MOLECULAR EVOLUTION

"Describe the concept of taxonomy in biology."

"Taxonomy is the identification, naming, and assignment of organisms to groups based on overall similarity, without taking evolutionary history into account."

"Explain the significance of Carl Linnaeus in the field of classification."

"Carl Linnaeus was the creator of a system of hierarchical classification, which laid the foundation for modern taxonomy."

"Define homoplasy in the context of molecular evolution."

"Homoplasy, or convergent evolution, refers to the independent acquisition of similar characters in different organisms, which can lead to similarities that do not reflect common ancestry."

"How do homologous features differ from analogous features?"

"Homologous features are similar due to common ancestry, while analogous features are similar due to convergent evolution and do not indicate a shared lineage."

"Explain the concept of orthologous genes."

"Orthologous genes are found in different species and are derived from the same gene in a common ancestor, often retaining similar functions."

"Describe the fate of paralogous genes after gene duplication."

"Paralogous genes can become an extra copy of the gene, gradually acquire mutations leading to a new function, or become a non-functioning pseudogene."

"What is the importance of comparing orthologs when studying genes across species?"

"When making comparisons of genes in different species, it is crucial to compare orthologs to ensure that the genes being compared are truly homologous and reflect evolutionary relationships."

"Define monophyletic groups in phylogenetics."

"Monophyletic groups contain a common ancestor and all of its descendants, reflecting a complete lineage."

"What are paraphyletic groups and how do they differ from monophyletic groups?"

"Paraphyletic groups do not include all descendants of a common ancestor, thus failing to accurately reflect evolutionary history."

"Explain the role of Charles Darwin's observations in understanding molecular evolution."

"Charles Darwin's observations of similarities in living organisms provided evidence for descent with modification, suggesting that all living things are related through a chain of common ancestors."

"Describe the concept of homology in evolutionary biology."

"Homology refers to features present in different organisms that are similar due to inheritance from a common ancestor."

"What is the Hox complex and its significance in molecular evolution?"

"The Hox complex in Drosophila is an example of a set of paralogous genes, illustrating how gene duplication can lead to functional diversification within a species."

"How does convergent evolution challenge the robustness of similarity-based classifications?"

"Convergent evolution can lead to similar traits arising independently in different lineages, which may not be repeatable and can mislead classifications based on similarity alone."

"What is the relationship between homologous features and common ancestors?"

"Homologous features are those that were present in a common ancestor shared by different organisms, indicating a shared evolutionary history."

"Explain the concept of sister taxa in phylogenetics."

"Sister taxa are groups of organisms that are more closely related to each other than to any other group, sharing a more recent common ancestor."

"Describe the science of systematic biology."

"Systematic biology is the science of classifying organisms into groupings based on their evolutionary relationships."

"Explain the significance of the 1950s in the context of taxonomy."

"The 1950s marked the Age of Numerical Taxonomy (Phenetics), which grouped organisms based on their overall similarity, although it faced challenges such as convergent evolution."

"Define molecular evolution and its two main questions."

"Molecular evolution refers to changes in biomolecules over time. It addresses two questions: how do molecules change over time (evolve), and how can the historical record in biomolecules help us understand the history of life on Earth?"

"How does cladistics classify organisms?"

"Cladistics classifies organisms based on shared derived characters, known as synapomorphies, which indicate common ancestry."

"Explain Hennig's Grouping Rule."

"Hennig's Grouping Rule states that synapomorphies are evidence of common ancestry, while symplesiomorphies, convergences, and parallelisms do not provide useful evidence of common ancestry."

"What is Ocham's Razor and its relevance in systematic biology?"

"Ocham's Razor is the principle that the simplest explanation is preferable to more complicated ones, which is relevant in parsimony methods of systematic biology."

"Describe the concept of parsimony in the context of phylogenetic trees."

"Parsimony in phylogenetics suggests that simpler hypotheses are preferable, and the tree with the shortest number of steps, representing the simplest explanation, is favored."

"How do distance methods contribute to molecular systematic methodology?"

"Distance methods are one of the approaches used in molecular systematic methodology to analyze evolutionary relationships among organisms."

"Explain the role of molecular evolution in reconstructing evolutionary history."

"Molecular evolution plays a crucial role in reconstructing evolutionary history by using changes in biomolecules to trace the lineage and relationships of different organisms."

"What is the significance of shared derived characters in cladistics?"

"Shared derived characters, or synapomorphies, are significant in cladistics as they provide evidence of common ancestry among organisms."

"How does Hennig's Auxiliary Principle guide assumptions in evolutionary biology?"

"Hennig's Auxiliary Principle advises that one should never assume convergence or parallel evolution without contrary evidence, and instead assume homology."

"Describe the concept of population aggregation analysis as presented by Davis and Nixon."

