Resprouters Versus Reseeders: Are Wild Rooibos Ecotypes Genetically Distinct?

Aspalathus linearis (Burm. F.) R. Dahlgren (Fabaceae) or rooibos, is a strict endemic species, limited to areas of the Cederberg (Western Cape) and the southern Bokkeveld plateau (Northern Cape) in the greater Cape Floristic Region (CFR) of South Africa. Wild rooibos, unlike the cultivated type, is variable in morphology, biochemistry, ecology and genetics, and these ecotypes are broadly distinguished into two main groups, namely, reseeders and resprouters, based on their fire-survival strategy. No previous assessment of genetic diversity or population structure using microsatellite markers has been conducted in A. linearis. This study aimed to test the hypothesis that wild rooibos ecotypes are distinct in genetic variability and that the ecotypes found in the Northern Cape are differentiated from those in the Cederberg that may be linked to a fire-survival strategy as well as distinct morphological and phytochemical differences. A phylogeographical and population genetic analyses of both chloroplast (trnLF intergenic region) and newly developed species-specific nuclear markers (microsatellites) was performed on six geographically representative wild rooibos populations. From the diversity indices, it was evident that the wild rooibos populations have low-to-moderate genetic diversity (He: 0.618–0.723; Ho: 0.528–0.704). The Jamaka population (Cederberg, Western Cape) had the lowest haplotype diversity (H = 0.286), and the lowest nucleotide diversity (π = 0.006) even though the data revealed large variations in haplotype diversity (h = 0.286–0.900) and nucleotide diversity (π = 0.006–0.025) between populations and amongst regions where wild rooibos populations are found. Our data suggests that populations of rooibos become less diverse from the Melkkraal population (Suid Bokkeveld, Northern Cape) down towards the Cederberg (Western Cape) populations, possibly indicative of clinal variation. The largest genetic differentiation was between Heuningvlei (Cederberg, Western Cape) and Jamaka (FST = 0.101) localities within the Cederberg mountainous region, and, Blomfontein (Northern Cape) and Jamaka (Cederberg) (FST = 0.101). There was also a significant isolation by distance (R2 = 0.296, p = 0.044). The presence of three main clusters is also clearly reflected in the discriminant analysis of principal components (DAPC) based on the microsatellite marker analyses. The correct and appropriate management of wild genetic resources of the species is urgently needed, considering that the wild Cederberg populations are genetically distinct from the wild Northern Cape plants and are delineated in accordance with ecological functional traits of reseeding or resprouting, respectively. The haplotype divergence of the ecotypes has also provided insights into the genetic history of these populations and highlighted the need for the establishment of appropriate conservation strategies for the protection of wild ecotypes.

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Genetic diversity analysis and phylogenetic reconstruction of groupers Epinephelus spp. from Madura Island, Indonesia based on partial sequence of CO1 gene

Biodiversitas Journal of Biological Diversity ◽

10.13057/biodiv/d221020 ◽

2021 ◽

Vol 22 (10) ◽

Author(s):

ABDUL BASITH ◽

Abinawanto Abinawanto ◽

ENI KUSRINI ◽

YASMAN YASMAN

Keyword(s):

