| Literature DB >> 31341743 |
Hideyuki Ito1,2, Miho Inoue-Murayama2,3.
Abstract
We examined genetic diversity of the wild Tsushima leopard cat-a regional population of the Amur leopard cat-using microsatellite markers. In addition, we compared genetic diversity of the Tsushima leopard cat with that of the Korean population of Amur leopard cat. Although bias should be considered when applying cross-species amplification, the Tsushima leopard cat showed a lower index of molecular genetic diversity than did the Korean population. These results were consistent with those obtained using other genetic markers, such as mitochondrial DNA and Y chromosome sequences. This low genetic diversity of the wild Tsushima leopard cat may be derived from the founding population. Furthermore, our results suggest that the captive populations held in Japanese zoos may show extremely low genetic diversity, leading to difficulties in genetic management of the Tsushima leopard cat. Moreover, the two regional populations were clearly separated using these marker sets. In the present study, we demonstrated that the genetic diversity of the Tsushima leopard cat is extremely low compared with that of the continental regional population. Importantly, the Japanese captive population for ex situ conservation was derived from a founding population with extremely low genetic diversity; hence, we assume that both the captive and wild populations showed extremely low genetic diversities. Our findings emphasize the need to develop carefully considered management strategies for genetic conservation.Entities:
Keywords: Genetic diversity; Molecular genetic analysis; Tsushima leopard cat
Year: 2019 PMID: 31341743 PMCID: PMC6637929 DOI: 10.7717/peerj.7297
Source DB: PubMed Journal: PeerJ ISSN: 2167-8359 Impact factor: 2.984
Figure 1Location of Tsushima Island.
This map shows the location and magnified view of Tsushima in East Asia.
Primers of 12 microsatellite loci.
| Locus | Labeled primer | Panel of multiplex PCR | Forward primer (5′-3′) | Reverse primer (5′-3′) | Repeat motif | GenBank |
|---|---|---|---|---|---|---|
| Tail C | 1 | tggagtttggcccgttcatt | acatgtctcagaaccgcaga | (AAAC)5 | KU290367 | |
| M13F | 1 | tggaaaagctcatttctttccact | gttgcactttgtaactttagttctaac | (AAGA)5 | KU290368 | |
| M13F | 2 | ctatgacccacactgccagg | ccctcaagatgcttaatatcagct | (ATAG)6 | KU290369 | |
| M13F | 2 | gcagggactcagtaaatgtttagc | ccggttggatctcatctgga | (TGAA)5 | KU290371 | |
| Tail C | 2 | ggaaaacttgaggactgccc | ggctctttgatgcccactttc | (AAAT)9 | KU290372 | |
| Tail C | 2 | agtgaaagttgctggactctga | acaagggaacattacaaccact | (AACA)5 | KU290375 | |
| M13F | 3 | gagctttgagcagcaatggg | tggccagccacaatattaca | (AAGG)12 | KU290376 | |
| Tail C | 3 | gcaaatctgcggatgttggg | caggccgagaccagttaagg | (GGAA)11 | KU290379 | |
| M13F | 3 | cagtcagcatcgatcatgacc | gcaaataaggtttggatattggtgc | (TAAA)10 | KU290381 | |
| Tail C | 3 | acccacacttgtgtctctgc | cctgcagttacaatcaaactcgt | (AATG)8 | KU290387 | |
| M13F | 1 | gcttgctaatgtcaggggtt | gcttcagatgcagatttgggt | (GATA)5 | KU290392 | |
| M13F | 1 | gcttttcaggtttcacgatatgc | tctctctgttctttctggggc | (GTTT)5 | KU290393 |
Notes.
Sequences of M13F and Tail C are 5′-GTTGTAAAACGACGGCCAGT-3′ and 5′-CAGGACCAGGCTACCGTG-3′, respectively. Reverse primers are labeled at the 5′ end with pigtail sequences (5′-GTTTCTT-3′).
Genbank accession number from Eo et al. (2016).
