Short Communication: Strong genetic differentiation of the endemic rosin-producing tree Styrax sumatrana (Styracaceae) in North Sumatra, Indonesia

Rachmat HH, Susilowati A, Elfiati D, Hartini KS, Faradillah WN. 2017. Short Communication: Strong genetic differentiation of the endemic rosin-producing tree Styrax sumatrana (Styracaceae) in North Sumatra, Indonesia. Biodiversitas 18: 1331-1335. Styrax sumatrana is an economically important rosin-producing tree endemic to North Sumatra, Indonesia. Distribution of this species is very limited, and the high rate of forest degradation in Sumatra is increasing the necessity for conservation. To quantify genetic variation and population structuring, we collected individuals from 3 populations namely Pakpak Bharat, Humbang Hasundutan (Humbahas) and Tapanuli Utara in which each of the population was represented by 10 individuals. However, the successful rate of amplification was varied among populations and for later analysis, we only took an account those sequences showing clear electropherograms and disposed those which showed ambiguity. We sequenced trnL-trnF chloroplast DNA (cpDNA) region yielded 941 bp after alignment. The trnL-trnF assigned the species into 4 haplotypes in which Pakpak Bharat was differentiated significantly and not shared any similar haplotypes with two others populations. Humbahas and Tapanuli Utara was shared one common haplotype. Mean nucleotide diversity at silent sites ranged 0 - 3.33 x 10-3, while nucleotide diversity at non-synonymous site ranged 0 - 5.9 x 10-4. Strong genetic differentiation was also found among 3 origin populations, with the highest pairwise genetic differentiation found on Pakpak Bharat and Tapanuli Utara (FST= 0.80952). Clear and apparent genetic structuring was possibly caused by geographical barriers such as highland and mountain ranges (Bukit Barisan mountain ranges) which acted as effective barriers to gene flow among population. The findings suggest that conservation efforts should focus on every population because each of the population maintains distinct genetic identity.

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Genetic melting pot and importance of long-distance dispersal indicated in the Gladiolus imbricatus L. populations in the Polish Carpathians

Scientific Reports ◽

10.1038/s41598-021-96135-8 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Agnieszka Sutkowska ◽

Józef Mitka ◽

Tomasz Warzecha ◽

Jakub Bunk ◽

Julia Rutkowska ◽

...

Keyword(s):

Genetic Diversity ◽

Diversity Indices ◽

Western Carpathians ◽

Genetic Structuring ◽

Long Distance ◽

Plant Populations ◽

Genetic Stock ◽

Melting Pot ◽

Mountain Ranges ◽

Eastern Carpathians

AbstractThe genetic diversity in 11 populations of Gladiolus imbricatus in five mountain ranges, including the Tatra, Pieniny, Gorce, Beskid Niski (Western Carpathians) and Bieszczady Mts (Eastern Carpathians), was studied with inter-simple sequence repeat (ISSR) markers. The species is a perennial plant occurring in open and semi-open sites of anthropogenic origin (meadows and forest margins). We checked a hypothesis on the microrefugial character of the plant populations in the Pieniny Mts, a small calcareous Carpathian range of complicated relief that has never been glaciated. Plant populations in the Tatra and Pieniny Mts had the highest genetic diversity indices, pointing to their long-term persistence. The refugial vs. the non-refugial mountain ranges accounted for a relatively high value of total genetic variation [analysis of molecular variance (AMOVA), 14.12%, p = 0.003]. One of the Pieniny populations was of hybridogenous origin and shared genetic stock with the Tatra population, indicating there is a local genetic melting pot. A weak genetic structuring of populations among particular regions was found (AMOVA, 4.5%, p > 0.05). This could be an effect of the frequent short-distance and sporadic long-distance gene flow. The dispersal of diaspores between the remote populations in the Western Carpathians and Eastern Carpathians could be affected by the historical transportation of flocks of sheep from the Tatra to Bieszczady Mts.

