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Understanding how genetic variation in the Tree Swallow (Tachycineta bicolor) is geographically structured is informative because this broadly distributed North American bird is increasingly used as a model for studies of mating systems, life-history traits, and physiology. We explored patterns of phylogeographic differentiation across the Tree Swallow's breeding range by using nine microsatellite loci and a mitochondrial DNA sequence marker. Contrary to this species' high population-level variation in life-history traits and other ecologically important characteristics, we found no genetic structuring across the majority of its distribution, spanning Tennessee, New York, and Alaska, but we found that birds from California form a distinct yet subtly differentiated genetic cluster. The Tree Swallow can be characterized as a species with both continent-wide genetic panmixia and slight differentiation at one edge of its breeding distribution. This pattern of genetic variation has implications for u...

The delimitation of populations, defined as groups of individuals linked by gene flow, is possible by the analysis of genetic markers and also by spatial models based on dispersal probabilities across a landscape. We combined these two complimentary methods to define the spatial pattern of genetic structure among remaining populations of the threatened Florida scrub-jay, a species for which dispersal ability is unusually well-characterized. The range-wide population was intensively censused in the 1990s, and a metapopulation model defined population boundaries based on predicted dispersal-mediated demographic connectivity. We subjected genotypes from more than 1000 individual jays screened at 20 microsatellite loci to two Bayesian clustering methods. We describe a consensus method for identifying common features across many replicated clustering runs. Ten genetically differentiated groups exist across the present-day range of the Florida scrub-jay. These groups are largely consistent with the dispersal-defined metapopulations, which assume very limited dispersal ability. Some genetic groups comprise more than one metapopulation, likely because these genetically similar metapopulations were sundered only recently by habitat alteration. The combined reconstructions of population structure based on genetics and dispersal-mediated demographic connectivity provide a robust depiction of the current genetic and demographic organization of this species, reflecting past and present levels of dispersal among occupied habitat patches. The differentiation of populations into 10 genetic groups adds urgency to management efforts aimed at preserving what remains of genetic variation in this dwindling species, by maintaining viable populations of all genetically differentiated and geographically isolated populations.

Single nucleotide polymorphisms (SNPs) are becoming more commonly used as molecular markers in conservation studies. However, relatively few studies have employed SNPs for species with little or no existing sequence data, partly due to the practical challenge of locating appropriate SNP loci in these species. Here we describe an application of SNP discovery via shotgun cloning that requires no pre-existing sequence data and is readily applied to all taxa. Using this method, we isolated, cloned and screened for SNP variation at 90 anonymous sequence loci (51 kb total) from the banded wren (Thryothorus pleurostictus), a Central American species with minimal pre-existing sequence data and a documented paucity of microsatellite allelic variation. We identified 168 SNPs (a mean of one SNP/305 bp, with SNPs unevenly distributed across loci). Further characterization of variation at 41 of these SNP loci among 256 individuals including 37 parent–offspring families suggests that they provide substantial information for defining the genetic mating system of this species, and that SNPs may be generally useful for this purpose when other markers are problematic.

We describe 15 polymorphic microsatellite loci from the white-ruffed manakin Corapipo altera, a common understory bird of Neotropical lowland and montane evergreen forests from eastern Honduras to northwestern Colombia. These markers were developed in order to assess population structure and genetic diversity in a fragmented landscape, and to study gene flow between forest fragments. Primers were tested on a population of 159 individuals from the Coto Brus region of southwestern Costa Rica. We found between four and 23 alleles per locus, and observed heterozygosities ranging from 0.23 to 0.93.

