control region
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Zootaxa ◽  
2022 ◽  
Vol 5087 (2) ◽  
pp. 335-356
Author(s):  
JING LIU ◽  
XIANGYI WU ◽  
XUN BIAN

Based on the specimens from Guangxi and Yunnan deposited in the Guangxi Normal University, the paper is firstly reported the female sex of two known species from China, viz. Furcilarnaca armata (Bey-Bienko, 1957) and Furcilarnaca forceps (Bey-Bienko, 1962). The female of Furcilarnaca armata (Bey-Bienko, 1957) is very similar to Furcilarnaca chiangdao in seventh abdominal tergite and subgenital plate, and they may belong to the same species. After examining the female subgenital plate of Furcilarnaca chirurga (Bey-Bienko, 1962), we treat Furcilarnaca hirta as a valid species. Mitochondrial genomes of six specimens of three Furcilarnaca species were sequenced and annotated in this study. The organization and gene content of new sequenced mitogenomes were conserved, except for significant variation of the control region. All the PCGs started with the typical ATN codons and most ended with complete TAA or TAG codons. Combined with five mitogenomes in NCBI, a total of twelve specimens (including one outgroup) were used in phylogenetic analysis based on 13 PCGs. The result revealed that Furcilarnaca was a monophyletic group. These data will provide more meaningful genetic information and validate the phylogenetic relationships within the Gryllacrididae.  


10.6036/10115 ◽  
2022 ◽  
Vol 97 (1) ◽  
pp. 71-78
Author(s):  
Li-Pang Chen ◽  
Syamsiyatul Muzayyanah ◽  
SU-FEN YANG ◽  
Bin Wang ◽  
Ting-An Jiang ◽  
...  

Control charts are effective tools for detecting out-of-control conditions of process parameters in manufacturing and service industries. The development of distribution-free control charts is important in statistical process control when the process quality variable follows an unknown or a non-normal distribution. This research thus proposes to use a distribution-free technology to establish a new control region based on the exponentially weighted moving average median statistic and exponentially weighted moving average interquartile range statistic for simultaneously monitoring the process location and dispersion and further sets up a corresponding new control chart. We compute the out-of-control average run length to evaluate out-of-control detection performance of the proposed control region and also compare the proposed control region with some existing location and dispersion control charts. Results show that our proposed chart always exhibits superior detection performance when the shifts in process location and/or dispersion are small or moderate. The new control region is thus recommended. Keywords: control chart, distribution-free, dispersion and location, EWMA, kernel control region, kernel density estimation.


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 ◽  
...  

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.


Author(s):  
Jeffrey A. Rappaport ◽  
Ariana A. Entezari ◽  
Adi Caspi ◽  
Signe Caksa ◽  
Aakash V. Jhaveri ◽  
...  

2021 ◽  
Author(s):  
◽  
Jana Wold

<p>The Diomedeidae (Albatrosses) family is comprised of 22 recognised species, 13 are of high conservation concern because they are experiencing population declines. The taxonomy of albatrosses has always been problematic, which makes it difficult to estimate the number and size of breeding groups within a species. The Northern Buller’s Albatross (Thalassarche bulleri platei) and Southern Buller’s Albatross (Thalassarche bulleri bulleri) (Robertson & Nunn 1998; Turbott 1990) were recognised as separate species until 2006. A review of morphological data provided a basis for defining them as one species (Thalassarche bulleri); a result that was supported by international conservation agreements. However, there was no genetic data available at the time to corroborate the taxonomic change. The species status of Buller’s Albatross ssp. is an important issue because they are consistently recorded in the top five observed seabird interactions with commercial fishing vessels within New Zealand's Exclusive Economic Zone. Despite their prevalence in fisheries interactions, the relative impact of commercial fishing activity on northern and southern populations is unknown. Incidental mortality of albatrosses in commercial fisheries is recognised as a primary source of population disturbance.  The overall goal of this thesis research was to investigate the genetic differences between the two sub-species of Buller’s Albatross. DNA was isolated from blood samples collected from a total of 73 birds from two Northern Buller’s Albatross colonies (n = 26) and two Southern Buller’s Albatross colonies (n = 47). The degree of genetic differentiation between the Northern and Southern taxa was estimated using DNA sequences from a 221 bp fragment of the mitochondrial control region, Domain II (CRII). The genetic differentiation between regional colony groups was high (pairwise ΦST = 0.621, p < 0.00001). Two haplogroups were identified within Northern Buller’s Albatross, while Southern Buller’s Albatross samples composed a single haplogroup. An analysis of molecular variance did not find any significant population structuring at the colony level. All individuals sampled from fisheries bycatch (n = 97) were assigned with maximum probability to either Northern (n = 19) or Southern Buller’s Albatross (n = 78; P = 1.00). The DNA sequences differences found in the mitochondrial control region can be used to assign provenance of T. bulleri ssp. samples, which will be a useful conservation management tool.  In addition, a genome wide set of markers was obtained using a Genotyping by Sequencing approach. DNA was digested using restriction enzymes, fragments were labeled adaptor sequences, and shotgun sequenced on an Illumina platform by AgResearch. The Stacks pipeline was used to filter the sequences and obtain a set of single nucleotide polymorphism (SNP) markers across the genome. Estimates of genetic diversity and gene flow were conducted for 26 319 putative loci comprised of 54,061 single nucleotide polymorphisms. Estimates of genetic diversity were consistent across datasets with both taxa exhibiting similar levels of nucleotide diversity (Northern π ≈ 0.002 – 0.004; Southern π ≈ 0.002 – 0.003). However, estimates of genetic differentiation increased slightly as filtering protocols became increasingly restrictive (FST ≈ 0.019 – 0.048). This low level of differentiation was supported by admixture analyses, which identified two distinct ‘clusters’, one corresponding to T. b. platei and the second to T. b. bulleri. The results of this research demonstrate that Northern and Southern Buller’s Albatrosses are two genetically distinct groups.</p>