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Population structuring of the endemic black-cheeked gnateater, Conopophaga melanops melanops (Vieillot, 1818) (Aves, Conopophagidae), in the Brazilian Atlantic Forest

Brazilian Journal of Biology ◽

10.1590/s1519-69842007000500009 ◽

2007 ◽

Vol 67 (4 suppl) ◽

pp. 867-872 ◽

Cited By ~ 2

Author(s):

VO. Lunardi ◽

MR. Francisco ◽

PM. Galetti Jr.

Keyword(s):

Genetic Differentiation ◽

Atlantic Forest ◽

Rapd Markers ◽

Nonparametric Test ◽

Brazilian Atlantic Forest ◽

Randomly Amplified Polymorphic Dna ◽

Molecular Variance ◽

Local Populations ◽

Population Structuring ◽

Significant Genetic Divergence

Randomly amplified polymorphic DNA (RAPD) markers were used to analyze genetic differentiation among three populations of the endemic Black-cheeked Gnateater (Conopophaga melanops melanops) within a larger pristine reminiscent of the Brazilian Atlantic Forest. Analyses of molecular variance (AMOVA) (phiST = 0.13149, P < 0.0001) and the nonparametric test for homogeneity of the molecular variance (HOMOVA) (B = 0.32337; P = 0.0019) showed a statistically significant genetic divergence among the three Black-cheeked Gnateater populations in a continuous transect of 250 km. Some hypothetic explanations for these results are the sedentary nature of the species and the historical isolation of the populations in refuges during the Pleistocene. The present results suggest that the local populations were naturally differentiated along the entire original range before the recent process of massive deforestation.

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Elucidating the drivers of genetic differentiation in Malaysian torrent frogs (Anura: Ranidae: Amolops): a landscape genomics approach

Zoological Journal of the Linnean Society ◽

10.1093/zoolinnean/zlz151 ◽

2019 ◽

Vol 190 (1) ◽

pp. 65-78 ◽

Cited By ~ 2

Author(s):

Kin Onn Chan ◽

Rafe M Brown

Keyword(s):

Genetic Variation ◽

Gene Flow ◽

Genetic Differentiation ◽

Isolation By Distance ◽

Variance Partitioning ◽

Nucleotide Polymorphisms ◽

Landscape Genomics ◽

Mountain Ranges ◽

Historical Factors ◽

Environmental Attributes

Abstract The interplay between environmental attributes and evolutionary processes can provide valuable insights into how biodiversity is generated, partitioned and distributed. This study investigates the role of spatial, environmental and historical factors that could potentially drive diversification and shape genetic variation in Malaysian torrent frogs. Torrent frogs are ecologically conserved, and we hypothesize that this could impose tight constraints on dispersal routes, gene flow and consequently genetic structure. Moreover, levels of gene flow were shown to vary among populations from separate mountain ranges, indicating that genetic differentiation could be influenced by landscape features. Using genome-wide single nucleotide polymorphisms, in conjunction with landscape variables derived from Geographic Information Systems, we performed distance-based redundancy analyses and variance partitioning to disentangle the effects of isolation-by-distance (IBD), isolation-by-resistance (IBR) and isolation-by-colonization (IBC). Our results demonstrated that IBR contributed minimally to genetic variation. Intraspecific population structure can be largely attributed to IBD, whereas interspecific diversification was primarily driven by IBC. We also detected two distinct population bottlenecks, indicating that speciation events were likely driven by vicariance or founder events.

