scholarly journals Genetic diversity, genetic structure, and demographic history of Cinnamomum chago, a plant species with extremely small populations in China

2021 ◽  
pp. e01808
Author(s):  
Xue Zhang ◽  
Liu Yang ◽  
Yuan-Huan Liu ◽  
Xiong-Li Zhou ◽  
Li-Qin Zhang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Plant Species ◽  
Demographic History ◽  
Small Populations ◽  
History Of

scholarly journals Population Genetic Structure and Genetic Diversity in Twisted-Jaw Fish, Belodontichthys truncatus Kottelat & Ng, 1999 (Siluriformes: Siluridae), from Mekong Basin

2017 ◽  
Vol 2017 ◽  
pp. 1-7 ◽  
Author(s):  
Surapon Yodsiri ◽  
Komgrit Wongpakam ◽  
Adisak Ardharn ◽  
Chadaporn Senakun ◽  
Sutthira Khumkratok
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Demographic History ◽  
Hydropower Plant ◽  
Mekong River ◽  
Demographic Expansion ◽  
High Genetic Diversity ◽  
History Analysis ◽  
History Of ◽  
Important Food Source

The Mekong River and its tributaries possess the second highest diversity in fish species in the world. However, the fish biodiversity in this river is threatened by several human activities, such as hydropower plant construction. Understanding the genetic diversity and genetic structure of the species is important for natural resource management. Belodontichthys truncatus Kottelat & Ng is endemic to the Mekong River basin and is an important food source for people in this area. In this study, the genetic diversity, genetic structure, and demographic history of the twisted-jaw fish, B. truncatus, were investigated using mitochondrial cytochrome b gene sequences. A total of 124 fish specimens were collected from 10 locations in the Mekong and its tributaries. Relatively high genetic diversity was found in populations of B. truncatus compared to other catfish species in the Mekong River. The genetic structure analysis revealed that a population from the Chi River in Thailand was genetically significantly different from other populations, which is possibly due to the effect of genetic drift. Demographic history analysis indicated that B. truncatus has undergone recent demographic expansion dating back to the end of the Pleistocene glaciation.

scholarly journals One Step Away From Extinction: A Population Genomic Analysis of A Narrow Endemic, Tropical Plant Species

2021 ◽  
Vol 12 ◽  
Author(s):  
Thais M. Teixeira ◽  
Alison G. Nazareno
Keyword(s):  
Genetic Diversity ◽  
Missing Data ◽  
Plant Species ◽  
Threatened Species ◽  
Demographic History ◽  
Small Population ◽  
Narrow Endemic ◽  
Population Genomic ◽  
Genomic Study ◽  
History Of

Intraspecific genetic variation plays a fundamental role in maintaining the evolutionary potential of wild populations. Hence, the assessment of genetic diversity patterns becomes essential to guide biodiversity conservation policies, particularly for threatened species. To inform management strategies for conservation of Mimosa catharinensis – a narrow endemic, critically endangered plant species – we identified 1,497 unlinked SNP markers derived from a reduced representation sequencing method (i.e., double digest restriction site associated DNA sequencing, or ddRADseq). This set of molecular markers was employed to assess intrapopulation genetic parameters and the demographic history of one extremely small population of M. catharinensis (N=33) located in the Brazilian Atlantic Forest. Contrary to what is expected for narrow endemic and threatened species with small population sizes, we observed a moderate level of genetic diversity for M. catharinensis [uHE(0%missing data)=0.205, 95% CI (0.160, 0.250); uHE(30%missing data)=0.233, 95% CI (0.174, 0.292)]. Interestingly, M. catharinensis, which is a lianescent shrub with no indication of seed production for at least two decades, presented high levels of outcrossing [t(0%missing data)=0.883, SE±0.0483; t(30%missing data)=0.909, SE±0.011] and an apparent absence of inbreeding [F(0%missing data)=−0.145, 95% CI (−0.189, −0.101); F(30%missing data)=−0.105, 95% CI (−0.199, −0.011)]. However, the reconstruction of demographic history of M. catharinensis indicated that the population should be suffered a recent bottleneck. Our population genomic study tackles a central issue in evolution and conservation biology and we expect that it will be useful to help safeguard the remaining genetic diversity reported for this unique genetic resource.

