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Chapter 1: Adaptation by Natural Selection Explaining Adaptation before Darwin Animals and Plants adapted to conditions Adaptation: Feature of an organism created by the process of natural selection ○ Ex. the human eye that allows us to locate critical resources and avoid dangers...

Chapter 1: Adaptation by Natural Selection Explaining Adaptation before Darwin Animals and Plants adapted to conditions Adaptation: Feature of an organism created by the process of natural selection ○ Ex. the human eye that allows us to locate critical resources and avoid dangers Adaptations are complex and require a special kind of explanation ○ ex. how the Grand Canyon may be quite different given another geologic history Originally many people weren’t troubled as it was common belief adaptations were divine creation ○ William Paley 1802 argued that human eye structure was evidence of God Darwin’s Theory of Adaptation Darwin’s trip established his reputation as a skilled naturalist ○ Observations of living and fossil animals convinced him that plants and animals sometimes change slowly through time ○ Evolutionary change was key to understanding how new species came into existence It was considered heretical at the time Original theory of how species change over time ○ Follows 3 postulates: Struggle for existence Populations grow until they are checked by the dwindling supply of resources in environment Ex. food to grow and reproduce is necessary and explains population trends Variation in fitness Some individuals will be able to survive and reproduce more successfully than others Inheritance of variation If advantageous traits are inherited by offspring, they are more common in succeeding generations Natural Selection: the process that produces adaptation ○ Used the pattern of Galapagos finches to prove this theory Based on capturing and counting the number of birds with different beaks and types of food they get Distribution of seeds of various sizes and observed birds’ behavior  ○ Morphology: the form and structure of an organism ○ When numbers of populations splits are achieved, there is an equilibrium (steady state at which the population doesn’t change) ○ Stabilizing selection: pressures that favor average phenotypes ○ traits/characters: attribute of an organism According to Darwin’s theory, a species is a dynamic population of individuals ○ Characteristics of a particular species will be status, unchanged, or a long time Stasis (State of stability during which little evolutionary change occurs) Selection benefits individuals rather than a population or species The Evolution of Complex Adaptations Continuous Variation: Phenotypic variation in which there is a continuum of types ○ Ex. human heights ○ Essential for the evolution of complex adaptation Discontinuous variation: Phenotypic variation in which there is a discrete number of phenotypes with no intermediate types ○ Ex. pea color Natural selection over time can lead to complex adaptations ○ But only if each small change is adaptive ○ Evolution produces adaptations like a tinkerer Convergence: Evolution of similar adaptation in unrelated species or distantly related populations of the same species ○ Best evidence that selection is a powerful process for generating complex adaptations ○ Ex. marsupial fauna of Australia and placental faunas of the rest of the world with similar features ○ Ex. evolution of eyes for light-gathering Rates of Evolutionary Change Natural selection can cause evolutionary change that is much more rapid than we commonly observe in the fossil record Darwin’s Difficulties Explaining Variation Only a minority endorsed Darwin’s view at the time that major changes occur through the accumulation of small variation Objection to Darwin’s theory: actions of blending inheritance and selection would deplete variation in populations and make it impossible for natural selection to continue ○ Blending inheritance: model of inheritance that assumes the mother and father each contribute a hereditary substances that mixes to determine the characteristics of the offspring  ○ Later, we discovered that genetics can account for the fact that offspring are intermediate between their parents without assuming any blending Second objection: selection works by removing variants from populations and therefore no evolution by natural selection ○ Natural selection destroys the variation required to create adaptations ○ No explanation how a population might evolve beyond its original range of variation How can selection lead to new types not present in the original population Darwin believed that complex adaptations could arise from accumulation of small variations and disregarded discontinuous variation ○ Many thought that discontinuous variants were the key to evolution because they solved the blending effect Solution to criticisms against Darwin was genetics John Edmonstone (1790-?) ○ Born into slavery on a timber plantation in Diana ○ Worked on the plantation, owned by a Scottish guy Charles Edmonstone ○ One of the most wealthy plantation owners Charles Waterton, Charles Edmonstone’s nephew ○ Very well known taxidermist (very fine-tuned skill back then) ○ Was an outcast ○ In a visit to Edmonstone, he visits the rainforest to collect specimens ○ In order to collect as many specimens, he gets help from John Edmonstone John knows the landscape In exchange Charles Waterton is teaching John taxidermy Used a mercury solution to cure the animals Later, when Edmonstone moves back to Scotland, he takes John (now an expert taxidermist) ○ When John arrives, he becomes a free man and puts his skills to use ○ Sets up a relationship with the museum nearby there ○ Also takes up a side gig teaching university students taxidermy and naturalist things Charles Darwin (1809-1882) ○ Only sixteen when he took John’s class; but set to be a doctor ○ Went to Cambridge University to be a priest (did graduate with a degree in religious studies) ○ Spends most of his time collecting beetles ○ Fresh out of undergrad, a ship (Beagle) asks him to be their naturalist Takes a five year voyage around the world, mostly South America ○ After the voyage, he became a recluse  ○ Presented a testable mechanism for how populations change and continue to change Named it Natural Selection About Darwin’s finches (adaptation by natural selection) Evolution ○ The process by which different kinds of the living organisms are thought to have developed, adapted, and diversified from earlier forms during the history of the earth ○ The cumulative change in the inherited characteristics of a population ○ More like a bush or tree with all of it emerging from a common ancestor Diversity is “different branches” Natural Selection ○ Aka “survival of the fittest” ○ One driver of evolution, using adaptations ○ Allow them to adapt to an environment, survive, and reproduce ○ Needs 3 things Struggle for Existence Since the ability of populations to expand is infinite, there has to be a cap to drive this Variation in Fitness Need to have some variations that are more beneficial given an environment Inheritance of Variation Reproduction capacity (genetic) Discontinuous and continuous variation ○ Has no foresights; not a conscious process Simples causes organisms to change so that they are better adapted to their environment ○ Many times environments fluctuate, and selection tracks these fluctuations Jean-Baptiste Lamarack (1744-1829) ○ French naturalist ○ Theory of inheritance of acquired characteristics ○ “Use it or lose it”; incorrect mechanism ○ Ex. Elongation of neck in Giraffe according to Lamarck Original short-necked ancestor got longer to reach higher leaves Thomas Malthus (1766 1834) ○ Demographer and economist ○ Argued that the human population was too large to be supported by current resources  Alfred Russel Walllace (1823-1913) ○ British (Welsh) biologist ○ Leading authority on the geographic distribution of animals ○ Independently conceived the theory of evolution through natural selection ○ Impact of humans on the environment Just a theory? ○ Formal definition of a theory: a comprehensive explanation of some aspect of nature that is supported by a vast body of evidence ○ Many scientific theories are so well established that no new evidence is likely to alter them substantially ○ Ex. Earth does orbit around the sun Fact: observation, measurement, or other form of evidence that can be expected to occur the same way under similar circumstances ○ A scientific explanation that has been tested and confirmed so many times, there is no need for additional testing or examples Why study natural selection ○ Understanding other evolutionary processes ○ How it shapes our species and relevant to our behavior and human mind Chapter 2: Genetics Mendelian Genetics The key experiments necessary to understand how genetic inheritance worked was performed by monk Gregor Mendel ○ Discovered how inheritance works with common garden pea plant ○ He isolated several traits with only two forms or variants Ex. a trait of pea color or textures ○ Cultivated populations of plants in which those traits bred true (no change) ○ Crosses (matings) between plants that bore green peas always produced offspring with green peas and etc ○ Way of keeping track of results of matings: Original founding populations: F0 generation Offspring is F1 generation and so on ○ Derived two insightful conclusions: Observed characteristics of organisms are determined jointly by two particles, one inherited from the mother and one from the father  Particles later named genes Each of these two genes are equally likely to be transmitted when gametes (eggs and sperms) are formed, the process called independent assortment ○ Also proved the scientific method Multiple trials are necessary to see patterns in experimental data There is a lot of variation in the measurements of one experiment A large sample size “N” is required to make any quantitative comparisons or conclusions ○ Mendel’s 3 founding principles of inheritance Principle of Uniformity (Law of Dominance) States that all the progeny of a cross where the parents differ by only one trait will appear identical Crossed homozygous pea plants Early conceptions of DNA “Elementen”: believed the plants contained this that carried the information about these traits from one generation to the next “Gemmules” ○ Darwin proposed that traits could be passed on to successive generation in packets he referred to as gemmules ○ Speculates that they traveled from every body part to the sexual organs, where they were stores Principle of Segregation States that the particles or alleles that determine traits are separated into gametes during meiosis, and meiosis produces equal numbers of egg or sperm cells that contain each allele Crossed two heterozygous pea plants Principle of Independent Assortment States that alleles at one locus segregate into gametes independently of alleles at other locus ○ Such gametes are formed in equal frequencies Not always true Wrinkled green and wrinkled yellow are passed down separate of each dominance Dihybrid cross Traits that don’t follow this are considered non-Mendelian traits Mendelian Traits are monogenic  Ex. dimples, hitchhiker's thumb Polygenic traits: characteristics produced by the complex interaction of two or more genes or loci Ex. skin pigment, stature Pleiotropic traits: Characteristics produced by two or more genes A single locus affects two or more apparently unrelated phenotypic traits Often a result of a single mutation Ex. Sickle Cell anemia Polygenic and Pleiotropic traits Ex. PKU Patient ○ Incomplete dominance: distinct gene products from the two codominant alleles in a heterozygote blend to form a phenotype between those of the two homozygotes Ex. straight hair and curly hair parents produce wavy hair Occurs since neither of the alleles is dominant over the other one ○ Codominance: refers to a type of inheritance in which two versions (alleles of the same gene are expressed separately to yield different traits in an individual) Ex. red and white cows produce a red-white spotted cows Both traits show up Both alleles can be dominant or recessive ○ Epistasis: Expression of one gene is modified (masked, inhibited, or suppressed) by the expression of one or more genes Cell Division and the Role of Chromosomes in Inheritance Mendel’s theory of inheritance did not receive recognition by Karl Wilhelm von Nageli at the time and gave up In 1896, Dutch botanist Hugo de Vries unknowingly repeated the experiment with poppies and immediately published By the time Mendel’s experiments were rediscovered in 1900, it was well known that all living organisms are built out of cells and embryological work through cell division ○ Mendel’s discovery on inheritance was a crucial feature of cellular anatomy called the chromosome Chromosomes are small linear bodies contained in every cell and replicated through cell division (like that in gamete) When plants and animals grow, their cells divide ○ Cells contain nucleus (contains chromosomes) which divide in a process called mitosis Ordinary somatic cell division  Original set of chromosomes is duplicated to an exact copy in the daughter cell Different organisms have different numbers of chromosomes, but diploid organisms only have homologous pairs (with similar shapes and staining patterns) 2 features of mitosis suggest that chromosomes play an important role in determining the properties of organisms ○ Each new daughter cell is an exact copy of the parent chromosome when duplicating ○ Material that makes up the chromosome is present even when they aren’t dividing The sequence of events that occur during mitosis is different from meiosis ○ Meiosis is a special for of cell division leading to gametes production Occurs within sex organs Reduces the number of chromosomes by ½ ○ Each gamete only contains one copy of each chromosome, unlike mitosis which has a pair of homologous chromosomes ○ Cells that only contain one copy of each chromosome are haploid ○ When a new individual is conceived, a haploid sperm from the father and the haploid egg from the mother produce a diploid zygote Zygote: single cell that divides mitotically multiple times to produce the individual’s body In 1902, Walter Sutton made the connection between chromosome and the properties of inheritance ○ An organism's observable characteristics are determined by particles acquired from each of the parents ○ Genes segregate independently so meiosis involves the creation of gametes with only one of two possible chromosomes; this is consistent with the ideas: One gene is inherited from each parent Each of these genes is equally likely to be transmitted to gametes ○ In gametes, humans, we have 23 sets with haploid cells Genes: particles carrying chromosomes ○ Genes are made of molecules called DNA ○ Alleles are varieties of a single gene ○ Individuals with two copies of the same allele are homozygous for that allele ○ Individuals carrying two different alleles are called heterozygotes ○ Genotype: particular combination of genes or alleles that an individual carries ○ Phenotype: observable characteristics of the organisms ○ Dominant: the A allele because individuals with only one copy of the A allele have the same phenotype as individuals with two copies  Trait expressed in the phenotype even when the organism is carrying only one copy of the underlying hereditary material ○ Recessive: a allele because that allele has no effect on phenotype in heterozygotes Trait that is expressed in the phenotype only when the organism is carrying two copies of the underlying hereditary materials ○ Punnett Square: diagram that uses gene (or allele) frequencies to calculate the genotypic frequencies of the next generation ○ Recombination: the creation of new genotypes as a result of the random segregation of chromosomes and the crossing-over ○ Genes for a particular trait occur at a particular site on a particular chromosome (Locus) Mendel’s conclusion that traits segregate independently is true if the loci that affect the traits are on different chromosomes When loci for different traits occur close to each other on the same chromosome, they are linked On different chromosome: Unlinked ○ Genome: all of the genes carried on all of the chromosomes All of the DNA of an organism 2001 first human genome mapped Identify the genetic makeup of different people around the world and skeletal DNA (deceased humans and human ancestors) Extreme variability No consistent correlation between biological complexity and genome size Karyotype: The characteristics of the chromosomes for an individual organism or a species, such as number, size, and type Typically presented as a photograph of a person’s chromosomes that have been arranged in homologous pairs and put in numerical order by size Chromosomes frequently tangle and break as they are replicated during meiosis and sometimes shifted from one member of a homologous pair to another, a process called crossing-over ○ Errors in Meiosis Translocation: rearrangement of chromosomes due to the insertion of genetic material from one chromosome to another Disjunction: the failure of the chromosomes to properly segregate during meiosis, creating some gametes with abnormal numbers of chromosome  Monosomy (chromosome loss) Trisomy (chromosome gain) symptom of Down Syndrome Monogenic Traits: Characteristics encoded by a single gene, or locus Single Nucleotide Polymorphisms (SNPS) ○ Single DNA base pairings that produce genetics differences between individuals ○ Spread uniformly throughout the genome ○ Play critical role in determining various attributes, like hair color DNA has two jobs ○ Replicate itself and serve as a template for protein synthesis ○ Crossing Over: the exchange of genetic material between homologous chromosomes during meiosis Creates new combination of alleles on the chromosome (recombination) ○ Linkage: Linked genes sit closely together on a chromosome, making them likely to be inherited together Genes on separate chromosomes are never linked ○ Haplotypes: A group of alleles that tend to be inherited as a unit because of their closely space loci on a single chromosome Haplogroups: large set of haplotypes (ie. the Y chromosome, mitochondrial DNA) that may be used to define the population Maternal Haplogroups ○ Determined by defining variants in your mitochondrial DNA ○ Mitochondrial DNA is the only type of DNA found outside the nucleus, and does not recombine with other types of DNA ○ Share the same maternal haplogroups with any relative you share a direct maternal line with Paternal Haplogroups ○ Determined by defining variants in your Y chromosome (if you have a Y chromosome) ○ The Y chromosome does undergo recombination with the X chromosome, but only at the ends (about 95% of the Y chromosome remains intact across generations) ○ Share a paternal haplogroup with any male relative you share a direct paternal line with Molecular Genetics Genes are segments of a long molecule called DNA, contained in chromosomes DNA (deoxyribonucleic acid) contains information essential to life Using molecular genetics is a field of great intellectual excitement ○ Connects physical and geochemical evolution to Darwinian processes DNA is well suited to be the chemical basis of inheritance ○ Each