1. The document discusses three main questions regarding human evolutionary genetics: the debate between hybridization models vs. the Southern dispersal route out of Africa, the coevolution of cultural and biological diversity, and challenges to the persistence of racial paradigms given genomic data.
2. Regarding the first question, the author notes several problems with hybridization hypotheses and presents evidence supporting an earlier dispersal of modern humans out of Africa via a Southern route, avoiding contact with Neanderthals.
3. For the second question, the author reviews evidence that increases in brain size did not necessarily correlate with genes associated with cognitive functions, and that cultural and linguistic changes likely evolved in parallel with biological changes.
4.
1. The document compares genetic and linguistic diversity in Europe and finds some correlations between the two.
2. Structural features of languages may provide a better basis for comparison than vocabulary. Principal component analysis of genetic and linguistic data show some similarities in clustering.
3. Recent population mixing can account for some inconsistencies between the genetic and linguistic patterns. Overall, geography, genetics, and language are interrelated but influenced by separate evolutionary processes over long time periods.
1. The human genome is very similar to the chimpanzee genome, with individual genetic diversity among humans being the lowest of all primates.
2. While population differences among humans are also relatively low, genetic studies show inconsistent clustering of genotypes across genes and loci.
3. Models of human migration out of Africa best explain observed genetic patterns, with gradients of diversity correlated with distance from Africa.
This document summarizes research on human genetic population structure and diversity. The key points are:
- 85% of human genetic variation exists within populations, 10% among continental groups, and 5% among populations within the same continent.
- Clustering analyses of genetic data yield inconsistent groupings depending on the traits or markers used, and populations form a continuous gradient without clear boundaries.
- The patterns of genetic diversity are consistent with an origin of modern humans in Africa followed by serial founder effects during dispersal, around 56,000 years ago.
This document summarizes research on the origins of Ashkenazi Levites based on analysis of Y-chromosome DNA from 66 Ashkenazi Levites with carefully constructed genealogies. It finds that over 50% of contemporary Ashkenazi Levites belong to a single lineage, Haplogroup R1a, which shows a close genetic relationship to non-Jewish populations in Eastern Europe. The research aims to determine if 4 individuals claiming descent from Yeshaya Horowitz are direct male-line descendants by comparing their Y-DNA to a worldwide phylogeny of R1a lineages. Preliminary results place the Ashkenazi Levites within the European branch of R1a and indicate a most recent common ancestor for the Hor
Bio380 Human Evolution: Waking the deadMark Pallen
Bio380 Human Evolution, genes and genomes lecture on contribution of archaic populations to gene pool of anatomically modern humans, including Neanderthals and Denisovan
My first lecture on the second year Bio263 module on human evolution. An overview of human evolution and palaeoanthropology. Taxonomy and humanity's place in nature. Who is our closest living relative? Evidence from morphology and molecules.
See also Slidecast on YouTube
http://www.youtube.com/watch?v=28bLQIGRbWU
1. The document compares genetic and linguistic diversity in Europe and finds some correlations between the two.
2. Structural features of languages may provide a better basis for comparison than vocabulary. Principal component analysis of genetic and linguistic data show some similarities in clustering.
3. Recent population mixing can account for some inconsistencies between the genetic and linguistic patterns. Overall, geography, genetics, and language are interrelated but influenced by separate evolutionary processes over long time periods.
1. The human genome is very similar to the chimpanzee genome, with individual genetic diversity among humans being the lowest of all primates.
2. While population differences among humans are also relatively low, genetic studies show inconsistent clustering of genotypes across genes and loci.
3. Models of human migration out of Africa best explain observed genetic patterns, with gradients of diversity correlated with distance from Africa.
This document summarizes research on human genetic population structure and diversity. The key points are:
- 85% of human genetic variation exists within populations, 10% among continental groups, and 5% among populations within the same continent.
- Clustering analyses of genetic data yield inconsistent groupings depending on the traits or markers used, and populations form a continuous gradient without clear boundaries.
- The patterns of genetic diversity are consistent with an origin of modern humans in Africa followed by serial founder effects during dispersal, around 56,000 years ago.
This document summarizes research on the origins of Ashkenazi Levites based on analysis of Y-chromosome DNA from 66 Ashkenazi Levites with carefully constructed genealogies. It finds that over 50% of contemporary Ashkenazi Levites belong to a single lineage, Haplogroup R1a, which shows a close genetic relationship to non-Jewish populations in Eastern Europe. The research aims to determine if 4 individuals claiming descent from Yeshaya Horowitz are direct male-line descendants by comparing their Y-DNA to a worldwide phylogeny of R1a lineages. Preliminary results place the Ashkenazi Levites within the European branch of R1a and indicate a most recent common ancestor for the Hor
Bio380 Human Evolution: Waking the deadMark Pallen
Bio380 Human Evolution, genes and genomes lecture on contribution of archaic populations to gene pool of anatomically modern humans, including Neanderthals and Denisovan
My first lecture on the second year Bio263 module on human evolution. An overview of human evolution and palaeoanthropology. Taxonomy and humanity's place in nature. Who is our closest living relative? Evidence from morphology and molecules.
See also Slidecast on YouTube
http://www.youtube.com/watch?v=28bLQIGRbWU
1) The document discusses ancient DNA evidence from Europe that shows three ancestral components - Western Hunter-Gatherer (WHG), Early European Farmer (EEF), and Ancient North Eurasian (ANE).
