Using DNA Barcodes to Identify Bird Species Involved in Birdstrikes

Abstract: We determined effectiveness of using mitochondrial DNA barcodes (cytochrome c oxidase subunit 1 [CO1]) to identify bird-aircraft collision (birdstrike) cases that lacked sufficient feather evidence for morphological diagnosis. From September through December 2006, 821 samples from birdstrike events occurring in the United States were submitted for DNA analysis. We successfully amplified a CO1 DNA barcode product from 554 (67.5%) of the samples; 267 (32.5%) did not contain viable DNA and depended on morphological methods (microscopy) for Order or Family level identification. We deemed 19 cases inconclusive either because the DNA barcode recovered from the sample did not meet our 98% match criteria when compared to the Barcode of Life Database (BoLD) or because the DNA barcode matched to a set of ≥ 2 closely related species with overlapping barcodes, preventing complete species identification. Age of the sample (≤6 months) did not affect DNA viability, but initial condition of the sample and the collection method was critical to DNA identification success. The DNA barcoding approach has great potential in aiding in identification of birds (and wildlife) for airfield management practices, particularly in regions of the world that lack the vast research collections and individual expertise for morphologic identifications.     

Y chromosome microsatellite markers identified from the tammar wallaby (Macropus eugenii) and their amplification in three other macropod species

Microsatellites were identified from three fully sequenced Y chromosome‐specific bacterial artificial chromosome clones from the tammar wallaby, Macropus eugenii. Ten microsatellites were genotyped in male tammar wallabies. Four loci were polymorphic with between two and six alleles per locus. Eleven different haplotypes were identified from 22 male tammar wallabies. No amplifications were obtained from female samples. Each microsatellite was also shown to amplify reliably in at least one other macropod species. These markers may therefore prove useful as some of the first male‐specific genetic markers for marsupials, with potential application to studies of male‐biased dispersal and mating systems.     

Microsatellite loci from the Caribbean Fruit Fly,Anastrepha suspensa (Diptera: Tephritidae)

The lack of polymorphic genetic markers suitable for genotyping sperm, eggs, and all life stages of the important agricultural pest, Anastrepha suspensa, have prevented detailed genetic studies of its breeding system, reproductive dynamics, and population dynamics. We describe polymerase chain reaction (PCR) primers and reaction conditions for amplifying nine polymorphic microsatellite DNA loci isolated from this species. The PCR primers were tested on four to five individuals each collected from five geographically distant locations in Florida. Heterozygosity values and the number of alleles per locus varied from 0.11 to 0.89, and from two to 12, respectively.     

Development and optimization of microsatellite DNA primers for boreal owls (Aegolius funereus)

We developed 22 microsatellite loci for boreal owls (Aegolius funereus). We genotyped 275 unrelated boreal owls (Aegolius f. richardsoni) and 36 unrelated Tengmalm's owls (Aegolius f. funereus) using seven loci that were polymorphic and did not have detectable null alleles. Among North American and Scandinavian boreal owls, respectively, allelic diversity ranged from three to 11 alleles and from one to 11 alleles, observed heterozygosity ranged from 0.31 to 0.80 and from 0.00 to 0.81, and expected heterozygosity ranged from 0.28 to 0.81 and from 0.00 to 0.81. These markers appeared to amplify DNA in six other Strigidae species.     

Fourteen polymorphic microsatellite loci characterized in the house sparrow Passer domesticus (Passeridae,Aves)

We characterized 14 polymorphic microsatellite loci in the house sparrow Passer domesticus. Four loci were isolated from house sparrow genomic libraries and 10 loci were identified by testing 100 loci that had been originally isolated in other passerine species. Loci were characterized in 37–54 unrelated sparrows from British and Norwegian populations. Each locus displayed between two and 31 alleles, with the observed heterozygosity ranging between 0.30 and 0.91.     

