scholarly journals Taxonomic and genetic assessment of captive White-Handed Gibbons (Hylobates lar) in Peninsular Malaysia with implications towards conservation translocation and reintroduction programmes

ZooKeys ◽  
2021 ◽  
Vol 1076 ◽  
pp. 25-41
Author(s):  
Millawati Gani ◽  
Jeffrine J. Rovie-Ryan ◽  
Frankie Thomas Sitam ◽  
Noor Azleen Mohd Kulaimi ◽  
Chew Cheah Zheng ◽  
...  
Keyword(s):  
Control Region ◽  
Phylogenetic Trees ◽  
Peninsular Malaysia ◽  
Hylobates Lar ◽  
Northern Population ◽  
Complete Control ◽  
Network Methods ◽  
Region Segment ◽  
Genetic Assessment ◽  
Two Populations

Conservation translocation and reintroduction for the purpose of repopulating and reinforcing extirpated or depleted populations has been recognised as an important conservation tool, particularly for gibbon conservation in the immediate future. Feasibility assessments involving multiple factors, including taxonomic and genetic assessment of rescued and captive gibbons, are imperative prior to translocation and reintroduction programmes. In this study, we attempt to determine the subspecies and origin of captive Hylobates lar, White-handed gibbons, from Peninsular Malaysia to assist in future translocation and reintroduction programmes. A total of 12 captive and rescued H. lar samples were analysed using the control region segment of mitochondrial DNA. Sequence analyses and phylogenetic trees constructed using neighbour-joining, maximum likelihood, Bayesian inference, and network methods congruently differentiate all 12 captive individuals used in this study from other H. lar subspecies suggesting that these individuals belong to the H. lar lar subspecies. In addition, two populations of H. l. lar were observed: (1) a southern population consisting of all 12 individuals from Peninsular Malaysia, and (2) a possible northern population represented by three individuals (from previous studies), which might have originated from the region between the Isthmus of Kra, Surat Thani-Krabi depression, and Kangar-Pattani. Our findings suggest that the complete control region segment can be used to determine the subspecies and origin of captive H. lar.

scholarly journals Why TKI Therapy Targeting Minority Population of Tumor Cells Could Achieve Complete Control of Entire Tumor: The Self-Driven and Non-Autonomous Replication in Cancer and Their Connection through Inflammation

2020 ◽  
Vol 5 (3) ◽  
Keyword(s):  
Tumor Cells ◽  
Kinase Inhibitors ◽  
Extended Period ◽  
Target Population ◽  
Minority Population ◽  
Complete Control ◽  
Therapy Efficacy ◽  
The Common ◽  
Two Populations ◽  
Cancer Clinic

Despite wide application of targeted therapy with small molecule tyrosine kinase inhibitors (TKI) in cancer clinic, some questions for the mechanisms of these inhibitors remain unresolved. For example, how can a tumor be completely controlled for extended period (more than a year) by the drug when the target population in the tumor is not even in majority? Here we report our observations in one such case of lung cancer and provide explanation for this long-awaited clinical puzzle. Our analyses indicate that in many of the similar cases, the cancer is composed of two populations of tumor cells, one capable of autonomous (or self-driven) replication through the known mutation, and the replication of the other is inflammationdependent. The connection is through inflammation induced by the tumor cells capable of self-driven replication. The control of this population by TKI terminates induction of inflammation thus results in control of the non-autonomous population. The identification of these two replicating tumor cells and their relationship holds many answers to current clinical confusions in many cancer cases where accelerated tumor progression, high inflammation and loss of therapy efficacy are often the common feature. By understanding these processes, we can begin to manage cancer in a more proactive manner to avoid the once recognized unavoidable fate of cancer

scholarly journals Male parental investment reflects the level of partner contributions and brood value in tree swallows

2017 ◽  
Author(s):  
Ádám Z. Lendvai ◽  
Çağlar Akçay ◽  
Mark Stanback ◽  
Mark F. Haussmann ◽  
Ignacio T. Moore ◽  
...  
Keyword(s):  
Parental Care ◽  
Interesting Case ◽  
Temporary Increase ◽  
Southern Population ◽  
Tree Swallows ◽  
Parental Effort ◽  
Northern Population ◽  
Nestling Begging ◽  
Two Populations ◽  
Partial Compensation

AbstractBiparental care presents an interesting case of cooperation and conflict between unrelated individuals. Several models have been proposed to explain how parents should respond to changes in each other’s parental care to maximize their own fitness, predicting no change, partial compensation, or matching effort as a response. Here, we present an experiment in tree swallows (Tachycineta bicolor) in which we increased the parental care of females by presenting them, but not their mates, with additional nestling begging calls using automated playbacks. We performed this experiment in two populations differing in future breeding opportunities and thus the intensity of conflict over current parental care. We found that in response to a temporary increase in female parental effort, males in the northern population with lower sexual conflict matched the increased effort, whereas males in the southern population did not. We also found that increases in parental care during playbacks were driven by the females (i.e., females initiated the increased effort and their mates followed them) in the northern population but not the southern population. These results support the idea that with incomplete information about the brood value and need, cues or signals from the partner might become important in coordinating parental care.

