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Imperialism Rise in Nationalism • During the French and Industrial Revolution, nationalism continued to inspire nations to increase their political and economic power. • Nationalism became the ideal force in the political, economic, and cultural life in the world, becoming the first universal ideology-organizing all people into a nation state. Nationalism Defined • The strong belief that the interest of a particular nation-state is of primary importance. o Nation-State – a state where the vast majority shares the same culture and is conscious of it. It is an ideal in which cultural boundaries match up with political ones. • As an ideology, it is based on the idea that the individual’s loyalty and devotion to the nation-state surpass other individual/group interests. • Exalting one nation’s belief above all others and placing primary emphasis on promotion of its culture and interests, excluding the interests of others. Changing the World through a Nationalistic Vision • The French Revolution significantly changed the political world and how countries govern. • The Industrial Revolution significantly changed the economic world. • The Age of Imperialism (1870-1914) dramatically changed the political, economic, and social world. What is Imperialism? • Imperialism- The policy of extending the rule of authority of an empire or nation over foreign countries, or of acquiring and holding colonies and dependencies. Power and influence are done through diplomacy or military force. Reasons for Imperialism • There are 5 main motives for empires to seek to expand their rule over other countries or territories: 1. Exploratory • Imperial nations wanted to explore territory unknown to them. • The main purpose for this exploration of new lands was for resource acquisition, medical or scientific research. o Charles Darwin • Other reasons: o Cartography (map making) o Adventure 2. Ethnocentric • Europeans acted on the concept of ethnocentrism o Ethnocentrism- the belief that one race or nation is superior to others. • Ethnocentrism developed out of Charles Darwin’s “survival of the fittest” theory. Philosophers used the theory to explain why there were superior races and inferior races. o This became known as Social Darwinism. • Most imperial nations believed that their cultural values or beliefs were superior to other nations or groups. • Believed imperial conquest would bring successful culture to inferior people. 3. Religious • Imperial expansion promoted a religious movement of people setting out to convert new members of conquered territories. • With the belief that Christianity was superior, missionaries believed it was their duty to spread Christianity to the world. • Christian missionaries established churches, and in doing so, they spread Western culture values as well. • Typically, missionaries spread the imperial nation's language through education and religious interactions. 4. Political • Patriotism and Nationalism helped spur our imperial growth, thus creating competition against other supremacies. • It was a matter of national pride, respect, and security. • Furthermore, European rivalry spurred nations for imperial conquest. Since land equaled power, the more land a country could acquire the more prestige they could wield across the globe. • Empires wanted strategic territory to ensure access for their navies and armies around the world. • The empire believed they must expand, thus they needed to be defended. 5. Economic • With the Industrial Revolution taking place during the same time, governments and private companies contributed to find ways to maximize profits. • Imperialized countries provided European factories and markets with natural resources (old and new) to manufacture products. • Trading posts were strategically placed around imperialized countries to maximize and increase profits. o Such places as the Suez Canal in Egypt which was controlled by the British provided strategic choke hold over many European powers. o Imperial powers competed over the best potential locations for resources, markets, and trade. History of Imperialism • Ancient Imperialism 600 BCE-500 CE o Roman Empire, Ancient China, Greek Empire, Persian Empire, Babylonian Empire. • Middle Age Imperialism (Age of Colonialism-1400-1800s) o Great Britain, Spain, Portugal, France, Netherlands (Dutch), Russia. • Age of Imperialism 1870-1914 o Great Britain, Spain, Portugal, France, Germany, Belgium, Italy, Japan, United States, Ottoman Empire, Russia. • Current Imperialism...? o U.S. Military intervention (i.e. Middle East) o Russia’s Invasion of Ukraine. Imperialism Colonialism • Refers to political or economic control, either legally or illegally. • Refers to where one nation assumes control over the other. • Creating an empire, expanding into neighboring regions and expanding the dominance far outside its borders. • Where a country conquers and rules over other regions for exploiting resources from the conquered country for the conqueror's benefit. • Foreign government controls/governs a territory without significant settlement. • Foreign government controls/governs the territory from within the land being colonized. • Little to no new settlement established on fresh territory. • Movement to settle to fresh territory. Age of Colonialism WHEN? • Started around the late 1400s and ended around the late 1700s/early 1800s. WHY? • Primary Reason: European countries, wished to find a direct trade route to Asia (China & India) and the East Indies. o Quicker and relatively more effective than land routes over Asia. • Secondary Reason: Empire expansion (land power) WHO? • Countries involved: Great Britain, France, Spain, the Dutch & Portugal. • Individuals’ knowns as Mercantilists believed that maintaining imperialized territory and colonizing the region could serve as a source of wealth, while personal motives by rulers, explorers, and missionaries could therefore promote their own agenda. o This agenda being “Glory, God and Gold”. Mercantilism • Mercantilism was a popular and main economic system for many European nations during the 16th to 18th centuries. • The main goal was to increase a nation’s wealth by promoting government rule of a nation’s economy for the purpose of enhancing state power at the expense of rival national power. • It was the