Soo Hyung Eo

Complete mitochondrial genome of white-backed woodpecker Dendrocopos leucotos (Piciformes: Picidae) and its phylogenetic position

Abstract The white-backed woodpecker (Dendrocopos leucotos) is an ecologically important bird in Eurasian forest ecosystems. In this study, the complete mitochondrial genome of the species was sequenced using next-generation sequencing technology. The genome was 16,838 bp in length, consisting of 13 protein coding genes, two rRNAs, 22 tRNAs, a non-coding control region and a repeat region. Phylogenetic analysis using available complete mitochondrial genomes of the Coraciimorphae supported the monophyly of the Piciformes. The complete mitochondrial genome of D. leucotos will be a useful genetic resource for population genetics, phylogenetic analysis and conservation of the species.

The complete mitochondrial genome sequence of Japanese murrelet (Aves: Alcidae) and its phylogenetic position in Charadriiformes

Abstract The Japanese murrelet (Synthliboramphus wumizusume) is a threatened bird endemic to Japan, Korea, and Russia. We generated the complete mitochondrial genome sequence to provide molecular genetic information for phylogeny and conservation of the species. The S. wumizusume mitochondrial genome is 16 714 bp in length and comprises 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, a non-coding control region, and a repeat region. Gene composition and order in the genome is consistent with that of other mitochondrial genomes of the order Charadriiformes currently available in the GenBank. Phylogenetic analysis using all available Charadriiform mitochondrial genomes revealed that interfamilial relationships of the birds based on mitochondrial genes were in agreement with those based on multilocus nuclear genes. The complete mitochondrial genome of S. wumizusume we sequenced might be a useful genetic resource for phylogenetic relationships, evolutionary biology, and conservation of the species.

Altitudinal range-size distribution of breeding birds and environmental factors for the determination of species richness: An empirical test of altitudinal Rapoport’s rule and rescue effect on a local scale

Range-size distributions are important for understanding species richness patterns and led to the development of the controversial Rapoport’s rule and Rapoport-rescue effect. This study aimed to understand the relationship between species richness and range-size distribution in relation to environmental factors. The present study tested the following: (1) altitudinal Rapoport’s rule, (2) climatic and ambient energy hypotheses, (3) non-directional rescue effect, and (4) effect of environmental factors on range-size group. Altitudinal species range-size distribution increased with increasing altitude and showed a negative relationship with climatic variables and habitat heterogeneity, and a positive relationship with primary productivity. These results support the altitudinal Rapoport’s rule and climatic hypothesis; however, they do not fully support the ambient energy hypothesis. Results from testing the non-directional rescue effect showed that the inflow intensity of species from both directions (high and low elevations) affected species richness. And we found that the 2nd and 3rd quartile species distribution were the main cause of a mid-peak of species richness and the non-directional rescue effect. Additionally, the 2nd quartile species richness was highly related to minimum temperature and possessed thermal specialist species features, and the 3rd quartile species richness was highly related to habitat heterogeneity and primary productivity. Although altitudinal range-size distribution results were similar to the altitudinal Rapoport’s rule, the mid-peak pattern of species richness could not be explained by the Rapoport’s-rescue effect; however, the non-directional rescue effect could explain a mid-peak pattern of species richness.

Altitudinal patterns in breeding bird species richness and density in relation to climate, habitat heterogeneity, and migration influence in a temperate montane forest (South Korea)

Altitudinal patterns in the population ecology of mountain bird species are useful for predicting species occurrence and behavior. Numerous hypotheses about the complex interactions among environmental factors have been proposed; however, these still remain controversial. This study aimed to identify the altitudinal patterns in breeding bird species richness or density and to test the hypotheses that climate, habitat heterogeneity (horizontal and vertical), and heterospecific attraction in a temperate forest, South Korea. We conducted a field survey of 142 plots at altitudes between 200 and 1,400 m a.s.l in the breeding season. A total of 2,771 individuals from 53 breeding bird species were recorded. Altitudinal patterns of species richness and density showed a hump-shaped pattern, indicating that the highest richness and density could be observed at moderate altitudes. Models constructed with 13 combinations of six variables demonstrated that species richness was positively correlated with vertical and horizontal habitat heterogeneity. Density was positively correlated with vertical, but not horizontal habitat heterogeneity, and negatively correlated with migratory bird ratio. No significant relationships were found between spring temperature and species richness or density. Therefore, the observed patterns in species richness support the hypothesis that habitat heterogeneity, rather than climate, is the main driver of species richness. Also, neither habitat heterogeneity nor climate hypotheses fully explains the observed patterns in density. However, vertical habitat heterogeneity does likely help explain observed patterns in density. The heterospecific attraction hypothesis did not apply to the distribution of birds along the altitudinal gradient. Appropriate management of vertical habitat heterogeneity, such as vegetation cover, should be maintained for the conservation of bird diversity in this area.

