Seon-Deok Jin

The first whole genome and transcriptome of the cinereous vulture reveals adaptation in the gastric and immune defense systems and possible convergent evolution between the Old and New World vultures

BackgroundThe cinereous vulture, Aegypius monachus, is the largest bird of prey and plays a key role in the ecosystem by removing carcasses, thus preventing the spread of diseases. Its feeding habits force it to cope with constant exposure to pathogens, making this species an interesting target for discovering functionally selected genetic variants. Furthermore, the presence of two independently evolved vulture groups, Old World and New World vultures, provides a natural experiment in which to investigate convergent evolution due to obligate scavenging.ResultsWe sequenced the genome of a cinereous vulture, and mapped it to the bald eagle reference genome, a close relative with a divergence time of 18 million years. By comparing the cinereous vulture to other avian genomes, we find positively selected genetic variations in this species associated with respiration, likely linked to their ability of immune defense responses and gastric acid secretion, consistent with their ability to digest carcasses. Comparisons between the Old World and New World vulture groups suggest convergent gene evolution. We assemble the cinereous vulture blood transcriptome from a second individual, and annotate genes. Finally, we infer the demographic history of the cinereous vulture which shows marked fluctuations in effective population size during the late Pleistocene.ConclusionsWe present the first genome and transcriptome analyses of the cinereous vulture compared to other avian genomes and transcriptomes, revealing genetic signatures of dietary and environmental adaptations accompanied by possible convergent evolution between the Old World and New World vultures.

Additional file 1: Table S1. of The first whole genome and transcriptome of the cinereous vulture reveals adaptation in the gastric and immune defense systems and possible convergent evolution between the Old and New World vultures

Sequencing and analysis statistics of the cinereous vultureâ s WGS relative to the bald eagle genome. Table S2 17-mer statistics. Table S3 Summary of SNVs and small indel in the cinereous vulture. Table S4 PSGs list of the Accipitrimorphae using a branch-site model. Table S5 PSGs list of the Accipitrimorphae using a branch model. Table S6 Functional annotation chart of PSGs of the Accipitrimorphae. Table S7 PSGs list of the cinereous vulture using a branch-site model. Table S8 PSGs list of the cinereous vulture using a branch model. Table S9 PSGs list of the turkey vulture using a branch-site model. Table S10 PSGs list of the turkey vulture using a branch model. Table S11 Functional annotation chart of PSGs of the cinereous vulture. Table S12 Functional annotation chart of PSGs of the turkey vulture. Table S13 Unique amino acid changes of the turkey vulture. Table S14 Unique amino acid changes of the cinereous vulture Table S15 Unique amino acid changes of the Accipitridae. Table S16 Unique amino acid changes on sites between Accipitridae and Cathartidae of the digestive system-related proteins. Table S17 Unique amino acid changes on sites between Accipitridae and Cathartidae of the gastric acid secretion-related proteins. Table S18 Statistics regarding whole-transcriptome sequences and unigene construction. Table S19 GO analysis for the blood transcriptome of the cinereous vulture. Table S20 KEGG pathway analysis for the blood transcriptome of the cinereous vulture. Table S21 Gene expression in the cinereous vulture compared to the other avian species. Table S22 Immune related genes expression in the cinereous vulture compared to the other avian species. (XLSX 635 kb)

Bird Community of Tandong Stream in Daejeon Metropolitan City

This study carried out over two times in February and May in 2009 was aimed at the survey of the birds inhabiting in the whole region of Tandongcheon (Stream) that runs through Daedeok Science Town in Daejeon Metropolitan city to Gapcheon (Stream) and the adjacent area such as Maebongsan and Seongdusan urban parks. The number of birds observed during the period reached 11 orders, 23 families, 37 species, and 799 individuals (Total sum of maximum individuals). The highest dominant species was Anas crecca that was counted in 153 individuals (19.15%), while the others were Paradoxornis webbianus in 125 individuals (15.64%), Pica pica in 101 individuals (12.64%), Passer montanus in 91 individuals (11.39%), Anas poecilorhyncha in 66 individuals (8.26%), and Hypsipetes amaurotis in 41 individuals (5.13%). By seasons, 28 species 742 individuals were observed in winter while 24 species 337 individuals in spring. Especially it was notable that Amaurornis phoenicurus was observed in winter (February), which is known as a passage migrant not easily seen in Korea. In addition, the legally protected species designated as Korean National Monument in Korea such as Falco tinnunculus, Otus scops, and Ninox scutulata were observed, too.

