Phylogenomics With Hyb-Seq Unravels Korean Hosta Evolution

The genus Hosta (Agavoideae and Asparagaceae) is one of the most popular landscaping and ornamental plants native to temperate East Asia. Their popularity has led to extensive hybridization to develop various cultivars. However, their long history of hybridization, cultivation, and selection has brought about taxonomic confusion in the Hosta species delimitation along with their indistinguishable morphology. Here, we conducted the first broad phylogenetic analyses of Hosta species based on the most comprehensive genomic data set to date. To do so, we captured 246 nuclear gene sequences and plastomes from 55 accessions of Korean Hosta species using the Hyb-Seq method. As a result, this study provides the following novel and significant findings: (1) phylogenetic analyses of the captured sequences retrieved six species of Hosta in South Korea compared to five to eleven species based on the previous studies, (2) their phylogenetic relationships suggested that the large genome size was ancestral and the diversification of Korean Hosta species was accompanied by decreases in genome sizes, (3) comparison between nuclear genes and plastome revealed several introgressive hybridization events between Hosta species, and (4) divergence times estimated here showed that Hosta diverged 35.59 million years ago, while Korean Hosta species rapidly diversified during the late Miocene. Last, we explored whether these genomic data could be used to infer the origin of cultivars. In summary, this study provides the most comprehensive genomic resources to be used in phylogenetic, population, and conservation studies of Hosta, as well as for unraveling the origin of many cultivars.

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Systematic relationships of five newly sequenced cervid species

PeerJ ◽

10.7717/peerj.2307 ◽

2016 ◽

Vol 4 ◽

pp. e2307 ◽

Cited By ~ 23

Author(s):

Nicola S. Heckeberg ◽

Dirk Erpenbeck ◽

Gert Wörheide ◽

Gertrud E. Rössner

Keyword(s):

Comparative Anatomy ◽

Phylogenetic Analyses ◽

Molecular Data ◽

Data Set ◽

Systematic Uncertainties ◽

Mitochondrial Cytochrome B ◽

In The Wild ◽

History Of ◽

Systematic Relationships ◽

Partial Consensus

Cervid phylogenetics has been puzzling researchers for over 150 years. In recent decades, molecular systematics has provided new input for both the support and revision of the previous results from comparative anatomy but has led to only partial consensus. Despite all of the efforts to reach taxon-wide species sampling over the last two decades, a number of cervid species still lack molecular data because they are difficult to access in the wild. By extracting ancient DNA from museum specimens, in this study, we obtained partial mitochondrial cytochrome b gene sequences forMazama bricenii,Mazama chunyi,Muntiacus atherodes,Pudu mephistophiles, andRusa marianna, including three holotypes. These new sequences were used to enrich the existing mitochondrial DNA alignments and yielded the most taxonomically complete data set for cervids to date. Phylogenetic analyses provide new insights into the evolutionary history of these five species. However, systematic uncertainties withinMuntiacuspersist and resolving phylogenetic relationships withinPuduandMazamaremain challenging.

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Introgressive hybridization facilitates adaptive divergence in a recent radiation of monkeyflowers

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2015.1666 ◽

2015 ◽

Vol 282 (1814) ◽

pp. 20151666 ◽

Cited By ~ 53

Author(s):

Sean Stankowski ◽

Matthew A. Streisfeld

Keyword(s):