Studies on the feeding ecology of vampire bats (Phyllostomidae: Desmodontinae) have been limited by the diagnostic techniques available for identifying host taxa. A precipitin-based test has been the standard method for determining their domestic host preferences (e.g., Cardoso, 1995). This postmortem immunological assay provides a presence or absence indication of a particular host’s blood in a vampire bat’s gut contents (Greenhall, 1970). However, the precipitin test has significant limitations. The bat must be sacrificed for its stomach sample, a particular difficulty for the rare species Diaemus youngi and Diphylla ecaudata. The precipitin test has low utility for identifying wild hosts (Greenhall, 1970), as it requires the harvesting of antibodies, usually in rabbits, using serum collected from all potential host organisms. For this reason, antibody techniques are generally considered too costly (time-wise and financially) for investigating a diverse potential prey range (Symondson, 2002). Indeed, harvesting antibodies of all the potential sympatric avian host species of a vampire bat would be unfeasible. Third, cross-reactivity among related host taxa is expected, and the precipitin technique is therefore unlikely to be diagnostic at the level of families or genera. An alternative and potentially powerful approach is to use the host DNA as a marker for host identification. Although previous studies demonstrate that prey DNA can be isolated and amplified via PCR from feces (Hoss et al., 1992; Sutherland, 2000; Jarman et al., 2002, 2004; Jarman and Wilson, 2004; Deagle et al., 2005) and even fossilized feces (e.g., Kuch et al., 2002), vampire bat fecal samples are a uniquely implausible PCR template due to the lack of robust tissue and very high concentration of PCR-inhibiting heme compounds. The resistance of prey tissue to digestion is a factor determining the extent to which the targeted fecal DNA is degraded (Jarman et al., 2004). Past successful PCR-based Acta Chiropterologica, 8(1): 255–274, 2006 PL ISSN 1508-1109 © Museum and Institute of Zoology PAS

Feathers are increasingly collected as a nondestructive source of DNA for avian genetic research. Although feather samples are not optimal in some important ways than more robust blood or tissue samples, feather sampling requires less training for field workers, results in shorter handling times for the organism, generates no hazardous wastes, and requires simpler storage procedures. Along with these largely positive attributes comes a set of challenges, particularly the relatively low copy number of DNA present in feather samples. We compared the utility and reliability of feathers to the more traditional blood samples as sources of DNA for polymerase chain reaction (PCR)-based molecular sexing of Black-capped Chickadees (Poecile atricapilla). DNA from 102 individuals was extracted separately from both single rectrices and from blood samples, and the sex of each bird was then determined using standard PCR-based methods. We found complete agreement between sex determinations based on feather versus blood DNA extractions. Slight variations in lab protocols were necessary to obtain consistent results from these two DNA sources; and we briefly discuss other sources of error that could occur in feather-based molecular sexing studies. This controlled comparison of feather versus blood samples demonstrates that plucked rectrices provide a highly reliable source of DNA for molecular sexing of wild birds. SINOPSIS Se esta incrementando la modalidad de usar plumas como una fuente no destructiva de ADN para llevar a cabo investigacion genetica en aves. Aunque las muestras tomadas de plumas, en algunas instancias no son optimas que muestras mas robustas como sangre y tejido, el uso de estas no requiere adiestramiento especial, toman menos tiempo en la manipulacion del ave, no generan desperdicios peligrosos y requieren un almacenaje sencillo. Aunque hay atributos positivos en el uso de plumas, tambien existe el problema de obtener una muestra baja de ADN. Examinamos la utilidad y confiabilidad de muestras de plumas en comparacion con tecnicas mas tradicionales como obtencion de muestras de sangre como una fuente de ADN para el sexado de Poecile atricapilla utilizando PCR. A tales efectos se extrajo ADN, de rectrices, de 102 individuos y un numero similar de muestras de sangre para determinar el sexo usando PCR. Encontramos resultados similares con ambos metodos. Sin embargo, fueron necesarios pequenas variaciones en el protocolo de laboratorio para obtener resultados consistentes, de ambas fuentes de ADN. Discutimos algunas fuentes de error que pueden ocurrir cuando se utilizan plumas para la determinacion del sexo utilizando tecnicas moleculares. Este estudio demuestra que las rectrices son una fuente confiable para obtener buenas muestras de ADN y poder determinar el sexo en aves silvestres.

