Plastome data reveal multiple geographic origins of Quercus Group Ilex

Nucleotide sequences from the plastome are currently the main source for assessing taxonomic and phylogenetic relationships in flowering plants and their historical biogeography at all hierarchical levels. One exception is the large and economically important genus Quercus (oaks). Whereas differentiation patterns of the nuclear genome are in agreement with morphology and the fossil record, diversity patterns in the plastome are at odds with established taxonomic and phylogenetic relationships. However, the extent and evolutionary implications of this incongruence has yet to be fully uncovered. The DNA sequence divergence of four Euro-Mediterranean Group Ilex oak species (Quercus ilex L., Q. coccifera L., Q. aucheri Jaub. & Spach., Q. alnifolia Poech.) was explored at three chloroplast markers (rbcL, trnK-matK, trnH-psbA). Phylogenetic relationships were reconstructed including worldwide members of additional 55 species representing all Quercus subgeneric groups. Family and order sequence data were harvested from gene banks to better frame the observed divergence in larger taxonomic contexts. We found a strong geographic sorting in the focal group and the genus in general that is entirely decoupled from species boundaries. Main plastid haplotypes shared by distinct oak lineages from the same geographic region and high plastid diversity in members of Group Ilex are indicative for a polyphyletic origin of their plastomes. The results suggest that incomplete lineage sorting and repeated phases of unidirectional introgression among ancestral lineages of Group Ilex and two other main Groups of Eurasian oaks (Cyclobalanopsis and Cerris) caused this complex pattern. Comparison with the current phylogenetic synthesis also suggests an initial high- versus mid-latitude biogeographic split within Quercus. High plastome plasticity of Group Ilex reflects geographic area disruptions, possibly linked with high tectonic activity of past and modern distribution ranges, that did not leave imprints in the nuclear genome of modern species and infrageneric lineages.

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Plastome data reveal multiple geographic origins of Quercus Group Ilex

10.7287/peerj.preprints.1615v1 ◽

2015 ◽

Author(s):

Marco Cosimo Simeone ◽

Guido W Grimm ◽

Alessio Papini ◽

Federico Vessella ◽

Simone Cardoni ◽

...

Keyword(s):

Phylogenetic Relationships ◽

Sequence Data ◽

Incomplete Lineage Sorting ◽

Nuclear Genome ◽

Sequence Divergence ◽

Geographic Area ◽

Geographic Region ◽

Tectonic Activity ◽

Lineage Sorting ◽

Distribution Ranges

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Plastome data reveal multiple geographic origins ofQuercusGroup Ilex

PeerJ ◽

10.7717/peerj.1897 ◽

2016 ◽

Vol 4 ◽

pp. e1897 ◽

Cited By ~ 43

Author(s):

Marco Cosimo Simeone ◽

Guido W. Grimm ◽

Alessio Papini ◽

Federico Vessella ◽

Simone Cardoni ◽

...

Keyword(s):

Phylogenetic Relationships ◽

Sequence Data ◽

Incomplete Lineage Sorting ◽

Nuclear Genome ◽

Sequence Divergence ◽

Geographic Area ◽

Tectonic Activity ◽

Lineage Sorting ◽

Geographic Origins ◽

Distribution Ranges

Nucleotide sequences from the plastome are currently the main source for assessing taxonomic and phylogenetic relationships in flowering plants and their historical biogeography at all hierarchical levels. One major exception is the large and economically important genusQuercus(oaks). Whereas differentiation patterns of the nuclear genome are in agreement with morphology and the fossil record, diversity patterns in the plastome are at odds with established taxonomic and phylogenetic relationships. However, the extent and evolutionary implications of this incongruence has yet to be fully uncovered. The DNA sequence divergence of four Euro-Mediterranean Group Ilex oak species (Quercus ilexL.,Q. cocciferaL.,Q. aucheriJaub. & Spach.,Q. alnifoliaPoech.) was explored at three chloroplast markers (rbcL, trnK/matK, trnH-psbA). Phylogenetic relationships were reconstructed including worldwide members of additional 55 species representing allQuercussubgeneric groups. Family and order sequence data were harvested from gene banks to better frame the observed divergence in larger taxonomic contexts. We found a strong geographic sorting in the focal group and the genus in general that is entirely decoupled from species boundaries. High plastid divergence in members ofQuercusGroup Ilex, including haplotypes shared with related, but long isolated oak lineages, point towards multiple geographic origins of this group of oaks. The results suggest that incomplete lineage sorting and repeated phases of asymmetrical introgression among ancestral lineages of Group Ilex and two other main Groups of Eurasian oaks (Cyclobalanopsis and Cerris) caused this complex pattern. Comparison with the current phylogenetic synthesis also suggests an initial high- versus mid-latitude biogeographic split withinQuercus. High plastome plasticity of Group Ilex reflects geographic area disruptions, possibly linked with high tectonic activity of past and modern distribution ranges, that did not leave imprints in the nuclear genome of modern species and infrageneric lineages.

