Fish Genetics

Question 1

Locus / loci and alleles

Answer 1

diploids, each locus has two alleles
- homozygous (same alleles – AA)
- heterozygous (different alleles – Aa)
* In populations, there are many alleles, and in species even more

Question 2

Genotypes/haplotypes and heterozygosity

Answer 2

At any given locus, the combination of alleles represents the genotype (e.g., Cc, bb, Aa, Dd)
* Haplotypes, is the genotype at a single copy gene or locus (e.g., mitochondrial DNA, or Y-chromosome)

Question 3

Which is more diverse, heterozygotes or homozygotes?

Answer 3

At the individual level, Heterozygotes more genetically diverse than Homozygotes * At the population level, proportion of heterozygotes indicates:
- Population index of genetic diversity H’obs (Observed heterozygosity)
- Index allows populations to be genetically compared to others, and to expectations based on population allele frequencies (H’exp)

Question 4

Allozymes

Answer 4

• a type of molecular marker
  derived from mashing tissue and running mash on a gel
• Gel stained with reagents that fluoresce when bound to specific enzyme

Locus is the enzyme that binds the fluorescent dye, and alleles are the different sizes of the enzymes observed within individuals
* Polymorphisms – represent gene products and underlying difference in DNA sequences
* Product likely under some selection and cannot easily discern population structure from selection

Question 5

Populations don’t always form based on ___

Answer 5

selective pressures

Question 6

Polymerase Chain Reaction PCR

Answer 6

Uses cycles of heating and cooling with primers (DNA bits) and DNA replicating enzyme (Taq polymerase) to serially copy target

Targets only single locus
* Mostly done on single copy DNA (mitochondrial DNA) because no easy way to parse out different alleles (haplotypes)

Question 7

Sanger sequencing

Answer 7

Sanger Sequencing Steps

(1) The double-stranded DNA (dsDNA) is denatured into two single-stranded DNA (ssDNA). (2) A primer that corresponds to one end of the sequence is attached. (3) Four polymerase solutions with four types of dNTPs but only one type of ddNTP are added.

Question 8

RFLPs

Answer 8

a molecular marker

Restriction enzyme Fragment Length Polymorphisms
* Specific piece of DNA amplified and cut with restriction enzymes

Locus is the piece of DNA amplified and the restriction enzyme cut site
* Alleles are the fragment patterns that are produced
Cheap and can be diagnostic, but typically
produce either too few or too many loci
* Not used much anymore

Question 9

Microsatellites

Answer 9

a molecular marker

Genomic DNA segments composed of short nucleotide
repeats
* Originate from “slips” mistakes during DNA replication and occur mostly in non-coding regions
* Have Mendelian Inheritance and high mutation rates making them excellent to track population changes
* Locus is DNA regions with repeats and Alleles are the number of repeats that can vary even in single population (2-30+)

Question 10

How are errors in microsatellites resolved?

Answer 10

Resolved by running produced DNA fragments through gel
electrophoretic methods

Question 11

NGS-μsat 1.0

Answer 11

R-based platform for converting scoring NGS generated μsat data
Provides
- Automatic scoring & evaluation
- Interactive re-scoring/adjusting
- Produces data as .txt usable format

Question 12

SNPs

Answer 12

a molecular marker

Single nucleotide polymorphisms – Difference in base pair at specific location on a chromosome
* Happen throughout genome and in both coding and non- coding regions
* Locus is the SNP location and bp difference are the alleles – but thousands can be identified and digitised – simultaneously
* Each produced fragments of DNA is tracked to an individual and sequenced – no gel separation
* Easy to produce but bioinformatics intensive to identify and to filter from other noise in DNA sequencing processesàproduce very large datasets

Question 13

Applications of genetics to fish ecology

Answer 13

Used for genetic identification coupled with other data
* Assess parentage, track or identify individuals, determine phylogeographic phenomena
relationships, identify genes related to adaptation etc,…

Question 14

Resolution of mating systems

Answer 14

Used to assess reproductive biology of many fishes
e.g., monogamy, paternity, maternity, egg thievery and cuckoldry by

assessing genotype of eggs and fish caring for, or in vicinity of eggs * Microsatellites especially useful in parentage analyses

