A new feather mite species of the genus Mycterialges Gaud & Atyeo, 1981 (Acari, Xolalgidae) from the Oriental Stork, Ciconiaboyciana (Ciconiiformes, Ciconiidae) in Korea.

A new feather mite species, Mycterialgesboycianaesp. nov. (Xolalgidae), was identified from the Oriental Stork, Ciconiaboyciana Swinhoe, 1873, in Korea. Males of M.boycianaesp. nov. are distinguished from Mycterialgesmesomorphus Gaud & Atyeo, 1981, in having a single triangular prodorsal shield, sinuous margins of the opisthosoma located between setae e2 and h2 on the hysteronotal shield, an oval-shaped epiandrum without posterior extensions, a shorter tibia + tarsus IV than femoragenu IV, and an absent ambulacral disc of leg IV. Females differ in having a prodorsal shield with a posterior margin that is blunt-angular, and a concave posterior margin of the hysteronotal shield with posterior extensions. This study presents the first record of the feather mite genus Mycterialges in birds of the genus Ciconia (Ciconiidae). Additionally, we determined the phylogenetic relationship among Ingrassiinae using the mitochondrial cytochrome c oxidase subunit (COI).

Microsatellite analyses across three diverse vertebrate transcriptomes (Acipenser fulvescens, Ambystoma tigrinum, and Dipodomys spectabilis).

Historically, many population genetics studies have utilized microsatellite markers sampled at random from the genome and presumed to be selectively neutral. Recent studies, however, have shown that microsatellites can occur in transcribed regions, where they are more likely to be under selection. In this study, we mined microsatellites from transcriptomes generated by 454-pyrosequencing for three vertebrate species: lake sturgeon (Acipenser fulvescens), tiger salamander (Ambystoma tigrinum), and kangaroo rat (Dipodomys spectabilis). We evaluated (i) the occurrence of microsatellites across species; (ii) whether particular gene ontology terms were over-represented in genes that contained microsatellites; (iii) whether repeat motifs were located in untranslated regions or coding sequences of genes; and (iv) in silico polymorphism. Microsatellites were less common in tiger salamanders than in either lake sturgeon or kangaroo rats. Across libraries, trinucleotides were found more frequently than any other motif type, presumably because they do not cause frameshift mutations. By evaluating variation across reads assembled to a given contig, we were able to identify repeat motifs likely to be polymorphic. Our study represents one of the first comparative data sets on the distribution of vertebrate microsatellites within expressed genes. Our results reinforce the idea that microsatellites do not always occur in noncoding DNA, but commonly occur in expressed genes.

The effects of contig length and depth on the estimation of SNP frequencies, and the relative abundance of SNPs in protein-coding and non-coding transcripts of tiger salamanders (Ambystoma tigrinum).

BACKGROUND: Next-generation sequencing methods have contributed to rapid progress in the fields of genomics and population genetics. Using this high-throughput and cost-effective technology, a number of studies have estimated single nucleotide polymorphism (SNP) frequency by calculating the mean number of SNPs per unit sequence length (e.g., mean SNPs/kb). However, both read length and contig depth are highly variable and thus raise doubt about simple methods of SNP frequency estimation. RESULTS: We used 454 pyrosequencing to identify 2,980 putative SNPs in the eastern tiger salamander (Ambystoma tigrinum tigrinum) transcriptome, then constructed analytical models to estimate SNP frequency. The model which considered only contig length (i.e., the method employed in most published papers) was evaluated with very poor likelihood. Our most robust model considered read depth as well as contig length, and was 7.5 × 1055 times more likely than the length-only model. Using this novel modeling approach, we estimated SNP frequency in protein-coding (mRNA) and non-coding transcripts (e.g., small RNAs). We found little difference in SNP frequency in the contigs, but we found a trend of a higher frequency of SNPs in long contigs representing non-coding transcripts relative to protein-coding transcripts. These results support the hypothesis that long non-coding transcripts are less conserved than long protein-coding transcripts. CONCLUSIONS: A modeling approach (i.e., using multiple model construction and model selection approaches) can be a powerful tool for identifying selection on specific functional sequence groups by comparing the frequency and distribution of polymorphisms.

The influencing factors for distribution patterns of resident and migrant bird species richness along elevational gradients.