"Population aggregation analysis involves examining specific genetic markers in populations, such as the presence of certain nucleotides in the genome of different species."

"What does the term 'Black Box' refer to in the context of evolutionary traits?"

"In the context of evolutionary traits, 'Black Box' refers to various anatomical features such as the backbone, jaws, walking legs, amniotic egg, and hair."

"Explain the challenges faced by numerical taxonomy in the 1950s."

"Numerical taxonomy faced challenges such as the issue of convergent evolution, which complicated the classification of organisms based solely on overall similarity."

"How can molecular evolution help us understand the history of life on Earth?"

"Molecular evolution can help us understand the history of life on Earth by analyzing the changes in biomolecules, which serve as a historical record of evolutionary processes."

"Define microevolution and its significance in evolutionary biology."

"Microevolution refers to changes in allele frequencies within a population over time, and it is significant as it provides insight into the mechanisms of evolution at the population level."

"Describe the significance of red and black bars in phylogenetic trees."

"Red bars represent convergent evolution, while black bars indicate characters with a single origin."

"Explain why the tree with 7 steps is preferred over the tree with 8 steps."

"The tree with 7 steps is preferred because it provides a simpler explanation, representing the shortest tree."

"Define the formula for estimating the number of possible trees based on taxa."

"The formula is N_R = (2n - 3)! / [2^(n - 2) * (n - 2)!], where n is the number of taxa."

"How does adding more species affect the number of possible phylogenetic trees?"

"Adding more species increases the number of possible trees exponentially; for example, adding a fourth species results in 15 possible trees."

"Explain the challenges faced when analyzing phylogenetic trees beyond 12 species."

"Beyond 12 species, heuristic search methods are employed, which only approximate the best result due to the complexity of possible arrangements."

"What are the advantages of using parsimony in phylogenetic analysis?"

"Advantages include making the fewest assumptions, retaining all character information, and effectively combining different data sources."

"Identify the objections to parsimony in phylogenetic studies."

"Objections include ignoring information present in the data, susceptibility to long branch attraction problems, and difficulty in comparing alternative hypotheses."

"Describe the implications of long branches in phylogenetic trees."

"Long branches represent taxa that diverged far back in the past, which can lead to high rates of convergence by chance."

"What is an important caveat regarding phylogenetic trees?"

"Phylogenetic trees are hypotheses of relationships, and their accuracy cannot be completely determined without the ability to travel back in time."

"Summarize the main methods used in molecular systematic methodology."

"The main methods include distance methods, statistical methods (like Maximum Likelihood), and parsimony methods (Cladistics)."

"How do distance methods work in phylogenetic analysis?"

"Distance methods calculate the genetic distance between each pair of taxa, identifying the pair with the shortest distance as the most closely related."

"What is the role of the sister group in distance methods?"

"The taxa that has the shortest distance from the most closely related pair is identified as the sister group to them."

"Explain the concept of convergence in the context of phylogenetic trees."

"Convergence refers to the phenomenon where different species independently evolve similar traits, complicating the interpretation of evolutionary relationships."

"Discuss the implications of Andrew Van Zandt Brower's quote on truth in phylogenetics."

"The quote suggests that understanding the true relationships in phylogenetics is complex and may be elusive, emphasizing the hypothetical nature of phylogenetic trees."

"What is the relationship between homology and convergence in phylogenetic analysis?"

"Homology refers to traits inherited from a common ancestor, while convergence involves traits that arise independently; convergence is generally less common than homology."

"How does the number of taxa (n) affect the factorial calculations in the tree formula?"

"The number of taxa (n) directly influences the factorial calculations, as it determines the complexity and number of possible arrangements in the phylogenetic tree."

"Describe the concept of genetic distance in molecular biology."

"Genetic distance is a measure of how different two taxa are in a genetic sense, often calculated by counting nucleotide substitutions."

"Explain the significance of distance methods in grouping taxa."

"Distance methods group taxa based on overall genetic similarity, but they must account for convergent evolution to avoid misleading results."

"Define the unique problems associated with molecular data."

"Molecular data can include sequences of nucleotides or amino acids, with limited character states for DNA (4 states) and amino acids (20 states), complicating analysis."

"How do mutations differ from substitutions in genetics?"

"A mutation is an error in DNA replication or repair, while a substitution is a mutation that has been fixed in a population through selection."

"Explain the process of DNA sequence alignment."

"DNA sequence alignment involves matching nucleotides to identify common ancestry, accounting for substitutions, insertions, and deletions by inserting gaps to maximize similarity."

"What is the role of alignment algorithms in sequence alignment?"

"Alignment algorithms maximize matches and minimize insertions or deletions by finding the alignment with the lowest score, often using sophisticated computer programs."

"Describe the Jukes Cantor model of molecular evolution."