• helping to distinguish social mating systems from genetic mating systems

Question 15

Nesting fishes (oviparous) resolution

Answer 15

Evidence of multiple paternity, maternity and even egg
stealing in multiple species using microsatellites

Question 16

Live bearing fishes (viviparous) resolution

Answer 16

• Thought to have more restricted in parentage – especially with internal fertilization but genetic show high variability here too
• mosquito fishes ~ 100% of multiple paternity
• Lemon shark = 86% of litters sired by multiple fathers

Question 17

Importance (or not) of pelagic life stages

Answer 17

Pelagic Larval Dispersal (PLD) * More pronounced in marine fishes
* Paternity, maternity difficult to determine in broadcast spawners * But some reef fishes form stable monogamous pairings (e.g.,
butterflyfish – according to microsatellite studies)

Question 18

Can sibling larvae stay together during PLD?

Answer 18

PLD= pelagic life dispersal
* Not in Giant Red Sea Groupers or Orange Clownfishes according to microsatellites surveys
* Other studies show larval kin groups navigate and recruit back to same home regions for sturgeon and american eel

Question 19

Molecular Ecology

Answer 19

Using molecular (now mostly genetic/genomic) tools to clarify the ecology and evolution of species (meta-population dynamics)
* Basic ecological features of species can be assessed with genetic tools
- population structure (number, size and connectivity) - adaptive potential (standing genetic diversity)

Question 20

Populations Genetics:

Answer 20

population genetics= used to distinguish groups

Populations are a groups of interbreeding individuals rarely exchanging individuals with
other groups of the same species
* Mostly applied to stock (population) identification for managed species
* Population = management units, where species operate using meta-population dynamics within distribution

Question 21

Population number: F-Statistics

Answer 21

Designed to assess departures from random mating among groups
Also assess level of genetic variation within vs. among groups
* FST –> Allele frequency differences among different populations assessed through
population level heterozygosities (Wright 1951)
* Ranges from 0 – 1;
0 = no differentiation between population
1 = populations fixed for different alleles

Question 22

Population number: Variants on F-Statistics:

Answer 22

GST -> Modification to account for haploid data (Takahata & Palumbi 1985)
𝝓ST -> Incorporates allele frequency shifts and DNA sequence divergence between
haplotype (Excoffier et al. 1992)
RST -> More appropriate for microsatellites (but seldom used)
DJost -> More accurate and capable of reaching 1 most in situations where other indices cannot (maximum differentiation)

Question 23

Effective population size (Ne) vs. (NC)

Answer 23

NC – Census population size: total # of individuals regardless of age,
sex or condition (no survival)
Ne –Effective population size:#of individuals contributing to next generation– depends implicitly on age, sex or condition (implies fitness)

Question 24

Ne size meaning

Answer 24

Small
* Low Standing Genetic Diversity (SGD)
* Less stable
* More prone to collapse

Large
* High SGD
* Greater stability
* Higher prob. of adaptation

Question 25

Effective number of migrants (Nem):

Answer 25

Ne can be used to determine ~ effective number of migrants per
generation when multiplied by proportion of migrants (m)

Like Ne, actual migrants ≠ Nem –> not all migrants contribute effectively to gene exchange

Question 26

Nem value meaning

Answer 26

if Nem > 1 then thought to be enough to maintain high connectivity among populations

Question 27

Population genetics information

Answer 27

• Important indices helping to understand populations/species in nature
• Describes basic ecology of the species (meta-population dynamics)
• Used to better identify those in need of special conservation status/resources for sustainability/survival

Question 28

Genetic diversity and population structure trends in fishes

Answer 28

• Genetic diversity: Marine > Anadromous > Freshwater fishes
• Likely related to large Nes and high connectivity in marine species
• Less susceptible to genetic drift (loss/fixation of alleles), high rates of genetic exchange

Question 29

Habitat preferences

Answer 29

1. Migratory overlap: where populations mix (e.g., feeding grounds) or during migrations
   at sea or offshore – do they interbreed?
2. Sex-biased dispersal: gene flow disparity between genders
   - In some fish males disperse prior to reproduction, while females are philopatric
   (remain in natal areas)

Question 30

The main goals of geometric morphometrics :

Answer 30

study how specimens are similar or different in overall shape and to perform statistical analyses of these shape differences.