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Biodiversitas Journal of Biological Diversity
Published by Universitas Sebelas Maret
ISSN : 1412033X     EISSN : 20854722     DOI : https://doi.org/10.13057/biodiv/d230231
Core Subject : Science, Agriculture,
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology
The Biodiversitas Journal was first published in 2000 by the Department of Biology, FMNS, Universitas Sebelas Maret, Surakarta, Indonesia, then in 2006 it was co-published by the Society for Indonesian Biodiversity and that department; since 2017 it was also hosted by Smujo. From 2003-2012 it was accredited by DGHE, Ministry of Education, R.I., since 2014 was indexed by Scopus, where DOAJ and Google Scholar was indexed first.
Arjuna Subject : Biokimia, Genetika dan Biologi Molekuler - Biokimia, Genetika dan Biologi Molekuler (Lain-Lain)
Articles 6,315 Documents
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The evidence of cloaca display as an indicator to validate breeding behavior during the matchmaking phase on local Indonesia female White-rumped Shama (Copsychus malabaricus) Heri Dwi Putranto; ‪Nurmeiliasari‬ ‪Nurmeiliasari‬; ‪Ahmad Saleh Harahap‬; Bieng Brata; Sutriyono Sutriyono; ‪Yossie Yumiati
Biodiversitas Journal of Biological Diversity Vol. 24 No. 1 (2023)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d240156

Abstract

Abstract. Putranto HD, Nurmeilliasari, Harahap AS, Brata B, Sutriyono, Yumiati Y. 2023. The evidence of cloaca display as an indicator to validate breeding behavior during the matchmaking phase on local Indonesia female White-rumped Shama (Copsychus malabaricus). Biodiversitas 24: 486-491. White-rumped Shama bird, which Indonesian bird lovers call the Murai Batu bird (Copsychus malabaricus), has been a favorite bird for almost a decade. This bird is well-known among bird keepers for its colors and male singing voices. Generally, we recognize some biological behaviors that are trusted as avian behaviors. However, some specific behaviors in wild and domesticated birds are still not detected and unclear. The objective of this study was to validate and analyze the scientific evidence, frequency, and duration of cloaca display appearance as indicators of the female White-rumped Shama birds breeding behavior during the matchmaking phase. By animal focal sampling method, 18 sexually mature females of local White-rumped Shama captivated and observed by the research peer team were observed intensively for cloaca display activity during 22 days of matchmaking observation duration. Those 18 female samples were treated for matchmaking with another 8 males. For the cloaca display frequency and duration parameter, a time sampling method was used by dividing a total of 6 hours of daily behavior observation into 3 hours of observation duration, 2 times a day with 6 hours of distance between one observation and to next observation. Daily behavior observation conducted between 06.00 am to 09.00 am continued from 03.00 pm to 06.00 pm. Cloaca display frequency was counted as how often a female shows a cloaca exposure to her male matchmaking partner during the daily observation period. Then, a cloaca display duration was measured in the unit of seconds for each cloaca display behavior confirmed. Seventeen (17) female White-rumped Shama birds (94% samples) exhibited motion of cloaca display, with 21 motions of cloaca display behaviors confirmed. The earliest cloaca display behavior was confirmed on day 15 after matchmaking began, and the latest behavior was confirmed on day 22 after matchmaking began. These behaviors were seen on average of day 18.9±2.256 after matchmaking began. The shortest duration of cloaca display behavior lasted for 1.62 seconds, and the longest lasted for 6.26 seconds, with an average duration of 4.37 seconds for each motion. The average daily confirmed cloaca display frequency among that female White-rumped Shama was 0.053 times in 22 days of matchmaking observation duration. Cloaca display motion is seen daily (21 days) during 22 days of observation conducted, and the relative frequency percentage of cloaca display behavior was 95.45%. There is no proven info about the breeding behavior of this bird, and based on our scientific results, we strongly believe cloaca display motion can be validated as the main indicator of Indonesia's local female White-rumped Shama birds' breeding behavior. It can be read from the relative frequency percentage of cloaca display motion of female White-rumped Shama, which is overtopped 95% or dominant motion in its breeding behavior.
Application of selection index for rice mutant screening under a drought stress condition imposed at reproductive growth phase MAMIK SARWENDAH; ISKANDAR LUBIS; AHMAD JUNAEDI; BAMBANG SAPTA PURWOKO; DIDY SOPANDIE; AZRI KUSUMA DEWI
Biodiversitas Journal of Biological Diversity Vol. 23 No. 10 (2022)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d231056

