bluuebunny/crossref_metadata_2025_split huggingface dataset:
Selection outweighs drift at a fine scale: Lack of MHC differentiation within a family living lizard across geographically close but disconnected rocky outcrops
Authors: Pearson Sarah K. , Bull C. Michael , Gardner Michael G. 
Published: March 2018

AbstractThe highly polymorphic genes of the major histocompatibility complex (MHC) are involved in disease resistance, mate choice and kin recognition. Therefore, they are widely used markers for investigating adaptive variation. Although selection is the key driver, gene flow and genetic drift also influence adaptive genetic variation, sometimes in opposing ways and with consequences for adaptive potential. To further understand the processes that generate MHC variation, it is helpful to compare variation at the MHC with that at neutral genetic loci. Differences in MHC and neutral genetic variation are useful for inferring the relative influence of selection, gene flow and drift on MHC variation. To date, such investigations have usually been undertaken at a broad spatial scale. Yet, evolutionary and ecological processes can occur at a fine spatial scale, particularly in small or fragmented populations. We investigated spatial patterns of MHC variation among three geographically close, naturally discrete, sampling sites of Egernia stokesii, an Australian lizard. The MHC of E. stokesii has recently been characterized, and there is evidence for historical selection on the MHC. We found E. stokesii MHC weakly differentiated among sites compared to microsatellites, suggesting selection, acting similarly at each site, has outweighed any effects of low gene flow or of genetic drift on E. stokesii MHC variation. Our findings demonstrate the strength of selection in shaping patterns of MHC variation or consistency at a fine spatial scale.
Comparisons of behavioural and TRPA1 heat sensitivities in three sympatric Cuban Anolis lizards
Authors: Akashi Hiroshi D. , Saito Shigeru , Cádiz Díaz Antonio , Makino Takashi , Tominaga Makoto , Kawata Masakado 
Published: March 2018

AbstractThermal tolerances of organisms play a role in defining geographic ranges and occurrence of species. In Cuba, three sympatric species of Anolis lizards (Anolis allogus, Anolis homolechis and Anolis sagrei) inhabit different thermal microhabitats. A previous study found that these species showed distinct gene expression patterns in response to temperature stimuli, suggesting the genetically distinct thermal physiology among species. To investigate whether the Anolis species inhabiting locally distinct thermal habitats diverge their thermal tolerances, we first conducted behavioural experiments to analyse the temperatures at which the three Anolis species escape from heat source. Then, for each of the three species, we isolated cDNA encoding a putative molecular heat sensor, transient receptor potential ion channel ankyrin 1 (TRPA1), which has been suggested to play a role on eliciting behavioural responses to heat stimuli. We performed electrophysiological analysis to quantify activation temperature of Anolis TRPA1 to see whether the pattern of divergence in TRPA1 responses is congruent with that of divergence in behavioural responses. We found that temperatures triggering behavioural and TRPA1 responses were significantly lower for shade‐dwelling species (A. allogus) than for sun‐dwelling species (A. homolechis and A. sagrei). The ambient temperature of shade habitats where A. allogus occurs stays relatively cool compared to that of open habitats where A. homolechis and A. sagrei occur and bask. The high temperature thresholds of A. homolechis and A. sagrei may reflect their heat tolerances that would benefit these species to inhabit the open habitats.
Diversification of African tree frogs (genus Leptopelis) in the highlands of Ethiopia
Authors: Reyes‐Velasco Jacobo , Manthey Joseph D. , Freilich Xenia , Boissinot Stéphane 
Published: March 2018

