Find research datasets worth reusing

opencc-zeroJul 2021View details →

Data for Concordance-based approaches in phylogenomics

Gene tree conflict is common and finding methods to analyze and alleviate the negative effects that conflict has on species tree analysis is a crucial part of phylogenomics. This study aims to expand the discussion of inferring species trees and molecular branch lengths when conflict is present. Conflict is typically examined in two ways: inferring its prevalence, and inferring the influence of the individual genes (how strongly one gene supports any given topology compared to an alternative topology). Here, we examine a procedure for incorporating both conflict and the influence of genes in order to infer evolutionary relationships. All supported relationships in the gene trees are analyzed and the likelihood of the genes constrained to these relationships is summed to provide a likelihood for the relationship. Consensus tree assembly is conducted based on the sum of likelihoods for a given relationship and choosing relationships based on the most likely relationship assuming it does not conflict with a relationship that has a higher likelihood score. If it is not possible for all most likely relationships to be combined into a single bifurcating tree then multiple trees are produced and a consensus tree with a polytomy is created. This procedure allows for more influential genes to have greater influence on an inferred relationship, does not assume conflict has arisen from any one source, and does not force the dataset to produce a single bifurcating tree. Using this approach on three empirical datasets, we examine and discuss the relationship between influence and prevalence of gene tree conflict. We find that in one of the datasets, assembling a bifurcating consensus tree solely composed of the most likely relationships is impossible. To account for conflict in molecular rate analysis we also introduce a concordance-based approach to the summary and estimation of branch lengths suitable for downstream comparative analyses. We demonstrate through simulation that even under high levels of stochastic conflict, the mean and median of the concordant rates recapitulate the true molecular rate better than using a supermatrix approach. Using a large phylogenomic dataset, we examine rate heterogeneity across concordant genes with a focus on the branch subtending crown angiosperms. Notably, we find highly variable rates of evolution along the branch subtending crown angiosperms. The approaches outlined here have several limitations, but they also represent some alternative methods for harnessing the complexity of phylogenomic datasets and enrich our inferences of both species' relationships and evolutionary processes.

opencc-zeroDec 2017View details →

Data from: Museum specimens provide phylogenomic data to resolve relationships of sack-bearer moths (Lepidoptera, Mimallonoidea, Mimallonidae)

Mimallonidae, the sack‐bearer moths, are a family of predominantly Neotropical moths containing nearly 300 described species. Mimallonidae feed on over 40 host plant families and are found in a variety of environments, but phylogenetic relationships of species within the family have never been investigated. We sequenced 515 loci using anchored hybrid enrichment target capture on ethanol‐preserved and dried museum specimens, with dates of collection ranging from 1985 to 2017. We sampled 47 species, representing 32 of the 36 described mimallonid genera. By incorporating 19 dry museum specimens, and recovering an average of over 400 loci for each, we illustrate the utility of natural history collections in anchored hybrid enrichment‐based phylogenomics. Maximum likelihood and multi‐species coalescent analyses provide robust support for the recognition of six higher‐level groups within Mimallonidae, which we designate as subfamilies: Zaphantinae St Laurent & Kawahara subfam.n., Aurorianinae St Laurent & Kawahara subfam.n., Mimalloninae Burmeister, Lacosominae Dyar, Druenticinae St Laurent & Kawahara subfam.n. and Cicinninae Schaus stat.n. Our phylogenetic results also robustly support eight new tribes: Lacosominae: Trogopterini St Laurent & Kawahara tribe n., Lacosomini Dyar stat.n., Alheitini St Laurent & Kawahara tribe n.; Druenticinae: Luramini St Laurent & Kawahara tribe n., Druenticini St Laurent & Kawahara tribe n.; Cicinninae: Bedosiini St Laurent & Kawahara tribe n., Psychocampini St Laurent & Kawahara tribe n., Cicinnini Schaus stat.n. Three new genera are also described based on our phylogenetic results: Herbinalla St Laurent & Kawahara, gen.n., Ulaluma St Laurent & Kawahara, gen.n., Bedosiallo St Laurent & Kawahara, gen.n. Naniteta Franclemont, syn.n. is a synonym of Lacosoma Grote. Six genera are paraphyletic, and in total 19 new combinations are proposed: Macessoga laxa comb.n., Lacosoma elassa comb.n., Thaelia anysia comb.n., Thaelia subrubiginosa comb.n., Herbinalla caudina comb.n., Druentica brosica comb.n., Ulaluma valva comb.n., Cicinnus eminens comb.n., Roelmana pluridiscata comb.n., Roelmana laguerrei comb.n., Psychocampa joanna comb.n., Psychocampa unalca comb.n., Psychocampa hamata comb.n., Psychocampa marona comb.n., Bedosiallo eugenia comb.n., Bedosiallo forbesi comb.n., Bedosiallo moengus comb.n., Bedosiallo styx comb.n. and Bedosiallo sylvia comb.n. This study is the first to implement the LEP1 probe set on a comprehensive taxonomic dataset that includes many museum specimens, and our results demonstrate that museum specimens can be used in anchored hybrid enrichment studies. Importantly, these data produce a robust phylogeny that will serve as a foundation for future studies on mimallonid evolution, such as host plant relationships and biogeography.