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MetaCurator: A hidden Markov model-based toolkit for extracting and curating sequences from taxonomically-informative genetic markers

10.1101/672782 ◽

2019 ◽

Cited By ~ 1

Author(s):

Rodney T. Richardson ◽

Douglas B. Sponsler ◽

Harper McMinn-Sauder ◽

Reed M. Johnson

Keyword(s):

Markov Models ◽

Sequence Data ◽

Hidden Markov ◽

Incomplete Lineage Sorting ◽

Genetic Material ◽

Sequence Divergence ◽

Reference Sequence ◽

Sequence Classification ◽

Lineage Sorting ◽

Link Type

SummaryThe community-level analysis of samples containing diverse genetic material, via metabarcoding and metagenomic approaches, is increasingly popular. While the production of sequence data for such studies has become straightforward, questions remain about how best to analyze and taxonomically characterize sequence data. For many sequence classification approaches, an important component of the workflow involves the curation of reference sequences. Ideally, this involves trimming away extraneous sequence at the 3 prime and 5 prime ends of the target marker of interest, as well as the removal of reference sequence duplicates. Here, we present MetaCurator, a software package written in Python, designed for automated reference sequence curation and highly generalizable across markers and study systems. MetaCurator is organized in a modular fashion, so users can implement tools individually in addition to utilizing the automated and flexible MetaCurator parental code. Aside from modules used to organize and format taxonomic lineage data, MetaCurator contains two signature tools. IterRazor utilizes profile hidden Markov models and an iterative search framework to exhaustively identify and extract the precise amplicon marker of interest from available reference sequence data. DerepByTaxonomy then facilitates sequence dereplication using a taxonomically aware approach, removing duplicates only when they belong to the same taxon. This is important for cases of incomplete lineage sorting between species and for highly conserved markers, such as plantrbcLandtrnL, which often display no sequence divergence across taxa, even at the genus level.Availability and implementationMetaCurator is supported on OSX and Linux (RedHat/CentOS) and is freely available under a GPL v3.0 license athttps://github.com/RTRichar/[email protected] informationCode associated with this work is available athttps://github.com/RTRichar/MetabarcodeDBsV2and additional analysis is presented in supplementary files.

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Phylogeography of Canada Geese (Branta Canadensis) in Western North America

The Auk ◽

10.1093/auk/120.3.889 ◽

2003 ◽

Vol 120 (3) ◽

pp. 889-907

Author(s):

Kim T. Scribner ◽

Sandra L. Talbot ◽

John M. Pearce ◽

Barbara J. Pierson ◽

Karen S. Bollinger ◽

...

Keyword(s):

North America ◽

Sequence Data ◽

Incomplete Lineage Sorting ◽

Molecular Genetic ◽

Sequence Divergence ◽

Branta Canadensis ◽

Canada Geese ◽

Western North America ◽

Gene Trees ◽

Lineage Sorting

Abstract Using molecular genetic markers that differ in mode of inheritance and rate of evolution, we examined levels and partitioning of genetic variation for seven nominal subspecies (11 breeding populations) of Canada Geese (Branta canadensis) in western North America. Gene trees constructed from mtDNA control region sequence data show that subspecies of Canada Geese do not have distinct mtDNA. Large and small-bodied forms of Canada Geese were highly diverged (0.077 average sequence divergence) and represent monophyletic groups. A majority (65%) of 20 haplotypes resolved were observed in single breeding locales. However, within both large and small-bodied forms certain haplotypes occurred across multiple subspecies. Population trees for both nuclear (microsatellites) and mitochondrial markers were generally concordant and provide resolution of population and subspecific relationships indicating incomplete lineage sorting. All populations and subspecies were genetically diverged, but to varying degrees. Analyses of molecular variance, nested-clade and coalescencebased analyses of mtDNA suggest that both historical (past fragmentation) and contemporary forces have been important in shaping current spatial genetic distributions. Gene flow appears to be ongoing though at different rates, even among currently recognized subspecies. The efficacy of current subspecific taxonomy is discussed in light of hypothesized historical vicariance and current demographic trends of management and conservation concern.

