This study analyzed genetic and environmental data from two slow worm lizard species, Anguis greaca and A. cephallonica, that are morphologically similar but have distinct evolutionary histories. Genomic analysis showed no genetic admixture or gene flow between the species and population structure correlated with geographic distance. Species distribution models found little niche overlap, with each species associated with different climatic variables. The results reject hypotheses of recent hybridization or convergent evolution, and instead suggest morphological similarity reflects ancient shared ancestry.
First attempts using NGS in Senecio (Asteraceae)
Building a robust phylogeny of Culcitium group: a baseline for addressing further evolutionary questions for the genus in the Andes
First attempts using NGS in Senecio (Asteraceae)
Building a robust phylogeny of Culcitium group: a baseline for addressing further evolutionary questions for the genus in the Andes
“Distributional patterns of the order Gomphales (fungi: basidiomycota) in Nor...astridGonzalez29
ASTRID GONZÁLEZ-ÁVILA and DAVID ESPINOSA-ORGANISTA
Facultad de Estudios Superiores Zaragoza, Universidad Nacional Autónoma de México, Batalla del 5 de mayo s/n, Ejército de Oriente, Iztapalapa, CP 09230, Ciudad de México, México.
Diversification of the genus Dolichothele (Araneae: Theraphosidae) in the Bra...WendyArroyo8
Wendy Y. Arroyo-Pérez1,2, Vera Nisaka Solferini2
1Genetics and Molecular Biology Program, University of Campinas, Brazil.
2Department of Genetics, Evolution, Microbiology and Immunology – University of Campinas, Brazil
*vera.solferini@gmail.com
*wendyarroyo2015@gmail.com
Magpali et al (2020) Adaptive evolution of hearing genes in echolocating dolp...Letícia Magpali
Candidate poster for presentation at the I Meeting of Systematics, Biogeography and Evolution (SBE), in the category Phylogenomics and molecular evolution.
Magpali, L.; Freitas, L.; Ramos, E. K. S.; de Souza, E. M. S.; Nery, M. F.
University of Campinas / Biology Institute, Brazil
Supporting evidence for a cryptic species within the Neotropical freshwater f...Izabela Mendes
Presentation by Izabela Santos Mendes for the I Virtual Meeting of Systematics, Biogeography and Evolution (SBE).
Authors: Izabela Santos Mendes, Bruno Francelino de Melo, Daniel Fonseca Teixeira, Júnio Damasceno Souza, Daniel Cardoso Carvalho.
Phylogeny of Bacterial and Archaeal Genomes Using Conserved Genes: Supertrees...Jonathan Eisen
Lang JM, Darling AE, Eisen JA (2013) Phylogeny of Bacterial and Archaeal Genomes Using Conserved Genes: Supertrees and Supermatrices. PLoS ONE 8(4): e62510. doi:10.1371/journal.pone.0062510
Memorial lecture to University of Delhi HYM H.Y. Mohan Ram giving results about our molecular cytogenetics and cytogenomics research in University of Leicester and South China Botanical Garden
“Distributional patterns of the order Gomphales (fungi: basidiomycota) in Nor...astridGonzalez29
ASTRID GONZÁLEZ-ÁVILA and DAVID ESPINOSA-ORGANISTA
Facultad de Estudios Superiores Zaragoza, Universidad Nacional Autónoma de México, Batalla del 5 de mayo s/n, Ejército de Oriente, Iztapalapa, CP 09230, Ciudad de México, México.
Diversification of the genus Dolichothele (Araneae: Theraphosidae) in the Bra...WendyArroyo8
Wendy Y. Arroyo-Pérez1,2, Vera Nisaka Solferini2
1Genetics and Molecular Biology Program, University of Campinas, Brazil.
2Department of Genetics, Evolution, Microbiology and Immunology – University of Campinas, Brazil
*vera.solferini@gmail.com
*wendyarroyo2015@gmail.com
Magpali et al (2020) Adaptive evolution of hearing genes in echolocating dolp...Letícia Magpali
Candidate poster for presentation at the I Meeting of Systematics, Biogeography and Evolution (SBE), in the category Phylogenomics and molecular evolution.
Magpali, L.; Freitas, L.; Ramos, E. K. S.; de Souza, E. M. S.; Nery, M. F.