chromosome contains a single DNA molecule in a double helix Each strand hsa alternating sequences of sugar and phosphate molecules with bases (adenine, guanine, cytosine, or thymine) Repeating four-base structure allows the molecule to assume a vast number of distinct forms ○ Messages need to be preserved over time and transmitted faithfully Messages encoded in DNA affect phenotypes in several ways ○ Protein-coding genes that specify the structure of proteins (necessary for machinery of life)  Proteins can be enzymes that regulate much of biochemical machinery of organisms ○ Regulatory genes determining the conditions under which the message encoded in a protein-coding gene will be expressed ○ Several kinds of ribonucleic acid (RNA) molecules that perform important cellular functions Enzymes influence an organism’s biochemistry ○ Determine what raw materials are transformed into when cells are built ○ Play roles virtually in all cellular processes Proteins play other important roles like the structural functions in living things like hair Proteins are constructed of amino acids that have the same chemical backbone but differ in chemical composition ○ Complex chemicals that make up tissues and bring about the functions, repairs, and growth of tissues Consist of amino acids (20) Essential amino acids: not produced by the body, must be acquired nutritionally Each kind is defined by its particular combination and number of linked amino acids ○ Primary structure: sequence of amino acids that make up a protein ○ Tertiary structure of a protein is crucial to its catalytic function that depends on the sequence of amino acids ○ Hemoglobin molecule: protein that transport oxygen from the lungs to the tissues via red blood cells DNA specifies the primary structure of protein (codons) which are three-letter words that specifies a particular amino acid ○ Codon: essential genetic unit of life; that acts as the template for the amino acid synthesis required for protein expression Made up of 3 DNA or RNA nucleotides 64 possible combinations of the four nucleotides (A,C,G,T) to code for 20 amino acids (61 code form amino acids, 3 for start and stop signals) redundancy ○ Before DNA is translated into proteins its message is first transcribed into messenger RNA (ribonucleic acid) with a different chemical backbone (uracil for thymine)  ○ Ribosome then synthesizes a particular protein by reading the messenger RNA (mRNA) as its bound to a transfer RNA (tRNA) with a triplet of bases called an anticodon ○ tRNA is bound to amino acid whose mRNA codon binds to the anticodon on the tRNA ○ Ribosomes (small cellular organelles) that bind to mRNA (bound to tRNA) and is detached from tRNA and added to the growing protein chain In eukaryotes (organisms with a cell nucleus like people), the DNA that codes for proteins is interrupted by noncoding sequences called introns (noncoding sequences as opposed to exons which are protein-coding sequences) Introns are snipped out and mRNA is spliced back together to code for more than one protein Prokaryotes: don’t have a chromosome or cell nucleus so the process is uninterrupted DNA sequence in regulatory genes determines when protein-coding genes are expressed ○ For example, lactose intolerance When there is no lactose in the environment, a repressor protein binds to one of two regulatory sequences If glucose is present, the activator protein doesn’t bind Combinational control: control of gene expression in which more than one regulatory protein is used and expression is allowed only in a specific combination of conditions Not all DNA sequences code for functional RNA molecules ○ Some RNA molecules bind together with proteins to perform a variety of cellular functions Ex. spliceosomes: organelles that splice the mRNA in eukaryotes after the introns have been snipped out Chromosomes also contain long strings of simple repeated sequences At some point, there is some danger of losing sight of the genes amid the discussion of introns, exons, and repeat sequences Chapter 3: The Modern Synthesis Population Genetics Evolutionary change in a phenotype reflects change in the underlying genetic composition of the population  Phenotypes are observable characteristics or organisms and genotypes are the underlying genetic compositions Evolutionary processes must entail changes in the genetic composition of populations When evolution alters the morphology of a trait, there must be a corresponding change in distribution of genes to control development within the population Population genetics: what happens to genes in the population undergoing natural selection ○ Ex. PKU (genetically inherited disease) is determined by the substitution of one allele for another at a single locus Individuals who are homozygous are for PKU allele are missing a crucial enzyme in the biochemical pathway that allow them to metabolize the amino acid Genotypic frequency: the fraction of the population that carries that genotype Must add up to 1.0 because every individual has to have a genotype Provides a description of the genetic composition of populations independent of population size q= (# of a gametes)/(total # of a gametes) Where q= frequency of a and the frequency of A as p to that p+q=1 q= (# 𝑔𝑎𝑚𝑒𝑡𝑒𝑠 𝑝𝑒𝑟 𝑎𝑎 𝑝𝑎𝑟𝑒𝑛𝑡)(# 𝑜𝑓 𝑎𝑎 𝑝𝑎𝑟𝑒𝑛𝑡𝑠)+(#𝑎 𝑔𝑎𝑚𝑒𝑡𝑒𝑠 𝑝𝑒𝑟 𝐴𝑎 𝑝𝑎𝑟𝑒𝑛𝑡)(# 𝐴𝑎 𝑝𝑎𝑟𝑒𝑛𝑡𝑠) (# 𝑔𝑎𝑚𝑒𝑡𝑒𝑠 𝑝𝑒𝑟 𝑝𝑎𝑟𝑒𝑛𝑡)(𝑡𝑜𝑡𝑎𝑙 # 𝑝𝑎𝑟𝑒𝑛𝑡𝑠) ○ Variety of events in the lives of plants and animals may change the frequency of alternative genotypes ○ Most important mechanisms are sexual reproduction, natural selection, mutation, and genetic drift Sexual Reproduction (random mating) ○ If members of the F1 generation mate at random, the distribution of genotypes in F2 will be the same as F1 Genotypic frequencies remain constant Godfrey Harold Hardy and Wilhelm Weinberg recognized constant frequencies, now called the Hardy-Weinberg equilibrium In general the proportions for a genetic locus with two alleles are Freq(aa)=q2 Freq(Aa)=2pq freq(AA)= p2 Where p is the frequency of A and q is the frequency of a  If no other processes change genotypic frequencies, the Hardy-Weinberg equilibrium frequencies will be reached after only one generation and remain unchanged If the proportions are altered by chance, the population will return to Hardy-Weinberg proportions in one generation Natural Selection ○ Genotypic frequencies will remain at Hardy-Weinberg proportions as long as all genotypes are equally likely to survive and produce gametes ○ If q’ is the frequency of an allele among a population # 𝑜𝑓 𝑎𝑙𝑙𝑒𝑙𝑒 𝑔𝑎𝑚𝑒𝑡𝑒𝑠 𝑝𝑟𝑜𝑑𝑢𝑐𝑒𝑑 𝑏𝑦 𝑎𝑑𝑢𝑙𝑡𝑠 𝑖𝑛 𝑛𝑥𝑡 𝑔𝑒𝑛𝑒𝑟𝑎𝑡𝑖𝑜𝑛 q’ = 𝑇𝑜𝑡𝑎𝑙 # 𝑜𝑓 𝑔𝑎𝑚𝑒𝑡𝑒𝑠 𝑝𝑟𝑜𝑑𝑢𝑐𝑒𝑑 𝑏𝑦 𝑎𝑑𝑢𝑙𝑡𝑠 𝑖𝑛 𝑡ℎ𝑒 𝑛𝑒𝑥𝑡 𝑔𝑒𝑛𝑒𝑟𝑎𝑡𝑖𝑜𝑛 ○ Selection cannot produce change unless there is variation in the population If all individuals are homozygous for the normal allele, gene frequencies won’t change Selection doesn’t operate directly on genes and doesn’t change gene frequencies directly Changes the frequency of different phenotypes Strength and direction of selection depend on the environment Modern Synthesis Darwin believed evolution proceeded by gradual accumulation of small changes Mendel elucidated the structure of the genetic system around the turn of the 20th century were dealing with genes that had a noticeable effect on the phenotype ○ Substitution of one allele for another changed phenotype ○ Genetics proved that inheritance was fundamentally discontinuous and Darwinism declined as people couldn’t reconcile it with his theory of accumulation of small variations (no intermediates) In early 1930s, Ronald A Fisher and JBS Haldane and Sewall Wright showed how Mendelian genetics could be used to explain continuous variation ○ 2 main objections to Darwin’s theory of evolution Absence of a theory of inheritance The problem of accounting for how variation is maintained in populations ○ Modern synthesis: explanation for the evolution of continuously varying traits that combine the theory and empirical evidence of Mendelian genetics and Darwinism Environmental variation: phenotypic differences between individuals that exist because those individuals developed in different environments ○ Ex. bird’s beak  In the absence of selection, genotypic frequencies reach equilibrium after one generation and sexual reproduction produces no blending in the genes Genes are copied with amazing fidelity, but every once in a while, when a mistake in copying is made and goes unrepaired, a new allele is introduced into the population ○ Genes are pieces of DNA and certain forms of ionizing radiation and chemicals can damage the DNA Mutations: spontaneous change in the chemical structure of DNA Add variation to a population to a population by continuously introducing new alleles ○ For characters affected by genes at many loci, low rates of mutation can maintain variation in populations Many genotypes generate intermediate phenotypes favored by stabilizing selection Natural Selection and Behavior Evolution of morphological characters (beak depth and eye morphology that don’t change once we reach adulthood) Behavior is different from morphology as it is flexible and allows individuals to adjust their behavior Ex. soapberry bug have mate guarding behavior to defend his mate after copulation to prevent other males from mating with her ○ Relative magnitude of the cost and benefits of mate guarding depends on the sex ratio (relative numbers of males and females) ○ If the mate-guarding trait were canalized (quality of being insensitive to environmental conditions during development) ○ Plastic traits: sensitive to environmental conditions, resulting in different phenotypes in different environments Behavioral flexibility evolves by selective retention