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A Noninvasive Hair Sampling Technique to Obtain High Quality DNA from Elusive Small Mammals

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Demographic History and Inbreeding in Two Declining Sea Duck Species Inferred From Whole-Genome Sequence Data.

María I Cádiz¹, Aja Noersgaard Buur Tengstedt¹, Iben Hove Sørensen²

¹Department of Biology Aarhus University Aarhus Denmark.

Evolutionary Applications

|September 11, 2024

Summary

Genomic analysis reveals long-tailed ducks (Clangula hyemalis) show stable populations, while velvet scoters (Melanitta fusca) faced glacial impacts. Both species exhibit recent declines, but inbreeding remains low, highlighting Allee effects as a key conservation concern.

Keywords:

demographic history effective population size inbreeding population decline runs of homozygosity whole‐genome sequencing

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Area of Science:

Conservation genetics
Population genomics
Avian ecology

Background:

Long-tailed ducks (Clangula hyemalis) and velvet scoters (Melanitta fusca) are vulnerable sea ducks facing significant population declines.
Anthropogenic impacts are increasingly threatening even once-abundant species.

Purpose of the Study:

To sequence and analyze genomes of C. hyemalis and M. fusca to understand their demographic history and genetic diversity.
To assess inbreeding levels and identify conservation priorities for these declining sea duck populations.

Main Methods:

Genome sequencing and resequencing of 15 individuals per species.
Analysis of site frequency spectra and sequential Markovian coalescence to infer demographic history.
Runs of homozygosity (ROH) analysis to quantify inbreeding (F_ROH).

Main Results:

C. hyemalis exhibits historical demographic stability, while M. fusca was significantly impacted by the Last Glaciation.
Both species show evidence of long-term declines, with recent acceleration potentially linked to anthropogenic pressures.
Inbreeding levels (F_ROH) are low to moderate, suggesting background inbreeding rather than recent severe population bottlenecks.

Conclusions:

Despite significant population declines, strong inbreeding and genetic erosion have not yet occurred in these sea duck species.
The primary conservation concern may be density-dependent (Allee) effects, rather than genetic factors.
Monitoring inbreeding using ROH analysis is recommended as a cost-effective method for tracking future population health and informing conservation strategies.