University of Campinas / Biology Institute, Brazil
Supporting evidence for a cryptic species within the Neotropical freshwater f...Izabela Mendes
Presentation by Izabela Santos Mendes for the I Virtual Meeting of Systematics, Biogeography and Evolution (SBE).
Authors: Izabela Santos Mendes, Bruno Francelino de Melo, Daniel Fonseca Teixeira, Júnio Damasceno Souza, Daniel Cardoso Carvalho.
Phylogeny of Bacterial and Archaeal Genomes Using Conserved Genes: Supertrees...Jonathan Eisen
Lang JM, Darling AE, Eisen JA (2013) Phylogeny of Bacterial and Archaeal Genomes Using Conserved Genes: Supertrees and Supermatrices. PLoS ONE 8(4): e62510. doi:10.1371/journal.pone.0062510
Memorial lecture to University of Delhi HYM H.Y. Mohan Ram giving results about our molecular cytogenetics and cytogenomics research in University of Leicester and South China Botanical Garden
Based on the given abstract and introduction to this journal article.pdfeyelineoptics
Based on the given abstract and introduction to this journal article, what is/are:
a.) The goals and need of the study?
b.) The theory/theories used to frame the research? MOLECULAR ECOLOGY Molecular
Eoology (20ts) 24,5813-SE28 Genetic diversity loss in a biodiversity hotspot: ancient DNA
quantifies genetic decline and former connectivity in a critically endangered marsupial NTOFT, t
TIMOTHY G. VAUGHAN MORTEN E. ALLE CARLO PACIONI HELEN HUNT ADRIAN
F. WAYNE, ALEXANDER BAYNES, DALAL HAOUCHAR, JOE DORTCH\" and
MICHAEL BUNCE tt wA 62ss, Australie, sniedem Antralinn Masnam. Lacked Beg 49,
Weldrpool DC, WA 6986, Parker and Willlife, Marjamap, M257, unirersiyof western Auestralia.
35 Stirling Highnny, Nindlamas, WA 6009, Australia. DTartwamt Eneinartment and
Agricalturer. Tror and Environmental DNA Laboratory, Kent Street. Bently, Perti, WA Abstract
The extent of genetic diversity loss and former connectivity between fragmented popu- lations
are often unknown factors when studying endangered species. While genetic commonly applied
in extant Populations to assess temporal and spatial it is no substitute for directly measuring past
diversity using emographic changes, ancient DNA (aDNA. We analysed both mitochondrial
DNA (mtDNA) and nuclear microsatellite loci from 64 historical fossil and skin samples of the
critically endan- gered Western Australian woylie (Bettongia penicillata ogilbyi, and compared
them with 231 152 for mtDNA) modem samples. In modern woylie Populations 15 mito-
chondrial control region (CR) haplotypes were identified. Interestingly, mtDNA CR data from
only 29 historical samples demonstrated 15 previously unknown haplotypes and detected extinct
divergent clade. Through modelling we estimated the loss of CR mtDNA diversity to be between
46% and 91% and estimated this to have occurred in the past 2000-4000 years in association
with a dramatic population decline. In addi tion, we obtained near-com plete 11-oci
microsatellite profiles from 21 historical sam- ples. In agreement with the mtDNA data, a
number of new\" microsatellite alleles was only detected in the historical populations despite
extensive modem sampling indicat. ing a nuclear genetic diversity loss 20%. Calculations of
genetic diversity 0heterozy gosity and alleli rarefaction) showed that these were significantly
higher in the past and that there was a high degree of gene flow across the woylie\'s historical
range. These findings have an immediate impact on how the extant populations are managed and
we recommend the implementation of an assisted migration programme further of genetic
diversity. our study demonstrates the value of integrating data conservation strategies. ancient
DNA Bettorgia, biodiversity loss, genetic diversity, population botdeneck Racinad 22 May 2014
reision receioed 7 October 2015. accepted 13 october 2015 Introduction spedes and populations
that are adversely affected by Correspondence Michael Bunce, Fax: +él 8926 2495; E-mail
anthropogenic activit.
Effects of density on spacing patterns and habitat associations of a Neotropi...Nicole Angeli
Presentation at Ecological Society of America, August 2013. Minneapolis, USA. –Oral Paper
Angeli, N. F., K. Lips, G. V. DiRenzo, and A. Cunha. “Effects of density on spacing patterns
and habitat associations in the Neotropical Glassfrog Espadarana prosoblepon.”
