scholarly journals Novel Intron Phylogeny Supports Plumage Convergence in Orioles (Icterus)

The Auk ◽  
2003 ◽  
Vol 120 (4) ◽  
pp. 961-969 ◽  
Author(s):  
Eva Sanders Allen ◽  
Kevin E. Omland
Keyword(s):  
New World ◽  
Mitochondrial Gene ◽  
Gene Tree ◽  
Nuclear Gene ◽  
Gene Trees ◽  
Mt Dna ◽  
Single Linkage ◽  
Mitochondrial Data ◽  
Phylogenetic Resolution ◽  
Phylogenetic Hypotheses

Abstract A recent study of New World orioles (Icterus spp.), which traced a large number of plumage characters onto a mitochondrial DNA phylogeny, reported high frequencies of evolutionary convergence and reversal of plumage characters (Omland and Lanyon 2000). Although those results are consistent with other smaller scale studies that have documented plumage homoplasy, the mitochondrial genome is inherited as a single linkage group, so mitochondrial data represent only one gene tree. The mitochondrial (mt) DNA tree may not reflect the true evolutionary history of a lineage; therefore, it remains possible that the plumage characters could reflect the true species phylogeny. Other rapidly evolving regions of DNA can provide independent phylogenetic hypotheses useful for evaluating mitochondrial gene trees. A novel phylogenetic marker, a region of the nuclear gene ornithine decarboxylase (ODC) spanning from exon 6 to exon 8, was sequenced in 10 oriole species. The resultant nuclear gene tree reconstructs the same three major oriole clades as the mtDNA tree (Omland et al. 1999), supporting the conclusion that plumage evolution in the New World orioles has been highly homoplastic. Although most phylogenetic studies that have employed introns report greatest resolution at the genus or family level, ODC appears to offer some degree of phylogenetic resolution for infrageneric analyses. However, that intron has clearly not sorted to monophyly within or between closely related species.

A new living species of degu, genus Octodon (Hystricomorpha: Octodontidae)

2020 ◽  
Author(s):  
Guillermo D’Elía ◽  
Pablo Teta ◽  
Diego H Verzi ◽  
Richard Cadenillas ◽  
James L Patton
Keyword(s):  
New Species ◽  
Mitochondrial Gene ◽  
Gene Tree ◽  
Nuclear Gene ◽  
Qualitative Assessment ◽  
Large Set ◽  
Gene Trees ◽  
Cranial Measurements ◽  
Living Species ◽  
Gene Data

Abstract We combine morphological (qualitative and quantitative data) and genetic (one mitochondrial and one nuclear gene) data from a large set of specimens of Octodon from the four currently recognized living species of the genus. The integration of the results (qualitative assessment, multivariate analysis of cranial measurements, and gene trees) allows us to state that 1) the current taxonomic scheme does not reflect the species diversity of Octodon; 2) in particular, as currently understood O. bridgesii likely is a complex of three species; 3) one of these, encompassing the southern populations of the genus, in the Araucanía Region (Chile) and Neuquén Province (Argentina), is named and described here as a new species; and 4) the mitochondrial gene tree departs from the nuclear gene tree with respect to O. pacificus and the new species here described.

scholarly journals Cytonuclear discordance in the crowned-sparrows, Zonotrichia atricapilla and Zonotrichia leucophrys: a mitochondrial selective sweep?

2020 ◽  
Author(s):  
Rebecca S. Taylor ◽  
Ashley C. Bramwell ◽  
Rute Clemente-Carvalho ◽  
Nicholas A. Cairns ◽  
Frances Bonier ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Environmental Changes ◽  
Incomplete Lineage Sorting ◽  
Mitochondrial Gene ◽  
Nuclear Gene ◽  
Phylogeographic Structure ◽  
Gene Trees ◽  
Lineage Sorting ◽  
Reciprocal Monophyly ◽  
Mitochondrial Introgression

ABSTRACTThe golden-crowned (Zonotrichia atricapilla) and white-crowned (Z. leucophrys) sparrows have been presented as a compelling case for rapid speciation. They display divergence in song and plumage with overlap in their breeding ranges implying reproductive isolation, but have almost identical mitochondrial genomes. Previous research proposed hybridization and subsequent mitochondrial introgression as an alternate explanation, but lacked robust nuclear gene trees to distinguish between introgression and incomplete lineage sorting. We test for signatures of these processes between Z. atricapilla and Z. leucophrys, and investigate the relationships among Z. leucophrys subspecies, using mitochondrial sequencing and a reduced representation nuclear genomic dataset. Contrary to the paraphyly evident in mitochondrial gene trees, we confirmed the reciprocal monophyly of Z. atricapilla and Z. leucophrys using large panels of single nucleotide polymorphism (SNPs). The pattern of cytonuclear discordance is consistent with limited, historical hybridization and mitochondrial introgression, rather than a recent origin and incomplete lineage sorting between recent sister species. We found evidence of nuclear phylogeographic structure within Z. leucophrys with two distinct clades. Altogether, our results support the true species status of Z. atricapilla and Z. leucophrys, and indicate deeper divergences between the two species than inferred using mitochondrial markers. Our results demonstrate the limitations of relying solely on mitochondrial DNA for taxonomy, and raise questions about the possibility of selection on the mitochondrial genome during temperature oscillations (e.g. during the Pleistocene). Historical mitochondrial introgression facilitated by past environmental changes could cause erroneous dating of lineage splitting in other taxa when based on mitochondrial DNA alone.

scholarly journals Variation Across Mitochondrial Gene Trees Provides Evidence for Systematic Error: How Much Gene Tree Variation Is Biological?

