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opennotspecifiedApr 2021View details →

Fig. 1 in Phylogenomics of Ichneumoninae (Hymenoptera, Ichneumonidae) reveals pervasive morphological convergence and the shortcomings of previous classifications

Fig. 1. Morphological diversity in Ichneumoninae. (A–C) Live habitus of representative species; photos by Steve Marshall (University of Guelph), used with permission. (A) Centeterus sp. in Canada; (B) Ichneumon promissorius in Australia; (C) Aucklandella sp. in New Zealand. (D–F) habitus images. (D) Alomya debellator; (E) Notosemus bohemani; (F) Abzaria latipetiolaris; (G) Probolus concinnus; (H) Eutanyacra sp.; (I) Joppa sp.; (J) Lophojoppa sp.; (K) Platylabops fraterculus; (L) Trogomorpha trogiformis. [Colour figure can be viewed at wileyonlinelibrary.com].

Data from: Phylogenomics and continental biogeographic disjunctions – insight from the Australian starflowers (Calytrix: Myrtaceae)

PREMISE OF THE STUDY: Continental-scale disjunctions and associated drivers is a core research interest in biogeographic studies. Here, we selected a species-rich Australian plant genus (Calytrix; Myrtaceae) as a case study to investigate these patterns in an Australian context. The endemic Australian starflower genus has a disjunct distribution across the mesic fringes of the continent and is absent from the arid centre. METHODS: We used high-throughput sequencing to generate unprecedented resolution and near complete species-level nuclear and plastid phylogenies for Calytrix. BioGeoBEARS and biogeographic stochastic mapping (BSM) were used to infer ancestral areas, the relative contributions of vicariance and dispersal events, and directionality of dispersal. KEY RESULTS: Present-day disjunctions in Calytrix are explained by a combination of scenarios: (1) retreat of multiple lineages from the continental centre to the more mesic fringes as Australia became progressively more arid, with subsequent extinction in the centre, and also (2) origination of ancestral lineages in southwestern Australia (SWA) for species-rich clades. The SWA biodiversity hotspot is a major diversification centre and the most common source area of dispersals, with multiple lineages originating in SWA and subsequently spreading to the adjacent arid Eremaean region. CONCLUSIONS: Our results suggest major extinction as a result of cooling and drying of the Australian continent in the Eocene–Miocene shaped the present-day biogeography of Calytrix. We hypothesise that this peripheral vicariance pattern, which is similar to the African Rand flora, may explain the disjunctions of many other Australian plant groups. Further studies with densely sampled phylogenies are required to test this hypothesis.

A phylogenomic perspective on the evolutionary history of the stonefly genus Suwallia (Plecoptera: Chloroperlidae) revealed by ultraconserved genomic elements

Evolutionary biologists have long sought to disentangle phylogenetic relationships among taxa spanning the tree of life, an increasingly important task as anthropogenic influences have caused, and are expected to continue to cause, population declines and species extinctions, particularly in insects. Advances in DNA sequencing techniques have increasingly facilitated the ability of researchers to apply genomic methods to phylogenetic analyses, even for non-model organisms which have historically lacked the genomic resources to do so. Phylogenetic relationships within the stonefly genus Suwallia (Insecta: Plecoptera: Chloroperlidae) are poorly understood, and have never been assessed using molecular data. We used DNA sequence data from genome-wide ultraconserved element loci to generate the first molecular phylogeny for the group and assess its monophyly. Our results reveal that the monospecific chloroperlid Neaviperla forcipata renders Suwallia paraphyletic, and we recommend a taxonomic revision for its inclusion in Suwallia. We also found that Palearctic and Nearctic Suwallia do not form reciprocally monophyletic clades, and that a biogeographic history including dispersal, vicariance, and founder event speciation via jump dispersal best explains the geographic distribution of this group. Moreover, some Suwallia species (e.g., S. amoenacolens, S. kerzhneri, S. marginata, S. pallidula, and S. starki) exhibit pronounced cryptic diversity that is worthy of further investigation. These findings provide a first glimpse into the evolutionary history of Suwallia, improve our understanding of stonefly diversity, and highlight areas where additional research is needed.