Abstract

Abstract. Sarwendah M, Lubis I, Junaedi A, Purwoko BS, Sopandie D, Dewi AK. 2022. Application of selection index for rice mutant screening under a drought stress condition imposed at reproductive growth phase. Biodiversitas 23: 5446-5452. Drought is a condition of limited availability of water that can reduce rice growth and productivity, and may threaten food security. Therefore, efforts are needed to produce drought-tolerant rice genotypes. This study aimed to select drought tolerant of the M3 mutant upland rice population at the reproductive growth phase. This research was carried out in dryland at BATAN, Indonesia, from September 2020 to February 2021, using an augmented design. The study employed 360 ??genotypes of mutant upland rice and 5 check varieties, namely Salumpikit, IR20, IR64, Limboto, and Situgintung. The selection index was constructed based on multivariate analyses such as correlation, path, and Principal Component Analysis (PCA). The coefficient of the selected main component can be used as a selection index. Before selecting the character values of each genotype, the values were standardized to obtain the same degree of value. The results showed that grain weight per hill (W.G.), panicle density (P.D.), panicle length (P.L.), and the number of filled grains per panicle (NFG) could be used as selection criteria for mutant upland rice tolerant to drought at reproductive growth phase. The selection index formula was I = (5*0.44*WG) + (2*0.41*PD) + (0.23*PL) + (0.42*NFG). Selection of genotypes of mutant upland rice based on weighted index selection resulted in 89 genotypes with high yields and good agronomic characteristics so that they could be tested in further research.
Genetic diversity of eight maize (Zea mays) cultivars from East Nusa Tenggara (Indonesia) based on inter simple sequence repeat markers AHMAD YANI; ABDUL RAZAQ CHASANI; BUDI SETIADI DARYONO
Biodiversitas Journal of Biological Diversity Vol. 23 No. 8 (2022)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d230833

Abstract

Abstract. Yani A, Chasani AR, Daryono BS. 2022. Genetic diversity of eight maize Zea mays L. cultivars from East Nusa Tenggara based on inter simple sequence repeat markers. Biodiversitas 23: 4124-4130. East Nusa Tenggara (NTT) is one of Indonesia's island that has many local maize cultivars. However, the existence of this local corn is threatened by the presence of high-yielding maize seeds. Therefore, characterization of local maize cultivars using molecular marker is needed to conserve the germplasm. This study aims to determine the genetic diversity of local maize cultivars (Zea maysL.) from  East Nusa Tenggara based on ISSR markers. This research used eight local maize cultivars (Watar Ohaq, Watar Puluq, Wata Bura, Wata Kuma, Wata Bunga, Pena Muti, Boti Pulut, and Latun Wara). Young leaves of maize were used for DNA isolation. Total genomic DNA was isolated using Genomic DNA Mini Kit for Plant (Geneaid). DNA was then amplified using 5 ISSR molecular markers (ISSR-807, ISSR-808, UBC-809, UBC-811, UBC-834). DNA band profiles were scored based on the presence or absence of bands. Genetic variability was analyzed based on the UPGMA method using the MVSP ver application. 3.1. Local maize from NTT has high genetic diversity (similarity index between 0.29-0.65). Local maize cultivars were separated into two main clusters at a similarity index of 0.43 and the grouping pattern was not influenced by the geographic location of local maize origin.
Potential bioactivity evaluation of Arytera littoralis Blume (Sapindaceae) PRAPTIWI PRAPTIWI; F. I. WINDADRI; DIAH SULISTIARINI; N. P. Q. ERSALIANY
Biodiversitas Journal of Biological Diversity Vol. 23 No. 10 (2022)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d231003

