bluuebunny/crossref_metadata_2025_split huggingface dataset:
The deep divergences of neornithine birds: a phylogenetic analysis of morphological characters
Authors: Mayr Gerald , Clarke Julia 
Published: July 2005

AbstractConsensus is elusive regarding the phylogenetic relationships among neornithine (crown clade) birds. The ongoing debate over their deep divergences is despite recent increases in available molecular sequence data and the publication of several larger morphological data sets. In the present study, the phylogenetic relationships among 43 neornithine higher taxa are addressed using a data set of 148 osteological and soft tissue characters, which is one of the largest to date. The Mesozoic non‐neornithine birds Apsaravis, Hesperornis, and Ichthyornis are used as outgroup taxa for this analysis. Thus, for the first time, a broad array of morphological characters (including both cranial and postcranial characters) are analyzed for an ingroup densely sampling Neornithes, with crown clade outgroups used to polarize these characters. The strict consensus cladogram of two most parsimonious trees resultant from 1000 replicate heuristic searches (random stepwise addition, tree‐bisection‐reconnection) recovered several previously identified clades; the at‐one‐time contentious clades Galloanseres (waterfowl, fowl, and allies) and Palaeognathae were supported. Most notably, our analysis recovered monophyly of Neoaves, i.e., all neognathous birds to the exclusion of the Galloanseres, although this clade was weakly supported. The recently proposed sister taxon relationship between Steatornithidae (oilbird) and Trogonidae (trogons) was recovered. The traditional taxon “Falconiformes” (Cathartidae, Sagittariidae, Accipitridae, and Falconidae) was not found to be monophyletic, as Strigiformes (owls) are placed as the sister taxon of (Falconidae + Accipitridae). Monophyly of the traditional “Gruiformes” (cranes and allies) and ”Ciconiiformes” (storks and allies) was also not recovered. The primary analysis resulted in support for a sister group relationship between Gaviidae (loons) and Podicipedidae (grebes)—foot‐propelled diving birds that share many features of the pelvis and hind limb. Exclusion of Gaviidae and reanalysis of the data set, however, recovered the sister group relationship between Phoenicopteridae (flamingos) and grebes recently proposed from molecular sequence data.
Brooks Parsimony Analysis: a valiant failure
Authors: Siddall Mark E , Perkins Susan L 
Published: July 2005

AbstractA recent comparison of two methods for examining correlated host and parasite phylogenies, namely TreeMap 1.0 and Brooks Parsimony Analysis concluded that the latter method performed better and is to be preferred. Reevaluation of the examples contrived for that study demonstrates that the two methods were only compared on one kind of problem (widespread parasite) for which there is an easy fix for TreeMap 1.0. Other kinds of problems like host‐switching among sister taxa or host‐switching over great distances across a host tree befuddle BPA even as they are readily resolved parsimoniously by TreeMap 1.0. These difficulties, compounded with inaccurate counting of ad hoc hypotheses required by its solutions render BPA unsuitable for comparison of host and parasite phylogenies.
The origin of photic behavior and the evolution of sexual communication in fireflies (Coleoptera: Lampyridae)
Authors: Branham Marc A , Wenzel John W 
Published: July 2005

AbstractThrough a phylogenetic analysis using adult morphological characters, we show that the origin of bioluminescence in cantharoid beetles appears to predate the origin of the family Lampyridae. The ability to produce and emit photic signals was first gained by larvae and appears to function as an aposematic warning display; it was subsequently gained in adults and is used as a sexual signal. Our analysis also suggests that while pheromonal sexual signals are used basally in the family, they are used in conjunction with and then subsequently replaced by photic signals in some lampyrid lineages. Both photic signals and the photic organs used to produce them have become greatly elaborated in the fireflies that no longer employ pheromonal sexual signals. In addition, the ability to produce a flashed sexual signal appears to have arisen at least three times in the family Lampyridae. Convergent evolution is also evident in a number of adult male photic organ morphologies. Further, we recommend that individual signal system components be compared rather than overall signal system complexity. The use of this strategy may allow one to recognize and better interpret adaptive correlations despite convergence or loss. We demonstrate that phylogenetic analysis is a powerful tool even for rapidly evolving traits.
Identification and molecular characterization of defensin gene from the ant Formica aquilonia
Authors: Viljakainen L. , Pamilo P. 
Published: July 2005