scholarly journals Population Genetics of New Zealand Nemadactylus macropterus (tarakihi) and Characterisation of their Mitochondrial Genome

2021 ◽  
Author(s):  
◽  
Alexander Halliwell
Keyword(s):  
Genetic Diversity ◽  
New Zealand ◽  
Genetic Structure ◽  
East Coast ◽  
Demographic History ◽  
Variable Region ◽  
Sequencing Data ◽  
Commercial Catch ◽  
History Of ◽  
Hyper Variable Region

<p>Nemadactylus macropterus, commonly known as tarakihi in New Zealand is highly regarded by commercial and recreational fishers and considered a taonga by iwi and customary fisheries. For many years N. macropterus was New Zealand’s second most important commercial catch and is currently the third most valuable inshore commercial finfish fishery in which 90% is consumed by the domestic market. However, despite the apparent importance, relatively little is known about the population structure of the N. macropterus. In 2017 the first fully quantitative stock assessment was conducted on the east coast N. macropterus fisheries as one stock. Alarmingly, the east coast fishery was estimated to be 15.9% of the unexploited spawning biomass and predicted to have been declining for the past thirty years. In an effort to rebuild the fishery, several rebuild plans have been purposed and commercial catch limits have been reduced. In order to rebuild and successfully manage a viable future N. macropterus fishery, an understanding of demographic connectivity and genetic connectivity among N. macropterus populations is essential.  The overall goal of this thesis research was to investigate the population genetic structure, genetic diversity and demographic history of N. macropterus using fish sampled from around New Zealand. This was achieved by analysing hyper variable region one of mitochondrial DNA for 370 N. macropterus collected from 14 locations. No genetic differentiation was observed among the 14 locations, an indication that N. macropterus have a panmictic genetic structure. Furthermore, N. macropterus display a relatively high level of genetic diversity and appear to have a large stable population with a long evolutionary history. The Bayesian skyline analysis indicates the N. macropterus historic population has gone through two expansions. The mostly likely cause of this is an expansion before and after the last glacial maximum.  The genetic diversity and demographic history of N. sp was also studied using samples collected from around the Three Kings Islands of New Zealand. The complete mitochondrial genome of N. macropterus was reconstructed from bulk DNA sequencing data and a set of specific mtDNA primers were developed to amplify hyper variable region one. The DNA sequencing data provided by these primers with the addition of published control region sequences was used to reconstruct the Nemadactylus phylogeny.</p>

scholarly journals Population Genetics of New Zealand Nemadactylus macropterus (tarakihi) and Characterisation of their Mitochondrial Genome

2021 ◽  
Author(s):  
◽  
Alexander Halliwell
Keyword(s):  
Genetic Diversity ◽  
New Zealand ◽  
Genetic Structure ◽  
East Coast ◽  
Demographic History ◽  
Variable Region ◽  
Sequencing Data ◽  
Commercial Catch ◽  
History Of ◽  
Hyper Variable Region

<p>Nemadactylus macropterus, commonly known as tarakihi in New Zealand is highly regarded by commercial and recreational fishers and considered a taonga by iwi and customary fisheries. For many years N. macropterus was New Zealand’s second most important commercial catch and is currently the third most valuable inshore commercial finfish fishery in which 90% is consumed by the domestic market. However, despite the apparent importance, relatively little is known about the population structure of the N. macropterus. In 2017 the first fully quantitative stock assessment was conducted on the east coast N. macropterus fisheries as one stock. Alarmingly, the east coast fishery was estimated to be 15.9% of the unexploited spawning biomass and predicted to have been declining for the past thirty years. In an effort to rebuild the fishery, several rebuild plans have been purposed and commercial catch limits have been reduced. In order to rebuild and successfully manage a viable future N. macropterus fishery, an understanding of demographic connectivity and genetic connectivity among N. macropterus populations is essential.  The overall goal of this thesis research was to investigate the population genetic structure, genetic diversity and demographic history of N. macropterus using fish sampled from around New Zealand. This was achieved by analysing hyper variable region one of mitochondrial DNA for 370 N. macropterus collected from 14 locations. No genetic differentiation was observed among the 14 locations, an indication that N. macropterus have a panmictic genetic structure. Furthermore, N. macropterus display a relatively high level of genetic diversity and appear to have a large stable population with a long evolutionary history. The Bayesian skyline analysis indicates the N. macropterus historic population has gone through two expansions. The mostly likely cause of this is an expansion before and after the last glacial maximum.  The genetic diversity and demographic history of N. sp was also studied using samples collected from around the Three Kings Islands of New Zealand. The complete mitochondrial genome of N. macropterus was reconstructed from bulk DNA sequencing data and a set of specific mtDNA primers were developed to amplify hyper variable region one. The DNA sequencing data provided by these primers with the addition of published control region sequences was used to reconstruct the Nemadactylus phylogeny.</p>