AbstractThe frog genus Leptopelis is composed of ~50 species that occur across sub‐Saharan Africa. The majority of these frogs are typically arboreal; however, a few species have evolved a fossorial lifestyle. Most species inhabit lowland forests, but a few species have adapted to high elevations. Five species of Leptopelis occupy the Ethiopian highlands and provide a good opportunity to study the evolutionary transition from an arboreal to a fossorial lifestyle, as well as the diversification in this biodiversity hot spot. We sequenced 14 nuclear and three mitochondrial genes, and generated thousands of SNPs from ddRAD sequencing to study the evolutionary relationships of Ethiopian Leptopelis. The five species of highland Leptopelis form a monophyletic group, which diversified during the late Miocene and Pliocene. We found strong population structure in the fossorial species L. gramineus, with levels of genetic differentiation between populations similar to those found between arboreal species. This could indicate that L. gramineus is a complex of cryptic species. We propose that after the original colonization of the Ethiopian highlands by the ancestor of the L. gramineus group, episodes of vicariance fragmented the ancestral populations of this group. We also report the re‐evolution of arboreality in L. susanae, which evolved from a fossorial ancestor, a rare ecological switch in frogs that had previously been reported only once.
Genetic footprints of adaptive divergence in the bracovirus of Cotesia sesamiae identified by targeted resequencing
Authors: Gauthier Jérémy , Gayral Philippe , Le Ru Bruno Pierre , Jancek Séverine , Dupas Stéphane , Kaiser Laure , Gyapay Gabor , Herniou Elisabeth A. 
Published: March 2018

AbstractThe African parasitoid wasp Cotesia sesamiae is a generalist species structured in locally adapted populations showing differences in host range. The recent discovery of Cotesia typhae, a specialist, sister species to C. sesamiae, provides a good framework to study the genetic determinants of parasitoid host range. To investigate the genomic bases of divergence between these populations and species, we used a targeted sequencing approach on 24 samples. We targeted the bracovirus genomic region encoding virulence genes involved in the interaction with the lepidopteran hosts of the wasps. High sequencing coverage was obtained for all samples, allowing the study of genetic variation between wasp populations and species. By combining population genetic estimations, such as nucleotide diversity (π), relative differentiation (FST) and absolute divergence (dxy), with branch‐site dN/dS measures, we identified six of 98 bracovirus genes showing significant divergence and evidence of positive selection. These genes, belonging to different gene families, are potentially involved in host adaptation and in the specialization process. Fine‐scale analyses of genetic variation also revealed mutations and large deletions in certain genes inducing pseudogenization and loss of function. The image emerging from these results is that adaptation mediated by bracovirus genes happens through selection of particularly adaptive alleles and loss of nonadaptive genes. These results highlight the central role of the bracovirus in the molecular interactions between the wasps and their hosts and in the evolutionary processes of specialization.
Soil abiotic variables are more important than Salicaceae phylogeny or habitat specialization in determining soil microbial community structure
Authors: Erlandson Sonya , Wei Xiaojing , Savage Jessica , Cavender‐Bares Jeannine , Peay Kabir 
Published: March 2018

AbstractPredicting the outcome of interspecific interactions is a central goal in ecology. The diverse soil microbes that interact with plants are shaped by different aspects of plant identity, such as phylogenetic history and functional group. Species interactions may also be strongly shaped by abiotic environment, but there is mixed evidence on the relative importance of environment, plant identity and their interactions in shaping soil microbial communities. Using a multifactor, split‐plot field experiment, we tested how hydrologic context, and three facets of Salicaceae plant identity—habitat specialization, phylogenetic distance and species identity—influence soil microbial community structure. Analysis of microbial community sequencing data with generalized dissimilarity models showed that abiotic environment explained up to 25% of variation in community composition of soil bacteria, fungi and archaea, while Salicaceae identity influenced <1% of the variation in community composition of soil microbial taxa. Multivariate linear models indicated that the influence of Salicaceae identity was small, but did contribute to differentiation of soil microbes within treatments. Moreover, results from a microbial niche breadth analysis show that soil microbes in wetlands have more specialized host associations than soil microbes in drier environments—showing that abiotic environment changed how plant identity correlated with soil microbial communities. This study demonstrates the predominance of major abiotic factors in shaping soil microbial community structure; the significance of abiotic context to biotic influence on soil microbes; and the utility of field experiments to disentangling the abiotic and biotic factors that are thought to be most essential for soil microbial communities.
Co‐evolution with recombination affects the stability of mobile genetic element insertions within gene families of Salmonella
Authors: Brandis Gerrit , Cao Sha , Hughes Diarmaid 
Published: March 2018