Genetic Diversity ◽

Phylogenetic Tree ◽

Nucleotide Diversity ◽

Haplotype Diversity ◽

Phylogenetic Reconstruction ◽

Partial Sequence ◽

Diversity Analysis ◽

Epinephelus Coioides ◽

Substitution Model ◽

Genetic Diversity Analysis

Abstract. Basith A, Abinawanto, Kusrini E, Yasman. 2021. Genetic diversity analysis and phylogenetic reconstruction of groupers Epinephelus spp. from Madura Island, Indonesia based on partial sequence of CO1 gene. Biodiversitas 22: 4282-4290. Groupers populations in Indonesia, particularly from Madura Island, East Java are indicated to be over-fished, thereby requiring data collection of more accurate genetic resources as an important step for grouper conservation. A total of 14 samples of the Epinepheplus groupers were obtained from the fish landing port on Madura Island. The 617 bp CO1 gene sequence was utilized for genetic diversity analysis and phylogenetic tree reconstruction. Genetic diversity is based on the value of haplotype diversity (Hd) and nucleotide diversity (?). Reconstruction of the phylogenetic tree includes neighbor-joining (NJ) implementing K2P substitution model, while maximum likelihood (ML) is conducted by implementing HKY+G+I substitution model, both of which were evaluated by employing a bootstrap of 1000 replications. Analysis of genetic distance between species indicated that the farthest distance between E. heniochus and E. fasciatus was 0.189, while the closest distance between E. erythrurus and E. ongus was 0.099. Intrapopulation genetic diversity indicated a high value with details of Hd=0.978 and ?=0.12107. Furthermore, NJ and ML phylogenetic tree demonstrated similar topology in the observed Epinephelus spp. obtained from Madura Island grouped into 7 clades, that is Epinephelus coioides, E. bleekeri, E. areolatus, E. erythrurus, E. heniochus, E. fasciatus, and E. ongus.

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Genetic Diversity and Population Divergence of a Rare, Endemic Grass (Elymus breviaristatus) in the Southeastern Qinghai-Tibetan Plateau

Sustainability ◽

10.3390/su11205863 ◽

2019 ◽

Vol 11 (20) ◽

pp. 5863 ◽

Cited By ~ 2

Author(s):

Qingqing Yu ◽

Qian Liu ◽

Yi Xiong ◽

Yanli Xiong ◽

Zhixiao Dong ◽

...

Keyword(s):

Genetic Diversity ◽

Tibetan Plateau ◽

Isolation By Distance ◽

Genetic Distances ◽

Conservation Strategy ◽

Conservation Strategies ◽

Grass Species ◽

Population Divergence ◽

High Genetic Diversity ◽

Widespread Species

Elymus breviaristatus is a grass species only distributed in the southeast of Qinghai-Tibetan Plateau (QTP), which has suffered from serious habitat fragmentation. Therefore, understanding patterns of genetic diversity within and among natural E. breviaristatus populations could provide insight for future conservation strategies. In this study, sequence-related amplified polymorphism markers were employed to investigate the genetic diversity and hierarchical structure of seven E. breviaristatus populations from QTP, China. Multiple measures of genetic diversity indicated that there is low to moderate genetic variation within E. breviaristatus populations, consistent with its presumed mating system. In spite of its rarity, E. breviaristatus presented high genetic diversity that was equivalent to or even higher than that of widespread species. Bayesian clustering approaches, along with clustering analysis and principal coordinate analysis partitioned the studied populations of E. breviaristatus into five genetic clusters. Differentiation coefficients (Fst, GST, etc.) and AMOVA analysis revealed considerable genetic divergence among different populations. BARRIER analyses indicated that there were two potential barriers to gene flow among the E. breviaristatus populations. Despite these patterns of differentiation, genetic distances between populations were independent of geographic distances (r = 0.2197, p = 0.2534), indicating little isolation by distance. Moreover, despite detecting a common outlier by two methods, bioclimatic factors (altitude, annual mean temperature, and annual mean precipitation) were not related to diversity parameters, indicating little evidence for isolation caused by the environment. These patterns of diversity within and between populations are used to propose a conservation strategy for E. breviaristatus.

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Integrating population genetics to define conservation units from the core to the edge of Rhinolophus ferrumequinum western range

10.1101/662643 ◽

2019 ◽

Author(s):

Orianne Tournayre ◽

Jean-Baptiste Pons ◽

Maxime Leuchtmann ◽

Raphael Leblois ◽

Sylvain Piry ◽

...

