Ecological Research最新文献

CUSCO: A Tool for Curating Single-Copy Orthologs and Extracting Marker Genes for Phylogenetic Tree Construction With Extra Samples 库斯科：一个工具，用于管理单拷贝同源物和提取标记基因与额外样本的系统发育树建设

IF 1.4 4区环境科学与生态学

Ecological Research Pub Date : 2025-10-09 DOI: 10.1111/1440-1703.70015

Takashi Seiko, Koki Nagasawa, Ken Naito

{"title":"CUSCO: A Tool for Curating Single-Copy Orthologs and Extracting Marker Genes for Phylogenetic Tree Construction With Extra Samples","authors":"Takashi Seiko, Koki Nagasawa, Ken Naito","doi":"10.1111/1440-1703.70015","DOIUrl":"https://doi.org/10.1111/1440-1703.70015","url":null,"abstract":"Single-copy orthologs are often used to reconstruct phylogenetic trees of life. A set of single-copy orthologs can be prepared by building a new database including the species/strains of interest and performing a homology search, but these steps are time-consuming when working with a large number of samples. To address this issue, more efficient and practical approaches are needed. Here, we developed a new pipeline called CUSCO, which reconstructs phylogenetic trees from the genome sequences of desired samples, including polyploid genomes or those without annotation using a reference set of protein sequences. As a benchmark, we compared the CUSCO pipeline with OrthoFinder. The CUSCO pipeline reproduced the same tree topologies that were reconstructed using single-copy orthologs selected by OrthoFinder in a significantly shorter runtime. The pipeline is implemented with a function to identify a minimal set of marker genes that reconstruct a species tree, which is comparable to the one reconstructed from single-copy orthologs. We also verified that the minimal set of marker genes identified by CUSCO accurately reproduces the tree topology obtained from the whole genome dataset. Sequencing these marker genes enables rapid and cost-effective inference of the phylogenetic position of newly sampled species. Now that the genomes can be sequenced easily and inexpensively, the speed and accuracy of CUSCO facilitate large-scale phylogenomic analyses on a desktop computer. Availability and implementation https://github.com/seikot345/CUSCO/.","PeriodicalId":11434,"journal":{"name":"Ecological Research","volume":"40 6","pages":""},"PeriodicalIF":1.4,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://esj-journals.onlinelibrary.wiley.com/doi/epdf/10.1111/1440-1703.70015","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145272472","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genetic Diversity in the Wrinkled Frog, Glandirana rugosa, Evaluated Using Microsatellite Markers Identified by Nanopore Sequencing 用纳米孔测序鉴定的微卫星标记评价皱纹蛙的遗传多样性

IF 1.4 4区环境科学与生态学

Ecological Research Pub Date : 2025-10-08 DOI: 10.1111/1440-1703.70014

Yuzuna Fukatsu, Takeshi Igawa, Kaito Sasaki, Satoshi Yamagishi, Teruhiko Takahara

