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opencc-zeroSep 2022View details →

How the Easter Egg Weevils got their spots: Phylogenomics reveals Müllerian mimicry in Pachyrhynchus (Coleoptera, Curculionidae)

The evolutionary origins of mimicry in the Easter Egg weevil, Pachyrhynchus, have fascinated researchers since first noted more than a century ago by Alfred Russel Wallace. Müllerian mimicry, or mimicry in which two or more distasteful species look similar, is widespread throughout the animal kingdom. Given the varied but discrete color patterns in Pachyrhynchus, this genus presents one of the best opportunities to study the evolution of both perfect and imperfect mimicry. We analyzed more than 10,000 UCE loci using a novel partitioning strategy to resolve the relationships of closely related species in the genus. Our results indicate that many of the mimetic color patterns observed in sympatric species are due to convergent evolution. We suggest that this convergence is driven by positive frequency-dependent selection.

opencc-zeroDec 2021View details →

Phylogenomic analysis of the hemp family (Cannabaceae) reveals deep cyto-nuclear discordance and provides new insights into generic relationships

Cannabaceae are a relatively small family of angiosperms, but they include several species of huge economic and cultural significance: marijuana or hemp (Cannabis sativa) and hops (Humulus lupulus). Previous phylogenetic studies clarified most deep relationships in Cannabaceae, but relationships remain ambiguous among several major lineages. Here, we sampled 83 species representing all genera of Cannabaceae and utilized a new dataset of 90 nuclear genes and 82 chloroplast loci from Hyb-Seq to investigate the phylogenomics of Cannabaceae. Nuclear phylogenetic analyses revealed a robust and consistent backbone for Cannabaceae. We observed nuclear gene-tree conflict at several deep nodes in inferred species trees, also cyto-nuclear discordance concerning the relationship between Gironniera and Lozanella and the relationships among Trema s.l. (including Parasponia), Cannabis + Humulus, and Chaetachme + Pteroceltis. Coalescent simulations and network analyses suggest that observed deep cyto-nuclear discordances likeliest stem from incomplete lineage sorting (ILS); nuclear gene-tree conflict might be caused by both ILS and gene flow between species. All genera of Cannabaceae were recovered as monophyletic, except for Celtis, which consisted of two distinct clades: Celtis I (including most Celtis species) and Celtis II (including Celtis gomphophylla and Celtis schippii). We suggest that Celtis II should be recognized as the independent genus Sparrea based on both molecular and morphological evidence. Our work provides the most comprehensive and reliable phylogeny to date for Cannabaceae, enabling further exploration of evolutionary patterns across this family and highlighting the necessity of comparing nuclear with chloroplast data to examine the evolutionary history of plant groups.

opencc-by-4.0Feb 2017View details →

Signal, Uncertainty, and Conflict in Phylogenomic Data for a Diverse Lineage of Microbial Eukaryotes (Diatoms, Bacillariophyta)

This data depository contains analysis results from Parks, Wickett, and Alverson 2017 (Signal, Uncertainty, and Conflict in Phylogenomic Data for a Diverse Lineage of Microbial Eukaryotes (Diatoms, Bacillariophyta) (Mol. Biol. Evol. doi:10.1093/molbev/msx268)), and is made freely available to the research community. The file and subfolders here are as follows: gene_alignments - contains compressed (tarred and gzipped) folders with all gene alignments at 0.2, 0.5 and 0.8 alignment column occupancy cutoffs. In each folder, there are also text files listing which gene alignments fall under which taxon occupancy subsetting strategy (i.e., 10-20% taxon occupancy, 40-60% taxon occupancy, 80-100% taxon occupancy, etc). gene_trees - contains all (compressed) gene trees (bootstrapped versions, 100 bootstrap pseudo-replicates)) used in Astral analyses for each alignment column occupancy cutoff (0.2, 0.5, 0.8); nodes with less than 33% bootstrap support are collapsed. hmms.mafft_aligned - contains (compressed) hmm specifications for each major diatom morphotype (radial and polar centrics, araphid and raphid pennates) from the 0.2 alignment column occupancy subset of the data. A summary of the sampling scheme and the hmm results/counts are also available in HMM_sampling.docx. mmetsp_nuclear_transcriptome_assemblies - these are the compressed nuclear transcriptome assemblies that were done in-house (i.e., mostly MMETSP samples). Assemblies do not include organellar or rDNA loci. species_trees - contains (compressed) species trees for all phylogenetic strategies and alignment column occupancy cutoff/data subset strategies. Suppl_1.MMETSP_basic_summaries.xlsx - this an identical file to Parks, Wickett and Alverson 2017 supplementary file 1. This file contains taxon, strain and SRA information for all assembled taxa, and a variety of assembly metric information.