2018 ◽  
Vol 67 (5) ◽  
pp. 847-860 ◽  
Author(s):  
Emilie J Richards ◽  
Jeremy M Brown ◽  
Anthony J Barley ◽  
Rebecca A Chong ◽  
Robert C Thomson
Keyword(s):  
Systematic Error ◽  
Mitochondrial Gene ◽  
Gene Tree ◽  
Gene Trees

scholarly journals Ancient and recent introgression shape the evolutionary history of pollinator adaptation and speciation in a model monkeyflower radiation (Mimulus section Erythranthe)

PLoS Genetics ◽  
2021 ◽  
Vol 17 (2) ◽  
pp. e1009095
Author(s):  
Thomas C. Nelson ◽  
Angela M. Stathos ◽  
Daniel D. Vanderpool ◽  
Findley R. Finseth ◽  
Yao-wu Yuan ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Gene Tree ◽  
Nuclear Gene ◽  
Evolutionary Genetics ◽  
Species Tree ◽  
Pollination Syndrome ◽  
Gene Trees ◽  
Genome Wide ◽  
Hummingbird Pollination ◽  
History Of

Inferences about past processes of adaptation and speciation require a gene-scale and genome-wide understanding of the evolutionary history of diverging taxa. In this study, we use genome-wide capture of nuclear gene sequences, plus skimming of organellar sequences, to investigate the phylogenomics of monkeyflowers in Mimulus section Erythranthe (27 accessions from seven species). Taxa within Erythranthe, particularly the parapatric and putatively sister species M. lewisii (bee-pollinated) and M. cardinalis (hummingbird-pollinated), have been a model system for investigating the ecological genetics of speciation and adaptation for over five decades. Across >8000 nuclear loci, multiple methods resolve a predominant species tree in which M. cardinalis groups with other hummingbird-pollinated taxa (37% of gene trees), rather than being sister to M. lewisii (32% of gene trees). We independently corroborate a single evolution of hummingbird pollination syndrome in Erythranthe by demonstrating functional redundancy in genetic complementation tests of floral traits in hybrids; together, these analyses overturn a textbook case of pollination-syndrome convergence. Strong asymmetries in allele-sharing (Patterson’s D-statistic and related tests) indicate that gene-tree discordance reflects ancient and recent introgression rather than incomplete lineage sorting. Consistent with abundant introgression blurring the history of divergence, low-recombination and adaptation-associated regions support the new species tree, while high-recombination regions generate phylogenetic evidence for sister status for M. lewisii and M. cardinalis. Population-level sampling of core taxa also revealed two instances of chloroplast capture, with Sierran M. lewisii and Southern Californian M. parishii each carrying organelle genomes nested within respective sympatric M. cardinalis clades. A recent organellar transfer from M. cardinalis, an outcrosser where selfish cytonuclear dynamics are more likely, may account for the unexpected cytoplasmic male sterility effects of selfer M. parishii organelles in hybrids with M. lewisii. Overall, our phylogenomic results reveal extensive reticulation throughout the evolutionary history of a classic monkeyflower radiation, suggesting that natural selection (re-)assembles and maintains species-diagnostic traits and barriers in the face of gene flow. Our findings further underline the challenges, even in reproductively isolated species, in distinguishing re-use of adaptive alleles from true convergence and emphasize the value of a phylogenomic framework for reconstructing the evolutionary genetics of adaptation and speciation.

scholarly journals Target enrichment improves phylogenetic resolution in the genus Zanthoxylum (Rutaceae) and indicates both incomplete lineage sorting and hybridization events

2021 ◽  
Author(s):  
Niklas Reichelt ◽  
Jun Wen ◽  
Claudia Paetzold ◽  
Marc Appelhans
Keyword(s):  
High Throughput Sequencing ◽  
Incomplete Lineage Sorting ◽  
Phylogenetic Analyses ◽  
Gene Tree ◽  
Single Copy ◽  
Reticulate Evolution ◽  
Gene Trees ◽  
Target Enrichment ◽  
Lineage Sorting ◽  
Phylogenetic Resolution

Background and aims: Zanthoxylum L. 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. Methods: We developed a custom bait set for target enrichment of 745 exons in Zanthoxylum and applied it to 45 Zanthoxylum species and one Tetradium species as the outgroup. Illumina reads were processed via the HybPhyloMaker pipeline. Phylogenetic inferences were conducted using coalescent and concatenated methods. Concordance was assessed using quartet sampling. Off-target reads were assembled and putative single- and low-copy genes were extracted. Additional phylogenetic analyses were performed based on these alignments. Key results: Four 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 for 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. Conclusion: Target enrichment is suitable to assess 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.

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