Keyword(s):

Genetic Diversity ◽

Isolation By Distance ◽

Demographic History ◽

Large Population ◽

Conservation Strategies ◽

Conservation Units ◽

Management Units ◽

Rhinolophus Ferrumequinum ◽

Northern France ◽

History Of

AbstractThe greater horseshoe bat (Rhinolophus ferrumequinum) is among the most widespread bat species in Europe but it has experienced severe declines, especially in Northern Europe. This species is listed Near Threatened in the European IUCN Red List of Threatened Animals and it is considered to be highly sensitive to human activities and particularly to habitat fragmentation. Therefore, understanding the population boundaries and demographic history of populations of this species is of primary importance to assess relevant conservation strategies. In this study, we used 17 microsatellite markers to assess the genetic diversity, the genetic structure and the demographic history of R. ferrumequinum colonies in the Western European part of its distribution. We found high levels of genetic diversity and large population size on the European mainland and lower estimates in England and Northern France. Analyses of clustering and isolation by distance showed a barrier effect of the Channel and potentially of the Mediterranean Sea on R. ferrumequinum bat dispersal. Conversely, we could not reveal any gene flow disruption from both sides of the Western Pyrenees. These results provide important information to improve the delineation of R. ferrumequinum management units in its western range. We suggest that a large management unit corresponding to the European mainland population must be considered. Particular attention should be given to mating territories as they seem to play a key role in maintaining the high levels of genetic mixing between colonies. Smaller management units corresponding to English and Northern France colonies must also be implemented. These insular or peripheral colonies could be at higher risk of extinction in a near future.

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Short Communication: Genetic diversity and phylogenetic analysis of two Indonesian local cattle breeds based on cytochrome b gene sequences

Biodiversitas Journal of Biological Diversity ◽

10.13057/biodiv/d200103 ◽

2018 ◽

Vol 20 (1) ◽

pp. 17-22

Author(s):

TETY HARTATIK ◽

DWI NUR HAPPY HARIYONO ◽

YUDI ADINATA

Keyword(s):

Genetic Diversity ◽

Phylogenetic Analysis ◽

Cytochrome B ◽

Nucleotide Diversity ◽

Haplotype Diversity ◽

Cytochrome B Gene ◽

Cyt B ◽

Gene Sequences ◽

Cattle Breeds ◽

Cyt B Gene

Hartatik T, Hariyono DNH, Adinata Y. 2019. Genetic diversity and phylogenetic analysis of two Indonesian local cattle breeds based on cytochrome b gene sequences. Biodiversitas 20: 17-22. Genetic diversity and phylogenetic relationships of two Indonesian local cattle breeds (Pasundan and Pacitan cattle) were investigated using mitochondrial DNA (mtDNA) cytochrome b (cyt b) gene analysis. Partial sequences of cyt b gene, 404 bp in length, were determined for 21 individuals from the two breeds. Genetic diversity of the breeds was assessed based on the number of polymorphic sites, number of haplotypes, haplotype diversity, nucleotide diversity and average number of differences. In addition, a neighbour-joining (NJ) haplotype tree was constructed based on Kimura’s two-parameter model. Among the two breeds, haplotype and nucleotide diversity of Pacitan cattle were the highest with values of 0.3778 and 0.00099, respectively. In contrast, Pasundan cattle had the lowest value for haplotype (0.1818) and nucleotide (0.00045) diversity. Four haplotypes (Hap_16, Hap_17, Hap_18 and Hap_19) were found across the two breeds and around 85.71% of investigated individuals were classified as Hap_16. Phylogenetic analysis with the inclusion of the cyt b sequences from 39 cattle breeds from Genbank database, showed that Indonesian cattle made a separated lineage together with Bos javanicus, B. bison, and B. bonasus. Pasundan and Pacitan cattle were considered from the same lineage based on haplotype distribution as well as phylogenetic analysis. This study may help the future researchers and livestock breeders for designing a breeding program based on a better understanding of the genetic diversity and history of local breeds.