"The Jukes Cantor model assumes that all substitutions occur at the same rate, providing a simple framework for estimating genetic distances."

"How does the Kimura 2 parameter model differ from the Jukes Cantor model?"

"The Kimura 2 parameter model accounts for unequal rates of transitions and transversions, providing a more nuanced approach to molecular evolution."

"What are synonymous substitutions and their significance?"

"Synonymous substitutions are mutations that do not change the amino acid sequence of a protein and likely reflect the actual substitution rate in the genome."

"Explain the importance of aligning sequences before analyzing molecular data."

"Aligning sequences is crucial for identifying homology and accurately assessing genetic differences, as it allows for the detection of substitutions, insertions, and deletions."

"What challenges arise from convergent evolution in molecular data analysis?"

"Convergent evolution can lead to similar genetic changes in unrelated lineages, complicating the interpretation of genetic distance and similarity."

"How are parameters for models of molecular evolution estimated?"

"Parameters can be estimated from substitution patterns in the data matrix using sophisticated computer programs, allowing for more accurate modeling of evolutionary processes."

"Describe the concept of gap cost in sequence alignment."

"Gap cost refers to the penalty incurred for inserting gaps in a sequence alignment, which must exceed the cost of mismatches to ensure optimal alignment."

"What is the significance of identifying transitions vs. transversions in molecular evolution models?"

"Identifying transitions vs. transversions allows for a more detailed understanding of substitution patterns and rates, which can improve the accuracy of evolutionary models."

"Explain the role of computer programs in molecular data analysis."

"Sophisticated computer programs are used to align multiple sequences and estimate parameters for models of molecular evolution, enhancing the analysis of genetic data."

"Describe the difference between transitions and transversions in molecular evolution."

"Transitions are changes between two purines (A <-> G) or two pyrimidines (C <-> T), while transversions are changes between a purine and a pyrimidine (A <-> C, A <-> T, G <-> C, G <-> T). In the example, transitions occur twice as often as transversions."

"Explain the General Time Reversible model of Molecular Evolution."

"The General Time Reversible model allows for the calculation of substitution rates for each possible change from one base to another, accommodating different rates for forward and reverse changes."

"How is the rate of substitution calculated in molecular evolution?"

"The rate of substitution is calculated for each possible change from one base to another, taking into account the specific rates of transitions and transversions."

"What are some parameters considered in molecular evolution analysis?"

"Parameters include base composition percentages, the percentage of invariable sites, and the gamma distribution."

"Discuss the objections to distance methods in molecular evolution."

"Distance methods have less information content as they reduce entire sequences to a single piece of information and depend on the correct model being chosen."

"Define Maximum Likelihood in the context of molecular evolution."

"Maximum Likelihood is a statistical method that evaluates which hypothesis of relationships under a specific model would best explain the observed data."

"How do you perform a Maximum Likelihood Analysis?"

"1. Collect and align gene sequences for a group of taxa. 2. Use a computer program to determine the appropriate model of molecular evolution. 3. Estimate model parameters. 4. Build a random tree and calculate its likelihood. 5. Repeat until the highest likelihood value is found."

"What are the advantages of using Maximum Likelihood in evolutionary studies?"

"Advantages include the ability to determine if one hypothesis is significantly better than another, a statistical value indicating the relationship among the tree, model, and data, and no loss of character information."

"Identify some objections to Maximum Likelihood methods."

"Objections include being computationally intensive, model dependence, and difficulty in combining different types of data such as morphology and molecular data."

"Explain the difference between mutations and substitutions."

"A mutation is an error in DNA replication or repair, while a substitution is a mutation that has been fixed in a population through the filter of selection."

"Describe the variation in evolutionary rates among different gene regions."

"Different gene regions evolve at different rates, with coding regions evolving at varying rates, and the 3rd position of codons typically having the highest rates."

"What does the term 'synonymous substitution' refer to?"

"A synonymous substitution is a mutation that does not change the amino acid sequence of a protein, often reflecting the actual mutation rate in the genome."

"How does the rate of transitions compare to transversions in molecular evolution?"

"Transitions generally occur more frequently than transversions, with the example indicating a rate of 2 for transitions and 1 for transversions."

"What is the significance of the gamma distribution in molecular evolution analysis?"

"The gamma distribution is used to model rate variation among sites, allowing for a more accurate representation of evolutionary processes."

"Discuss the implications of applying probabilities to historical events, as mentioned in the content."

"Applying probabilities to historical events is considered foolish because such events either occurred or did not occur, leading to only two possible probabilities: 100% or 0%."

"Describe the difference between synonymous and non-synonymous substitutions."

"Synonymous substitutions code for chemically similar amino acids and do not cause an amino acid change, while non-synonymous substitutions cause an amino acid change, which can be neutral or missense."

"Explain the concept of codon usage bias."