Abstract

Abstract. Praptiwi Windadri FI, Sulistiarini D, Ersaliany NPQ. 2022. Potential bioactivity evaluation of Arytera littoralis Blume (Sapindaceae). Biodiversitas 23: 4977-4983. Bioactivity of Arytera littoralis (Sapindaceae) and its chemical compounds from different parts of the plants (flower, leaves, and stem) using the different polarities of solvents was carried out in this study. Phytochemical analysis was performed using the standard method. Total phenolic content (TPC) and total flavonoid contents (TFC) were analyzed using spectrophotometry method. Out a qualitative assay for antioxidant and antibacterial activity against Streptococcus aureus and Escherichia coli was carried out by Bioautography-Thin Layer Chromatography (TLC). The minimum inhibitory concentration (MIC) value and IC50 value for antioxidant was carried out by microdilution methods on a 96-well microtiter plate. The results showed that different parts of the plant contained different phytochemical compounds. The highest TPC and TFC were obtained from stem extract, followed by leaves and flowers. The antibacterial activity of A. littoralis extracts against S. aureus and E. coli was categorized as weak antibacterial, while their antioxidant activity was categorized as a strong antioxidant. The antioxidant activity index (AAI) has a very strong correlation with TPC, TFC, and IC50 value.
Molecular authentication of Etlingera spp. (Zingiberaceae) in Aceh Province, Indonesia using DNA barcoding SAUDAH SAUDAH; ZUMAIDAR ZUMAIDAR; DARUSMAN DARUSMAN; FITMAWATI FITMAWATI; DEWI INDRIYANI ROSLIM; ERWINA JULIANTARI
Biodiversitas Journal of Biological Diversity Vol. 23 No. 8 (2022)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d230815

Abstract

Abstract. Saudah, Zumaidar, Darusman, Firmawati, Rislim DI, Juliantari E. 2022. Molecular authentication of Etlingera spp. (Zingiberaceae) in Aceh Province, Indonesia using DNA barcoding. Biodiversitas 23: 3976-3983. Etlingera spp.or locally known as Etlingera spp.(Acehnese) already has strong basic evidence in the treatment of traditional tribes in Aceh such as cough medicine, fever and sprains, and used to food and spices. Etlingera spp. used in various places varies based on morphological characteristics. On the other hand, for the development of phytopharmaceutical, the use of Etlingera spp. as plant herb requires authentication about the names. This study aimed to authenticate Etlingera spp. from Aceh using DNA barcoding. Nuclear ITS and trnL-F DNA sequences were used to authenticate among species of Etlingera spp. In this study different species of Etlingera spp. can be differentiated effectively by comparing the DNA barcoding regions. ITS sequence data can identify two different species of Etlingera (E. elatior and E. hemisphaerica). The two identified Etlingera spp.species can be used as important information for further research related to their pharmacological studies. One marker and combined analysis of ITS and trnL-F data proved that the Etlingeraspp. is a monophyletic group and provided phylogenetic information in closely related species. The intraspecific and interspecific variation of ITS markers were more discriminatory regions, while trnL-F IGS were of lower divergences. Our findings indicated that DNA barcoding is efficient and powerful to authenticate herbal medicine Etlingera spp..
Diversity of reef fish species in presence of mangrove habitat in Ternate, North Maluku, Indonesia RIZKIE SATRIYA UTAMA; JEVERSON RENYAAN; DONI NURDIANSAH; PETRUS CHRISTIANUS MAKATIPU; SUYADI SUYADI; BETALINI WIDHI HAPSARI; EKA MARTHA DELLA RAHAYU; ARWAN SUGIHARTO; NEBUCHADNEZZAR AKBAR
Biodiversitas Journal of Biological Diversity Vol. 23 No. 10 (2022)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d231026