{"title":"Genetic Diversity in the Wrinkled Frog, Glandirana rugosa, Evaluated Using Microsatellite Markers Identified by Nanopore Sequencing","authors":"Yuzuna Fukatsu, Takeshi Igawa, Kaito Sasaki, Satoshi Yamagishi, Teruhiko Takahara","doi":"10.1111/1440-1703.70014","DOIUrl":"https://doi.org/10.1111/1440-1703.70014","url":null,"abstract":"Wrinkled frogs (Glandirana rugosa) are a common species found in various freshwater habitats across Japan. Due to multiple sex chromosome turnovers and the discovery of cryptic species, understanding the historical population dynamics of this species is crucial for studying its genomic evolution and speciation. On the other hand, in some populations, urbanization has led to a decline in both population size and their distribution range. To better understand the historical population dynamics and recent population decline of G. rugosa, it can be helpful to conduct novel genetic analyses. As a crucial first step, we primarily focused on developing 14 microsatellite markers using nanopore sequencing. These markers were then validated by assessing the genetic diversity of G. rugosa in four populations: three from mainland Japan (two from Shimane and one from Gunma Prefectures) and one from an island (Oki Islands, Shimane Prefecture). The total number of alleles per locus ranged from 4 to 36, and the observed heterozygosity ranged from 0 to 0.950. Population genetic analyses using these markers revealed substantial genetic diversity among populations and a weak correlation between intra-population diversity and geographical features. We believe that the microsatellite markers developed in this study would be useful in exploring their genetic diversity in other populations and contribute to the conservation of this species in the future.","PeriodicalId":11434,"journal":{"name":"Ecological Research","volume":"40 6","pages":""},"PeriodicalIF":1.4,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://esj-journals.onlinelibrary.wiley.com/doi/epdf/10.1111/1440-1703.70014","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145271979","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Life-Cycle Plasticity Underlying the Survival of Glandirana rugosa Tadpoles in Intensively Managed Rice Fields 集约化管理稻田中绿蛙蝌蚪生存的生命周期可塑性

IF 1.4 4区环境科学与生态学

Ecological Research Pub Date : 2025-10-02 DOI: 10.1111/1440-1703.70013

Kaede Kimura, Teiji Sota

{"title":"Life-Cycle Plasticity Underlying the Survival of Glandirana rugosa Tadpoles in Intensively Managed Rice Fields","authors":"Kaede Kimura, Teiji Sota","doi":"10.1111/1440-1703.70013","DOIUrl":"https://doi.org/10.1111/1440-1703.70013","url":null,"abstract":"<div>\u0000 \u0000 Rice field intensification in recent decades has negatively impacted wetland species, partly due to the shortened hydroperiods caused by effective water drainage during mid-summer, harvesting, and fallow seasons, which increase mortality risks for amphibian larvae. To investigate potentially adaptive responses to these altered conditions, we tested whether Glandirana rugosa, a species with long tadpole stages, accelerates metamorphosis in rice fields to avoid desiccation. We surveyed larval growth and adult breeding phenology across contrasting habitats and conducted a series of rearing experiments to identify factors determining the duration of the larval period. We found G. rugosa larvae often metamorphose before winter in certain rice fields and in a river, whereas larval overwintering commonly occurred in other sites. Frequent larval overwintering was associated with low water temperatures rather than permanent water bodies. In the experiments, larvae metamorphosed earlier at higher temperatures, while population origin, water level, photoperiod, and sex had no clear effects on the larval period. Because G. rugosa larvae possess traits associated with permanent water bodies (e.g., long larval period and no response to reduced water level), the observed developmental plasticity may not be a direct adaptation to temporal pools. Rather, it likely represents a coincidental adaptive expression of thermal reaction norms in rice fields with harvesting drainage. However, their development rate is not fast enough to complete metamorphosis before mid-summer drainage, possibly precluding their occurrence in many typical rice fields. This study highlights larval life-history plasticity as an understudied mechanism of population persistence during the nationwide land transformation in Japan.\u0000 </div>","PeriodicalId":11434,"journal":{"name":"Ecological Research","volume":"40 6","pages":""},"PeriodicalIF":1.4,"publicationDate":"2025-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145223873","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

National-scale terrestrial biodiversity and ecosystem monitoring with essential biodiversity variables in Japan and Finland 日本和芬兰国家尺度陆地生物多样性和生态系统监测与基本生物多样性变量

IF 1.4 4区环境科学与生态学

Ecological Research Pub Date : 2025-09-24 DOI: 10.1111/1440-1703.70011

Yayoi Takeuchi, Lea Végh, Hibiki Noda, Kristin Böttcher, Petteri Vihervaara, Jamie M. Kass, Ichiro Hama, Yusuke Saito

