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An examination of introgression and incomplete lineage sorting among three closely related species of chocolate-dipped damselfish (genus: Chromis).

ABSTRACT: Aim:To determine the impact of ecological and environmental histories on the evolution of coral reef damselfishes at two adjacent marine biogeographic suture zones. Location:Indo-West Pacific, notably including two suture zones: Socotra and Christmas and Cocos/Keeling Islands. Taxon:Chromis dimidiata, Chromis margaritifer, and Chromis fieldi. Methods:We utilized a combination of nuclear and mitochondrial genetic markers in addition to visual abundance survey data of these fishes. Results:Despite genetic patterns consistent with incomplete lineage sorting and relatively low genetic differentiation among the three studied Chromis species, there is evidence of hybridization between C. margaritifer and C. fieldi at Christmas Island based on molecular and visual identification. Introgression appears to be spreading westwards to other C. fieldi populations based on COI haplotype comparison. Moreover, the genetic distance between C. margaritifer and C. fieldi suggests that Pleistocene sea-level fluctuations may have contributed to allopatric divergence and secondary contact between these two closely related species. Main conclusions:Our study highlights that evolutionary processes in coral reef fishes operate differently between suture zones, possibly due to different ecological and environmental predispositions regulating secondary contact of sister species. While secondary contact likely led to hybridization and introgression at Christmas and Cocos/Keeling Islands, none of those processes seem present at Socotra for the chocolate-dipped damselfish. This difference is likely due to an environmental barrier caused by hydrodynamic regimes in the Gulf of Aden.

SUBMITTER: He S

PROVIDER: S-EPMC6509375 | biostudies-literature | 2019 May

REPOSITORIES: biostudies-literature

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An examination of introgression and incomplete lineage sorting among three closely related species of chocolate-dipped damselfish (genus: <i>Chromis</i>).

He Song S Robitzch Vanessa V Hobbs Jean-Paul A JA Travers Michael J MJ Lozano-Cortés Diego D Berumen Michael L ML DiBattista Joseph D JD

Ecology and evolution 20190419 9

<h4>Aim</h4>To determine the impact of ecological and environmental histories on the evolution of coral reef damselfishes at two adjacent marine biogeographic suture zones.<h4>Location</h4>Indo-West Pacific, notably including two suture zones: Socotra and Christmas and Cocos/Keeling Islands.<h4>Taxon</h4><i>Chromis dimidiata</i>, <i>Chromis margaritifer</i>, and <i>Chromis fieldi</i>.<h4>Methods</h4>We utilized a combination of nuclear and mitochondrial genetic markers in addition to visual abun ...[more]

PMID: 31110695

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Project description:Background and aimsZanthoxylum is the only pantropical genus within Rutaceae, with a few species native to temperate eastern Asia and North America. Efforts using Sanger sequencing failed to resolve the backbone phylogeny of Zanthoxylum. In this study, we employed target-enrichment high-throughput sequencing to improve resolution. Gene trees were examined for concordance and sectional classifications of Zanthoxylum were evaluated. Off-target reads were investigated to identify putative single-copy markers for bait refinement, and low-copy markers for evidence of putative hybridization events.MethodsA custom bait set targeting 354 genes, with a median of 321 bp, was designed for Zanthoxylum and applied to 44 Zanthoxylum species and one Tetradium species as the outgroup. Illumina reads were processed via the HybPhyloMaker pipeline. Phylogenetic inferences were conducted using coalescent and maximum likelihood methods based on concatenated datasets. Concordance was assessed using quartet sampling. Additional phylogenetic analyses were performed on putative single and low-copy genes extracted from off-target reads.Key resultsFour major clades are supported within Zanthoxylum: the African clade, the Z. asiaticum clade, the Asian-Pacific-Australian clade and the American-eastern Asian clade. While overall support has improved, regions of conflict are similar to those previously observed. Gene tree discordances indicate a hybridization event in the ancestor of the Hawaiian lineage, and incomplete lineage sorting in the American backbone. Off-target putative single-copy genes largely confirm on-target results, and putative low-copy genes provide additional evidence for hybridization in the Hawaiian lineage. Only two of the five sections of Zanthoxylum are resolved as monophyletic.ConclusionsTarget enrichment is suitable for assessing phylogenetic relationships in Zanthoxylum. Our phylogenetic analyses reveal that current sectional classifications need revision. Quartet tree concordance indicates several instances of reticulate evolution. Off-target reads are proven useful to identify additional phylogenetically informative regions for bait refinement or gene tree based approaches.

Project description:We investigated genetic variation and evolutionary history of closely related taxa of Picris subsect. Hieracioides with major focus on the widely distributed P. hieracioides and its closely related congeners, P. hispidissima, P. japonica, P. olympica, and P. nuristanica. Accessions from 140 sample sites of the investigated Picris taxa were analyzed on the infra- and the inter-specific level using nuclear (ITS1-5.8S-ITS2 region) and chloroplast (rpl32-trnL(UAG) region) DNA sequences. Genetic patterns of P. hieracioides, P. hispidissima, and P. olympica were shown to be incongruent and, in several cases, both plastid and nuclear alleles transcended borders of the taxa and genetic lineages. The widespread P. hieracioides was genetically highly variable and non-monophyletic across both markers, with allele groups having particular geographic distributions. Generally, all gene trees and networks displayed only a limited and statistically rather unsupported resolution among ingroup taxa causing their phylogenetic relationships to remain rather unresolved. More light on these intricate evolutionary relationships was cast by the Bayesian coalescent-based analysis, although some relationships were still left unresolved. A combination of suite of phylogenetic analyses revealed the ingroup taxa to represent a complex of genetically closely related and morphologically similar entities that have undergone a highly dynamic and recent evolution. This has been especially affected by the extensive and recurrent gene flow among and within the studied taxa and/or by the maintenance of ancestral variation. Paucity of phylogenetically informative signal further hampers the reconstruction of relationships on the infra- as well as on the inter-specific level. In the present study, we have demonstrated that a combination of various phylogenetic analyses of datasets with extremely complex and incongruent phylogenetic signal may shed more light on the interrelationships and evolutionary history of analysed species groups.

Dataset Information

An examination of introgression and incomplete lineage sorting among three closely related species of chocolate-dipped damselfish (genus: Chromis).

Publications

An examination of introgression and incomplete lineage sorting among three closely related species of chocolate-dipped damselfish (genus: <i>Chromis</i>).

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