scholarly journals Mitochondrial dna diversity of crossbanded barb Puntioplites bulu (Bleeker, 1851) from natural populations in peninsular Malaysia

2021 ◽  
Vol 4 ◽  
Author(s):  
Intan A Ghani ◽  
Adibah Abu Bakar ◽  
Arshad Aziz ◽  
Christianus Annie ◽  
Harmin Sharr ◽  
...  
Keyword(s):  
Selective Breeding ◽  
Habitat Degradation ◽  
Natural Populations ◽  
Peninsular Malaysia ◽  
Cyt B ◽  
Haplotype Sharing ◽  
High Demand ◽  
Migration Ability ◽  
Genetic Lineages ◽  
Base Study

Puntoplites bulu is a freshwater Cyprinidae and widely distributed in Southeast Asia. It has attracted considerable interest due to high demand and price. However, an apparent decline in its distribution and abundance is observed and this is due to several factors, such as habitat degradation, pollution, and overfishing. Intraspecific variation of P.bulu from three major rivers in Peninsular Malaysia were determined based on genetic divergence by using mtDNA Cyt b. Two distinct genetic lineages were apparent viz Central West and East Peninsular Malaysia with natural barriers (the Titiwangsa Range) acted as natural dividers between these two lineages. Alternatively, the close genetic relation and haplotype sharing that were observed between Perak and Kelantan populations could be due to human translocations. Further, haplotype sharing between Kelantan and Pahang populations revealed the migration ability of P. bulu through ancient connectivity. These findings provide an important base study for initiating a selective breeding program

scholarly journals Genome-wide shifts in climate-related variation underpin responses to selective breeding in a widespread conifer

2021 ◽  
Vol 118 (10) ◽  
pp. e2016900118
Author(s):  
Ian R. MacLachlan ◽  
Tegan K. McDonald ◽  
Brandon M. Lind ◽  
Loren H. Rieseberg ◽  
Sam Yeaman ◽  
...  
Keyword(s):  
Gene Flow ◽  
Selective Breeding ◽  
Natural Populations ◽  
Cold Injury ◽  
Nucleotide Polymorphisms ◽  
Phenotypic Differences ◽  
Climatic Regions ◽  
Breeding Populations ◽  
Trade Offs ◽  
Growth Initiation

Locally adapted temperate tree populations exhibit genetic trade-offs among climate-related traits that can be exacerbated by selective breeding and are challenging to manage under climate change. To inform climatically adaptive forest management, we investigated the genetic architecture and impacts of selective breeding on four climate-related traits in 105 natural and 20 selectively bred lodgepole pine populations from western Canada. Growth, cold injury, growth initiation, and growth cessation phenotypes were tested for associations with 18,600 single-nucleotide polymorphisms (SNPs) in natural populations to identify “positive effect alleles” (PEAs). The effects of artificial selection for faster growth on the frequency of PEAs associated with each trait were quantified in breeding populations from different climates. Substantial shifts in PEA proportions and frequencies were observed across many loci after two generations of selective breeding for height, and responses of phenology-associated PEAs differed strongly among climatic regions. Extensive genetic overlap was evident among traits. Alleles most strongly associated with greater height were often associated with greater cold injury and delayed phenology, although it is unclear whether potential trade-offs arose directly from pleiotropy or indirectly via genetic linkage. Modest variation in multilocus PEA frequencies among populations was associated with large phenotypic differences and strong climatic gradients, providing support for assisted gene flow polices. Relationships among genotypes, phenotypes, and climate in natural populations were maintained or strengthened by selective breeding. However, future adaptive phenotypes and assisted gene flow may be compromised if selective breeding further increases the PEA frequencies of SNPs involved in adaptive trade-offs among climate-related traits.

Cryptic Lineages and a Population Dammed to Incipient Extinction? Insights into the Genetic Structure of a Mekong River Catfish

2019 ◽  
Vol 110 (5) ◽  
pp. 535-547 ◽  
Author(s):  
Amanda S Ackiss ◽  
Binh T Dang ◽  
Christopher E Bird ◽  
Ellen E Biesack ◽  
Phen Chheng ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Natural Populations ◽  
Principal Component ◽  
Flood Pulse ◽  
Mekong River ◽  
Effective Population ◽  
Long Distance ◽  
Genetic Lineages ◽  
Low Genetic Diversity ◽  
Population Size Estimates

