This document discusses issues with using morphological data to construct phylogenetic trees for bat species. It finds that morphological characters can be highly convergent due to similarities in ecology and function. This saturation of morphological signal over time makes resolving relationships difficult. However, the study finds that dental characters provide a strong phylogenetic signal, likely because they are repeated across the dentition and show less convergence than other traits. The repetition of dental characters amplifies phylogenetic signal and helps resolve relationships that would otherwise be unresolved using morphology alone.
Chromosomal Variations, Continuous and Discontinuous Variations, Genotypic & ...Muhammad Mubashir Ali
Chromosomal Variations, Continuous and Discontinuous Variations, Genotypic & Phenotypic Variations. Hardy-Weinberg law of random mating, Recombination technology
It also explains the main points for a variation.
Has Milwaukee\'s Riverwest neighborhood reached a condo development saturation point? What is the impact of income and job growth on the sustainability of the condo building boom in this diverse area of Milwaukee?
Chromosomal Variations, Continuous and Discontinuous Variations, Genotypic & ...Muhammad Mubashir Ali
Chromosomal Variations, Continuous and Discontinuous Variations, Genotypic & Phenotypic Variations. Hardy-Weinberg law of random mating, Recombination technology
It also explains the main points for a variation.
Has Milwaukee\'s Riverwest neighborhood reached a condo development saturation point? What is the impact of income and job growth on the sustainability of the condo building boom in this diverse area of Milwaukee?
Evolution of North American MicruracarusRachel Shoop
My research focuses on the evolution of North American water mites in the genus Arrenurus, Subgenus Micruracarus. In this presentation, I discuss why I chose to study these little known critters, and present some preliminary findings. Please contact me for more info.
Ecology of Ranaviruses: State of Understandingmgray11
Presentation on the basic ecology of ranaviruses and mechanisms that may be contribute to this pathogen's emergence. By Dr. Matt Gray (University of Tennessee, Center for Wildlife Health)
Evolution of North American MicruracarusRachel Shoop
My research focuses on the evolution of North American water mites in the genus Arrenurus, Subgenus Micruracarus. In this presentation, I discuss why I chose to study these little known critters, and present some preliminary findings. Please contact me for more info.
Ecology of Ranaviruses: State of Understandingmgray11
Presentation on the basic ecology of ranaviruses and mechanisms that may be contribute to this pathogen's emergence. By Dr. Matt Gray (University of Tennessee, Center for Wildlife Health)
Labs without Borders: Methods for Extracting, Amplifying, and Sequencing in t...Liliana Davalos
Genomic methods have revolutionized current understanding of the evolution and ecology of bats worldwide. At the same time, air travel restrictions and concerns about emerging diseases have made transporting bat tissues an increasingly expensive and fraught pursuit. To both overcome these restrictions and build capacity in high biodiversity countries, we implemented field-based molecular protocols. First, we sequenced the prokaryotic microbiome of multiple individuals in the field using a standard centrifuge, mini-PCR and mini-gel rigs, and a MinIon sequencer. Modifications to lab protocols included: 1) centrifugation steps robust at high- or mini-centrifuge speed, 2) extending proteinase-K incubation at ambient temperature and evaluating the elimination of ethanol in clean-up during extraction, 3) using lyophilized mastermix in amplification, and 4) eluting in molecular-grade water in library prep. The lack of a high-sensitivity method for quantifying DNA, however, limited the efficiency of multiplexing and reduced the life of the cell in sequencing. Second, we generated mtDNA barcodes using a cheaper, hybrid approach of extracting and amplifying in the field, with subsequent lab-based Sanger sequencing. We added a temperature control ceramic mug and Qubit fluorometer to the kit. By modifying standard procedures, and substituting some equipment with modestly priced consumer products (e.g., the mug), our protocols make critical steps in molecular genetics field-accessible, and open possibilities for future research on genomics, transcriptomics, and disease surveillance in bats.