Phylogenomic Convergence Detection - Evolutionary Biology Meeting in Marseill...Joe Parker
Invited talk presented at the 18th EBM in Marseille, 16th September 2014.
I outline the state-of-the-art in methods of genomic convergence detection, including adaptive molecular convergence, and highlight some of the next challenges in developing these techniques, including recent results.
Here, we describe a learning strategy that results an excellent choice for a first approach of students to produce scientific knowledge that can be confronted in the scientific field as well as recognize in this knowledge the transferability to the natural resources management. Nowadays, the availability of several Population Genetics software together with public molecular database represents a valuable tool of great assistance for teachers of this discipline. In this way, we implemented a
lecture where the students worked with empirical data set from a recent published article. The students joined theoretical concepts learned, computational software free available and empirical data set. The development of the activity comprised four steps: i) estimate population genetics parameters using software recommended by teachers, ii) understand results in a biological sense, iii) read the original manuscript from dataset authors and iv) compare both results in a comprehensive way. The students assumed the challenge under a reflective look and they kept a very fruitful discussion playing a role of population geneticists. Their exchange of ideas allowed them arrive to the conclusion that Manilkara zapota populations keep high levels of genetic diversity, although Ancient Maya left traces in the genetic makeup of these non-native populations with different management histories.
Modeling the biosphere: the natural historian's perspectiveRutger Vos
Natural history collections of specimens are a rich source of data for discovering the patterns of biodiversity in space and time and for furthering our understanding of the underlying processes that generate these patterns. Modeling the biosphere in this manner can help address global challenges in relation to climate change, food security, emerging disease and conservation. (Talk to the 3rd annual eScience symposium, 8 October 2015).
Phylogenetic diversity—patterns of phylogenetic relatedness among organisms in ecological communities—provides important insights into the mechanisms underlying community assembly. Studies that measure phylogenetic diversity in microbial communities have primarily been limited to a single marker gene approach, using the small subunit of the rRNA gene (SSU-rRNA) to quantify phylogenetic relationships among microbial taxa. In this study, we present an approach for inferring phylogenetic relationships among microorganisms based on the random metagenomic sequencing of DNA fragments. To overcome challenges caused by the fragmentary nature of metagenomic data, we leveraged fully sequenced bacterial genomes as a scaffold to enable inference of phylogenetic relationships among metagenomic sequences from multiple phylogenetic marker gene families. The resulting metagenomic phylogeny can be used to quantify the phylogenetic diversity of microbial communities based on metagenomic data sets. We applied this method to understand patterns of microbial phylogenetic diversity and community assembly along an oceanic depth gradient, and compared our findings to previous studies of this gradient using SSU-rRNA gene and metagenomic analyses. Bacterial phylogenetic diversity was highest at intermediate depths beneath the ocean surface, whereas taxonomic diversity (diversity measured by binning sequences into taxonomically similar groups) showed no relationship with depth. Phylogenetic diversity estimates based on the SSU-rRNA gene and the multi-gene metagenomic phylogeny were broadly concordant, suggesting that our approach will be applicable to other metagenomic data sets for which corresponding SSU-rRNA gene sequences are unavailable. Our approach opens up the possibility of using metagenomic data to study microbial diversity in a phylogenetic context.
Cancer cell metabolism: special Reference to Lactate PathwayAADYARAJPANDEY1
Normal Cell Metabolism:
Cellular respiration describes the series of steps that cells use to break down sugar and other chemicals to get the energy we need to function.
Energy is stored in the bonds of glucose and when glucose is broken down, much of that energy is released.
Cell utilize energy in the form of ATP.
The first step of respiration is called glycolysis. In a series of steps, glycolysis breaks glucose into two smaller molecules - a chemical called pyruvate. A small amount of ATP is formed during this process.
Most healthy cells continue the breakdown in a second process, called the Kreb's cycle. The Kreb's cycle allows cells to “burn” the pyruvates made in glycolysis to get more ATP.
The last step in the breakdown of glucose is called oxidative phosphorylation (Ox-Phos).
It takes place in specialized cell structures called mitochondria. This process produces a large amount of ATP. Importantly, cells need oxygen to complete oxidative phosphorylation.
If a cell completes only glycolysis, only 2 molecules of ATP are made per glucose. However, if the cell completes the entire respiration process (glycolysis - Kreb's - oxidative phosphorylation), about 36 molecules of ATP are created, giving it much more energy to use.