Genetic diversity indices of two regional populations of the Amur leopard cat with 12 microsatellite markers.
| Locus | Korea | Japan | ||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 30 | 2 | 1 | 1.301 | 0.267 | 0.231 | 2.000 | 0.618 | 0.789 | 28 | 1 | 0 | 1.000 | 0.000 | 0.000 | 1.000 | 1.000 | 1.000 | |
| 30 | 3 | 2 | 1.835 | 0.467 | 0.455 | 2.933 | 0.386 | 0.619 | 28 | 1 | 0 | 1.000 | 0.000 | 0.000 | 1.000 | 1.000 | 1.000 | |
| 30 | 5 | 3 | 2.532 | 0.667 | 0.605 | 4.993 | 0.214 | 0.501 | 28 | 2 | 0 | 2.000 | 0.714 | 0.500 | 2.000 | 0.375 | 0.594 | |
| 30 | 2 | 1 | 1.142 | 0.133 | 0.124 | 2.000 | 0.774 | 0.881 | 28 | 1 | 0 | 1.000 | 0.000 | 0.000 | 1.000 | 1.000 | 1.000 | |
| 29 | 3 | 2 | 2.393 | 0.690 | 0.582 | 3.000 | 0.240 | 0.519 | 28 | 1 | 0 | 1.000 | 0.000 | 0.000 | 1.000 | 1.000 | 1.000 | |
| 30 | 2 | 0 | 1.260 | 0.233 | 0.206 | 2.000 | 0.652 | 0.810 | 28 | 3 | 1 | 1.244 | 0.214 | 0.196 | 3.000 | 0.656 | 0.816 | |
| 30 | 7 | 6 | 4.327 | 0.867 | 0.769 | 6.996 | 0.085 | 0.387 | 28 | 1 | 0 | 1.000 | 0.000 | 0.000 | 1.000 | 1.000 | 1.000 | |
| 30 | 4 | 2 | 2.359 | 0.500 | 0.576 | 3.933 | 0.255 | 0.526 | 28 | 2 | 0 | 1.036 | 0.036 | 0.035 | 2.000 | 0.932 | 0.965 | |
| 30 | 5 | 4 | 2.442 | 0.533 | 0.591 | 4.933 | 0.205 | 0.506 | 28 | 1 | 0 | 1.000 | 0.000 | 0.000 | 1.000 | 1.000 | 1.000 | |
| 30 | 2 | 1 | 1.514 | 0.300 | 0.339 | 2.000 | 0.494 | 0.704 | 28 | 2 | 1 | 1.036 | 0.036 | 0.035 | 2.000 | 0.932 | 0.965 | |
| 30 | 4 | 3 | 1.410 | 0.300 | 0.291 | 3.930 | 0.524 | 0.736 | 28 | 1 | 0 | 1.000 | 0.000 | 0.000 | 1.000 | 1.000 | 1.000 | |
| 30 | 3 | 2 | 1.448 | 0.300 | 0.309 | 2.997 | 0.508 | 0.722 | 28 | 1 | 0 | 1.000 | 0.000 | 0.000 | 1.000 | 1.000 | 1.000 | |
| Average | 3.50 | 2.25 | 1.997 | 0.438 | 0.423 | 3.476 | 0.413 | 0.642 | 1.42 | 0.07 | 1.110 | 0.083 | 0.064 | 1.417 | 0.908 | 0.945 | ||
Notes.
number of individuals
number of alleles
number of private alleles
the number of effective alleles
observed heterozygosity
expected heterozygosity
allelic richness
probability of identity
Pid among siblings
In Korean population, three variables (Na, He and Ho) were cited data from the previous study (Eo et al., 2016), while the other variables were calculated as part of this study.
Figure 2Bayesian analysis of the genetic structure showing the differentiation of the two regional populations of the Amur leopard cat based on 12 microsatellite loci.
This figure was obtained using Structure Plot and CLUMPP to align the 10 replicates for optimal K = 2 (all runs were performed using the Markov chain Monte Carlo method running for 500,000 generations and an initial burn-in of 250,000 generations). K1-K30: Korean population. J1-J28: Tsushima leopard cat.
Figure 3First and second components of principal coordinate analysis of 12 microsatellite loci in the two regional populations of the Amur leopard cat.
Percentages of variation explained by the first two axes were 53.27% and 7.36%, respectively. Diamond symbols: Tsushima leopard cat. Circle symbols: Korean population.