SummaryBacteria can have multiple copies of a gene at separate locations on the same chromosome. Some of these gene families, including tuf (translation elongation factor EF‐Tu) and rrl (ribosomal RNA), encode functions critically important for bacterial fitness. Genes within these families are known to evolve in concert using homologous recombination to transfer genetic information from one gene to another. This mechanism can counteract the detrimental effects of nucleotide sequence divergence over time. Whether such mechanisms can also protect against the potentially lethal effects of mobile genetic element insertion is not well understood. To address this we constructed two different length insertion cassettes to mimic mobile genetic elements and inserted these into various positions of the tuf and rrl genes. We measured rates of recombinational repair that removed the inserted cassette and studied the underlying mechanism. Our results indicate that homologous recombination can protect the tuf and rrl genes from inactivation by mobile genetic elements, but for insertions within shorter gene sequences the efficiency of repair is very low. Intriguingly, we found that physical distance separating genes on the chromosome directly affects the rate of recombinational repair suggesting that relative location will influence the ability of homologous recombination to maintain homogeneity.
Regulons and protein–protein interactions of PRD‐containing Bacillus anthracis virulence regulators reveal overlapping but distinct functions
Authors: Raynor Malik J. , Roh Jung‐Hyeob , Widen Stephen G. , Wood Thomas G. , Koehler Theresa M. 
Published: March 2018

SummaryBacillus anthracis produces three regulators, AtxA, AcpA and AcpB, which control virulence gene transcription and belong to an emerging class of regulators termed ‘PCVRs’ (Phosphoenolpyruvate‐dependent phosphotransferase regulation Domain‐Containing Virulence Regulators). AtxA, named for its control of toxin gene expression, is the master virulence regulator and archetype PCVR. AcpA and AcpB are less well studied. Reports of PCVR activity suggest overlapping function. AcpA and AcpB independently positively control transcription of the capsule biosynthetic operon capBCADE, and culture conditions that enhance AtxA level or activity result in capBCADE transcription in strains lacking acpA and acpB. We used RNA‐Seq to assess the regulons of the paralogous regulators in strains constructed to express individual PCVRs at native levels. Plasmid and chromosome‐borne genes were PCVR controlled, with AtxA, AcpA and AcpB having a ≥ 4‐fold effect on transcript levels of 145, 130 and 49 genes respectively. Several genes were coregulated by two or three PCVRs. We determined that AcpA and AcpB form homomultimers, as shown previously for AtxA, and we detected AtxA‐AcpA heteromultimers. In co‐expression experiments, AcpA activity was reduced by increased levels of AtxA. Our data show that the PCVRs have specific and overlapping activity and that PCVR stoichiometry and potential heteromultimerization can influence target gene expression.
Distribution and abundance of beaked whales (Family Ziphiidae) Off Cape Hatteras, North Carolina, U.S.A.
Authors: McLellan William A. , McAlarney Ryan J. , Cummings Erin W. , Read Andrew J. , Paxton Charles G. M. , Bell Joel T. , Pabst D. Ann 
Published: March 2018

AbstractBeaked whales are vulnerable to the impacts of disturbance from several sources of anthropogenic sound. Here we report the distribution and abundance of beaked whales off Cape Hatteras, North Carolina, U.S.A., an area utilized by the U.S. Navy for training exercises, and of particular interest for seismic geophysical surveys. From May 2011 through November 2015, monthly aerial surveys were conducted at the site. Beaked whales were encountered 74 times (n = 205 individuals) during these surveys.Ziphius cavirostris, the most commonly encountered species, was observed in every month of the year.Mesoplodonspp. were encountered in ten months of the year. Photographs of adult males with erupted teeth permitted six sightings to be identified conclusively asM. europaeus;M. miruswas also photographed just outside the study area. Beaked whale surface densities stratified by depth (0.005–0.007/km2) were among the highest reported in the world for small ziphiids. A quantitative comparison of sightings and stranding records suggests that strandings do not accurately reflect the relative abundance of beaked whale species in this area. We conclude that Cape Hatteras, at the convergence of the Labrador Current and Gulf Stream, is a particularly important year‐round habitat for several species of beaked whales.
The status of Demodex cornei: description of the species and developmental stages, and data on demodecid mites in the domestic dog Canis lupus familiaris
Authors: Izdebska J. N. , Rolbiecki L. 
Published: March 2018