IN CANCER CELL:
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
introduction to WARBERG PHENOMENA:
WARBURG EFFECT Usually, cancer cells are highly glycolytic (glucose addiction) and take up more glucose than do normal cells from outside.
Otto Heinrich Warburg (; 8 October 1883 – 1 August 1970) In 1931 was awarded the Nobel Prize in Physiology for his "discovery of the nature and mode of action of the respiratory enzyme.
WARNBURG EFFECT : cancer cells under aerobic (well-oxygenated) conditions to metabolize glucose to lactate (aerobic glycolysis) is known as the Warburg effect. Warburg made the observation that tumor slices consume glucose and secrete lactate at a higher rate than normal tissues.
THE IMPORTANCE OF MARTIAN ATMOSPHERE SAMPLE RETURN.Sérgio Sacani
The return of a sample of near-surface atmosphere from Mars would facilitate answers to several first-order science questions surrounding the formation and evolution of the planet. One of the important aspects of terrestrial planet formation in general is the role that primary atmospheres played in influencing the chemistry and structure of the planets and their antecedents. Studies of the martian atmosphere can be used to investigate the role of a primary atmosphere in its history. Atmosphere samples would also inform our understanding of the near-surface chemistry of the planet, and ultimately the prospects for life. High-precision isotopic analyses of constituent gases are needed to address these questions, requiring that the analyses are made on returned samples rather than in situ.
Richard's aventures in two entangled wonderlandsRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
Professional air quality monitoring systems provide immediate, on-site data for analysis, compliance, and decision-making.
Monitor common gases, weather parameters, particulates.
Multi-source connectivity as the driver of solar wind variability in the heli...Sérgio Sacani
The ambient solar wind that flls the heliosphere originates from multiple
sources in the solar corona and is highly structured. It is often described
as high-speed, relatively homogeneous, plasma streams from coronal
holes and slow-speed, highly variable, streams whose source regions are
under debate. A key goal of ESA/NASA’s Solar Orbiter mission is to identify
solar wind sources and understand what drives the complexity seen in the
heliosphere. By combining magnetic feld modelling and spectroscopic
techniques with high-resolution observations and measurements, we show
that the solar wind variability detected in situ by Solar Orbiter in March
2022 is driven by spatio-temporal changes in the magnetic connectivity to
multiple sources in the solar atmosphere. The magnetic feld footpoints
connected to the spacecraft moved from the boundaries of a coronal hole
to one active region (12961) and then across to another region (12957). This
is refected in the in situ measurements, which show the transition from fast
to highly Alfvénic then to slow solar wind that is disrupted by the arrival of
a coronal mass ejection. Our results describe solar wind variability at 0.5 au
but are applicable to near-Earth observatories.
Observation of Io’s Resurfacing via Plume Deposition Using Ground-based Adapt...Sérgio Sacani
Since volcanic activity was first discovered on Io from Voyager images in 1979, changes
on Io’s surface have been monitored from both spacecraft and ground-based telescopes.
Here, we present the highest spatial resolution images of Io ever obtained from a groundbased telescope. These images, acquired by the SHARK-VIS instrument on the Large
Binocular Telescope, show evidence of a major resurfacing event on Io’s trailing hemisphere. When compared to the most recent spacecraft images, the SHARK-VIS images
show that a plume deposit from a powerful eruption at Pillan Patera has covered part
of the long-lived Pele plume deposit. Although this type of resurfacing event may be common on Io, few have been detected due to the rarity of spacecraft visits and the previously low spatial resolution available from Earth-based telescopes. The SHARK-VIS instrument ushers in a new era of high resolution imaging of Io’s surface using adaptive
optics at visible wavelengths.
The increased availability of biomedical data, particularly in the public domain, offers the opportunity to better understand human health and to develop effective therapeutics for a wide range of unmet medical needs. However, data scientists remain stymied by the fact that data remain hard to find and to productively reuse because data and their metadata i) are wholly inaccessible, ii) are in non-standard or incompatible representations, iii) do not conform to community standards, and iv) have unclear or highly restricted terms and conditions that preclude legitimate reuse. These limitations require a rethink on data can be made machine and AI-ready - the key motivation behind the FAIR Guiding Principles. Concurrently, while recent efforts have explored the use of deep learning to fuse disparate data into predictive models for a wide range of biomedical applications, these models often fail even when the correct answer is already known, and fail to explain individual predictions in terms that data scientists can appreciate. These limitations suggest that new methods to produce practical artificial intelligence are still needed.