Evolutionary Biology ◽

De Novo ◽

Phylogenetic Analyses ◽

Introgressive Hybridization ◽

Flower Colour ◽

Adaptive Divergence ◽

Evolutionary Mechanisms ◽

Standing Variation ◽

Regulatory Mutations ◽

History Of

A primary goal in evolutionary biology is to identify the historical events that have facilitated the origin and spread of adaptations. When these adaptations also lead to reproductive isolation, we can learn about the evolutionary mechanisms contributing to speciation. We reveal the complex history of the gene MaMyb2 in shaping flower colour divergence within a recent radiation of monkeyflowers. In the Mimulus aurantiacus species complex, red-flowered M. a. ssp . puniceus and yellow-flowered M. a. ssp. australis are partially isolated because of differences in pollinator preferences. Phylogenetic analyses based on genome-wide variation across the complex suggest two origins of red flowers from a yellow-flowered ancestor: one in M. a. ssp . puniceus and one in M. a. ssp. flemingii . However, in both cases, red flowers are caused by cis -regulatory mutations in the gene MaMyb2 . Although this could be due to distinct mutations in each lineage, we show that the red allele in M. a. ssp. puniceus did not evolve de novo or exist as standing variation in its yellow-flowered ancestor. Rather, our results suggest that a single red MaMyb2 allele evolved during the radiation of M. aurantiacus that was subsequently transferred to the yellow-flowered ancestor of M. a. ssp. puniceus via introgressive hybridization. Because gene flow is still possible among taxa, we conclude that introgressive hybridization can be a potent driver of adaptation at the early stages of divergence that can contribute to the origins of biodiversity.

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Phylogenomics reveals a complex evolutionary history of lobed-leaf white oaks in western North America

Genome ◽

10.1139/gen-2016-0206 ◽

2017 ◽

Vol 60 (9) ◽

pp. 733-742 ◽

Cited By ~ 21

Author(s):

John D. McVay ◽

Duncan Hauser ◽

Andrew L. Hipp ◽

Paul S. Manos

Keyword(s):

Phylogenetic Analyses ◽

Introgressive Hybridization ◽

Sympatric Species ◽

Robust Estimate ◽

History Of ◽

Tree Space ◽

Quercus Gambelii ◽

Lobed Leaf ◽

The Impact ◽

Historical Range

Species within the genus Quercus (oak) hybridize in complex patterns that have yet to be fully explored with phylogenomic data. Analyses to date have recovered reasonable divergent patterns, suggesting that the impact of introgression may not always be obvious in inferred oak phylogenies. We explore this phenomenon using RADseq data for 136 samples representing 54 oak species by conducting phylogenetic analyses designed to distinguish signals of lineage diversification and hybridization, focusing on the lobed-leaf species Quercus gambelii, Q. lobata, and Q. garryana in the context of a broad sampling of allied white oaks (Quercus section Quercus), and particularly the midwestern Q. macrocarpa. We demonstrate that historical introgressive hybridization between once sympatric species affects phylogeny estimation. Historical range expansion during periods of favorable climate likely explains our observations; analyses support genetic exchange between ancestral populations of Q. gambelii and Q. macrocarpa. We conclude that the genomic consequences of introgression caused the attraction of distant lineages in phylogenetic tree space, and that introgressive and divergent signals can be disentangled to produce a robust estimate of the phylogenetic history of the species.

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Perizomini (Lepidoptera: Geometridae: Larentiinae) are polyphyletic

Insect Systematics & Evolution ◽

10.1163/1876312x-00002301 ◽

2020 ◽

Vol 51 (3) ◽

pp. 489-516

Author(s):

Erki Õunap ◽

Toomas Tammaru ◽

Andro Truuverk

Keyword(s):

Maximum Likelihood ◽

Molecular Systematics ◽

New World ◽

Phylogenetic Analyses ◽

Nuclear Gene ◽

Morphological Evidence ◽

Worldwide Distribution ◽

The Family ◽

History Of ◽

Open Question

Recent advances in molecular systematics have led to an emerging understanding of the phylogenetic history of the family Geometridae. These studies have basically confirmed the traditional subdivision of the subfamily Larentiinae into tribes but unsolved problems remain. Here we test the monophyly of the tribe Perizomini, and evaluate the division of this tribe into genera using Bayesian and maximum likelihood analyses of one mitochondrial and eight nuclear gene fragments. We show that the Eurasian members of Perizoma Hübner, 1825, Mesotype Hübner, 1825 and Gagitodes Warren, 1893 together form a monophyetic tribe Perizomini. However, Martania Mironov, 2000 is not closely related to these genera, but is considered to belong to Melanthiini according to the results of the phylogenetic analyses. Morphological evidence supporting this rearrangement is discussed. The Nearctic Larentia basaliata Walker, 1862 was shown to belong in the genus Martania as M. basaliata (Walker, 1862) comb. nov. and being specifically distinct from the morphologically similar Palaearctic M. taeniata. Three other studied ‘Perizoma’ species from the New World were similarly placed far from Perizomini in the phylogenetic tree, and were not related to each other. We conclude that both the tribe Perizomini and the genus Perizoma are polyphyletic which indicates that the group needs a global revision. It remains an open question whether Perizomini have a worldwide distribution as previously assumed, or is this tribe confined to the Palaearctic region.