"Codon usage bias refers to the phenomenon where certain codons are used more frequently in specific organisms, such as 60% of Leu codons in bacteria being CUG and 80% in yeast being UUG."

"How does the abundance of tRNAs relate to codon usage bias?"

"The abundance of tRNAs may influence codon usage bias, as different tRNAs can have varying bonding energies, affecting the frequency of codon usage."

"Define the factors that cause variation in evolutionary rates among different genes."

"Variation in evolutionary rates among genes is influenced by different selective pressures, functional constraints, and the generation times of organisms, with shorter generation times generally leading to higher rates."

"What role do histones and apolipoproteins play in relation to substitutions?"

"Histones bind DNA, and substitutions can decrease their efficiency, while apolipoproteins bind lipids using hydrophobic domains, and as long as substitutions produce hydrophobic amino acids, they remain functional."

"Explain how selective pressure can favor variation in certain genes."

"Selective pressure can favor variation in genes like the Major Histocompatibility Complex (MHC), where greater variation leads to the production of more types of antibodies and a higher rate of nonsynonymous substitutions."

"Describe the rate of evolution in mitochondrial DNA compared to nuclear DNA."

"The rate of evolution is higher in mitochondrial DNA due to factors such as lack of proofreading during replication, less efficient DNA mismatch repair mechanisms, higher levels of mutagens, and reduced selective pressure."

"How is the evolutionary substitution rate estimated using the formula r = K/(2T)?"

"In the formula r = K/(2T), K represents the number of substitutions, and T is the time measured in generations, with 2T accounting for two lineages evolving over the same period."

"What does genetic distance (D) measure in evolutionary biology?"

"Genetic distance (D) measures how genetically different two species are and can be used to calculate the rate of evolutionary change, defined as D = 2μt, where μ is the rate and t is time in generations."

"Calculate the estimated number of generations since divergence given a divergence of 500,000 years and a rate of 3.5 generations per year."

"The estimated number of generations since divergence is calculated as 500,000 years x 3.5 generations/year = 1,750,000 generations."

"Explain how to derive the rate of evolution from genetic distance and time."

"The rate of evolution can be derived from genetic distance (D) and time (t) using the equation D/t = 2μ, allowing for the calculation of the substitution rate per site per generation."

"What is the significance of time in estimating evolutionary rates?"

"Time is a critical parameter in estimating evolutionary rates, as it can be calculated using various methods, including fossil records and biogeographic events, and is essential for back-calculating the timing of evolutionary events."

"How is the percentage of substitutions per site calculated over time since species divergence?"

"The percentage of substitutions per site is calculated by dividing the number of substitutions (0.2) by the total number of generations (1,750,000), resulting in a rate of 1.14 x 10^-6."

"Define the relationship between genetic distance (D), rate (μ), and time (t)."

"The relationship is defined by the equation D = 2μt, indicating that genetic distance is a function of the rate of substitutions and the time in generations."

"Describe the conditions necessary for using molecular clocks to estimate divergences among species."

"Substitutions must occur at a constant rate, rates should be similar in closely related species, evidence of the divergence date must be available, and the rate should be consistent in other species."

"Explain how molecular clocks can theoretically recover divergence events in the history of life on Earth."

"By using consistent substitution rates and divergence dates, molecular clocks can estimate the timing of divergence events across different species."

"Define the method for estimating rates of molecular evolution."

"Rates are estimated by calculating genetic distance divided by historical events, using fossil dates for minimum estimates and biogeography for maximum estimates."

"How does biogeography contribute to estimating the age of species?"

"Biogeography indicates that species endemic to a specific locale cannot be older than the age of that locality, providing a maximum estimate for their age."

"What is the significance of the Hawaiian Archipelago in the context of molecular clocks?"

"The Hawaiian Archipelago is home to various species that can be studied to understand their evolutionary history and divergence through molecular clocks."

"List some species from the planitibia species group."

"D.hanaulae, D.ingens, D.cyrtoloma, D.melanocephala, D.obscuripes, D.neoperkinsi, D.oahuensis, D.nigribasis, D.neopicta, D.substenoptera, D.hemipeza, D.silvestris, D.heteroneura, D.differens, D.planitibia, D.picticornis, D.setosifrons, D.primaeva, D.adunca."

"What are the estimated rates of molecular evolution for mt DNA and nuc DNA?"

"mt DNA has a rate of 0.004-0.044 substitutions per site per million years (mean=0.016), while nuc DNA has a rate of 0.003-0.015 substitutions per site per million years (mean=0.007)."

"How much faster is mt DNA compared to nuc DNA?"

"mt DNA is estimated to be 1.7-2.8 times faster than nuc DNA."

"What do molecular clock tests reveal about rate estimates?"

"Molecular clock tests show that minimum rate estimates can be too slow, maximum rates can be too fast, but mean rates are often just right."