Macroevolution of the plant-hummingbird pollination system.

Plant-hummingbird interactions are considered a classic example of coevolution, a process in which mutually dependent species influence each other's evolution. Plants depend on hummingbirds for pollination, whereas hummingbirds rely on nectar for food. As a step towards understanding coevolution, this review focuses on the macroevolutionary consequences of plant-hummingbird interactions, a relatively underexplored area in the current literature. We synthesize prior studies, illustrating the origins and dynamics of hummingbird pollination across different angiosperm clades previously pollinated by insects (mostly bees), bats, and passerine birds. In some cases, the crown age of hummingbirds pre-dates the plants they pollinate. In other cases, plant groups transitioned to hummingbird pollination early in the establishment of this bird group in the Americas, with the build-up of both diversities coinciding temporally, and hence suggesting co-diversification. Determining what triggers shifts to and away from hummingbird pollination remains a major open challenge. The impact of hummingbirds on plant diversification is complex, with many tropical plant lineages experiencing increased diversification after acquiring flowers that attract hummingbirds, and others experiencing no change or even a decrease in diversification rates. This mixed evidence suggests that other extrinsic or intrinsic factors, such as local climate and isolation, are important covariables driving the diversification of plants adapted to hummingbird pollination. To guide future studies, we discuss the mechanisms and contexts under which hummingbirds, as a clade and as individual species (e.g. traits, foraging behaviour, degree of specialization), could influence plant evolution. We conclude by commenting on how macroevolutionary signals of the mutualism could relate to coevolution, highlighting the unbalanced focus on the plant side of the interaction, and advocating for the use of species-level interaction data in macroevolutionary studies.

Population genetics of wild Macaca fascicularis with low-coverage shotgun sequencing of museum specimens.

OBJECTIVES: Long-tailed macaques (Macaca fascicularis) are widely distributed throughout the mainland and islands of Southeast Asia, making them a useful model for understanding the complex biogeographical history resulting from drastic changes in sea levels throughout the Pleistocene. Past studies based on mitochondrial genomes (mitogenomes) of long-tailed macaque museum specimens have traced their colonization patterns throughout the archipelago, but mitogenomes trace only the maternal history. Here, our objectives were to trace phylogeographic patterns of long-tailed macaques using low-coverage nuclear DNA (nDNA) data from museum specimens. METHODS: We performed population genetic analyses and phylogenetic reconstruction on nuclear single nucleotide polymorphisms (SNPs) from shotgun sequencing of 75 long-tailed macaque museum specimens from localities throughout Southeast Asia. RESULTS: We show that shotgun sequencing of museum specimens yields sufficient genome coverage (average ~1.7%) for reconstructing population relationships using SNP data. Contrary to expectations of divergent results between nuclear and mitochondrial genomes for a female philopatric species, phylogeographical patterns based on nuclear SNPs proved to be closely similar to those found using mitogenomes. In particular, population genetic analyses and phylogenetic reconstruction from the nDNA identify two major clades within M. fascicularis: Clade A includes all individuals from the mainland along with individuals from northern Sumatra, while Clade B consists of the remaining island-living individuals, including those from southern Sumatra. CONCLUSIONS: Overall, we demonstrate that low-coverage sequencing of nDNA from museum specimens provides enough data for examining broad phylogeographic patterns, although greater genome coverage and sequencing depth would be needed to distinguish between very closely related populations, such as those throughout the Philippines.

Statistical Modeling of Distribution Patterns: A Markov Random Field Implementation and Its Application on Areas of Endemism.

A statistical framework to infer areas of endemism from geographic distributions is proposed. This novel method is based on hidden Markov random fields (HMRFs), a type of undirected graph model commonly used in computer vision. This framework assumes areas of endemism are the states of the hidden layer of the model, whereas taxon distributions are emitted values in the observed layer. Taxon distributions are associated to the observed layer through a clustering procedure based on the extent of overlap. Observations are emitted by the hidden layer according to a Gaussian distribution, whereas the joint distribution of the hidden layer follows a Potts model. State and parameter inference of the maximum a posteriori configuration is performed through a modified version of the expectation-maximization algorithm. The optimal number of areas of endemism in the data set is estimated through the pseudolikelihood information criterion, a model selection procedure that uses an approximation to likelihood. The performance of the new algorithm was assessed on simulated data, and compared with the most popular methods for delimitation of areas of endemism: biotic element analysis, parsimony analysis of endemism, and endemicity analysis. HMRFs efficiently recovered the true pattern across a wide range of uncertainty values. The performance was also examined on empirical data: South African weevils (Sciobius) and Central American ground beetles and funnel-web tarantulas (Carabidae and Dipluridae, respectively). HMRFs uncovered six areas of endemism from the weevil data set, whereas eight were estimated for the Central American arthropods (compared with 3-5 and 3-14 from the other methods, respectively).