Phylogenomics of Fargesia and Yushania reveals a history of reticulate evolution

Reticulate evolution is a common and important driving force in angiosperm evolution. In this study, we analyzed the phylogenetic signals of genomic regions with different inheritance patterns to understand the evolutionary process of organisms using species‐rich Himalaya–Hengduan taxa of bamboos (Fargesia Franchet and Yushania Keng). We constructed phylogenetic trees using different sampling strategies and reconstruction methods based on genome skimming and double digest restriction‐site‐associated DNA sequencing data. We assessed the congruence of topologies generated from different datasets and employed several approaches to reveal the causes of phylogenetic incongruence, including the detection of hybridization and introgression using PhyloNetworks and the D‐ statistic test (ABBA‐BABA test). We found that, in the plastome‐based phylogeny, Fargesia bamboos can be clustered into three groups and Yushania was nested within one of them, which contradicts the nuclear–double digest restriction‐site‐associated DNA sequencing‐based phylogeny. Moreover, the genetic variation of chloroplast DNA is significantly correlated with geographical distribution. The strong signal of incomplete lineage sorting, hybridization, introgression, and cytoplasmic gene flow found among genera and species suggests that reticulate evolution is the main cause for the phylogenetic incongruence between nuclear and chloroplast datasets. Our results add evidence that genomes with different inheritance patterns can reveal distinct evolutionary histories of species and suggest that reticulate evolution is prevalent in rapidly diversifying groups.

opencc-zeroNov 2021View details →

Valenzuela phylogenomic dataset from: Illumina whole genome sequencing indicates ploidy level differences within the Valenzuela flavidus (Psocodea: Psocomorpha: Caeciliusidae) species complex

This contains data for the manuscript: "Illumina Whole Genome Sequencing indicates Ploidy Level Differences within the Valenzuela flavidus (Psocodea: Psocomorpha: Caeciliusidae) Species Complex". Valenzuela flavidus is a species of bark louse which is known to have asexual parthenogenetic populations in Europe but is believed to have sexual and asexual populations in North America as well. Historically, Valenzuela aurantiacus was the species epithet recognized for North American members until reports of asexual reproduction surfaced in certain North American populations. Cytogenetic studies have demonstrated European all-female populations are triploid. However, males are often reported in North America suggesting diploidy for sexual populations. With the use of Illumina whole genome sequencing, genetic diversity among North American and European populations was explored with phylogenomic methods. Ploidy level was estimated by examining allele frequencies of read-mapped homologous gene regions. Results indicate divergent populations between Europe and North America. North American populations containing males are estimated to be diploid suggesting a different mechanism of genomic reproduction. These results suggest divergent population structure among European asexual and North American sexual members of V. flavidus providing insight for future studies to understand patterns of asexuality reported within the complex. The following file contains all gene alignments, concatenated supermatrix, and mitochondrial alignment for this manuscript. In addition, the BAM files used to estimate allele frequencies. Also, gene trees for coalescent analysis, resultant treefiles from IQ-tree searches, and MCMCtree result.

Data from: Phylogeny of gracillariid leaf-mining moths: evolution of larval behaviour inferred from phylogenomic and Sanger data