Nitrogen Deficiency Slows Leaf Development and Delays Flowering in Narrow-leafed Lupin

Effects of nitrogen (N) supply on leaf and flower developmentinLupinus angustifolius L. cv Merrit were examined in a temperature-controlledglasshouse. Low N supply (0.05 or 0.4 mM N) had little effecton leaf initiation but slowed leaf emergence on the main stemcompared with plants receiving high N supply (6.0 or 6.4 mMN), or with symbiotic N₂-fixation. Plants experiencing transientN deficiency had slower leaf emergence than plants with a continuoussupply of 6.4 mM N. Nitrogen supply did not affect the timeof floral initiation, which occurred within 4 weeks of sowing,by which time nine to ten leaves had emerged. However, the floweringof low-N plants was delayed by 68 to 220 °C d (i.e. 4–14d) even though they had fewer leaves. The effect of N deficiencyon flowering time was largely a result of slower leaf emergence. Lupinus angustifolius L.; nitrogen; leaf; flower initiation; thermal time; plastochron; phyllochron     

The Distribution of Chromosome Races of Ranunculus ficaria L. in the British Isles

The chromosome numbers of 889 plants from 222 British populationsof Ranunculus ficaria were counted. 66.1 per cent of the populationscontained diploids (49.1 per cent of plants), 4.1 per cent containedtriploids (5.5 per cent of plants) and 43.2 per cent tetraploids(45.4 per cent of plants); 13.1 per cent of the populationscontained two or more polyplotypes. At the fruiting stage, tetraploidplants can be reliably distinguished from diploids by the presenceof axillary bulbils in the tetraploids and their absence inthe diploids. The production of well-developed heads of achenes,which is more characteristic of the diploids than of the tetraploids,is a less reliable character. Diploid plants are widespreadthroughout the British Isles but tetraploids are more commonin the east than in the west; 17.6 per cent of the diploid plantshad B-chromosomes and these plants were virtually confined tosouthern England and the Midlands. The occurrence of triploidsand of mixed populations of diploids and tetraploids are bothshown to be more common than previously supposed.     

Stress Proteins in Mammalian Hibernation

Many organisms whose body temperatures (T_b) vary when they areexposed to a wide range of environmental temperatures exhibitdifferential expression of stress (heat shock) proteins, presumablyto minimize protein damage during thermal stress. In contrast,we know relatively little about natural variation in stressproteins in homeotherms (i.e., birds and mammals), perhaps dueto the relatively constant T_b that is the hallmark of this vertebrategroup. The significant changes in T_b and metabolism characteristicof mammalian hibernators suggest they could provide insightinto the ecological relevance of stress proteins in mammals.Here we examined differential expression of stress proteinsin several tissues of active and torpid 13-lined ground squirrels.There were few significant differences in expression of inducibleHsp70 protein in liver, kidney, heart, intestine, and skeletalmuscle between active and torpid squirrels, and neither fastingin active squirrels nor torpor bout length in hibernators significantlyaltered Hsp70 abundance in these tissues. However, Hsp70 proteinwas lower in brown adipose tissue (BAT) of torpid compared withactive squirrels. In contrast, abundance of GRP75, the mitochondria]form of Hsp70, was greater in liver, skeletal muscle and intestineof torpid compared with active squirrels, with the greatestchange in intestine. Because GRP75 has been shown to be inducedby non-thermal stressors including glucose deprivation and oxidativestress, these results suggest that the ecological significanceof stress proteins for hibernators may be more closely associatedwith the metabolic demands of heterothermy rather than thermalstress per se.     

White-Tailed Deer Movements in a Chronic Wasting Disease Area in South-Central Wisconsin

Abstract: To focus white-tailed deer (Odocoileus virginianus) management within a chronic wasting disease-infected area in south-central Wisconsin, USA, we assessed deer movements and related dispersal to variation in landscape pattern, deer density, and harvest intensity. We radiocollared and monitored 165 deer between 2003 and 2005. Yearling males that dispersed (45%) had greater forest edge (i.e., fragmentation) within natal home ranges. Exploratory movements were rare for adult females. Transient and migratory movements were rare among all deer (<5%). Although yearling males have low chronic wasting disease prevalence rates, they may be infected before dispersal due to variable incubation times. Managers should increase yearling male harvest and consider removing young males in areas of higher forest edge.     

