Some mitochondrial genes perform better for damselfly phylogenetics: species- and population-level analyses of four complete mitogenomes of Euphaea sibling species

Yun Chieh Cheng, Ming Yu Chen, Jo Fan Wang, Ai Ping Liang, Chung-Ping Lin

研究成果: 雜誌貢獻文章

1 引文 (Scopus)

摘要

Animal mitochondrial genes continue to provide an efficient and inexpensive assessment of genetic diversity. However, which mitochondrial genes should be selected to best estimate species phylogeny and population genealogy remains uncertain for most under-sampled taxa. We analysed four complete mitochondrial genomes of sibling species of Euphaea damselflies, E. decorata, E. ornata, E. formosa and E. yayeyamana (Insecta, Odonata, Euphaeidae), to examine the patterns of selection and to evaluate the phylogenetic utility of the mitochondrial genes compared with nuclear genes. The results indicated that mitochondrial protein-coding nad2 (NADH dehydrogenase subunit 2) and noncoding A + T-rich (control region) genes have the highest mutation rates and more phylogenetic utility [higher parsimony-informative sites; higher α (the shape parameter of gamma distribution); lower rates of heterogeneity among sites; and higher relative substitution rates] than all the other mitochondrial and nuclear genes analysed. In contrast, the animal DNA barcoding gene cytochrome c oxidase subunit 1 (cox1) had average values for all estimated parameters of phylogenetic performance and was sometimes outperformed by other mitochondrial genes. The majority of the mitochondrial and nuclear genes in Euphaea damselflies have experienced frequent purifying selection, except for two cases of potential positive selection in NADH dehydrogenase subunit 3 (nad3) and elongation factor 1α (EF1α), and all mitochondrial genes had experienced stronger purifying selection than nuclear genes. Our findings indicated that mitochondrial nad2 and the A + T-rich region should be selected to provide efficient and high-resolution phylogenetic markers for damselflies at the species and population level.

原文英語
頁(從 - 到)702-715
頁數14
期刊Systematic Entomology
43
發行號4
DOIs
出版狀態已發佈 - 2018 十月 1

指紋

damselfly
Zygoptera
sibling species
phylogenetics
gene
phylogeny
genes
NADH dehydrogenase
mitochondrial genome
genealogy
animal
DNA barcoding
Odonata
Insecta
cytochrome-c oxidase
cytochrome
mutation
animals
substitution
genome

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Insect Science

引用此文

Some mitochondrial genes perform better for damselfly phylogenetics : species- and population-level analyses of four complete mitogenomes of Euphaea sibling species. / Cheng, Yun Chieh; Chen, Ming Yu; Wang, Jo Fan; Liang, Ai Ping; Lin, Chung-Ping.

於: Systematic Entomology, 卷 43, 編號 4, 01.10.2018, p. 702-715.

研究成果: 雜誌貢獻文章

@article{943469c0464b431784abe9c507ec9e5d,
title = "Some mitochondrial genes perform better for damselfly phylogenetics: species- and population-level analyses of four complete mitogenomes of Euphaea sibling species",
abstract = "Animal mitochondrial genes continue to provide an efficient and inexpensive assessment of genetic diversity. However, which mitochondrial genes should be selected to best estimate species phylogeny and population genealogy remains uncertain for most under-sampled taxa. We analysed four complete mitochondrial genomes of sibling species of Euphaea damselflies, E. decorata, E. ornata, E. formosa and E. yayeyamana (Insecta, Odonata, Euphaeidae), to examine the patterns of selection and to evaluate the phylogenetic utility of the mitochondrial genes compared with nuclear genes. The results indicated that mitochondrial protein-coding nad2 (NADH dehydrogenase subunit 2) and noncoding A + T-rich (control region) genes have the highest mutation rates and more phylogenetic utility [higher parsimony-informative sites; higher α (the shape parameter of gamma distribution); lower rates of heterogeneity among sites; and higher relative substitution rates] than all the other mitochondrial and nuclear genes analysed. In contrast, the animal DNA barcoding gene cytochrome c oxidase subunit 1 (cox1) had average values for all estimated parameters of phylogenetic performance and was sometimes outperformed by other mitochondrial genes. The majority of the mitochondrial and nuclear genes in Euphaea damselflies have experienced frequent purifying selection, except for two cases of potential positive selection in NADH dehydrogenase subunit 3 (nad3) and elongation factor 1α (EF1α), and all mitochondrial genes had experienced stronger purifying selection than nuclear genes. Our findings indicated that mitochondrial nad2 and the A + T-rich region should be selected to provide efficient and high-resolution phylogenetic markers for damselflies at the species and population level.",
author = "Cheng, {Yun Chieh} and Chen, {Ming Yu} and Wang, {Jo Fan} and Liang, {Ai Ping} and Chung-Ping Lin",
year = "2018",
month = "10",
day = "1",
doi = "10.1111/syen.12299",
language = "English",
volume = "43",
pages = "702--715",
journal = "Systematic Entomology",
issn = "0307-6970",
publisher = "Wiley-Blackwell",
number = "4",