Gracillariidae is the most taxonomically diverse cosmopolitan leaf-mining moth family, consisting of nearly 2000 named species in 105 described genera, classified into eight extant subfamilies. The majority of gracillariid species are internal plant feeders as larvae, creating mines and galls in plant tissue. Despite their diversity and ecological adaptations, their phylogenetic relationships, especially at the subfamily level, remain largely uncertain. Genomic data (83 taxa and 589 loci) were integrated with Sanger data (130 taxa and 22 loci), to reconstruct a phylogeny of Gracillariidae. Based on analyses of both data sets combined and analyzed separately, the monophyly of Gracillariidae and all its subfamilies, and the monophyly of the clade 'LAMPO' (subfamilies: Lithocolletinae, Acrocercopinae, Marmarinae, Phyllocnistinae, and Oecophyllembiinae) and relationships of its subclade 'AMO' (subfamilies: Acrocercopinae, Marmarinae, and Oecophyllembiinae) were strongly supported. A sister group relationship of Ornixolinae to the remainder of the family, and a monophyletic leaf roller lineage (Callicercops Vári + Parornichinae) + Gracillariinae, as sister to the 'LAMPO' clade were supported by the best hypotheses. Based on these results, a new subfamily, Callicercopinae Li, Ohshima et Kawahara, is established to accommodate the enigmatic genus Callicercops. Dating analyses indicate a mid-Cretaceous (105.3 Ma) origin of the family, followed by a rapid diversification into the nine subfamilies predating the K-Pg extinction. We hypothesize that advanced larval behaviours, such as making keeled or tentiform blotch mines, rolling leaves, and making galls, accelerated the diversification of Gracillariidae by avoiding larval parasitoids.

opencc-zeroNov 2021View details →

Phylogenomic discordance suggests polytomies along the backbone of the large genus Solanum

Premise of the study: Evolutionary studies require solid phylogenetic frameworks, but increased volumes of phylogenomic data have revealed incongruent topologies among gene trees in many organisms both between and within genomes. Some of these incongruences indicate polytomies that may remain impossible to resolve. Here we investigate the degree of gene-tree discordance in Solanum, one of the largest flowering plant genera that includes the cultivated potato, tomato, and eggplant, as well as 24 minor crop plants. Methods: A densely sampled species-level phylogeny of Solanum is built using unpublished and publicly available Sanger sequences comprising 60% of all accepted species (742 spp.) and nine regions (ITS, waxy, and seven plastid markers). The robustness of this topology is tested by examining a full plastome dataset with 140 species and a nuclear target-capture dataset with 39 species of Solanum (Angiosperms353 probe set). Key results: While the taxonomic framework of Solanum remained stable, gene tree conflicts and discordance between phylogenetic trees generated from the target-capture and plastome datasets were observed. The latter correspond to regions with short internodal branches, and network analysis and polytomy tests suggest the backbone is composed of three polytomies found at different evolutionary depths. The strongest area of discordance, near the crown node of Solanum, could potentially represent a hard polytomy. Conclusions: We argue that incomplete lineage sorting due to rapid diversification is the most likely cause for these polytomies, and that embracing the uncertainty that underlies them is crucial to understand the evolution of large and rapidly radiating lineages.

opencc-zeroNov 2021View details →

Spatial phylogenomics of acrobat ants in Madagascar—mountains function as cradles for recent diversity and endemism

Aim: A crucial step to protecting biodiversity is assessing species diversity and endemism. We delineate spatial patterns of diversity in Malagasy ants on a phylogenetic and taxonomic level to identify centers of diversity and endemism, and evaluate the 'museum vs cradle' hypothesis with regard to ant endemism. Location: Madagascar Taxon: Ants, genus Crematogaster. Methods: We estimated distribution models for 33 Crematogaster species and generated a phylogeny based on ultraconserved elements. We calculated species richness (SR), phylogenetic diversity (PD), weighted (WE), phylogenetic endemism(PE), randomized phylogenetic diversity (PD-sig), and relative phylogenetic diversity (RPD) and endemism (RPE). Categorical analyses of neo- and paleo-endemism (CANAPE) and the phylo-jaccard index were used to delineate centers of neo- and paleo-endemism. We correlated these measures with elevation metrics to investigate the role of mountains in generating ant endemism. Results: We found extensive phylogenetic clustering (significantly low PD-sig) and short branches (low RPD) at higher elevations in central and south-central to southern Madagascar. In contrast, phylogenetic overdispersion (significantly high PD-sig) and long branches (high RPD) predominate at lower elevations in eastern humid and northern western dry forests. CANAPE and phylo-jaccard estimated five centers of endemism, whereby neo- and mixed endemism were significantly correlated with higher elevations, and paleo-endemism with lower elevations. Main Conclusions: Centers of ant endemism are located in western dry and humid forests of northern Madagascar, eastern humid forests, and in the southern Central Highland region. Mountainous areas appear to be cradles of recent diversification for acrobat ants, whereas lower elevations may be regarded as centers of paleo-endemism and thus museums for relict lineages. Species diversification among acrobat ants may have coincided with the arrival of a new biome in the central highlands of Madagascar.

