Treemap Versus BPA (Again): A Response to Dowling

TreeMap is a computer program for analysing host-parasite cospeciation. We respond to Dowling’s (Cladistics, 18: 416-435) recent comparison of TreeMap and Brooks Parsimony Analysis (BPA) by showing that Dowling’s comparison suffers from several mistakes and flaws. We discuss the problems with both BPA and TreeMap, and show that BPA incorrectly counts the true number coevolutionary events more often than TreeMap 1. We also discuss the two main limitations of TreeMap 1 correctly identified by Dowling, namely its inability to handle widespread parasites, and its coarse optimality criterion (the number of cospeciation events). We suggest a simple fix for widespread parasites. The newly released TreeMap 2 uses a more sensitive optimality criterion than TreeMap 1, addressing Dowling’s second concern

On the Computational Complexity of the Reticulate Cophylogeny Reconstruction Problem

The cophylogeny reconstruction problem is that of finding minimal cost explanations of differences between evolutionary histories of ecologically linked groups of biological organisms. We present a proof that shows that the general problem of reconciling evolutionary histories is NP-complete and provide a sharp boundary where this intractability begins. We also show that a related problem, that of finding Pareto optimal solutions, is NP-hard. As a byproduct of our results, we give a framework by which meta-heuristics can be applied to find good solutions to this problem

Wing patterning genes and coevolution of Müllerian mimicry inHeliconiusbutterflies: Support from phylogeography, cophylogeny, and divergence times

Examples of long-term coevolution are rare among free-living organisms. Müllerian mimicry in Heliconius butterflies had been suggested as a key example of coevolution by early genetic studies. However, research over the last two decades has been dominated by the idea that the best-studied comimics, H. erato and H. melpomene, did not coevolve at all. Recently sequenced genes associated with wing color pattern phenotype offer a new opportunity to resolve this controversy. Here, we test the hypothesis of coevolution between H. erato and H. melpomene using Bayesian multilocus analysis of five color pattern genes and five neutral genetic markers. We first explore the extent of phylogenetic agreement versus conflict between the different genes. Coevolution is then tested against three aspects of the mimicry diversifications: phylogenetic branching patterns, divergence times, and, for the first time, phylogeographic histories. We show that all three lines of evidence are compatible with strict coevolution of the diverse mimicry wing patterns, contrary to some recent suggestions. Instead, these findings tally with a coevolutionary diversification driven primarily by the ecological force of Müllerian mimicry

Extracting the MESA SR4000 Calibrations

Time-of-flight range imaging cameras are capable of acquiring depth images of a scene. Some algorithms require these cameras to be run in `raw mode', where any calibrations from the off-the-shelf manufacturers are lost. The calibration of the MESA SR4000 is herein investigated, with an attempt to reconstruct the full calibration. Possession of the factory calibration enables calibrated data to be acquired and manipulated even in “raw mode.” This work is motivated by the problem of motion correction, in which the calibration must be separated into component parts to be applied at different stages in the algorithm. There are also other applications, in which multiple frequencies are required, such as multipath interference correction. The other frequencies can be calibrated in a similar way, using the factory calibration as a base. A novel technique for capturing the calibration data is described; a retro-reflector is used on a moving platform, which acts as a point source at a distance, resulting in planar waves on the sensor. A number of calibrations are retrieved from the camera, and are then modelled and compared to the factory calibration. When comparing the factory calibration to both the “raw mode” data, and the calibration described herein, a root mean squared error improvement of 51:3mm was seen, with a standard deviation improvement of 34:9mm. © (2015) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only

BAGANI, 1892-1896: Mga Aral Mula kay Rizal Para sa Makabagong Panahon ng Lockdown

Ang papel ay paglalagom ng itinuturing na pinakamahalagang yugto ng buhay ni José Rizal—ang kanyang pagkakatapon sa Dapitan, sa lente ng konseptong “bagani” ng ating mga ninuno. Sa pagbanggit sa lang nauna nang pag-aaral ukol kay Rizal, ipapakitang kung papaanong ang yugto sa Dapitan ay ang katuparan ng kanyang mga layunin sa La Liga Filipina, na kanyang isinabuhay kasama ang bayan. Sa lente ng kasalukuyang pandemyang COVID 19, makikita natin na tila naranasan din ni Rizal sa kanyang pagkakatapon ang ilang bagay na ating dinaranas ngayon, na tila siya isang frontliner na nasa lockdown, inilagay sa kuwarentena, nag-homeschooling, nagkaroon ng lockdown sickness at namahagi ng ayudang pangkabuhayan sa mga mamamayan ng isang natutulog na bayan upang ito ay sumiglang muli. Nawa ay maging inspirasyon sa bayan na anuman ang hamon at mga balakid, walang makapipigil sa isang Pilipino na magsilbi sa bayan gamit ang kanyang mga talento at manatiling liwanag ng katotohanan at kaalaman