opencc-zeroApr 2024View details →

Data from: Phylogenomic analyses of the Cucujiformia

The Cucujiformia, with remarkable morphological, ecological, and behavioral diversity, is the most evolutionarily successful group within Coleoptera. However, the phylogenetic relationships among superfamilies within Cucujiformia remain elusive. To address the issues, we conducted a transcriptome-based macro-evolutionary study of this lineage. We sequenced the genomes and transcriptomes of three species from the superfamily Curculionoidea (two from Curculionidae and one from Brentidae), and obtained a dataset of more than 569,990 amino acid alignments from 143 species of Cucujiformia. With the most complete collection of whole-genomes and transcriptomes so far, we compared the performance of different data matrices with universal-single-copy orthologs (USCO). The resultant trees based on different datasets were consistent for the majority of deep nodes. Two USCO amino acid matrices (i.e., USCO75 and USCO750-abs80) provided well-resolved topology. The analyses confirm that old Cucujoidea sensu is a non-monophyletic group, consisting of Erotyloidea, Nitiduloidea and Cucujoidea sensu. Moreover, Erotyloidea is the early-diverging group in Cucujoidea sensu, followed by the clade Nitiduloidea. The preferred topologies supported a "basal" split of Coccinelloidea from the remaining superfamilies, and Cleroidea formed the second splitting group. The following phylogeny was supported at the superfamily level in Cucujiformia: (Coccinelloidea, (Cleroidea, ((Lymexyloidea, Tenebrionoidea), (Erotyloidea, (Nitiduloidea, (Cucujoidea, (Chrysomeloidea, Curculionoidea))))))). Our comprehensive analyses recovered well-resolved higher-level phylogenetic relationships within the Cucujiformia, providing a stable framework for comprehending its evolutionary history.

opencc-zeroDec 2023View details →

Ultraconserved element data for phylogenomic placement of the jumping spider genus Iranattus Prószyński, 1992 (Salticidae, Plexippini, Plexippina)

The jumping spider genus Iranattus Prószyński, 1992 has been placed in the Harmochirina based on morphology. We use phylogenomic evidence based on ultraconserved element (UCE) data to show that it belongs instead in the subtribe Plexippina.

opencc-zeroApr 2024View details →

Data from: Plastid phylogenomics and cytonuclear discordance in Rubioideae, Rubiaceae

In this study of evolutionary relationships in the subfamily Rubioideae (Rubiaceae), we take advantage of the off-target proportion of reads generated via previous target capture sequencing projects based on nuclear genomic data to build a plastome phylogeny and investigate cytonuclear discordance. The assembly of off-target reads resulted in a comprehensive plastome dataset and robust inference of phylogenetic relationships, where most intratribal and intertribal relationships are resolved with strong support. While the phylogenetic results were mostly in agreement with previous studies based on plastome data, novel relationships in the plastid perspective were also detected. For example, our analyses of plastome data provide strong support for the SCOUT clade and its sister relationship to the remaining members of the subfamily, which differs from previous results based on plastid data but agrees with recent results based on nuclear genomic data. However, several instances of highly supported cytonuclear discordance were identified across the Rubioideae phylogeny. Coalescent simulation analysis indicates that, while ILS could by itself explain the majority of the discordant relationships, plastome introgression may be the better explanation in some cases. Our study further indicates that plastomes across the Rubioideae are with few exceptions highly conserved and mainly conform to the structure, gene content, and gene order present in the majority of the flowering plants.