Inhabiting Condition and Preservation of Black-faced Spoonbill around Ganghwa County

Regular monitoring on the Black-faced Spoonbill and survey on their breeding were performed in the vicinity of Ganghwa County from August 2002 till July 2003 in order to understand the inhabiting conditions of the endangered species of the bird (EN) defined by IUCN. Maximum 230 individuals of the Black-faced Spoonbill around the County were observed at the southern tidal flat of Ganghwa, which was the largest and 51 at Gyodongdo Island, 55 at Boreumdo Island while one at Seokmodo Island. No Black-faced Spoonbill was observed at Jumundo Island. For the inhabiting status of the bird as per the time of survey, 203 individuals were observed in August 2002, which was recorded as the largest of its kinds, on the other hand, only 5 individuals were found in March, which was the least. No Black-faced Spoonbill was observed from November till February of the following year. For the areas of survey, more individuals of the endangered bird were observed at the southern tidal flat of Ganghwa during the period of survey than other areas and it is because the bird took a rest at the southern tidal flat of Ganghwa and fed their foods. Breeding of the bird was verified at Yudo Island, Seokdo Island, Bido Island and Suribongdol Island and the breeding status as per each island is 100 individuals at Yudo Island, 10 at Seokdo Island, 8 at Bido Island and 5 at Suribongdol Island. On the other hand, the Black-faced Spoonbill found at the southern tidal flat of Ganghwa fed their foods at the nearby rice paddy during May and June. Heavy rainfall in 2007 and the pressure on developing the area surrounding Ganghwdo Island may force the endangered birds to breed at the artificial island of the Incheon Songdo International City or the main inhibiting place is in danger of vanishing. In order to protect the Black-faced Spoonbill, therefore, development and use of not only the tidal flat but also the rice paddy that is the wetland with fresh water and shallow tidal flat should be minimized. Also, converting to the eco-friendly development plan of the reclaimed land and collecting information to restore the inhabiting place of Black-faced Spoonbill is essential.

Avifauna of Manisan (Mt.) in Ganghwado

In June and September of 2009, a total of 179 individuals of 25 species, 14 families and 6 orders were found in the region of Manisan (Mt.) of Ganghwado (island). Dominant species included Aegithalos caudatus (20.11%, 36 individuals), Hypsipetes amaurotis (15.08%, 27 individuals), Parus palustris (10.06%, 18 individuals), Parus major (6.70%, 12 individuals), Parus varius (6.15%, 11 individuals), Pica pica (5.59%, 10 individuals) and more. In the 1st survey (June), a total of 108 individuals of 22 species were recorded, and in the 2nd survey (September), a total of 112 individuals of 17 species were recorded. The 1st survey, which showed a higher number of species, showed higher species diversity (2.70) and species richness (4.49) than those of the 2nd survey.

Avifauna in the Orkhon River basin - A World Heritage site in Mongol

Birds observed in the Orkhon River basin during Aug. 15 through Aug. 26, 2007 were 5,538 individuals in 68 species in total. Dominant species were Corvus dauuricus in 3,009 individuals (54.33%), Passer montanus in 499 individuals (9.01%), Pyrrhocorax pyrrhocorax in 213 individuals (3.85%), Corvus corax in 203 individuals (3.67%), and Milvus migrans in 198 individuals (3.58%) in order from the most dominant. As result of observation by habitat types, it appeared 20 species 541 individuals in residential area, 33 species 362 individuals in forest, 39 species 745 individuals in wetland, 26 species 3,373 individuals in steppe and 24 species 517 individuals in rocky area. From the aspect of species diversity, it showed 2.78 in wetland (highest), 2.72 in forest, 2.40 in residential area 1.82 in rocky area, and 1.00 in steppe.

Avifauna of southern coast of Ganghwado, Seokmodo and Gyodongdo.

Abstract In June and September of 2009, a total of 11,590 individuals (sum of maximum individuals by each species) of 68 species of 31 families and 12 orders were found in the southern coast of Ganghwado (island), Seokmodo (island) and Gyodongdo (island). Dominant species included, in decreasing order of, Larus crassirostris (29.18%, 3,382 individuals), Larus saundersi (10.52%, 1,219 individuals), Egretta garzetta (9.19%, 1,065 individuals), Egretta alba modesta (9.01%, 1,044 individuals) and Numenius madagascariensis (8.57%, 993 individuals). In June of 2009 (1st survey), the study recorded a total of 4,915 individuals of 50 species, and in September of 2009 (2nd survey), a total of 8,246 individuals of 45 species were recorded. The number of birds was relatively low in the 1st survey, but its species diversity (H′) of 2.35 and species richness (Da) of 4.76 were higher than those of the 2nd survey, with the H’ of 2.22 and Da of 4.87. Furthermore, depending on the region, Seokmodo (island) recorded the highest species diversity (37 species) in the 1st survey, with H’ of 2.57 and Da of 5.59, and in the 2nd survey, Gyodongdo (island) recorded the highest species diversity of 36 species, at H’ of 2.46 and Da of 4.79. In this study, Egretta eulophote and Platalea minor, natural mouments numbers 361 and 205-1, as well as 1st grade endangered species, along with 13 government protected species, were found.