AbstractThe effectors of the insect immune system are antimicrobial peptides. With the aim of studying the evolution of immune system genes, we identified a gene encoding the antimicrobial peptide defensin from a social insect, the wood ant Formica aquilonia. In this article we report the identification and characterization of this gene. We also compare the ant defensin gene structure to that previously obtained from two other hymenopteran species, the honeybee, Apis mellifera, and the bumblebee, Bombus ignitus. The ant defensin gene structure differs from both of these bee defensins with respect to the number and length of introns and exons.
Partial deletions of the W chromosome due to reciprocal translocation in the silkworm Bombyx mori
Authors: Abe H. , Seki M. , Ohbayashi F. , Tanaka N. , Yamashita J. , Fujii T. , Yokoyama T. , Takahashi M. , Banno Y. , Sahara K. , Yoshido A. , Ihara J. , Yasukochi Y. , Mita K. , Ajimura M. , Suzuki M. G. , Oshiki T. , Shimada T. 
Published: July 2005

AbstractIn the silkworm, Bombyx mori (female, ZW; male, ZZ), femaleness is determined by the presence of a single W chromosome, irrespective of the number of autosomes or Z chromosomes. The W chromosome is devoid of functional genes, except the putative female‐determining gene (Fem). However, there are strains in which chromosomal fragments containing autosomal markers have been translocated on to W. In this study, we analysed the W chromosomal regions of the Zebra‐W strain (T(W;3)Ze chromosome) and the Black‐egg‐W strain (T(W;10)+w−2 chromosome) at the molecular level. Initially, we undertook a project to identify W‐specific RAPD markers, in addition to the three already established W‐specific RAPD markers (W‐Kabuki, W‐Samurai and W‐Kamikaze). Following the screening of 3648 arbitrary 10‐mer primers, we obtained nine W‐specific RAPD marker sequences (W‐Bonsai, W‐Mikan, W‐Musashi, W‐Rikishi, W‐Sakura, W‐Sasuke, W‐Yukemuri‐L, W‐Yukemuri‐S and BMC1‐Kabuki), almost all of which contained the border regions of retrotransposons, namely portions of nested retrotransposons. We confirmed the presence of eleven out of twelve W‐specific RAPD markers in the normal W chromosomes of twenty‐five silkworm strains maintained in Japan. These results indicate that the W chromosomes of the strains in Japan are almost identical in type. The Zebra‐W strain (T(W;3)Ze chromosome) lacked the W‐Samurai and W‐Mikan RAPD markers and the Black‐egg‐W strain (T(W;10)+w−2 chromosome) lacked the W‐Mikan RAPD marker. These results strongly indicate that the regions containing the W‐Samurai and W‐Mikan RAPD markers or the W‐Mikan RAPD marker were deleted in the T(W;3)Ze and T(W;10)+w−2 chromosomes, respectively, due to reciprocal translocation between the W chromosome and the autosome. This deletion apparently does not affect the expression of Fem; therefore, this deleted region of the W chromosome does not contain the putative Fem gene.
SINE insertion polymorphism on the X chromosome differentiates Anopheles gambiae molecular forms
Authors: Barnes M. J. , Lobo N. F. , Coulibaly M. B. , Sagnon N′F. , Costantini C. , Besansky N. J. 
Published: July 2005