Preliminary phylogenetic analysis of the Andean clade and the placement of new Colombian blueberries (Ericaceae, Vaccinieae).

The blueberry tribe Vaccinieae (Ericaceae) is particularly diverse in South America and underwent extensive radiation in Colombia where many endemics occur. Recent fieldwork in Colombia has resulted in valuable additions to the phylogeny and as well in the discovery of morphologically noteworthy new species that need to be phylogenetically placed before being named. This is particularly important, as the monophyly of many of the studied genera have not been confirmed. In order to advance our understanding of the relationships within neotropical Vaccinieae and advice the taxonomy of the new blueberry relatives, here we present the most comprehensive phylogenetic analysis for the Andean clade. Anthopterus, Demosthenesia, and Pellegrinia are among the putative Andean genera recovered as monophyletic, while other eight Andean genera were not. The analyses also showed that genera that have been traditionally widely defined are non-monophyletic and could be further split into more discrete groups. Four newly discovered Colombian Vaccinieae are placed in the monophyletic Satyria s.s. and the Psammisia I clade. Although these new species are endemic to the Colombian Western Cordillera and Chocó biogeographic region and three are not known outside of Las Orquídeas National Park, they do not form sister pairs.

2matrix: A utility for indel coding and phylogenetic matrix concatenation(1.).

PREMISE OF THE STUDY: Phylogenetic analysis of DNA and amino acid sequences requires the creation of files formatted specifically for each analysis package. Programs currently available cannot simultaneously code inferred insertion/deletion (indel) events in sequence alignments and concatenate data sets. • METHODS AND RESULTS: A novel Perl script, 2matrix, was created to concatenate matrices of non-molecular characters and/or aligned sequences and to code indels. 2matrix outputs a variety of formats compatible with popular phylogenetic programs. • CONCLUSIONS: 2matrix efficiently codes indels and concatenates matrices of sequences and non-molecular data. It is available for free download under a GPL (General Public License) open source license (https://github.com/nrsalinas/2matrix/archive/master.zip).

Electric LAMP: Virtual Loop-Mediated Isothermal AMPlification.

We present eLAMP, a PERL script, with Tk graphical interface, that electronically simulates Loop-mediated AMPlification (LAMP) allowing users to efficiently test putative LAMP primers on a set of target sequences. eLAMP can match primers to templates using either exact (via builtin PERL regular expressions) or approximate matching (via the tre-agrep library). Performance was tested on 40 whole genome sequences of Staphylococcus. eLAMP correctly predicted that the two tested primer sets would amplify from S. aureus genomes and not amplify from other Staphylococcus species. Open source (GNU Public License) PERL scripts are available for download from the New York Botanical Garden's website.

[Prospective study and comparative of surgical and oncologic outcome between laparoscopic and retropubical radical prostatectomy]. / Estudio prospectivo no randomizado comparando los resultados funcionales y oncológicos entre la prostatectomía radical retropúbica y laparoscópica.