The latitudinal and elevational patterns of species richness of resident and migrant birds have been of interest to researchers over the past few decades, and various hypotheses have been proposed to explain the factors that may affect these patterns. This study aimed to shed light on the elevational distribution patterns of resident and migrant bird species richness by examining biotic and abiotic factors such as climate, and habitat heterogeneity using a piecewise structural equation model (pSEM). The overall pattern of resident species richness showed a decreasing trend with increasing elevation, whereas that of migrant species richness showed an increasing trend. The mid-peak pattern of species richness was affected by a combination of resident and migrant species and not by either resident or migrant species. Our results showed that resident species were distributed in lower elevation regions with higher mean spring temperatures, whereas migrant species were found in higher elevation regions with lower mean spring temperatures and higher overstory vegetation coverage. Although high elevation conditions might adversely affect the reproduction of migrant birds, higher overstory vegetation coverage at high elevations seemed to compensate for this by providing a better nesting and roosting environment. Despite the significance of habitat diversity and understory vegetation coverage in univariate linear regression models, multiple regression models of the interconnection of ecological processes demonstrated that mean spring temperature and overstory vegetation coverage were more explanatory than other variables.

Population genetic structure and conservation management of hill pigeons (Columba rupestris) recently endangered in South Korea.

BACKGROUND: Hill pigeons (Columba rupestris) are close to local extinction (ca. less than 100 individuals) in South Korea where a variety of conservation management procedures are urgently required. OBJECTIVE: This study was aimed at determining the conservation direction of captive propagation and reintroduction of hill pigeons using genetic information based on mitochondrial DNA. We also evaluated the extent of hybridization between hill pigeons and cohabiting domestic pigeons. METHODS: We used 51 blood samples of hill pigeons from Goheung (GH), Gurye (GR), and Uiryeong (UR), and domestic pigeons cohabiting with hill pigeon populations. Genetic diversity, pairwise Fst, analysis of molecular variance, and haplotype network analysis were used to examine the genetic structure of hill pigeons. RESULTS: Hill pigeons that inhabited South Korea were not genetically distinct from Mongolian and Russian populations and showed relatively low genetic diversity compared with other endangered species in Columbidae. The GR population that exhibited the largest population size showed lower genetic diversity, compared to the other populations, although the pairwise Fst values of the three populations indicated low genetic differentiation. The GH and GR populations were confirmed to lack hybridization, relatively, whereas the UR population was found to exhibit some degrees of hybridization. CONCLUSION: To conserve hill pigeons with low genetic diversity and differentiation in South Korea, the conservation process of captive propagation and reintroduction may require artificial gene flows among genetically verified populations in captivity and wildness. The introduction of foreign individuals from surrounding countries is also considered an alternative strategy for maintaining genetic diversity.

Development of InDel markers for interspecific hybridization between hill pigeons and feral pigeons based on whole-genome re-sequencing.

Interspecific hybridization occurs among birds, and closely related sister taxa tend to hybridize at a high rate. Genomic hybridization markers are useful for understanding the patterns and processes of hybridization and for conserving endangered species in captivity and the wild. In this study, we developed genomic hybridization markers for the F1 progeny of the sister taxa feral pigeons (Columba livia var. domestica) and endangered hill pigeons (Columba rupestris) (family Columbidae). Using whole-genome re-sequencing data, we performed genome-wide analysis for insertion/deletion (InDel) polymorphisms and validated using primers. We conducted polymerase chain reaction (PCR) and agarose gel electrophoresis to identify species-specific InDels. We produced eight F1 hybrids of hill and feral pigeons, and their samples were tested by re-performing analyses and sequencing using 11 species-specific InDel polymorphisms. Eight InDel markers simultaneously amplified two DNA fragments from all F1 hybrids, and there was no abnormality in the sequencing results. The application of genomic tools to detect hybrids can play a crucial role in the assessment of hybridization frequency in the wild. Moreover, systematic captive propagation efforts with hybrids can help control the population decline of hill pigeons.

Technical note: Polyvinylpyrrolidone (PVP) and proteinase-K improve the efficiency of DNA extraction from Japanese larch wood and PCR success rate.

