Questions & explanations
1. Why might a gene tree disagree with a species tree, and how do scientists handle this?
A gene tree might disagree with a species tree due to incomplete lineage sorting, hybridization, or gene duplication. Incomplete lineage sorting happens when ancestral genetic variation is not fully sorted before species split, so some gene copies are more similar between different species than within the same species. Scientists handle this by using multiple genes from across the genome and building a consensus tree. They also use statistical methods that account for the probability of different gene trees given a species tree. For example, they might sequence many genes and use coalescent-based methods to estimate the species tree that best fits all the gene trees. This gives a more accurate picture of species relationships.
2. Compare the role of northern versus southern refugia during the Pleistocene.
Northern refugia were located in areas that were not covered by ice but were still cold, like parts of Alaska and Siberia. They were often small and had harsh conditions, so only hardy species survived there. Southern refugia, like those in southern Europe, Asia, and North America, were larger and had milder climates. They supported more species and acted as the main sources for recolonization after the ice melted. For example, in Europe, most species recolonized from southern refugia, while northern refugia contributed less. In North America, some species survived in Beringia (Alaska and Siberia) and others in the southern United States. The southern refugia generally had greater impact on modern biodiversity.
3. Compare the recolonization routes of a fast-dispersing animal versus a slow-dispersing plant.
Fast-dispersing animals, like birds or large mammals, can recolonize quickly after the ice retreats. They can fly or walk long distances, so they may reach new areas in a few generations. Their recolonization routes are often straight and fast. Slow-dispersing plants, like trees with heavy seeds, spread slowly. Their seeds might only travel a few meters per year, so recolonization takes thousands of years. Their routes follow favorable habitats like river valleys. For example, after the last ice age, red deer (a fast animal) recolonized Europe quickly, while beech trees (a slow plant) took much longer and followed specific paths. The animal's route is less constrained by geography than the plant's.
4. Compare Bagnold's treatment of bedload and suspended load.
In Bagnold's model, bedload transport occurs when grains are moved along the bed by rolling or saltation, and the energy is dissipated by grain collisions. The efficiency for bedload is higher (about 10-20%) because the grains are in contact with the bed. Suspended load occurs when grains are lifted by turbulence and carried in the flow; the efficiency is lower (about 1-2%) because energy is used to keep grains aloft against gravity. Bagnold assumed that suspended load transport requires the flow to do work to lift the sediment, while bedload mainly uses the flow's momentum. Both are driven by stream power, but the formulas differ in the efficiency factor and the threshold condition.
5. What is the first step in the nitrogen cycle when organic matter like dead leaves breaks down in soil?
The first step is mineralization, where microbes turn organic nitrogen from dead plants into ammonium (NH4+). This ammonium can then be used by plants or changed by other microbes. Immobilization is the opposite: microbes take up ammonium or nitrate for their own growth, making nitrogen unavailable to plants. Nitrification is a two-step process where Nitrosomonas bacteria convert ammonium to nitrite, then Nitrobacter convert nitrite to nitrate (NO3-). Denitrification happens in waterlogged soil where bacteria turn nitrate into nitrogen gas (N2) that escapes to the air. Volatilization is when ammonium turns into ammonia gas and is lost from soil, especially if the soil is alkaline.
6. What is Bagnold's energetics-based sediment transport model about?
Bagnold's model describes sediment transport as a process where flowing water does work to move sediment. It separates transport into bedload (grains rolling or bouncing along the bed) and suspended load (grains carried in the water column). The model assumes that the power of the flow (energy per time) is used to lift and transport sediment. The transport rate is proportional to the stream power (τ u, where τ is shear stress and u is flow velocity) minus a threshold for initiation of motion. Bagnold derived formulas for bedload and suspended load based on efficiency factors. This model is widely used because it is physically based and works for both rivers and coastal flows.
7. What is a molecular clock?
A molecular clock is a method that uses the rate of genetic mutations to estimate when two species or populations diverged from a common ancestor. The idea is that DNA changes accumulate at a roughly constant rate over time, like a clock ticking. By counting the number of differences between two DNA sequences, scientists can estimate how long ago they shared a common ancestor. For example, if two species have many genetic differences, they likely diverged long ago. The molecular clock must be calibrated using known dates from fossils or geological events. It is a powerful tool for studying evolutionary history and timing events like the split between humans and chimpanzees.
8. What is the difference between a gene tree and a species tree?
A gene tree shows the evolutionary history of a particular gene or DNA region. It traces how different versions of that gene are related. A species tree shows the evolutionary history of the species themselves. Gene trees and species trees can be different because genes can be inherited differently. For example, a gene tree might show that a human gene is more similar to a chimpanzee gene than to another human gene, but the species tree shows humans and chimpanzees as separate branches. This can happen due to incomplete lineage sorting, where ancestral genetic variation is passed on to different descendant species. So, gene trees are not always the same as species trees.
9. What is the difference between a leading edge and a rear edge in recolonization?
The leading edge is the front of a population as it expands into new territory. At the leading edge, individuals are often fast-moving colonizers that can quickly establish in open areas. The rear edge is the back of the population, near the original refugium. At the rear edge, populations are often stable and may have high genetic diversity because they have been there for a long time. For example, when a tree species spreads north after an ice age, the northernmost trees are the leading edge, while the southernmost trees near the refugium are the rear edge. Leading edge populations may be less genetically diverse because they come from a few pioneers.
10. What is phylogeography?
Phylogeography is the study of the geographic distribution of genetic lineages within and among species. It combines genetics, geography, and history to understand how past events like ice ages, mountain building, and sea level changes shaped where species live today. Scientists look at DNA sequences from populations across a species' range and build family trees (gene trees) to see how they are related. By mapping these trees onto geography, they can infer where populations came from and how they moved. For example, phylogeography can show that a bird species in South America spread from the Andes to the Amazon. It helps explain biodiversity patterns.
11. How do scientists calibrate a molecular clock?
Scientists calibrate a molecular clock by using known dates from the fossil record or geological events. They find a fossil that is confidently assigned to a particular branch of the evolutionary tree and has a known age. Then they compare the DNA of that lineage with its relatives to see how much genetic change has occurred since the fossil date. For example, if a fossil of a primate is 50 million years old, scientists can measure the genetic difference between that primate lineage and others to estimate the mutation rate. This rate is then used to date other divergences. Multiple calibration points from different fossils make the clock more reliable.
12. What is a Pleistocene refugium?
A Pleistocene refugium is a place where plants and animals survived during the ice ages of the Pleistocene epoch, which lasted from about 2.6 million to 11,700 years ago. During glacial periods, ice sheets covered large parts of the northern continents, making them too cold for many species. Refugia were areas that stayed ice-free and had a milder climate, like southern Europe, parts of Asia, and North America. Species that could not live in the cold retreated to these refugia. When the ice melted, they spread out again from these safe places. Refugia are important for understanding how species survived and where their genetic diversity came from.