opencc-zeroDec 2023View details →

Mitochondrial phylogenomics of liverworts

Premise: Liverworts, with approximately 7,300 species worldwide, exhibit remarkable morphological diversity, in terms of growth form, ontogeny and architecture. Based on phylogenetic inferences drawn from DNA data, including recent genomic-scale data, the relationships among families and orders have been constantly revised and refined, although new topological incongruences have emerged. The liverwort mitochondrial genome exhibits lower average substitution rates compared to their nuclear and plastid genomes, and shows less structural variation, suggesting its suitability for inferring relationships at higher taxonomic levels. Methods: The mitochondrial genomes of 112 liverworts were sequenced, covering 105 species, 52 families and 18 orders. We analysed the structures of the liverwort mitogenomes using Mauve alignment. Maximum likelihood and Bayesian inference methods were used to infer a family-level phylogeny of liverworts. Results: We assembled the complete mitochondrial genome for 23 species and identified four new structural variants. Phylogenetic inferences from mitochondrial genome sequences confirmed the monophyly of most suprafamilial taxa, with the expectations of Porellales, Ptilidiales, and Pelliidae. Herzogianthus (Ptilidiales) was well-supported as a sister group to Jungermanniales sensu lato, rather than forming a monophyletic lineage with Ptilidium (Ptilidiales). Given its distinct morphological traits, this genus should be singled out and elevated to a new order. Conclusions: The overall architecture of liverwort mitogenomes remains highly conserved, with taxa that diverged over 470 Mya still having co-linear mitogenomes. This study provides a genetic resource for future evolutionary research across the liverworts and highlights the utility of mitogenome across lineages diversifying for 470 Mya, including for family‐level classification.

opencc-zeroJun 2024View details →

Phylogenomic discordance is driven by wide-spread introgression and incomplete lineage sorting during rapid species diversification within rattlesnakes (Viperidae: Crotalus and Sistrurus)

Phylogenomics allows us to uncover the historical signal of evolutionary processes through time and estimate phylogenetic networks accounting for these signals. Insight from genome-wide data further allows us to pinpoint the contributions to phylogenetic signal from hybridization, introgression, and ancestral polymorphism across the genome. Here, we focus on how these processes have contributed to phylogenetic discordance among rattlesnakes (genera Crotalus and Sistrurus), a group for which there are numerous conflicting phylogenetic hypotheses based on a diverse array of molecular datasets and analytical methods. We address the instability of the rattlesnake phylogeny using genomic data generated from transcriptomes sampled from nearly all known species. These genomic data, analyzed with coalescent and network-based approaches, reveal numerous instances of rapid speciation where individual gene trees conflict with the species tree. Moreover, the evolutionary history of rattlesnakes is dominated by incomplete speciation and frequent hybridization, both of which have likely influenced past interpretations of phylogeny. We present a new framework in which the evolutionary relationships of this group can only be understood in light of genome-wide data and network-based analytical methods. Our data suggest that network radiations, like those seen within the rattlesnakes, can only be understood in a phylogenomic context, necessitating similar approaches in our attempts to understand evolutionary history in other rapidly radiating species. La filogenómica nos permite descubrir la señal histórica de los procesos evolutivos a través del tiempo y estimar redes filogenéticas tomando en cuenta estas señales. El conocimiento de datos genómicos incluso permiten distinguir la contribución de la señal filogenética de la hibridación, introgresión, y de polimorfismos ancestrales a lo largo del genoma. En este trabajo nos enfocamos en como estos procesos han contribuido a la discordancia filogenética entre las serpientes de cascabel, un grupo en el que hay numerosos conflictos en las hipótesis filogenéticas obtenidas de un grupo variado de datos moleculares y métodos analíticos. Nosotros abordamos la inestabilidad de la filogenia de las serpientes de cascabel (generos Crotalus y Sistrurus) usando datos genómicos generados de transcriptomas muestreados en la mayoría de las especies conocidas. Estos datos genómicos, analizados con métodos basados en coalescencia y redes filogenéticas, revelaron numerosos casos de especiación rápida donde los arboles de genes individuales conflictúan con el árbol de especies. Además, la historia evolutiva de las serpientes de cascabel esta dominada por una especiación incompleta y una frecuente hibridación, las cuales probablemente han influenciado interpretaciones pasadas de las filogenias. Nosotros presentamos un nuevo marco en el que las relaciones evolutivas de este grupo solo pueden ser entendidas en base a datos de genomicos y métodos analíticos basados en redes filogenéticas. Nuestros datos sugieren que la radiación en redes filogenéticas, como se ha visto dentro de las serpientes de cascabel, solo puede ser entendida en un contexto filogenómico, necesitando aproximaciones similares en nuestro intento de entender la historia evolutiva en otras especies con radiaciones rápidas.

opencc-zeroJun 2024View details →

Supplementary data for: Phylogenomics, male internal genitalia, a new species, and other notes on new world Stenopelmatus Jerusalem crickets (Orthoptera: Stenopelmatoidea: Stenopelmatini)