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Lack of Genetic Structuring among Tropical Brazilian Wood Stork Populations and Low Genetic Differentiation from North American Populations

Biotropica ◽

10.1111/j.1744-7429.2004.tb00316.x ◽

2004 ◽

Vol 36 (2) ◽

pp. 248-258 ◽

Cited By ~ 1

Author(s):

Cristiano Dosualdo Rocha ◽

Silvia Nassif Lama ◽

Luciana Correia de Almeida Regitano

Keyword(s):

Genetic Differentiation ◽

North American ◽

Genetic Structuring ◽

Wood Stork

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Diet breadth and its relationship with genetic diversity and differentiation: the case of southern beech aphids (Hemiptera: Aphididae)

Bulletin of Entomological Research ◽

10.1079/ber2004298 ◽

2004 ◽

Vol 94 (3) ◽

pp. 219-227 ◽

Cited By ~ 14

Author(s):

C. Gaete-Eastman ◽

C.C. Figueroa ◽

R. Olivares-Donoso ◽

H.M. Niemeyer ◽

C.C. Ramírez

Keyword(s):

Genetic Diversity ◽

Genetic Differentiation ◽

Diet Breadth ◽

Aphid Species ◽

Insect Species ◽

Herbivorous Insect ◽

Genetic Structuring ◽

Closely Related Species ◽

Single Host ◽

Southern Beech

AbstractHerbivorous insect species with narrow diet breadth are expected to be more prone to genetic differentiation than insect species with a wider diet breadth. However, a generalist can behave as a local specialist if a single host-plant species is locally available, while a specialist can eventually behave as a generalist if its preferred host is not available. These problems can be addressed by comparing closely related species differing in diet breadth with overlapping distributions of insect and host populations. In this work, diet breadth, genetic diversity and population differentiation of congeneric aphid species from southern beech forests in Chile were compared. While at the species level no major differences in genetic diversity were found, a general trend towards higher genetic diversity as diet breadth increased was apparent. The aphid species with wider diet breadth, Neuquenaphis edwardsi (Laing), showed the highest genetic diversity, while the specialist Neuquenaphis staryi Quednau & Remaudière showed the lowest. These differences were less distinct when the comparisons were made in the same locality and over the same host. Comparison of allopatric populations indicates that genetic differentiation was higher for the specialists, Neuquenaphis similis Hille Ris Lambers and N. staryi, than for the generalist N. edwardsi. Over the same host at different locations, genetic differentiation among populations of N. edwardsi was higher than among populations of N. similis. The results support the assumption that specialists should show more pronounced genetic structuring than generalists, although the geographical distribution of host plants may be playing an important role.

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Development and application of 14 microsatellite markers in the burying beetle Nicrophorus vespilloides reveals population genetic differentiation at local spatial scales

PeerJ ◽

10.7717/peerj.3278 ◽

2017 ◽

Vol 5 ◽

pp. e3278 ◽

Cited By ~ 7

Author(s):

Sonia Pascoal ◽

Rebecca M. Kilner

Keyword(s):

Genetic Differentiation ◽

Microsatellite Markers ◽

Parental Care ◽

Social Evolution ◽

Spatial Scales ◽

Burying Beetle ◽

Genetic Structuring ◽

Population Genetic Differentiation ◽

Nicrophorus Vespilloides ◽

Limited Dispersal

Burying beetles (genus Nicrophorus) are relatively rare among insects in providing sophisticated parental care. Consequently, they have become model species in research analysing social evolution, the evolution of parental care and mating systems. We used the recently published N. vespilloides genome and transcriptome to develop microsatellite markers. Specifically, we developed 14 polymorphic markers with five to 13 alleles per locus and used them to investigate levels of genetic differentiation in four south Cambridgeshire (UK) populations of N. vespilloides, separated by 21 km at most. The markers revealed significant genetic structuring among populations (global FST = 0.023) with all but one of the pairwise comparisons among populations being significant. The single exception was the comparison between the two closest populations, which are approximately 2.5 km apart. In general, the microsatellite markers showed lower observed heterozygosity than expected. We infer that there is limited dispersal between populations and potentially also some inbreeding within them and suggest that this may be due to habitat fragmentation. We discuss these results in the context of recent laboratory experiments on inbreeding and beetle flight.