economic counterpart of political absolutism. Why did mercantilists want colonies? • Mercantilists believed that a country must have an excess of exports over imports. • By colonizing territory, it provided the nation with indispensable wealth of precious raw materials. • Therefore, the claimed territory served as a market and supplier of raw materials for the mother country. Which, in time, provided an excess of exports for the nation and thus created wealth. o Development of Trading Companies to support this economic system. Hudson Bay Company – (1670). Controlled primarily North America. o Dutch East Indie Trading Company (1682) o East Indian Trading Company (1600) o Royal African Trade Company (1672) WHERE? • European nations begun to colonize the America, India and the East Indies to create a direct trade route. • Great Britain was the leading power in India, Australia and North America, South Africa. • Spain colonized central and South America. • French held Louisiana, coastal land of Africa and French Guinea. • The Dutch built an empire in the East Indies. • The Portuguese was able to take control of present-day Brazil and the southern tip of South America and Japan. Age of Colonialism • As countries started to imperialize these regions, eventually the concept of colonization took hold: • This is what makes the Age of Colonialism extremely different! End of Colonialism • By 1800, colonialism became less popular • Why? o Revolutions (Spain, France & American) o The Napoleonic Wars o Struggle for nationalism and democracy. o Exhausted all money and energy to supervise their colonies. Waiting to wake again • Imperialism would stay quiet for close to 50 years before Great Britain and France’s economies revitalized. • The outbreak of the Industrial Revolution only encouraged and revitalized European nations to begin their conquest for new territory and resources. Age of Imperialism THE SCRAMBLE FOR AFRICA 1870-1914 Conditions Prior to Imperialism of Africa  European interest in exploiting Africa was minimal.  Their economic interests & profit in Africa primarily came through coastal trade that took place during the 1500-1700s.  The slave trade became the main source of European profit.  Furthermore, disease, political instability, lack of transportation and unpredictable climate all discouraged Europeans from seeking territory. Slave Trade & the Trans-Atlantic Slave Voyages  Forced labor was not uncommon during the 13-17th Centuries. Africans and Europeans had been trading goods and people across the Mediteranea for centuries.  This all changed from 1526 to 1867, as a new system of slavery was introduced that became highly “commercialized, racialized and inherited”  By 1690, the America and West Indies saw approximately 30,000 African people shipped from Africa. A century later, that number grew to 85,000 people per year.  By 1867, approximately 12.5 million people (about twice the population of Arizona) left Africa in a slave ship. What Changed? 1. End of the Slave Trade- Left a need for trade between Europe and Africa. 2. Innovation in technology- The steam engine and iron hulled boats allowed Europe 3. Discovery of new raw materials- Explorers located vast raw materials and resources and this only spurred imperialism with Europe in the wake of the Industrial Revolution. 4. Politics- Unification of Germany and Italy left little room to expand in Europe. Germany and Italy both needed raw materials to “catch up” with Britain and France so they looked to Africa. The Scramble for Africa  The scramble started in 1870.  Although some coastal land had previously been acquired before 1870, the need for territory quickly accelerated as European countries looked t get deeper into Africa.  Within 20 years, nearly all continents were placed under imperialistic rule. Who was Involved?  Great Britain  France  Germany  Italy  Portugal  Belgium  Spain (kind) Violent Affairs  Violence broke out multiple times when European nations looked to claim the same territory.  Germ Chancellor. Otto van Bismarck. Attempted to avert the possibility of violence against the European powers.  In 1884, Bismarck organized a conference in Berlin for the European nations. The Berlin Conference (1884-85)  The conference looked to set ground rules for future annexation of African territory by European Nations.  Annexation is the forcible acquisition and assertion of legal title over one state’s territory by another state, usually following military occupation of the territory.  From a distant perspective, it looked like it would reduce tensions among European nations and avert war.  At the heart of the meeting, these European countries negotiated their claims to African territory, made it official and then mapped their regions.  Furthermore, the leaders agreed to allow free trade among imperialized territory and some homework for negotiating future European claims in Africa was established. Further Path  After the conference, european powers continued to expand their claims in Africa so that by 1900. 90% of the African territory had been claimed. A Turn towards Colonization?  Upon the imperialization of African territory, European nations and little interest in African land unless it produced economic wealth.  Therefore, European governments put little effort and expertise into these imperialized regions.  In most cases, this emat a form of indirect rule. Thus, governing the natin without sufficient settlement and government from within the mother country. Some Exceptions  There were some exemptions through in Africa as colonization was a necessary for some regions i n Africa.  Some regions where diamonds and gold were present. Government looked to protectorate the regions and establish rule and settlement in the regions.  Protectorates: A state controlled and protected by another state for defense against aggression and other law violations. Would  Some examples include South Africa, Botswana, Zimbabwe and Congo. Conclusion  Although it may appear that the Berlin Conference averted war amid the African Scramble, imperialism eventually brought the world into worldwide conflict.  With the continued desire to create an empire by European nations. World War 1 would break out which can be linked to this quest at imperialism.
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Molecular Evolution Notes

