Week 4: Thu: Conservation Genomics in Practice – Decoding the past to safeguard the future : Bosse

Conservation genomics

Use of genome-wide data to understand and manage biodiversity and conservation

Sixth mass extinction

Current rapid global loss of species largely driven by human activity

Hidden biodiversity loss

Loss of genetic diversity that is not immediately visible at species level

Conservation genetics vs genomics

Genetics focuses on specific markers while genomics uses whole-genome data

Genomics potential in conservation

Can provide detailed insights into population history

Genetic diversity importance

Fundamental for evolution

Pairwise differences

Number of nucleotide differences between two DNA sequences

Heterozygosity

Proportion of loci with different alleles in an individual

Genome-wide heterozygosity

Measure of overall genetic diversity across the genome

Heterozygosity as proxy

Indicator of past population size and adaptive potential

High heterozygosity

Suggests large historical population and higher adaptive capacity

Low heterozygosity

Suggests small population size and reduced adaptive potential

Debate on heterozygosity importance

Overall heterozygosity alone may not fully reflect conservation risk

Run of homozygosity (ROH)

Continuous stretches of homozygous DNA in the genome

ROH meaning

Indicates inbreeding and shared ancestry

Short ROH

Reflect older inbreeding events

Long ROH

Reflect recent inbreeding events

ROH length interpretation

Length corresponds to timing of inbreeding event

ROH as proxy

Indicator of recent inbreeding and small population size

Inbreeding

Mating between related individuals

Inbred offspring

Individuals with increased homozygosity

Inbreeding effect

Leads to more homozygous regions in genome

Inbreeding depression

Reduced fitness due to expression of harmful recessive mutations

Cause of inbreeding depression

Harmful mutations become homozygous and expressed

Neutral mutation

Mutation with no effect on fitness

Harmful mutation

Mutation that reduces fitness

Exposure of harmful mutations

Inbreeding increases chance that harmful alleles are expressed

Fitness consequence

Increased disease

Sensitivity to inbreeding

Varies between species

Purging

Process where harmful mutations are removed by selection in small populations

Role of past demography

Determines whether purging has occurred

Genomic signal of harmful mutations

Identification of deleterious variants in genome

Bioinformatics prediction

Use of computational tools to predict harmful mutations

Functional mutation

Mutation affecting gene/protein function

Truncating mutation

Mutation causing incomplete (shortened) protein

Harmful mutations as proxy

Indicator of inbreeding depression

Genomic footprints of decline

Patterns in genome reflecting population size changes over time

Population bottleneck

Sharp reduction in population size

Genomic signature of bottleneck

Reduced diversity and specific heterozygosity patterns

Past bottleneck vs recent inbreeding

Same heterozygosity but different genomic patterns

Conservation implication

Recent inbreeding is often more harmful than ancient bottlenecks

Adapted alleles

Alleles shaped by natural selection

Positive selection

Increase in frequency of beneficial alleles

Local adaptation

Genetic adaptation to local environment (e.g. climate

Genomic signal of selection

Regions with unusual patterns indicating selection

Hybridization

Mixing of genomes from different populations or species

Introgression

Gene flow between populations/species through hybridization

Using genomic information

Combine diversity

Zoo genomics

Use of genomic data in captive (ex-situ) populations

Ex-situ populations

Populations in captivity (zoos

In-situ populations

Wild populations

Applications in zoos

Study founder relatedness

Studbook

Record of pedigree and breeding history in captive populations

Representative for the wild

Whether captive population reflects wild genetic diversity

Applications in wild

Study evolutionary history

Asian elephant decline

50% population decline over last 3 generations

Habitat fragmentation

Populations split into smaller isolated groups

Captive population issue

Many individuals in captivity with unclear origins

Founder effect

Limited number of founders reduces genetic diversity

Population structure

Genetic subdivision into groups or clusters

PCA analysis

Statistical method to visualize genetic structure

SNP (single nucleotide polymorphism)

Single base pair variation in genome

Genome dataset

Large-scale data (millions of SNPs) used for analysis

Genetic health

Assessment of diversity

Window-pi

Measure of genetic diversity in genomic windows

Bornean elephants

Population with low diversity and high concern

Genetic load

Accumulation of harmful mutations in a population

Reconnect populations

Strategy to increase gene flow and diversity

Isolation vs hybridization

Conservation dilemma between preserving uniqueness vs increasing diversity

Genome structure compatibility

Whether genomes can mix without major issues

Structural differences

Large-scale genomic differences (e.g. inversions

Local adaptation concern

Mixing populations may disrupt locally adapted genes

Origin debate (Borneo elephants)

Question whether population is native or introduced

Molecular clock

Method to estimate timing of evolutionary events

Inbreeding timing analysis

Estimating when inbreeding occurred using ROH length

Strong bottleneck signal

Indicates severe past population reduction

Genomics-assisted connectivity

Using genomic data to guide corridor creation and reconnection

Elephant corridors

Landscape connections to allow gene flow

Non-invasive sampling

Using dung DNA for genomic analysis