SimPhy: Phylogenomic Simulation of Gene, Locus, and Species Trees

We present a fast and flexible software package--SimPhy--for the simulation of multiple gene families evolving under incomplete lineage sorting, gene duplication and loss, horizontal gene transfer--all three potentially leading to species tree/gene tree discordance--and gene conversion. SimPhy implements a hierarchical phylogenetic model in which the evolution of species, locus, and gene trees is governed by global and local parameters (e.g., genome-wide, species-specific, locus-specific), that can be fixed or be sampled from a priori statistical distributions. SimPhy also incorporates comprehensive models of substitution rate variation among lineages (uncorrelated relaxed clocks) and the capability of simulating partitioned nucleotide, codon, and protein multilocus sequence alignments under a plethora of substitution models using the program INDELible. We validate SimPhy's output using theoretical expectations and other programs, and show that it scales extremely well with complex models and/or large trees, being an order of magnitude faster than the most similar program (DLCoal-Sim). In addition, we demonstrate how SimPhy can be useful to understand interactions among different evolutionary processes, conducting a simulation study to characterize the systematic overestimation of the duplication time when using standard reconciliation methods. SimPhy is available at https://github.com/adamallo/SimPhy, where users can find the source code, precompiled executables, a detailed manual and example cases

Diversity and genetic struture in cajá tree (Spondias mombin L.) populations in Northeastern Brazil.

Spondias mombinL. is a fruit tree from the American continent from the Anacardiaceae family. In Brazil it is common in different vegetation types but is more frequent in the Atlantic and Amazonian rainforests. It is economically important because of its fruits, which are widely consumed raw or processed as fruit jellies, juices and ice creams. The leaves have great importance in the pharmaceutical industry because of their antibacterial properties. In the state of Pernambuco, cajá tree is widely distributed in the Zona da Mata region and less frequently in the Agreste and Sertão areas. In this work diversity and genetic structure were studied in four populations of cajá tree from Pernambuco?s Zona da Mata, Northeast Brazil, using isozymes polymorphism analyses from electrophoreses. The result showed 100% of polymorphism (P) for nine alleles (A)and the average of alleles per locus s was 2.4. The expected heterozygosity (He) ranged from 0.530 to 0.574 and the observed heterozygosity (Ho), from 0.572 to 0.735. It was not observedin breeding and the average FIT was -0.175, whereas within population inbreeding (f) varied from -0.08 to - 0.37. The genetic divergence among the populations (FST) ranged from 0.006 to 0.028 and the average was 0.026. The average of estimated gene flow (Nm) was high (5.27). The CG-IPA population, corresponding to the germplasm collection of IPA, showed more than 96% of genetic similarity with other populations; therefore, it is a good representative of the existent genetic diversity in the Zona da Mata region

Evolutionary Process of Deep-Sea Bathymodiolus Mussels

BACKGROUND: Since the discovery of deep-sea chemosynthesis-based communities, much work has been done to clarify their organismal and environmental aspects. However, major topics remain to be resolved, including when and how organisms invade and adapt to deep-sea environments; whether strategies for invasion and adaptation are shared by different taxa or unique to each taxon; how organisms extend their distribution and diversity; and how they become isolated to speciate in continuous waters. Deep-sea mussels are one of the dominant organisms in chemosynthesis-based communities, thus investigations of their origin and evolution contribute to resolving questions about life in those communities. METHODOLOGY/PRINCIPAL FINDING: We investigated worldwide phylogenetic relationships of deep-sea Bathymodiolus mussels and their mytilid relatives by analyzing nucleotide sequences of the mitochondrial cytochrome c oxidase subunit I (COI) and NADH dehydrogenase subunit 4 (ND4) genes. Phylogenetic analysis of the concatenated sequence data showed that mussels of the subfamily Bathymodiolinae from vents and seeps were divided into four groups, and that mussels of the subfamily Modiolinae from sunken wood and whale carcasses assumed the outgroup position and shallow-water modioline mussels were positioned more distantly to the bathymodioline mussels. We provisionally hypothesized the evolutionary history of Bathymodilolus mussels by estimating evolutionary time under a relaxed molecular clock model. Diversification of bathymodioline mussels was initiated in the early Miocene, and subsequently diversification of the groups occurred in the early to middle Miocene. CONCLUSIONS/SIGNIFICANCE: The phylogenetic relationships support the "Evolutionary stepping stone hypothesis," in which mytilid ancestors exploited sunken wood and whale carcasses in their progressive adaptation to deep-sea environments. This hypothesis is also supported by the evolutionary transition of symbiosis in that nutritional adaptation to the deep sea proceeded from extracellular to intracellular symbiotic states in whale carcasses. The estimated evolutionary time suggests that the mytilid ancestors were able to exploit whales during adaptation to the deep sea

Off-axis retrieval of orbital angular momentum of light stored in cold atoms

We report on the storage of orbital angu- lar momentum (OAM) of light of a Laguerre-Gaussian mode in an ensemble of cold cesium atoms and its re- trieval along an axis different from the incident light beam. We employed a time-delayed four-wave mixing configuration to demonstrate that at small angle (2o), after storage, the retrieved beam carries the same OAM as the one encoded in the input beam. A calculation based on mode decomposition of the retrieved beam over the Laguerre-Gaussian basis is in agreement with the experimental observations done at small angle values. However, the calculation shows that the OAM retrieving would get lost at larger angles, reducing the fidelity of such storing-retrieving process. In addition, we have also observed that by applying an external magnetic field to the atomic ensemble the retrieved OAM presents Larmor oscillations, demonstrating the possibility of its manipulation and off-axis retrieval.Comment: 9 pages, 4 figure

Caracterização morfológica de híbridos interespecíficos de maracujazeiro (Passiflora spp.).

O presente trabalho teve como objetivo utilizar descritores morfológicos de 17 híbridos interespecíficos provenientes do cruzamento entre Passiflora edulis Sims e Passiflora cincinnatta Mast. Os parentais P. edulis (BGM330) e P. cincinnatta (BGM077), bem como os 21 híbridos resultantes deste cruzamento foram caracterizados com uso de 27 descritores qualitativos incluindo atributos relacionados à folha e flor, no período de abril a julho de 2011. As flores foram coletadas obedecendo-se o horário de abertura para cada acesso e, as medições foram obtidas com o auxílio de paquímetro.PDF. 083_11

Estimação de componentes de variância em características de crescimento utilizando-se máxima verossimilhança restrita e inferência bayesiana.

Diversos métodos para estimação dos componentes de variância tem sido proposto, os métodos apresentam, por vezes, limitações de implementação computacional, dificuldade na determinação e testes dos modelos estatísticos apropriados. No entanto, o procedimento estimação de componentes de ( co )variância apresenta-se como fase essencial no processo de avaliação genética, sendo necessário a sua implementação. O objetivo do trabalho foi estimar componentes de variância para características de crescimento em bovinos, utilizando maxíma verossimilhança : a restrita e inferência bayesiana