2) Analysis of ancient DNA from Mesolithic Europeans showed they carried Y-chromosome haplogroup I, while Neolithic farmers carried haplogroup G. Metal Age samples had more diversity including haplogroups R1b and R1a.
3) The data supports a model where WHG ancestry was most prominent in Northern Europeans, EEF ancestry increased towards the South, and ANE ancestry from Siberian populations entered the gene pool after the Neolithic, reaching highest levels in Northern Europeans.
Poster at the International Biogeography Society Meetings in Bayreuth 2015Liliana Davalos
This document summarizes a study that tested the hypothesis that glacial refugia in the Neotropics drove increased speciation during the Pleistocene. The study found that:
1) Simulations using constant speciation and extinction rates always resulted in more speciation events occurring in the Pleistocene, even without refugia.
2) Simply comparing the ages of sister species fails to properly test the refugia hypothesis.
3) To truly test the hypothesis, models are needed that allow diversification rates to change over time.
There are two main competing theories for early human origins: the multiregional hypothesis and the Out-of-Africa hypothesis. The multiregional hypothesis proposes that modern humans evolved simultaneously from early Homo species in different regions with gene flow between populations. The Out-of-Africa hypothesis suggests that anatomically modern humans arose in Africa and later migrated out, replacing indigenous populations. Evidence from morphology, archaeology, and genetics has been debated, but recent genetic studies provide support for multiple migrations out of Africa with some limited interbreeding.
Segunda presentación del Seminario impartido por Daniel Turbón en el Grupo Ciencia, Razón y Fe, el 29 de mayo de 2013.
Los estudios de linajes de mtDNA -el materno- en poblaciones humanas actuales, habían permitido construir un mapa de la diversidad genética y de las probables rutas migratorias. Nuevos estudios, utilizando 3,2 millones de distintos polimorfismos genéticos de un solo locus (SNPs), han conseguido completar el mapa genético y calcular la separación más antigua detectada que se cifra en superior a 100.000 desde el presente, entre los actuales africanos Khoe-San (antes Bosquimanos) y los melanoafricanos que de lenguas de raíz Bantú.
Por estudios de paleogenética de Neandertales sabemos que éstos comparten más variantes genéticas con los seres humanos de hoy en día, en Eurasia, que con los seres humanos actuales en África subsahariana, lo que sugiere que el flujo genético de los Neandertales a los ancestros de los No Africanos se produjo antes de la divergencia de los actuales grupos euroasiáticos entre sí. Los europeos tenemos un 2,5% de nuestro genoma de los Neandertales.
Ha sido una sorpresa el descubrimiento de los Denisovanos, un grupo humano nuevo. Se trata de dos restos esqueléticos hallados en Denisova, una cueva del sur de Siberia, cerca del Himalaya, en los que se ha preservado bien el ADN. Están datados en 50.000 años. No eran ni Neandertales ni humanos modernos, y coexistieron con ambos, y con Homo sapiens incluso se aparearon. Es muy extraño que, para tener entre 30.000 y 50.000 años, el genoma de los Denisovanos esté tan bien conservado. En Neandertales de esta antigüedad, es habitual que solo el 1% del genoma que analizamos sea original y que el 99% restante corresponda a microbios que han contaminado la muestra, lo que dificulta y limita el trabajo. En el caso de Denisova, el 70% del genoma es original, una joya.
El descubrimiento de que el 5% del genoma de las poblaciones de Melanesia es herencia de los Denisovanos indica que, en algún momento, tuvieron que estar en algún lugar donde se encontraron con los ancestros de los Melanesios, y presumiblemente esto no ocurrió en el sur de Siberia. Se cree que los Denisovanos se extendieron por Asia de modo similar a como los Neandertales se extendieron por Europa y, al igual que los Neandertales, se extinguieron tras la llegada de los humanos modernos.
Se han detectado introgresiones de genomas de Neandertales y Denisovanos en nuestro genoma. Concretamente, el sistema de antígenos leucocitarios humanos (HLA) clase I muestra cómo los humanos modernos adquirimos la variante HLA-B *73 en el oeste de Asia a través de una mezcla con Denisovanos. Los Homo sapiens (ancestros del humano moderno), los Denisovanos y los Neandertales debieron separarse hace unos 400.000 años. Los Neandertales emigraron de África hacia Europa y Asia occidental; los Denisovanos dejaron África por Asia oriental. Los ancestros de los humanos modernos salieron de África hace sólo 65.000 años.
This study analyzed genetic differentiation between Ethiopian and Nigerian village chicken populations using genome-wide genotyping data from 52 samples across 14 populations. Principal component and admixture analyses showed genetic separation between the two countries, with Ethiopian chickens exhibiting more diversity. Incomplete genetic differentiation was observed between countries despite large geographical distance. Higher molecular variation was found within Ethiopian populations compared to Nigerian populations. The results support some level of genetic differentiation between village chicken populations in Ethiopia and Nigeria.
Colloquium Presentation 2009 Fall BongsooBongsoo Park
The document summarizes a study that analyzed genetic differences between human populations to understand patterns of human adaptation. The study found that:
1) Most genetic differences between populations can be explained by neutral processes like genetic drift rather than strong positive selection.
2) There are very few examples of alleles reaching near fixation between populations due to strong selection.
3) Population bottlenecks and weak selective pressures along with drift likely explain more of the genetic differences observed between human populations than strong positive selection alone.
