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Nuclear genomes distinguish cryptic species suggested by their DNA barcodes and ecology.

ABSTRACT: DNA sequencing brings another dimension to exploration of biodiversity, and large-scale mitochondrial DNA cytochrome oxidase I barcoding has exposed many potential new cryptic species. Here, we add complete nuclear genome sequencing to DNA barcoding, ecological distribution, natural history, and subtleties of adult color pattern and size to show that a widespread neotropical skipper butterfly known as Udranomia kikkawai (Weeks) comprises three different species in Costa Rica. Full-length barcodes obtained from all three century-old Venezuelan syntypes of U. kikkawai show that it is a rainforest species occurring from Costa Rica to Brazil. The two new species are Udranomia sallydaleyae Burns, a dry forest denizen occurring from Costa Rica to Mexico, and Udranomia tomdaleyi Burns, which occupies the junction between the rainforest and dry forest and currently is known only from Costa Rica. Whereas the three species are cryptic, differing but slightly in appearance, their complete nuclear genomes totaling 15 million aligned positions reveal significant differences consistent with their 0.00065-Mbp (million base pair) mitochondrial barcodes and their ecological diversification. DNA barcoding of tropical insects reared by a massive inventory suggests that the presence of cryptic species is a widespread phenomenon and that further studies will substantially increase current estimates of insect species richness.

SUBMITTER: Janzen DH

PROVIDER: S-EPMC5547596 | biostudies-literature | 2017 Aug

REPOSITORIES: biostudies-literature

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Nuclear genomes distinguish cryptic species suggested by their DNA barcodes and ecology.

Janzen Daniel H DH Burns John M JM Cong Qian Q Hallwachs Winnie W Dapkey Tanya T Manjunath Ramya R Hajibabaei Mehrdad M Hebert Paul D N PDN Grishin Nick V NV

Proceedings of the National Academy of Sciences of the United States of America 20170717 31

DNA sequencing brings another dimension to exploration of biodiversity, and large-scale mitochondrial DNA cytochrome oxidase I barcoding has exposed many potential new cryptic species. Here, we add complete nuclear genome sequencing to DNA barcoding, ecological distribution, natural history, and subtleties of adult color pattern and size to show that a widespread neotropical skipper butterfly known as <i>Udranomia kikkawai</i> (Weeks) comprises three different species in Costa Rica. Full-length ...[more]

PMID: 28716927

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Project description:BackgroundMajority of the species within Senecioneae are classified in Senecio, making it the tribe's largest genus. Certain intergeneric relationships within the tribe are vaguely defined, with the genus Senecio being partly linked to this ambiguity. Infrageneric relationships within Senecio remain largely unknown and consequently, the genus has undergone continuous expansion and contraction over the recent past due to addition and removal of taxa. Dendrosenecio, an endemic genus in Africa, is one of its segregate genera. To heighten the understanding of species divergence and phylogeny within the tribe, the complete chloroplast genomes of the first five Senecio and six Dendrosenecio species were sequenced and analyzed in this study.ResultsThe entire length of the complete chloroplast genomes was?~?150 kb and?~?151 kb in Dendrosenecio and Senecio respectively. Characterization of the 11 chloroplast genomes revealed a significant degree of similarity particularly in their organization, gene content, repetitive sequence composition and patterns of codon usage. The chloroplast genomes encoded an equal number of unique genes out of which 80 were protein-coding genes, 30 transfer ribonucleic acid, and four ribosomal ribonucleic acid genes. Based on comparative sequence analyses, the level of divergence was lower in Dendrosenecio. A total of 331 and 340 microsatellites were detected in Senecio and Dendrosenecio, respectively. Out of which, 25 and five chloroplast microsatellites (cpSSR) were identified as potentially valuable molecular markers. Also, through whole chloroplast genome comparisons and DNA polymorphism tests, ten divergent hotspots were identified. Potential primers were designed creating genomic tools to further molecular studies within the tribe. Intergeneric relationships within the tribe were firmly resolved using genome-scale dataset in partitioned and unpartitioned schemes. Two main clades, corresponding to two subtribes within the Senecioneae, were formed with the genus Ligularia forming a single clade while the other had Dendrosenecio, Pericallis, Senecio and Jacobaea. A sister relationship was revealed between Dendrosenecio and Pericallis whereas Senecio, and Jacobaea were closely placed in a different clade.ConclusionBesides emphasizing on the potential of chloroplast genome data in resolving intergeneric relationships within Senecioneae, this study provides genomic resources to facilitate species identification and phylogenetic reconstructions within the respective genera.

Project description:DNA barcoding has been used worldwide to identify biological specimens and to delimit species. It represents a cost-effective, fast, and efficient way to assess biodiversity with help of the public Barcode of Life Database (BOLD) accounting for more than 236,000 animal species and more than 10 million barcode sequences. Here, we performed a meta-analysis of available barcode data of central European Coleoptera to detect intraspecific genetic patterns among ecological groups in relation to geographic distance with the aim to investigate a possible link between infraspecific variation and species ecology. We collected information regarding feeding style, body size, as well as habitat and biotope preferences. Mantel tests and two variants of Procrustes analysis, both involving the Principal Coordinates Neighborhood Matrices (PCNM) approach, were applied on genetic and geographic distance matrices. However, significance levels were too low to further use the outcome for further trait investigation: these were in mean for all ecological guilds only 7.5, 9.4, or 15.6% for PCNM + PCA, NMDS + PCA, and Mantel test, respectively, or at best 28% for a single guild. Our study confirmed that certain ecological traits were associated with higher species diversity and foster stronger genetic differentiation. Results suggest that increased numbers of species, sampling localities, and specimens for a chosen area of interest may give new insights to explore barcode data and species ecology for the scope of conservation on a larger scale. We performed a meta-analysis of available barcode data of central European beetles to detect intraspecific genetic patterns among ecological groups in relation to geographic distance, regarding feeding style, body size, as well as habitat and biotope preferences. Our study confirmed that certain ecological traits were associated with higher species diversity and foster stronger genetic differentiation. However, significance levels were too low to further use the outcome for further trait investigation.

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Nuclear genomes distinguish cryptic species suggested by their DNA barcodes and ecology.

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Nuclear genomes distinguish cryptic species suggested by their DNA barcodes and ecology.

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