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Speciation and introgression between Mimulus nasutus and Mimulus guttatus

10.1101/000109 ◽

2013 ◽

Cited By ~ 1

Author(s):

Yaniv Brandvain ◽

Amanda M Kenney ◽

Lex Fagel ◽

Graham Coop ◽

Andrea L Sweigart

Keyword(s):

Ecological Model ◽

Negative Relationship ◽

Genomic Data ◽

Mimulus Guttatus ◽

Species Pair ◽

Data Set ◽

Genomic Signatures ◽

Population Genomic ◽

History Of ◽

Biological Differentiation

Mimulus guttatus and M. nasutus are an evolutionary and ecological model sister species pair differentiated by ecology, mating system, and partial reproductive isolation. Despite extensive research on this system, the history of divergence and differentiation in this sister pair is unclear. We present and analyze a novel population genomic data set which shows that M. nasutus "budded" off of a central Californian M. guttatus population within the last 200 to 500 thousand years. In this time, the M. nasutus genome has accrued numerous genomic signatures of the transition to predominant selfing. Despite clear biological differentiation, we document ongoing, bidirectional introgression. We observe a negative relationship between the recombination rate and divergence between M. nasutus and sympatric M. guttatus samples, suggesting that selection acts against M. nasutus ancestry in M. guttatus.

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Compositional heterogeneity and outgroup choice influence the internal phylogeny of the ants

10.1101/173393 ◽

2017 ◽

Cited By ~ 6

Author(s):

Marek L. Borowiec ◽

Christian Rabeling ◽

Seán G. Brady ◽

Brian L. Fisher ◽

Ted R. Schultz ◽

...

Keyword(s):

Molecular Phylogenetics ◽

Phylogenetic Analyses ◽

Nuclear Gene ◽

Phylogenetic Inference ◽

Death Process ◽

Compositional Heterogeneity ◽

Data Set ◽

Key Species ◽

Divergence Dating ◽

Birth Death

AbstractKnowledge of the internal phylogeny and evolutionary history of ants (Formicidae), the world’s most species-rich clade of eusocial organisms, has dramatically improved since the advent of molecular phylogenetics. A number of relationships at the subfamily level, however, remain uncertain. Key unresolved issues include placement of the root of the ant tree of life and the relationships among the so-called poneroid subfamilies. Here we assemble a new data set to attempt a resolution of these two problems and carry out divergence dating, focusing on the age of the root node of crown Formicidae. For the phylogenetic analyses we included data from 110 ant species, including the key species Martialis heureka. We focused taxon sampling on non-formicoid lineages of ants to gain insight about deep nodes in the ant phylogeny. For divergence dating we retained a subset of 62 extant taxa and 42 fossils in order to approximate diversified sampling in the context of the fossilized birth-death process. We sequenced 11 nuclear gene fragments for a total of ~7.5 kb and investigated the DNA sequence data for the presence of among-taxon compositional heterogeneity, a property known to mislead phylogenetic inference, and for its potential to affect the rooting of the ant phylogeny. We found sequences of the Leptanillinae and several outgroup taxa to be rich in adenine and thymine (51% average AT content) compared to the remaining ants (45% average). To investigate whether this heterogeneity could bias phylogenetic inference we performed outgroup removal experiments, analysis of compositionally homogeneous sites, and a simulation study. We found that compositional heterogeneity indeed appears to affect the placement of the root of the ant tree but has limited impact on more recent nodes. We put forward a novel hypothesis regarding the rooting of the ant phylogeny, in which Martialis and the Leptanillinae together constitute a clade that is sister to all other ants. After correcting for compositional heterogeneity this emerges as the best-supported hypothesis of relationships at deep nodes in the ant tree. The results of our divergence dating under the fossilized birth-death process and diversified sampling suggest that the crown Formicidae originated during the Albian or Aptian ages of the Lower Cretaceous (103–124 Ma). In addition, we found support for monophyletic poneroids comprising the subfamilies Agroecomyrmecinae, Amblyoponinae, Apomyrminae, Paraponerinae, Ponerinae, and Proceratiinae, and well-supported relationships among these subfamilies except for the placement of Proceratiinae and (Amblyoponinae + Apomyrminae). Our phylogeny also highlights the non-monophyly of several ant genera, including Protanilla and Leptanilla in the Leptanillinae, Proceratium in the Proceratiinae, and Cryptopone, Euponera, and Mesoponera within the Ponerinae.