scholarly journals Structure and Evolution of the Mitochondrial DNA Complete Control Region in the Lizard Lacerta dugesii (Lacertidae, Sauria)

2003 ◽  
Vol 56 (1) ◽  
pp. 46-53 ◽  
Author(s):  
António Brehm ◽  
D. James Harris ◽  
Cíntia Alves ◽  
José Jesus ◽  
Fabienne Thomarat ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Control Region ◽  
Complete Control

scholarly journals Phylogenetic Analysis of Mitochondrial Genes of Malaysian Tupaia Reveals Composite Species in Tupaia Glis

2021 ◽  
Vol 3 (1) ◽  
pp. 197-203
Author(s):  
Jayaraj Vijaya Kumaran ◽  
Ahmad Sofiman Othman ◽  
Shahrul-Anuar Mohd Sah ◽  
Seri Intan Mokhtar
Keyword(s):  
Phylogenetic Analysis ◽  
Mitochondrial Dna ◽  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Mitochondrial Genes ◽  
Peninsular Malaysia ◽  
Universal Primers ◽  
Cyt B ◽  
Southern Thailand ◽  
Tupaia Glis

Recent morphometric analysis on T. glis in Peninsular Malaysia indicates that there were more than one morphotypes in this species. Thus this study attempts to examine this phenomenon using mitochondrial DNA sequences of Cyt b and CO1 genes. A total of 74 DNA sequences for both genes were generated using available universal primers. Samples from Southern Thailand were found to be misidentified as T. glis when in fact these samples clustered with T. belangeri while one T. tana from Borneo was miss-identified as T. minor. The phylogenetic trees showed that there are at least one confirmed morphotype of Tupaia (new Tupaia sp.) that have yet to be described. The results also showed that the separation of T. glis morphotype 1 and 11 were visible in the combined genes tree, congruent with the morphometric phylogeny but had poor phylogenetic support.

scholarly journals Notes on the leaf insects of the genus Phyllium of Sumatra and Java, Indonesia, including the description of two new species with purple coxae (Phasmatodea, Phylliidae)

ZooKeys ◽  
2020 ◽  
Vol 913 ◽  
pp. 89-126 ◽  
Author(s):  
Royce T. Cumming ◽  
Sarah Bank ◽  
Stephane Le Tirant ◽  
Sven Bradler
Keyword(s):  
Cryptic Species ◽  
Morphological Difference ◽  
Nuclear Gene ◽  
Molecular Data ◽  
Mitochondrial Genes ◽  
Peninsular Malaysia ◽  
The Other ◽  
Two New Species ◽  
First Time ◽  
Two Populations

Within the last two years, the leaf insects of the genus Phyllium of both the islands of Java and Sumatra have been reviewed extensively based on morphological observations. However, cryptic species which cannot be differentiated morphologically may be present among the various populations. Since it has frequently been demonstrated that analyses based on molecular data can bring clarity in such cases, we conducted a phylogenetic analysis based on three genes (nuclear gene 28S and mitochondrial genes COI and 16S) from the Phyllium species of these islands. The results show distinct molecular divergence for several populations and suggest the presence of two new cryptic species, morphologically inseparable from Phyllium hausleithneri Brock, 1999. From Sumatra, the population originally thought to be a range expansion for Phyllium hausleithneri, is now here described as Phyllium nisussp. nov., with the only consistent morphological difference being the color of the eggs between the two populations (dark brown in P. hausleithneri and tan in P. nisussp. nov.). Further, an additional population with purple coxae from Java was morphologically examined and found to have no consistent features to separate it morphologically from the other purple coxae species. This cryptic species from Java was however shown to be molecularly distinct from the other purple coxae populations from Sumatra and Peninsular Malaysia and is here described as Phyllium gardabagusisp. nov. In addition, Phyllium giganteum is here officially reported from Java for the first time based on both historic and modern records of male specimens.

scholarly journals Complete mitochondrial genomes of five raptors and implications for the phylogenetic relationships between owls and nightjars

2019 ◽  
Author(s):  
Gang Liu ◽  
Lizhi Zhou ◽  
Guanghong Zhao
Keyword(s):  
Control Region ◽  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Stop Codon ◽  
Mitochondrial Genomes ◽  
Closely Related Species ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Independent Families ◽  
Complete Mitochondrial Genomes