Past, present, and future of deforestation in the northwestern AmazonLiliana Davalos
With the largest extent of tropical forest in the world, the dynamics of forest loss and fragmentation in Brazil have been the focus of attention for over 50 years. Global shifts in trade to the Pacific and growing infrastructure, however, threaten the western end of the forests in the Andean region, including the Amazon. Research combining spatial and socioeconomic analyses, as well as exploring the 20th-century history of the region, reveals three surprising findings. First, wedges of deforestation are strongly associated with directed colonization projects more than 40 years old. Second, although pastures are the end state of much formerly forested land, demand for beef is a poor predictor of this process and urbanization following infrastructure upgrade is a better correlate. Finally, coca cultivation, widely believed to be a motor of forest loss, contributes little to the process both directly and indirectly. Instead, the clearing of these forests corresponds to the transformation of nominally state-owned forests into private properties, and occurs in tandem with local urbanization and despite overall rural depopulation.
Extinction, Extinction: How it Was and How to Stop it From the Miocene to TodayLiliana Davalos
The central question of our time is whether we can manage global ecosystems to support us today and into the future. While many current challenges, such as massive carbon dioxide emissions or nitrogen fixation, are unprecedented, others have in fact been unfolding for thousands of years. Here I show the results of studies combining the fossil record with DNA analyses and advanced statistical techniques to discover the footprint of human activities deep into the past. Using the islands of the Caribbean as a microcosm offers crucial lessons for the future: the signature of human landscape transformation on biodiversity is extinction, and it would take nature millions of years to restore what was lost over only a few hundred years.
Twenty million years of extinction and survival in the Caribbean (v.2)Liliana Davalos
Whether equilibrium dynamics between extinction and processes generating new species governs biodiversity, or instead stochastic changes shape diversity over time is one of the central questions in evolutionary biology. But tests of equilibrium dynamics since MacArthur and Wilson formulated their model have primarily involved colonization and extinction, neglecting speciation. Analyses using recently developed algorithms fitted to branching times for both extant and extinct bats from the Greater Antilles reveal a 20-40-million year equilibrium between high extinction rates offset by both colonization and speciation. Since at least 13 species have gone extinct over the last 20,000 years, however, this fauna is no longer in equilibrium. It would take millions of years for dynamics were to restore the lost diversity to their equilibrium preceding the Holocene. There is a longstanding debate on whether this pulse of mammalian extinction, which extended to all of North America, is linked to human colonization, or instead corresponds to the loss of island area and climate change at the end of the last glaciation. On the islands, however, humans only arrived a few thousand years ago, providing an opportunity to test these hypotheses. Bayesian models of the difference between faunal last appearance and human first appearance, together with the largest database of archaeological and paleontological radiocarbon dates reveal the majority of extinction events occurred after human arrival. While some large bodied species were lost soon after human colonization and may have been hunted, others may have been vulnerable to pre-Columbian agriculture, and many more to predators introduced during European colonization. The demise of the Caribbean mammal fauna as a result of increasing human transformation of local ecosystems provides lessons for our own time and the extinction events today and into the future.
¿De dónde viene y para dónde va la deforestación en Colombia?Liliana Davalos
Talk given at ICESI university in Cali, Colombia on 17 July. En las últimas décadas la deforestación en Colombia a menudo se explica como una consecuencia, directa o indirecta, de los cultivos ilícitos. Sin embargo, la influencia de los cultivos ilícitos y especialmente de los sembrados de coca sobre la deforestación requiere un contexto con otras actividades agrícolas, además de comparaciones entre los tres países productores: Colombia, Perú y Bolivia. Esta presentación examina los resultados de múltiples estudios sobre deforestación para evaluar el impacto de los ilícitos sobre la deforestación utilizando modelos cuantitativos. Aunque los cultivos de coca son responsables de una fracción importante de la deforestación directa, esta es mínima comparada con otras actividades, especialmente la praderización de todas las regiones forestales del país. Al mismo tiempo, la coca actúa como punta de lanza de la frontera agrícola en la Amazonía y puede tener consecuencias nefastas para la flora y fauna endémica de bosques andinos y del Chocó biogeográfico. Ya que el PIB de ganadería se desplomó al dispararse la pérdida de bosque, tampoco es el mercado del ganado el responsable de la deforestación, por lo menos en el departamento del Guaviare. Por tanto la praderización en Guaviare y probablemente en otras regiones está más ligada a la urbanización y desarrollo de mercados locales de tierras que a la ganadería. La principal conclusión de este análisis es que la causa última de buena parte de la deforestación es la conversión de la reserva forestal a propiedades privadas en zonas de rápido desarrollo. Paradójicamente, la coca es ancilar a este motor de deforestación.