AbstractDemodecosis canina is one of the most important dog parasitoses, but its aetiology is still not well known. There are currently two known species of demodecid mite specific to the domestic dog Canis lupus familiaris Linnaeus, 1758 (Carnivora: Canidae). These are Demodex canis Leydig, 1859 (Acariformes: Demodecidae) and Demodex injai Desch & Hillier, 2003. There have also been many reports of the so‐called ‘short form’, considered to be a separate species functioning under the name Demodex cornei nomen nudum, for which, however, no formal valid description has been documented. Taxonomic analysis of short forms of dog demodecid mites, associated with the stratum corneum, was performed, in line with the taxonomic criteria of Demodecidae systematics. This form was found to be a distinct species with features that differ from those of the other known species of this family. The species, including the adult and immature stages, is described. It is likely that different Demodex species parasitizing the domestic dog may be responsible for differentiated symptoms and different courses of demodecosis. However, the basis for clarifying this issue should be the correct, unambiguous identification of the species causing parasitosis.
On God in Lacan: A Response to Tina Beattie
Authors: Dalzell Thomas 
Published: March 2018

AbstractTina Beattie has re-read Aquinas in the light of Lacanian theory and found the later Lacan's transition to what he calls the register of “the Real” to be significant for a revitalised theology beyond traditional intellectual categories. She argues for a maternal Trinity which she believes to lie hidden in Thomas and, in support of this, she contends that Lacan left behind Freud's paternal preoccupations in favour of maternity. This response to Beattie will re-examine Lacan's trajectory from “the Symbolic” register to “the Real” through the lens of what he said in his year-long seminars about Moses, whom he regarded as a representative of “the Symbolic”, and it will demonstrate that paternity remained a constant in Lacan, who even came to see “the Real” itself as a name of the father.
Francisco Suárez and His Sources on the Gift of Tongues
Authors: Salas Victor 
Published: March 2018

AbstractThis paper considers the grace of the gift of tongues both as it is currently practiced among many members of the Catholic Charismatic Renewal (CCR) and how it has traditionally been understood in medieval and post-medieval theology. The paper especially considers the perspective of Francisco Suárez on the subject insofar as he, as in most matters, is able to frame the status quaestionis of the topic and presents a uniform view of the Catholic theological tradition's understanding of the gift. Ultimately, I point out that there are significant points of divergence between the nature of this gift as the CCR understands and practices it and as it has traditionally been understood historically.
Phylogenomic analyses reveal a deep history of hybridization and polyploidy in the Neotropical genus Lachemilla (Rosaceae)
Authors: Morales‐Briones Diego F. , Liston Aaron , Tank David C. 
Published: March 2018

Summary

Hybridization, incomplete lineage sorting, and phylogenetic error produce similar incongruence patterns, representing a great challenge for phylogenetic reconstruction. Here, we use sequence capture data and multiple species tree and species network approaches to resolve the backbone phylogeny of the Neotropical genus Lachemilla, while distinguishing among sources of incongruence.

We used 396 nuclear loci and nearly complete plastome sequences from 27 species to clarify the relationships among the major groups of Lachemilla, and explored multiple sources of conflict between gene trees and species trees inferred with a plurality of approaches.

All phylogenetic methods recovered the four major groups previously proposed for Lachemilla, but species tree methods recovered different topologies for relationships between these four clades. Species network analyses revealed that one major clade, Orbiculate, is likely of ancient hybrid origin, representing one of the main sources of incongruence among the species trees. Additionally, we found evidence for a potential whole genome duplication event shared by Lachemilla and allied genera.