opencc-by-4.0Jul 2021View details →

Supplementary tables and figures - Excluding loci with substitution saturation improves inferences from phylogenomic data

Supplementary tables and figures - Excluding loci with substitution saturation improves inferences from phylogenomic data

opencc-zeroAug 2021View details →

Phylogenomic reconstruction reveals new insights into the evolution and biogeography of Atta leaf-cutting ants (Hymenoptera: Formicidae)

Atta Fabricius is an ecologically dominant leaf-cutting ant genus, the major herbivore of the Neotropics, and an agricultural pest of great economic importance. Phylogenetic relationships within Atta have until now remained uncertain, and the delimitation and identification of a subset of Atta species are problematic. To address these phylogenetic uncertainties, we reconstruct the most comprehensive phylogenetic estimate to date of Atta by employing ultraconserved elements (UCEs). We recovered 2340 UCE loci from 224 Atta specimens, which include 14 out of the 15 identifiable species from across their geographic distributions, and 49 outgroup specimens. Our results strongly support the monophyly of Atta and of the four clades that coincide with the previously recognized subgenera Archeatta Gonçalves, Atta s.s. Emery, Epiatta Borgmeier, and Neoatta Gonçalves. The Archeatta clade contains three species occurring in North and Central America and the Caribbean and is the sister group of the remainder of all other Atta species. The Atta s.s. clade is composed of two species occupying North, Central, and South America. The Epiatta clade contains seven entirely South American species and the two species of the Neoatta clade occur in Central and South America. Divergence-dating analyses identify a series of major events in the Miocene, such as the divergence of Acromyrmex Mayr and Atta 16.7 million years ago (Ma) and the crown-group origin of Atta around 8.5 Ma. Extant Atta species evolved very recently, originating in the early Pleistocene, approximately 1.8 to 0.3 Ma (crown-group ages). We provide the first evidence that Atta goiana Gonçalves belongs to the Epiatta clade and that Atta robusta Borgmeier is the species with the youngest crown-group age of 0.3 Ma. The very young ages of Atta and its component species indicate a recent, rapid radiation. Biogeographic analyses suggest that the range of the most recent common ancestor of Atta consisted of the combined North/Central America and NW South America bioregions and that one daughter lineage subsequently dispersed into South America, rapidly diversifying in the newly formed Cerrado biome and Chaco, and further dispersing into the Atlantic Forest, Caatinga, and Pampas bioregions.

opencc-zeroAug 2021View details →

Unveiling the Patterns of Reticulated Evolutionary Processes with Phylogenomics: Hybridization and Polyploidy in the genus Rosa

Reticulation, caused by hybridization and allopolyploidization, is considered an important and frequent phenomenon in the evolution of numerous plant lineages. Although both processes represent important driving forces of evolution, they are mostly ignored in phylogenetic studies involving a large number of species. Indeed only a scattering of methods exists to recover a comprehensive reticulated evolutionary history for a broad taxon sampling. Plastid markers, sometimes combined with a few nuclear sequences, are therefore favored, even though they restrict in-depth studies of hybridization and polyploidization. The genus Rosa encompasses c. 150 species widely distributed throughout the northern hemisphere and represents a challenging taxonomic group in which hybridization and polyploidization are prominent. Our main objective was to develop a general framework that would take patterns of reticulation into account in the study of the phylogenetic relationships among Rosa species. Using amplicon sequencing we targeted allele variation in the nuclear genome as well as haploid sequences in the chloroplast genome. A stepwise diploids-first approach was developed to reconstruct the reticulate evolutionary history of the genus Rosa. We successfully recovered robust plastid and nuclear phylogenies and performed in-depth tests for several scenarios of hybridization. Using this strategy, we were able to resolve most of the evolutionary relationships among Rosa subgenera, sections, and selected species, and we provide new directions for a future revision of the infrageneric classification in Rosa. The stepwise strategy proposed here can be used to reconstruct the phylogenetic relationships of other challenging taxonomic groups with large numbers of hybrid and polyploid taxa.