Illegal distribution of timber disrupts the timber market and depletes forest resources. DNA markers are used to verify the legal distribution of wood. However, it is difficult to obtain the quantity and quality of DNA suitable for genetic analysis because of the physicochemical properties of wood; therefore, an efficient wood DNA extraction method is required. In this study, to prepare an efficient DNA extraction method from Japanese larch (Larix kaempferi) wood, we investigated the ability of polyvinylpyrrolidone (PVP) and proteinase-K to improve DNA extraction efficiency and PCR success rate. It was found that the addition of PVP resulted in a significant increase in the DNA concentration of the treatment group compared to that of the control group, while the purity (A260/A280) showed no difference. Moreover, the addition of proteinase-K significantly increased both the DNA concentration and purity of the treatment group compared to those of the control group. Further analysis showed that the PCR success rate of psbC (approximately 350 bp) was higher than 90% in the control, PVP treatment, and proteinase-K treatment groups. However, in the PCR success rate of rbcL (approximately 1.3 kb) was higher in the proteinase-K and PVP treatment groups than in the control group. The addition of PVP and proteinase-K increased the success rate of PCR amplification for long regions by preventing DNA damage caused by phenolic compounds and proteins in the wood. The results of this study can thus develop DNA extraction methods to identify the species and origin of woods.

Testing the causal mechanism of the peninsular effect in passerine birds from South Korea.

The peninsular effect is a geographical phenomenon that explains patterns of species richness. Given that spatial variation in species richness along a peninsular may be driven by multiple processes, we aimed to identify the sources of latitudinal patterns in passerine species richness and test hypotheses regarding (1) recent deterministic processes (climate, primary productivity, forest area, and habitat diversity), (2) anthropogenic processes (habitat fragmentation), and (3) stochastic processes (migration influence) in the Korean peninsula. We used the distribution data of 147 passerine species from 2006 to 2012. Single regression between passerine species richness and latitude supported the existence of the peninsular effect. Mean temperature increased with decreasing latitude, as did habitat diversity but leaf area index and forest area decline. However, mean temperature and forest area only influenced passerine species richness. Although habitat diversity influenced passerine species richness, it was counter to the expectations associated with peninsular effect. The number of habitat patches decreased as latitude increased but it had no effect on passerine species richness. Ratio of migrant species richness showed no significant relationship with leaf area index, forest area, and habitat diversity. However, the ratio of migrant species richness increased with decreasing mean temperature and that contributed to the increase in passerine species. Overall, our finding indicate that the observed species richness pattern in peninsulas with the tip pointing south (in the northern hemisphere) counter to the global latitudinal gradient. These results were caused by the peninsular effect associated with complex mechanism that interact with climate, habitat area, and migrant species inflow.

Evolutionary rates of mitochondrial genomes correspond to diversification rates and to contemporary species richness in birds and reptiles.

Rates of biological diversification should ultimately correspond to rates of genome evolution. Recent studies have compared diversification rates with phylogenetic branch lengths, but incomplete phylogenies hamper such analyses for many taxa. Herein, we use pairwise comparisons of confamilial sauropsid (bird and reptile) mitochondrial DNA (mtDNA) genome sequences to estimate substitution rates. These molecular evolutionary rates are considered in light of the age and species richness of each taxonomic family, using a random-walk speciation-extinction process to estimate rates of diversification. We find the molecular clock ticks at disparate rates in different families and at different genes. For example, evolutionary rates are relatively fast in snakes and lizards, intermediate in crocodilians and slow in turtles and birds. There was also rate variation across genes, where non-synonymous substitution rates were fastest at ATP8 and slowest at CO3. Family-by-gene interactions were significant, indicating that local clocks vary substantially among sauropsids. Most importantly, we find evidence that mitochondrial genome evolutionary rates are positively correlated with speciation rates and with contemporary species richness. Nuclear sequences are poorly represented among reptiles, but the correlation between rates of molecular evolution and species diversification also extends to 18 avian nuclear genes we tested. Thus, the nuclear data buttress our mtDNA findings.

