Exam 2: Variations in Chromosome Structure and Number

What is the rationale behind the bootstrap procedure, where trees are repeatedly reconstructed following resampling with replacement of the original data?

In a molecular-evolutionary analysis, you estimate the number of base substitutions per site (K) at 0.82. Given an estimated divergence time (T) of 10 million years based on the fossil record, what is the substitution rate (r)?

One problem commonly experienced in phylogeny reconstruction arises when two or more of the groups being compared have accumulated far more genetic changes (mutations) than the others in the comparison. This situation often results in a phenomenon known as "long branch attraction," where the highly mutated lineages end up grouping together in a phylogenetic analysis even if in fact they are distantly related. What do you think causes long branch attraction? How might it be compensated for?

Codon bias suggests that

Homologous proteins

Genetic distance refers to the proportion of dissimilar nucleotides between two homologous sequences.

In the unweighted pair group method (UPGMA) of determining evolutionary relationships,

The average synonymous substitution rate in mammalian mitochondrial genes is ________ the average rate for nuclear genes.

Substitutions in the 3' flanking region of a gene

In molecular evolution analyses, the single most informative variable to estimate is

Pseudogenes tend to have lower average substitution rates than functional genes.

Given the following sequence alignment: G T C C A T C G G G T C G A T C-- G Which of the following is not true?

The noncoding 5' flanking region of genes is more constrained by selection than the noncoding 3' flanking region.

The "three domain" classification advocated by Carl Woese and his colleagues is based on molecular-evolutionary data. What are the domains and the arguments for formally recognizing them in classification?

High molecular similarity reflects evolutionary relatedness.

The McDonald-Kreitman test is an important tool in molecular evolutionary analysis. What is this test, and what kinds of insights can it provide?

Nuclear DNA sequence is more abundant than mtDNA and is therefore preferable for use in reconstructing events like domestication or human migration.

Which type of protein evolves at the slowest rate?

Natural selection favors variability in ________ genes.

Describe briefly the mechanisms that are thought to give rise to gene duplication and multigene families.