Using de novo transcriptomes to decipher the relationships in cutthroat trout subspecies (Oncorhynchus clarkii)

IF 3.5 2区 生物学 Q1 EVOLUTIONARY BIOLOGY
Andrea L. Kokkonen, Peter C. Searle, Dennis K. Shiozawa, R. Paul Evans
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引用次数: 0

Abstract

For almost 200 years, the taxonomy of cutthroat trout (Oncorhynchus clarkii), a salmonid native to Western North America, has been in flux as ichthyologists and fisheries biologists have tried to describe the diversity within these fishes. Starting in the 1950s, Robert Behnke reexamined the cutthroat trout and identified 14 subspecies based on morphological traits, Pleistocene events, and modern geographic ranges. His designations became instrumental in recognizing and preserving the remaining diversity of cutthroat trout. Over time, molecular techniques (i.e. karyotypes, allozymes, mitochondrial DNA, SNPs, and microsatellite arrays) have largely reinforced Behnke's phylogenies, but have also revealed that some relationships are consistently weakly supported. To further resolve these relationships, we generated de novo transcriptomes for nine cutthroat subspecies, as well as a Bear River Bonneville form and two Colorado River lineages (blue and green). We present phylogenies of these subspecies generated from multiple sets of orthologous genes extracted from our transcriptomes. We confirm many of the relationships identified in previous morphological and molecular studies, as well as discuss the importance of significant differences apparent in our phylogenies from these studies within a geological perspective. Specific findings include three distinct clades: (1) Bear River Bonneville form and Yellowstone cutthroat trout; (2) Bonneville cutthroat trout (n = 2); and (3) Greenback and Rio Grande cutthroat trout. We also identify potential gene transfer between Bonneville cutthroat trout and a population of Colorado River green lineage cutthroat trout. Using these findings, it appears that additional groups warrant species-level consideration if other recent species elevations are retained.

Abstract Image

利用全新转录组破译切喉鳟亚种(Oncorhynchus clarkii)之间的关系
切喉鳟(Oncorhynchus clarkii)是一种原产于北美西部的鲑科鱼类,近 200 年来,随着鱼类学家和渔业生物学家试图描述这些鱼类的多样性,其分类学一直在不断变化。从 20 世纪 50 年代开始,罗伯特-贝恩克(Robert Behnke)重新研究了切喉鳟,并根据形态特征、更新世事件和现代地理范围确定了 14 个亚种。他的命名在确认和保护割喉鳟残存的多样性方面发挥了重要作用。随着时间的推移,分子技术(即核型、同工酶、线粒体 DNA、SNPs 和微卫星阵列)在很大程度上加强了 Behnke 的系统进化论,但也揭示出一些关系始终得不到有力的支持。为了进一步理清这些关系,我们为九个割喉亚种、一个熊河邦纳维尔种和两个科罗拉多河种(蓝色和绿色)生成了全新的转录组。我们展示了从我们的转录组中提取的多组直向同源基因生成的这些亚种的系统发生图。我们确认了之前形态学和分子研究中发现的许多关系,并从地质学的角度讨论了这些研究中系统发育明显不同的重要性。具体发现包括三个不同的支系:(1)熊河邦纳维尔形态和黄石切喉鳟;(2)邦纳维尔切喉鳟(n = 2);以及(3)绿背和格兰德河切喉鳟。我们还发现了博纳维尔切喉鳟与科罗拉多河绿系切喉鳟之间的潜在基因转移。根据这些发现,如果保留其他最近的物种等级,似乎还有更多的群体值得在物种级别上加以考虑。
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来源期刊
Evolutionary Applications
Evolutionary Applications 生物-进化生物学
CiteScore
8.50
自引率
7.30%
发文量
175
审稿时长
6 months
期刊介绍: Evolutionary Applications is a fully peer reviewed open access journal. It publishes papers that utilize concepts from evolutionary biology to address biological questions of health, social and economic relevance. Papers are expected to employ evolutionary concepts or methods to make contributions to areas such as (but not limited to): medicine, agriculture, forestry, exploitation and management (fisheries and wildlife), aquaculture, conservation biology, environmental sciences (including climate change and invasion biology), microbiology, and toxicology. All taxonomic groups are covered from microbes, fungi, plants and animals. In order to better serve the community, we also now strongly encourage submissions of papers making use of modern molecular and genetic methods (population and functional genomics, transcriptomics, proteomics, epigenetics, quantitative genetics, association and linkage mapping) to address important questions in any of these disciplines and in an applied evolutionary framework. Theoretical, empirical, synthesis or perspective papers are welcome.
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