Abstract An understanding of the genetic composition of populations across management boundaries is vital to developing successful strategies for sustaining biodiversity and food resources. This is especially important in ecosystems where habitat fragmentation has altered baseline patterns of gene flow, dividing natural populations into smaller subpopulations and increasing potential loss of genetic variation through genetic drift. River systems can be highly fragmented by dams built for flow regulation and hydropower. We used reduced-representation sequencing to examine genomic patterns in an exploited catfish, Hemibagrus spilopterus, in a hotspot of biodiversity and hydropower development—the Mekong River basin. Our results revealed the presence of 2 highly divergent coexisting genetic lineages which may be cryptic species. Within the lineage with the greatest sample sizes, pairwise FST values, principal component analysis, and a STRUCTURE analysis all suggest that long-distance migration is not common across the Lower Mekong Basin, even in areas where flood-pulse hydrology has limited genetic divergence. In tributaries, effective population size estimates were at least an order of magnitude lower than in the Mekong mainstream indicating these populations may be more vulnerable to perturbations such as human-induced fragmentation. Fish isolated upstream of several dams in one tributary exhibited particularly low genetic diversity, high amounts of relatedness, and a level of inbreeding (GIS = 0.51) that has been associated with inbreeding depression in other outcrossing species. Our results highlight the importance of assessing genetic structure and diversity in riverine fisheries populations across proposed dam development sites for the preservation of these critically important resources.

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 Genetic diversity and structure of the narrow endemic Seseli farrenyi (Apiaceae): implications for translocation

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10521
Author(s):  
Núria Garcia-Jacas ◽  
Jèssica Requena ◽  
Sergi Massó ◽  
Roser Vilatersana ◽  
Cèsar Blanché ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Decline ◽  
Natural Populations ◽  
Ex Situ ◽  
Endemic Plant ◽  
Genetic Lineages ◽  
Narrow Endemic ◽  
Management Measures ◽  
Genetic Diversity And Structure ◽  
Nw Mediterranean

Seseli farrenyi (Apiaceae) is an extremely narrow endemic plant, which is considered as one of the species of most conservation concern in Catalonia (NW Mediterranean Basin). Given the accelerated fragmentation and reduction of population size (of over 90%), the environmental agency of Catalonia is currently preparing a recovery plan that includes reinforcements of the extant populations. The present study is aimed at providing the necessary knowledge to carry out genetically-informed translocations, by using microsatellites as genetic markers. Fourteen microsatellites have been specifically developed for S. farrenyi, of which nine have been used. Besides the extant natural populations, the three ex situ collections that are known to exist of this species have also been studied, as they would be the donor sources for translocation activities. Our main finding is that levels of genetic diversity in the natural populations of S. farrenyi are still high (He = 0.605), most likely as a result of a predominantly outcrossing mating system in combination with the limited time elapsed since the population decline. However, population fragmentation is showing the first genetic signs, as the values of genetic differentiation are relatively high, and two well-differentiated genetic lineages have been found even in such a narrow geographic range. These genetic results provide important information when designing conservation management measures.

scholarly journals Genetic Identification and Diversity of Stocks of The African Bonytongue, Heterotis Niloticus (Osteoglossiformes: Arapaiminae), in Nigeria, West Africa

2021 ◽  
Author(s):  
Tofunmi E. Oladimeji ◽  
Isabel C. Caballero ◽  
Mariana Mateos ◽  
Michael O. Awodiran ◽  
Kirk O. Winemiller ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
West Africa ◽  
Habitat Degradation ◽  
Natural Populations ◽  
Central Africa ◽  
Genetic Identification ◽  
Inland Fisheries ◽  
Genetic Patterns ◽  
Genetic Stocks ◽  
Kainji Lake

Abstract Inland fisheries are an important source of protein and income for people in Africa, and sustainable fisheries management requires knowledge of regional stocks. Presently, information regarding genetic diversity of African freshwater fishes is very limited. Here we present findings from a spatial analysis of genetic patterns in the African bonytongue, Heterotis niloticus, an important component of inland fisheries in West Africa. The species is common throughout Western and Central Africa and the Nile Basin; and has been introduced for aquaculture in locations across Africa. Nigeria has the largest fishery for African bonytongues, representing ~86% of the global total. Recent declines in yields at some Nigerian locations, however, suggest current levels of exploitation may be unsustainable. Habitat degradation also may be impacting some stocks. Despite its commercial and nutritional importance, the African bonytongue has been the subject of scant research to support management. We examined patterns of genetic diversity in natural populations of H. niloticus at four locations in Nigeria, including Kainji Lake, a reservoir on the Niger River in north-central Nigeria, and three southtern localities (Ethiope River, Igbokoda River, and Epe Lagoon), as well fish from the Ouémé River delta near Porto Novo, Benin. Eighty-five specimens were genotyped for nine microsatellite-loci. Genetic diversity estimates were highest at Kainji Lake, and substantially lower at southern localities. High levels of genetic differentiation were detected between samples from Kainji Lake and those from the southern localities. Low, yet significant FST values were observed among samples from southern Nigerian localities that were more differentiated from the sample from nearby coastal Benin. We thus recommend that African bonytongues from the five locations be considered distinct genetic stocks and managed accordingly.