The Florida Scrub-Jay (Aphelocoma coerulescens), a habitat specialist listed as Threatened by the U.S. Fish and Wildlife Service, exhibits extremely limited natal dispersal. We hypothesize that this behaviour results in a correlation of genetic and geographical distance. To test this, we are sampling intensively along the north–south orientated Lake Wales Ridge of central Florida. We describe the isolation and characterization of 31 microsatellite loci developed to determine the minimum distance at which genetic structure can be detected, and to test for isolation by distance. There are 3–15 alleles per locus, with expected heterozygosities from 0.16 to 0.86.

We describe 10 microsatellite loci developed from Crematogaster mimosae, an ant species that nests mutualistically in Acacia drepanolobium trees in east Africa. Polymorphism ranged from 4 to 16 alleles per locus (mean = 7.3). Observed and expected heterozygosities ranged from 0.485 to 0.813 (mean 0.626), and from 0.502 to 0.894 (mean 0.674), respectively. These markers will foster studies of the population structure, colony structure, and reproductive strategies of these ants.

We describe nine microsatellite loci from the chestnut-backed antbird (Myrmeciza exsul), and one locus from the spotted antbird (Hylophylax naevioides) that cross-amplifies in chestnut-backed antbirds. The chestnut-backed antbird is a common understorey insectivore in Neotropical lowland rain forests ranging from eastern Nicaragua to western Ecuador. Primers were developed in order to assess population structure in a fragmented landscape and to study dispersal at a local scale. Primers were tested on 60–62 individuals from a single population in the Sarapiqui Province of Costa Rica. Loci had varying degrees of polymorphism, ranging from two to 19 alleles.

Many species of Thryothorus wrens are renowned for their highly coordinated male-female song duets; the banded wren (T. pleurostictus) is one of the few Thryothorus that does not duet, with this loss a likely derived trait (Mann et al., submitted). Freedom from the constraints of duetting is associated with vigorous immediate-variety singing by the male banded wren, in contrast to the repeat-mode singing of all duetting relatives (Molles & Vehrencamp 1999). Markers for investigating the species’ genetic mating system will help distinguish among adaptive scenarios for the loss of duetting, including selection on the male to increase song versatility for the purposes of attracting extra-pair copulations, selection on the female to relinquish joint territorial defense, release from male mate-guarding, or female preference for versatile male singers (Hall 2004; Mennill & Vehrencamp 2005). Many of these scenarios predict that extra-pair paternity should be higher in the banded wren compared to duetting congeners. Banded wren DNA was isolated from whole blood in lysis buffer (Hoelzel 1992), using DNeasy™ Tissue Kits (Qiagen Inc., Valencia, CA). A microsatellite library from genomic DNA was constructed following the enrichment procedure described in Stenzler and Fitzpatrick (2002) with the modifications described in Stenzler et al. (2004). One hundred positive plasmid clones were sequenced. PCR primers were designed and tested for the 30 microsatellite-containing sequences. Of those, 11 microsatellite loci appeared suitable for further development and were tested for variability on a panel of 11 banded wrens (Table 1). Table 1 Characteristics of microsatellite loci in Thryothororus pleurostictus and cross-species allele size ranges and number of alleles in Troglodytes aedon and Thryothorus rufalbus Polymerase chain reactions (PCRs) were performed in eight-strip 0.2 mL tubes or 96-well plates using a DYAD® thermal cycler (MJ Research). The cycling profile was 1 cycle at 95° C for three min, 35 cycles of 1 min at 95° C, 1 minute at the locus-specific annealing temperature (see Table 1), and 1 min at 72° C, followed by a final extension cycle of 5 min at 72° C. Reactions (10 μL) contained 10–100 ng of genomic DNA, 0.25 units of Jumpstart™ Taq Polymerase (Sigma, St. Louis, MO), 10 mM Tris-HCL (pH 8.3), 50 mM KCl, MgCl2 specific to each locus (Table 1), 200 μM of dNTPs (Invitrogen), and 2.0 pmol each of forward and reverse primers, one of which was modified at the 5′ end by addition of a fluorescent label (PET, 6-FAM, VIC, or NED -Applied Biosystems). Labeled PCR products were analyzed on an ABI Prism 3100 Genetic Analyser (Applied Biosystems), and allele sizes were estimated using GENEMAPPER™ version 3.0 (Applied Biosystems). During preliminary screening of microsatellite loci isolated from the banded wren we noted that an unusually large proportion of loci were invariant, and in subsequent screening with primers developed for other wren taxa (song wren (Cyphorhinus phaeocephalus; Hughes and Robinson 2001) and house wren (Troglodytes aedon; Cabe and Marshall 2001), we similarly found little to no variation at the subset of those loci that amplified robustly in the banded wren. To explore whether this pattern of low variation was taxon-specific, we used the same protocols to test amplification and variability of the banded wren markers in panels of individuals of two additional wren taxa: the rufous-and-white wren (T. rufalbus), which occurs sympatrically with Thryothorus pleurostictus at our Costa Rica study site (Mennill & Vehrencamp 2005), and the southern house wren (Troglodytes aedon bonariae) from southern Buenos Aires Province, Argentina. A total of 11 banded wrens, 15 rufous-and-white wrens, and 15 house wrens were genotyped at each of the 11 banded wren-specific loci (Table 1). Of the primers that produced a PCR product, the number of variable loci in each species was: banded wren, 3 (2–3 alleles); rufous-and-white wren, 6 (2–7 alleles); and house wren, 3 (2–11 alleles). While allelic variation was present at 27% of banded wren loci in banded wrens, multiple alleles were found at 60% and 50% of loci that amplified in the rufousand-white and house wrens, respectively. Given the higher variability of these markers in related species, we suspect that the low microsatellite variability in this banded wren population stems from past demographic bottlenecks, despite the relative abundance of this species at the present time. The banded wren is a habitat specialist of lowland tropical dry-forests, whereas the rufous-and-white wren is a semi-humid and gallery forest specialist and the southern house wren is a generalist of semi-open habitat ranging from arid to humid and from lowland to montane areas. During the Last Glacial Maximum and subsequent Early Holocene, the Pacific lowlands of southern Central America experienced multiple rapid and extreme changes in climate and vegetation (Piperno and Jones 2003). During this period, the expansion of the humid lowland forest and concomitant fragmentation of dry forest habitats may have reduced and fragmented the banded wren’s populations more strongly than the populations of the other two wren species. In subsequent screening, we genotyped 40 complete banded wren families (246 individuals) with ThPl-14, ThPl-27, and ThPl-37. The numbers of alleles at these loci were 3, 6, and 3, respectively, in this larger pool of individuals. All loci were in Hardy-Weinberg equilibrium and there was no evidence of linkage among the loci (all P > 0.05, n = 70 adult males and females – offspring excluded; tests done in GENEPOP (Raymond & Rousset 1999).