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Genetic Diversity of Mitochondrial DNA Cytochrome b in Indonesian Native and Local Cattle Populations

Jurnal Ilmu Ternak dan Veteriner ◽

10.14334/jitv.v25i2.2496 ◽

2020 ◽

Vol 25 (2) ◽

pp. 39

Author(s):

Peni Wahyu Prihandini ◽

A Primasari ◽

M Luthfi ◽

J Efendy ◽

D Pamungkas

Keyword(s):

Genetic Diversity ◽

Bos Taurus ◽

Phylogenetic Analyses ◽

Bos Indicus ◽

Haplotype Diversity ◽

Genetic Distances ◽

Conservation Strategies ◽

Bos Javanicus ◽

Reverse Primer ◽

Relationship Of

Information on the genetic diversity of native and local cattle in Indonesia is vital for the development of breeding and conservation strategies. This study was aimed to assess the genetic diversity and phylogenetic relationship of the Indonesian native (Bali) and local [(Donggala, Madura, Sragen, Galekan, Rambon, dan Peranakan Ongole Grade x Bali (POBA)] cattle populations. Genomic DNA was extracted from blood samples (n= 75). Partial sequences of mtDNA cyt b, 464 bp, were amplified using the polymerase chain reaction technique (forward primer: L14735 and reverse primer: H15149). Thirty-four reference sequences of Bos taurus, Bos indicus, and Bos javanicus were included in the phylogenetic analyses. A total of 55 polymorphic sites and 13 haplotypes were observed in the whole breeds. No variable sites of mtDNA cyt b were observed in Galekan (kept in BCRS) and Rambon cattle. Overall haplotype diversity and nucleotide diversity were 0.515 ± 0.070 and 0.0184 ± 0.0045, respectively. The highest (0.092) and the lowest (0.000) genetic distances were between Bali and Donggala cattle populations and among Galekan (kept in BCRS), Rambon, and POBA cattle populations, respectively. Both mtDNA network and phylogenetic analyses revealed two major maternal lineages (A and B) of the studied population. Most of the sampled individuals (69.33%, present in haplotype H8-H19) were linked to lineage B, which belonged to the same cluster with Bos javanicus. Overall, most of the Indonesian native and local cattle populations had a considerable genetic diversity and shared a common maternal origin with Bos javanicus.

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Diversitas Genetika dan Identifikasi Jenis Kelamin Burung Pelikan (Pelecanus conspicillatus Temminck, 1824) di Penangkaran Taman Margasatwa Ragunan Jakarta

Jurnal Biologi Indonesia ◽

10.47349/jbi/17022021/105 ◽

2021 ◽

Vol 17 (2) ◽

pp. 105-114

Author(s):

Anik Budhi Dharmayanthi ◽

Achmad Muchsinin ◽

Afriana Pulungan ◽

Moch Syamsul Arifin Zein

Keyword(s):

Genetic Diversity ◽

Nucleotide Diversity ◽

Haplotype Diversity ◽

Population Expansion ◽

Bird Populations ◽

Low Genetic Diversity ◽

In Captivity ◽

D Loop ◽

Haplotype 1

Pelicans (Pelecanus conspicillatus) is one of the wild species that have a widely distribution. This bird has been successfully bred in Ragunan Zoo, Jakarta. The indicator of inbreeding in the captive population is shown by the decrease of nucleotide diversity and number of haplotypes. The result of genetic diversity analysis using D-loop fragment sequences showed low genetic diversity with nucleotide diversity (p) = 0.00064 ± 0.00010 and haplotype diversity (Hd) = 0.532 ± 0.061 in Pelecanus conspicillatus populations in the Ragunan Zoo. However, negative Fu's Fs value (-3,246) indicates population expansion. We found that there were seven haplotypes in bird populations in the captivity: haplotype 1, 2 and 3 consist of 43 individuals (65.15%), five individuals (7.57%), and 14 individuals (21.21%), respectively. For each haplotype 4, 5, 6 and 7 is only represented by one individual of Pelecanus conspicillatus (1.51%). The sex ratio of males to females is 1: 8.86 with four males identified as haplotype 1, and one male on haplotypes 3, 5 and 7, respectively. Genetic diversity data of the population is an important way for designing long-term plans and goals in efforts to maintain genetic diversity of the Pelecanus conspicillatus population in captivity.

