Population structure, inbreeding and stripe pattern abnormalities in plains zebras.

Area of Science:

• Conservation genetics
• Wildlife biology
• Population genetics

Background:

• Plains zebra (Equus quagga) populations have declined significantly, with phenotypic diversity in stripe patterns historically used for subspecies classification.
• Abnormal stripe patterns have been observed, but their connection to population demography and genetics remains unclear.
• Understanding genetic health and structure is crucial for effective plains zebra conservation strategies.

Purpose of the Study:

• To investigate the relationships between population structure, genetic diversity, inbreeding, and abnormal phenotypes in plains zebras.
• To assess the impact of habitat fragmentation on plains zebra genetic health.
• To determine the genetic basis of abnormal stripe patterns.

Main Methods:

• DNA was collected from 140 plains zebras across nine locations.
• Restriction site-associated and whole genome sequencing (RAD-seq, WGS) were employed.
• Genetic structure, diversity, and inbreeding levels were analyzed, including individuals with abnormal stripe patterns.

Main Results:

• Genetic structure did not align with traditional subspecific classifications.
• Habitat fragmentation was associated with reduced gene flow and increased inbreeding, particularly in East Africa.
• Zebras with abnormal striping showed higher inbreeding levels compared to normally striped individuals from the same populations.

Conclusions:

• Abnormal stripe patterns in plains zebras likely have a genetic cause, linked to increased inbreeding.
• Habitat fragmentation poses a significant threat, leading to reduced gene flow and negative genetic consequences.
• Conservation strategies must address habitat fragmentation to preserve plains zebra genetic diversity and health.