Molecular Evolution

Assisstant Prof. Cemalettin Bekpen's lecture on Molecular Evolution, part of Computational Biology II MBG2004.

Central Premise

Significant sequence similarity implies function assignment to unknown proteins based on known proteins due to evolutionary relationships.

Homolog

A gene/protein related to a second gene/protein by descent from a common ancestral gene via speciation.

Ortholog

Genes/proteins in different species evolved from a common ancestor via speciation, retaining the same function.

Paralog

Genes/proteins related by duplication of a common ancestral gene. These evolve new functions, which may or may not relate to that of the ancestor.

Speciation

Evolution of new gene/protein that is genetically independent from the ancestral gene.

Convergent Evolution

Evolution of similar features/properties in genes/proteins of different genetic lineages.

Divergent and Convergent Evolution Among the Serine Proteases

Examples include Trypsin (3NKK), Chymotrypsin (1ACB), and Subtilisin (1SBT).

Mechanisms of Molecular Evolution of Genes/Proteins

Mutation

Stochastic single point changes in genetic material due to:

  • Errors in DNA replication during mitosis
  • Radiation exposure
  • Chemical or environmental stressors
  • Viruses and transposable elements

Slow but constant rate (molecular clock) of 10^{-9} to 10^{-8} mutations per base per generation. Includes splicing errors in eukaryotes that retain introns.

Recombination

Exchange of genes (or portions) between different chromosomes to create new combinations.

Gene Duplication

Duplication of a gene (or portion). One copy retains the original function, while the other evolves and acquires new functions.

Retrotransposition

Incorporation of mRNA sequences back into DNA, often inserting into new locations with different expression patterns.

The mechanisms by which new genes/proteins arise enable sequence analysis to infer functional and structural relationships.

Evolutionary Selection

Natural Selection vs. Artificial Selection

Consider watching the YouTube video on this topic. Also review the Khan Academy article on Darwin, evolution, & natural selection.

Anagenesis

(Phyletic evolution): A single population transforms enough to be designated a new species.

Cladogenesis

Branching evolution: A new species arises from a small population that buds from a parent species. Most new species probably evolve by cladogenesis, the branching evolution that is the basis for biological diversity.

Directional, Disruptive, and Stabilizing Selection

  • Directional Selection: Favors individuals at one end of the phenotypic range.
  • Disruptive Selection: Favors individuals at both extremes of the phenotypic range.
  • Stabilizing Selection: Favors intermediate variants and acts against extreme phenotypes.
Directional Selection Example

The shift in moth population color from light to dark during the Industrial Revolution in England is an example of directional selection.

Disruptive Selection Example

Yearling male lazuli buntings with either bright or dull coloration being able to establish territories and breed, while those with intermediate plumage do not mate.

Stabilizing Selection Example

Stabilizing selection favors the most common phenotype as best adapted. It reduces variation by selecting against alleles that produce more extreme phenotypes. An example is birth weight; babies with weights too low or too high face increased risks.

Woodpeckers and wasps influence gall-fly populations, applying pressure that results in stabilizing selection.

Artificial Selection

Examples include the domestication of wolves into various dog breeds and the selective breeding of wild mustard into cabbage, brussel sprouts, cauliflower, broccoli, kale, and kohlrabi.

Lamarck's Giraffe vs Natural Selection

Contrast Lamarck's inheritance of acquired characteristics with natural selection, using the example of giraffe neck length. Also, consider the evolution of modern corn from Teosinte.

Adaptive Evolution

When natural selection favors a single allele and the allele frequency continuously shifts in one direction.