Abstract

Abstract. Utama RS, Renyaan J, Nurdiansah D, Makatipu PC, Suyadi, Hapsari BW, Martha E, Rahayu EMD, Sugiharto A. Akbar N. 2022. Diversity of reef fish species in presence of mangrove habitat in Ternate, North Maluku, Indonesia. Biodiversitas 23: 5184-5193. Research on reef fish has been widely reported, where information about reef fish communities is an important factor for evaluating fisheries management and coral reef management. Mangroves as the nursery, foraging, and growing areas were also important to assure sustainable reef fish fisheries. This paper studies reef fish abundance and diversity in Ternate Waters in the presence of mangrove in coral reef habitats. To determines coral reef condition underwater photo transect was performed while an underwater visual census (UVC) was used to determine the abundance and diversity of reef fishes in Ternate waters between 2017 and 2018. A total of 14 stations were used, with eight stations near the mangroves and six stations that did not contain mangroves. Based on the observation, fish species richness in mangrove absence was higher than in the presence of mangroves, with 68 and 65 species in 2017 and 66 and 62 species in 2018. However, the abundance of reef fish was recorded high in the presence of mangroves than in the absence of mangroves, with 390 and 289 individual differences in 2017 and 2018. Mangroves' complexity affected part of reef fish communities in Ternate water, particularly Lutjanidae, Serranidae, and Scaridae, which might influence the abundance of reef fishes rather than the species richness. In addition, carnivore shows a negative effect in the presence of mangroves, in contrast with herbivores. It is related to mangrove functioning as a temporary shelter when high-pressure presence in their natural habitat (reef) and a place for foraging. Therefore, mangrove management must be a consideration in the coral reef or fisheries management program.
DNA barcoding of Macrocephalon maleo originating from Sulawesi, Indonesia Abdul Samad; DEDY D. SOLIHIN; CECE SUMANTRI; BAMBANG PURWANTARA
Biodiversitas Journal of Biological Diversity Vol. 23 No. 9 (2022)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d230904

Abstract

Abstract. Samad A, Solihin DD, Sumantri C, Purwantara B. 2022. DNA barcoding of Macrocephalon maleo originating from Sulawesi, Indonesia. Biodiversitas 23: 4400-4408. Conservation of Maleo Senkawor (Macrocephalon maleo Sal. Muller, 1846) continues to be carried out to sustain this bird species. The genetic information from this study can be used to support future conservation activities. This study aimed to provide information on the genetic characteristics of the endangered Maleo Senkawor based on the partial sequence of the Cytochrome Oxidase 1 (COI) gene in mitochondrial DNA. Samples were collected from Central Sulawesi, Southeast Sulawesi, and North Sulawesi. Total DNA isolation was performed using the Dneasy® Blood and Tissue kit through a modified Qiagen protocol. PCR amplification used a forward primer MMCOI_F (5'-ccgatgattattctcaacca-3') and a reverse primer MMCOI_R (5'- gtagccgaatggttcttttt-3'). Analysis was performed on the partial sequences of the M. maleo COI mtDNA gene and its amino acid sequences. The genetic distance between the M. maleo population from North Sulawesi, Southeast and Central Sulawesi is 0.001 (0.1%). Macrocephalon maleo population of Southeast and Central Sulawesi have 0% genetic distance. Analysis of the COI M. maleo gene from 3 population locations showed that they came from the same species. Based on the genetic distance of the Kimura model with 2 parameters in the 3 populations, the M. maleo formed the same group (ingroup species) but had a different haplotype. These differences can be used as characterizing markers in each population. Furthermore, the conservation of M. maleo from these 3 populations was better treated as a separate group based on the mitochondrial DNA COI gene to avoid the negative impact of interpopulation breeding.
Floristic composition, structure, and diversity of mangroves in the coastal areas of Mabini, Davao de Oro, Philippines ALEXA MAE B. MANUAL; NEIL ALDEN S. GABATO; QUEZZEY B. JETUYA; JEMER A. ALIMBON
Biodiversitas Journal of Biological Diversity Vol. 23 No. 9 (2022)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d230958

Abstract

Abstract. Manual AMB, Gabato NAS, Jetuya QB, Alimbon JA. 2022. Floristic composition, structure, and diversity of mangroves in the coastal areas of Mabini, Davao de Oro, Philippines. Biodiversitas 23: 4887-4893. Biodiversity and stand structure assessments of mangrove communities are important for their management and conservation. However, this aspect of mangrove ecology in the Davao Gulf is not yet fully explored, particularly in the coastal areas of Mabini, Davao de Oro, Philippines, despite being proclaimed as a protected area. Hence, this study assessed the species composition, structure and diversity of mangroves in the coastal areas of Mabini, Davao de Oro, Philippines. Using the belt transect method, 35 plots with 10 m x 10 m each were established and surveyed. Results revealed that the area is home to eight species belonging to six genera and five families. One vulnerable species, Avicennia rumphiana, was recorded on the study site. Of the identified species, Rhizophora apiculata was the most important species, with an importance value index of 144.41 %. Meanwhile, the surveyed mangrove communities had a mean diameter at breast height of 10.96 cm, a basal area of 27.93 m² ha?¹, and a mean density of 4192 stems ha?¹. Diversity analysis indicated that the sampled sites had low species biodiversity (H’ = 1.098), low species richness (R = 0.9601), and less even species distribution (J = 0.5280). These results add to the existing knowledge about mangrove communities in Davao Gulf. More importantly, they serve as important baseline information relevant to the management, protection, and conservation of mangroves within the Mabini Protected Landscape and Seascape.
Relation between resistance of Klebsiella pneumoniae to certain antibiotics and ESBL/PBP genes ZEINA S. M. AL-HADEITHI; SAADE ABDALKAREEM JASIM; OMAR DHEYAULDEEN SALAHDIN
Biodiversitas Journal of Biological Diversity Vol. 23 No. 8 (2022)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d230806