Bare-bones summaries of current research papers. Basic data, graphics and links only. News items to be fleshed out on tour. Part 1 addresses the genomic basis for understanding early humans in Franco-Iberia. We are at the peak of modeling ancient gene flow based on modern and 'fossil' DNA. Addressed is the genetic makeup of prehistoric modern humans Neandertals and Denisovans. Presentation generally follows publication order. Includes links to the original abstracts--the online papers usually lie behind a paywall.
This document discusses using ancient DNA analysis to study archaeological remains. It notes that ancient DNA is typically fragmented into small pieces 100-500 base pairs long. Contamination from other sources is also a major issue. However, ancient DNA analysis can be used to study species phylogenies, hominin evolution, past diets and behaviors, origins of domestication, and population histories. As a case study, the document discusses analyzing ancient DNA from pygmy hippopotamus remains on Cyprus to learn about population dynamics and what caused their extinction 12,000 years ago alongside human arrival and climate change. Stable isotope analysis of bones and teeth can also provide clues about past diets.
A presentation as a webinar for the Winn Feline Foundation that focuses on recent findings related to the signatures of selection in the domestic cat genome
This ppt clarifies the differences and similarities of DNA of human and ape. Gives a conclusion that how the minimum differences gives major differences among human and ape.
Evolutionary Genetics by: Kim Jim F. Raborar, RN, MAEd(ue)Kim Jim Raborar
This presentation was created as a partial fulfillment of the requirements in the subject Advanced Genetics. Everything that was here were kinda symbolic. I mean, you could recognize that this was a product of so much data interpretation. I therefore suggest you read and read a lot first before you go back to this presentation. Or you could just contact me so i could send you the key-pointers.
Have a super nice day.
Kimy
I investigated the assumption that race and ancestry can be determined using DNA sequence analysis. I was able to present the results of my senior project at Luther College Research Symposium in April 2010.
This study aims to quantify and compare the gut microbiome diversity among populations of the endangered Channel Island fox. Scat samples were collected from all six inhabited Channel Islands and genomic DNA was extracted. The DNA was amplified using cytochrome b and 16S rRNA V4 region primers, confirming the presence of canid DNA and microorganisms. The 16S rRNA V4 region from available genomes will be sequenced and microbial diversity quantified and compared among populations. It is hypothesized that more phylogenetically similar populations will have more similar gut microbiomes, and foxes with lower body conditions will have less diverse microbiota.
Phyllostomidae and the evolution of dietYann Gager
This document describes a study on the evolution of diet in the bat family Phyllostomidae. It presents the goals, sampling methods, phylogenetic analyses, and results of the study. The study constructed a phylogenetic tree of 120 phyllostomid bat species using 5 genes. Ancestral character estimation was used to infer the evolution of diet across the tree and found specialization in diet but also opportunistic omnivory. Future work could improve resolution by adding more taxa and genes.
This presentation was my Senior Biology Major Capstone and was given along with a written paper. The presentation discusses three scientific papers following the ebola virus from fruit bats to carriers such as gorillas, chimpanzees, and humans.
Mitochondrial DNA is used to study human population genetics and evolution. The document discusses two examples:
1) Analysis of mitochondrial DNA from 31 bone remains from the Taforalt cave in Morocco dated to 12,000 years ago found both Eurasian and North African components, showing genetic continuity with modern Moroccan populations.
2) Analysis of Neanderthal mitochondrial DNA found it to be distinct from modern human DNA, indicating Neanderthals were a separate species and did not directly contribute to the modern human gene pool.
1) The document discusses ancient DNA evidence from Europe that shows three ancestral components - Western Hunter-Gatherer (WHG), Early European Farmer (EEF), and Ancient North Eurasian (ANE).
2) Analysis of ancient DNA from Mesolithic Europeans showed they carried Y-chromosome haplogroup I, while Neolithic farmers carried haplogroup G. Metal Age samples had more diversity including haplogroups R1b and R1a.
3) The data supports a model where WHG ancestry was most prominent in Northern Europeans, EEF ancestry increased towards the South, and ANE ancestry from Siberian populations entered the gene pool after the Neolithic, reaching highest levels in Northern Europeans.
Poster at the International Biogeography Society Meetings in Bayreuth 2015Liliana Davalos
This document summarizes a study that tested the hypothesis that glacial refugia in the Neotropics drove increased speciation during the Pleistocene. The study found that:
1) Simulations using constant speciation and extinction rates always resulted in more speciation events occurring in the Pleistocene, even without refugia.
2) Simply comparing the ages of sister species fails to properly test the refugia hypothesis.
3) To truly test the hypothesis, models are needed that allow diversification rates to change over time.
There are two main competing theories for early human origins: the multiregional hypothesis and the Out-of-Africa hypothesis. The multiregional hypothesis proposes that modern humans evolved simultaneously from early Homo species in different regions with gene flow between populations. The Out-of-Africa hypothesis suggests that anatomically modern humans arose in Africa and later migrated out, replacing indigenous populations. Evidence from morphology, archaeology, and genetics has been debated, but recent genetic studies provide support for multiple migrations out of Africa with some limited interbreeding.
Segunda presentación del Seminario impartido por Daniel Turbón en el Grupo Ciencia, Razón y Fe, el 29 de mayo de 2013.
Los estudios de linajes de mtDNA -el materno- en poblaciones humanas actuales, habían permitido construir un mapa de la diversidad genética y de las probables rutas migratorias. Nuevos estudios, utilizando 3,2 millones de distintos polimorfismos genéticos de un solo locus (SNPs), han conseguido completar el mapa genético y calcular la separación más antigua detectada que se cifra en superior a 100.000 desde el presente, entre los actuales africanos Khoe-San (antes Bosquimanos) y los melanoafricanos que de lenguas de raíz Bantú.