The Human Genome and Positive Selection

Human Genome Build 38

  • ~3 billion nucleotides or basepairs, ~3 million vary among random 2 humans
  • ~25,000 genes
  • only about 2 % of genome encodes for proteins

Chimpanzee Genome

  • Human and chimps diverged 5-6 million years ago (mya).
  • ~99% identical overall to the human genome.
  • ~30,000,000 nucleotide differences.
  • 29% of genes identical to human homologue (6,250 genes).
  • Average divergence per gene: 2 amino acid difference; one per lineage since human/chimp divergence.

Genome Wide McDonald-Kreitman Test

Red bars on the selection map indicate loci under negative selection. Blue bars represent loci under positive selection (95% credibility level). Strong evidence of selection at >99%.

Using Genetic Variation to Understand Natural Selection

To understand the presence and form of natural selection on genes by:

  1. Inferring ancestral states for genes.
  2. Inferring selection on amino acids in proteins with important functions and relating gene selection to phenotype selection.
  3. Inferring recent selective sweeps or balancing selection in the human genome.

Inferring Lineage Specific Evolution

Compare a gene of interest for different species

Measuring Positive Selection

Rate of synonymous mutations and rate of non-synonymous mutations

Changes in Protein Sequence

Changes in a protein sequence come from changes in the nucleotide sequence

Genetic Code and Synonymous/Nonsynonymous Changes

  • Synonymous Change: Does not change the amino acid encoded (e.g., TCT -> TCC, both coding for Serine).
  • Nonsynonymous Change: Changes the amino acid encoded (e.g., TCT -> TTC, changing from Serine to Phenylalanine).

Nonsynonymous changes are more likely to have functional consequences and are generally deleterious, thus removed from populations more rapidly. The rate of nonsynonymous change will be slower than the rate of synonymous change.

Inferring Adaptive Amino Acid Change in Proteins

Measuring selection on protein-coding genes:

-->Selection ‘for’ particular amino acid changes.

Changes are synonymous or non-synonymous

AAA \rightarrow AAG \text{ (Lysine)}

AAA \rightarrow GAA \text{ (Glutamic Acid)}

Synonymous or Nonsynonymous Change: dN/dS

  • dS: rate of synonymous change (e.g., per gene). Because synonymous changes do not affect the protein, most have little or no effect on organism fitness.
    • They are selectively neutral and accumulate at a constant rate (clock-like).
    • If species are far apart, correct for ‘multiple hits’ using a statistical model of sequence change.
  • dN: rate of nonsynonymous change (e.g., per gene). Nonsynonymous changes affect the protein, most are deleterious and lost.
    • So, dN rate is generally slower than dS. Hence dN/dS is generally less than 1.
  • If dN > dS, there have been many nonsynonymous changes, which is rare and a signature of adaptive evolution.

*What if dN/dS = 1?

Quantifying Non-Synonymous Variation

Estimate of positive selection

  • Synonymous mutations: neutral mutations.
  • Non-synonymous mutations: non-neutral mutations.

Codon Usage

Frequencies of different codons for the same amino acid are different.

Codon usage bias is caused by:

  • Translation machinery tends to use abundant tRNA (and codons corresponding).
    • Codon usage bias is the same for all highly expressed genes in the same organism.
  • Mutation pressure: Difference between mutation rates between GC à AT and AT à GC.
    • GC-content is different in different organisms.

The genetic code is redundant.

*Some amino acids coded by more than one codon.

*Proteins are more conserved during evolution.

DNA \rightarrow 4 \text{ letter alphabet}

Proteins \rightarrow 20 \text{ letter alphabet}

  • Two random DNA sequences 25% identical on average.
  • Two random protein sequences 5% identical on average.

dN/dS Interpretation

  • dN/ dS < 1 : replacements are deleterious (very few changes in amino acids, along lineage)
  • dN/ dS = 1 : replacements are neutral (changes just happen randomly)
  • dN/ dS > 1 : replacements are advantageous (lots of changes in amino acids along lineage)
  • Ratio of non-synonymous to synonymous changes=dN/ dS=Ka/Ks

dN/dS, Ka/Ks

Nei and Gojobori, 1986

  • Nd = Counts of non-synonymous mutations for each gene
  • Sd = Counts of synonymous mutations for each gene
  • N = Counts of potential non-synonymous sites for each gene
  • S = Counts of potential synonymous sites for each gene

KA = Nd / N and KS = Sd / S

Ratio KA/KS as an indicator of evolutionary mode in each gene Basic analyses of the proportion of non-synonymous to synonymous divergence KA/KS

Purifying, Neutral, and Positive Selection

  • dN/dS < 1: Purifying Selection
  • dN/dS = 1: Neutral Evolution
  • dN/dS > 1: Positive Selection

KA or dN: rate of non-synonymous divergence and KS or dS: rate of synonymous divergence between species