{"title":"National-scale terrestrial biodiversity and ecosystem monitoring with essential biodiversity variables in Japan and Finland","authors":"Yayoi Takeuchi, Lea Végh, Hibiki Noda, Kristin Böttcher, Petteri Vihervaara, Jamie M. Kass, Ichiro Hama, Yusuke Saito","doi":"10.1111/1440-1703.70011","DOIUrl":"https://doi.org/10.1111/1440-1703.70011","url":null,"abstract":"Essential biodiversity variables (EBVs) have emerged as a crucial tool for monitoring biodiversity change and provide a framework for standardized and integrated data that align with national and global conservation targets. While EBVs have static definitions, they offer flexibility in data products, allowing regions to develop unique implementation strategies. To guide the development of EBV lists for Japan, we compare data availability with Finland, a country with a similar environment. We review the status of primary data for EBVs in terrestrial ecosystems in these two countries and then compare data for Japan with the Group on Earth Observations Biodiversity Observation Network EBVs and the EBV lists recommended by Europa Biodiversity Observation Network and Finland. Furthermore, we summarize EBVs, remote sensing and modeling applications employed to produce them, and provide ideas for regional EBV priority lists. We found that Japan has medium-to-high data availability across several EBV classes, particularly for species distributions, phenology, and environmental disasters, which include unique datasets. For Japan, we identified data gaps in the EBV classes, Genetic composition, Species traits, and Ecosystem structure. We then discuss how EBVs can contribute to calculating indicators for Japan, such as the “30 by 30,” and highlight the remaining data gaps required to realize their implementation. Finally, we provide our perspectives on calculating EBVs at the national scale, focusing on Japan. With several countries and regions developing EBV lists, comparative regional analyses can help elucidate key commonalities and differences to inform more coordinated and effective responses to the global biodiversity crisis.","PeriodicalId":11434,"journal":{"name":"Ecological Research","volume":"40 6","pages":""},"PeriodicalIF":1.4,"publicationDate":"2025-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://esj-journals.onlinelibrary.wiley.com/doi/epdf/10.1111/1440-1703.70011","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145129368","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Impact of livestock grazing on soil potential net C and N mineralization during the dry season in a cultivated subhumid tropical grassland ecosystem 牲畜放牧对半湿润热带草地生态系统旱季土壤潜在净碳氮矿化的影响

IF 1.4 4区环境科学与生态学

Ecological Research Pub Date : 2025-09-18 DOI: 10.1111/1440-1703.70012

América Ortiz-Carmona, Heidi Patricia Medorio-García, Bruno Chávez-Vergara, Ofelia Beltrán-Paz, Yareni Perroni

{"title":"Impact of livestock grazing on soil potential net C and N mineralization during the dry season in a cultivated subhumid tropical grassland ecosystem","authors":"América Ortiz-Carmona, Heidi Patricia Medorio-García, Bruno Chávez-Vergara, Ofelia Beltrán-Paz, Yareni Perroni","doi":"10.1111/1440-1703.70012","DOIUrl":"10.1111/1440-1703.70012","url":null,"abstract":"Cultivated tropical grasslands have been hypothesized to have great soil carbon (C) and nutrient storage potential. However, global change and the resulting seasonal soil drying–wetting shifts may affect this potential. Limited data exist to predict the biogeochemical responses of these ecosystems under different management and climate conditions. Our objectives were (1) to explore the relationship between total and available C, nitrogen (N), and phosphorus (P), microbial biomass C, and C and N transformation in surface soil during the dry season under the two livestock species influence (water buffaloes [WB]; and Nellore cattle [NC]) and (2) to explore the livestock species effect on soil C transformation patterns across time and during a water pulse in the dry season. The results suggest that there is a seasonal pattern response and a differentiation in soil microbial activity shaped by livestock type and soil wetting. Furthermore, a high potential net C mineralization rate (PNCMR) (20.03 ± 1.13 μg C g−1 d−1) and retention of ammonium (0.04 ± 0.005 mg g−1), nitrate (0.04 ± 0.005 mg g−1), and soluble P (12.51 ± 0.9 μg g−1) appear to be associated with the ecosystem with WB. In the case of NC, a lower PNCMR (9.54 ± 0.60 μg C g−1 d−1) and high N mineralization (84.34 ± 12.35 μg g−1) may promote N losses in dry soil. These results could help to better understand the conservation and soil nutrient availability of complex grazing ecosystems in the subhumid tropics.","PeriodicalId":11434,"journal":{"name":"Ecological Research","volume":"40 5","pages":""},"PeriodicalIF":1.4,"publicationDate":"2025-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://esj-journals.onlinelibrary.wiley.com/doi/epdf/10.1111/1440-1703.70012","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145101481","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Influence of land use evolution on ecological environment quality in the mountainous areas of Shiqian, Southwest China: Spatiotemporal characteristics and driving exploration 石阡山区土地利用演变对生态环境质量的影响：时空特征及驱动力探索