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Introgression from Gorilla caused the Human-Chimpanzee split (Preprint)

10.2196/preprints.12038 ◽

2018 ◽

Author(s):

Johan Nygren

Keyword(s):

Gene Transfer ◽

Phylogenetic Relationships ◽

Sequence Data ◽

Incomplete Lineage Sorting ◽

Genome Project ◽

Genome Comparison ◽

Lineage Sorting ◽

Chromosome 5 ◽

Speciation Model ◽

Introgression Event

BACKGROUND ABSTRACT: The Gorilla Genome Project (Scally, 2012) showed that 30% of the gorilla genome introgressed into the ancestor of humans and chimpanzees, and that the two species diverged through lineage sorting with 15% ending up in Pan and another 15% in Homo. That introgression is the Pan-Homo split, hybridization, which led to speciation as the new hybrid lineages became reproductively isolated from one another. The NUMT on chromosome 5 (“ps5”) (Popadin, 2017) fits perfectly with the introgression speciation model, it was formed from mtDNA that had diverged from the common ancestor of Pan-Homo for 1.8 Myr at the time of insertion into the nuclear genome, and originated in the Gorilla lineage. The ps5 pseudogene was transferred to Pan and Homo during the introgression event that led to the Pan-Homo split, 6 million years ago. OBJECTIVE Genome sequencing has been evolving along the law of accelerating returns (Kurzweil, 2004), the total amount of sequence data produced doubling approximately every seven months. (Stephens, 2015) With the genetic revolution, phylogenetic relationships are no longer limited to morphological characters, they can instead be read like an open book. This thesis will explore a new chapter, with roots in genetic data from the Gorilla Genome Project (Scally, 2012). The Gorilla Genome Project was the first complete genome of Gorilla, from a female western lowland gorilla, and it revealed a closer relationship between humans and gorilla than what morphological analyses had shown: in 30% of the genome, gorilla is closer to human or chimpanzee than the latter are to each other. At the time interpreted as incomplete lineage sorting (Scally, 2012), genetic evidence of gene transfer between Gorilla, Pan and Homo around the time of the Pan-Homo split (Popadin, 2017) shows that the lineage sorting is more parsimonious as a result of introgression. Introgression may lead to speciation, in which the new hybrid lineages become reproductively isolated from parental populations (Baack, 2007), and since Pan and Homo have diverged through lineage sorting, with 15% of the introgressed genes ending up in Pan and another 15% in Homo, it is reasonable to conclude that the introgression caused the Pan-Homo split (Fig. 1), and therefore that it occurred at the time of the Pan-Homo split, around 6 million years ago. METHODS Phylogenetic relationships can be read from genome comparison. That there was gene transfer between Gorilla, Pan and Homo around the time of the Pan-Homo split can be read from a NUMT on chromosome 5 (ps5), which diverged between Gorilla, Pan and Homo at the time of the split. (Popadin, 2017) The ps5 NUMT as evidence of gene flow shows that introgression is a more parsimonious explanation for the lineage sorting from Gorilla than incomplete lineage sorting (ILS), and since Pan and Homo diverged through lineage sorting, it can be read that the introgression caused the Pan-Homo split. (Fig. 1) RESULTS The lineage sorting of 30% of the gorilla genome that is seen in humans and chimpanzees (Scally, 2012) is a result of introgression, an event that caused the speciation of Pan and Homo (Fig. 1), and the two lineages diverged through lineage sorting with 15% of the introgressed genes ending up in Pan and another 15% in Homo CONCLUSIONS The indisputable evidence that an introgression event caused the speciation of Pan and Homo is made possible by the genome revolution, and it provides a map, a reference frame, that makes it possible to read the world in ways that were previously out of sight, and can provide an important reference for continued research into hominin evolution. The fossil record shows that there were multiple lineages of hominin coexisting throughout the Pliocene and Pleistocene (Haile-Selassie, 2016), and the introgression speciation model can provide clues to how those lineages relate to one another. What remains to be understood is what environmental and ecological factors triggered the hybridization.

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Morphological, Ecological, and Molecular Divergence of Conogethes pinicolalis from C. punctiferalis (Lepidoptera: Crambidae)

Insects ◽

10.3390/insects12050455 ◽

2021 ◽

Vol 12 (5) ◽

pp. 455

Author(s):

Na Ra Jeong ◽

Min Jee Kim ◽

Sung-Soo Kim ◽

Sei-Woong Choi ◽

Iksoo Kim

Keyword(s):