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Evolutionary history of trypanosomes from South American caiman (Caiman yacare) and African crocodiles inferred by phylogenetic analyses using SSU rDNA and gGAPDH genes

Parasitology ◽

10.1017/s003118200800512x ◽

2008 ◽

Vol 136 (1) ◽

pp. 55-65 ◽

Cited By ~ 16

Author(s):

L. B. VIOLA ◽

R. S. ALMEIDA ◽

R. C. FERREIRA ◽

M. CAMPANER ◽

C. S. A. TAKATA ◽

...

Keyword(s):

Phylogenetic Analyses ◽

Divergence Time ◽

Ssu Rdna ◽

Tsetse Flies ◽

South American ◽

Data Set ◽

Divergence Time Estimates ◽

Time Estimates ◽

History Of ◽

Brazilian Pantanal

SUMMARYIn this study, using a combined data set of SSU rDNA and gGAPDH gene sequences, we provide phylogenetic evidence that supports clustering of crocodilian trypanosomes from the Brazilian Caiman yacare (Alligatoridae) and Trypanosoma grayi, a species that circulates between African crocodiles (Crocodilydae) and tsetse flies. In a survey of trypanosomes in Caiman yacare from the Brazilian Pantanal, the prevalence of trypanosome infection was 35% as determined by microhaematocrit and haemoculture, and 9 cultures were obtained. The morphology of trypomastigotes from caiman blood and tissue imprints was compared with those described for other crocodilian trypanosomes. Differences in morphology and growth behaviour of caiman trypanosomes were corroborated by molecular polymorphism that revealed 2 genotypes. Eight isolates were ascribed to genotype Cay01 and 1 to genotype Cay02. Phylogenetic inferences based on concatenated SSU rDNA and gGAPDH sequences showed that caiman isolates are closely related to T. grayi, constituting a well-supported monophyletic assemblage (clade T. grayi). Divergence time estimates based on clade composition, and biogeographical and geological events were used to discuss the relationships between the evolutionary histories of crocodilian trypanosomes and their hosts.

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Phylogenomics of the adaptive radiation of Triturus newts supports gradual ecological niche expansion towards an incrementally aquatic lifestyle

10.1101/463752 ◽

2018 ◽

Author(s):

B. Wielstra ◽

E. McCartney-Melstad ◽

J.W. Arntzen ◽

R.K. Butlin ◽

H.B. Shaffer

Keyword(s):

Adaptive Radiation ◽

Phylogenetic Analyses ◽

Gene Tree ◽

Data Set ◽

Internal Branch ◽

Branch Lengths ◽

History Of ◽

Tree Estimation ◽

Probe Set ◽

Short Timeframe

AbstractNewts of the genus Triturus (marbled and crested newts) exhibit substantial variation in the number of trunk vertebrae (NTV) and a higher NTV corresponds to a longer annual aquatic period. Because the Triturus phylogeny has thwarted resolution to date, the evolutionary history of NTV, annual aquatic period, and their potential coevolution has remained unclear. To resolve the phylogeny of Triturus, we generated a c. 6,000 transcriptome-derived marker data set using a custom target enrichment probe set, and conducted phylogenetic analyses using: 1) data concatenation with RAxML, 2) gene-tree summary with ASTRAL, and 3) species-tree estimation with SNAPP. All analyses produce the same, highly supported topology, despite cladogenesis having occurred over a short timeframe, resulting in short internal branch lengths. Our new phylogenetic hypothesis is consistent with the minimal number of inferred changes in NTV count necessary to explain the diversity in NTV observed today. Although a causal relationship between NTV, body form, and aquatic ecology has yet to be experimentally established, our phylogeny indicates that these features have evolved together, and suggest that they may underlie the adaptive radiation that characterizes Triturus.