Untying the Gordian Knot of plastid phylogenomic conflict: a case from ferns

Phylogenomic studies based on plastid genome have resolved the recalcitrant relationships among various plants, yet the phylogeny of Dennstaedtiaceae at the taxonomic level remains unresolved due to conflicting plastid genes, limited molecular data and incomplete taxon sampling of previous studies. The present study generated 31 new plastid genomes of Dennstaedtiaceae (9 genera, 30 species) and combined 41 publicly available sequences of plastid genome (including 24 families, 26 genera, 41 species) to solve and explore the evolution of Dennstaedtiaceae. In order to minimize the impact of systematic errors on the resolution of phylogenetic inference, we applied six strategies to generate 30 datasets based on CDS, Spacer, and All datasets, and two tree inference methods (maximum-likelihood, ML; and multispecies coalescent, MSC) to comprehensively analyze the plastome-scale data. Besides, the phylogenetic signal among all loci was quantified for the controversial node using the ML framework, and the phylogenetic hypotheses among all datasets were tested. In the species tree based on different data sets and methods, obvious conflicts were detected at the base of the polypod ferns. Meanwhile, the topology of the "CDS-codon-align-rm3" (CDS removed the third codon) matrix was selected as the primary reference or summary tree due to its analysis results are consistent, and similar to the topological structure of the amino-acid matrix. The final phylogenetic tree supported Dennstaedtiaceae as the sister group to eupolypods, and Dennstaedtia (sen. lat.) can divided into smaller genera, which was also supported by geographical distribution and plastid structure. This robust reconstructed phylogenetic backbone established a framework for future studies on Dennstaedtiaceae classification, evolution and diversification. The present study suggests considering plastid phylogenomic conflict when using plastid genomes. From our results, reducing saturated genes or sites can effectively mitigate the tree conflicts of distantly related taxa. Moreover, amino acid sequences may verify the accuracy of nucleotide-based phylogeny.

Whence came these plants most foul? Phylogenomics and biogeography of Lowiaceae (Zingiberales)

Lowiaceae (order Zingiberales) is a small family of forest herbs in Southeast Asia. All species belong to the genus Orchidantha. They are known for possessing orchid-like flowers that are smelly, apparently mimicking dead animals, feces, or mushrooms. Little is known of the biogeographic patterns or character evolution of the family. We sampled the family extensively, including many recently discovered species, and reconstructed the phylogeny of the family using HybSeq with Lowiaceae-specific RNA baits. Our phylogenetic reconstructions confirm that the family is most closely related to Strelitziaceae, and that species with dark, foul-smelling flowers form a grade in which a clade of species with paler smelling flowers are embedded. The pale-flowered species produce a distinct odor, resembling edible mushrooms. Apart from a single species, the species from Borneo form a clade, and the same is true for Indochinese species. The remaining species form a more widespread clade. A biogeographic analysis shows that the distribution of Lowiaceae can explained by vicariance and gradual dispersal from a shared ancestral range of Borneo and Indochina. There is no evidence of long-distance dispersal, only a later extension in distribution to Peninsular Malaysia which coincides with the presence of a land bridge. Different directions of spread are possible, but none require long-distance dispersal. The results are consistent with the geological history of Southeast Asia. In particular, the relatively early isolation between Indochina and Borneo could be explained by the presence of a sea barrier that developed 10–15 MYA, and the continuous movement of plant species between Borneo and Peninsular Malaysia could be explained by a land bridge that existed until c. 5 MYA. The lack of an extensive land bridge with a suitable habitat may explain the absence of this genus from Sumatra and other Indonesian islands aside from Borneo. The strict reliance on a continuous habitat for the range expansion of Lowiaceae can be explained by their fruits and seeds, which lack obvious adaptations for long-distance dispersal. The inability to disperse to new areas may also explain why the extant species have very restricted distributions.