In this talk, I will discuss our work in (1) building an integrative knowledge infrastructure to prepare FAIR and "AI-ready" data and services along with (2) neurosymbolic AI methods to improve the quality of predictions and to generate plausible explanations. Attention is given to standards, platforms, and methods to wrangle knowledge into simple, but effective semantic and latent representations, and to make these available into standards-compliant and discoverable interfaces that can be used in model building, validation, and explanation. Our work, and those of others in the field, creates a baseline for building trustworthy and easy to deploy AI models in biomedicine.
Bio
Dr. Michel Dumontier is the Distinguished Professor of Data Science at Maastricht University, founder and executive director of the Institute of Data Science, and co-founder of the FAIR (Findable, Accessible, Interoperable and Reusable) data principles. His research explores socio-technological approaches for responsible discovery science, which includes collaborative multi-modal knowledge graphs, privacy-preserving distributed data mining, and AI methods for drug discovery and personalized medicine. His work is supported through the Dutch National Research Agenda, the Netherlands Organisation for Scientific Research, Horizon Europe, the European Open Science Cloud, the US National Institutes of Health, and a Marie-Curie Innovative Training Network. He is the editor-in-chief for the journal Data Science and is internationally recognized for his contributions in bioinformatics, biomedical informatics, and semantic technologies including ontologies and linked data.
So close no matter how far: sympatric slow worm lizards look alike but share little else
1. So close no matter how far: sympatric slow
worm lizards look alike but share little else
Vassilis Kypraios-Skrekas, Sinos Giokas,
Evanthia Thanou*
Virtual Meeting of Systematics, Biogeography and Evolution
28-30 July 2020
Dep. of Biology, University of Patras, Greece
* Corresponding author: thanouevanthia@gmail.com
This research is co-financed by Greece and the European Union (European Social Fund- ESF) through the
Operational Programme «Human Resources Development, Education and Lifelong Learning 2014-2020» in the
context of the project “Phylogeography in the genomics era and the role of barriers in speciation (MIS 5047129)”
2. Introduction
• Anguis greaca and A. cephallonica are Balkan endemics, originally treated as
conspecifics due to morphological similarity and co-distribution.
• mtDNA phylogenies1,2,3 show 2 distinct lineages that possibly reached secondary
contact after past population expansion
• However, the question remains. Could morphological similarity and
co-distribution reflect common ancenstry or convergent evolution?
A. cephallonica
A. greaca
1. Gvozdic et al. 2010, MPE 55:460-472; 2. Thanou et al. 2014, Amph-Rept , 35:263-269; 3. Jablonsky et al. 2016, BMC Evol. Biol, 16:99-117
ImagesfromGvozdicetal.
2013,MPE69:1077-1092.
Here we tested two hypotheses:
1. Morphological similarity suggests gene flow
and hybridization between the two lineages.
2. Co-distribution suggests similar environmental
preferences and convergent evolution.
3. Materials & Methods
• 37 ddRAD libraries of A. cephallonica and A. graeca; approx.
75K sites in total, 4K loci and 1,000 unlinked SNPs per lineage
• ML phylogeny (IQ-tree, SVDquartets) with genomic markers
compared to known mtDNA phylogenies
• Test for admixture between lineages and population structure
within (hierarchical STRUCTURE analyses, DAPC); test for
Isolation-By-Distance (IBD; Mantel tests)
• Test for niche overlap and predict distribution maps based on
19 bioclimatic variables with Species Distribution Models
(SDM; Maxent analysis on 181 occurrence points)
4. Results & Discussion
Congruent mtDNA and genomic phylogenies
No admixture between cephallonica & greaca
Gene flow within each lineage
Population structure reflects IBD
A. cephallonica
P<0.00001
A. greaca
P<0.001
Regression plots of Genetic distances vs. Geographic distances
5. Conclusion
No niche overlap (Schoener's D = 0.47)
Both lizards’ distribution is associated with high
precipitation
Only A. greaca distribution is restricted by high
temperatures (30% contribution to SDM)
Results & Discussion
We reject both hypotheses of genetic admixture and niche convergence.
Most plausible explanation: morphological similarity due to retained ancient traits.
Next step: extensive morphometric comparisons!
A. cephallonica
AUC= 0.87
A. greaca
AUC= 0.81
- 0.2
- 0.8