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High Genetic Diversity and Low Differentiation in Michelia shiluensis, an Endangered Magnolia Species in South China

Forests ◽

10.3390/f11040469 ◽

2020 ◽

Vol 11 (4) ◽

pp. 469 ◽

Cited By ~ 1

Author(s):

Yanwen Deng ◽

Tingting Liu ◽

Yuqing Xie ◽

Yaqing Wei ◽

Zicai Xie ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Variation ◽

Human Disturbance ◽

Haplotype Diversity ◽

Conservation Strategy ◽

Ex Situ ◽

Conservation Strategies ◽

High Genetic Diversity ◽

Cpdna Markers

Research Highlights: This study is the first to examine the genetic diversity of Michelia shiluensis (Magnoliaceae). High genetic diversity and low differentiation were detected in this species. Based on these results, we discuss feasible protection measures to provide a basis for the conservation and utilization of M. shiluensis. Background and Objectives: Michelia shiluensis is distributed in Hainan and Guangdong province, China. Due to human disturbance, the population has decreased sharply, and there is thus an urgent need to evaluate genetic variation within this species in order to identify an optimal conservation strategy. Materials and Methods: In this study, we used eight nuclear single sequence repeat (nSSR) markers and two chloroplast DNA (cpDNA) markers to assess the genetic diversity, population structure, and dynamics of 78 samples collected from six populations. Results: The results showed that the average observed heterozygosity (Ho), expected heterozygosity (He), and percentage of polymorphic loci (PPL) from nSSR markers in each population of M. shiluensis were 0.686, 0.718, and 97.92%, respectively. For cpDNA markers, the overall haplotype diversity (Hd) was 0.674, and the nucleotide diversity was 0.220. Analysis of markers showed that the genetic variation between populations was much lower based on nSSR than on cpDNA (10.18% and 77.56%, respectively, based on an analysis of molecular variance (AMOVA)). Analysis of the population structure based on the two markers shows that one of the populations (DL) is very different from the other five. Conclusions: High genetic diversity and low population differentiation of M. shiluensis might be the result of rich ancestral genetic variation. The current decline in population may therefore be due to human disturbance rather than to inbreeding or genetic drift. Management and conservation strategies should focus on maintaining the genetic diversity in situ, and on the cultivation of seedlings ex-situ for transplanting back to their original habitat.

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Distribution and Genetic Diversity of Aedes aegypti Subspecies across the Sahelian Belt in Sudan

Pathogens ◽

10.3390/pathogens10010078 ◽

2021 ◽

Vol 10 (1) ◽

pp. 78

Author(s):

Sara Abdelrahman Abuelmaali ◽

Jamsari Amirul Firdaus Jamaluddin ◽

Kheder Noaman ◽

Mushal Allam ◽

Hind Mohammad Abushama ◽

...

Keyword(s):

Genetic Diversity ◽

Aedes Aegypti ◽

Nucleotide Diversity ◽

Isolation By Distance ◽

Haplotype Network ◽

Mitochondrial Marker ◽

Cross Sectional Survey ◽

Cross Sectional ◽

Disease Vector ◽

Arboviral Disease

Aedes aegypti is the most important arboviral disease vector worldwide. In Africa, it exists as two morphologically distinct forms, often referred to as subspecies, Aaa and Aaf. There is a dearth of information on the distribution and genetic diversity of these two forms in Sudan and other African Sahelian region countries. This study aimed to explore the distribution and genetic diversity of Aedes aegypti subspecies using morphology and Cytochrome oxidase-1 mitochondrial marker in a large Sahelian zone in Sudan. An extensive cross-sectional survey of Aedes aegypti in Sudan was performed. Samples collected from eight locations were morphologically identified, subjected to DNA extraction, amplification, sequencing, and analyses. We classified four populations as Aaa and the other four as Aaf. Out of 140 sequence samples, forty-six distinct haplotypes were characterized. The haplotype and nucleotide diversity of the collected samples were 0.377–0.947 and 0.002–0.01, respectively. Isolation by distance was significantly evident (r = 0.586, p = 0.005). The SAMOVA test indicated that all Aaf populations are structured in one group, while the Aaa clustered into two groups. AMOVA showed 53.53% genetic differences within populations and 39.22% among groups. Phylogenetic relationships indicated two clusters in which the two subspecies were structured. Thus, the haplotype network consisted of three clusters.