Metagenomic approach revealed effects of forest thinning on bacterial communities in the forest soil of Mt. Janggunbong, South Korea

The soil microbiome that plays important ecological roles in mountains and forests is influenced by anthropogenic and natural causes. Human activity, particularly harvesting or thinning, affects the soil microbiome in forests by altering environmental conditions, such as vegetation, microclimate, and soil physicochemical properties. The purpose of this study was to investigate the effects on forest thinning on the diversity and composition of the soil bacterial community. From next-generation sequencing results of the 16S rRNA gene, we examined differences in soil bacterial diversity and community composition before and after thinning at Mt. Janggunbong, South Korea. We identified 40 phyla, 103 classes, 192 orders, 412 families, 947 genera, and 3,145 species from the soil samples. Acidobacteria and Proteobacteria were the most dominant bacterial phyla in the forest soil of Mt. Janggunbong. Soil bacterial diversity measures (richness, Shannon diversity index, and evenness) at the phylum level increased after thinning, whereas species-level taxonomic richness decreased after thinning. Thinning provided new opportunities for bacterial species in Chloroflexi, Verrucomicrobia, Nitrospirae, and other nondominant bacterial taxa, especially for those not found in Mt. Janggunbong before thinning, to settle and adapt to the changing environment. Our results suggested that thinning affected the diversity and composition of soil bacterial communities in forests and mountains.

Microsatellite DNA analysis reveals lower than expected genetic diversity in the threatened leopard cat (Prionailurus bengalensis) in South Korea

To optimize conservation efforts, it is necessary to determine the risk of extinction by collecting reliable population information for a given species. We developed eight novel, polymorphic microsatellite markers and used these markers in conjunction with twelve existing markers to measure genetic diversity of South Korean populations of leopard cat (Prionailurus bengalensis), a species for which population size and habitat area data are unknown in the country, to assess its conservation status. The average number of alleles and the observed heterozygosity of the species were 3.8 and 0.41, respectively, and microsatellite diversity was lower than the average genetic diversity of 57 populations of 12 other felid species, and lower than that of other mammal populations occurring in South Korea, including the raccoon dog (Nyctereutes procyonoides), water deer (Hydropotes inermis), and endangered long-tailed goral (Naemorhedus caudatus). Furthermore, analysis of genetic structure in the national leopard cat population showed no clear genetic differentiation, suggesting that it is not necessary to divide the South Korean leopard cat population into multiple management units for the purposes of conservation. These results indicate that the genetic diversity of the leopard cat in South Korea is unexpectedly low, and that the risk of local extinction is, as a result, substantial. Thus, it is necessary to begin appropriate conservation efforts at a national level to conserve the leopard cat population in South Korea.

Mitochondrial genome sequence of black paradise flycatcher (Aves: Monarchidae) and its phylogenetic position

Abstract We generated the complete mitochondrial genome of the black paradise flycatcher (Terpsiphone atrocaudata; Family: Monarchidae), an ecologically important insectivorous bird in Asian forest ecosystems. The mitogenome was 16,984 bp in length and consisted of 13 protein-coding genes, 22 tRNAs, two rRNAs and a control region. Gene composition and arrangement in the mitogenome were similar to those of related families Corvidae and Laniidae available in GenBank. However, tRNAAla was located between COXII and ATP8 genes in the mitogenome of T. atrocaudata while tRNALys, was in the same location in the mitogenomes of Corvidae and Laniidae. The phylogenetic tree based on the mitogenomes of T. atrocaudata and the related families supported that Monarchidae was the sister taxa to the clade of Laniidae and Corvidae. The mitogenome of T. atrocaudata will be a valuable genetic resource for phylogenetic analyses and implication of conservation and management of the species.