bluuebunny/crossref_metadata_2025_split huggingface dataset:
Power and sample size for nested analysis of molecular variance
Authors: FITZPATRICK BENJAMIN M. 
Published: September 2009

AbstractAnalysis of molecular variance (amova) is a widely used tool for quantifying the contribution of various levels of population structure to patterns of genetic variation. Implementations of amova use permutation tests to evaluate null hypotheses of no population structure within groups and between groups. With few populations per group, between‐group structure might be impossible to detect because only a few permutations of the sampled populations are possible. In fact, with fewer than six total populations, permutation tests will never result in P‐values <0.05 for higher‐level population structure. I present minimum numbers of replicates calculated from multinomial coefficients and an r script that can be used to evaluate the minimum P‐value for any sampling scheme. While it might seem counterintuitive that a large sample of individuals is uninformative about hierarchical structure, the power to detect between‐group differences depends on the number of populations per group and investigators should sample appropriately.
The allopolyploidArabidopsis kamchaticaoriginated from multiple individuals ofArabidopsis lyrataandArabidopsis halleri
Authors: SHIMIZU‐INATSUGI RIE , LIHOVÁ JUDITA , IWANAGA HIROKO , KUDOH HIROSHI , MARHOLD KAROL , SAVOLAINEN OUTI , WATANABE KUNIAKI , YAKUBOV VALENTIN V. , SHIMIZU KENTARO K. 
Published: September 2009

AbstractPolyploidization, or genome duplication, has played a critical role in the diversification of animals, fungi and plants. Little is known about the population structure and multiple origins of polyploid species because of the difficulty in identifying multiple homeologous nuclear genes. The allotetraploid speciesArabidopsis kamchaticais closely related to the model speciesArabidopsis thalianaand is distributed in a broader climatic niche than its parental species. Here, we performed direct sequencing of homeologous pairs of the low‐copy nuclear genesWERandCHSby designing homeolog‐specific primers, and obtained also chloroplast and ribosomal internal transcribed spacer sequences. Phylogenetic analysis showed that 50 individuals covering the distribution range including North America are allopolyploids derived fromArabidopsis lyrataandArabidopsis halleri. Three major clusters withinA. kamchaticawere detected using Bayesian clustering. One cluster has widespread distribution. The other two are restricted to the southern part of the distribution range including Japan, where the parentA. lyratais not currently distributed. This suggests that the mountains in Central Honshu and surrounding areas in Japan served as refugia during glacial–interglacial cycles and retained this diversity. We also found that multiple haplotypes of nuclear and chloroplast sequences ofA. kamchaticaare identical to those of their parental species. This indicates that multiple diploid individuals contributed to the origin ofA. kamchatica. The haplotypes of low‐copy nuclear genes in Japan suggest independent polyploidization events rather than introgression. Our findings suggest that self‐compatibility and gene silencing occurred independently in different origins.
Molecular insights into the colonization and chromosomal diversification of Madeiran house mice
Authors: FÖRSTER D. W. , GÜNDÜZ İ. , NUNES A. C. , GABRIEL S. , RAMALHINHO M. G. , MATHIAS M. L. , BRITTON‐DAVIDIAN J. , SEARLE J. B. 
Published: September 2009

AbstractThe colonization history of Madeiran house mice was investigated by analysing the complete mitochondrial (mt) D‐loop sequences of 156 mice from the island of Madeira and mainland Portugal, extending on previous studies. The numbers of mtDNA haplotypes from Madeira and mainland Portugal were substantially increased (17 and 14 new haplotypes respectively), and phylogenetic analysis confirmed the previously reported link between the Madeiran archipelago and northern Europe. Sequence analysis revealed the presence of four mtDNA lineages in mainland Portugal, of which one was particularly common and widespread (termed the ‘Portugal Main Clade’). There was no support for population bottlenecks during the formation of the six Robertsonian chromosome races on the island of Madeira, and D‐loop sequence variation was not found to be structured according to karyotype. The colonization time of the Madeiran archipelago by Mus musculus domesticus was approached using two molecular dating methods (mismatch distribution and Bayesian skyline plot). Time estimates based on D‐loop sequence variation at mainland sites (including previously published data from France and Turkey) were evaluated in the context of the zooarchaeological record of M. m. domesticus. A range of values for mutation rate (μ) and number of mouse generations per year was considered in these analyses because of the uncertainty surrounding these two parameters. The colonization of Portugal and Madeira by house mice is discussed in the context of the best‐supported parameter values. In keeping with recent studies, our results suggest that mutation rate estimates based on interspecific divergence lead to gross overestimates concerning the timing of recent within‐species events.
Prevalence and diversity patterns of avian blood parasites in degraded African rainforest habitats
Authors: CHASAR ANTHONY , LOISEAU CLAIRE , VALKIŪNAS GEDIMINAS , IEZHOVA TATJANA , SMITH THOMAS B. , SEHGAL RAVINDER N. M. 
Published: September 2009