Estimating Non-Synonymous and Synonymous Polymorphisms

Estimates of non-synonymous and synonymous polymorphisms and substitutions provide insight into evolutionary processes By Analysing divergence and polymorphism:

  • KA / KS ratios > 1 indicate positive selection
  • KA / KS ratios < 1 indicate negative selection
  • KA / KS ratios = 1 indicates neutral evolution

KA and dN: rate of non-synonymous substitutions , KS and dS: rate of synonymous substitutions, PN: Amount of non-synonymous polymorphisms, PS: Amount of synonymous polymorphisms KA/Ks branch-specific estimate

Analogy Between Phenotype-Level and Genetic-Level Selection

  • Selection ‘for’ change in one direction
    • Directional selection on phenotype: Ala->Glu, Tyr->Ser (examples)
    • Positive selection on a gene:
  • Selection ‘for’ remaining the same
    • Stabilizing selection on phenotype
    • Purifying selection on a gene - Ala, Tyr, retained despite mutations to other amino acids

Positive selection is selection on a particular trait - and the increased frequency of an allele in a population

Excess of Function-Altering Mutations Example

In PRM1 exon 2, there are six differences between humans and chimpanzees, five of which alter amino acids.

Branch-Specific dN/dS Estimates Example

branch-specific dN/dS estimates for OGP (oviductal glycoprotein) for multiple species

Selective Sweeps and Balancing Selection

Alleles and Haplotypes that increase in frequency rapidly due to positive selection will carry lots of “hitch-hiking”, flanking DNA, creating a linkage disequilibrium signature

Infer Selection

Geographic variation in allele frequencies and patterns

Examples of Genes with Geographic Selection

Genes such as AGT, CYP3A, SLC24A5, FY, IL4, IL13, CASP12, NAT2, LCT, TRPV6, and MMP3, show evidence of geographically restricted selection in humans related to climate, pathogens, or diet.

Extreme Population Differences

Extreme population differences in FYO allele frequency; The FYO allele, which confers resistance to P. vivax malaria.

Studies of Selection Signatures in the Human Genome

Brains, food, reproduction and parasites

Genome-Wide Analysis

Most-significant categories showing positive selection in the human lineage include:

  • Immune system: parasites and pathogens
  • Reproduction: genes expressed in reproductive tissues
  • Nervous system genes: expressed in brain
  • Amino-acid metabolism: diet
  • Olfaction: sense of smell
  • Development: such as skeletal
  • Hearing: for speech perception

Biological Processes with Significant Excess of Positively Selected Genes

Immunity and defense, T-cell-mediated immunity, Chemosensory perception, Biological process unclassified, Olfaction, Gametogenesis, Natural killer-cell-mediated immunity, Spermatogenesis and motility, Inhibition of apoptosis, Interferon-mediated immunity, Sensory perception and B-cell- and antibody-mediated immunity.

Enrichment of GO Categories Example

Chemosensory perception, Olfaction, Gametogenesis, Spermatogenesis and motility, Fertilization, Other carbohydrate metabolism, Electron transport, Chromatin packaging/remodeling, MHC-I-mediated immunity, Steroid metabolism, Lipid and fatty acid binding, mRNA transcription initiation , Protein modification, Vitamin/cofactor transport, Phosphate metabolism and Peroxisome transport

Adaptive Evolution of Young Gene Duplicates

Human-specific duplicates evolving under adaptive natural selection include a surprising number of genes involved in neuronal and cognitive functions.

Hominid-Specific Gene Families Under Positive Selection Examples

Neuroblastoma breakpoint family NBPF and others such as, FAM75A ,Williams Beuren syndrome region 19 and etc.

Specific Genes Affecting Brain Size: Microcephaly Genes

Small (~430 cc v ~1,400 cc) but otherwise ~normal brain, only mild mental retardation. Can be due to loss of activity of the ASPM gene, Abnormal spindle-like microcephaly associated, or MCPH1 gene

Positive Selection of MCPH1 in Primate Evolution

Positive Selection of ASPM in Primate Evolution

ASPM is still evolving adaptively in human lineage?! and May related to forms of human language, tonal and non-tonal convergence

Genes related to Brain and Language Example: FOXP2

relating human adaptive molecular evolution to human disease, Crespi 2010, Evol. Appl. Genes subject to recent positive selection in humans are differentially involved in neurological diseases

Inheritance of a Language/Speech Defect

FOXP2

  • FOXP2 mutations results in an autosomal dominant communication disorder
  • Phenotype includes problems with speech articulation and deficits in many aspects of language and grammar
  • Intelligence varies among affected individuals but speech/language impairment is always present
  • Interestingly, deficits with language are not restricted to speech but influence writing and comprehension/expression Chromosome 7 7q31