Anchored phylogenomics and a revised classification of the Planidial Larva Clade of Jewel Wasps (Hymenoptera: Chalcidoidea)

Planidia are free-living, mobile first-instar larvae that are notable in their ability to transition on a single host between different larval stadia, and for completing their development on the host prepupa as ectoparasitoids, effectively acting as larval-pupal external koinobionts. Within Chalcidoidea, a mega-diverse superfamily of parasitoid wasps, taxa with a planidium form a monophyletic group, the Planidial-Larva-Clade (PLC), which has been comprised of three recognized groups: Eutrichosomatinae (Pteromalidae), Perilampidae (Chrysolampinae, Perilampinae, Philomidinae and the unplaced genus Jambiya), and Eucharitidae (Akapalinae, Eucharitinae, Gollumiellinae and Oraseminae). To clarify the classification and better understand the evolution of this clade, we conducted a phylogenomic study of the PLC using anchored hybrid enrichment data. The phylogenetic analyses support the backbone relationship of PLC as: (Eutrichosomatinae, ((Philomidinae, Chrysolampinae), (Perilampinae, Eucharitidae))). Although excluded from the main analyses, the genus Jambiya, based on only 11 loci recovered, was placed as the sister of Chrysolampinae + Philomidinae or Perilampinae + Eucharitidae. Our results support the placement of Eutrichosomatinae at the base of the PLC phylogeny and demonstrate that Perilampidae (Philomidinae, Chrysolampinae and Perilampinae) are paraphyletic. In contrast to other studies, anchored enrichment data fail to recover the Ponerinae- Ectatomminae-Myrmeciinae (PEM) parasitoid clade within Eucharitinae, which may indicate a more complicated evolutionary history of ant-host shifts. Traits explored using Likelihood Ancestral State Reconstruction include the evolution of host associations, direct versus indirect hyperparasitism, ability to attack a host within a cocoon, soft versus hard planidial forms, and mobility of the planidium. Divergence dating based on four calibration fossils suggests that the planidial clade arose approximately 111 Ma and the evolution of ant parasitism at least 64 Ma. A revised higher-level classification of the planidial larva clade is proposed with Eutrichosomatinae elevated to Eutrichosomatidae (Rev. Stat.), Chrysolampinae and Philomidinae placed in Chrysolampidae (Rev. Stat.), Perilampidae (Rev. Stat.) restricted to what was referred to as Perilampinae, and Eucharitidae maintained with four subfamilies, with Akapalinae (unknown biology) as sister group to the core Eucharitidae, all of which are ant parasitoids. Jambiya is treated as an incertae sedis taxon within the planidial clade.

opencc-by-4.0Nov 2021View details →

Data from: Schneider et al. (2021). Predominantly eastward long-distance dispersal in pantropical Ochnaceae inferred from ancestral range estimation and phylogenomics. Frontiers in Ecology and Evolution.

The data contains (a) DNA sequence alignments of concatenated nuclear loci, near-complete plastid genomes and plastid genomes with sites removed at a 10% gap threshold; (b) maximum clade credibility trees obtained from divergence time estimation in BEAST with each of the alignments; (c) area codings and the input tree (nuclear DNA only) for the ancestral area analysis in BioGeoBears.