Phylogenetic Analysis ◽

First Generation ◽

Incomplete Lineage Sorting ◽

Divergence Time ◽

Sequence Divergence ◽

Lineage Sorting ◽

Mitochondrial Coi ◽

Feeding Type ◽

Pine Trees ◽

Yellow Peach Moth

Conogethes pinicolalis has long been considered as a Pinaceae-feeding type of the yellow peach moth, C. punctiferalis, in Korea. In this study, the divergence of C. pinicolalis from the fruit-feeding moth C. punctiferalis was analyzed in terms of morphology, ecology, and genetics. C. pinicolalis differs from C. punctiferalis in several morphological features. Through field observation, we confirmed that pine trees are the host plants for the first generation of C. pinicolalis larvae, in contrast to fruit-feeding C. punctiferalis larvae. We successfully reared C. pinicolalis larvae to adults by providing them pine needles as a diet. From a genetic perspective, the sequences of mitochondrial COI of these two species substantially diverged by an average of 5.46%; moreover, phylogenetic analysis clearly assigned each species to an independent clade. On the other hand, nuclear EF1α showed a lower sequence divergence (2.10%) than COI. Overall, EF1α-based phylogenetic analysis confirmed each species as an independent clade, but a few haplotypes of EF1α indicated incomplete lineage sorting between these two species. In conclusion, our results demonstrate that C. pinicolalis is an independent species according to general taxonomic criteria; however, analysis of the EF1α sequence revealed a short divergence time.

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Multi-gene incongruence consistent with hybridisation in Cladocopium (Symbiodiniaceae), an ecologically important genus of coral reef symbionts

10.7287/peerj.preprints.27614 ◽

2019 ◽

Author(s):

Joshua I Brian ◽

Simon K Davy ◽

Shaun P Wilkinson

Keyword(s):

Sequence Data ◽

Incomplete Lineage Sorting ◽

Reticulate Evolution ◽

Next Generation Sequencing Data ◽

Putative Hybrid ◽

Its2 Region ◽

Sequencing Data ◽

Lineage Sorting ◽

Evolutionary Potential ◽

Unbiased Test

Coral reefs rely on their intracellular dinoflagellate symbionts (family Symbiodiniaceae) for nutritional provision in nutrient-poor waters, yet this association is threatened by thermally stressful conditions. Despite this, the evolutionary potential of these symbionts remains poorly characterised. In this study, we tested the potential for divergent Symbiodiniaceae types to sexually reproduce (i.e. hybridise) within Cladocopium, the most ecologically prevalent genus in this family. With sequence data from three organelles (cob gene, mitochondria; psbAncr region, chloroplast; and ITS2 region, nucleus), we utilised the Incongruence Length Difference test, Approximately Unbiased test, tree hybridisation analyses and visual inspection of raw data in stepwise fashion to highlight incongruences between organelles, and thus provide evidence of reticulate evolution. Using this approach, we identified three putative hybrid Cladocopium samples among the 158 analysed, at two of the seven sites sampled. These samples were identified as the common Cladocopium types C40 or C1 with respect to the mitochondria and chloroplasts, but the rarer types C3z, C3u and C1# with respect to their nuclear identity. These five Cladocopium types have previously been confirmed as evolutionarily distinct and were also recovered in non-incongruent samples multiple times, which is strongly suggestive that they sexually reproduced to produce the incongruent samples. A concomitant inspection of Next Generation Sequencing data for these samples suggests that other plausible explanations, such as incomplete lineage sorting, are much less likely. The approach taken in this study allows incongruences between gene regions to be identified with confidence, and brings new light to the evolutionary potential within Symbiodiniaceae.

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Phylogenetic relationships based on nuclear and plastid DNA sequences reveal recent diversification and discordant patterns of morphological evolution of the Chilean genera of Gilliesieae (Amaryllidaceae: Allioideae)

Botanical Journal of the Linnean Society ◽

10.1093/botlinnean/boaa035 ◽

2020 ◽

Vol 194 (1) ◽

pp. 84-99

Author(s):

Inelia Escobar ◽

Eduardo Ruiz-Ponce ◽

Paula J Rudall ◽

Michael F Fay ◽

Oscar Toro-Núñez ◽

...