of beneficial genetic variants For any character to evolve: ○ Character must vary ○ Variation must impact reproductive success ○ Variation must be heritable Constraints on Adaptation 5 reasons why evolution doesn’t lead to the best possible phenotype ○ When individuals that have particular variants of one character also tend to have particular variants of a second character, the two are said to be correlated  If natural selection acts on more than one character simultaneously, and characters are nonrandomly associated or correlate On a plot If the cloud of points were round or randomly scattered, then the characters are uncorrelated If the cloud orients from lower left to upper right, it is positively correlated If the variables have points from upper left to lower right, it is negatively correlated Pleiotropic effects: genes that affect more than one character Correlated response: When two characters are correlated, selection that changes the mean value of one character in the population also changes the mean value of the correlated character Can cause other characters to change in a maladaptive (less fit) direction ○ Selection produces optimal adaptations only at equilibrium If the environment changed recently, there is every reason to suspect that morphology or behavior of residents is not adaptive under current conditions Disequilibrium is important because there have been big changes in the lives of humans When populations are small, genetic drift may cause random changes in gene frequencies ○ Sampling variation: variation in the composition of small samples drawn from a large population Same things happens during genetic transmission in small populations ○ Genetic drift: random change in gene frequencies due to sampling variation that occurs in any finite population More rapid in small populations ○ Causes isolated populations to become genetically different from each other ○ Some populations are said to reach fixation (state in which all the individuals in the population are homozygous for the same allele at a particular locus) ○ Populations must be small to lead to significant maladaptation Local versus Optimal Adaptations ○ Natural selection may lead to evolutionary equilibrium where the most common phenotype isn’t the best possible one ○ Natural selection doesn’t take into account long-term consequences of the alterations Ex. humans have camera-type eyes versus insects with compound type eyes  ○ Some local adaptations are called developmental constraints Development: processes by which the single-celled zygote is transformed into a multicellular adult DNA has two main jobs ○ Replicate itself ○ Serve as a template for protein synthesis Proteins ○ Complex chemicals that make up tissues and bring about functions, repairs and growth of tissues ○ Consist of amino acids (20) Body produces 12 by itself and other 8 comes from what we eat ○ Each kind of protein is defined by its particular combination and number of linked amino acid ○ Make enzymes ○ Essential amino acids: not produced by the body, must be acquired nutritionally Codons; proteins made with codons ○ Essential genetic unit of life that acts as the template for the amino acid synthesis required for protein expression ○ Made up of a sequence of 3 nucleotides ○ 64 possible combination of the four nucleotides to code for 20 amino acids ACGT nucleotides 61 code for amino acids and 3 are for start and stop signals ○ Redundancy Making proteins ○ DNA makes proteins through a 2 step process Transcription: enzymes read the information in a codon of DNA molecules and the genetic information is copied into messenger RNA (mRNA) by enzymes in the nucleus Translation: mRNA is carried to the ribosomes in the cytoplasm of the cell, where codons are translated into amino acid chain Amino acids are added in sequence by transfer RNA molecules Final protein is form when the chain folds up 2 main categories of proteins constantly being made ○ Structural genes; code for structural proteins that contribute to the cell’s structure and function ○ Regulatory genes; code for proteins that control the expression of other genes  Turn other genes on or off Starting or stopping transcription and translation from occurring Darwin ○ Blended traits (intermediate) ○ Natural selection- Galapagos Mendel ○ Worked in a lab, manipulating genetics ○ Basic principles of inheritance Traits aren’t blended Parents each contribute alleles (one version of their genes) Dominance, recessive alleles Modern synthesis ○ Combining Mendel’s laws of inheritance to explain Darwin’s natural selection and how it works in real time ○ Neo-darwinism ○ Brought together genetics, paleontology, systematics, and other sciences into one explanation of evolution Population Genetics ○ Study of how populations of a species change genetically over time, leading to evolution ○ Population: group of individuals of a species that can interbreed Allele (gene) frequency: how often a specific allele shows up in a certain population How does allele frequency change within a population ○ Natural selection Main selector Makes organisms the strongest, smartest, and more likely to survive ○ Sexual selection Seems like a subcategory of natural selection Certain individuals are more attractive mates than others because of certain traits Not random mating- specific traits are preferred, even though they make not make an organism technically more fit for survival Alleles of the most successful maters are going to show up more often in the gene pool ○ Mutation  Errors in DNA replication Can be caused by mutagens (ex. cigarettes) Ex. lactose intolerance in the enzyme ○ Genetic drift: allele frequency change in a population due to random chance Greater when the population is small Happens more quickly when a population decreases due to natural disasters and diseases Doesn’t make the population more fit Just shifts genetic variation and gene frequency ○ Gene flow: due to things like migration ○ These don’t act in phases, but overall all the time Hardy-Weinberg law ○ Mathematical model in population genetics that reflects the relationship between frequencies of alleles and of genotypes ○ Can be used to determine whether a population is undergoing evolutionary changes If there are only 2 alleles for a trait p2+2pq+q2=1 P is the dominant allele, q is the recessive allele ○ Assume no genetic drift, natural selection, sexual selection, mutation, gene flow Where evolution isn’t happening Epigenetics ○ Refers to how your behaviors and environment can cause changes that affect the way your genes work Chemical changes in the genome affect how the underlying DNA is used in the production of proteins, but without altering the DNA sequences ○ Unlike genetic mutation (mutations), epigenetic changes are reversible ○ Methylation: mechanism in which a methyl group attaches to a DNA site and represses or fully stops gene expression ○ Like volume controls for your gene expression ○ Not altering genetic code, but how it is read ○ Trauma Methylation can be activated by exposure to extreme temperatures, environmental chemicals, disease, poor nutrition, behaviors (smoking, alcohol consumption, inactivity), stress Chromosomes  ○ Chromosomes: densely packed bundles of DNA and proteins in the nucleus of the cell that carry the cell’s genetic information ○ Homologous: pairs of chromosomes that have similar size, shape, and gene content ○ Chromatid: one half of a replicated chromosomes Any chromosome that isn’t a sex chromosome (XX or XY) is an autosome Mendelian genetics ○ Genetics: study of biological inheritance and passing biological information from parents to offspring ○ Experience revealed basic principles of inheritance Law of dominance, segregation, and independent assortment ○ Gene: basic unit of heredity Alleles: varieties of a single gene ○ Homozygous: two copies of the same allele ○ Heterozygous: two different alleles for a gene ○ Phenotype vs. genotype ○ Dominant vs. recessive ○ Genotypic ratio: homozygous dominant: heterozygous: homozygous recessive Evolution ○ Evolution: descent with inherited modification ○ Mechanisms of change Mutation, natural selection, migration, genetic drift Chapter 4: Speciation and Phylogeny What are Species? Microevolution: evolution of populations within a species affecting morphology, physiology, and behavior of individuals in particular species in particular environments Macroevolution: evolution of new species, families, and higher taxa ○ Interpret fossil record to reconstruct lineage of humans Species aren’t always easy to identify ○ Biological species concept: species are a group of organisms that have the potential to reproduce with one another and produce fertile offspring, and that are reproductively isolated from other such groups ○ Gene flow: introduction of genetic material from one population or species to another through successful reproduction of migrating individuals Ex. gorillas and apes Speciation:  ○ Anagenesis: single lineage evolves with a daughter species replacing its parent species without branching ○ Cladogenesis: single ancestral lineage branches into two or more descendant lineages Species classifications are neither impossible nor useless ○ It can be challenging to precisely identify when 2 diverging populations are different enough to warrant assignment to different species Lineages, subspecies, or species Origin of Species Considerable uncertainty about how new species arise ○ Speciation occurs much too rapidly to be detected in fossil record If a geographic or environmental barriers isolate populations and selection favors different phenotypes, a new species may evolve ○ Allopatric speciation: occurs when 