Genetic investigations of laboratory stocks of the complex of Anopheles balabacensis Baisas (Diptera: Culicidae)

1985 ◽  
Vol 75 (2) ◽  
pp. 185-197 ◽  
Author(s):  
Jeffrey L. K. Hii
Keyword(s):  
Genetic Analysis ◽  
Reproductive Isolation ◽  
X Chromosome ◽  
Polytene Chromosomes ◽  
Natural Populations ◽  
Peninsular Malaysia ◽  
Distinct Population ◽  
Anopheles Dirus ◽  
Genetic Changes ◽  
Anopheles Balabacensis

AbstractExamination of the polytene chromosomes and cross-breeding data confirmed the specific status of Anopheles dirusPeyton & Harrison within the complex of A. balabacensis Baisas. The data also strongly suggested that A. dirus itself is a complex of at least two species, one of which, a hitherto unrecognized species, provisionally designated A. dirus species B, previously known as the Perlis form, occurs in northern Peninsular Malaysia. A distinct population from Thailand was designated A. dirus species A. The mosquitoes studied also include material from natural populations in Sabah, here provisionally designated A. balabacensis s.s., and may represent the first genetic analysis of this species. The Sabah material is distinct from either of the A. dirus forms. Hybrid males from crosses of A. balabacensis × A. dirus species A and of A. dirus species B females × A. dirus species A males were sterile. Chromosome studies also showed that reproductive isolation was accompanied by genetic changes in both the autosomesand X chromosome in the hybrid larvae.

Extinction risks and conservation status of Corybas (Orchidaceae; Orchidoideae; Diurideae) in Peninsular Malaysia

Phytotaxa ◽  
2015 ◽  
Vol 233 (3) ◽  
pp. 273 ◽  
Author(s):  
RUSEA GO ◽  
TAN MUI CHING ◽  
AHMAD AINNUDIN NURUDDIN ◽  
JANNA ONG ABDULLAH ◽  
NG YONG JIN ◽  
...  
Keyword(s):  
Climate Change ◽  
Temperature Rise ◽  
Conservation Status ◽  
Natural Populations ◽  
Peninsular Malaysia ◽  
Small Population ◽  
Highly Sensitive ◽  
In The Wild ◽  
Population Sizes ◽  
Herbarium Collections

Corybas is an elusive terrestrial orchid genus mostly inhabiting the high peaks in Peninsular Malaysia, which is the most vulnerable habitat to climate change. Nine species, of which seven are endemic, were studied based on natural populations, whereas information on another two was obtained from herbarium collections. Corybas caudatus was excluded from the study due to insufficient materials, and the type was not located. The species investigated were growing in small populations in the remaining moss-covered forests in the highlands. Human activities and temperature rise are two major threats to the wild populations. Our field observations revealed that Corybas species are good indicators of climate change as they are highly sensitive to temperature rise and drop in relative humidity. Judging from the current small number of specimens recollected, the small population sizes and degraded habitats where they grow, Corybas species in Peninsular Malaysia are all threatened by extinction in the wild.

scholarly journals Allozyme variation of the endemic and vulnerable Dyera lowii Hook.f. in Central Kalimantan: Implications for genetic resources conservation

2015 ◽  
Vol 19 (1) ◽  
pp. 79
Author(s):  
Tri Suwarni Wahyudiningsih ◽  
Mohammad Naiem ◽  
Sapto Indrioko ◽  
Issirep Sumardi
Keyword(s):  
Genetic Diversity ◽  
Natural Populations ◽  
Allozyme Variation ◽  
Peninsular Malaysia ◽  
Private Allele ◽  
Effective Management ◽  
High Genetic Diversity ◽  
Central Kalimantan ◽  
Habitat Conversion ◽  
Resources Conservation

Dyera lowii is an endemic and vulnerable tree species of commercial value as chewing gum found inpeat swamp forests, scatteredly distributed in Sumatra, Kalimantan, and Peninsular Malaysia. Their existenceis now under severe threat due to habitat conversion. This study is aimed to assess genetic diversity withinfour natural populations (Hampangen, Parahangan, Sebangau, Selat Nusa ) and one plantation in CentralKalimantan based on allozyme variation. Electrophoresis procedures were conducted with an isoelectricfocusing polyacrylamide slab gel system. The result showed high genetic diversity (HE=0.52) and gene fl ow(3.402) seemed to be effective. A total of 14 alleles were found among all the analysed population. Meannumber of alleles per locus (Aa) was 3.206, and the effective number of alleles per locus (Ae) was 2.21. Geneticdifferentiation between populations (FST) was signifi cant at the moderately level (0.0685). Most allozymevariation was found within population (93.2%). Special attention is essential to conserve a private allele ofGot-1-e (9%) at Selat Nusa population. Sebangau population missed the alleles of Est-2-b and Got-1-a, as foundin other populations. Selat Nusa population is expected to enhance the effective management for geneticresources conservation of this vulnerable species in the future.