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Short Communication: The mitochondrial cytochrome c oxidase subunit I (COI) for identification of batoids collected from landed sites in Medan, Indonesia

Biodiversitas Journal of Biological Diversity ◽

10.13057/biodiv/d211149 ◽

2020 ◽

Vol 21 (11) ◽

Author(s):

MUFTI SUDIBYO ◽

Khairiza Lubis ◽

ACHMAD FARAJALLAH ◽

NISFA HANIM

Keyword(s):

Cytochrome C ◽

Cytochrome C Oxidase ◽

Short Communication ◽

East Coast ◽

Morphological Trait ◽

Coi Gene ◽

Mitochondrial Cytochrome ◽

Landing Sites ◽

Dna Fragment ◽

North Sumatra

Abstract. Lubis K, Sudibyo M, Farajallah A, Hanim N. 2020. Short Communication: The mitochondrial cytochrome c oxidase subunit I (COI) for identification of batoids collected from landing sites in Medan, Indonesia. Biodiversitas 21: 5414-5421. Batoids are member of Elsamoranch subclass which consist of many species. Most of batoids species are overexploited, especially in Medan Indonesia. Up to presents, the information about diversity of rays on the east coast of North Sumatra, Indonesia was very limited. Therefore, this research aimed to investigate the diversity of rays on the east coast of North Sumatra. We examined the morphological trait of 82 individuals of batoid from three landing sites on the east coast of North Sumatra, namely: Tanjung Balai, Belawan, and Percut, then identify its species based on determination key. After that, we collected pectoral muscle tissue from an individual in each species which successfully identified to extract its genomic DNA. Molecular based identification was carried out by using DNA fragment form COI gene. The successfully amplificated COI gene DNA fragment then was sequenced and analyzed. Based on morphological trait, we successfully identifying nine species of batoid, which is Maculabatis gerrardi, Gymnura poecilura, Dasyatis zugei, Brevitrygon heterura, Neotrygon kuhlii, Hemitrygon bennettii, Rhinobatos jimbaranensis, Rhinoptera javanica, and Taeniura lymma. The result of identification based on COI gene DNA fragment was in congruent with morphological-based identification based on data BLAST-N and genetic distance value within same species. The nucleotide diversity within same species ranged from 0-15 nucleotide variants.

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GENETIC DIFFERENTIATION AMONG POPULATIONS OF Chromobotia macracanthus BLEEKER FROM SUMATRA AND KALIMANTAN BASED ON SEQUENCING GENE OF MTDNA CYTOCHROME B AND NUCLEUS DNA RAG2

Indonesian Aquaculture Journal ◽

10.15578/iaj.3.2.2008.107-117 ◽

2008 ◽

Vol 3 (2) ◽

pp. 107 ◽

Cited By ~ 1

Author(s):

Sudarto Sudarto ◽

Kafi Hidonis ◽

Emmanuel Paradis

Keyword(s):