}

TY - JOUR

T1 - Some mitochondrial genes perform better for damselfly phylogenetics

T2 - species- and population-level analyses of four complete mitogenomes of Euphaea sibling species

AU - Cheng, Yun Chieh

AU - Chen, Ming Yu

AU - Wang, Jo Fan

AU - Liang, Ai Ping

AU - Lin, Chung-Ping

PY - 2018/10/1

Y1 - 2018/10/1

N2 - Animal mitochondrial genes continue to provide an efficient and inexpensive assessment of genetic diversity. However, which mitochondrial genes should be selected to best estimate species phylogeny and population genealogy remains uncertain for most under-sampled taxa. We analysed four complete mitochondrial genomes of sibling species of Euphaea damselflies, E. decorata, E. ornata, E. formosa and E. yayeyamana (Insecta, Odonata, Euphaeidae), to examine the patterns of selection and to evaluate the phylogenetic utility of the mitochondrial genes compared with nuclear genes. The results indicated that mitochondrial protein-coding nad2 (NADH dehydrogenase subunit 2) and noncoding A + T-rich (control region) genes have the highest mutation rates and more phylogenetic utility [higher parsimony-informative sites; higher α (the shape parameter of gamma distribution); lower rates of heterogeneity among sites; and higher relative substitution rates] than all the other mitochondrial and nuclear genes analysed. In contrast, the animal DNA barcoding gene cytochrome c oxidase subunit 1 (cox1) had average values for all estimated parameters of phylogenetic performance and was sometimes outperformed by other mitochondrial genes. The majority of the mitochondrial and nuclear genes in Euphaea damselflies have experienced frequent purifying selection, except for two cases of potential positive selection in NADH dehydrogenase subunit 3 (nad3) and elongation factor 1α (EF1α), and all mitochondrial genes had experienced stronger purifying selection than nuclear genes. Our findings indicated that mitochondrial nad2 and the A + T-rich region should be selected to provide efficient and high-resolution phylogenetic markers for damselflies at the species and population level.

AB - Animal mitochondrial genes continue to provide an efficient and inexpensive assessment of genetic diversity. However, which mitochondrial genes should be selected to best estimate species phylogeny and population genealogy remains uncertain for most under-sampled taxa. We analysed four complete mitochondrial genomes of sibling species of Euphaea damselflies, E. decorata, E. ornata, E. formosa and E. yayeyamana (Insecta, Odonata, Euphaeidae), to examine the patterns of selection and to evaluate the phylogenetic utility of the mitochondrial genes compared with nuclear genes. The results indicated that mitochondrial protein-coding nad2 (NADH dehydrogenase subunit 2) and noncoding A + T-rich (control region) genes have the highest mutation rates and more phylogenetic utility [higher parsimony-informative sites; higher α (the shape parameter of gamma distribution); lower rates of heterogeneity among sites; and higher relative substitution rates] than all the other mitochondrial and nuclear genes analysed. In contrast, the animal DNA barcoding gene cytochrome c oxidase subunit 1 (cox1) had average values for all estimated parameters of phylogenetic performance and was sometimes outperformed by other mitochondrial genes. The majority of the mitochondrial and nuclear genes in Euphaea damselflies have experienced frequent purifying selection, except for two cases of potential positive selection in NADH dehydrogenase subunit 3 (nad3) and elongation factor 1α (EF1α), and all mitochondrial genes had experienced stronger purifying selection than nuclear genes. Our findings indicated that mitochondrial nad2 and the A + T-rich region should be selected to provide efficient and high-resolution phylogenetic markers for damselflies at the species and population level.

UR - http://www.scopus.com/inward/record.url?scp=85045324240&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85045324240&partnerID=8YFLogxK

U2 - 10.1111/syen.12299

DO - 10.1111/syen.12299

M3 - Article

AN - SCOPUS:85045324240

VL - 43

SP - 702

EP - 715

JO - Systematic Entomology

JF - Systematic Entomology

SN - 0307-6970

IS - 4

ER -