Based on past and expanded DNA sampling, the orthopteran families Stenopelmatidae and Anostostomatidae, as currently structured, are shown to be non-monophyletic. The splay-footed cricket genus Comicus, is confirmed to be genetically distinct from all Stenopelmatidae. We add two specimens to our previously published phylogenetic tree for New World Stenopelmatus Jerusalem cricket species and report the first multilocus DNA recovery for S. ater from Costa Rica. Male internal genitalia may be of systematic value in Jerusalem crickets, but we believe they should be analyzed when in their unfolded, "physiologically functional" state, where morphological characters can be seen in more detail when compared to their preserved, folded state. We describe Stenopelmatus nuevoguatemalae n. sp. from Guatemala.

opencc-zeroJun 2024View details →

Data from: Phylogenomic perspectives on speciation in a North American biodiversity hotspot: An example using the California sages (Salvia subgenus Audibertia; Lamiaceae)

The California Floristic Province (CA-FP) is the most species-rich region of North American north of Mexico. Several hypotheses have been proposed to explain why this region is exceptionally diverse, including that it harbors many recently diverged clades with weak or no barriers to reproduction. Salvia subgenus Audibertia is a conspicuous element of the CA-FP, with multiple species often occurring in sympatry. Using 305 nuclear loci and both organellar genomes, we reconstruct species trees, examine genomic discordance, conduct divergence-time estimation, and analyze contemporaneous patterns of geneflow and mechanical reproductive isolation. Despite strong genomic discordance, an underlying bifurcating tree is supported. Organellar genomes capture additional introgression events not detected in the nuclear genome. Most interfertility is found within clades and species are generally not mechanically isolated. Rapid, recent speciation with some horizontal geneflow during the rise of Mediterranean climate is the underlying cause of extant diversity in subgenus Audibertia. Geneflow has largely not facilitated speciation. Its signal in the nuclear genome seems to mostly be erased by backcrossing, but organellar genomes each capture different events of historical geneflow, perhaps characteristic of many lineages in the CA-FP. Mechanical reproductive isolation is likely only part of a mosaic of factors limiting geneflow.

opencc-zeroDec 2023View details →

Phylogenomic analyses of ochrophytes (stramenopiles) with an emphasis on neglected lineages

Ochrophyta is a photosynthetic lineage that crowns the phylogenetic tree of stramenopiles, one of the major eukaryotic supergroups. Due to their ecological impact as a major primary producer, ochrophytes are relatively well-studied compared to the rest of the stramenopiles, yet their evolutionary relationships remain poorly understood. This is in part due to a number of missing lineages in large-scale multigene analyses, and an apparently rapid radiation leading to many short internodes between ochrophyte subgroups in the tree. These short internodes are also found across deep-branching lineages of stramenopiles with limited phylogenetic signal, leaving many relationships controversial overall. We have addressed this issue with other deep-branching stramenopiles recently, and now examine whether contentious relationships within the ochrophytes may be resolved with the help of filling in missing lineages in an updated phylogenomic dataset of ochrophytes, along with exploring various gene filtering criteria to identify the most phylogenetically informative genes. We generated ten new transcriptomes from various culture collections and single-cell isolation from an environmental sample, added these to an existing phylogenomic dataset, and examined the effects of selecting genes with high phylogenetic signal or low phylogenetic noise. For some previously contentious relationships, we find a variety of analyses and gene filtering criteria consistently unite previously unstable grouping with strong statistical support. For example, we recovered a robust grouping of Eustigmatophyceae with Raphidophyceae-Phaeophyceae-Xanthophyceae while Olisthodiscophyceae formed a sister lineage to Pinguiophyceae. Selecting genes with high phylogenetic signal or data quality recovered more stable topologies. Overall, we find that adding under-represented groups across different lineages is still crucial in resolving phylogenomic relationships, and discrete gene properties affect lineages of stramenopiles differently which may be further explored to better understand the molecular evolution of stramenopiles.

