity was also observed in multiple pathotypes. Insensitivity was not complete, however, because quantitative analysis of the number of lesions on older plants revealed that applications of fosetyl-aluminum could reduce the levels of disease by 50%. Therefore, while fosetyl-aluminum may have utility under low disease pressure in the field, other control measures are required to provide control under conditions favorable to the disease.

The domestic dog fulfills many functions for their human companions, such as hauling, guarding, and protection. Consequently, humans have taken dogs to nearly every corner of the globe. Recent translocations of Western dogs stemming from the Victorian era dog fancy have erased some of the ancient genetic signatures of these earlier migrations. Here we used DNA of ancient and modern dogs from the North American Arctic of Alaska and Greenland to assess their genetic continuity in time and space. We successfully sequenced 23 archaeological (ca. AD 1250–1910) and recent (ca. AD 1930–1990) surface-collected Canis bone and tooth samples and compared them to 51 modern Inuit Sled Dogs and to published sequences of modern Alaskan Malamutes (and additional Inuit Sled Dogs) to test for evidence of lineage replacement or genetic continuity through time. Ancient samples from Alaska and Greenland and modern sequences from Greenland all contained a high frequency of haplotype A31, which was previously described only in modern North American Arctic dogs. Thus, A31 was a common thread tying the entire North American Arctic together prior to European colonization and, in the Eastern Arctic, indicates genetic continuity between past and present dogs as well. However, A31 is rare in modern Alaskan dogs, consistent with post-colonization replacement by Eurasian matrilines.

Heterokaryon incompatibility (HI) is a nonself recognition phenomenon occurring in filamentous fungi that is important for limiting resource plundering and restricting viral transfer between strains. Nonself recognition and HI occurs during hyphal fusion between strains that differ athetloci. If two strains undergo hyphal fusion, but differ in allelic specificity at ahetlocus, the fusion cell is compartmentalized and undergoes a rapid programmed cell death (PCD). Incompatible heterokaryons show a macroscopic phenotype of slow growth and diminished conidiation, and a microscopic phenotype of hyphal compartmentation and cell death. To understand processes associated with HI and PCD, we used whole-genome microarrays forNeurospora crassato assess transcriptional differences associated with induction of HI mediated by differences inhet-c pin-chaplotype. Our data show that HI is a dynamic and transcriptionally active process. The production of reactive oxygen species is implicated in the execution of HI and PCD inN. crassa, as are several genes involved in phosphatidylinositol and calcium signalling pathways. However, genes encoding mammalian homologues of caspases or apoptosis-inducing factor (AIF) are not required for HI or programmed cell death. These data indicate that PCD during HI occurs via a novel and possibly fungal-specific mechanism, making this pathway an attractive drug target for control of fungal infections.

The contemporary genetic structure of animal populations is sculpted by past events, including demographic bottlenecks and expansions and movement of animals by humans. In an analysis of microsatellite DNA of black bears (Ursus americanus; n 5 540) across California, we discovered distinct population structure and genetic evidence of 2 historic colonization events. First, genotypes of bears sampled in southern California are most related to those from the Yosemite National Park region and not with spatially intervening populations. Historical records recount the translocation of 28 black bears from the Yosemite National Park area of the central Sierra Nevada to the San Bernardino Mountains in southern California in the 1930s. Second, before colonization of California by Europeans, the Central Coast region was inhabited by the now extinct California grizzly bear (Ursus arctos californiensis), but not black bears. Following an apparent competitive release and range expansion during the past century, black bears now inhabit the Central Coast region of California. Black bears in California’s Central Coast display lower genetic diversity (founder effect) and a genetic signature most closely allied with black bears from the southern Sierra Nevada. In both these cases, molecular genetic techniques allowed historical reconstruction of anthropogenic events leading to changes in animal distributions.

The dusky-footed woodrat (Neotoma fuscipes) is an endemic North American rodent belonging to the family Cricetidae. We present here the first complete mitogenome within the Neotoma genus. The mitogenome is 16,199 bp in length, and has a structure and gene organization similar to other rodent species (e.g. Mus musculus, Peromyscus maniculatus and Microtus fortis calamorum). The overall base composition is A (35.2%), C (25.5%), G (12.3%), T (27.0%), with a GC content of 37.8%, similar to other rodents. This mitogenome serves as a foundation for future phylogenetic, phylogeographic and population genetic studies.

