Genome Organization and Inheritance

• Different genome parts possess alternative transmission modes.
• Mitochondrial DNA (mtDNA) and Y chromosomes are uniparentally inherited, while autosomes and X chromosomes are biparentally inherited.
• mtDNA, autosomes, and X chromosomes exist in all population members, whereas Y chromosomes are present in half of the population.
• Low recombination areas are inherited as a unit; high recombination areas break up and are inherited independently.

Application of Genome Data

• Biparentally inherited regions infer contributions from both parents.
• Uniparentally inherited genomes track specific contributions from one parent.
• mtDNA tracks maternal lineages.
• Y chromosomes track paternal lineages.
• Genetic markers help understand the evolutionary process.
• Behavior and ecology data helps to understand patterns in genetic data.

Elephant Social System

• Females often live with 2-20 maternal kin in their natal group with juveniles.
• Males leave their natal groups in adolescence and do not join other social groups.
• Males are drawn to females in estrous and are seen with their natal group.
• Male reproductive lifespan is long, and many males are still reproductive when their daughters mature.

Elephant Inbreeding Avoidance

• Hypothesis 1: Male elephants evolved inbreeding avoidance due to severe inbreeding depression.
• Hypothesis 2: Selection has not led to inbreeding avoidance due to weak inbreeding depression and/or highly variable male reproductive success.
• Experiments with elephants are infeasible due to long gestation (22 months) and lifespan (62 years).
• Measuring inbreeding depression or fitness directly is not feasible.
• Genetic markers can be used to apply an inferential approach.
• The key question is whether male elephants behave in a way suggesting inbreeding avoidance.
• Elephant behavior must be observed to quantify mating behaviors to assess if behaviors are directed away from kin.
• Maternity is a certainty, while paternity requires genetic analysis.

Possible Outcomes of Elephant Mating Behaviour

• Males observed towards NON-kin and kin can be compared in terms of courtship and offspring fathered.
• No difference in behavior could indicate random mating.
• More courtship and offspring between kin may indicate inbreeding preference.
• More courtship and offspring between non-kin may indicate inbreeding avoidance.

Elephant Mating Behaviour Results

• Male elephants avoid their kin, even paternal kin.
• Male reproductive success is highly skewed, creating strong costs of inbreeding avoidance.
• Despite these costs, males avoid inbreeding.
• Males compete strongly for mating, sometimes leading to death.
• Although males outweigh females (by 2x), females may exhibit some choice and avoid mating with close relatives, but this is harder to assess.

Species Mobility

• Species differ in mobility, lifespan, offspring number, and sensitivity to human disturbance.
• These differences affect patterns of genetic variation.

Gene Flow and Differentiation

• Gene flow erodes differences between populations.
• Restricting gene flow leads to the accumulation of genetic differences.

Coyotes

• Coyotes (Canis latrans) are a species of Canid (wolves, dogs, foxes) native to North America.
• They are smaller than wolves, generalist mesopredators, and tolerant of human disturbance.

Coyote Study

• Study collected ~1,000 scats in greater Seattle area.
• Seattle is divided by roads and major waterways.
• DNA was extracted from scats for microsatellite analysis.
• Microsatellites are repetitive DNA motifs that can be used as genetic markers.
• Null hypothesis: Natural and human barriers have no effect on Coyote patterns of genetic variation.
• Alternative hypothesis #1: Natural and human barriers lead to genetic differences between Coyote populations due to reduced gene flow.
• Alternative hypothesis #2: Natural and human barriers lead to slight genetic differences between Coyote populations due to reduced gene flow.

Genetic Differentiation in Coyotes

• Colors indicate groups of genetically similar coyotes.
• Circles represent individual coyotes.
• A cluster of blue circles indicates a group of genetically similar coyotes.
• Fst is a measurement metric for genetic differentiation.
• Fst ranges from 0 (pan-mixia) to 1 (complete genetic differentiation).
• Fst in Coyotes was moderate (~0.08).

Human Dispersal

• Features affecting human dispersal affect our genetic variation.
• These features might be cultural or physical (oceans, mountain ranges, etc.).
• These features might have differential effects on different components of our genomes– mtDNA, Y chromosome, X chromosome, autosome

Cultural trends

• Patrilocality: Females move to the location of their male reproductive partner.
• Matrilocality: Males move to the location of their female reproductive partner.

Patrilocality vs Matrilocality

• Patrilocality (females move, males stay) leads to lower Y chromosome variation within populations and higher Y chromosome differentiation between populations.
• Patrilocality leads to higher mtDNA variation within populations and lower mtDNA differentiation between populations.
• Matrilocality (males move, females stay) leads to higher Y chromosome variation within populations and lower Y chromosome differentiation between populations.
• Matrilocality leads to lower mtDNA variation within populations and higher mtDNA differentiation between populations.

Human Genetic Differentiation

• In an early view study, higher Fst at long distances for Y-chromosome means less male gene flow.
• Lower Fst at long distances for mtDNA, means more female gene flow.
• A later study found gene flow among populations is similar for males and females.
• Similar rates of divergence for Y chromosome and mtDNA (slightly faster rate in mtDNA).
• Most regional level studies suggest female-biased dispersal and patrilocality.
• A wide variety of outcomes suggests lots of cultural variation affecting the results.

Hill People of Northern Thailand

• The Hill People provide a best-case scenario to test the prediction.
• They are in the same geographic region, speak related Sino-Tibetan languages, and practice similar modes of agriculture.
• Approach: Compare genetic diversity on mtDNA and Y chromosome for matrilocal and patrilocal ethnic groups in the same region.
• In markers carried by the sex that stays in their natal home, there is reduced genetic diversity.
• In markers carried by the sex that moves to their partner’s natal home, there is greater genetic diversity.
• Trends are concordant for matrilocal and patrilocal dispersal.

General Conclusions

• Genetic markers can be used to understand fitness components (mating and paternity) and illuminate the evolutionary process in long-lived organisms.
• Knowledge of habitat barriers and genomic transmission will affect differentiation.
• Human social behavior affects patterns of genetic differentiation and diversity among and within populations.

Recap

• Genome transmission modes / who gets what
• Using markers to infer mating / fitness; movement; human migration
• Variation within populations; differentiation between populations
• Gene flow affects differentiation and variation

Different genome parts possess alternative transmission modes. mtDNA tracks maternal lineages, while Y chromosomes track paternal lineages. Genetic markers and behavior/ecology data help understand the evolutionary process.