用于Cervidae条形码物种识别的通用mtDNA片段,使用树系学和机器学习方法的初步分析进行识别
Ewa Filip1,2, Tomasz Strzała3, Edyta Stępień4
1Institute of Biology, University of Szczecin, Wąska 13, 71-415, Szczecin, Poland. ewa.filip@usz.edu.pl.
Scientific reports
|June 5, 2023
概括
这项研究成功地使用线粒体DNA (mtDNA) 测序和先进的生物信息学从退化的骨DNA中识别出自由生活的动物物种. 机器学习方法,特别是BLOG和WEKA.
科学领域:
- 分子生物学分子生物学
- 生物信息学是一种生物信息学.
- 野生动物法医学 野生动物法医学
背景情况:
- 从退化的骨样本中鉴定物种是具有挑战性的.
- 线粒体DNA (mtDNA) 条形编码对于野生动物的识别至关重要.
- 需要先进的计算方法来准确分析短的DNA片段.
研究的目的:
- 用退化骨DNA识别自由生活的动物物种.
- 评估分子和生物信息学工具用于物种识别的有效性.
- 将机器学习方法与DNA条形码准确性的传统方法进行比较.
主要方法:
- 从骨物质中提取总DNA.
- 线粒体细胞染色体b (Cytb) 基因片段的测序.
- 生物信息学工具的应用,包括贝叶斯推断,机器学习 (BLOG,WEKA),基于距离 (TaxonDNA) 和基于树的 (NJ树) 方法.
主要成果:
- 从退化的骨样本中成功识别了Capreolus capreolus,Dama dama和Cervus elaphus的物种.
- 产生了部分Cytb基因序列,丰富了Cervidae物种的GenBank数据库.
- 与TaxonDNA相比,机器学习分类器 (BLOG,WEKA的SMO) 和NJ树显示出更高的区分精度.
结论:
- 短 mtDNA 片段与先进的生物信息学相结合,可以从退化的骨中准确识别物种.
- 机器学习方法为DNA条形码和野生动物法医中的物种歧视提供了高度有效的工具.
- 该研究为Cervidae mtDNA数据库提供了有价值的数据,并验证了新的分析方法.
相关概念视频
Evolutionary Relationships through Genome Comparisons
5.9K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
5.9K
Modern Molecular Taxonomy
56
Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
56
Animal Mitochondrial Genetics
7.7K
Among all the organelles in an animal cell, only mitochondria have their own independent genomes. Animal mitochondrial DNA is a double-stranded, closed-circular molecule with around 20,000 base pairs. Mitochondrial DNA is unique in that one of its two strands, the heavy, or H, -strand is guanine rich, whereas the complementary strand is cytosine rich and called the light, or L, -strand. Compared to nuclear DNA, mitochondrial DNA has a very low percentage of non-coding regions and is marked by...
7.7K
Applications of Molecular Taxonomy
42
Molecular taxonomy has revolutionized the understanding and classification of bacteria, providing precise insights into their diversity, evolutionary relationships, and ecological roles. By utilizing molecular techniques such as DNA sequencing and fingerprinting, researchers have made significant strides in various fields related to bacterial studies.Resolving Taxonomic AmbiguitiesMolecular taxonomy has been instrumental in distinguishing closely related bacterial species initially thought to...
42
Gene Evolution - Fast or Slow?
7.2K
The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
In contrast, regions which code...
7.2K
Multi-species Conserved Sequences
4.0K
Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
4.0K