Genetic variability and demographic history of Heliothis virescens (Lepidoptera: Noctuidae) populations from Brazil inferred by mtDNA sequences

2011 ◽  
Vol 102 (3) ◽  
pp. 333-343 ◽  
Author(s):  
K.C. Albernaz ◽  
K.L. Silva-Brandão ◽  
P. Fresia ◽  
F.L. Cônsoli ◽  
C. Omoto
Keyword(s):  
Genetic Structure ◽  
Genetic Variability ◽  
Heliothis Virescens ◽  
Demographic History ◽  
Haplotype Diversity ◽  
Low Frequency ◽  
Haplotype Network ◽  
Demographic Expansion ◽  
Significant Genetic Structure ◽  
History Of

AbstractIntra- and inter-population genetic variability and the demographic history of Heliothis virescens (F.) populations were evaluated by using mtDNA markers (coxI, coxII and nad6) with samples from the major cotton- and soybean-producing regions in Brazil in the growing seasons 2007/08, 2008/09 and 2009/10. AMOVA indicated low and non-significant genetic structure, regardless of geographical scale, growing season or crop, with most of genetic variation occurring within populations. Clustering analyzes also indicated low genetic differentiation. The haplotype network obtained with combined datasets resulted in 35 haplotypes, with 28 exclusive occurrences, four of them sampled only from soybean fields. The minimum spanning network showed star-shaped structures typical of populations that underwent a recent demographic expansion. The recent expansion was supported by other demographic analyzes, such as the Bayesian skyline plot, the unimodal distribution of paired differences among mitochondrial sequences, and negative and significant values of neutrality tests for the Tajima's D and Fu's FS parameters. In addition, high values of haplotype diversity (Ĥ) and low values of nucleotide diversity (π), combined with a high number of low frequency haplotypes and values of θπ<θW, suggested a recent demographic expansion of H. virescens populations in Brazil. This demographic event could be responsible for the low genetic structure currently found; however, haplotypes present uniquely at the same geographic regions and from one specific host plant suggest an initial differentiation among H. virescens populations within Brazil.

scholarly journals The Genetic History of France

2019 ◽  
Author(s):  
Aude Saint Pierre ◽  
Joanna Giemza ◽  
Matilde Karakachoff ◽  
Isabel Alves ◽  
Philippe Amouyel ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Demographic History ◽  
Migration Routes ◽  
Effective Population ◽  
Genetic Studies ◽  
Independent Population ◽  
Genome Wide Data ◽  
Population Sizes ◽  
History Of ◽  
Exhaustive Study

ABSTRACTThe study of the genetic structure of different countries within Europe has provided significant insights into their demographic history and their actual stratification. Although France occupies a particular location at the end of the European peninsula and at the crossroads of migration routes, few population genetic studies have been conducted so far with genome-wide data. In this study, we analyzed SNP-chip genetic data from 2 184 individuals born in France who were enrolled in two independent population cohorts. Using FineStructure, six different genetic clusters of individuals were found that were very consistent between the two cohorts. These clusters match extremely well the geography and overlap with historical and linguistic divisions of France. By modeling the relationship between genetics and geography using EEMS software, we were able to detect gene flow barriers that are similar in the two cohorts and corresponds to major French rivers or mountains. Estimations of effective population sizes using IBDNe program also revealed very similar patterns in both cohorts with a rapid increase of effective population sizes over the last 150 generations similar to what was observed in other European countries. A marked bottleneck is also consistently seen in the two datasets starting in the fourteenth century when the Black Death raged in Europe. In conclusion, by performing the first exhaustive study of the genetic structure of France, we fill a gap in the genetic studies in Europe that would be useful to medical geneticists but also historians and archeologists.

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