The phylogenetic relationships between owls and nightjars are rather complex and controversial. To clarify these relationships, we determined the complete mitochondrial genomes of Glaucidium cuculoides, Otus scops, Glaucidium brodiei, Caprimulgus indicus, and Strix leptogrammica, and estimated phylogenetic trees based on the complete mitochondrial genomes and aligned sequences from closely related species that were obtained in GenBank. The complete mitochondrial genomes were 17392, 17317, 17549, 17536, and 16307 bp in length. All mitochondrial genomes contained 13 protein-coding genes, two rRNAs, 22 tRNAs, and a putative control region. All mitochondrial genomes except for that of Strix leptogrammica contained a pseudo-control region. ATG, GTG, and ATA are generally start codons, whereas TAA is the most frequent stop codon. All tRNAs in the new mtDNAs could be folded into canonical cloverleaf secondary structures except for tRNASer (AGY) and tRNALeu (CUN) , which missing the “DHU” arm. The phylogenetic relationships demonstrated that Strigiformes and Caprimulgiformes are independent orders, and Aegothelidae is a family within Caprimulgiformes. The results also revealed that Accipitriformes is an independent order, and Pandionidae and Sagittariidae are independent families. The results also supported that Apodiformes is polyphyletic, and hummingbirds (family Trochilidae) belong to Apodiformes. Piciformes was most distantly related to all other analyzed orders.

scholarly journals Genetic variations among selected wild Asian elephant populations in Peninsular Malaysia based on mitochondrial D-loop region DNA sequences

2019 ◽  
Vol 20 (9) ◽  
Author(s):  
KAYAL VIZI KARUPPANNAN ◽  
NOR AIFAT RAHMAN ◽  
KHAIRUL AMIRIN MOHAMED ◽  
NURUL FARAH DIYANA AHMAD TAHIR ◽  
FATIN MARDHIAH NORDIN ◽  
...  
Keyword(s):  
National Parks ◽  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Haplotype Diversity ◽  
Mitochondrial Control Region ◽  
Genetic Variations ◽  
Peninsular Malaysia ◽  
Asian Elephant ◽  
Loop Region ◽  
D Loop

Abstract. Karuppannan KV, Aifat NR, Mohamed KA,  Ahmad-Tahir NFD,  Nordin FM, Yaakop S, Maldonado JE, Md-Zain BM. 2019. Genetic variations among selected wild Asian elephant populations in Peninsular Malaysia based on mitochondrial D-loop region DNA sequences. Biodiversitas 20: 2494-2502. Asian elephant (Elephas maximus) is an important large mammal in Peninsular Malaysia and is completely protected by the Wildlife Conservation Act 2010 (Act 716). The conservation of this species requires strong information-based research, such as genetic evaluations. The aim of this study was to compare mitochondrial control region variation among selected elephants from the Taman Negara National Parks (TNNP) population with other selected populations in Peninsular Malaysia. DNA materials were extracted from fecal samples and amplified using partial mitochondrial D-loop region. Total 13 haplotypes with haplotype diversity (Hd) of 0.7524 were observed. A total of 34 base pair (bp) segregation sites were formed in 547 bp sequences. Both phylogenetic trees showed that a few individual elephants from the TNNP formed a clade together with individuals from other populations. The remaining individual elephants from TNNP formed a monophyletic clade supported by a high bootstrap value. Low genetic distance was detected among the tested populations, which proved that both individuals from the TNNP and other selected populations have similar genetic patterns. High gene flow among tested populations would impact on fitness and long-term resilience of the populations. This highly significant outcome provides strong baseline data for Department of Wildlife and National Parks (DWNP) in monitoring elephant populations in order to reduce number of human-elephant conflicts which indirectly minimize translocating conflict elephants to TNNP.

scholarly journals Low Genetic Diversity in Turkish Populations of Wels Catfish Silurus glanis L., 1758 (Siluridae, Pisces) Revealed by Mitochondrial Control Region Sequences

2020 ◽  
Vol 20 (10) ◽  
pp. 767-776
Author(s):  
Yusuf Bektas ◽  
Ismail Aksu ◽  
Gokhan Kalayci ◽  
Davut Turan
Keyword(s):  
Genetic Diversity ◽  
Control Region ◽  
Mismatch Distribution ◽  
Phylogenetic Trees ◽  
Goodness Of Fit ◽  
Haplotype Diversity ◽  
Mitochondrial Control Region ◽  
Haplotype Network ◽  
Silurus Glanis ◽  
Low Genetic Diversity