2 or more populations of a single species are geographically isolated from each other and diverse to form 2 or more species ○ Gene flow cannot homogenize the subpopulations, they diverge genetically from another ○ Mechanisms of reproductive isolation reduce or eliminate successful interbreeding between populations, contributing to genetic divergence ○ Genetic drift plays a role in reproductive isolation when one subpopulation is composed of a small number of individuals ○ Classify mechanisms of reproductive isolation according to Prezygotic: they act before formation of zygote Due to lack of encounters, different courtship/preferences, genitals differ to much, incompatible sperm Postzygotic: after the formation of a zygote Prevent hybrid zygote from developing into a healthy fertile adult, typically because of mismatched chromosomes (no complete set of genetic information) Exists on a continuum ○ Character displace and reinforcement help maintain boundaries between previously isolated species experiencing gene flow upon recontact ○ Character displacement: if competition over food, mates, or other resources increases the morphological differences between immigrants and residents ○ Reinforcement: may also reduce the extent of gene flow between populations Process in which selection acts against the likelihood of hybrids occurring between members of two phenotypically distinctive populations, leads to evolution of mechanisms that prevent interbreeding ○ Most speciation is allopatric Parapatric speciation: when populations diverge because they experience different natural selection pressures in their differing environments or as a result of genetic drift  ○ Populations may have overlapping ranges and continue to experience gene flow throughout the process of speciation ○ Scientists would need information about the species’ historical ranging patterns Sympatric speciation: hypothesis that speciation can result from selective pressures favoring different phenotypes within a population without posting geographic isolation as a factor ○ Thought to occur when a trait is advantageous in one part of a species’ range but strongly disadvantageous in another part of the range Adaptive radiation: process where a single lineage diversifies into several species, each characterized by distinctive adaptation ○ Niche: the way of life or trade of a particular species Tree of Life Organisms can be classified hierarchically on the basis of similarities, not related to adaptation ○ Remarkable property of life of patterns of similarity is the basis for system of classification devised by Carolus Linnaeus Speciation explains why organisms can be classified hierarchically ○ Clearly new species originate by splitting off from older ones and we can arrange a group of species that share a common ancestor into a family tree or phylogeny ○ Ex. hominoids a superfamily that includes apes and humans ○ However, when two daughter species diverge, they don’t differ in all phenotypic details Most other traits retain their original form ○ Each time one species splits to become two new species, the new daughter species differ in some way and continue to diverge through time because one speciation has occurred, two lineages evolve independently Why Reconstruct Phylogenies? Phylogenetic reconstruction plays 3 roles in the study of organic evolution ○ Phylogeny is the basis for identification and classification of organisms Taxonomy: branch of biology concerned with the use of phylogenies for naming and classifying organisms ○ Explain why a species evolved certain adaptation and not others Ex. apes influenced by the evolution of locomotion (way animals move) They are all quadrupedal (walk on hands and feet) However, gorillas and chimpanzees knuckle walk (type of quadrupedal locomotion where weight is supported by knuckles Humans are bipedal, walking on two legs Phylogeny accounts that is is possible that the common ancestor of humans, chimpanzees, and gorillas was a knuckle walker ○ Deduce the function of morphological features or behaviors by comparing traits of different species  Comparative method: establishes the function of a phenotypic trait by comparing species Some scientists argue that terrestrial (ground-dwelling) primates live in larger groups that arboreal (tree-dwelling) primates since they are more vulnerable to predators Systematics: branch of biology concerned with the procedures for constructing phylogenies Whereas taxonomy means the use of phylogenies in naming and classifying All living organisms can be placed on a phylogenetic tree to trace their ancestry How to Reconstruct Phylogenies Construct phylogenies on the assumption that species with many phenotypic similarities are more closely related than those with fewer phenotypic similarities Must avoid basing decisions on characters that are similar because of convergent evolution (separate adaptations independently produced by natural selection) ○ Analogous: similarity between traits due to convergent evolution, not common descent ○ Homologous: similarity between traits due to common ancestry Important to ignore similarity based on ancestral characters, traits that also characterized by common ancestor of species benign classified ○ Ex. egg laying is an ancestral trait (characterized the common ancestor) ○ Derived traits: features that have evolved since the time of the last common ancestor of the species under consideration Systematists have developed 3 criteria for distinguishing ancestral characters from derived characters ○ Ancestral characters appear earlier in organismal development Evolution often proceeds by modifying the ends of existing developmental pathways ○ Ancestral characters appear earlier in fossil records ○ Ancestral characters are seen in out-groups Out-groups: taxonomic group that is related to a group of interest and can be used to determine which traits are ancestral and which are derived If out-groups have a trait, it is reasonable to infer that the common of ancestor has it Genetic distance measures the overall genetic similarity of two species ○ One way is measure this is DNA sequence data If there are homologous DNA segments, they are descended from the same DNA sequence in the common ancestry DNA segments are sequences and the number of nucleotide sites at the site where they differ is used to compute genetic distance ○ Molecular clocks: the hypothesis that genetic change occurs at a constant rate and thus can be used to measure the time that has elapsed since two species shared a common ancestor Based on observed regularities in the rate of genetic change along different phylogenetic lines  As long as genetic distances are not too big or small, the assumption is a useful approximation Drift and mutation are key factors influencing rates of change, but others argue that molecular clock are mainly controlled by natural selection If the molecular clock hypothesis is correct, then knowing the genetic distance between two living species allows us to estimate how long ago the two lineages diverged ○ One method for determining rates of change is fossil calibration (uses known divergence times based on fossil records to calibrate molecular clock) ○ Recent advances in genetic tech have made it possible to estimate the rate of change directly Sequencing the genomes of large set of relatives, or pedigree, containing trios of parents and offspring nd counting the number of times an offspring has an allele neither of its parents have Need to distinguish between differences causing by sequencing errors and those representing true mutations Yields lower estimates of rate of change, but generates older divergence times between lineages ○ Uncertain which estimates of the rates of change result in accurate divergence times Taxonomy: Naming Names Hierarchical pattern of similarity created by evolution provides the basis for the way science classifies and names organisms Scientific system for naming animals is based on the hierarchy of descent ○ Species closely related are grouped together in the same genus ○ Closely related genera are grouped in a higher unit, often the family ○ Closely related families are then grouped in a more inclusive unit, often a superfamily Most taxonomists agree that descent should play a major role in classifying organisms ○ Disagree about whether descent should be the only factor used Cladistic taxonomy: school of thought that argue only descent should matter ○ Both informative and unambiguous Tells us how an organism is related to others but ambiguous because the position of each organism is given by the actual pattern of descent Evolutionary taxonomy: school believing that classification should be based on descent and overall similarity ○ Ambiguous because judgments of overall similarity are necessarily subjective Species ○ Group of organisms that have the potential to reproduce with one another and produce fertile offspring ○ Reproductively isolated from one another Life changes over time and evolution means that there are common ancestry between species Phylogeny  ○ The evolutionary relationships of a group of organisms ○ Based on shared characteristics including physical traits, genetics, and behavior ○ Organisms with shared genetics will be closer than others Reconstructing phylogenies ○ Characters: heritable traits that can be compared across organisms Physical characteristics (morphology) Genetic sequences Behavioral traits Phylogeny ○ Evolutionary relationship of a group of organisms ○ Based on shared characteristics including physical traits, genetics, and behavior Directional patterns of traits ○ Plesiomorphy: characteristic present in common ancestor