Isolation and characterization of microsatellite loci in the Amami rabbit (Pentalagus furnessi)

Nagata, Junco; Sonoda, Youichi; Hamaguchi, Keiko; Ohnishi, Naoki; Kobayashi, Soh; Sugimura, Ken; Yamada, Fumio

doi:10.1007/s10592-008-9723-x

Cited by 2 publications

(2 citation statements)

References 7 publications

(6 reference statements)

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“…For microsatellite genotyping, we designed 8 microsatellite primers (Table S1, available online in Supporting Information) based on the sequences of the microsatellite loci isolated by Nagata et al () to amplify fragments shorter than the original length presented by Nagata et al (). This altered design is because short fragments are amplified easily from degraded fecal DNA.…”

Section: Methodsmentioning

confidence: 99%

Historical and recent impacts on genetic structure of an island rabbit

Ando

Tsuda²,

Kaneko

et al. 2018

J Wildl Manag

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Population fragmentation can reduce genetic diversity and increase the extinction risk of island endemic mammals, especially those with low dispersal ability. However, the intra‐island genetic structure and demographic history of mammals have not yet been well evaluated, especially on small geographic scales. We performed a genetic analysis of isolated island populations of the Amami rabbit (Pentalagus furnessi) on Tokunoshima Island using mitochondrial D‐loop region sequences and 8 nuclear microsatellite markers. Using data from fecal samples, we detected 2 genetic groups that corresponded with the northern and southern forested areas of the island based on the mitochondrial and nuclear genomes. We detected some admixture between the 2 groups in the nuclear genomes but did not detect gene flow between the 2 groups in the mitochondrial genomes. Although genetic diversity was higher in the southern population than in the northern population, the fixation index showed higher levels of inbreeding in the southern area with a signal of a recent bottleneck. We inferred the divergence time between the northern and southern groups (∼4,320 years ago) using approximate Bayesian computations. These genetic structure patterns may have been generated by a combination of the demographic history of the species in relation to the geology of the island, human activities in the stone age, deforestation due to sugar plantations (beginning approximately 300 years ago), and recent human activities. This study highlights the importance of considering genetic structure in relation to complex factors within a single‐island habitat for appropriate genetic management of endemic mammals on islands. © 2018 The Wildlife Society.

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Section: Methodsmentioning

confidence: 99%

Historical and recent impacts on genetic structure of an island rabbit

Ando

Tsuda²,

Kaneko

et al. 2018

J Wildl Manag

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“…The genotypes at eight microsatellite DNA loci (PF002, PF003, PF010, PF015, PF033, PF070, PF088, and PF098) were determined for all fecal samples using PCR following Nagata et al (2009). To avoid mistyping, we amplified each sample a few times.…”

Section: Dna Investigationsmentioning

confidence: 99%

The influence of invasive mongoose on the genetic structure of the endangered Amami rabbit populations

Ohnishi

Kobayashi

Nagata

et al. 2017

Ecological Research

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Invasive carnivores often cause heavy damage to native species on small islands. Endangered Amami rabbit (Pentalagus furnessi) populations have been fragmented into a north‐isolated population (NI) and a south‐large population (SL) caused by predation pressure from the invasive small Indian mongoose (Herpestes auropunctatus) on Amami Oshima Island in southern Japan. We investigated the genetic structure of these rabbit populations to determine the effects of fragmentation. We collected rabbit feces from most of the Amami Oshima Island habitat and sequenced the mitochondrial DNA (mtDNA) control region along with its 5′‐flanking region (312 bp) and genotyped eight microsatellite DNA loci. Genetic diversity was lower in the NI than that in the SL population, and FST values between the two populations were significantly higher than zero in both the mtDNA and microsatellite DNA. Bayesian clustering analyses suggested four ancestral clusters of Amami rabbit, but clear genetic structure was not observed. A partial Mantel test supported isolation‐by‐distance but not habitat fragmentation. These results suggest that the low genetic diversity in the NI population was caused by the small population size after fragmentation; however, the difference in genetic structure between the two populations was caused by isolation‐by‐distance and the structure has been maintained.

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Isolation and characterization of microsatellite loci in the Amami rabbit (Pentalagus furnessi)

Cited by 2 publications

References 7 publications

Historical and recent impacts on genetic structure of an island rabbit

Historical and recent impacts on genetic structure of an island rabbit

The influence of invasive mongoose on the genetic structure of the endangered Amami rabbit populations

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