Por estudios de paleogenética de Neandertales sabemos que éstos comparten más variantes genéticas con los seres humanos de hoy en día, en Eurasia, que con los seres humanos actuales en África subsahariana, lo que sugiere que el flujo genético de los Neandertales a los ancestros de los No Africanos se produjo antes de la divergencia de los actuales grupos euroasiáticos entre sí. Los europeos tenemos un 2,5% de nuestro genoma de los Neandertales.
Ha sido una sorpresa el descubrimiento de los Denisovanos, un grupo humano nuevo. Se trata de dos restos esqueléticos hallados en Denisova, una cueva del sur de Siberia, cerca del Himalaya, en los que se ha preservado bien el ADN. Están datados en 50.000 años. No eran ni Neandertales ni humanos modernos, y coexistieron con ambos, y con Homo sapiens incluso se aparearon. Es muy extraño que, para tener entre 30.000 y 50.000 años, el genoma de los Denisovanos esté tan bien conservado. En Neandertales de esta antigüedad, es habitual que solo el 1% del genoma que analizamos sea original y que el 99% restante corresponda a microbios que han contaminado la muestra, lo que dificulta y limita el trabajo. En el caso de Denisova, el 70% del genoma es original, una joya.
El descubrimiento de que el 5% del genoma de las poblaciones de Melanesia es herencia de los Denisovanos indica que, en algún momento, tuvieron que estar en algún lugar donde se encontraron con los ancestros de los Melanesios, y presumiblemente esto no ocurrió en el sur de Siberia. Se cree que los Denisovanos se extendieron por Asia de modo similar a como los Neandertales se extendieron por Europa y, al igual que los Neandertales, se extinguieron tras la llegada de los humanos modernos.
Se han detectado introgresiones de genomas de Neandertales y Denisovanos en nuestro genoma. Concretamente, el sistema de antígenos leucocitarios humanos (HLA) clase I muestra cómo los humanos modernos adquirimos la variante HLA-B *73 en el oeste de Asia a través de una mezcla con Denisovanos. Los Homo sapiens (ancestros del humano moderno), los Denisovanos y los Neandertales debieron separarse hace unos 400.000 años. Los Neandertales emigraron de África hacia Europa y Asia occidental; los Denisovanos dejaron África por Asia oriental. Los ancestros de los humanos modernos salieron de África hace sólo 65.000 años.
This study analyzed genetic differentiation between Ethiopian and Nigerian village chicken populations using genome-wide genotyping data from 52 samples across 14 populations. Principal component and admixture analyses showed genetic separation between the two countries, with Ethiopian chickens exhibiting more diversity. Incomplete genetic differentiation was observed between countries despite large geographical distance. Higher molecular variation was found within Ethiopian populations compared to Nigerian populations. The results support some level of genetic differentiation between village chicken populations in Ethiopia and Nigeria.
Colloquium Presentation 2009 Fall BongsooBongsoo Park
The document summarizes a study that analyzed genetic differences between human populations to understand patterns of human adaptation. The study found that:
1) Most genetic differences between populations can be explained by neutral processes like genetic drift rather than strong positive selection.
2) There are very few examples of alleles reaching near fixation between populations due to strong selection.
3) Population bottlenecks and weak selective pressures along with drift likely explain more of the genetic differences observed between human populations than strong positive selection alone.
Bare-bones summaries of current research papers. Basic data, graphics and links only. News items to be fleshed out on tour. Part 1 addresses the genomic basis for understanding early humans in Franco-Iberia. We are at the peak of modeling ancient gene flow based on modern and 'fossil' DNA. Addressed is the genetic makeup of prehistoric modern humans Neandertals and Denisovans. Presentation generally follows publication order. Includes links to the original abstracts--the online papers usually lie behind a paywall.
This document discusses using ancient DNA analysis to study archaeological remains. It notes that ancient DNA is typically fragmented into small pieces 100-500 base pairs long. Contamination from other sources is also a major issue. However, ancient DNA analysis can be used to study species phylogenies, hominin evolution, past diets and behaviors, origins of domestication, and population histories. As a case study, the document discusses analyzing ancient DNA from pygmy hippopotamus remains on Cyprus to learn about population dynamics and what caused their extinction 12,000 years ago alongside human arrival and climate change. Stable isotope analysis of bones and teeth can also provide clues about past diets.
A presentation as a webinar for the Winn Feline Foundation that focuses on recent findings related to the signatures of selection in the domestic cat genome
This ppt clarifies the differences and similarities of DNA of human and ape. Gives a conclusion that how the minimum differences gives major differences among human and ape.
Evolutionary Genetics by: Kim Jim F. Raborar, RN, MAEd(ue)Kim Jim Raborar
This presentation was created as a partial fulfillment of the requirements in the subject Advanced Genetics. Everything that was here were kinda symbolic. I mean, you could recognize that this was a product of so much data interpretation. I therefore suggest you read and read a lot first before you go back to this presentation. Or you could just contact me so i could send you the key-pointers.
Have a super nice day.
Kimy
I investigated the assumption that race and ancestry can be determined using DNA sequence analysis. I was able to present the results of my senior project at Luther College Research Symposium in April 2010.
This study aims to quantify and compare the gut microbiome diversity among populations of the endangered Channel Island fox. Scat samples were collected from all six inhabited Channel Islands and genomic DNA was extracted. The DNA was amplified using cytochrome b and 16S rRNA V4 region primers, confirming the presence of canid DNA and microorganisms. The 16S rRNA V4 region from available genomes will be sequenced and microbial diversity quantified and compared among populations. It is hypothesized that more phylogenetically similar populations will have more similar gut microbiomes, and foxes with lower body conditions will have less diverse microbiota.