Nexos desarrollo - cultivos ilícitos y tres propuestas para el siguiente sigloLiliana Davalos
Talk given as part of the cultural program of Banco de la República in Cali and Medellín, Colombia on 17 and 18 July. The talk includes three approaches to tackle the challenge of tropical deforestation for the next 100 years.
ESR spectroscopy in liquid food and beverages.pptxPRIYANKA PATEL
With increasing population, people need to rely on packaged food stuffs. Packaging of food materials requires the preservation of food. There are various methods for the treatment of food to preserve them and irradiation treatment of food is one of them. It is the most common and the most harmless method for the food preservation as it does not alter the necessary micronutrients of food materials. Although irradiated food doesn’t cause any harm to the human health but still the quality assessment of food is required to provide consumers with necessary information about the food. ESR spectroscopy is the most sophisticated way to investigate the quality of the food and the free radicals induced during the processing of the food. ESR spin trapping technique is useful for the detection of highly unstable radicals in the food. The antioxidant capability of liquid food and beverages in mainly performed by spin trapping technique.
The use of Nauplii and metanauplii artemia in aquaculture (brine shrimp).pptxMAGOTI ERNEST
Although Artemia has been known to man for centuries, its use as a food for the culture of larval organisms apparently began only in the 1930s, when several investigators found that it made an excellent food for newly hatched fish larvae (Litvinenko et al., 2023). As aquaculture developed in the 1960s and ‘70s, the use of Artemia also became more widespread, due both to its convenience and to its nutritional value for larval organisms (Arenas-Pardo et al., 2024). The fact that Artemia dormant cysts can be stored for long periods in cans, and then used as an off-the-shelf food requiring only 24 h of incubation makes them the most convenient, least labor-intensive, live food available for aquaculture (Sorgeloos & Roubach, 2021). The nutritional value of Artemia, especially for marine organisms, is not constant, but varies both geographically and temporally. During the last decade, however, both the causes of Artemia nutritional variability and methods to improve poorquality Artemia have been identified (Loufi et al., 2024).
Brine shrimp (Artemia spp.) are used in marine aquaculture worldwide. Annually, more than 2,000 metric tons of dry cysts are used for cultivation of fish, crustacean, and shellfish larva. Brine shrimp are important to aquaculture because newly hatched brine shrimp nauplii (larvae) provide a food source for many fish fry (Mozanzadeh et al., 2021). Culture and harvesting of brine shrimp eggs represents another aspect of the aquaculture industry. Nauplii and metanauplii of Artemia, commonly known as brine shrimp, play a crucial role in aquaculture due to their nutritional value and suitability as live feed for many aquatic species, particularly in larval stages (Sorgeloos & Roubach, 2021).
Remote Sensing and Computational, Evolutionary, Supercomputing, and Intellige...University of Maribor
Slides from talk:
Aleš Zamuda: Remote Sensing and Computational, Evolutionary, Supercomputing, and Intelligent Systems.
11th International Conference on Electrical, Electronics and Computer Engineering (IcETRAN), Niš, 3-6 June 2024
Inter-Society Networking Panel GRSS/MTT-S/CIS Panel Session: Promoting Connection and Cooperation
https://www.etran.rs/2024/en/home-english/
This presentation explores a brief idea about the structural and functional attributes of nucleotides, the structure and function of genetic materials along with the impact of UV rays and pH upon them.
Seminar of U.V. Spectroscopy by SAMIR PANDASAMIR PANDA
Spectroscopy is a branch of science dealing the study of interaction of electromagnetic radiation with matter.
Ultraviolet-visible spectroscopy refers to absorption spectroscopy or reflect spectroscopy in the UV-VIS spectral region.
