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Diversification rate

Todd H Oakley
Novelty and innovation are fundamental yet relatively understudied concepts in evolution. We may study the history and provenance of novelty using phylogenetics, where key questions include when evolution occurs by tree-like branching and when it occurs by movement of distantly related parts in processes akin to horizontal transfer. Perfectly vertical inheritance, often an assumption of evolutionary trees, requires simultaneous co-duplication of the parts of a duplicating or speciating (processes I collectively call 'furcating') biological feature...
September 15, 2017: Developmental Biology
Qing Li, Neda Barghi, Aiping Lu, Alexander E Fedosov, Pradip K Bandyopadhyay, Arturo O Lluisma, Gisela P Concepcion, Mark Yandell, Baldomero M Olivera, Helena Safavi-Hemami
The genus Conus comprises approximately 700 species of venomous marine cone snails that are highly efficient predators of worms, snails, and fish. In evolutionary terms, cone snails are relatively young with the earliest fossil records occurring in the Lower Eocene, 55 Ma. The rapid radiation of cone snail species has been accompanied by remarkably high rates of toxin diversification. To shed light on the molecular mechanisms that accompany speciation, we investigated the toxin repertoire of two sister species, Conus andremenezi and Conus praecellens, that were until recently considered a single variable species...
September 1, 2017: Genome Biology and Evolution
Andrew L Hipp, Paul S Manos, Antonio González-Rodríguez, Marlene Hahn, Matthew Kaproth, John D McVay, Susana Valencia Avalos, Jeannine Cavender-Bares
Oaks (Quercus, Fagaceae) are the dominant tree genus of North America in species number and biomass, and Mexico is a global center of oak diversity. Understanding the origins of oak diversity is key to understanding biodiversity of northern temperate forests. A phylogenetic study of biogeography, niche evolution and diversification patterns in Quercus was performed using 300 samples, 146 species. Next-generation sequencing data were generated using the restriction-site associated DNA (RAD-seq) method. A time-calibrated maximum likelihood phylogeny was inferred and analyzed with bioclimatic, soils, and leaf habit data to reconstruct the biogeographic and evolutionary history of the American oaks...
September 18, 2017: New Phytologist
James P Herrera
Biodiversity arises from the balance between speciation and extinction. Fossils record the origins and disappearance of organisms, and the branching patterns of molecular phylogenies allow estimation of speciation and extinction rates, but the patterns of diversification are frequently incongruent between these two data sources. I tested two hypotheses about the diversification of primates based on ∼600 fossil species and 90% complete phylogenies of living species: 1) diversification rates increased through time; 2) a significant extinction event occurred in the Oligocene...
September 14, 2017: Evolution; International Journal of Organic Evolution
M Arista, R Berjano, J Viruel, M Á Ortiz, M Talavera, P L Ortiz
Background and aims: The transition from outcrossing to selfing is a repeated pattern in angiosperm diversification and according to general theory this transition should occur quickly and mixed reproductive systems should be infrequent. However, a large proportion of flowering plants have mixed reproductive systems, even showing inbreeding depression. Recently, several theoretical studies have shown that mixed mating systems can be stable, but empirical studies supporting these assumptions are still scarce...
September 1, 2017: Annals of Botany
Christopher D Beatty, Melissa Sánchez Herrera, Jeffrey H Skevington, Arash Rashed, Hans Van Gossum, Scott Kelso, Thomas N Sherratt
The study of island fauna has greatly informed our understanding of the evolution of diversity. We here examine the phylogenetics, biogeography, and diversification of the damselfly genera Nesobasis and Melanesobasis, endemic to the Fiji Islands, to explore mechanisms of speciation in these highly speciose groups. Using mitochondrial (COI, 12S) and nuclear (ITS) replicons, we recovered garli-part maximum likelihood and mrbayes Bayesian phylogenetic hypotheses for 26 species of Nesobasis and eight species/subspecies of Melanesobasis...
September 2017: Ecology and Evolution
Clément Rougeux, Louis Bernatchez, Pierre-Alexandre Gagnaire
Parallel divergence across replicated species pairs occurring in similar environmental contrasts may arise through distinct evolutionary scenarios. Deciphering whether such parallelism actually reflects repeated parallel divergence driven by divergent selection or a single divergence event with subsequent gene flow needs to be ascertained. Reconstructing historical gene flow is therefore of fundamental interest to understand how demography and selection jointly shaped genomic divergence during speciation. Here, we use an extended modeling framework to explore the multiple facets of speciation-with-gene-flow with demo-genetic divergence models that capture both temporal and genomic variation in effective population size and migration rate...