Phyllostomidae and the evolution of dietYann Gager
This document describes a study on the evolution of diet in the bat family Phyllostomidae. It presents the goals, sampling methods, phylogenetic analyses, and results of the study. The study constructed a phylogenetic tree of 120 phyllostomid bat species using 5 genes. Ancestral character estimation was used to infer the evolution of diet across the tree and found specialization in diet but also opportunistic omnivory. Future work could improve resolution by adding more taxa and genes.
This presentation was my Senior Biology Major Capstone and was given along with a written paper. The presentation discusses three scientific papers following the ebola virus from fruit bats to carriers such as gorillas, chimpanzees, and humans.
Mitochondrial DNA is used to study human population genetics and evolution. The document discusses two examples:
1) Analysis of mitochondrial DNA from 31 bone remains from the Taforalt cave in Morocco dated to 12,000 years ago found both Eurasian and North African components, showing genetic continuity with modern Moroccan populations.
2) Analysis of Neanderthal mitochondrial DNA found it to be distinct from modern human DNA, indicating Neanderthals were a separate species and did not directly contribute to the modern human gene pool.
This study examined 79 dry crania (55 male and 24 female) from southern Nigeria to determine the incidence and dimensions of single and double hypoglossal canals, and whether these dimensions differ between sexes. Measurements were taken of the internal and external diameters of the hypoglossal canals. The results showed significant differences in all dimensions between males and females. Bilateral single hypoglossal canals were most prevalent. In conclusion, the size of the hypoglossal canal is sex-specific, with significant differences found between males and females in this population.
This study examined 79 dry crania (55 male and 24 female) from southern Nigeria to determine the incidence and dimensions of single and double hypoglossal canals, and whether these dimensions differ between sexes. Measurements were taken of the internal and external diameters of the hypoglossal canals. The results showed significant differences in all dimensions between males and females. Bilateral single hypoglossal canals were most prevalent. In conclusion, the size of the hypoglossal canal is sex-specific, with significant differences found between males and females in this population.
Talk at Institut Jean Nicod on 6 October 2010Robin Ryder
1. The document discusses using phylogenetic methods from evolutionary biology to model and analyze the diversification and development of languages over time.
2. These methods allow for quantitative dating of language relationships and splits, accounting for uncertainty and factors like borrowing between languages.
3. When applied to Indo-European language data, phylogenetic analysis strongly supports an Anatolian origin for Proto-Indo-European around 8000BP rather than the Kurgan hypothesis.
Analysis of dense genome-wide single nucleotide polymorphisms unlocks the gen...Takele Desta
The two Ethiopian chicken populations, Horro and Jarso, show genetic divergence likely due to limited gene flow, different demographic histories, and management under different ecological conditions. Horro chickens show less genetic diversity than Jarso chickens. Analysis of single nucleotide polymorphisms found significant genetic differentiation between the two populations, with 28% of genetic variation explained between populations. The results indicate the populations descended from different ancestral origins and developed independently under different environmental and management conditions.
The climbing vine kudzu, a member of the leguminous
pea family (Fabaceae), was introduced into the USA
from its native Asia in the 1800s. It was initially lauded
for efficacy in erosion control along highways and as a
high-quality grazing crop for livestock. P. montana var.
lobata has since become a truculent invasive, spreading
via vegetative runners and seed dispersal. Seven
million acres of the American southeast are now
plagued by this vine.
Project Overview: Ecological & Evolutionary Genetics of Southwestern White Pi...Justin C. Bagley
This project studies the ecological and evolutionary processes influencing the distribution, genetic diversity, adaptation, and persistence of southwestern white pine across its range. The researchers are analyzing genome-wide data from samples of southwestern white pine and limber pine using demographic modeling to infer the timing and influence of processes shaping divergence between the species. The best-supported model found speciation with gene flow between the species approximately 11 million years ago, with ongoing gene flow between the peripheral southwestern white pine lineage and limber pine. This supports speciation consistent with a model of bounded hybrid superiority rather than genomic islands of differentiation forming between the lineages.
The document discusses recent findings in ancient DNA research. It summarizes a 2014 Nature article that analyzed ancient human genomes from present-day Europeans and suggested three ancestral populations. It also lists 27 other relevant published ancient DNA studies from the past few years. Key criteria for evaluating the reliability of ancient DNA analyses are discussed, such as the journal and researchers involved, sample handling, contamination controls, and consistency of results.
Episode 5(2): Genomics, our African genesis and family tree - Meetup session 17William Hall
This is the 17th of 23 presentations in a series introducing and outlining my hypertext book project, "Application Holy Wars or a New Reformation - A Fugue on the Theory of Knowledge". The project explores the interactions of technology and cognition in the extraordinary evolutionary history of the human species.
The growing fossil record and detailed genomic evidence provides an increasingly detailed understanding of our ancestry and genealogy.
Fossils and lost tools recovered from the geological record give us hints as to what kinds of humans were present in particular geographic areas. Various forms of dating based on the decay rates of a variety of different radioactive elements together with geology and stratigraphy tell us when they were there. This record grows more detailed through time as more paleoanthropologists study more areas in more detail and as Moore's law speeds up the publication cycle.