A study on the bird community in Chilgap Mountain Provincial Park.

In this result, from May, 2007 to January, 2008, important points for bird habitation in Mt. Chilgap Provincial Park area (Cheonjang reservoir, climbing paths of Mt. Chilgap, Chilgap reservoir, and Janggok temple, etc.) were established and investigated once every season. It was found that observed birds were 65species-4,999 individuals and dominant species were Anas poecilorhyncha(926 individuals, 18.52%), Emberiza elegans (553 individuals, 11.06%), Anas platyrhynchos (504 individuals, 10.08%), Paradoxornis webbianus (420 individuals, 8.40%), Passer montanus (358 individuals, 7.16%) (Table 1). By migratory features of birds, it was found that they were 29 species of resident birds (44.62%), 22 species of winter migratory birds (33.85%), 12 species of summer migratory birds (18.46%), and 2 species of passage birds (s3.08%). By seasons, it was found that there were 48 species-680 individuals in spring, 32 species-530 individuals in summer, 35 species-1,616 individuals in autumn, and 38 species-2200 individuals in winter. By investigation areas, it was found that there were 45 species-1,444 individuals in A area, 49 species-2,691 individuals in B areas, and 41 species-64 individuals in C area. The overall species diversity was 3.02. It was found that the species diversity indexes by seasons were 3.31 in spring, 2.79 in summer, 2.72 in autumn, and 2.52 in winter, and they were 3.05 in A area, 2.50 in B area, and 2.98 in C area, by areas. As endangered species, 7 species including Aix galericulata, Anas formosa, Accipiter soloensis, Accipiter gentilis, Buteo buteo, Falco tinnunculus, and Charadrius placidus were observed.

Avifauna of Geumo Archipelago

A total of 3,248 individuals of 51 species were observed in the Geumo Archipelago (Geumodo, Ando, Yeondo) in Yeosu, Jeollanamdo in two rounds of study conducted from June to September 2008. The dominant species was Larus crassirostris with 1,145 individuals (35.25%) followed by Hirundo rustica with 385 individuals (11.85%), Paradoxornis webbianus with 356 individuals (10.96%), Hypsipetes amaurotis with 219 individuals (6.74%), and Hirundo daurica with 168 individuals (5.17%). Resident birds showed the highest migration of 54.90% followed by summer vagrant birds (31.37%), passage migratory birds (9.8%), winter vagrant birds (1.96%) and vagrant birds (1.96%). The Species biodiversity was 2.43 and the species richness was 6.18.

First Discovery of European White Storks in Korea

Chungnam Federation Environmetal MovementA brace of European white stork ( Ciconia ciconia ciconia )was observed for the first time in Korea, staying inMangyeonggang basin, Hwapo-ri, Jellabuk-do, from Sept.2008. The Mangyeonggang (river) basin was an intertidalmudflat and is turning into a salty grassland in the processof the Saemangeum reclamation project now underway.The birds in Picture 1 are resting on a mudflat in the rivermade by high and low tides .The pair repeat hunting and resting in an area within theradius of 4~5 km. Their feather looks rougher comparedwith wild birds. It seems they are still young or notexperienced in preening feather. Some suggest they haveescaped from a zoo, because Korea is too far away from the other n . O way t their em to have los th ider ns co Europe to hand, some think they are wild birds because theirbehaviors of hunting and warning in the wild are naturallydeveolped rather than trained in a zoo. The appearance of the European white storks in Korea,through whatever route, interests Koreans who have lovedwhite storks since long time ago.In Korea, a white stork ( Ciconia boyciana ) means alarge, auspicious bird, and represents longevity, happiness,noble man, wealthiness, eternal youth, and noble spirit.Until the liberation from Japanese Imperial rule in 1945,white storks were native birds commonly found living inHwanghae-do and Chungcheongbuk-do regions. Most ofthem were killed in the Korean War and poached in the1960s. The male stork of the last brace in Eumseong,Chungcheongbuk-do, wapoached in Aprs il, 1974, thus, thefemale failed to breed. White designated ae wr sstore k natural a s monument No.199, in 1968 for protection. The European white storksfound last September, Family Ciconiidae under OrderCiconiiformes, are almost the same as the migratory whitestorks, except they are a little smaller in size. They areexpected to stay in Korea for some time as they seem tohave no problem in fylnig and eating.