Data from: The influence of the number of tree searches on maximum likelihood inference in phylogenomics

Maximum likelihood (ML) phylogenetic inference is widely used in phylogenomics. As heuristic searches most likely find suboptimal trees, it is recommended to conduct multiple (e.g., ten) tree searches in phylogenetic analyses. However, beyond its positive role, how and to what extent multiple tree searches aid ML phylogenetic inference remains poorly explored. Here, we found that a random starting tree was not as effective as the BioNJ and parsimony starting trees in inferring ML gene tree and that RAxML-NG and PhyML were less sensitive to different starting trees than IQ-TREE. We then examined the effect of the number of tree searches on ML tree inference with IQ-TREE and RAxML-NG, by running 100 tree searches on 19,414 gene alignments from 15 animal, plant, and fungal phylogenomic datasets. We found that the number of tree searches substantially impacted the recovery of the best-of-100 ML gene tree topology among 100 searches for a given ML program. In addition, all of the concatenation-based trees were topologically identical if the number of tree searches was ≥ 10. Quartet-based ASTRAL trees inferred from 1 to 80 tree searches differed topologically from those inferred from 100 tree searches for 6 /15 phylogenomic datasets. Lastly, our simulations showed that gene alignments with lower difficulty scores had a higher chance of finding the best-of-100 gene tree topology and were more likely to yield the correct trees.

Data from: Phylogenomic loci define the generic boundaries of Gochnatieae and improve resolution at the species level in Moquiniastrum (Compositae)

Understanding the evolution of the tribe Gochnatieae (Compositae) has been the subject of considerable effort in the past decade. This is due to the key position of this tribe in the phylogeny of the sunflower family and the corresponding implications for biogeographic and morphological evolution of Compositae. Previous studies have confirmed the monophyly of this tribe as well as most of the genera that belong to it. However, phylogenetic resolution of Gochnatieae at both the genus- and species-level has remained poor. A subset of new phylogenomic loci used in this study has proven effective and has improved phylogenetic resolution in this group. The results of this work demonstrate Gochnatieae is a well-supported clade comprised of nine genera (Anastraphia, Cnicothamnus, Cyclolepis, Gochnatia, Moquiniastrum, Nahuatlea, Pentaphorus, Richterago, Tehuasca). One recently described genus, Vickia, was not included in this study; but its placement in Gochnatieae as a tenth genus in the tribe is well-justified. The monospecific Cyclolepis, which had been circumscribed within the tribe since its inception but was subsequently removed and designated as incertae sedis since 2014, is also shown to belong to Gochnatieae. We confirmed the monophyletic Moquiniastrum with two well-supported subclades. Ancestral area reconstruction analyses show that Gochnatieae originated in Eastern South America about 53 my. Apparently, except for Cyclolepis and Richterago, the ancestors of the other genera of Gochnatieae originated about 44 my from an area that now corresponds to the central Andes. The presence of the genera in the Chaco phytogeographic province, central Chile, and Mexico-United States-Caribbean is a result of dispersal from the central Andes. The ancestral distribution of Moquiniastrum corresponds to a large area comprising Eastern South America and the current central Andes, about 32 my. Ancestral character state reconstruction that included four characters indicates several states associated with complex plant reproductive biology such as gynodioecy, gynomonoecy, and polygamodioecy are derived in Gochnatieae as are heterogamous capitula (in Moquiniastrum and Richterago), dimorphic and subdimorphic corollas (in Cnicothamnus, Moquiniastrum, and Richterago), and the presence of marginal female corollas (in Moquiniastrum and Richterago). Within Moquiniastrum, two subclades (Densicephalum and Polymorphum) exhibit divergent patterns of trait evolution associated with these reproductive characters which suggests this genus can serve as a model to understand the sexual system evolution in plants.

Phylogenomics of Brachystegia (Fabaceae, Detarioideae): Insights into the origin of African miombo woodlands

Premise of study: Phylogenetic approaches can provide valuable insights on how and when a biome emerged and developed using its structuring species. In this context, Brachystegia Benth, a dominant genus of trees in miombo woodlands, appears as a key witness of the history of the largest woodland and savanna biome of Africa. Methods: We reconstructed the evolutionary history of the genus using targeted-enrichment sequencing on 60 Brachystegia specimens for a near complete species sampling. Phylogenomic inferences used supermatrix (RAxML-NG) and summary-method (ASTRAL-III) approaches. Conflicts between species and gene trees were assessed and the phylogeny was time-calibrated in BEAST. Introgression between species was explored using Phylonet. Key results: Phylogenies are globally congruent regardless of the method used. Most of the species were recovered as monophyletic, unlike previous plastid phylogenetic reconstructions where lineages were shared among geographically close individuals independently of species identity. Still, most of the individual gene trees have low levels of phylogenetic information and are mostly in conflict with the reconstructed species trees, when informative. It suggests incomplete lineage sorting and/or reticulate evolution, the latter being supported by network analyses. BEAST analysis supports a Pliocene origin for the genus, with most of the diversification events dated to the Pliocene-Pleistocene. Conclusions: These results suggest a recent origin of species of the miombo, congruently with their spatial expansion documented from plastid data. Brachystegia species appear to behave potentially as a syngameon, a group of interfertile but still relatively well-delineated species, an aspect that deserves further investigations.