primitive/ancestral trait ○ Symplesiomorphy: plesiomorphy shared by two or more lineages in particular clade ○ Apomorphy: novel characteristic that they evolved from (and is now differed from) its ancestral form (plesiomorphy) Derived trait ○ Synapomorphy: apomorphy shared by two or more lineages in a particular clade, and is hypothesized to have evolved in their most recent common ancestor Why construct phylogenies ○ Phylogeny is the basis for the identification and classification of organisms ○ Knowing phylogenetic relationships often helps explain why a species evolved certain adaptations and not others ○ We can deduce the function of morphological features or behaviors by comparing the traits of different species (comparative method) ○ Biologists collect data on different traits of the species they are examining Reconstructing phylogenies ○ Characteristics: heritable traits that can be compared across organisms Physical characteristics (morphology) Genetic sequences Behavioral traits ○ Categorized into Derived traits (apomorphies) Traits that arise during the evolution of a group and differ from the traits of the ancestor; may appear through loss or gain of a feature ○ Categorize into primitive/ancestral traits Appear earlier in organismal development Appear earlier in the fossil record Seen in outgroups  Phylogenetic trees versus Cladograms ○ Phylogenetic: evolutionary relationship in a set of organisms ○ Cladograms: group of organisms that include an ancestor Section of phylogenetic tree Biological similarity ○ Homologous traits Traits inherited by two different organisms from a common ancestor Structures that share a similar embryonic origin ○ Analogous traits Similar characteristics in different evolutionary origins and are not due to a close evolutionary relationship Evolution ○ Convergent evolution: independent evolution of similar features in species of different periods of epochs over time ○ Divergent evolution: when two species share a common ancestor and evolved one or more characteristics that make them different to each other ○ Microevolution: small scale evolution; a change in gene frequency within a single population ○ Macroevolution: large scale evolution; evolution above the species level Patterns of macroevolution ○ Stasis: lack of evolutionary change or very slow evolutionary change ○ Character change: (Character displacement) two similar species that inhabit the same environment are undergoing natural selection and it is favoring divergence in characteristics When competing species evolve in response to one another ○ lineage -splitting (AKA speciation) How new species are created when a group within a species separates from other members of its species and develops its own characteristics Due to geographic isolation, reduction of gene flow, and adaptive radiation Allopatric speciation: occurs when a contiguous population become split into 2 geographically isolated subpopulations by a physical or environmental barrier to migration Adaptive radiation: process of rapid divergence of multiple species from a single ancestral lineage ○ Increases number of species we see diverging from common ancestor ○ Extinction: really important and in terms of the whole tree of line Every lineage has the potential to go extinct; over 99% of species on Earth are extinct Speciation and Phylogeny ○ Microevolution; acts at the level of individuals within populations Natural selection, genetic drift, mutation, migration Cause changes in allele frequency over time  ○ Macroevolution: evolution applied to more than one species How do new species come into existence? Species ○ Biological species concept: group of organisms that has the potential to reproduce with one another and produce fertile offspring ○ Can be regular exchange of genes between closely related species ○ Lumpers versus splitters Disagreement even among scientists about phylogeny ○ Doesn’t mean it’s useless Types of speciation ○ Allopatric speciation: geographically isolated populations ○ Parapatric speciation: continuously distributed populations ○ Sympatric speciation: new species within the same range Phylogeny ○ A map/theory of evolutionary relationships among a set of organisms, called taxa ○ Why make a phylogeny? Helps with taxonomy, efforts to identify and classify organisms Helps explain why certain adaptations evolved It helps to understand the function of morphological features or behaviors by comparing the traits of different species ○ Assumption: species with many phenotypic similarities are more closely related than species with fewer phenotypic similarities ○ Avoid confusion from convergent evolution and ancestral traits ○ How to distinguish ancestral characters from derived characters Ancestral characters appear earlier in organismal development Earlier in the fossil record and seen in out-groups Measuring genetic distance with molecular clocks ○ Molecular clock: genetic distances with a constant rate or change ○ Useful as an approximation ○ Allows us to estimate how long ago two lineages diverged Chapter 5: Primate Diversity and Ecology Two Reasons to Study Primates Studies of nonhuman primates help understand human evolution for two complementary but distinct reasons ○ Closely related species tend to be similar as they acquire traits from a common ancestor  Ex. viviparity (bearing live young) and lactation are shared by placental and marsupial mammals ○ Natural selection favors similar adaptations in similar environments See how evolution shapes adaptation in response to different selective pressures Humans and other primates share many characteristics so other primates provide valuable insights about early humans ○ Share aspects of morphology, physiology, and development ○ Developed vision and grasping hands and feet ○ Behavior is similar as physiologic and cognitive structures are more similar to those of other primates than to members of other taxonomic groups Diversity within primate order helps understand how natural selection shapes behavior All primate species have evolved adaptations that enable them to meet basic challenges of life ○ There is still much morphological, ecological, and behavioral diversity among species ○ Few are solitary and most are highly gregarious ○ Some are nocturnal (active at night) and others are diurnal (active at day) ○ Some species actively defend territories from incursions by other remembers of their own species (conspecifics) ○ In some species, only females provide care for their young In others males actively participate Evidence of diversity among closely related organisms help researchers understand how evolution shapes behavior ○ Differences in closely related species are likely to represent adaptive responses to specific ecological conditions ○ Similarities among more distantly related creatures under similar ecological conditions are likely the product of convergence Comparative method: important form of analysis as researchers ○ Researchers explain patterns of variation in morphology and behavior observed in nature ○ Behavior leaves little trace in the fossil record, so testing hypotheses about lives of hominin ancestors is the way ○ Ex. sexual dimorphism: males compete over access to females and form groups that contain one male and multiple females Features that Define the Primates Members of the primate order are characterized by several shared, derived characters, but not all primates share all of these traits  Primates are a nondescript mammalian order that cannot be unambiguously characterized by a single derived feature shared by all members Most important derived traits of primates ○ Opposable toes and thumbs ○ Locomotion is hind-limb dominated (hind limbs do most of the work) ○ Unspecialized olfactory (smelling) apparatus reduced in diurnal primates ○ Visual sense is highly developed ○ Females have small litters and gestation and juvenile periods are longer ○ Brain is larger than similarly sized mammals ○ Molars are relatively unspecialized ○ Subtle anatomical characteristics useful to systematists Humans differ from most nonhuman primates in that they move upright along the ground ○ Some primates swing along underneath branches using a form of locomotion called brachiation Most primates are characterized by a greater reliance on visual stimuli and less reliance on olfactory stimuli than other mammals Binocular vision: fields of vision of two eyes overlap so both eyes perceive the same image Stereoscopic vision: each eye sends a signal of visual image to both hemispheres in the brain to create an image with depth (not uniformly expressed within primate order) Primates have longer pregnancies, mature at later ages, live longer, and have larger brains ○ Progressive trend toward increased dependence on complex behavior, learning, and behavioral flexibility 2 points in mind about characteristics ○ None of the traits makes primates unique ○ Not every primate possess all the traits Primate Biogeography Primates are restricted mainly to tropical regions of the world ○ Continents of Asia, Africa, and South America and islands that lie near the coasts are home to most of the world’s nonhuman primates ○ Nonhuman primates were once found in southern Europe, but no natural populations survive there now Nonhuman primates are found mainly in tropical regions, where fluctuations in temperature from day to night greatly exceed fluctuations in temperature across the year ○ Some species extend their ranges into temperate areas of Africa and Asia, where they cope with substantial seasonal fluctuations in environmental conditions  Nonhuman primate species occupy an extremely diverse set of habitats, including tropical