August 1, 2017: Genome Biology and Evolution
Séverin Hatt, Pierre Mouchon, Thomas Lopes, Frédéric Francis
Landscape diversification is a key element for the development of sustainable agriculture. This study explores whether the implementation of habitats for pest natural enemies enhances conservation biological control in an adjacent field. In the present study conducted in Gembloux (Belgium) in 2016, the effect of two different habitats (wildflower strips and a forest) and aphid abundance on the density of aphid natural enemies, mummified aphids and parasitism on pea plants was assessed through visual observations...
September 13, 2017: Insects
Edward D Burress, Milton Tan
The uneven distribution of diversity is a conspicuous phenomenon across the tree of life. Ecological opportunity is a prominent catalyst of adaptive radiation and therefore may alter patterns of diversification. We evaluated the distribution of shifts in diversification rates across the cichlid phylogeny and the distribution of major clades across phylogenetic space. We also tested if ecological opportunity influenced these patterns. Colonization-associated ecological opportunity altered the tempo and mode of diversification during the adaptive radiation of cichlid fishes...
September 12, 2017: Evolution; International Journal of Organic Evolution
Zhonglou Sun, Tao Pan, Chaochao Hu, Lu Sun, Hengwu Ding, Hui Wang, Chenling Zhang, Hong Jin, Qing Chang, Xianzhao Kan, Baowei Zhang
The Anseriformes is a well-known and widely distributed bird order, with more than 150 species in the world. This paper aims to revise the classification, determine the phylogenetic relationships and diversification patterns in Anseriformes by exploring the Cyt b, ND2, COI genes and the complete mitochondrial genomes (mito-genomes). Molecular phylogeny and genetic distance analyses suggest that the Dendrocygna species should be considered as an independent family, Dendrocygnidae, rather than a member of Anatidae...
2017: PloS One
Stephen A Smith, Joseph W Brown, Ya Yang, Riva Bruenn, Chloe P Drummond, Samuel F Brockington, Joseph F Walker, Noah Last, Norman A Douglas, Michael J Moore
The role played by whole genome duplication (WGD) in plant evolution is actively debated. WGDs have been associated with advantages such as superior colonization, various adaptations, and increased effective population size. However, the lack of a comprehensive mapping of WGDs within a major plant clade has led to uncertainty regarding the potential association of WGDs and higher diversification rates. Using seven chloroplast and nuclear ribosomal genes, we constructed a phylogeny of 5036 species of Caryophyllales, representing nearly half of the extant species...
September 11, 2017: New Phytologist
Subir B Shakya, Jérôme Fuchs, Jean-Marc Pons, Frederick H Sheldon
Molecular phylogenetic studies of woodpeckers (Picidae) have generally focused on relationships within specific clades or have sampled sparsely across the family. We compared DNA sequences of six loci from 203 of the 217 recognized species of woodpeckers to construct a comprehensive tree of intrafamilial relationships. We recovered many known, but also numerous unknown, relationships among clades and species. We found, for example, that the three picine tribes are related as follows (Picini, (Campephilini, Melanerpini)) and that the genus Dinopium is paraphyletic...
September 7, 2017: Molecular Phylogenetics and Evolution
Yanis Bouchenak-Khelladi, H Peter Linder
The enormous species richness in the Cape Floristic Region (CFR) of Southern Africa is the result of numerous radiations, but the temporal progression and possible mechanisms of these radiations are still poorly understood. Here, we explore the macroevolutionary dynamics of the Restionaceae, that include 340 species which are found in all vegetation types in the Cape flora and are ecologically dominant in fynbos. Using an almost complete (i.e. 98%) species-level time calibrated phylogeny and models of diversification dynamics, we show that species diversification is constant through the Cenozoic, with no evidence of an acceleration with the onset of the modern winter-wet climate, or a recent density-dependent slowdown...
September 8, 2017: Evolution; International Journal of Organic Evolution
Vivian Triana, Ratmir Derda
In this paper, we developed a tandem of two carbon-carbon bond-forming reactions to chemically diversify the libraries of peptides displayed on a bacteriophage. The Wittig reaction of a biotin-ester from a stabilized phosphorane ylide with model peptides containing N-terminal glyoxal exhibits reaction rates of 0.07 to 5 M(-1) s(-1) in water at pH 6.5-8. The log(k) scaled linearly with pH from pH 6 to 8; above pH 9 the reaction is accompanied by the hydrolysis of the ester functionality. Capture of the phage displaying the biotinylated product by streptavidin beads confirmed the rate of this reaction in a library of 10(8) peptides (k = 0...