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Genetic analysis of mitochondrial ND5 gene of siberian ibex (Capra Sibirica, Pallas, 1776) population in Mongolia

Proceedings of the Mongolian Academy of Sciences ◽

10.5564/pmas.v59i3.1246 ◽

2019 ◽

pp. 48-53

Author(s):

Tsenddorj Bilguun ◽

Baatar Delgerzul ◽

Zunduibaatar Unudbayasgalan ◽

Baranz Galbadrakh ◽

Batsukh Tserendulam

Keyword(s):

Genetic Diversity ◽

Genetic Analysis ◽

Phylogenetic Tree ◽

Central Asia ◽

Nucleotide Diversity ◽

Population Decline ◽

Haplotype Diversity ◽

Desert Steppe ◽

Nd5 Gene ◽

Different Parts

The Siberian ibex (Capra sibirica) from Central Asia is believed to be the most ancient species of the genus Capra. In Mongolia, it is distributed in the areas of Mongolian Altai, Gobi-Altai, Dzungaria, Altai, Khan Khuhii, Khoridal Saridag and Ulaan Taiga as well as in the desert and semi-desert steppe zones of Dundgobi and Dornogobi aimags (provinces). In the current study, we investigated the mitochondrial ND5 gene fragments of the Siberian ibex population from different parts of Mongolia. Nine haplotypes, including 6 shared and 3 unique haplotypes were identified among these populations. Furthermore, Tajima’s statistics and Fu’s statistics did not reveal significant positive value across the population, indicating population decline and balancing selection.In the phylogenetic tree by 9 haplotypes, no separated clusters were generated. In addition, nucleotide diversity was 0.015, haplotype diversity was 0.86 and the average number of differences in nucleotides was 8.2 in the overall population. These results suggest that genetic diversity across all the populations was low, while haplotype diversity and the average number of differences in nucleotides were high.

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Study on Genetic Diversity of Phellodendron amurense based on cpDNA

E3S Web of Conferences ◽

10.1051/e3sconf/202127103059 ◽

2021 ◽

Vol 271 ◽

pp. 03059

Author(s):

Hongsheng Yang ◽

Donghong Yang ◽

Xuewen Yang ◽

Qingbo Zhou ◽

Haitao Cheng ◽

...

Keyword(s):

Genetic Diversity ◽

Northeast China ◽

Mismatch Distribution ◽

Nucleotide Diversity ◽

North China ◽

Haplotype Diversity ◽

Common Origin ◽

Ancestral Haplotype ◽

Phellodendron Amurense ◽

Tajima’S D

In this study, 3 haplotypes were found in populations of Phellodendron amurense based on two combined cpDNA regions (psbA-trnH and trnT-trnL). Nucleotide diversity and haplotype diversity were 0.43×10-3 and 0.41, respectively at the level of species. The AMOVA revealed that only 8.53% of the variation was explained by differences among geographical groups, whereas inter-population and intrapopulation differences explained 18.32% and 71.35% of the variation, respectively. Phylogeographical relationships showed that all haplotypes were clustered into two lineages. Haplotype H1 and H2 cluster together, and Haplotype H3 composed a group. TCS network of haplotypes showed that haplotype H1 located in the center of the lineage, and it appears to be an ancestral haplotype. So we hypothesized that Northeast China populations and North China populations had a common origin. The mismatch distribution of this species suggested that all populations and populations in North China had not undergone recent expansion, but populations in Northeast China had undergone recent expansion. The results were consistent with the results of Tajima’s D and Fu’s and Li’s D test.

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