IF 1.4 4区环境科学与生态学

Ecological Research Pub Date : 2025-09-09 DOI: 10.1111/1440-1703.70008

Quan Wang, Xiu Li

{"title":"Influence of land use evolution on ecological environment quality in the mountainous areas of Shiqian, Southwest China: Spatiotemporal characteristics and driving exploration","authors":"Quan Wang, Xiu Li","doi":"10.1111/1440-1703.70008","DOIUrl":"10.1111/1440-1703.70008","url":null,"abstract":"Currently, rapid socioeconomic development has caused over-exploitation of mountain land, severely damaging the regional ecology. Rational development and ecological protection provide a scientific basis for precise land use planning, management, and restoration. This study focuses on Shiqian County, a typical mountainous area, using land data from 2005 to 2020 and employing land use models, ecological quality indices, and spatial autocorrelation to reveal spatiotemporal differences in land use-ecology interactions and explore internal mechanisms. The results show that, from 2005 to 2020, changes in rural residential land and other construction land were the most significant, followed by changes in urban construction land. During 2010–2015, 5.199 km2 of cultivated land was converted to other construction land. From 2015 to 2020, 7.104 km2 of forest land was converted to water area. The overall ecological environment of Shiqian County shows a deteriorating trend, mainly due to the conversion of cultivated land, forest land, and meadow to construction land, which has the highest contribution rates of 16.803%, 28.273%, and 13.60%, respectively. Between 2005 and 2020, the ecological environment quality was mainly dominated by “high-high” agglomeration areas, with a significant p-value of 0.001–0.05. Over time, the ecological environment has been affected by many factors, among which NDVI has the strongest impact. Thus, relevant government departments urgently need to implement policies for the precise adjustment of land use structure, optimize land use and planting patterns, and provide a decision-making basis for precise land use planning and ecological restoration.","PeriodicalId":11434,"journal":{"name":"Ecological Research","volume":"40 5","pages":""},"PeriodicalIF":1.4,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145022072","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The impact of slope position on the relationship between biodiversity and ecosystem multifunctionality in the Qinghai-Tibet Plateau subalpine meadows