We describe 12 microsatellite loci from the Golden-winged Warbler ( Vermivora chrysoptera ), a bird species of conservation concern owing to competition and hybridization with the Blue-winged Warbler ( V. pinus ). Directional mitochondral DNA introgression from V. pinus into V. chrysoptera has been reported within the hybrid zone. Frequent hybrid phenotypes suggest that nuclear introgression is also prevalent, although this has not been demonstrated conclusively with molecular markers. These microsatellites will foster explorations of the genetic interactions between these avian congeners, and amplification tests suggest that they have high cross-species utility for closely allied bird genera and families.

We describe 30 microsatellite loci developed from three species of swallows in the genus Tachycineta: T. bicolor (tree swallow), T. albilinea (mangrove swallow), and T. leucorrhoa (white-rumped swallow). These commonly studied birds nest in secondary cavities and are distributed from Alaska to Argentina. Primer pairs were designed for each species individually and tested for cross-amplification in 40-48 individuals of all three species. Polymorphism ranged from 5 to 65 alleles per locus (mean = 19.1). These markers will allow comparative studies of extra-pair paternity rates among members of the genus as well as the assessment of population structure.

We describe 11 microsatellite loci isolated from the Banded Wren (Thryothorus pleurostictus), a Neotropical species for which understanding the genetic mating system is important for testing questions about the species’ unusual vocal behavior. Screening of these loci revealed extremely low allelic variation in a Costa Rican population. Allelic variation at these and other previously developed loci is substantially higher in two other wren species, the southern house wren (Troglodytes aedon bonariae) and rufous-and-white wren (Thryothorus rufalbus), suggesting that the low allelic diversity in the banded wren results from demographic bottlenecks rather than locus-sampling artifacts.