AbstractPolymorphic SINE insertions can be useful markers for assessing population structure and differentiation. Maque is a family of SINE elements which, based on bioinformatic analysis, was suggested to have been active recently in Anopheles gambiae, the major vector of malaria. Here, we report the development of polymorphic Maque insertions as population genetic markers in A. gambiae, and the use of these markers to better characterize divergence on the X chromosome between A. gambiae M and S molecular forms in populations from Burkina Faso and Mali. Our data are consistent with the recent activity of Maque. Phylogenetic analysis suggests that at least two recently active lineages may have a role in mediating genome evolution. We found differences in element insertion frequency and sequence between the M and S populations analysed. Significant differentiation was observed between these two groups across a 6 Mb region at the proximal (centromeric) end of the X chromosome. Locus‐specific FST values ranged from 0.14 to 1.00 in this region, yet were not significantly different from zero in more distal locations on the X chromosome; the trend was consistent in populations from both geographical locales suggesting that differentiation is not due to local adaptation. Strong differentiation between M and S at the proximal end of the X chromosome, but not outside this region, suggests the action of selection counteracting limited gene flow between these taxa and supports their characterization as incipient species.
Microarray analysis of genes showing variable expression following a blood meal in Anopheles gambiae
Authors: Marinotti O. , Nguyen Q. K. , Calvo E. , James A. A. , Ribeiro J. M. C. 
Published: July 2005

AbstractA microarray analysis of 14 900 genes of the malaria vector mosquito, Anopheles gambiae, shows that as many as 33% (4924) of their corresponding transcription products vary in abundance within 24 h after a blood meal. Approximately half (2388) of these products increase in their accumulation and the remainder (2536) decrease. Expression dynamics of 80% of the genes analysed by expressed sequence tag (EST) projects reported previously are consistent with the observations from this microarray analysis. Furthermore, the microarray analysis is more sensitive in detecting variation in abundance of gene products expressed at low levels and is more sensitive overall in that a greater number of regulated genes are detected. Major changes in transcript abundance were seen in genes encoding proteins involved in digestion, oogenesis and locomotion. The microarray data and an electronic hyperlinked version of all tables are available to the research community at http://www.angagepuci.bio.uci.edu/1/.
Molecular cloning, characterization and regulation of the cockroach vitellogenin receptor during oogenesis
Authors: Tufail M. , Takeda M. 
Published: July 2005

AbstractThe vitellogenin receptor (VgR) belongs to the low density lipoprotein receptor (LDLR) superfamily, and mediates the uptake of vitellogenin (Vg) into developing oocytes of all oviparous species. We cloned and characterized a VgR from previtellogenic ovaries of the cockroach, Periplaneta americana (Pa). This is the first report on a VgR from a hemimetabolous insect. The cDNA, comprising 5722 bp, encoded a 1790‐residue mature protein with a predicted molecular mass of 200.5 kDa. We next characterized the ovarian expression pattern, developmental regulation and cellular distribution of the VgR mRNA and protein. Northern blot analysis confirmed that a ∼7.2 kb transcript was specifically expressed in ovarian tissues at high levels throughout ovarian development, especially in previtellogenic ovaries and in ovaries before adult emergence. RNA in situ hybridization and immunocytochemistry localized the VgR mRNA and protein to germ‐line derived cells, the oocytes, and revealed that VgR gene transcription and translation begin very early during oocyte differentiation in the germarium. Immunoblot analysis detected an ovary‐specific VgR protein of ∼210 kDa that was present in previtellogenic ovaries on the day of female emergence. The VgR protein signal strengthened every day and was intense after initiation of vitellogenesis and onset of Vg uptake. The immunoblotting of vitellins demonstrated that Vg uptake occurred on day 5, one day after Vg first appeared in the haemolymph, indicating that the receptor‐endocytotic machinery starts functioning soon after the ligand becomes available.
Identification of candidate sialome components expressed in ixodid tick salivary glands using secretion signal complementation in mammalian cells
Authors: Lambson B. , Nene V. , Obura M. , Shah T. , Pandit P. , Ole‐MoiYoi O. , Delroux K. , Welburn S. , Skilton R. , De Villiers E. , Bishop R. 
Published: July 2005

AbstractIxodid ticks manipulate mammalian host pathways by secreting molecules from salivary glands. Novel cDNAs containing functional secretion signals were isolated from ixodid tick salivary glands using a signal sequence trap. Only 15/61Rhipicephalus appendiculatusand 1/7Amblyomma variegatumcDNAs had significant identity (< 1e‐15) to previously identified sequences. Polypeptides that may interact with host pathways included a kinase inhibitor. Two proteins encoded homologues of the yolk protein vitellogenin and seventeen contained glycine‐rich motifs. Four proteins without sequence matches had conserved structural folds, identified using a Threading algorithm. Predicted secretion signals were between fifteen and fifty‐seven amino acids long. Four homologous polymorphic proteins contained conserved (26/27 residues) signal peptides. Ten functional tick secretion signals could not be unambiguously identified using predictive algorithms.
Quantitative real‐time RT‐PCR analysis in desert locusts reveals phase dependent differences in neuroparsin transcript levels
Authors: Claeys I. , Simonet G. , Breugelmans B. , Van Soest S. , Franssens V. , Sas F. , De Loof A. , Vanden Broeck J. 
Published: July 2005