Enabled by the application of Moore's law to automated gene sequencing technology, over the last 5 years the detail and volume of genomic evidence has doubled and redoubled several times over. We can now compare the exact sequence of nucleotides in every single gene in the entire genomes of individual people, apes, and even some of our extinct cousins who lived 50,000 years or more ago, and do this down to differences in single nucleotides (i.e., to identify single character differences between two texts that are about 3 billions of characters long - about 1.5 million pages of text). Comparing the genomes of these ancient deceased relatives tells us a lot about what happened as long as half a million years or more in the past.
From these kinds of evidence we now know a great deal more about our genealogical relationships than we did five years ago.
I am working with collaborators in Brazil, the U.S., and Mexico to complete genetic data analyses and manuscripts from two postdoctoral research fellowships. This slideshow presents a brief overview of the two main funded research projects that I am involved in.
This document summarizes a Darwin Day event held on February 11, 2011 that featured presentations from five researchers: James Mallet, Walter Salzburger, Eric Alm, Elisabeth Vrba, and a description of the new Science Library at the University of Oslo. It provides brief biographies of each researcher and lists some of their recent publications. It also includes a quote from Charles Darwin about the grandeur of evolution.
Biodiverse - Rosauer talk @ iEvoBio conference June 2010Dan Rosauer
Biodiverse is a tool for spatial analysis of biodiversity that calculates various biodiversity indices including species richness, endemism, phylogenetic diversity, and beta diversity. It was developed by researchers at UNSW to investigate patterns in Australian plants and animals. Biodiverse allows users to visualize species and phylogeny distributions, calculate biodiversity metrics for areas, cluster areas based on biological similarity, and test significance using randomization procedures. It has been used in studies of Australian flora, frogs, and primates.
THE HUMAN ANATOMY IN A THOUSAND YEARS (1).pptxAdebayoAbayomi3
The document summarizes the evolution of human anatomy over time and predictions for changes in the next 1000 years. It discusses theories of evolution, key stages in human evolution like Australopithecus and Homo Sapiens, and how humans have changed physically since our early ancestors. Tables compare features from the past, present and predicted future such as smaller brains and jaws, loss of hair and changes to bones, muscles and teeth. The document also notes limitations in predicting the future and references sources on human evolution.
Storyboard for "An Evolutionary Hypothesis for the Origins of Socio-Technical...William Hall
1) The document discusses the coevolution of technology, cognition, culture, and organizations in humans over millions of years, from tool-using savanna apes to today's socio-technical organizations.
2) Around 5 million years ago, climate change forced forest-dwelling apes out of East Africa, selecting for increased brain capacity and cultural adaptation on the savanna. Tool use and social cooperation allowed hunting and scavenging of large prey.
3) By 3-2 million years ago, hominins' competitive scavenging and hunting reduced other carnivore populations in East Africa, establishing hominins as top carnivores. The spread of tool-using hominins like Homo erect
The document discusses the Genome Russia Project, which aims to sequence and analyze the genomes of populations across the Russian Federation. This will fill one of the largest remaining gaps in mapping human genetic variation globally. Sequencing Russian populations is important because of their complex history involving migrations of Indo-Europeans, Uralic peoples, and Turkic peoples. It will provide insights into human population origins, disease studies, and evolutionary history. The Genome Russia Project is being endorsed by Russian scientific organizations and aims to become an example of international collaboration in genomics.
Mapping Biodiversity - The Atlas of Living AustraliaDonald Hobern
The document summarizes the Atlas of Living Australia project, which aims to provide open access to biodiversity data. It discusses challenges such as digitizing literature and specimens, standardizing data, integrating taxonomy, and developing tools for users. The Atlas will include a metadata repository, species pages, a regional atlas, and annotation tools to link data and comments. The goal is to make Australia's biological knowledge more accessible and usable.
Semantics of and for the diversity of life: Opportunities and perils of tryi...Hilmar Lapp
The document discusses using ontologies and reasoning to analyze biodiversity data at scale. It proposes using phyloreferences - a universal coordinate system for life based on phylogenetic trees - to unambiguously refer to taxa. It also describes representing phylogenetic clade definitions and the Tree of Life as an ontology, allowing taxon names and relationships to be rendered computable. The document outlines how ontologies and reasoning could be used to infer missing phenotypic data, synthesize knowledge about trait evolution, and generate hypotheses about genes involved in morphological diversity by linking model organism and comparative data. Scaling reasoning to the size of biodiversity knowledge is discussed, along with a proposed architecture using specialized reasoners and triplestores.
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Barbujani leicester
1. Human evolutionary
genetics
A few questions for the next
few years
Guido Barbujani
Dipartimento di Scienze della Vita e Biotecnologie
Università di Ferrara
g.barbujani@unife.it Leicester, April 1st, 2014
2. ER Mardis (2011) Nature 470: 198-203 doi:10.1038/nature09796
Revolutionary changes in our ability to generate genetic data over
the past decade
Date Time taken N authors Cost (US dollars)
2003 (HGP) 13 years 2,800 2.7 billion
2007 (Venter) 4 years 31 100 million
2008 (Watson) 4.5 months 27 1.5 million
Oct. 2008 342,502
Oct. 2009 little 70,333
Oct. 2010 29,092
Oct. 2012 6,618
Oct. 2013 2.5 days (exome) 5,096
http://www.genome.gov/sequencingcosts/
3. Questions concerning three things:
1. Hybridisation between human forms vs. the
Southern route of modern human expansion from
Africa
2. Evolution of cognitive functions vs. relationships
between cultural and biological diversity
3. Data on human genome diversity vs. persistence of
the racial paradigm
6. Hybridisation events proposed on the basis of HLA data.
Is this a parsimonious hypothesis?