Modern genetic samples are commonly used to trace dog origins, which entails untested assumptions that village dogs reflect indigenous ancestry or that breed origins can be reliably traced to particular regions. We used high-resolution Y chromosome markers (SNP and STR) and mitochondrial DNA to analyze 495 village dogs/dingoes from the Middle East and Southeast Asia, along with 138 dogs from >35 modern breeds to 1) assess genetic divergence between Middle Eastern and Southeast Asian village dogs and their phylogenetic affinities to Australian dingoes and gray wolves (Canis lupus) and 2) compare the genetic affinities of modern breeds to regional indigenous village dog populations. The Y chromosome markers indicated that village dogs in the two regions corresponded to reciprocally monophyletic clades, reflecting several to many thousand years divergence, predating the Neolithic ages, and indicating long-indigenous roots to those regions. As expected, breeds of the Middle East and East Asia clustered within the respective regional village dog clade. Australian dingoes also clustered in the Southeast Asian clade. However, the European and American breeds clustered almost entirely within the Southeast Asian clade, even sharing many haplotypes, suggesting a substantial and recent influence of East Asian dogs in the creation of European breeds. Comparison to 818 published breed dog Y STR haplotypes confirmed this conclusion and indicated that some African breeds reflect another distinct patrilineal origin. The lower-resolution mtDNA marker consistently supported Y-chromosome results. Both marker types confirmed previous findings of higher genetic diversity in dogs from Southeast Asia than the Middle East. Our findings demonstrate the importance of village dogs as windows into the past and provide a reference against which ancient DNA can be used to further elucidate origins and spread of the domestic dog.

5 pages; International audience; This article documents the addition of 411 microsatellite marker loci and 15 pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Acanthopagrus schlegeli, Anopheles lesteri, Aspergillus clavatus, Aspergillus flavus, Aspergillus fumigatus, Aspergillus oryzae, Aspergillus terreus, Branchiostoma japonicum, Branchiostoma belcheri, Colias behrii, Coryphopterus personatus, Cynogolssus semilaevis, Cynoglossus semilaevis, Dendrobium officinale, Dendrobium officinale, Dysoxylum malabaricum, Metrioptera roeselii, Myrmeciza exsul, Ochotona thibetana, Neosartorya fischeri, Nothofagus pumilio, Onychodactylus fischeri, Phoenicopterus roseus, Salvia officinalis L., Scylla paramamosain, Silene latifo, Sula sula, and Vulpes vulpes. These loci were cross-tested on the following species: Aspergillus giganteus, Colias pelidne, Colias interior, Colias meadii, Colias eurytheme, Coryphopterus lipernes, Coryphopterus glaucofrenum, Coryphopterus eidolon, Gnatholepis thompsoni, Elacatinus evelynae, Dendrobium loddigesii Dendrobium devonianum, Dysoxylum binectariferum, Nothofagus antarctica, Nothofagus dombeyii, Nothofagus nervosa, Nothofagus obliqua, Sula nebouxii, and Sula variegata. This article also documents the addition of 39 sequencing primer pairs and 15 allele specific primers or probes for Paralithodes camtschaticus.

The genetic map of Bremia lactucae was expanded utilizing 97 F(1) progeny derived from a cross between Finnish and Californian isolates (SF5xC82P24). Genetic maps were constructed for each parent utilizing 7 avirulence genes, 83 RFLP markers, and 347 AFLP markers, and a consensus map was constructed from the complete data set. The framework map for SF5 contained 24 linkage groups distributed over 835cM; the map for C82P24 contained 21 linkage groups distributed over 606cM. The consensus map contained 12 linkage groups with markers from both parents and 24 parent-specific groups. Six avirulence genes mapped to different linkage groups; four were located at the ends of linkage groups. The closest linkages between molecular markers and avirulence genes were 3cM to Avr4 and 1cM to Avr7. Mating type seemed to be determined by a single locus, where the heterozygote determined the B(2) type and the homozygous recessive genotype determined the B(1) type.