Al-resistant (alr) mutants of Arabidopsis thaliana were isolated and characterized to gain a better understanding of the genetic and physiological mechanisms of Al resistance. alr mutants were identified on the basis of enhanced root growth in the presence of levels of Al that strongly inhibited root growth in wild-type seedlings. Genetic analysis of the alr mutants showed that Al resistance was semidominant, and chromosome mapping of the mutants with microsatellite and random amplified polymorphic DNA markers indicated that the mutants mapped to two sites in the Arabidopsis genome: one locus on chromosome 1 (alr-108, alr-128, alr-131, and alr-139) and another on chromosome 4 (alr-104). Al accumulation in roots of mutant seedlings was studied by staining with the fluorescent Al-indicator dye morin and quantified via inductively coupled argon plasma mass spectrometry. It was found that the alr mutants accumulated lower levels of Al in the root tips compared with wild type. The possibility that the mutants released Al-chelating organic acids was examined. The mutants that mapped together on chromosome 1 released greater amounts of citrate or malate (as well as pyruvate) compared with wild type, suggesting that Al exclusion from roots of these alr mutants results from enhanced organic acid exudation. Roots of alr-104, on the other hand, did not exhibit increased release of malate or citrate, but did alkalinize the rhizosphere to a greater extent than wild-type roots. A detailed examination of Al resistance in this mutant is described in an accompanying paper (J. Degenhardt, P.B. Larsen, S.H. Howell, L.V. Kochian [1998] Plant Physiol 117: 19–27).

A sample of two-jet events from the UA1 experiment at the CERN pp Collider has been used to study the fragmentation of high-energy quark and gluon jets into charged hadrons. Compared with lower-energy jets observed in e + e − and pp collisions, the fragmentation function measured in the present experiment is softer (i.e. peaked to smaller values of z ) and the mean internal transverse momentum is larger, mainly because of the effects of the QCD scaling violations. Using our knowledge of the quark and gluon structure functions in the proton, together with the QCD matrix elements, a statistical separation of quark and gluon jets is achieved within the present experiment. The fragmentation function for the gluon jets is found to be softer, and the angular spread of the fragmentation products larger, than is the case for quark jets.

The equine trophoblast exists in two distinct forms. The non-invasive and major component constitutes the outer layer of the allantochorionic villi that interdigitate with the endometrial epithelium. The invasive and minor component consists of the chorionic girdle. This discrete, annulare band of tissue begins to differentiate at approximately day 25 of gestation, and it invades the endometrium between days 36 and 38 to form 10-20 endometrial cups (Allen et al., 1973). The large cells from the fetal endometrial cups secrete the high concentrations of equine Chorionic Gonadotrophin (eCG) that are present in the serum of pregnant mares between days 40 and 120. The cup cells also elicit a maternal cell mediated reaction which hastens the destruction of the cups and their deliverance from the endometrium between days 100 and 140. No such leukocyte reaction occurs at the interface between the endometrial epithelium and the normal trophoblast of the allantochorion (Allen, 1975).

The production properties of a sample of 172 charged intermediate vector bosons produced at the CERN Super Proton Synchrotron Collider are described. The production cross-section, the longitudinal- and transverse-momentum distributions and the properties of hadronic jet activity produced in association with the weak bosons are in agreement with the expectations of the QCD-improved Drell-Yan mechanism.

The nucleotide sequence of the DNA polymerase gene of the avipoxvirus fowlpox is presented and the predicted amino acid sequence compared with that of the orthopoxvirus vaccinia. The results have brought to light an error in the vaccinia sequence which has resulted in the ommission of 44 amino acids from the carboxy-terminus of the vaccinia DNA polymerase. There has been extensive conservation of amino acids throughout the enzymes, and regions identified as being present in DNA polymerases from a wide range of viruses are again present here. The method used to identify the fowlpoxvirus gene could have applications towards defining genomic organisations in other viral systems.