IF 1.4 4区环境科学与生态学

Ecological Research Pub Date : 2025-09-09 DOI: 10.1111/1440-1703.70006

Youyan Chen, Minxia Liu, Xin Zhang, Xuejiao Chen, Yingying Zhang

{"title":"The impact of slope position on the relationship between biodiversity and ecosystem multifunctionality in the Qinghai-Tibet Plateau subalpine meadows","authors":"Youyan Chen, Minxia Liu, Xin Zhang, Xuejiao Chen, Yingying Zhang","doi":"10.1111/1440-1703.70006","DOIUrl":"10.1111/1440-1703.70006","url":null,"abstract":"Plant and soil microbial communities are crucial in regulating various ecosystem functions. However, the specific effects of aboveground plant communities versus belowground microbial communities (e.g., protozoa, bacteria, and fungi) and their interactions on ecosystem multifunctionality (EMF) mediated by slope positions remain largely unknown. Here, we investigated the relationship between EMF and biodiversity indices on the upper, middle, and lower slopes of subalpine meadows on the Qinghai-Tibet Plateau and how changes in plant and soil biodiversity and other abiotic factors mediate EMF. The results showed that plant diversity (species, function, phylogeny) and soil microbial diversity (bacteria, ciliates) were significantly higher on the downslope site than on the upper slope site, and EMF was significantly higher with decreasing slope position. Phylogenetic diversity and ciliate diversity were the dimensions of plant and soil biodiversity, respectively, that contributed most to EMF, suggesting the critical role of ecological niche complementarity and protozoan-driven nutrient cycling in maintaining multifunctionality. Slope position alters the relationship between biodiversity and EMF by regulating resource allocation: soil biodiversity dominates EMF when relative slope position (RSP, i.e., the ratio of the relative elevation of the watershed) is <0.30; the role of plant diversity is enhanced when RSP is >0.34. Generally speaking, our study provides valuable insights into the critical role of multi-trophic biodiversity in conserving ecosystem multifunctionality in subalpine grassland communities, as well as strong support for the importance of biodiversity conservation.","PeriodicalId":11434,"journal":{"name":"Ecological Research","volume":"40 5","pages":""},"PeriodicalIF":1.4,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145022062","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Canopy cover instigating feces deposition on paved roads in urban areas 在市区铺砌的道路上盖上树冠导致粪便堆积

IF 1.4 4区环境科学与生态学

Ecological Research Pub Date : 2025-09-09 DOI: 10.1111/1440-1703.70009

Harsh Yadav, Yuki Iwachido, Takehiro Sasaki

{"title":"Canopy cover instigating feces deposition on paved roads in urban areas","authors":"Harsh Yadav, Yuki Iwachido, Takehiro Sasaki","doi":"10.1111/1440-1703.70009","DOIUrl":"10.1111/1440-1703.70009","url":null,"abstract":"Paved roads (PRs), a key feature of urbanization, adversely affect ecosystem processes, including seed dispersal. PRs can influence the ecological functions of urban forests because of their proximity to trees and forest fragments. Therefore, understanding the effects of two critical factors, canopy cover and proximity to a forest patch, on fecal deposition on PRs is essential for assessing the impact on animal-mediated seed dispersal. In this study, we quantified fecal deposition on PRs and analyzed the effects of canopy cover and distance from forest fragments on this deposition. We also estimated the potential seed loss resulting from fecal deposition on the PRs in urban forest fragments of Yokohama, Japan. In total, 1976 fecal samples were collected from the PRs. More of these samples were observed on PRs near forest patches (n = 1671) than on PRs distant from forest patches (n = 305). The canopy cover significantly influenced fecal deposition on PRs. Numerous bird fecal samples on the PRs were expected to contain at least one seed. In addition, approximately 949 seeds could be deposited in the feces of the birds. This study indicates that PRs are critical factors contributing to seed dispersal disservice within urban ecosystems. Urban forest management practices should also consider mitigating the impact of PRs on species interactions and the services they provide.","PeriodicalId":11434,"journal":{"name":"Ecological Research","volume":"40 5","pages":""},"PeriodicalIF":1.4,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145022070","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Response to Kishida et al. (2022): Asian black bears show stronger introgression signal with brown than American black bears 对Kishida et al.（2022）的回应：与美洲黑熊相比，亚洲黑熊表现出更强的棕色入侵信号

