Platypus Genomics and Wildlife Conservation

Flashcards about platypus genomics and wildlife conservation.

What is the first learning outcome related to genomics?

Students will be able to describe the main characteristics of experimental approaches and bioinformatic pipelines in genomics.

What is the second learning outcome related to genomics?

Students will be able to discuss the applications of genomic and bioinformatic pipelines in wildlife conservation.

What genomic approaches were used in the platypus case studies?

Genome resequencing and reduced representation sequencing.

Give examples of traditional markers.

Microsatellites; exon-priming intron-crossing markers

Give examples of qPCR-based SNP chips.

Fluidigm dynamic arrays; Illumina Golden Gate; Applied Biosystems OpenArray128

Give examples of high-density SNP chips.

Affymetrix GeneChip; Illumina BeadChip129

Give examples of targeted DNA sequencing.

Exon capture110

Give examples of anonymous DNA sequencing.

RAD sequencing127

What is the cost per sample of traditional markers?

US$10–50

What number of markers does Whole-genome resequencing examine?

Complete genome

What equipment is needed for traditional markers?

PCR machine; traditional sequencer

What is the possible genomic solution for reducing the amount of admixture in hybrid populations?

Genome scanning of many markers will help to identify individuals with greater amounts of admixture so that they can be removed from the breeding pool

What is the possible genomic solution for identification of units for conservation: species, ESU and MU?

The incorporation of adaptive genes and gene expression will augment our understanding of conservation units based on neutral genes. The use of individual-based landscape genetics will help to identify boundaries between conservation units more precisely

Define qPCR and RAD.

qPCR, quantitative PCR; RAD, restriction-site-associated DNA.

In what circumstances we should use complete/entire genome sequencing approaches instead of low genome representation approaches in wildlife research?

Interested to sequence the entire genome to develop a reference sequence. Have a comprehensive understanding of the genetic variation across the genome To make genome wide associations Investigate structural genome rearrangements

What are the steps in the development of bioinformatic pipelines for raw data?

Raw genomic data, Quality filtering of raw sequence data, Read alignment and mapping, Mapping statistics

What type of genetic data was used in the Akiyama (1998) platypus study?

Microsatellites

What was found in the Gongora et al. (2012) platypus study?

Two major groups (mainland vs TAS) 3-4 major genetic lineages/ESUs across the species’ range

What was found in the Furlan et al. (2013) platypus study?

Rivers act as discreet population units/MU

Give one rationale for using genome sequencing to understand platypus population dynamics and demographics?

A small number of markers gives limited information about the underlying population history

What are the specific aims of the platypus genome sequencing project?

Diversity, structure and differentiation between subpopulations, relative historical effective population sizes, relatedness between the individuals sampled, dispersal

Outline the library preparation and short-read genome resequencing pipeline

Mapping and variant calling

How many genetic distinct groups did Principle Component Analyses find within the platypus?

5

Name the platypus populations identified in the Principle Component Analyses

Dirran/Rifle/Barron, Running, Tasmania, Shoalhaven

What was now possible in the genomics era that was not possible in previous historical platypus genetic studies?

Genomics provides resolution to assess relatedness

What is the estimated de novo mutation rate in the platypus?

7.0 × 10−9 (95% CI 4.1 × 10−9–1.2 × 10−8/bp/generation)

Outline the functionality of the Structure program

Infers genetic population ancestries, Assigns individuals to populations, Identify admixed individuals, Identify migrants

Outline the study conducted by Mijangos et al. (2019)

Fragmentation by large dams and implications for the future viability of small platypus populations

What question does the second case study attempt to answer?

Do dams affect dispersal between populations?

Give the hypotheses for regulated (dammed) rivers

If dams affect platypus dispersal, genetic differentiation will be greater across the dam than along a similar stretch of the undammed river

Genetic differentiation is highly correlated to?

Dam age

How many genomic regions explained by scenarios a), b) and c) respectively?

115, 46, and 185

Name the genes found as probable selection sites in genes with metabolic and development functions ?

KCNIP4, ADAM10 and OXR1