Lachemilla shows clear evidence of ancient and recent hybridization throughout the evolutionary history of the group. Also, we show the necessity to use phylogenetic network approaches that can simultaneously accommodate incomplete lineage sorting and gene flow when studying groups that show patterns of reticulation.
Rare genotype advantage promotes survival and genetic diversity of a tropical palm
Authors: Browne Luke , Karubian Jordan 
Published: March 2018

Summary

Negative density dependence, where survival decreases as density increases, is a well‐established driver of species diversity at the community level, but the degree to which a similar process might act on the density or frequency of genotypes within a single plant species to maintain genetic diversity has not been well studied in natural systems.

In this study, we determined the maternal genotype of naturally dispersed seeds of the palm Oenocarpus bataua within a tropical forest in northwest Ecuador, tracked the recruitment of each seed, and assessed the role of individual‐level genotypic rarity on survival.

We demonstrate that negative frequency‐dependent selection within this species conferred a survival advantage to rare maternal genotypes and promoted population‐level genetic diversity. The strength of the observed rare genotype survival advantage was comparable to the effect of conspecific density regardless of genotype.

These findings corroborate an earlier, experimental study and implicate negative frequency‐dependent selection of genotypes as an important, but currently underappreciated, determinant of plant recruitment and within‐species genetic diversity. Incorporating intraspecific genetic variation into studies and theory of forest dynamics may improve our ability to understand and manage forests, and the processes that maintain their diversity.
Steal the light: shade vs fire adapted vegetation in forest–savanna mosaics
Authors: Charles‐Dominique Tristan , Midgley Guy F. , Tomlinson Kyle W. , Bond William J. 
Published: March 2018

Summary

Shade cast by trees, which suppresses grass growth, and fire fuelled by grass biomass, which prevents tree sapling establishment, are mutually exclusive and self‐reinforcing drivers of biome distribution in savanna–forest mosaics.

We investigated how shade depth, represented by canopy leaf area index (LAI), is generated by adult trees across savanna–forest boundaries and how a shade gradient filters tree functioning, and grass composition and biomass.

Forest trees exerted greater shading through increased stem density and greater light interception per unit biomass. A critical transition at LAI c. 1.5 was linked to tree shifts from savanna to forest species, functional shifts from fire‐tolerant to light‐competitive species, and grass composition shifts from C4 to C3 pathways. A second transition to grass fuel loads too low to support fires, occurred at a lower canopy density (LAI > 0.5), accompanied by shifts in C4 subtype dominance.

This pattern suggests that shade suppression of grass biomass is an essential first step for the maintenance of alternative stable states.
Biodiversity of arbuscular mycorrhizal fungi and ecosystem function
Authors: Powell Jeff R. , Rillig Matthias C. 
Published: March 2018

Contents

Summary
1059

I.
Introduction: pathways of influence and pervasiveness of effects
1060

II.
AM fungal richness effects on ecosystem functions
1062

III.
Other dimensions of biodiversity
1062

IV.
Back to basics – primary axes of niche differentiation by AM fungi
1066

V.
Functional diversity of AM fungi – a role for biological stoichiometry?
1067

VI.
Past, novel and future ecosystems
1068

VII.
Opportunities and the way forward
1071

Acknowledgements
1072

References
1072

SummaryArbuscular mycorrhizal (AM) fungi play important functional roles in ecosystems, including the uptake and transfer of nutrients, modification of the physical soil environment and alteration of plant interactions with other biota. Several studies have demonstrated the potential for variation in AM fungal diversity to also affect ecosystem functioning, mainly via effects on primary productivity. Diversity in these studies is usually characterized in terms of the number of species, unique evolutionary lineages or complementary mycorrhizal traits, as well as the ability of plants to discriminate among AM fungi in space and time. However, the emergent outcomes of these relationships are usually indirect, and thus context dependent, and difficult to predict with certainty. Here, we advocate a fungal‐centric view of AM fungal biodiversity–ecosystem function relationships that focuses on the direct and specific links between AM fungal fitness and consequences for their roles in ecosystems, especially highlighting functional diversity in hyphal resource economics. We conclude by arguing that an understanding of AM fungal functional diversity is fundamental to determine whether AM fungi have a role in the exploitation of marginal/novel environments (whether past, present or future) and highlight avenues for future research.