Taxonomic classification of the reef coral family Mussidae (Cnidaria: Anthozoa: Scleractinia)

Molecular analyses are transforming our understanding of the evolution of scleractinian corals and conflict with traditional classification, which is based on skeletal morphology. A new classification system, which integrates molecular and morphological data, is essential for documenting patterns of biodiversity and establishing priorities for marine conservation, as well as providing the morphological characters needed for linking present‐day corals with fossil species. The present monograph is the first in a series whose goal is to develop such an integrated system. It addresses the taxonomic relationships of 55 Recent zooxanthellate genera (one new) in seven families (one new), which were previously assigned to the suborder Faviina (eight genera are transferred to incertae sedis). The present monograph has two objectives. First, we introduce the higher‐level classification system for the 46 genera whose relationships are clear. Second, we formally revise the taxonomy of those corals belonging to the newly discovered family‐level clade (restricted today to the western Atlantic and Caribbean regions); this revised family Mussidae consists of ten genera (one of which is new) and 26 species that were previously assigned to the ‘traditional’ families Faviidae and Mussidae. To guide in discovering morphologic characters diagnostic of higher‐level taxa, we mapped a total of 38 morphologic characters [19 macromorphology, eight micromorphology, 11 microstructure] onto a molecular tree consisting of 67 species [22 Indo‐Pacific and seven Atlantic species in the traditional family Faviidae; 13 Indo‐Pacific and ten Atlantic species in the traditional family Mussidae; 13 species in the traditional families Merulinidae (5), Pectiniidae (7), and Trachyphylliidae (1); two Atlantic species of traditional Montastraea], and trace character histories using parsimony. To evaluate the overall effectiveness of morphological data in phylogeny reconstruction, we performed morphology‐based phylogenetic analyses using 27 (80 states) of the 38 characters, and compared morphological trees with molecular trees. The results of the ancestral state reconstructions revealed extensive homoplasy in almost all morphological characters. Family‐ and subfamily‐level molecular clades [previously identified as XVII?XXI] are best distinguished on the basis of the shapes of septal teeth and corresponding microstructure. The newly revised family Mussidae (XXI) has septal teeth with regular pointed tips (a symplesiomorphy) and a stout blocky appearance. It has two subfamilies, Mussinae and Faviinae. The subfamily Mussinae is distinguished by spine‐shaped teeth and widely spaced costoseptal clusters of calcification centres. The subfamily Faviinae is distinguished by blocky, pointed tricorne or paddle‐shaped teeth with elliptical bases, transverse structures such as carinae that cross the septal plane, and well‐developed aligned granules. Defining diagnostic characters for the broader data set is more challenging. In analyses of taxonomic subsets of the data set that were defined by clade, morphological phylogenetic analyses clearly distinguished the families Mussidae (XXI) and Lobophylliidae (XIX), as well as the two subfamilies of Mussidae (Mussinae, Faviinae), with one exception (Homophyllia australis). However, analyses of the entire 67‐species data set distinguished the family Lobophylliidae (XIX), but not the Merulinidae (XVII) and not the newly defined Mussidae (XXI), although the subfamily Mussinae was recovered as monophyletic. Some lower‐level relationships within the Merulinidae (XVII) agree with molecular results, but this particular family is especially problematic and requires additional molecular and morphological study. Future work including fossils will not only allow estimation of divergence times but also facilitate examination of the relationship between these divergences and changes in the environment and biogeography. Published 2012. This article is a U.S. Government work and is in the public domain in the USA. Zoological Journal of the Linnean Society, 2012, 166 , 465–529.