forests, savanna woodlands, mangrove swamps Almost all species are found in forested areas Taxonomy of Living Primates Scientists divide the primate order into two suborders, the Strepsirrhini and Haplorrhini Semiorders further divided into suborders ○ Strepsirrhine belong to a single suborder, Strepsirrhini ○ Haplorrhini is divided into 2 suborders Tarsiiformes and Anthropoidea reflecting evolutionary history of tarsiers because their lineage led to the evolution of other haplorrhine primates (including monkeys, apes, and humans) Primate Diversity Strepsirrhines ○ Infraorder: Lemuriformes Composed of small, nocturnal, arboreal residents of forests of Africa and Asia 2 families with different locomotion and activity patterns Galagos: active and agile Lorises and pottos move with ponderous deliberation and remain immobile for long periods ○ Possibly to help avoid detection by predators ○ Infraorder: Lorisiformes Feed on fruit, gum, and insect pray Dependent offspring in nests built in hollows of trees or hidden in masses of tangled vegetation Haplorrhines ○ Suborder: Tarsiiformes Includes tarsiers, which are enigmatic primates that live in the rainforests Small, nocturnal, arboreal, and move by vertical leaping Only primates that rely exclusively on animal matter for food ○ Suborder; anthropoidea Includes all of monkeys and apes Infraorder: Platyrrhini South and Central America and southern Mexico Share basic features of diurnal behavior, forested homes, mainly arboreal Superfamily: Ceboidea  ○ Ex. capuchins, owl monkeys, squirrel monkeys, marmosets, tamarins ○ Multimale, multifemale groups ○ Forage for fruit, leaves and insects Superfamily: Pithecoidea ○ Pair-bonded family groups ○ Specialized seed eaters Family: Atelidae ○ Ex. howler monkeys, spider monkeys, wooly monkey, and muriquis ○ Long-distance roars in intergroup interactions Infraorder: Catarrhini Reside in Africa and Asia, except for humans Catarrhine monkeys and apes have narrow nostrils that face downward Most are larger than most platyrrhine species Superfamily: Cercopithecoidea (monkeys) ○ Subfamily: Colobinae Ex. colobus monkeys, langurs, leaf monkeys Slender bodies, long legs, long tails, and beautifully colored coats Leaf and seed eaters Complex stomachs that allow them to maintain bacterial colonies One adult male and several females Infanticide is favoured by selection ○ Subfamily: Cercopithecinae Africa mostly Wide variety of habitats and variable in body size and dietary preferences Superfamily: Hominoidea (apes and humans) ○ Family: Hylobatidae Ex. gibbons and siamangs Slightly built with long arms Use arms to move through canopy (only true brachiators) Pair-bonded family groups  Feed on fruit, leaves, flowers, and insects ○ Family: Pongidae Ex. orangutans (only living genus) Largest and most solitary species of primates ○ Family: Hominidae Great apes, gorillas, bonobos, chimpanzees, humans Gorillas divided into 2 species, western and eastern gorilla (subspecies for mountain and lowland gorilla) Chimpanzees display a number of behaviors of particular interest Regularly hunt vertebrate prey Share meat with other group members Use tools for various tasks Behavioral traditions represent a form of culture Primate Ecology Primate life is driven by 2 concerns: food and safety from predators Food ○ Essential for growth, survival, reproduction ○ Total amount of energy an animal needs depends on 4 components Basal metabolic rate: rate at which an animal expends energy to maintain life when at rest Active metabolism: number of additional calories required when energy needs rise above baseline levels, depending on how much energy the animal expends Growth Rate: imposes further energetic demands on organisms Reproductive effort: energetic costs or reproduction ○ Diet must satisfy the animal’s energy requirements, provide specific types of nutrients, and minimize exposure to dangerous toxins Provides energy and essential nutrients animals cannot synthesize themselves Proteins, most amino acids, fats and oils, carbohydrates, vitamin, minerals, and trace amounts of certain elements play an essential role in regulating many metabolic functions ○ Must avoid toxins (substances in the environment that are harmful to animals) Many plants produce these called secondary compounds to protect themselves from being eaten  Ex. alkaloids are toxic and disrupt normal metabolic functions ○ Primates must obtain energy and essential nutrients from a variety of sources Carbohydrates from sugars in fruit Animal pre provide fats and oils Gum (substance that plants produce in response to physical injury) is an important ○ Generalizations about primate diet Rely on at least one type of food that is high in protein and another that is high in carbohydrates from fruit Most primates rely more heavily on some types of foods than on others Chimpanzees feed mainly on ripe fruit throughout their range from Tanzania to Ivory Coast Frugivore: diet is mostly fruits Folivore: diet is mostly leaves Insectivore: diet is mostly insects Gumnivore: diet is mostly gum Insectivores are smaller than frugivore than folivores Related to differences in energy requirements ○ Nature of dietary specializations and challenge of foraging influence ranging patterns Availability of preferred food varies widely in space and time Foliage is normally more abundant than fruit or flowers at a given time during the year ○ Activity patterns Primate activity patterns show regularity in seasonal and daily cycles Spend most of their time feeding, moving around their home range, and resting Morning is spent eating and moving between feeding sites Most species settle down in a shady spot to rest, socialize, and digest their morning meals ○ Ranging behavior All primates have home ranges, but only some species are territorial and defend their home range against incursion by other members of their species Home ranges: relatively fixed area where all members of a given group can be consistently found in a particular area over time Contain food, water, and safe sleeping sites  Territories: fixed area occupied by animals that defend the boundaries against intrusion by other individuals or groups of the same species Difficult for primatologists to study intergroup encounters because researchers need to monitor the behavior of multiple groups simultaneously Predation ○ Predation is believed to be a significant source of mortality among primates, but direct evidence of predation is difficult to obtain ○ Estimated rates of predation vary from less than 1% of the population per year to more than 15% ○ Small-bodied primates are more vulnerable to predation than larger ones ○ Terrestrial species are more vulnerable than arboreal species ○ Species that live in small groups are more vulnerable than arboreal species ○ Primates have evolved an array of defenses against predators Give alarm calls to alert others of danger Concealing Interspecific associations may enhance predator detection Primate Sociality Threat of predation and need to find food influence many aspects of primates’ lives and have also played a role in the evolution of primate sociality Most primates live in groups of some kind Predation is the primary factor favoring evolution of sociality ○ Intensity of predation pressure and the distribution of food influences the size and composition of groups ○ Groups are likely to detect predators sooner than individuals Power in numbers in conflicts Group life also poses some risk over resources like food and mates ○ Spend more time moving than searching for food ○ Group competition imposes upper limit on group size ○ Greater exposure to infectious diseases and pathogens Behavioral immunity and primates’ responses to biological contaminants, like feces Within-group competition leads to the formation of dominance hierarchies and disparities ○ Outcome of mating may be related to relative size, strength, experience, etc Dominance relationship: ability of one individual to intimidate or defeat another individual in a pairwise encounter Assessed from the outcome of aggressive encounters  ○ When dominance interactions have predictable outcomes, we assign dominance rankings to individuals Dominance matrix: square table to keep track of dominance interactions among a group of individuals Dominance relationships are said to be transitive (3-way relationship) between first and second elements and the second and third elements automatically determine the relationship between the first and third elements Most primates live in groups, social units that are composed of animals that share a common home range or territory and interact more with one another than other members Social organization: size, age-sex composition, and degree of cohesiveness of primate social groups ○ 4 types ○ Solitary: females maintain separate home ranges or territories and associate mainly with their dependent offspring Males establish their own territories and home ranges Both sexes disperse but in some species, females settler near their natal (birth) territories All solitary primates are strepsirrhines ○ Pairs: groups composed of one adult male, one female, and immature offspring Members of both sexes disperse from their natal groups ○ One male, multiple females: groups composed of several females, one resident adult male, and immature offspring Males compete over residence Characterized by polygyny, a mating system in which resident males mate with multiple females ○ Multiple males, multiple females: groups composed of several adult males and females and immature offspring Polygynandry: mating system where both sexes mate with more than one partner Reality is more complicated