2021 ◽  
Author(s):  
◽  
Jana Wold

<p>The Diomedeidae (Albatrosses) family is comprised of 22 recognised species, 13 are of high conservation concern because they are experiencing population declines. The taxonomy of albatrosses has always been problematic, which makes it difficult to estimate the number and size of breeding groups within a species. The Northern Buller’s Albatross (Thalassarche bulleri platei) and Southern Buller’s Albatross (Thalassarche bulleri bulleri) (Robertson & Nunn 1998; Turbott 1990) were recognised as separate species until 2006. A review of morphological data provided a basis for defining them as one species (Thalassarche bulleri); a result that was supported by international conservation agreements. However, there was no genetic data available at the time to corroborate the taxonomic change. The species status of Buller’s Albatross ssp. is an important issue because they are consistently recorded in the top five observed seabird interactions with commercial fishing vessels within New Zealand's Exclusive Economic Zone. Despite their prevalence in fisheries interactions, the relative impact of commercial fishing activity on northern and southern populations is unknown. Incidental mortality of albatrosses in commercial fisheries is recognised as a primary source of population disturbance.  The overall goal of this thesis research was to investigate the genetic differences between the two sub-species of Buller’s Albatross. DNA was isolated from blood samples collected from a total of 73 birds from two Northern Buller’s Albatross colonies (n = 26) and two Southern Buller’s Albatross colonies (n = 47). The degree of genetic differentiation between the Northern and Southern taxa was estimated using DNA sequences from a 221 bp fragment of the mitochondrial control region, Domain II (CRII). The genetic differentiation between regional colony groups was high (pairwise ΦST = 0.621, p < 0.00001). Two haplogroups were identified within Northern Buller’s Albatross, while Southern Buller’s Albatross samples composed a single haplogroup. An analysis of molecular variance did not find any significant population structuring at the colony level. All individuals sampled from fisheries bycatch (n = 97) were assigned with maximum probability to either Northern (n = 19) or Southern Buller’s Albatross (n = 78; P = 1.00). The DNA sequences differences found in the mitochondrial control region can be used to assign provenance of T. bulleri ssp. samples, which will be a useful conservation management tool.  In addition, a genome wide set of markers was obtained using a Genotyping by Sequencing approach. DNA was digested using restriction enzymes, fragments were labeled adaptor sequences, and shotgun sequenced on an Illumina platform by AgResearch. The Stacks pipeline was used to filter the sequences and obtain a set of single nucleotide polymorphism (SNP) markers across the genome. Estimates of genetic diversity and gene flow were conducted for 26 319 putative loci comprised of 54,061 single nucleotide polymorphisms. Estimates of genetic diversity were consistent across datasets with both taxa exhibiting similar levels of nucleotide diversity (Northern π ≈ 0.002 – 0.004; Southern π ≈ 0.002 – 0.003). However, estimates of genetic differentiation increased slightly as filtering protocols became increasingly restrictive (FST ≈ 0.019 – 0.048). This low level of differentiation was supported by admixture analyses, which identified two distinct ‘clusters’, one corresponding to T. b. platei and the second to T. b. bulleri. The results of this research demonstrate that Northern and Southern Buller’s Albatrosses are two genetically distinct groups.</p>


Viruses ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 2314
Author(s):  
Kazuo Nakamichi ◽  
Toshio Shimokawa