This study aimed to investigate the genetic diversity and population structure of Wels catfish Silurus glanis L. 1758 in Turkey using squences of the mitochondrial DNA control region The 887-bp fragment of D-loop was aligned for 112 S. glanis individuals from ten wild populations in Turkey, defined by 29 polymorphic sites comprising 16 haplotypes. The low haplotype diversity and nucleotide diversity within each population ranged from 0.000 to 0.378 and from 0.0000 to 0.0045, respectively. Analysis of molecular variance showed significant genetic differentiation among ten populations (FST =0.940; P<0.01). AMOVA revealed that the most of genetic variation was found between Thrace and Anatolia clades (74,07 %). The phylogenetic trees and haplotype network topologies were consistent with the results of AMOVA analysis. The non-significant negative Tajima's D (-0.875 P<0.05) and Fu's Fs (-0.381, P<0.02) values and mismatch distribution for S. glanis populations indicated no evidence for changes in population size. Furthermore, goodness-of-fit of the observed versus the theoretical mismatch distribution tested the sum of squared deviation (SSD; 0.00308, P>0.05), Harpending’s raggedness index (Hri; 0,300, P>0.05) and Ramos-Onsins & Rozas (R2; 0,0771, P>0.05), supporting population neutrality.

Population genetic structure of long-tailed pygmy rice rats (Oligoryzomys longicaudatus) from Argentina and Chile based on the mitochondrial control region

2010 ◽  
Vol 88 (1) ◽  
pp. 23-35 ◽  
Author(s):  
Raúl E. González-Ittig ◽  
Hernán J. Rossi-Fraire ◽  
Gustavo E. Cantoni ◽  
Eduardo R. Herrero ◽  
Rosendo Benedetti ◽  
...  
Keyword(s):  
Gene Flow ◽  
Genetic Structure ◽  
Control Region ◽  
Phylogenetic Trees ◽  
Mitochondrial Control Region ◽  
The Andes ◽  
Single Clade ◽  
The Last Glacial Maximum ◽  
Oligoryzomys Longicaudatus ◽  
The Last Glacial

The rodent Oligoryzomys longicaudatus (Bennett, 1832) (Rodentia, Cricetidae) inhabits southern forests of Argentina and Chile, a region severely affected by glaciations during the Pleistocene–Holocene periods. We evaluate here the diversity of the mitochondrial control region to characterize the genetic structure of this species from forests and bushy areas of seven populations from Argentina and four populations from Chile. Statistical analyses showed shallow haplotype trees and mismatch distributions compatible with recent range expansions. The presence of “private” haplotypes indicates that current levels of gene flow among populations of each country would be low to moderate. Significant differences in haplotype frequencies were detected between eastern and western populations, indicating that the Andes mountains would be an effective geographic barrier for gene flow despite the existing valleys that could act as corridors for dispersion. A single clade containing all the haplotypes was recovered in the phylogenetic trees, suggesting postglacial dispersion from a single refugium during the Last Glacial Maximum. The higher effective size and levels of polymorphism in populations from Chile suggest that the refugium was located in this country. The asymmetric gene flow from Chile to Argentina may reflect a recent colonization of the eastern populations.

scholarly journals Complete mitochondrial genomes of five raptors and implications for the phylogenetic relationships between owls and nightjars

2019 ◽  
Author(s):  
Gang Liu ◽  
Lizhi Zhou ◽  
Guanghong Zhao
Keyword(s):  
Control Region ◽  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Stop Codon ◽  
Mitochondrial Genomes ◽  
Closely Related Species ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Independent Families ◽  
Complete Mitochondrial Genomes

The phylogenetic relationships between owls and nightjars are rather complex and controversial. To clarify these relationships, we determined the complete mitochondrial genomes of Glaucidium cuculoides, Otus scops, Glaucidium brodiei, Caprimulgus indicus, and Strix leptogrammica, and estimated phylogenetic trees based on the complete mitochondrial genomes and aligned sequences from closely related species that were obtained in GenBank. The complete mitochondrial genomes were 17392, 17317, 17549, 17536, and 16307 bp in length. All mitochondrial genomes contained 13 protein-coding genes, two rRNAs, 22 tRNAs, and a putative control region. All mitochondrial genomes except for that of Strix leptogrammica contained a pseudo-control region. ATG, GTG, and ATA are generally start codons, whereas TAA is the most frequent stop codon. All tRNAs in the new mtDNAs could be folded into canonical cloverleaf secondary structures except for tRNASer (AGY) and tRNALeu (CUN) , which missing the “DHU” arm. The phylogenetic relationships demonstrated that Strigiformes and Caprimulgiformes are independent orders, and Aegothelidae is a family within Caprimulgiformes. The results also revealed that Accipitriformes is an independent order, and Pandionidae and Sagittariidae are independent families. The results also supported that Apodiformes is polyphyletic, and hummingbirds (family Trochilidae) belong to Apodiformes. Piciformes was most distantly related to all other analyzed orders.

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