AbstractLand use changes including deforestation, road construction and agricultural encroachments have been linked to the increased prevalence of several infectious diseases. In order to better understand how deforestation affects the prevalence of vector‐borne infectious diseases in wildlife, nine paired sites were sampled (disturbed vs. undisturbed habitats) in Southern Cameroon. We studied the diversity, prevalence and distribution of avian malaria parasites (Plasmodium spp.) and other related haemosporidians (species of Haemoproteus and Leucocytozoon) from these sites in two widespread species of African rainforest birds, the yellow‐whiskered greenbul (Andropadus latirostris, Pycnonotidae) and the olive sunbird (Cyanomitra olivacea, Nectariniidae). Twenty‐six mitochondrial cytochrome b lineages were identified: 20 Plasmodium lineages and 6 Haemoproteus lineages. These lineages showed no geographic specificity, nor significant differences in lineage diversity between habitat types. However, we found that the prevalence of Leucocytozoon and Haemoproteus infections were significantly higher in undisturbed than in deforested habitats (Leucocytozoon spp. 50.3% vs. 35.8%, Haemoproteus spp. 16.3% vs. 10.8%). We also found higher prevalence for all haemosporidian parasites in C. olivacea than in A. latirostris species (70.2% vs. 58.2%). Interestingly, we found one morphospecies of Plasmodium in C. olivacea, as represented by a clade of related lineages, showed increased prevalence at disturbed sites, while another showed a decrease, testifying to different patterns of transmission, even among closely related lineages of avian malaria, in relation to deforestation. Our work demonstrates that anthropogenic habitat change can affect host–parasite systems and result in opposing trends in prevalence of haemosporidian parasites in wild bird populations.
Population genetic analysis reveals a homoploid hybrid origin ofStephanomeria diegensis(Asteraceae)
Authors: SHERMAN NATASHA A. , BURKE JOHN M. 
Published: September 2009

AbstractHomoploid hybrid speciation has generally been viewed as a rare evolutionary phenomenon, with relatively few well‐documented cases in nature. Here, we investigate the origin ofStephanomeria diegensis, a diploid flowering plant species that has been proposed to have arisen as a result of hybridization betweenS. exiguaandS. virgata. Across the range ofS. diegensis, all individuals share a common chloroplast haplotype withS. virgatawhile showing a greater affinity forS. exiguain terms of nuclear genetic diversity. A prinicipal coordinates analysis (PCO) based on the nuclear data revealed thatS. diegensisis most similar to each parent along different axes. Moreover, a Bayesian clustering analysis as well as a hybrid index‐based analysis showed evidence of mixed ancestry, with approximately two thirds of theS. diegensisnuclear genome derived fromS. exigua. These results provide strong support for a homoploid hybrid origin ofS. diegensis. Finally, contrary to the finding that homoploid hybrid species are typically multiply‐derived, our results were most consistent with a single origin of this species.
Parallel evolution in the major haemoglobin genes of eight species of Andean waterfowl
Authors: McCRACKEN K. G. , BARGER C. P. , BULGARELLA M. , JOHNSON K. P. , SONSTHAGEN S. A. , TRUCCO J. , VALQUI T. H. , WILSON R. E. , WINKER K. , SORENSON M. D. 
Published: September 2009