opencc-zeroDec 2020View details →

Data from: Unravelling hybridization in Phytophthora using phylogenomics and genome size estimation

The genus Phytophthora comprises many economically and ecologically important plant pathogens. Hybrid species have previously been identified in at least six of the 12 phylogenetic clades. These hybrids can potentially infect a wider host range and display enhanced vigour compared to their progenitors. Phytophthora hybrids therefore pose a serious threat to agriculture as well as to natural ecosystems. Early and correct identification of hybrids is therefore essential for adequate plant protection but this is hampered by the limitations of morphological and traditional molecular methods. Identification of hybrids is also important in evolutionary studies as the positioning of hybrids in a phylogenetic tree can lead to suboptimal topologies. To improve the identification of hybrids we have combined genotyping-by-sequencing (GBS) and genome size estimation on a genus-wide collection of 614 Phytophthora isolates. Analyses based on locus- and allele counts and especially on the combination of species-specific loci and genome size estimations allowed us to confirm and characterize 27 previously described hybrid species and discover 16 new hybrid species. Our method was also valuable for species identification at an unprecedented resolution and further allowed correct naming of misidentified isolates. We used both a concatenation- and a coalescent-based phylogenomic method to construct a reliable phylogeny using the GBS data of 140 non-hybrid Phytophthora isolates. Hybrid species were subsequently connected to their progenitors in this phylogenetic tree. In this study we demonstrate the application of two validated techniques (GBS and flow cytometry) for relatively low cost but high resolution identification of hybrids and their phylogenetic relations.

opencc-by-4.0Dec 2020View details →

Figure 2 in Phylogenomic approaches in systematic studies

Figure 2. Summary of 1KITE phylotranscriptomic pipeline (aa—amino acid; nt—nucleotide).

opencc-zeroNov 2022View details →

No phylogenomic support for a Cenozoic origin of the "living fossil" Isoetes

Premise: The isoetalean lineage has a rich fossil record that extends to the Devonian, but the age of the living clade is unclear. Recent results indicate that it is young, from the Cenozoic, whereas earlier work based on less data from a denser taxon sample yielded Mesozoic median ages. Methods: We investigated node ages in Isoetes using two genomic datasets (plastome and nuclear ribosomal cistron) analyzed using three different clock models implemented in MrBayes (ILN, WN and TK02 models) and a conservative approach to calibration. Key results: While topological results are consistently resolved in Isoetes, estimated crown group ages range from the latest Paleozoic (mid-Permian) to the Mesozoic depending on datatype and clock model. The oldest estimates were retrieved using the autocorrelated TK02 clock model. An (early) Cenozoic age was only obtained under one specific condition (plastome data analyzed with the uncorrelated ILN clock model). That same plastome dataset also yielded the oldest (mid-Permian) age estimate when analyzed with the autocorrelated TK02 clock model. Adding the highly divergent recently established sister species Isoetes wormaldii to the dataset approximately doubled the average median node depth to the Isoetes crown group. Conclusions: There is no consistent support for a Cenozoic origin of the living clade Isoetes. We obtained seemingly well-founded, yet strongly deviating results, depending on datatype and clock model. The single most important future improvement is probably to add calibration points, which requires an improved understanding of the isoetalean fossil record or alternative bases for calibration.

opencc-zeroNov 2022View details →

Plastid phylogenomics shed light on intergeneric relationships and spatiotemporal evolutionary history of Melocanninae (Poaceae: Bambusoideae)

