Fish Genetics Flashcards
Locus / loci and alleles
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
Genotypes/haplotypes and heterozygosity
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)
Which is more diverse, heterozygotes or homozygotes?
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)
Allozymes
- 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
Populations don’t always form based on ___
selective pressures
Polymerase Chain Reaction PCR
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)
Sanger sequencing
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.
RFLPs
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
Microsatellites
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+)
How are errors in microsatellites resolved?
Resolved by running produced DNA fragments through gel
electrophoretic methods
NGS-μsat 1.0
R-based platform for converting scoring NGS generated μsat data
Provides
- Automatic scoring & evaluation
- Interactive re-scoring/adjusting
- Produces data as .txt usable format
SNPs
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
Applications of genetics to fish ecology
Used for genetic identification coupled with other data
* Assess parentage, track or identify individuals, determine phylogeographic phenomena
relationships, identify genes related to adaptation etc,…
Resolution of mating systems
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
Nesting fishes (oviparous) resolution
Evidence of multiple paternity, maternity and even egg
stealing in multiple species using microsatellites
Live bearing fishes (viviparous) resolution
- 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
Importance (or not) of pelagic life stages
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)
Can sibling larvae stay together during PLD?
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
Molecular Ecology
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)
Populations Genetics:
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
Population number: F-Statistics
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
Population number: Variants on F-Statistics:
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)
Effective population size (Ne) vs. (NC)
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)
Ne size meaning
Small
* Low Standing Genetic Diversity (SGD)
* Less stable
* More prone to collapse
Large
* High SGD
* Greater stability
* Higher prob. of adaptation
Effective number of migrants (Nem):
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
Nem value meaning
if Nem > 1 then thought to be enough to maintain high connectivity among populations
Population genetics information
- 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
Genetic diversity and population structure trends in fishes
- 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
Habitat preferences
- Migratory overlap: where populations mix (e.g., feeding grounds) or during migrations
at sea or offshore – do they interbreed? - Sex-biased dispersal: gene flow disparity between genders
- In some fish males disperse prior to reproduction, while females are philopatric
(remain in natal areas)
The main goals of geometric morphometrics :
study how specimens are similar or different in overall shape and to perform statistical analyses of these shape differences.