Plastid phylogenomics of tribe Perseeae (Lauraceae) yields insights into the evolution of East Asian subtropical evergreen broad-leaved forests

Background: The East Asian subtropical evergreen broad-leaved forests (EBLFs) harbor remarkable biodiversity. However, their historical assembly remains unclear. To gain new insights into the assembly of this biome, we generated a molecular phylogeny of one of its essential elements, the tribe Perseeae (Lauraceae). Results: Our plastid tree topologies were robust to analyses based on different plastid regions, data partitioning, nucleotide substitution saturation and gap handling strategies. We found that Perseeae comprised six major clades and started to colonize the subtropical EBLFs of east Asia in the early Miocene. The diversification rates of Perseeae accelerated twice in the late Miocene. Conclusions: Our findings suggest that the intensified precipitation in East Asia in the early Miocene might have facilitated range expansions of the drought-sensitive subtropical EBLFs and establishment of Perseeae within this biome. By the late Miocene, assembly and diversification within the EBLFs had become rapid.

opencc-zeroFeb 2022View details →

Phylogenomics in the hard pines (Pinus subsection Ponderosae; Pinaceae) confirms paraphyly in Pinus ponderosa, and places Pinus jeffreyi with the California big cone pines

We sampled 130 individuals (2 to 25 per taxon) of subsections Ponderosae and Sabinianae. Nucleotide sequences were obtained by targeting 703 low copy nuclear genes. From the unenriched portion of the short reads, we assembled nearly complete plastome nucleotide sequences. We used 600 nuclear genes and the plastome sequences to create phylogenies and species trees that we compared to evaluate cytonuclear concordance and reticulation. We found that Pinus jeffreyi belongs with subsect. Sabinianae based on morphological synapomorphies as well as strong molecular phylogenetic support. Pinus ponderosa sensu lato is paraphyletic, and we suggest treatment as threes species: P. ponderosa sensu stricto (with var. ponderosa, var. benthamiana, and var. washoensis), P. scopulorum, and P. brachyptera. The persistence of lineages with the footprints of ancient nuclear introgression (labeled bpw in clade N4) and chloroplast capture (labeled bpw in clade P1) should caution species identification in the Ponderosae based on limited molecular data. The hybrid frequency was low based on cytonuclear discordance, and the persistence of an ancient P1 plastid clade is a better explanation than hybridization between P. ponderosa and P. jeffreyi for unexpected plastid associations in the western Sierra Nevada, USA. We identified a new potential zone of ancient admixture between P. ponderosa and P. scopulorum in Idaho, USA. Some populations of P. arizonica, P. brachyptera, P. engelmannii, and P. scopulorum in the USA are more closely related to taxa with distributions limited to Mexico than they are to each other. To integrate phylogeny and taxonomy, future work should sample widely in Mexico and the USA, score morphological characters (including seedling characters from the known seed parent), on the same individual as used for molecular data, and use methods that are based on individuals rather than population frequencies.

opennotspecifiedDec 2020View details →

Fig. 2. Phylogenomic tree showing the relationship between strain CTD02-10-2T in Chryseoglobus indicus sp. nov., isolated from deep sea water

Fig. 2. Phylogenomic tree showing the relationship between strain CTD02-10-2T and closely related species. The phylogenetic relationship of the related genomes was determined using UBCG pipeline3 tool with GTR + CAT model based on concatenated alignment of 92 core genes. Genome sequences for each of the type strains are available from the NCBI databases, with the GenBank accession numbers shown in parentheses. Tropheryma whipplei Neuro14T (CAUR000000000) was used as an outgroup. Bootstrap values (expressed as percentages of 1000 replications) over 70% are shown at branching nodes. Bar, 0.05 substitutions per nucleotide position.

opencc-zeroFeb 2022View details →

Peeling back the layers: First phylogenomic insights into the Ledebouriinae (Scilloideae, Asparagaceae)