FOXP2 is highly conserved throughout mammals and beyond but for three nucleotide substitutions that change the FOXP2 protein between humans and the mouse, and two have occurred along the human lineage Examination of human genetic variation suggests that the region surrounding the gene underwent a selective sweep in the past 200,000 years
Brains of individuals with FOXP2 mutations have reduced grey matter in the frontal gyrus which includes Broca’s area and Functional abnormalities in Broca’s area during language tasks

Positive selection linked to Neandertals

The Derived FOXP2 Variant of Modern Humans Was Shared with Neandertals

FOXP2: two genetic variants (SNPs) are associated with risk of some neurodevelopmental disorders involving speech and language, schizophrenia and autism

Positive Selection Related to the Human Genome

Many genes related to primate brain development have been subject to positive selection Have identified several positively-selected genes related to brain size and language in humans, but we do not know how they work These same genes are also involved in human disorders related to the brain and language

The Gene Example LCT

All infants have high lactase enzyme activity to digest the sugar lactose in milk In most humans, activity declines after weaning, but in some it persists: LCT*P

Molecular Basis of Lactase Persistence

Linkage and LD studies show association of lactase persistence with the T allele of a T/C polymorphism 14 kb upstream of the lactase gene and Lactase level is controlled by a cis-acting element

Genetic Signatures-Lactase Gene

Genetic Signatures of Strong Recent Positive Selection at the Lactase Gene and Convergent adaptation of human lactase persistence in Africa and Europe show selection

A SNP Examples

A SNP in the gene encoding lactase (LCT) (C/T-13910) is associated with the ability to digest milk as adults (lactase persistence) in Europeans, These data provide a marked example of convergent evolution due to strong selective pressure resulting from shared cultural traits-animal domestication and adult milk consumption and Genotyping across a 3-Mb region demonstrated haplotype homozygosity extending >2.0 Mb on chromosomes carrying C-14010, consistent with a selective sweep over the past ~7,000 years

Dietary Adaptation

Diet and Adaptation Example of Use of Starches

Not just milk - use of starches also increased in human diet, Diet and the evolution of human amylase gene copy number variation and Evidence for selection of suite of genes 'for' meat-eating adaptation

Human Adaptation to Diet

Better food, smaller guts, adaptations to meat, Humans adapted genetically to a novel diet that includes dairy products, grains, and more meat The selection involved has been strong The molecular adaptations involved in dietary adaptations tend to be local geographically, and still exhibit genetic polymorphisms

Mammals Rapid Evolution of Reproductive Proteins

Rapid Evolution of Reproductive Proteins in Mammals, Rapid Evolution of Fertilization Proteins and Male-female conflicts, Egg laying (increased). Receptivity to mating sperm displacement and more

Correlation Between Evolution and Selection

Correlation between SEMG2 Evolution and Primate Sexual Traits, comparative evidence for molecular adaptation related to sperm mobility, with implications for human male fertility different primate species and Carlson et al, research in fertile

Strong balancing selection at HLA loci

Evidence from segregation in South Amerindian families: A strong signature of balancing selection in the 5' cis-regulatory region of CCR5

Maladaptation-Byproducts and Local Adaptations

How selection on the human genome is related to disease; Strong, recent positive selection can create maladaptations as byproducts (via pleiotropy); Balancing selection creates maladapted homozygotes (as a form of tradeoff); Locally-selected adaptations become maladaptive with changes in the environment (such as recent human migrations)-local adaptation is common; Selection on brain, dietary, reproductive and disease genes has generated very rapid, recent, ongoing change, which helps in understanding human adaptation and disease

Immune recognition molecules: KIRS, LIRAS, HLAS, TRs Multiple changes, Inactivation or deletion, Duplication and Functional amino acid changes