Abi-Rached et al. (2011) Science 334: 89-94
1. Hybridisation vs. Southern route
Population Freq.
Papua Wosera 20.5 %
Australia Kimberley 8.3 %
China Yunnan 9.0 %
Israeli Jews 3.0 %
Albanians 2.5 %
Finnish 1.1 %
7. A simpler, and currently rather standard, view of likely
hybridisation processes.
1. Hybridisation vs. Southern route
Stoneking and Krause (2011) Nature Rev Genet 12: 603-614
Wall, J. D. et al. (2013)
Genetics 194: 199–209
8. Henn et al. (2012) Proc Natl
Acad Sci USA 109: 17758-17764
1. Hybridisation vs. Southern route
Scally and Durbin (2012)
Nature Rev Genet 13: 745-753
9. Nei and Roychoudhury (1993) Mol Biol Evol. 10: 927-943
Separation times from African populations
PREDICTION: Under SD we expect equal separation times from Africa for Europe and Asia;
under MD we expect significantly different separation times from Africa for Europe and Asia
1. Hybridisation vs. Southern route
10. FST = Genetic distance
LINKAGE
DISEQUILIBRIUM
T = Separation time Ne = eff. population size
But things are not so simple
Hayes et al. (2003) Novel multilocus measure of linkage
disequilibrium to estimate past effective population size.
Genome Res 13: 635-643
McVean (2002) A genealogical interpretation of linkage
disequilibrium. Genetics 162: 987-991
1. Hybridisation vs. Southern route
13. Significantly older separation between Africa and East
Asia / Oceania than between Africa and Europe
Lower 5% CL Estimate
(years ago)
Higher 5% CL
Europe 69,768 74,209 77,448
East Asia + Oceania 79,007 82,862 87,925
Oceania 92,609 97,799 104,142
1 generation = 25 years
1. Hybridisation vs. Southern route
15. 1. Hybridisation vs. Southern route
Reyes-Centeno et al. Proc Natl
Acad Sci USA (2014) in press
16. If most Papuans’ ancestors arrived via a Southern route, they missed by 1,000 miles the
nearest Neandertal with whom they could hybridize
Any better hypothesis?
1. Hybridisation vs. Southern route
A problem with the hybridization models
18. Another little problem
In all well-studied cases of hybridization, females of the invaded population were
incorporated in the invading population. However, Neandertal mtDNA has never
been observed in any current human population
1. Hybridisation vs. Southern route
19. Perhaps that’s not a problem?
An interbreeding success smaller than 2% for Neanderthal-human hybrids is fully
compatible with limited Neanderthal nuclear introgression and with no
introgression of mtDNA.
But perhaps it is?
Observed statistics
ABC, Approximate
Bayesian Computations
Comparison of observed
diversity statistics with
those generated under
alternative models
Currat and Excoffier (2011) Proc Natl Acad Sci USA 105: 15129-15134
1. Hybridisation vs. Southern route
20. Model 4, with no Neandertals contribution
to the mitochondrial genealogy, is at least 8
times as likely as any alternative coalescent-
based model
1. Hybridisation vs. Southern route
Ghirotto et al. (2011) Am J Phys Anthropol 146: 242-252.
21. Adding gene flow from Neandertals into the modern mtDNA pool
decreases the posterior probability with respect to a model with no
admixture
1. Hybridisation vs. Southern route
Ghirotto et al. (2011) Am J Phys Anthropol 146: 242-252.
22. What about the effects of population structure?
Neandertals
Ancestors of Eurasians
Ancestors of Africans
1. Hybridisation vs. Southern route
23. Evolution of brain size
2. Coevolution of cultural and biological diversity
26. H. erectus
H. sapiens
Neandertals
Trees inferred from morphometrics
Neandertals
H. erectus
H. sapiens
LEFT SIDE RIGHT SIDE
2. Coevolution of cultural and biological diversity
Di Vincenzo, F., P. Piras & G. Manzi (2012) Proceedings of
the European Society for the study of Human Evolution 1: 70.
27. Castillo-Morales A et al. (2014) Proc. R. Soc. B 281: 20132428.
Increased brain size in Mammals correlates with
over-representation of gene families not obviously
associated with cognitive functions
2. Coevolution of cultural and biological diversity
28. Somel et al. (2013) Nature Rev. Neurosciences 14: 112-127.
2. Coevolution of cultural and biological diversity
So, do we have any evidence for nearly
simultaneous origin of language and of
the FOXP2 regulatory mutation?
29. Similarity between gene trees and language
trees suggests parallel evolutionary changess
Cavalli-Sforza et al. (1988) Proc
Natl Acad Sci USA 85: 6002-6006
Populations speaking related languages
are also genetically closer than
expected based on their spatial
distance
Sokal (1988) Proc
Natl Acad Sci USA 85:
1722-1726
2. Coevolution of cultural and biological diversity
30. Validation: Mantel Correlations among Indo-European speakers
Mantel correlation r P
Lexical-geographic 0.206 0.077
Syntactic-geographic 0.385 0.008
Lexical-genomic 0.514 0.0001
Syntactic-genomic 0.491 0.0004
Lexical-syntactic 0.822 0.0001
LanGeLin: Inferring linguistic relationships from structural
language features, in grammar and synthax
2. Coevolution of cultural and biological diversity
32. How come that black athletes always win in Olympic
running events? Isn’t that the sign of a racial difference?
