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Genes 2019, 10(1), 38; https://doi.org/10.3390/genes10010038

Highly Resolved Phylogenetic Relationships within Order Acipenseriformes According to Novel Nuclear Markers

1
Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing 400715, China
2
Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
3
Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research, 10315 Berlin, Germany
*
Authors to whom correspondence should be addressed.
Dehuai Luo and Yanping Li contributed equally to this work.
Received: 26 November 2018 / Revised: 28 December 2018 / Accepted: 2 January 2019 / Published: 10 January 2019
(This article belongs to the Special Issue Conservation Genetics and Genomics)
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Abstract

Order Acipenseriformes contains 27 extant species distributed across the northern hemisphere, including so-called “living fossil” species of garfish and sturgeons. Previous studies have focused on their mitochondrial genetics and have rarely used nuclear genetic data, leaving questions as to their phylogenetic relationships. This study aimed to utilize a bioinformatics approach to screen for candidate single-copy nuclear genes, using transcriptomic data from sturgeon species and genomic data from the spotted gar, Lepisosteus oculatus. We utilized nested polymerase chain reaction (PCR) and degenerate primers to identify nuclear protein-coding (NPC) gene markers to determine phylogenetic relationships among the Acipenseriformes. We identified 193 nuclear single-copy genes, selected from 1850 candidate genes with at least one exon larger than 700 bp. Forty-three of these genes were used for primer design and development of 30 NPC markers, which were sequenced for at least 14 Acipenseriformes species. Twenty-seven NPC markers were found completely in 16 species. Gene trees according to Bayesian inference (BI) and maximum likelihood (ML) were calculated based on the 30 NPC markers (20,946 bp total). Both gene and species trees produced very similar topologies. A molecular clock model estimated the divergence time between sturgeon and paddlefish at 204.1 Mya, approximately 10% later than previous estimates based on cytochrome b data (184.4 Mya). The successful development and application of NPC markers provides a new perspective and insight for the phylogenetic relationships of Acipenseriformes. Furthermore, the newly developed nuclear markers may be useful in further studies on the conservation, evolution, and genomic biology of this group. View Full-Text
Keywords: nuclear markers; phylogeny; Acipenseriformes; molecular clock nuclear markers; phylogeny; Acipenseriformes; molecular clock
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Luo, D.; Li, Y.; Zhao, Q.; Zhao, L.; Ludwig, A.; Peng, Z. Highly Resolved Phylogenetic Relationships within Order Acipenseriformes According to Novel Nuclear Markers. Genes 2019, 10, 38.

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