Pkr Evolution in Response to Viral Mimicry - YouTube

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Imperialism Rise in Nationalism • During the French and Industrial Revolution, nationalism continued to inspire nations to increase their political and economic power. • Nationalism became the ideal force in the political, economic, and cultural life in the world, becoming the first universal ideology-organizing all people into a nation state. Nationalism Defined • The strong belief that the interest of a particular nation-state is of primary importance. o Nation-State – a state where the vast majority shares the same culture and is conscious of it. It is an ideal in which cultural boundaries match up with political ones. • As an ideology, it is based on the idea that the individual’s loyalty and devotion to the nation-state surpass other individual/group interests. • Exalting one nation’s belief above all others and placing primary emphasis on promotion of its culture and interests, excluding the interests of others. Changing the World through a Nationalistic Vision • The French Revolution significantly changed the political world and how countries govern. • The Industrial Revolution significantly changed the economic world. • The Age of Imperialism (1870-1914) dramatically changed the political, economic, and social world. What is Imperialism? • Imperialism- The policy of extending the rule of authority of an empire or nation over foreign countries, or of acquiring and holding colonies and dependencies. Power and influence are done through diplomacy or military force. Reasons for Imperialism • There are 5 main motives for empires to seek to expand their rule over other countries or territories: 1. Exploratory • Imperial nations wanted to explore territory unknown to them. • The main purpose for this exploration of new lands was for resource acquisition, medical or scientific research. o Charles Darwin • Other reasons: o Cartography (map making) o Adventure 2. Ethnocentric • Europeans acted on the concept of ethnocentrism o Ethnocentrism- the belief that one race or nation is superior to others. • Ethnocentrism developed out of Charles Darwin’s “survival of the fittest” theory. Philosophers used the theory to explain why there were superior races and inferior races. o This became known as Social Darwinism. • Most imperial nations believed that their cultural values or beliefs were superior to other nations or groups. • Believed imperial conquest would bring successful culture to inferior people. 3. Religious • Imperial expansion promoted a religious movement of people setting out to convert new members of conquered territories. • With the belief that Christianity was superior, missionaries believed it was their duty to spread Christianity to the world. • Christian missionaries established churches, and in doing so, they spread Western culture values as well. • Typically, missionaries spread the imperial nation's language through education and religious interactions. 4. Political • Patriotism and Nationalism helped spur our imperial growth, thus creating competition against other supremacies. • It was a matter of national pride, respect, and security. • Furthermore, European rivalry spurred nations for imperial conquest. Since land equaled power, the more land a country could acquire the more prestige they could wield across the globe. • Empires wanted strategic territory to ensure access for their navies and armies around the world. • The empire believed they must expand, thus they needed to be defended. 5. Economic • With the Industrial Revolution taking place during the same time, governments and private companies contributed to find ways to maximize profits. • Imperialized countries provided European factories and markets with natural resources (old and new) to manufacture products. • Trading posts were strategically placed around imperialized countries to maximize and increase profits. o Such places as the Suez Canal in Egypt which was controlled by the British provided strategic choke hold over many European powers. o Imperial powers competed over the best potential locations for resources, markets, and trade. History of Imperialism • Ancient Imperialism 600 BCE-500 CE o Roman Empire, Ancient China, Greek Empire, Persian Empire, Babylonian Empire. • Middle Age Imperialism (Age of Colonialism-1400-1800s) o Great Britain, Spain, Portugal, France, Netherlands (Dutch), Russia. • Age of Imperialism 1870-1914 o Great Britain, Spain, Portugal, France, Germany, Belgium, Italy, Japan, United States, Ottoman Empire, Russia. • Current Imperialism...? o U.S. Military intervention (i.e. Middle East) o Russia’s Invasion of Ukraine. Imperialism Colonialism • Refers to political or economic control, either legally or illegally. • Refers to where one nation assumes control over the other. • Creating an empire, expanding into neighboring regions and expanding the dominance far outside its borders. • Where a country conquers and rules over other regions for exploiting resources from the conquered country for the conqueror's benefit. • Foreign government controls/governs a territory without significant settlement. • Foreign government controls/governs the territory from within the land being colonized. • Little to no new settlement established on fresh territory. • Movement to settle to fresh territory. Age of Colonialism WHEN? • Started around the late 1400s and ended around the late 1700s/early 1800s. WHY? • Primary Reason: European countries, wished to find a direct trade route to Asia (China & India) and the East Indies. o Quicker and relatively more effective than land routes over Asia. • Secondary Reason: Empire expansion (land power) WHO? • Countries involved: Great Britain, France, Spain, the Dutch & Portugal. • Individuals’ knowns as Mercantilists believed that maintaining imperialized territory and colonizing the region could serve as a source of wealth, while personal motives by rulers, explorers, and missionaries could therefore promote their own agenda. o This agenda being “Glory, God and Gold”. Mercantilism • Mercantilism was a popular and main economic system for many European nations during the 16th to 18th centuries. • The main goal was to increase a nation’s wealth by promoting government rule of a nation’s economy for the purpose of enhancing state power at the expense