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Phylogenetic relationships of xenodermid snakes (Squamata: Serpentes: Xenodermidae), with the description of a new genus

Vertebrate Zoology ◽

10.3897/vz.71.e75967 ◽

2021 ◽

Vol 71 ◽

pp. 747-763

Author(s):

V. Deepak ◽

Samuel Lalronunga ◽

Esther Lalhmingliani ◽

Abhijit Das ◽

Surya Narayanan ◽

...

Keyword(s):

Phylogenetic Relationships ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Strong Support ◽

Nuclear Gene ◽

Morphological Data ◽

Data Set ◽

Molecular Phylogenetic ◽

East And Southeast Asia ◽

Nuclear Gene Sequence

Xenodermidae is a generally poorly known lineage of caenophidian snakes found in South, East and Southeast Asia. We report molecular phylogenetic analyses for a multilocus data set comprising all five currently recognised genera and including new mitochondrial and nuclear gene sequence data for the recently described Stoliczkia vanhnuailianai. Our phylogenetic results provide very strong support for the non-monophyly of Stoliczkia, as presently constituted, with S. borneensis being more closely related to Xenodermus than to the Northeast Indian S. vanhnuailianai. Based on phylogenetic relationships and morphological distinctiveness, we transfer Stoliczkia borneensis to a new monotypic genus endemic to Borneo, Paraxenodermusgen. nov. We also present new morphological data for P. borneensis.

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Nuclear DNA diversity, population differentiation, and phylogenetic relationships in the California closed-cone pines based on RAPD and allozyme markers

Genome ◽

10.1139/g98-171 ◽

1999 ◽

Vol 42 (5) ◽

pp. 893-908 ◽

Cited By ~ 43

Author(s):

J Wu ◽

K V Krutovskii ◽

S H Strauss

Keyword(s):

Population Differentiation ◽

Rapd Markers ◽

Nuclear Dna ◽

Gene Diversity ◽

Phylogenetic Analyses ◽

Nuclear Gene ◽

Published Data ◽

Data Set ◽

Closed Cone ◽

Allozyme Loci

We studied nuclear gene diversity and population differentiation using 91-98 randomly amplified polymorphic DNA (RAPD) loci in the California closed-cone pines knobcone (Pinus attenuata Lemm.), bishop (P. muricata D. Don), and Monterey (P. radiata D. Don) pines. A total of 384 trees from 13 populations were analyzed for RAPDs and another sample of 242 trees from 12 of these 13 populations were analyzed at 32-36 allozyme loci, using a published data set. Twenty-eight of 30 (93%) comigrating RAPD fragments tested were found to be homologous by Southern hybridization in all three species. Using an enriched mitochondrial DNA (mtDNA) preparation and a chloroplast DNA (cpDNA) library as probes, two fragments of cpDNA origin, and one of mtDNA origin present among RAPD profiles were excluded from analysis of nuclear gene diversity. RAPD markers revealed moderately higher intrapopulation gene diversity and substantially higher total genetic diversity and population differentiation than did allozyme markers for each species. We performed a simulation study using allozyme data, which showed that the dominant and biallelic nature of RAPD markers could explain the differences observed in differentiation parameters, but not in gene diversity; RAPD phenotypes appear to represent more underlying gene diversity than do allozyme phenotypes. Results of joint phylogenetic analyses of both the RAPD and allozyme markers strongly supported a common ancestor for P. radiata and P. attenuata pines, and south-to-north migration histories for all three species.Key words: allozymes, dominance, gene diversity, Pinus attenuata, Pinus muricata, Pinus radiata, phylogeny, RAPDs.

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