Genetic Differentiation ◽

Genetic Distance ◽

Cytochrome B ◽

Nucleotide Diversity ◽

Population Group ◽

Fish Population ◽

Neighbor Joining ◽

R Language ◽

Estimation Of Time ◽

Two Populations

Research on genetic differentiation among populations of Chromobotia macracanthus Bleeker from Sumatra, based on sequencing gene of mtDNA Cytochrome b and nucleus DNA RAG2 has been done. The objectives of the study were to obtain the representation of genetic differentiation among population of clown loach fishes or botia (Chromobotia macracanthus) from Sumatra and Kalimantan and to estimate the time divergence of both population group of botia. Samples of botia population were taken from 3 rivers in Sumatra namely Batanghari, Musi, and Tulang Bawang and one river from Kalimantan namely Kapuas. The genetic analysis was based on the sequencing of mtDNA Cytochrome b and nucleus DNA RAG2. The statistical analysis was done by using APE package on R language. The parameters observed were: nucleotide diversity, genetic distance, and neighbor-joining tree. The result showed that the highest nucleotide diversity was fish population of Musi, while the other two populations, Tulang Bawang (Sumatra) and Kapuas (Kalimantan), were considered as the lowest genetic diversity especially based on nucleus DNA RAG2 sequencing. Based on mtDNA Cytochrome-b sequencing, the most distinct population among those populations based on genetic distance were fish populations of Musi and Kapuas. According to the result of neighbor-joining tree analysis, the populations of botia were classified into two groups namely group of Sumatra and group of Kalimantan. The estimation of time divergence among group of population of Sumatra and Kalimantan based on mtDNA Cytochrome b was about 9.25—9.46 million years (Miocene era). The high genetic differences between groups of Sumatra and Kalimantan suggested that the effort of restocking botia from Sumatra into Kalimantan has to be done carefully, because it may disturb the gene originality of both botia populations.

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Regional population structuring and conservation units in the platypus (Ornithorhynchus anatinus)

Australian Journal of Zoology ◽

10.1071/zo13029 ◽

2013 ◽

Vol 61 (5) ◽

pp. 378 ◽

Cited By ~ 7

Author(s):

Stephen H. Kolomyjec ◽

Tom R. Grant ◽

Christopher N. Johnson ◽

David Blair

Keyword(s):

Gene Flow ◽

Genetic Differentiation ◽

Large Scale ◽

Wide Distribution ◽

Conservation Units ◽

Genetic Structuring ◽

The North ◽

Contemporary Gene Flow ◽

Ornithorhynchus Anatinus ◽

Southern Island

The platypus (Ornithorhynchus anatinus) has a wide distribution in Australia, encompassing the southern island of Tasmania and a broad latitudinal range of the mainland from the temperate south to the tropical north. We used 12 microsatellite markers from 235 individuals sampled from 13 river systems to examine patterns of genetic differentiation and gene flow throughout the species’ range. Using a Bayesian approach we identified three large-scale groupings that correspond closely to geographically distinct regions of the species’ distribution: the tropical northern mainland, the subtropical and temperate southern mainland, and Tasmania. Six additional clusters were found within the regional groups, three in the northern, two in the southern mainland regions, and the last in Tasmania. These clusters coincided with major river drainages. Genetic differentiation was generally high, with pairwise Fst values ranging from 0.065 to 0.368 for regions and 0.037 to 0.479 for clusters. We found no evidence of contemporary gene flow among the three clusters in the north, but some migration may occur between the larger clusters in the south. Due to the high genetic structuring and lack of gene flow between these three regional populations of the platypus we recommend their treatment as evolutionarily significant units (ESUs) within the platypus species. We have also detailed several smaller management units (MUs) existing within our study area based on subregional clusters and geographically significant features.

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Evidence for geographical isolation of the early life stages of the white anglerfish, Lophius piscatorius, based on otolith microchemistry

Journal of the Marine Biological Association of the United Kingdom ◽

10.1017/s002531540401001xh ◽

2004 ◽

Vol 84 (4) ◽

pp. 827-830 ◽

Cited By ~ 6

Author(s):

S.C. Swan ◽

P.J. Wright ◽

D.A. Woodroffe ◽

J.D.M. Gordon ◽

T. Shimmield

Keyword(s):

Early Life ◽

Early Life History ◽

Life Stages ◽

Early Life Stages ◽

Geographical Isolation ◽

Genetic Structuring ◽

North East ◽

The North ◽

Population Structuring ◽

Limited Exchange

Concentrations of elements in the sagittal otoliths of juvenile white anglerfish (Lophius piscatorius) from five locations in the north-east Atlantic were measured to test for evidence of segregation in the early life stages. The concentrations of some elements, notably copper, were different between locations. As such, the results suggest limited exchange between locations during some period of the early life history. The relevance of these results to our understanding of population structuring is discussed in relation to recent information on anglerfish movements and genetic structuring.

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