IF 1.4 4区环境科学与生态学

Ecological Research Pub Date : 2025-09-09 DOI: 10.1111/1440-1703.70004

Emily E. Puckett

{"title":"Response to Kishida et al. (2022): Asian black bears show stronger introgression signal with brown than American black bears","authors":"Emily E. Puckett","doi":"10.1111/1440-1703.70004","DOIUrl":"10.1111/1440-1703.70004","url":null,"abstract":"The expansion of whole genome sequencing from single individuals per species to range-wide sampling of diversity now allows for nuanced investigation of the phylogeography of introgression. Analyses by Kishida et al. (2022) show gene flow between Alaskan American black bears (Ursus americanus) and both Korean and Japanese populations of Asian black bears (U. thibetanus). Further, they show no gene flow between Asian black and brown bears. Fundamental to these results was the use of four taxon D-statistics, which placed the polar bear (U. maritimus) as the outgroup species. As polar bears are not an outgroup to any of the focal species tested, this violated a main assumption of the D-statistic test. Thus, a new analysis of the phylogeography of introgression of Asian black, American black, and brown bears was undertaken, but with the divergent Andean bear (Tremarctos ornatus) serving as outgroup. I did not identify introgression between Asian black bear populations and intra-specific lineages of brown or American black bears. However, an ancient signature of introgression between Asian black and brown bears was observed and affected all intra-specific lineages of both species. Expanded aDNA resources for these species would aid in explaining the phylogeography of introgression and potential for adaptive introgression among bears.","PeriodicalId":11434,"journal":{"name":"Ecological Research","volume":"40 5","pages":""},"PeriodicalIF":1.4,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145022069","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genetic diversity and population structure of Shorea macrophylla using genome-wide single-nucleotide polymorphisms and microsatellite markers in Indonesia for conservation 利用全基因组单核苷酸多态性和微卫星标记对印尼大叶Shorea的遗传多样性和群体结构进行保护

IF 1.4 4区环境科学与生态学

Ecological Research Pub Date : 2025-09-09 DOI: 10.1111/1440-1703.70010

Singgih Utomo, Widiyatno, Sapto Indrioko, Mohamad Na'iem, Yoshihisa Suyama, Yunosuke Onuma, Takaki Aihara, Yoshihiko Tsumura

{"title":"Genetic diversity and population structure of Shorea macrophylla using genome-wide single-nucleotide polymorphisms and microsatellite markers in Indonesia for conservation","authors":"Singgih Utomo,  Widiyatno, Sapto Indrioko, Mohamad Na'iem, Yoshihisa Suyama, Yunosuke Onuma, Takaki Aihara, Yoshihiko Tsumura","doi":"10.1111/1440-1703.70010","DOIUrl":"10.1111/1440-1703.70010","url":null,"abstract":"In the tropical forests of Southeast Asia, the dipterocarp species stands out as the most significant tree group in terms of ecosystem stability and forestry management. Shorea macrophylla, found on Borneo Island, is particularly noteworthy for its rapid growth, high oil content nut production, and versatile timber characteristics, making it a prime candidate for plantation material in rehabilitating degraded forests. We collected population samples of S. macrophylla in Kalimantan Island and evaluated parameters such as genetic diversity, genetic structure, and estimated divergence times of the populations using SSR (simple sequence repeat) markers and SNPs (single-nucleotide polymorphisms). Interestingly, the estimated divergence time of genetic groups was similar between the two markers, with SNP markers likely offering a more accurate estimation owing to their higher marker count. Although SNP markers generally offer advantages over SSR markers in genetic studies, the latter remains valuable for assessing genetic diversity due to its high polymorphism. We conclude that SSR markers are still useful for identifying hotspot areas in terms of genetic diversity. Our study revealed that both DNA markers identified the Northeast Kalimantan population as the most genetically distinct population of S. macrophylla, which is important for the conservation of this species. By using multiple DNA markers with different characteristics, the history and features of the population can be more clearly explored. The result of species distribution modeling suggests that the habitat of this species may expand on Kalimantan Island due to future global warming.","PeriodicalId":11434,"journal":{"name":"Ecological Research","volume":"40 5","pages":""},"PeriodicalIF":1.4,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://esj-journals.onlinelibrary.wiley.com/doi/epdf/10.1111/1440-1703.70010","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145022021","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0