Not all groups of a particular species may have the same social organization or mating system Primate Conservation Many species of primates are in real danger of extinction in the wild Two primate species have become extinct, with many more endangered Primates are threatened because their habitats are disappearing  ○ Most live in the tropics and are directly affected by widespread destruction of the world’s forests ○ Trade in forest products also pose threats as humidity levels drop, tree mortality increases, risk of fires increases ○ Mining pollutes the soil and groundwater Primate Diversity and ecology Carl Linnaeus (17701-1778) ○ Swedish botanist ○ “Father of Taxonomy” Taxonomy ○ Branch of science concerned with classifying organisms ○ Binomial nomenclature ○ International Commission on Zoological Nomenclature ○ Genus species Order: Primata ○ Latin noun primat-/primus ○ Encompasses extant (living) lorises, lemurs, tarsiers, monkeys, and apes (including humans), as well as extinct primate species Primates ○ ~80MA ○ >600 species and subspecies ○ Our closest living relatives ○ Development explains a lot of our developmental processes ○ Divides primates into two orders 70 MA Haplorhini New world monkeys, old world monkeys, apes, tarsiers ○ Tarsiers were an out-group (nocturnal) Retinal fovea Higher order Have ancestral rhinarium ○ Face is pushed in and upper lip is freed to show teeth and facial expressions Orbital plate 25MA Platyrrhines ○ New world monkeys ○ Wide navel septum  Catarrhines ○ Apes, old world monkeys ○ Tiny septum and nostrils point down Sexual dimorphism (differences in male and female, ex color, canine size, sound) ○ Gorillas as the most sexual dimorphism (greater differences) Tarsiers ○ Half orbital plate ○ Dental formula 2.1.3.3./1.1.3.3. ○ Only purely carnivorous primates ○ Large hands, feet, tarsal bones Strepsirrhini Have open skull Have tapetum lucidum on their eyes that receive light May have grooming claw on their tow Nocturnal Orbital bar Wet noses (as opposed to Haplorrhinis which are dry) Primate order is incredibly diverse (3rd most diverse order of mammals after rodents and bats) Primate characteristics ○ Eyes Heavy reliance on vision (versus olfaction) Trichromacy Stereoscopic, binocular vision ○ Ears Auditory bulla (enclosure of middle ear) completely formed by petrosal bones (surrounds inner ear in all mammals) Ear tube ○ Teeth Generalized dentition (heterodont) Shape, size, kind allows us to infer diet, lifestyle, sex, species Dental formulas allow us to infer species Dental formulas (½ of your mouth) Incisors 2  ○ Located in the front of the mouth and used for nipping off pieces of food Canines 1 ○ Sharp and pointed ○ “Eye-teeth” ○ Primarily to puncture and rip Premolars 2 ○ Low and wide ○ Located behind the canines ○ Crushing and grinding food Molars 3 ○ Largest teeth found in the mouth ○ Located behind the premolars ○ Crushing and grinding food Outlier: tooth comb (pushed together incisor) for grooming or scrapping gum off trees Dental formulas Platyrrhines (new world monkeys) 2.1.3.3. Top and bottom Catarrhines (old world monkeys and apes) 2.1.2.3. Tarsiers top 2.3.3.3. Bottom is 1.1.3.3. Most Strepsirrhines 2.1.3.3. ○ Teeth and Diet Frugivory Lack of specialization Molar have broad chewing surfaces with low, rounded cusps Large incisors for slicing through fruit skins Folivory Highly specialized teeth and gut Broad molars with high, sharp cusps connected by shearing crests Allow physical breakdown of fibrous leaves Insectivory Small molars with pointed cusps for puncturing exoskeletons ○ Hands Prehensile digits (can move by themselves) (Most have 5) Must have opposable or pseudo-opposable thumbs or big toe Tactile pads  ○ Brains Large and dense (when adjusted for body size) compared to other mammals Sulci (folds) and gyri (between the folds) Neocortex: higher-order thinking wrapping around the limbic brain (emotions) and brain stem is for survival Bigger head=bigger brain Brain size is positively correlated with body size Brain size is correlated with diet ○ Foramen magnum (hole in the bottom of the skull where the spinal cord goes through) Position is indicative of level of bipedalism Chimps can walk bipedally (foramen magnum far back of the skull) ○ Primate behavior EXTREME sociality Group size ○ Tarsiers and orangutans are pretty solitary ○ Baboons live in huge groups and are indicative of primates Dominance Group composition/structure Life history/reproduction Number of offspring Number of nipples ○ Primate life span Life history: pattern of allocation of resources to maintenance, growth, and reproduction throughout its lifetime fertilization/ovulation, birth, infancy, weaning, juvenile, puberty, adulthood Primate life history Long lives (slow history) Modest reproductive rates Slow growth Extensive parental care Chapter 6: Primate Reproductive Strategies Why Reproduction Matters Reproduction is the central act in the life of every living thing  Perform a dizzying variety of behaviors All behaviors evolved for a single ultimate purpose: to enhance reproduction Darwin’s theory: complex adaptations exist because they evolved step by step through natural selection ○ Modifications increased reproductive success Understanding diverse reproductive systems illustrates human evolutions since we share many elements Reproductive strategies are influenced by phylogenetic heritage as mammals ○ All mammals reproduce sexually and carry young internally, then nursing born offspring ○ Considerable diversity in patterns of reproduction, mating, parenting ○ Amount of time, energy, resources that males and females invest in mating activities and offspring care has profound consequences for the evolution of virtually every aspect of social behavior and parts of their morphology Language of Adaptive Explanations Strategy: set of traits are designed to solve a particular adaptive problem, like finding food, avoiding predation, or rearing offspring ○ Conscious plan of action to achieve a goal Evolutionary biologists don’t think that nonhuman animals are consciously aware of reproductive goals, etc Behaviors we observe are the product of natural selection acting on individuals to shape their motivations, reactions, capacities, and decisions Behavioral tactics that led to greater reproductive success in ancestral populations have been favored by natural selection and represent adaptations Terms cost and benefit refer to how particular behavioral tactics affect reproductive success ○ Different behaviors have different impacts on an animal’s genetic fitness ○ Influence lifetime reproductive success Evolution of Reproductive Strategies Reproduction can be divided into two components: mating effort and parenting effort Mating effort: all of the activities leading up to conception, including the effort required to locate mates and gain access to them Parenting effort: all activities related to offspring care after conception occurs Expectation is that natural selection favors investment in both mating and parenting efforts If time, energy, and resources were unlimited, animals would invest heavily in these two efforts In most mammalian species, females benefit more from investing in parent effort than mating effort and the opposite for males If mammalian females laid eggs, the respective parenting strategies of the sexes might be quite different ○ In some family of fish, male parental care is more common, like sea horses Female Reproductive Tactics Primate females generally invest heavily in each of their offspring Pregnancy and lactation are time-consuming and energetically expensive activities for all female primates, including humans  Larger animals tend to have longer pregnancies an lactation periods Extended duration of pregnancy and lactation in primates is related to the fact that brain tissue develops very slowly Energy costs of pregnancy and lactation impose important constraints on female reproductive behavior If a mother produces many offspring, she will be unable to invest much in any individual offspring ○ As infants grow older, they become progressively more independent and more competent ○ Mothers use a variety of tactics to actively encourage their infants to become more independent ○ Reflect shifting balance between the requirements of the growing infant and the energy costs to the mother of catering to her infant’s needs ○ Female reproductive success depends partly on her ability to obtain enough resources to support herself and her offspring When monkeys were being intensively provisioned, groups grew very rapidly because the females grew faster, matured earlier, and had higher fertility rates ○ Interbirth intervals: period of time between the birth of one infant and the next The reproductive success of individual female varies ○ Its a product of the length of her reproductive career, length of the interval between successive births, and the proportion of her offspring that survive to reproduce themselves In most primate species, females continue to reproduce throughout their lives Dominance rank influences reproductive success in some species ○ Competition for access to food resources leads to formation of dominance hierarchies in which high-ranking individuals have priority access to resources ○ Influences various components of reproductive success in species forming social groups that include multiple breeding females ○ Ex. daughters of high-ranking female chimpanzees mature earlier than those of low-ranking females ○ Relationship between rank and reproductive success only captures a portion of reproductive careers o individual females and makes it difficult to assess the impact of dominance r