AbstractTheory predicts that parallel evolution should be common when the number of beneficial mutations is limited by selective constraints on protein structure. However, confirmation is scarce in natural populations. Here we studied the major haemoglobin genes of eight Andean duck lineages and compared them to 115 other waterfowl species, including the bar‐headed goose (Anser indicus) and Abyssinian blue‐winged goose (Cyanochen cyanopterus), two additional species living at high altitude. One to five amino acid replacements were significantly overrepresented or derived in each highland population, and parallel substitutions were more common than in simulated sequences evolved under a neutral model. Two substitutions evolved in parallel in the αA subunit of two (Ala‐α8) and five (Thr‐α77) taxa, and five identical βA subunit substitutions were observed in two (Ser‐β4, Glu‐β94, Met‐β133) or three (Ser‐β13, Ser‐β116) taxa. Substitutions at adjacent sites within the same functional protein region were also observed. Five such replacements were in exterior, solvent‐accessible positions on the A helix and AB corner of the αA subunit. Five others were in close proximity to inositolpentaphosphate binding sites, and two pairs of independent replacements occurred at two different α1β1intersubunit contacts. More than half of the substitutions in highland lineages resulted in the acquisition of serine or threonine (18 gains vs. 2 losses), both of which possess a hydroxyl group that can hydrogen bond to a variety of polar substrates. The patterns of parallel evolution observed in these waterfowl suggest that adaptation to high‐altitude hypoxia has resulted from selection on unique but overlapping sets of one to five amino acid substitutions in each lineage.
Phenotypic heterogeneity in expression of epitopes in the Cryptococcus neoformans capsule
Authors: Gates‐Hollingsworth Marcellene A. , Kozel Thomas R. 
Published: September 2009

SummaryThe opportunistic yeast Cryptococcus neoformans is surrounded by a polysaccharide capsule comprised primarily of glucuronoxylomannan (GXM). GXM is a key component of the antigenic character of the capsule. Expression of the epitope that allows for binding of mAbs that require O‐acetylation of GXM for mAb recognition was greatly influenced by cell age, growth conditions and serotype. Yeast cells of serotype A grown in vitro under capsule induction conditions showed considerable cell‐to‐cell variability in binding of two O‐acetyl‐dependent mAbs, and such mAbs uniformly failed to bind to GXM that covers yeast buds. Expression of the O‐acetyl‐dependent epitope increased with cell age. In contrast, all serotype A cells harvested from brain tissue bound the same O‐acetyl‐dependent mAbs. The ability of the cryptococcal capsule to activate the complement cascade and bind C3 occurred uniformly over the surface of all yeast cells, including the bud. Finally, the cell‐to‐cell variability in binding of O‐acetyl‐dependent mAbs with strains of serotype A was not found with strains of serotype D; almost all cells of serotype D showed homogeneous binding of O‐acetyl‐dependent mAbs. These results indicate that variability in expression of antigenic epitopes by GXM should be considered in selection of mAbs used for immunodiagnosis or immunotherapy.
The Great Barrier Reef: a 700 000 year diagenetic history
Authors: BRAITHWAITE COLIN J. R. , MONTAGGIONI LUCIEN F. 
Published: September 2009

AbstractA deep borehole through Ribbon Reef 5 in the Great Barrier Reef off north‐eastern Australia has identified a variety of cements, including epitaxial, radial prismatic and spherular aragonite, together with blocky, prismatic and fibrous calcite. These cements are discontinuously arranged within the sequence that consists predominantly of grainstones but locally includes clotted muddy and filamentous textures that may be of microbial origin. Calcite cements vary in morphology with groups of crystals that include acute scalenohedral, rhombohedral and flattened concordant terminations; these show varying densities of inclusions that locally define growth zones and in some terminations divide in the manner of ‘split crystals’ to form fibrous fringes. Morphological changes in calcite are inferred to reflect changes in water chemistry and crystal growth rates at the time of growth, allied to their relationship to the palaeo‐water table, and linked in turn to changes in sea‐level. Neomorphism and dissolution are widespread and variations in the severity of both imply response to the degree of undersaturation of pore waters that at times were probably balanced within very narrow limits. A total of 10 depositional units are identified. Those units at the base of the borehole reflect deposition and diagenesis within a marine environment. The influence of meteoric waters, indicated by stable isotopes, is first apparent at the top of Unit 1 and in Unit 2 (184 to 155 m below sea floor). Petrographic evidence of vadose conditions appears at the tops of Unit 3 (131 to 99 m below sea floor). Units 4 to 8, all deposited under marine conditions, provide isotopic evidence of meteoric or mixing‐zone waters and petrographic indicators of vadose conditions, typically at the top of the units. Evidence indicates that in Unit 5 the water table was mobile and Units 6a, 6b, 7 and 8, all characterized by ultraviolet fluorescent cements, are capped by sub‐aerial erosion surfaces. Unit 9 (the Holocene) reflects the recent re‐establishment of marine conditions. The extent of alteration of the entire sequence reflects the substantial and pervasive influence of meteoric waters. This effect is interpreted as a result of a greater rainfall and river flow from the mainland during early and late stages of interstadial periods. The study reflects progress in the ability to recognize the diagenetic signal generated by sea‐level change. However, whereas the isotopic results reflect the changing relationships between vadose and phreatic zones in groundwater systems beneath successive emergent surfaces, their correspondence with petrographic features is expressed only weakly and commonly lacks the systematic sequential overprinting implied by the distribution of cathodoluminescent zones of cements in many ancient limestones.
Impact of the shift from NCHS growth reference to WHO2006 growth standards in a therapeutic feeding programme in Niger
Authors: Minetti A. , Shams Eldin M. , Defourny I. , Harczi G. 
Published: September 2009