3. Racial paradigms
33. We are not identical, and our physical aspect contains
information on our likely place of origin
3. Racial paradigms
34. The study of morphology leads to contrasting racial
catalogs
Linnaeus (1735) 4 (europeus, luridus, afer, americanus) [+2]
Buffon (1749) 6 (european, lapp, tartar, asian, ethiopan, american)
Blumenbach (1795) 5 (caucasian, malay, afer, americanus, australianus)
Cuvier (1828) 3 (caucasoid, negroid, mongoloid)
Huxley (1875) 4 (mongoloid, xanthocroid, australoid, negroid)
Deniker (1900) 29
Von Eickstedt (1937) 38
Chicago Nat. Hist. Museum (1933) 107
USA census (2000) 6: White, Black or African-American, American Indian and Alaska Native, Asian,
Native Hawaiian and other Pacific Islander, Hispanic or Latino
USA census (2010) 15: White, Black or African-American, American Indian and Alaska Native, Asian
Indian, Chinese, Filipino, Japanese, Korean, Vietnamese, Other Asian, Native Hawaiian,
Guamanian, Samoan, Other Pacific Islander, Hispanic or Latino
3. Racial paradigms
36. Theodosius Dobzhansky:
Genetic diversity and human
equality
“Equality—as in equality in law and equality of
opportunity—pertains to the rights and the
sacredness of life of every human being and
not to the individual’s bodily or mental
features.
There are valid races in humans, but biology is
only beginning to properly define them”.
3. Racial paradigms
37. Pre- and post-genomic estimates of genetic variances
Lewontin (1972) 85% 8% 6%
Barbujani et al. (1997) 85% 5% 10%
Jorde et al. (2000) 85% 2% 13%
Romualdi et al. (2002) 83% 8% 9%
Rosenberg et al. (2002) 93% 3% 4%
Excoffier & Hamilton (2003) 88% 3% 9%
Ramachandran et al. (2005) 90% 5% 5%
Bastos-Rodriguez et al. (2006) 86% 2% 12%
Li et al. (2008) 89% 2% 9%
Barreiro et al. (2008) 89% 11%
Auton et al. (2009) 95% 5%
Xing et al. (2009) 88% 12%
MEDIAN
within populations
between populations
between races or continents
85% 5% 10%
3. Racial paradigms
38. At the genomic level, two people
from the same country can be
more different than people from
different continents
Within-population diversity is
very large
3. Racial paradigms
Ahn et al. (2008) Genome Res 19: 1622-1629
39. “To attain truly personalized medicine, the scientific community must leave behind
simplistic race-based approaches, and look instead for the genetic and
environmental factors contributing to individual drug reactions”
3. Racial paradigms
Ng et al. (2008) Clin Pharmacol Ther. 84: 306-309
40. Hence, the human genome produces a consistent
molecular architecture in the prefrontal cortex, despite
millions of genetic differences across individuals and races.
It's significantly possible that the Clovis population is
of mixed race -- and Kennewick Man and Spirit Cave
Man actually came with the Old Cordilleran
149352 papers as of March 13, 2014
3. Racial paradigms
41. Many thanks to:
Krishna Veeramah
Tomàs Marques-Bonet
Richard Nichols
Silvietta Ghirotto Fabio Di Vincenzo
42.
43. Denisova
Possible area of admixture with
Neandertal
Possible area of admixture with
Denisovans (H. heidelbergensis?)
Possible area of admixture with
H. rhodesiensis
Veeramah and Hammer (2014) Nature Reviews Genetics 15: 149–162
1. Hybridisation vs. Southern route
44. Initial dataset
871 populations
2471 individuals
> 1 million SNPs
Final dataset
63 populations
1672 individuals
95,401 SNPs
1. Hybridisation vs. Southern route
45. Harmonic means over arbitrary recombination classes; errors estimated comparing Ne
values inferred for the different chromosomes
Estimated population sizes inferred from LD values
1. Hybridisation vs. Southern route
46. Each of us shares 99.9% of her genome with everybody else
Two cells of the same person 0/1000
Two identical twins 0/1000
Two of us 1/1000
One of us and a chimp 10-30/1000
One of us and an artichoke 700/1000
3. Racial paradigms
47. In each individual, chromosomes are mosaics of DNA
traits of different origins
From the
23andme.com
and
Gedmatch.co
m sites
Editor's Notes
Abbiamo dovuto quindi trovare un’altra strada. Analisi LD.
È il verificarsi di alcune combinazioni di alleli o marcatori genetici in una popolazione più spesso di quanto ci si aspetterebbe da una formazione casuale di aplotipi secondo le frequenze dei singoli alleli.
LD separati da brevi distanze di ricombinazione permettono di calcolare una dimensione effettiva delle popolazioni molto indietro nel tempo
-possibilità di calcolare la dimensione effettiva delle popolazioni dal LD
-possibilità di calcolare il tempo di divergenza delle popolazioni da Ne e FST
Utilizzata tutta l’informazione genetica a disposizione e nn solo il sottoinsieme di snp in comune
Da queste 3 rotte di dispersione sono state create matrici di distanze geografiche a coppie di popolazioni
Ne è causato dalla deriva
Africa= ne accompagnato da un declino costante, che rispecchia l’Out of Africa
L’impatto della deriva genetica è determinato dalla funzione inversa di Ne (la deriva genetica ha un impatto maggiore nelle popolazioni con dimensioni ridotte) in entrambe le popolazioni e T
piccoli valori di Ne o grandi valori di T portano a valori maggiori di FST