JC virus (JCV), as an archetype, establishes a lifelong latent or persistent infection in many healthy individuals. In immunocompromised patients, prototype JCV with variable mutations in the non-coding control region (NCCR) causes progressive multifocal leukoencephalopathy (PML), a severe demyelinating disease. This study was conducted to create a database of NCCR sequences annotated with transcription factor binding sites (TFBSs) and statistically analyze the mutational pattern of the JCV NCCR. JCV NCCRs were extracted from >1000 sequences registered in GenBank, and TFBSs within each NCCR were identified by computer simulation, followed by examination of their prevalence, multiplicity, and location by statistical analyses. In the NCCRs of the prototype JCV, the limited types of TFBSs, which are mainly present in regions D through F of archetype JCV, were significantly reduced. By contrast, modeling count data revealed that several TFBSs located in regions C and E tended to overlap in the prototype NCCRs. Based on data from the BioGPS database, genes encoding transcription factors that bind to these TFBSs were expressed not only in the brain but also in the peripheral sites. The database and NCCR patterns obtained in this study could be a suitable platform for analyzing JCV mutations and pathogenicity.


2021 ◽  
Author(s):  
◽  
Rachel Zoe Wilcox

<p>Notolabrus celidotus (the New Zealand spotty) is a common rocky reef species that is endemic to New Zealand. This species is the most abundant demersal reef fish in New Zealand, and is distributed throughout the North and South Islands, and Stewart Island. Notolabrus celidotus consumes a wide variety of small invertebrates, and juveniles are reliant on coastal kelp forests as nursery habitats. Because N. celidotus is such a common species on New Zealand rocky reefs it is a good model species for population genetic studies.  The primary goal of this research was to investigate new genetic markers and add new sample locations to bolster previous genetic population data from N. celidotus. The thesis research utilised DNA sequences obtained from a 454 massively parallel DNA sequencer and reports six new microsatellite loci for N. celidotus. These loci are the first microsatellite DNA markers to be developed for this species. Additional mitochondrial DNA (mtDNA) control region sequences were obtained from new samples of N. celidotus and combined with previously reported mtDNA sequences. Increasing the sample size improved the genetic coverage of N. celidotus populations around coastal New Zealand. The mtDNA sequences were analysed to examine the population connectivity and demographic history of N. celidotus. The microsatellite DNA loci reported in this study were also used to examine the levels of genetic diversity and population structure in N. celidotus.  Results of the combined genetic analyses revealed extremely high levels of genetic diversity among the population sample of the mtDNA control region. Both the mitochondrial DNA and microsatellite DNA analyses showed a distinct lack of population genetic structuring, which suggests there is constant mixing of N. celidotus among sites. The results of this study have the potential to inform the expectations about the genetic structure of closely related wrasse species, such as Notolabrus fucicola, as well as other coastal species that have a similar life history, dispersal power, and New Zealand-wide distribution.</p>


2021 ◽  
Author(s):  
◽  
Rachel Zoe Wilcox

<p>Notolabrus celidotus (the New Zealand spotty) is a common rocky reef species that is endemic to New Zealand. This species is the most abundant demersal reef fish in New Zealand, and is distributed throughout the North and South Islands, and Stewart Island. Notolabrus celidotus consumes a wide variety of small invertebrates, and juveniles are reliant on coastal kelp forests as nursery habitats. Because N. celidotus is such a common species on New Zealand rocky reefs it is a good model species for population genetic studies.  The primary goal of this research was to investigate new genetic markers and add new sample locations to bolster previous genetic population data from N. celidotus. The thesis research utilised DNA sequences obtained from a 454 massively parallel DNA sequencer and reports six new microsatellite loci for N. celidotus. These loci are the first microsatellite DNA markers to be developed for this species. Additional mitochondrial DNA (mtDNA) control region sequences were obtained from new samples of N. celidotus and combined with previously reported mtDNA sequences. Increasing the sample size improved the genetic coverage of N. celidotus populations around coastal New Zealand. The mtDNA sequences were analysed to examine the population connectivity and demographic history of N. celidotus. The microsatellite DNA loci reported in this study were also used to examine the levels of genetic diversity and population structure in N. celidotus.  Results of the combined genetic analyses revealed extremely high levels of genetic diversity among the population sample of the mtDNA control region. Both the mitochondrial DNA and microsatellite DNA analyses showed a distinct lack of population genetic structuring, which suggests there is constant mixing of N. celidotus among sites. The results of this study have the potential to inform the expectations about the genetic structure of closely related wrasse species, such as Notolabrus fucicola, as well as other coastal species that have a similar life history, dispersal power, and New Zealand-wide distribution.</p>


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