ecol 335 exam 2 fill in the blanks

• When a mutation hits a gene, the protein resulting from that gene's expression may be altered. When this happens, the mutation is said to be nonsynonymous. Most mutations are neutral (no effect on fitness) or slightly deleterious (small decrease in fitness). Some mutations can be lethal (fitness drops to zero). Sometimes mutations can be beneficial (increase fitness). The effect of point mutations on proteins is dictated by the genetic code. Mutations that hit the 3rd base of a codon are often synonymous (they don't change the amino acid, no effect on the protein).
• Post-zygotic reproductive isolation tends to make speciation irreversible. It may result from the joint operation of genetic drift and Dobzhanski-Muller genetic incompatability, whereby neutral mutations that went to fixation in distinct populations have negative epistatic effects when brought together in hybrids. Sexual selection is an important mechanism to explain the evolution of pre-zygotic reproductive isolation, an area of research championed by Professor Maria Servedio and her team. 
• Species diversification often happens in patterns of adaptive radiation. This refers to the diversification of one ancestral species into a clade of multiple species following exposure and adaptation to multiple ecological opportunities, which may arise from major environmental changes. Evidence can be found by relating diversification events with environmental history. Examples include Darwin's finches in the Galapagos, the cichlids in the African Great Lakes, and the silversword plant alliance Hawai'i.
• If we find a number of synonymous substitutions (per nonsynonymous sites) larger than the number of synonymous substitutions (per synonymous sites), this is a strong signature of positive selection. This comparison is called the Ka/Ks (or dN/dS) test.
• The Small Subunit rRNA 16S is conserved across all roganisms. Carl Woese discovered it and used it to uncover the three domains of life: Bacteria, Archaea Eukaryotes. The most recent reconstructions of the tree of life suggest that Archaea are not monophyletic, with eukaryotes branching out of Archaea. Most of biodiversity is in lineages without isolated representatives. Based on their genomes, these unknown organisms are intracellular symbionts with very small genomes.
• Settlement of the American continent may not have occurred until ~15,000 ya, following the Last Glacial Maximum. Inter-breeding occurred between H. sapiens, Neanderthals and Denisovans. Even though Neanderthals and Denisovans went extinct thousands of years ago, their alleles are still with us!
• In the third wave out-of-Africa 100,000 - 50,000 ya, Homo sapiens began to spread worldwide. Non-African populations trace their genetic ancestry back to H. sapiens dispersal from Africa 60 - 50,000 ya. About 40,000 ya, Homo sapiens was co-existing with at least 4 other species of Homo. Neanderthals went extinct ~30,000 ya. Denisovans may have persisted until 14,500 ya.
• Evolutionary biology can help us make sense of HIV virulence. Within each host, the virus is likely to mutate. As within-host selection of non-neutral mutations occurs, the viral population evolves. Within-host virus evolution results in a viral population that replicates faster, is more apt at evading the host immune defenses, and can attack a broader range of cells. As a consequence, the harm caused by the virus to the patient's body worsens in the course of an infection.
• Chimpanzees are our closest living relatives; their lineage and our diverged 5-6 Mya. Synapomorphies of the Hominins include: erect posture; bipedalism with modified feet, thigh bone, pelvis, and spine; reduced canines (and teeth in general); complex social behavior. 
• Ardipithecus (5.5 - 4 Mya), Australopithecus (4 - 1.9 Mya), and Paranthropus (2.6 - 1 Mya) represent a complex group of transitional forms between chimps and the genus Homo. Australopithecus is monophyletic provided Ardipithecus, Paranthropus and Homo are grouped with them! The lineages of Australopithecus/Homo sediba, Homo floriensis and Homo habilis are the oldest human lineages in the fossil record. 
• Evolutionary biology can help us understand the origin of HIV. After someone's infection, the HIV virus forms a population that evolves in the body. Mutations occur and substitutions drive the divergence of different virus lineages within the patient's body.
• From a blood sample, a phylogeny of the virus evolving within the patient's body can be reconstructed. By reconstructing a virus phylogeny from strains sampled across different patients, we can infer a likely chain of transmission. Applied to HIV and SIV, this strongly support an origin of HIV from SIV in chimpanzees. The jump between species probably occurred in the first half of the 20th century, before 1940.
• Evolutionary biology can help us design treatment against AIDS. AZT was the first drug discovered to block HIV replication. But HIV mutants with a slightly different reverse transcriptase can be resistant to AZT. Sooner or later in the course of an infection, because the viral population is so large and the mutation rate is so high, such mutants will arise.