AbstractIn different parts of the world, locust swarms cause severe ecological and economic damage. However, the physiological mechanisms underlying this gregarization process remain elusive. In this study, we present a detailed quantitative analysis of two neuroparsin precursor (Scg‐NPP1 and Scg‐NPP2) transcripts in the brain, fat body, gut, gonads and accessory glands of male and female, gregarious and solitarious desert locusts (Schistocerca gregaria). These transcripts are generally more abundant in solitarious than in gregarious animals. In contrast to their gregarious congeners, solitarious locusts contain detectable Scg‐NPP1 and Scg‐NPP2 transcript levels in the fat body. Moreover, our data reveal temporal changes of neuroparsin mRNA levels in the brains and fat bodies of adult isolated‐reared locusts. This paper provides the first scientific evidence for phase‐dependent transcriptional regulation of neuropeptide hormone encoding genes.
Gene structure and expression profile of Manduca sexta prophenoloxidase‐activating proteinase‐3 (PAP‐3), an immune protein containing two clip domains
Authors: Zou Z. , Jiang H. 
Published: July 2005

AbstractProphenoloxidase‐activating proteinase‐3 (PAP‐3) is a component of the defence system in Manduca sexta. We have isolated genomic clones and elucidated the organization of this gene. The 3′ end of exon 2, the entire exon 3 and the 5′ end of exon 4 encode the two amino‐terminal clip domains. Southern blot analysis suggested a single copy of the PAP‐3 gene in the genome. We identified several putative immune‐responsive elements in the upstream region. The PAP‐3 gene is not highly expressed in the fat body during larval development until the wandering stage begins. The mRNA level is high in the epithelium, fat body and haemocytes. Tissue‐specific alternative splicing occurs in the fat body and trachea. A bacterial injection markedly induced the gene expression in the fat body and haemocytes.
Fertility, segregation at a herbicide‐resistance locus, and genome structure in BC1 hybrids from two important weedy Amaranthus species
Authors: TRUCCO F. , TATUM T. , RAYBURN A. L. , TRANEL P. J. 
Published: July 2005

AbstractField studies have established high potential for hybridization between two important and often coexisting weedy species, Amaranthus hybridus and Amaranthus tuberculatus. Prezygotic reproductive barriers between these species are believed to be limited to pollen competition and availability. A greenhouse study showed that a herbicide‐resistance gene (ALS) from A. hybridus could be introgressed into an advanced A. tuberculatus background (BC2). However, evidence is lacking in support of such transfer in nature. Postzygotic reproductive barriers may minimize, if not preclude, natural introgression. Indeed, A. hybridus ×A. tuberculatus hybrids are characterized by reduced fertility and even floral neuterism. The purpose of this study was to assess hybrid fertility in the BC1 generation and its relationship with genome structure and segregation at ALS. Fertility was assessed by measuring seed output and by pollen evaluation, and segregation at ALS was determined via a molecular marker system. The two parental species have the same ploidy (2n = 32) but differ in DNA content (2C) values, with A. tuberculatus chromosomes being on average 29% greater than those of A. hybridus. Given that most (98%) BC1s were homoploid, 2C values were used as indicators of relative genomic constitution. Fertility in the BC1 generation was greater than that of F1s, and 3% of BC1s had seed output similar to that of the parental species. Fertility in the BC1 did not correlate (in a strict way) with reconstitution of parental genomes. Hybrid sterility appeared to be controlled by relatively few loci. Heterozygosity at ALS was negatively correlated with fertility. Also, the A. tuberculatus ALS allele was not observed in the A. hybridus sexual condition, monoecism. Linkage of ALS to a locus associated (directly or via epistasis) with hybrid sterility may explain the fertility penalty observed with ALS introgression. Moreover, this linkage might explain why sequenced herbicide‐resistance ALS alleles from sympatric A. tuberculatus and A. hybridus populations show independent evolution.
Genomic tools and cDNA derived markers for butterflies
Authors: PAPANICOLAOU ALEXIE , JORON MATHIEU , MCMILLAN W. OWEN , BLAXTER MARK L. , JIGGINS CHRIS D. 
Published: July 2005