September 7, 2017: Organic & Biomolecular Chemistry
Olivia Munoz
OBJECTIVES: In Southeast (SE) Arabia, agriculture is supposed to expand around 3000 BC, but its tempo and its actual role in populations' subsistence is still debated by archaeologists. Here, we compare dental health conditions of 11 skeletal samples from coastal and inland sites, dated from the Late Neolithic (ca. 4500-3100 BC) to the Early Bronze Age (EBA), conventionally divided into Hafit (ca. 3100-2700 BC) and Umm an-Nar period (ca. 2700-2000 BC). The goal is to assess long-term trends in subsistence patterns and regional variability during the local transition to agriculture...
September 6, 2017: American Journal of Physical Anthropology
Christelle Tougard, Carmen R García Dávila, Uwe Römer, Fabrice Duponchelle, Frédérique Cerqueira, Emmanuel Paradis, Bruno Guinand, Carlos Angulo Chávez, Vanessa Salas, Sophie Quérouil, Susana Sirvas, Jean-François Renno
Evaluating biodiversity and understanding the processes involved in diversification are noticeable conservation issues in fishes subject to large, sometimes illegal, ornamental trade purposes. Here, the diversity and evolutionary history of the Neotropical dwarf cichlid genus Apistogramma from several South American countries are investigated. Mitochondrial and nuclear markers are used to infer phylogenetic relationships between 31 genetically identified species. The monophyly of Apistogramma is suggested, and Apistogramma species are distributed into four clades, corresponding to three morphological lineages...
2017: PloS One
Vivek Philip Cyriac, Ullasa Kodandaramaiah
Understanding how and why diversification rates vary across evolutionary time is central to understanding how biodiversity is generated and maintained. Recent mathematical models that allow estimation of diversification rates across time from reconstructed phylogenies have enabled us to make inferences on how biodiversity copes with environmental change. Here, we explore patterns of temporal diversification in Uropeltidae, a diverse fossorial snake family. We generate a time-calibrated phylogenetic hypothesis for Uropeltidae and show a significant correlation between diversification rate and paleotemperature during the Cenozoic...
September 1, 2017: Molecular Phylogenetics and Evolution
Peter Vďačný, Ľubomír Rajter, Shahed Uddin Ahmed Shazib, Seok Won Jang, Mann Kyoon Shin
Ciliates are a suitable microbial model to investigate trait-dependent diversification because of their comparatively complex morphology and high diversity. We examined the impact of seven intrinsic traits on speciation, extinction, and net-diversification of rhynchostomatians, a group of comparatively large, predatory ciliates with proboscis carrying a dorsal brush (sensoric structure) and toxicysts (organelles used to kill the prey). Bayesian estimates under the binary-state speciation and extinction model indicate that two types of extrusomes and two-rowed dorsal brush raise diversification through decreasing extinction...
August 30, 2017: Scientific Reports
Hudson T Pinheiro, Giacomo Bernardi, Thiony Simon, Jean-Christophe Joyeux, Raphael M Macieira, João Luiz Gasparini, Claudia Rocha, Luiz A Rocha
Studies on the distribution and evolution of organisms on oceanic islands have advanced towards a dynamic perspective, where terrestrial endemicity results from island geographical aspects and geological history intertwined with sea-level fluctuations. Diversification on these islands may follow neutral models, decreasing over time as niches are filled, or disequilibrium states and progression rules, where richness and endemism rise with the age of the archipelago owing to the splitting of ancestral lineages (cladogenesis)...
September 7, 2017: Nature
Ronald M Bonett, Andrea L Blair
Metazoans display a tremendous diversity of developmental patterns, including complex life cycles composed of morphologically disparate stages. In this regard, the evolution of life cycle complexity promotes phenotypic diversity. However, correlations between life cycle stages can constrain the evolution of some structures and functions. Despite the potential macroevolutionary consequences, few studies have tested the impacts of life cycle evolution on broad-scale patterns of trait diversification. Here we show that larval and adult salamanders with a simple, aquatic-only (paedomorphic) life cycle had an increased rate of vertebral column and body form diversification compared to lineages with a complex, aquatic-terrestrial (biphasic) life cycle...
August 29, 2017: Proceedings of the National Academy of Sciences of the United States of America
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