of rival national power. • It was the economic counterpart of political absolutism. Why did mercantilists want colonies? • Mercantilists believed that a country must have an excess of exports over imports. • By colonizing territory, it provided the nation with indispensable wealth of precious raw materials. • Therefore, the claimed territory served as a market and supplier of raw materials for the mother country. Which, in time, provided an excess of exports for the nation and thus created wealth. o Development of Trading Companies to support this economic system. Hudson Bay Company – (1670). Controlled primarily North America. o Dutch East Indie Trading Company (1682) o East Indian Trading Company (1600) o Royal African Trade Company (1672) WHERE? • European nations begun to colonize the America, India and the East Indies to create a direct trade route. • Great Britain was the leading power in India, Australia and North America, South Africa. • Spain colonized central and South America. • French held Louisiana, coastal land of Africa and French Guinea. • The Dutch built an empire in the East Indies. • The Portuguese was able to take control of present-day Brazil and the southern tip of South America and Japan. Age of Colonialism • As countries started to imperialize these regions, eventually the concept of colonization took hold: • This is what makes the Age of Colonialism extremely different! End of Colonialism • By 1800, colonialism became less popular • Why? o Revolutions (Spain, France & American) o The Napoleonic Wars o Struggle for nationalism and democracy. o Exhausted all money and energy to supervise their colonies. Waiting to wake again • Imperialism would stay quiet for close to 50 years before Great Britain and France’s economies revitalized. • The outbreak of the Industrial Revolution only encouraged and revitalized European nations to begin their conquest for new territory and resources. Age of Imperialism THE SCRAMBLE FOR AFRICA 1870-1914 Conditions Prior to Imperialism of Africa  European interest in exploiting Africa was minimal.  Their economic interests & profit in Africa primarily came through coastal trade that took place during the 1500-1700s.  The slave trade became the main source of European profit.  Furthermore, disease, political instability, lack of transportation and unpredictable climate all discouraged Europeans from seeking territory. Slave Trade & the Trans-Atlantic Slave Voyages  Forced labor was not uncommon during the 13-17th Centuries. Africans and Europeans had been trading goods and people across the Mediteranea for centuries.  This all changed from 1526 to 1867, as a new system of slavery was introduced that became highly “commercialized, racialized and inherited”  By 1690, the America and West Indies saw approximately 30,000 African people shipped from Africa. A century later, that number grew to 85,000 people per year.  By 1867, approximately 12.5 million people (about twice the population of Arizona) left Africa in a slave ship. What Changed? 1. End of the Slave Trade- Left a need for trade between Europe and Africa. 2. Innovation in technology- The steam engine and iron hulled boats allowed Europe 3. Discovery of new raw materials- Explorers located vast raw materials and resources and this only spurred imperialism with Europe in the wake of the Industrial Revolution. 4. Politics- Unification of Germany and Italy left little room to expand in Europe. Germany and Italy both needed raw materials to “catch up” with Britain and France so they looked to Africa. The Scramble for Africa  The scramble started in 1870.  Although some coastal land had previously been acquired before 1870, the need for territory quickly accelerated as European countries looked t get deeper into Africa.  Within 20 years, nearly all continents were placed under imperialistic rule. Who was Involved?  Great Britain  France  Germany  Italy  Portugal  Belgium  Spain (kind) Violent Affairs  Violence broke out multiple times when European nations looked to claim the same territory.  Germ Chancellor. Otto van Bismarck. Attempted to avert the possibility of violence against the European powers.  In 1884, Bismarck organized a conference in Berlin for the European nations. The Berlin Conference (1884-85)  The conference looked to set ground rules for future annexation of African territory by European Nations.  Annexation is the forcible acquisition and assertion of legal title over one state’s territory by another state, usually following military occupation of the territory.  From a distant perspective, it looked like it would reduce tensions among European nations and avert war.  At the heart of the meeting, these European countries negotiated their claims to African territory, made it official and then mapped their regions.  Furthermore, the leaders agreed to allow free trade among imperialized territory and some homework for negotiating future European claims in Africa was established. Further Path  After the conference, european powers continued to expand their claims in Africa so that by 1900. 90% of the African territory had been claimed. A Turn towards Colonization?  Upon the imperialization of African territory, European nations and little interest in African land unless it produced economic wealth.  Therefore, European governments put little effort and expertise into these imperialized regions.  In most cases, this emat a form of indirect rule. Thus, governing the natin without sufficient settlement and government from within the mother country. Some Exceptions  There were some exemptions through in Africa as colonization was a necessary for some regions i n Africa.  Some regions where diamonds and gold were present. Government looked to protectorate the regions and establish rule and settlement in the regions.  Protectorates: A state controlled and protected by another state for defense against aggression and other law violations. Would  Some examples include South Africa, Botswana, Zimbabwe and Congo. Conclusion  Although it may appear that the Berlin Conference averted war amid the African Scramble, imperialism eventually brought the world into worldwide conflict.  With the continued desire to create an empire by European nations. World War 1 would break out which can be linked to this quest at imperialism.
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