SummaryObjectives  To describe the implementation of the WHO2006 growth standards in a therapeutic feeding programme.Methods  Using programme monitoring data from 21 769 children 6–59 months admitted to the Médecins Sans Frontières therapeutic feeding programme during 2007, we compared characteristics at admission, type of care and outcomes for children admitted before and after the shift to the WHO2006 standards. Admission criteria were bipedal oedema, MUAC <110 mm, or weight‐for‐height (WFH) of <‐70% of the median (NCHS) before mid‐May 2007, and WFH <‐3 z score (WHO2006) after mid‐May 2007.Results  Children admitted with the WHO2006 standards were more likely to be younger, with a higher proportion of males, and less malnourished (mean WFH ‐3.6 z score vs. mean WFH ‐4.6 z score). They were less likely to require hospitalization or intensive care (28.4%vs. 77%; 12.8%vs. 36.5%) and more likely to be treated exclusively on an outpatient basis (71.6%vs. 23%). Finally, they experienced better outcomes (cure rate: 89%vs. 71.7%, death rate: 2.7%vs. 6.4%, default rate: 6.7%vs. 12.3%).Conclusions  In this programme, the WHO2006 standards identify a larger number of malnourished children at an earlier stage of disease facilitating their treatment success.
CD14 polymorphisms in mother and infant, soluble CD14 in breast milk and atopy development in the infant (KOALA Study)
Authors: Snijders Bianca E. P. , Stelma Foekje F. , Reijmerink Naomi E. , Thijs Carel , Van Der Steege Gerrit , Damoiseaux Jan G. M. C. , Van Den Brandt Piet A. , Van Ree Ronald , Postma Dirkje S. , Koppelman Gerard H. 
Published: September 2009

Snijders BEP, Stelma FF, Reijmerink NE, Thijs C, van der Steege G, Damoiseaux JGMC, van den Brandt PA, van Ree R, Postma DS, Koppelman GH. CD14 polymorphisms in mother and infant, soluble CD14 in breast milk and atopy development in the infant (KOALA Study). Pediatr Allergy Immunol 2010: 21: 541–549. © 2009 John Wiley & Sons A/SDifferent CD14 polymorphisms have been associated with atopic phenotypes in infants. In addition, CD14 genotypes of breastfeeding mothers have been associated with soluble CD14 (sCD14) levels in breast milk. The role of CD14 genotypes of infant and mother and their interaction with sCD14 levels in breast milk in atopy development remain to be established. We aimed to study the associations of CD14 single nucleotide polymorphisms (SNPs), and their interaction with breast milk sCD14, with atopy development until age two. In addition, we assessed whether levels of sCD14 in breast milk associated with SNPs in CD14. Four SNPs in CD14 gene were investigated in 698 infants and 188 mothers. Associations between these SNPs, sCD14 and atopy development were analyzed in multiple logistic or linear regression models. The CD14/‐1619 SNP was associated with eczema. CC homozygotes showed a lower risk of eczema vs. TT homozygotes (adjusted odds ratio = 0.56, 95% confidence interval 0.33–0.96) in a co‐dominant model. Breast milk sCD14 levels did not significantly modify the effect of the child’s CD14 genotype on atopy development (p interaction ≥0.10). Maternal CD14 SNPs were not significantly associated with sCD14 levels in breast milk (anova, p ≥ 0.48). We found only an association between CC homozygozity of SNP CD14/‐1619 and eczema. Our data did not support a modifying role of breast milk sCD14 levels on the relationship between CD14 genotype and atopy development until age 2 yr.
Diversity of the Vocal Signals of Concave‐Eared Torrent Frogs (Odorrana tormota): Evidence for Individual Signatures
Authors: Feng Albert S. , Riede Tobias , Arch Victoria S. , Yu Zulin , Xu Zhi‐Min , Yu Xin‐Jian , Shen Jun‐Xian 
Published: September 2009