Ultraviolet-visible spectroscopy is an analytical method that can measure the amount of light received by the analyte.
Travis Hills' Endeavors in Minnesota: Fostering Environmental and Economic Pr...Travis Hills MN
Travis Hills of Minnesota developed a method to convert waste into high-value dry fertilizer, significantly enriching soil quality. By providing farmers with a valuable resource derived from waste, Travis Hills helps enhance farm profitability while promoting environmental stewardship. Travis Hills' sustainable practices lead to cost savings and increased revenue for farmers by improving resource efficiency and reducing waste.
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.
Phenomics assisted breeding in crop improvementIshaGoswami9
As the population is increasing and will reach about 9 billion upto 2050. Also due to climate change, it is difficult to meet the food requirement of such a large population. Facing the challenges presented by resource shortages, climate
change, and increasing global population, crop yield and quality need to be improved in a sustainable way over the coming decades. Genetic improvement by breeding is the best way to increase crop productivity. With the rapid progression of functional
genomics, an increasing number of crop genomes have been sequenced and dozens of genes influencing key agronomic traits have been identified. However, current genome sequence information has not been adequately exploited for understanding
the complex characteristics of multiple gene, owing to a lack of crop phenotypic data. Efficient, automatic, and accurate technologies and platforms that can capture phenotypic data that can
be linked to genomics information for crop improvement at all growth stages have become as important as genotyping. Thus,
high-throughput phenotyping has become the major bottleneck restricting crop breeding. Plant phenomics has been defined as the high-throughput, accurate acquisition and analysis of multi-dimensional phenotypes
during crop growing stages at the organism level, including the cell, tissue, organ, individual plant, plot, and field levels. With the rapid development of novel sensors, imaging technology,
and analysis methods, numerous infrastructure platforms have been developed for phenotyping.
Lying through your teeth: saturation and non independence in morphological data, and what to do about it
1. Lying through your teeth: saturation and non
independence in morphological data, and what to
do about it
Liliana M. Dávalos —Stony Brook University
Paul M. Velazco —American Museum of Natural History
Omar M. Warsi —Stony Brook University
Peter D. Smits —University of Chicago
Nancy B. Simmons —American Museum of Natural History
3. Genome not always
available
•Majority of species are
extinct
•Fossils are all that
remain
•Phylogenies must use
morphology
•How?
Morgan Czaplewski 2012 Evolutionary
History of Bats
4. Total evidence Conditional combination
Hermsen Hendricks 2008 Ann Missouri Springer et al. 2007 Syst Biol
Bot Gard
5. Assumptions of
phylogeny
•Homology: character
changes reflect
common descent
•IID: Independent and
Identically Distributed
7. Saturation is not
everything
•If rates of evolution are
high, then signal
erased over time
•Results in
unresolved
phylogeny
•Other signal must
emerge to resolve
phylogeny
• First position
• Second position
o Third position
Dávalos Perkins 2008 Genomics
10. 19
9.5
0
3.9
2.6
1.3
0
Molecular Morphological
Frequency (percent)
A
Figure B
Pairwise dissimilarity between characters
Relative density between morphological characters
0.0 0.2 0.4 0.6 0.8 1.0
2.5
2.0
1.5
1.0
0.5
0.0
Signal is amplified by
repetition
•Measured dissimilarity
between pairs of
characters
•25% sequence
characters are
completely dissimilar
•Despite protein-coding
loci
•This is not the case for
dental characters
Dávalos et al. Accepted Syst Biol
12. Data models don’t
match
•Less is more when
collecting certain kinds of
characters
•Dental data violate key
assumptions of
phylogenetic models
•Saturation, convergence,
and non-independence
•= model failure
•New data models needed
Czaplewski et al. 2003 Caldasia
14. Thanks!
• Funding
• NSF—DEB
• CIDER—SBU
• Speciation diversification: A.
Cirranello, E. Dumont, A. Russell,
N. Simmons, P. Velazco
• N. Gerardo, A. Wilson
• Dávalos Lab
• Phylogenetics: B. Baird, S.
DelSerra, A. Goldberg, O.
Warsi, L. Yohe