The Ledebouriinae (Scilloideae, Asparagaceae) are a widespread group of bulbous geophytes found predominantly throughout seasonal climates in sub-Saharan Africa, with a handful of taxa in Madagascar, the Middle East, India, and Sri Lanka. Phylogenetic relationships within the groups have been historically difficult to elucidate. Here, we provide the first phylogenomic perspective into the Ledebouriinae. Using the Angiosperms353 targeted enrichment probe set, we consistently recovered four major clades (i.e., two Ledebouria clades, Drimiopsis, and Resnova). The two Ledebouria clades closely align with geography, either consisting almost entirely of sub-Saharan African taxa (Ledebouria Clade A), or East African and non-African taxa (Ledebouria Clade B). Our results suggest that the Ledebouriinae likely underwent a rapid radiation leading to rampant incomplete lineage sorting. We additionally find evidence for potential historical hybridization between Drimiopsis and a subclade within Ledebouria Clade A.

opencc-by-4.0Apr 2022View details →

Supporting information for Plant migration under long-lasting hyperaridity – phylogenomics unravels recent biogeographic history in one of the oldest deserts on Earth

R Scripts, input and parameter files as well as analysis results are provided for the publication: Böhnert et la. (2022) Plant migration under long-lasting hyperaridity – phylogenomics unravels recent biogeographic history in one of the oldest deserts on Earth. New Phyotologist.

opencc-zeroMar 2022View details →

Phylogenomics and fossil data inform the systematics and geographic range evolution of a diverse Neotropical ant lineage

Recent advances in phylogenomics allow for the use of large amounts of genetic information in phylogenetic inference. Ideally, the increased resolution and accuracy of such inferences facilitate improved understanding of macroevolutionary processes. Here, we integrate ultraconserved elements (UCEs) with fossil and biogeographic range data to explore diversification and geographic range evolution in the diverse turtle ant genus Cephalotes. We focus on the potential role of the uplift of the Panamanian land bridge and the putative ephemeral GAARlandia land bridge linking South America and the Antilles in shaping the evolution in this group. Our phylogenetic analyses provide new resolution to the backbone of the turtle ant phylogeny. We further found that a majority of geographic range shifts between the South America and Central America regions were temporally consistent with the development of the Panamanian land bridge, while we did not find support for the GAARlandia land bridge. Additionally, we did not infer any shifts in diversification rates associated with our focal land bridges, or any other historical events (we inferred a single diversification rate regime across the genus). Our findings highlight the impact of the Panamanian land bridge for Cephalotes geographic range evolution as well as the influence of taxonomic sampling on macroevolutionary inferences. Keywords: Formicidae, Hymenoptera, Biogeography, Biology, Evolution, Phylogeny, Systematics

opencc-zeroMar 2022View details →

A new approach using targeted sequence capture for phylogenomic studies across Cactaceae

Relationships within the major clades of Cactaceae are relatively well known based on DNA sequence data mostly from the chloroplast genome. Nevertheless, some nodes along the backbone of the phylogeny, and especially generic and species-level relationships, remain poorly resolved and are in need of more informative genetic markers. In this study, we propose a new approach to solve the relationships within Cactaceae, applying a targeted sequence capture pipeline. We designed a custom probe set for Cactaceae using MarkerMiner and complemented it with the Angiosperms353 probe set. We then tested both probe sets against 36 different transcriptomes using Hybpiper preferentially retaining phylogenetically informative loci and reconstructed the relationships using RAxML-NG and Astral. Finally, we tested each probe set through sequencing 96 accessions, representing 88 species across Cactaceae. Our preliminary analyses recovered a well-supported phylogeny across Cactaceae with a near identical topology among major clade relationships as that recovered with plastome data. As expected, however, we found incongruences in relationships when comparing our nuclear probe set results to plastome datasets, especially at the generic level. Our results reveal great potential for the combination of Cactaceae-specific and Angiosperm353 probe set application to improve phylogenetic resolution for Cactaceae and for other studies.