Effects of hatchery shading and nest depth on the development and quality of Chelonia mydas hatchlings: implications for hatchery management in Peninsular, Malaysia

2005 ◽  
Vol 53 (3) ◽  
pp. 205 ◽  
Author(s):  
Jason van de Merwe ◽  
Kamarruddin Ibrahim ◽  
Joan Whittier
Keyword(s):  
Sex Ratio ◽  
Sex Ratios ◽  
Natural Populations ◽  
Chelonia Mydas ◽  
Condition Index ◽  
Peninsular Malaysia ◽  
Sex Characteristics ◽  
Poor Correlation ◽  
Emergence Success ◽  
Nest Depth

One of the decisions made by hatchery managers around the world is what degree of shading and nest depth are required to maximise the production of high-quality hatchlings at optimal sex ratios. The primary objectives of this study were to determine the effects of (1) hatchery shading and nest depth on nest temperatures and emergence lag, and (2) nest temperatures and nest depth on hatchling sex ratio and quality. In 2001, 26 Chelonia mydas clutches from Ma’Daerah beach, Terengganu, Malaysia, were relocated alternatively at depths of 50 cm and 75 cm into a 70%-shaded and a 100%-shaded hatchery. Data loggers were placed into the centre of each relocated clutch to record the temperature every hour over the course of incubation. When the hatchlings emerged, a sample of the clutch was run, measured and weighed and a separate sample was examined histologically for sex characteristics. Nest temperatures ranged between 28°C and 30°C and generally showed increases over the second half of incubation due to metabolic heating of the clutch. There was no significant correlation found between nest temperature and any of the hatchling parameters measured. Hatchlings from 75-cm-deep nests had a longer emergence lag (46.4 (±10.2) h) than hatchlings from 50-cm-deep nests. Hatch and emergence success were similar to those of natural populations and hatchling sex ratios were male dominant, with an average of 72% males. There was a poor correlation between mean middle-third incubation temperatures and sex ratio. Hatchlings from 75-cm-deep nests had similar running speeds but lower condition index than their conspecifics from 50-cm-deep nests.

scholarly journals Checklist of vascular plants of Klang Gates Quartz Ridge, Malaysia, a 14-km long quartz dyke

PhytoKeys ◽  
2020 ◽  
Vol 166 ◽  
pp. 57-77
Author(s):  
Ruth Kiew ◽  
Lim Chung-Lu
Keyword(s):  
Vascular Plants ◽  
Habitat Degradation ◽  
Rocky Mountain ◽  
Peninsular Malaysia ◽  
Tree Canopy ◽  
World Heritage Site ◽  
Unesco World Heritage Site ◽  
Plant Area ◽  
Baeckea Frutescens ◽  
Threatened Habitat

The Klang Gates Quartz Ridge (KGQR) is proposed for protection as National Heritage and as a UNESCO World Heritage Site because of its spectacular size, exceptional beauty and significant biodiversity. The checklist of vascular plants documents 314 species that comprise a unique combination that grows on lowland quartz and that is distinct from the surrounding lowland equatorial rain forest by the absence of orchids, palms, gingers and tree canopy families. The Rubiaceae, Gramineae, Moraceae, Apocynaceae, Melastomataceae and Polypodiaceae are the most speciose families. The summit vegetation at 200–400 m elevation is dominated by Baeckea frutescens (Myrtaceae) and Rhodoleia championii (Hamamelidaceae) and shows similarities to the plant community on rocky mountain peaks above 1500 m. About 11% of its species are endemic in Peninsular Malaysia and four are endemic to KGQR: Aleisanthia rupestris (Rubiaceae), Codonoboea primulina (Gesneriaceae), Spermacoce pilulifera (Rubiaceae), and Ilex praetermissa (Aquifoliaceae). All four are provisionally assessed as Critically Endangered. Two, Eulalia milsumi (Gramineae) and Sonerila prostrata (Melastomataceae), are endemic to KGQR and a few neighbouring smaller quartz dykes. They are assessed as Endangered. The KGQR is a fragile habitat and conservation management is urgently required to halt the spread of the aggressive alien grass, Pennisetum polystachion and to prevent further habitat degradation from visitors. Based on KGQR being a threatened habitat, its biodiverse flora, and endangered species, it qualifies as an Important Plant Area.

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