AbstractThe Lepidoptera have long been used as examples in the study of evolution, but some questions remain difficult to resolve due to a lack of molecular genetic data. However, as technology improves, genomic tools are becoming increasingly available to tackle unanswered evolutionary questions. Here we have used expressed sequence tags (ESTs) to develop genetic markers for two Müllerian mimic species,Heliconius melpomeneandHeliconius erato. In total 1363 ESTs were generated, representing 330 gene objects inH. melpomeneand 431 inH. erato. User‐friendly bioinformatic tools were used to construct a nonredundant database of these putative genes (available athttp://www.heliconius.org), and annotate them withblastsimilarity searches, InterPro matches and Gene Ontology terms. This database will be continually updated with EST sequences for the Papilionideae as they become publicly available, providing a tool for gene finding in the butterflies. Alignments of theHeliconiussequences with putative homologues derived fromBombyx morior other public data sets were used to identify conserved PCR priming sites, and develop 55 markers that can be amplified from genomic DNA in bothH. eratoandH. melpomene. These markers will be used for comparative linkage mapping inHeliconiusand will have applications in other phylogenetic and genomic studies in the Lepidoptera.
Recombination and speciation
Authors: BUTLIN ROGER K. 
Published: July 2005

AbstractSpeciation can be viewed as the evolution of restrictions on the freedom of genetic recombination: new combinations of alleles can be generated within species, but alleles from different species cannot be brought together. Recently, there has been increasing realization that the role of chromosomal rearrangements in speciation might be primarily a result of their influence on recombination. I argue that ideas about the role of recombination in speciation should be considered in the context of the variability of recombination rates and patterns more generally and that genic as well as chromosomal causes of restricted recombination should be considered. I review patterns of variation in recombination rates and theoretical progress in understanding the conditions that favour increased or decreased rates. Although progress has been made in understanding conditions that alter overall rates of recombination, widespread variation in patterns of recombination remains largely unexplained. I consider three models for the role of locally restricted recombination in speciation and the evidence currently supporting them.
How do misassigned paternities affect the estimation of heritability in the wild?
Authors: CHARMANTIER ANNE , RÉALE DENIS 
Published: July 2005

AbstractStudies of birds have recently played an important role in the increasing success of quantitative genetics applied to natural populations. However, these studies mostly base their pedigree relationships on social information, despite the known widespread genetic polygamy in avian species. Here, we study the influence of misassigned paternities, combined with the effect of pedigree size and depth, on the estimation of heritability. First, we compute simulations of a polygenic trait for two levels of heritability (0.1 and 0.4), several extra‐pair paternity rates (ranging from 5% to 40%), and varying sample sizes (20, 50 and 100 broods) or pedigree depth (2 or 4 generations). We compare heritability estimates from the social and the genetic pedigree, running a restricted maximum‐likelihood ‘animal model’. Social pedigree underestimates heritability by an average of 0–17% for 5–20% extra‐pair paternities and by up to 18% for 40% extra‐pair paternities and a heritability of 0.4. Second, we identifyied extra‐pair offspring using microsatellite loci in two populations of blue tits (Parus caeruleus) showing high levels of extra‐pair paternities (15% and 25% of extra‐pair offspring). We compare heritabilities of tarsus length and body mass estimated with pedigrees of increasing accuracy. These analyses suggest that the bias induced by misassigned paternities on heritability estimation depends on the level of heritability and the rate of paternity error. Typical rates of extra‐pair paternities in birds (around 20% of offspring) should result in an underestimation of heritability of less than 15% when estimated over a minimum of 100 broods.