Melocanninae is sister to other subtribes of Paleotropical woody bamboos with some 90 species mainly concentrated in Asia. However, phylogenetic relationships within the subtribe are poorly known. Here, we filled the gaps in complete plastome data of Melocanninae, reconstructed the phylogeny of Melocanninae, and further estimated divergence time and ancestral distribution range. Our results showed that the two major genera, Cephalostachyum and Schizostachyum, were paraphyletic. Species of Cephalostachyum were resolved in two successive basal clades, while Annamocalamus was embedded in the Schizostachyum clade. Different plastid regions provided inconsistent signals for the relationship of Melocanna and Pseudostachyum. Conservative loci supported a successive divergence rather than sister relationship between them and the difference may be caused by long-branch attraction. We infer that Melocanninae originated in the East Himalaya to northern Myanmar in the early Miocene. Three routes were revealed in forming its present biogeographic pattern: in situ diversification on the Asian mainland; dispersing southwest to Sri Lanka and to the Western Ghats in South India; and spreading southeast to Malesia and Oceania via the Indo-China Peninsula. The rapid uplift of the Tibetan Plateau and the intensification of Asian monsoons since the Miocene and the sea-level-fall events since the late Miocene might be potential driving forces for diversification of Melocanninae and, particularly the latter event, for the species radiation of Schizostachyum.

opencc-zeroDec 2022View details →

A novel probe set for the phylogenomics and evolution of RTA spiders

Spiders are important models for evolutionary studies of web building, sexual selection and adaptive radiation. The recent development of probes for UCE-based phylogenomic studies has shed light on the phylogeny and evolution of spiders. However, the two available UCE probe sets for spider phylogenomics (Spider and Arachnida probe sets) have relatively low capture efficiency within spiders and are not optimized for the RTA clade, a hyperdiverse lineage that is key to understanding the evolution and diversification of spiders. In this study, we sequenced 15 genomes of species in the RTA clade, and using eight reference genomes, we developed a new UCE probe set (41,845 probes targeting 3802 loci, labelled as the RTA probe set). The performance of the RTA probes in resolving the phylogeny of the RTA clade was compared with the Spider and Arachnida probes through an in-silico test on 19 genomes. We also tested the new probe set empirically on 28 spider species of major spider lineages. The results showed that the RTA probes recovered twice and four times as many loci as the other two probe sets, and the phylogeny from the RTA UCEs provided higher support for certain relationships. This newly developed UCE probe set shows higher capture efficiency empirically and is particularly advantageous for phylogenomic and evolutionary studies of RTA clade and jumping spiders.

opencc-zeroDec 2022View details →

Plastid phylogenomics uncovers multiple species in Medicago truncatula (Fabaceae) germplasm accessions

Medicago truncatula is a model legume that has been extensively investigated in diverse subdisciplines of plant science. Medicago littoralis can interbreed with M. truncatula and M. italica; these three closely related species form a clade, i.e. TLI clade. Genetic studies have indicated that M. truncatula accessions are heterogeneous, but their taxonomic identities have not been verified. To elucidate the phylogenetic position of diverse M. truncatula accessions within the genus, we assembled 54 plastid genomes (plastomes) using publicly available next-generation sequencing data and conducted phylogenetic analyses using maximum likelihood. Five accessions showed high levels of plastid DNA polymorphism. Three of these highly polymorphic accessions contained sequences from both M. truncatula and M. littoralis. Phylogenetic analyses of sequences placed some accessions closer to distantly related species suggesting misidentification of source material. Most accessions were placed within the TLI clade and maximally supported the interrelationships of three subclades. Two Medicago accessions were placed within a M. italica subclade of the TLI clade. Plastomes with a 45-kb (rpl20-ycf1) inversion were placed within the M. littoralis subclade. Our results suggest that the M. truncatula accession genome pool represents more than one species due to possible mistaken identities and gene flow among closely related species.

FIGURE 2 in An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar

FIGURE 2. (Continued).

FIGURE 2 in An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar

FIGURE 2. (Continued).

FIGURE 2 in An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar

FIGURE 2. (Continued).

FIGURE 2 in An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar

FIGURE 2. (Continued).

FIGURE 2 in An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar

FIGURE 2. (Continued).

FIGURE 2 in An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar

FIGURE 2. (Continued).

FIGURE 2 in An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar

FIGURE 2. (Continued).

FIGURE 2 in An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar

FIGURE 2. (Continued).