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 non-directional 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, and a subsequent test on climatic and ambient energy hypotheses, (2) non-directional rescue effect, and a subsequent test on effect of environmental factors associated with the distribution of narrowest to widest-range species. Altitudinal species range-size distribution increased with increasing altitude and showed a negative relationship with climatic variables. 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 species with intermediate range-size, rather than narrowest or widest range-size were the main cause of a mid-peak of species richness and the non-directional rescue effect. Additionally, the richness of species with intermediate range-size was highly related to minimum temperature, habitat heterogeneity, or primary productivity. Although altitudinal range-size distribution results were similar to the phenomenon of altitudinal Rapoport's rule, the mid-peak pattern of species richness could not be explained by the underlying mechanism of Rapoport's-rescue effect; however, the non-directional rescue effect could explain a mid-peak pattern of species richness along altitudinal gradient.

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.

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.

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

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.

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.

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

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.

Comparative transcriptomics and gene expression in larval tiger salamander (Ambystoma tigrinum) gill and lung tissues as revealed by pyrosequencing.

Biologists are beginning to unravel the complexities of gene expression in model organisms by studying the transcriptome, the complement of genes that are transcribed in a given tissue. It is unclear, however, if findings from model systems apply to non-model organisms because of environmental effects on gene expression. Furthermore, there have been few efforts to quantify how transcriptome or gene expression varies across individuals and across tissues in natural environments. Herein, we describe transcriptomic profiling of gene expression in lung and gill tissue of three larval tiger salamanders. We do so with a hierarchical experimental design that captures variation in expression among genes, among tissues, and among individuals. Using 454 pyrosequencing, we produced high-quality sequence data of 59 megabases and assembled ~200,000 reads into 19,501 contigs. These contigs BLASTed to 3,599 transcripts, of which 721 were expressed in both tissues, 1,668 were unique to gill, and 1,210 unique to lung. Our data showed tissue-specific patterns in gene expression level with variation among transcripts and individuals. We identified genes and gene ontology terms related to respiration and compared their relative expression levels between gill and lung tissues. We also found evidence of exogenous genes associated with larval salamanders, and we identified ~1400 potential molecular markers (microsatellites and single nucleotide polymorphisms) that are associated with expressed genes. Given the tissue-specific differences we observed in transcriptomes, these data reinforce the idea that changes in gene expression serve as a primary mechanism underlying phenotypic plasticity.

A priori and a posteriori approaches for finding genes of evolutionary interest in non-model species: osmoregulatory genes in the kidney transcriptome of the desert rodent Dipodomys spectabilis (banner-tailed kangaroo rat).

One common goal in evolutionary biology is the identification of genes underlying adaptive traits of evolutionary interest. Recently next-generation sequencing techniques have greatly facilitated such evolutionary studies in species otherwise depauperate of genomic resources. Kangaroo rats (Dipodomys sp.) serve as exemplars of adaptation in that they inhabit extremely arid environments, yet require no drinking water because of ultra-efficient kidney function and osmoregulation. As a basis for identifying water conservation genes in kangaroo rats, we conducted a priori bioinformatics searches in model rodents (Mus musculus and Rattus norvegicus) to identify candidate genes with known or suspected osmoregulatory function. We then obtained 446,758 reads via 454 pyrosequencing to characterize genes expressed in the kidney of banner-tailed kangaroo rats (Dipodomys spectabilis). We also determined candidates a posteriori by identifying genes that were overexpressed in the kidney. The kangaroo rat sequences revealed nine different a priori candidate genes predicted from our Mus and Rattus searches, as well as 32 a posteriori candidate genes that were overexpressed in kidney. Mutations in two of these genes, Slc12a1 and Slc12a3, cause human renal diseases that result in the inability to concentrate urine. These genes are likely key determinants of physiological water conservation in desert rodents.

Population divergence in plant species reflects latitudinal biodiversity gradients.

The trend for increasing biodiversity from the poles to the tropics is one of the best-known patterns in nature. This latitudinal biodiversity gradient has primarily been documented so far with extant species as the measure of biodiversity. Here, we evaluate the global pattern in biodiversity across latitudes based on the magnitude of genetic population divergence within plant species, using a robust spatial design to compare published allozyme datasets. Like the pattern of plant species richness across latitudes, we expected the divergence among populations of current plant species would have a similar pattern and direction. We found that lower latitudinal populations showed greater genetic differentiation within species after controlling for geographical distance. Our analyses are consistent with previous population-level studies in animals, suggesting a high possibility of tropical peaks in speciation rates associated with observed levels of species richness.