Keyword(s):

Dna Sequences ◽

Phylogenetic Relationships ◽

Incomplete Lineage Sorting ◽

Morphological Evolution ◽

Strong Support ◽

Plastid Dna ◽

Lineage Sorting ◽

Generic Level ◽

Molecular Analyses ◽

Floral Diversity

Abstract Gilliesieae are a South American tribe of Amaryllidaceae characterized by high floral diversity. Given different taxonomic interpretations and proposals for generic and specific relationships, a representative phylogenetic analysis is required to clarify the systematics of this group. The present study provides a framework for understanding phylogenetic relationships and contributing to the development of an appropriate taxonomic treatment of Gilliesieae. Molecular analyses, based on nuclear (ITS) and plastid DNA sequences (trnL-F and rbcL), resolve with strong support the monophyly of the tribe and the differentiation of two major clades. Clade I comprises the genera Gilliesia, Gethyum and Solaria and Clade II includes Miersia and Speea. These well-supported clades are mostly congruent with vegetative and karyotype characters rather than, e.g., floral symmetry. At the generic level, all molecular analyses reveal the paraphyly of Gilliesia and Miersia. Gethyum was found to be paraphyletic, resulting in the confirmation of Ancrumia as a distinct genus. Several instances of incongruent phylogenetic signals were found among data sets. The calibrated tree suggests a recent diversification of the tribe (Pliocene–Pleistocene), a contemporary process of speciation in which instances of hybridization and incomplete lineage sorting could explain patterns of paraphyly and incongruence of floral morphology.

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Multilocus phylogeny of Gryllus field crickets (Orthoptera: Gryllidae: Gryllinae) utilizing anchored hybrid enrichment

Zootaxa ◽

10.11646/zootaxa.4750.3.2 ◽

2020 ◽

Vol 4750 (3) ◽

pp. 328-348 ◽

Cited By ~ 2

Author(s):

DAVID A. GRAY ◽

DAVID B. WEISSMAN ◽

JEFFREY A. COLE ◽

EMILY MORIARTY LEMMON

Keyword(s):

Sequence Data ◽

Incomplete Lineage Sorting ◽

The United States ◽

Field Cricket ◽

Future Research ◽

Gene Trees ◽

Lineage Sorting ◽

The Bahamas ◽

Field Crickets ◽

Anchored Hybrid Enrichment

We present the first comprehensive molecular phylogeny of Gryllus field cricket species found in the United States and Canada, select additional named Gryllus species found in Mexico and the Bahamas, plus the European field cricket G. campestris Linnaeus and the Afro-Eurasian cricket G. bimaculatus De Geer. Acheta, Teleogryllus, and Nigrogryllus were used as outgroups. Anchored hybrid enrichment was used to generate 492,531 base pairs of DNA sequence from 563 loci. RAxML analysis of concatenated sequence data and Astral analysis of gene trees gave broadly congruent results, especially for older branches and overall tree structure. The North American Gryllus are monophyletic with respect to the two Old World taxa; certain sub-groups show rapid recent divergence. This is the first Anchored Hybrid Enrichment study of an insect group done for closely related species within a single genus, and the results illustrate the challenges of reconstructing the evolutionary history of young rapidly diverged taxa when both incomplete lineage sorting and probable hybridization are at play. Because Gryllus field crickets have been used extensively as a model system in evolutionary ecology, behavior, neuro-physiology, speciation, and life-history and life-cycle evolution, these results will help inform, interpret, and guide future research in these areas.

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A Bayesian Implementation of the Multispecies Coalescent Model with Introgression for Phylogenomic Analysis

Molecular Biology and Evolution ◽

10.1093/molbev/msz296 ◽

2019 ◽

Vol 37 (4) ◽

pp. 1211-1223 ◽

Cited By ~ 8

Author(s):

Tomáš Flouri ◽

Xiyun Jiao ◽

Bruce Rannala ◽

Ziheng Yang

Keyword(s):

Gene Flow ◽

Genomic Sequence ◽

Sequence Data ◽

Incomplete Lineage Sorting ◽

Mosquito Species ◽

Phylogenomic Analysis ◽

Data Sets ◽

Lineage Sorting ◽

Coalescent Model ◽

Multispecies Coalescent

Abstract Recent analyses suggest that cross-species gene flow or introgression is common in nature, especially during species divergences. Genomic sequence data can be used to infer introgression events and to estimate the timing and intensity of introgression, providing an important means to advance our understanding of the role of gene flow in speciation. Here, we implement the multispecies-coalescent-with-introgression model, an extension of the multispecies-coalescent model to incorporate introgression, in our Bayesian Markov chain Monte Carlo program Bpp. The multispecies-coalescent-with-introgression model accommodates deep coalescence (or incomplete lineage sorting) and introgression and provides a natural framework for inference using genomic sequence data. Computer simulation confirms the good statistical properties of the method, although hundreds or thousands of loci are typically needed to estimate introgression probabilities reliably. Reanalysis of data sets from the purple cone spruce confirms the hypothesis of homoploid hybrid speciation. We estimated the introgression probability using the genomic sequence data from six mosquito species in the Anopheles gambiae species complex, which varies considerably across the genome, likely driven by differential selection against introgressed alleles.

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