INTRODUCTION: Radical prostatectomy (RP) is a potentially healing surgical procedure. OBJECTIVE: We evaluate and compare the surgical and oncologic outcomes between laparoscopic and retropubical radical prostatectomy in the Urology Department in DIPRECA Hospital. METHOD: We constructed a nonrandomised, prospective study between january 2003 and march 2007. A total of 115 patients, 56 operated laparoscopically and 59 by retropubical RP. Functional and oncologic results were compared according to standardized variables and their corresponding statistical analysis, for which we used SPSS 12.0 program. RESULTS: Mean operation time was 202,5 minutes for laparoscopic RP and 150,5 for retropubical RP (p<0.0001). Retropubical RP required more blood transfusions (p<0.0001), longer hospital stay (p=0,0073) and longer need for vesical catheter (p=0,0001) than laparoscopic RP. There were 23 complications, 15 attributable to laparoscopic RP. We found no significant differences in postsurgical sexual function and urinary continence. In respect to the oncologic variables, we found no statistically relevant differences in positive surgical margins nor biochemical relapse during follow up. CONCLUSION: We found no significant differences between retropubical and laparoscopic RP in the oncologic and functional variables analyzed. Nevertheless, our experience shows a distinct benefit in favour of the laparoscopic approach in relation to bleeding and recovery rate. Though retropubical RP has a shorter operating time, we believe this variable depends on the learning curve still developing for laparoscopic RP. According to our literary review, this is the first publication in Chile that compares both techniques.

Estudio prospectivo no randomizado comparando los resultados funcionales y oncológicos entre la prostatectomía radical retropúbica y laparoscópica / Prospective study and comparative of surgical and oncologic outcome between laparoscopic and retropubical radical prostatectomy

Introducción: La prostatectomía radical es un procedimiento quirúrgico potencialmente curativo. Objetivo: Evaluar y comparar los resultados quirúrgicos y oncológicos entre la prostatectomía radical retropúbica (PRR) y la prostatectomía radical laparoscópica (PRL) en el servicio de Urología del Hospital DIPRECA. Material y método: Un total de 115 pacientes, 56 para PRL y 59 PRR realizadas entre enero 2003 hasta marzo 2007.Estudio prospectivo, no randomizado. Se compararon los resultados funcionales y oncológicos de acuerdo a variables estandarizadas y su análisis estadístico correspondiente, usando programa estadístico SPSS 12.0. Resultados: El tiempo operatorio promedio fue de 202,5 minutos para PRL y 150,5 minutos en PRR (p<0,0001). Requerimiento de transfusiones mayor para la PRR (p<0,0001), al igual que en número de días de hospitalización (p=0,0073) y tiempo de requerimiento de sonda Foley (p=0,0001). Hubo 15 complicaciones en PRL y 8 en PRR (p=0,10). No hubo diferencias significativas en la conservación de la función sexual y continencia urinaria postcirugía. En el análisis oncológico el margen quirúrgico positivo no presento diferencias, tampoco en la recidiva bioquímica en el seguimiento. Conclusión: Nuestros resultados muestran que ambas cirugías tienen resultados similares en términos oncológicos, continencia y función sexual. Existe un claro beneficio a favor de la PRL en cuanto a menor sangrado, y recuperación precoz. Si bien la PRR supera a la PRL en tiempo operatorio, creemos que esta variable depende de la curva de aprendizaje. Según nuestra revisión, éste es el primer trabajo comparativo entre estas dos técnicas que se publica en Chile (AU)

Introduction: Radical prostatectomy (RP) is a potentially healing surgical procedure. Objective: We evaluate and compare the surgical and oncologic outcomes between laparoscopic and retropubical radical prostatectomy in the Urology Department in DIPRECA Hospital. Method: We constructed a non randomised, prospective study between january 2003 and march 2007. A total of 115patients, 56 operated laparoscopically and 59 by retropubical RP. Functional and oncologic results were compared according to standardized variables and their corresponding statistical analysis, for which we used SPSS 12.0 program. Results: Mean operation time was 202,5 minutes for laparoscopic RP and 150,5 for retropubical RP (p<0.0001). Retropubical RP required more blood transfusions (p<0.0001), longer hospital stay (p=0,0073) and longer need for vesical catheter (p=0,0001) than laparoscopic RP. There were 23 complications, 15 attributable to laparoscopic RP. We found no significant differences in postsurgical sexual function and urinary continence. In respect to the oncologic variables, we found no statistically relevant differences in positive surgical margins nor biochemical relapse during follow up. Conclusion: We found no significant differences between retropubical and laparoscopic RP in the oncologic and functional variables analyzed. Nevertheless, our experience shows a distinct benefit in favour of the laparoscopic approach in relation to bleeding and recovery rate. Though retropubical RP has a shorter operating time, we believe this variable depends on the learning curve still developing for laparoscopic RP. According to our literary review, this is the first publication in Chile that compares both techniques (AU)