Abstract

Abstract. Al-Hadeithi ZSM, Jasim SA, Salahdin OD. 2022. Relation between resistance of Klebsiella pneumoniae to certain antibiotics and ESBL/PBP genes. Biodiversitas 23: 3902-3906. One of the most effective antibiotics on microbes or in treating infections caused by these most resistant microbes, as it belongs to the beta-lactam group such as cephalosporin and carbapenems, which are considered among the most important antibiotics that have wide activity compared to the rest of the other antibiotics and their effectiveness against two types of negative and positive bacteria. Antibiotic resistance is a major public health concern because it happens when antibiotics are used too much or not in the right way. The improved resistance of Klebsiella pneumoniae against the antibiotics because of the virulence factors make K. pneumoniae is the most prevalent pathogenic bacteria behind nosocomial infections. Finding demonstrates that ?-lactamase is implicated in K. pneumoniae antimicrobial resistance to ?-lactam antibiotics. The purpose of this study was to look into the relation among Extended-spectrum beta-lactamase (ESBL), and the molecular biological mechanisms of antibiotic resistance in K. pneumoniae. Through the period from February to July 2021 a total of 100 out of 350 isolates were found to be K. pneumoniae. Cultural, morphological, and biochemical studies were used to identify growth on blood agar and MacConkey agar. The results revealed that the tested isolates were highly resistant to Imipenem (63%) and Amikacin (24%), while Amoxi-clav exhibited poor resistance (2%). The qualitative real-time approach was used to detect BlaR1 and Bla1 genes for positive isolates that’s possess gene/ resistant isolate , and the findings revealed that 2 (16%), 4 (33%), 16 (88%), 7 (38%), 24 (100%), 20 (83%), 2 (66%), 2 (100%), 2 (100%), 60 (95%), and 57 (90%) for CIP, CRO, AK, TMP, AMC, and IMP respectively.
Diversity of partial sequence leptin gene (Exon 3) in crossbred cattle compared to GenBank database DEVI ERMAWATI; PANJONO PANJONO; SIGIT BINTARA; TETY HARTATIK
Biodiversitas Journal of Biological Diversity Vol. 23 No. 11 (2022)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d231109

Abstract

Abstract. Ermawati D, Panjono, Bintara S, Hartatik T. 2022. Diversity of partial sequence leptin gene (Exon 3) in crossbred cattle compared to GenBank database. Biodiversitas 23: 5614-5620. Genetic marker method that is often used to select cattle is Single Polymorphism Nucleotide (SNP). Single Polymorphisms Nucleotide (SNP) has been found in various candidate genes, one of which is the leptin gene. Leptin is a gene that affects reproduction and cattle weight. Therefore, this research aims to identify SNP of the leptin gene (exon 3) in Crossbred cattle by comparison with GenBank data. A sample of Crossbred cattle was taken from Klaten in Central Java, Indonesia. Afterward, DNA sequencing results were analyzed with BioEdit to identify SNP. BioEdit software was used for DNA sequencing alignment part of intron 2, exon 3 and 3'UTR. The MEGA 11.1.1 program was used to analyze and edit the genetic distance and phylogenetic tree based on the SNP leptin gene. The result shows that nine variations of SNPs were found in exon 3. The phylogenetic tree shows that the Crossbred cattle, Bos taurus, Bos indicus, Hereford, Friesian Holstein and Bali, were in the same cluster. HindIII restriction enzyme can be recommended for genotyping Crossbred cattle using PCR RFLP. This research provides information on SNP in the leptin gene so that it can be used for further research on the association of the leptin gene to growth and reproduction.

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