Data from: Plastid phylogenomic analysis of Podostemaceae with an emphasis on Neotropical podostemoideae

Podostemaceae are a clade of aquatic flowering plants that form important components of tropical river ecosystems. Species in the family exhibit highly derived growth forms and high vegetative phenotypic plasticity, both of which contribute to taxonomic confusion. The backbone phylogeny of the family remains poorly resolved, many species remain to be included in a molecular phylogenetic analysis, and the monophyly of many taxa remains to be tested. To address these issues, we assembled sequence data for 73 protein-coding plastid genes from 132 samples representing 68 species (~23% of described species) that span the breadth of most major taxonomic, morphological, and biogeographic groups of Podostemaceae. With these data, we conducted the first plastid phylogenomic analysis of the family with broad taxon sampling. These analyses resolved most nodes with high support, including relationships not recovered in previous analyses. No evidence of widespread, well-supported conflict among individual plastid genes and the concatenated phylogeny was observed. We present new evidence that four genera (Apinagia, Marathrum, Oserya, and Podostemum), as well as four species, are not monophyletic. In particular, we show that Podostemum flagelliforme should not be included in Podostemum and is better recognized as Devillea flagelliformis, and that Marathrum capillaceum is embedded within Lophogyne s.l. and should be recognized as Lophogyne capillacea. We also place a previously unsampled and undescribed species that likely represents a new genus. In contrast to previous studies, the neotropical genera Diamantina, Ceratolacis, Cipoia, and Podostemum are resolved as successive sister groups to a clade of all paleotropical Podostemoideae taxa sampled, suggesting a single dispersal event from the neotropics to the paleotropics in the history of the subfamily. These results provide a strong basis for improving the classification of Podostemaceae and a framework for future phylogenomic studies of the clade employing data from the nuclear genome.

opencc-by-4.0Jun 2019View details →

Dataset for the phylogenomic analysis of Burkholderiaceae sp. PBA

File description: Genome_Information.txt - Complete information of the genomes used in this study phylophlan_Alignment.fna.contree - IQtree tree (newick format) based on the alignment of 400 conserved proteins Aligned_SCGs.faa.contree - IQtree tree (newick format) based on the alignment of 200+ conserved proteins Folder description (tar archive): GToTree_output - Intermediate and Output files from GToTree PhylophlAN_output - Intermediate and Output files from PhylophlAN

opencc-by-4.0Sep 2019View details →

LIchenothelia_Saxomyces_phylogenomic_alignments

Alignments used in  Ametrano et al. (2019) "Genome-scale data resolve ancestral rock-inhabiting lifestyle in Dothideomycetes"; IMAFungus

opencc-by-4.0Feb 2021View details →

Fig. 3 in Phylogenomics of the tropical plant family Ochnaceae using targeted enrichment of nuclear genes and 250+ taxa

Fig. 3. Continues. For caption, see next part.

opencc-zeroDec 2017View details →

Data from: Phylogenomic analyses reveal a deep history of hybridization and polyploidy in the Neotropical genus Lachemilla (Rosaceae)

Hybridization, incomplete lineage sorting, and phylogenetic error produce similar incongruence patterns, representing a great challenge for phylogenetic reconstruction. Here, we use sequence capture data and multiple species tree and species network approaches to resolve the backbone phylogeny of the Neotropical genus Lachemilla, while distinguishing among sources of incongruence. We used 396 nuclear loci and nearly complete plastome sequences from 27 species to clarify the relationships among the major groups of Lachemilla, and explored multiple sources of conflict between gene trees and species trees inferred with a plurality of approaches. All phylogenetic methods recovered the four major groups previously proposed for Lachemilla, but species tree methods recovered different topologies for relationships between these four clades. Species network analyses revealed that one major clade, Orbiculate, is likely of ancient hybrid origin, representing one of the main sources of incongruence among the species trees. Additionally, we found evidence for a potential whole genome duplication event shared by Lachemilla and allied genera. Lachemilla shows clear evidence of ancient and recent hybridization throughout the evolutionary history of the group. Also, we show the necessity to use phylogenetic network approaches that can simultaneously accommodate incomplete lineage sorting and gene flow when studying groups that show patterns of reticulation.