AbstractMale concave‐eared torrent frogs (Odorrana tormota) have an unusually large call repertoire and have been shown to communicate ultrasonically. We investigated the individual specificity of male advertisement calls in order to explore the acoustic bases of individual recognition, which was demonstrated in an accompanying study. Vocalizations of 15 marked males were recorded in the field. A quantitative analysis of the signals revealed eight basic call‐types. Two of them (the single‐ and multi‐note long‐calls) were investigated in more detail. Long‐calls were characterized by pronounced and varying frequency modulation patterns, and abundant occurrence of nonlinear phenomena (NLP), i.e., frequency jumps, subharmonics, biphonations and deterministic chaos. The occurrence of NLP was predictable from the contour of the fundamental frequency in the harmonic segment preceding the onset of the NLP, and this prediction showed individual‐specific patterns. Fifteen acoustic variables of the long calls were measured, all of which were significantly different among individuals, except biphonic segment duration. Discriminant function analysis (DFA) showed that 54.6% of the calls could be correctly assigned to individual frogs. The correct classification was above chance level, suggesting that individual specificity of calls underlie the ability of males to behaviorally discriminate the vocal signals of their neighbors from those of strangers, a remarkable feat for a frog species with a diverse vocal repertoire. The DFA classification results were lower than those for other anurans, however. We hypothesize that there is a tradeoff between an increase in the fundamental frequency of vocalizations to avoid masking by low‐frequency ambient background noise, and a decrease in individual‐specific vocal tract information extractable from the signal.
Diverging Cave‐ and River‐Dwelling Newts Exert the Same Mate Preference in their Native Light Conditions
Authors: Dreiss Amélie N. , Guillaume Olivier , Clobert Jean 
Published: September 2009

AbstractWhen colonizing a new habitat, populations must adapt their sexual behaviour to new ecological constraints. Because caves display drastically different conditions from surface habitats and cave animals are deprived from visual information, hypogean populations are expected to have modified their mate preference and signalling behaviour after cave colonization. Here, we experimentally examined the female preference and the sexual behaviour of brook newts Calotriton asper from different cave and river populations, either in light or in darkness. Our results suggest that females prefer large individuals in both hypogean and epigean populations, but that this preference is only expressed in the light conditions of their native habitat. Hence, some mate choice criteria would be maintained across genetically divergent populations and throughout dissimilar habitats. However, this sexual behaviour is likely to be expressed via a different sensory pathway in the different habitats, suggesting that a sensory shift has occurred in cave populations, enabling animals to communicate through a non‐visual channel.
Facultative Adjustment of Brood Sex Ratio in Response to Indirect Manipulation of Behaviour
Authors: Johannessen Lars Erik , Kristiansen Lena , Hansen Bo Terning , Slagsvold Tore 
Published: September 2009

AbstractSex allocation theory states that parents should adjust their offspring sex ratio according to the expected fitness returns from sons and daughters. Several recent studies indicate that such adaptive manipulation of offspring sex ratio is achievable, and that it may be influenced by e.g. morphological characters. Here we manipulate behaviour through interspecific cross‐fostering of great tits (Parus major) and blue tits (Cyanistes caeruleus), and investigate its effect on the offspring sex ratio of adults that were themselves cross‐fostered as chicks. The experience of being raised by a different species has previously been shown to result in aberrant species assortative behaviour and song, and a lowered dominance status during winter. Brood sex ratios of conspecifically breeding pairs with and without cross‐fostered members were compared. Broods with at least one cross‐fostered parent contained significantly more males than did control broods. Sex of cross‐fostered parents did not influence the brood sex ratio. We conclude that female great tits and blue tits seem to be able to adjust the sex ratio of their broods, and that changes in their own or their partners’ behaviour may elicit such adjustments.