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Figure 2 in A phylogenomic look into the systematics of oceanic squids (order Oegopsida)

Figure 2. Schematic representation of the contigs usually retrieved from NOVOPLASTY v.3.8.3 (A–D) and the two possible combinations of the same size including all the genes present on oegopsid mitogenomes (E, F). The plus (+) strand is represented in the direction 5′ → 3′. A, contig usually of ~6.3 kb including nad3, rrnS and transfer RNAs associated with both genes. B, contig usually of ~7.1 kb including nad2, rrnS and transfer RNAs associated with both genes. C, contig usually of ~13.1 kb including nad3, rrnL and transfer RNAs associated with both genes. D, contig usually of ~13.8 kb including nad2, rrnL and transfer RNAs associated with both genes. E, complete mitogenome after manually merging the contigs depicted in A, D. F, complete mitogenome after manually merging the contigs depicted in B, C. The non-coding regions are indicated in black; genes from the minus (−) strand of the mitogenome are coloured in light grey. Squares are not proportional to the size of the genes. See the Material and Methods section for gene abbreviations.

Figure 4. A, B in A phylogenomic look into the systematics of oceanic squids (order Oegopsida)

Figure 3 in A phylogenomic look into the systematics of oceanic squids (order Oegopsida)

Figure 3. Maximum likelihood phylogenetic tree of oceanic squids constructed with IQTREE v.2. Values on nodes represent bootstrap percentages from the maximum likelihood analysis and posterior probabilities from the Bayesian inference analysis, respectively. A, Ommastrephes caroli (Furtado, 1887) (Ommastrephidae). B, Thysanoteuthis rhombus (Thysanoteuthidae), modified from Fernández-Álvarez et al. (2021). C, Leachia sp. (Cranchiidae). Photograph by Steven Kovacs. D, Abraliopsis sp. B (Enoploteuthidae), from Young & Tsuchiya (2014). E, Chiroteuthis sp. (Chiroteuthidae), modified from Vecchione (2019). F, Pholidoteuthis massyae (Pholidoteuthidae). Photograph by Mark C. Benfield (Louisiana State University). G, Octopoteuthis sicula (Octopoteuthidae). H, Lepidoteuthis grimaldii (Lepidoteuthidae). Photograph by Alejandro Escánez (University of La Laguna). I, Brachioteuthis sp. (Brachioteuthidae). Photograph by David Shale. J, Cycloteuthis sirventi (Cycloteuthidae). K, Discoteuthis laciniosa (Cycloteuthidae). L, Neoteuthis theilei (Neoteuthidae), modified from Vecchione & Young (2019c). M, Architeuthis dux (Architeuthidae). Photograph by T. Kubodera, curator emeritus of National Museum of Nature and Science (Tokyo).

Figure 1 in A phylogenomic look into the systematics of oceanic squids (order Oegopsida)

Figure 1. Schematic representation of the mitogenome of oegopsid squids based on the Watasenia scintillans (Berry, 1911) mitogenome described by Yokobori et al. (2004). The plus (+) strand is represented in the direction 5′ → 3′. The duplicated gene blocks associated with NADH dehydrogenase subunit 3 (nad3) are coloured in green; the duplicated gene blocks associated with NADH dehydrogenase subunit 2 (nad2) are coloured in blue; the non-coding regions are indicated in black; and genes from the minus (−) strand of the mitogenome are coloured in light grey. Squares are not proportional to the size of the genes. See the Material and Methods section for gene abbreviations.

Figure 4. A, B in A phylogenomic look into the systematics of oceanic squids (order Oegopsida)

Figure 4. A, B, maximum parsimony (A) and maximum likelihood (B) ancient state reconstruction of the mitogenome gene order of oceanic squids implemented in MESQUITE v.3.61. C, hypothetical mitochondrion including the plesiomorphic positions for trnM and trnI. D, hypothetical mitochondrial gene order of Lampadioteuthis megaleia. E, hypothetical mitochondrial gene order of Histioteuthidae. F, hypothetical mitochondrial gene order of Cranchiidae, Ommastrephidae and Thysanoteuthidae. G, hypothetical mitochondrial gene order of Neoteuthidae. H, mitochondrial gene order of Lepidoteuthidae and Octopoteuthidae. I, mitochondrial gene order of Joubiniteuthidae. J, mitochondrial gene order of Architeuthidae based on Winkelmann et al. (2013) and the GenBank sequence FJ429092 (Elliger CA, Lebaric ZN, Gilly WF & Robison BH, unpublished). In all mitogenomes, the plus (+) strand is represented in the direction 5′ → 3′. Arrowheads indicate the points where one or more genes were lost; arrows signal the position of gene transposition (highlighted) and the position of that gene in the plesiomorphic gene order; diamonds signal the position of non-functional copies of genes. The non-coding regions are indicated in black; genes from the minus (−) strand of the mitogenome are coloured in light grey. Squares are not proportional to the size of the genes. See the Material and Methods section for gene abbreviations. Where multiple duplicate genes prevented NOVOPLASTY from returning a single circular contig, we curated the contigs obtained to match the gene order in Figure 2E (see the Material and Methods section). Almost all published oegopsid genomes follow the order depicted in Figure 2E, whereas those reported for Architeuthis dux (Winkelmann et al., 2013) and the bathyteuthid Bathyteuthis abyssicola Hoyle, 1885 (Kawashima et al., 2013) follow Figure 2F, and our assumption regarding the arrangement of blocks (but not the order of genes within them) could be wrong for some species.

opencc-zeroApr 2022View details →

Data from: Phylogenomics and historical biogeography of West Indian Rock Iguanas (genus Cyclura)

The genus Cyclura includes nine extant species and six subspecies of West Indian Rock Iguanas and is one of the most imperiled genera of squamate reptiles globally. An understanding of species diversity, evolutionary relationships, diversification, and historical biogeography in this group is crucial for implementing sound long-term conservation strategies. We collected DNA samples from 1–10 individuals per taxon from all Cyclura taxa (n = 70 ingroup individuals), focusing where possible on incorporating individuals from different populations of each species. We also collected 1–2 individuals from each of seven outgroup species of iguanas (Iguana delicatissima; five Ctenosaura species) and Anolis sagrei (n = 12 outgroup individuals). We used targeted genomic sequence capture to isolate and to sequence 1,872 loci comprising of 687,308 base pairs (bp) from each of the 82 individuals from across the nuclear genome. We extracted mitochondrial reads and assembled and annotated mitogenomes for all Cyclura taxa plus outgroup species. We present well-supported phylogenomic gene tree/species tree analyses for all extant species of Cyclura using ASTRAL-III, SVDQuartets, and starBEAST methods, and discuss the taxonomic, biogeographic, and conservation implications of these data. We find a most recent common ancestor of the genus 9.91 million years ago. The earliest divergence within Cyclura separates C. pinguis from a clade comprising all Cyclura except C. pinguis. Within the latter group, a clade comprising C. carinata from the southern Lucayan Islands and C. ricordii from Hispaniola is the sister taxon to a clade comprising the other Cyclura. Among the other Cyclura, the species C. cornuta and C. stejnegeri (from Hispaniola and Isla Mona) form the sister taxon to a clade of species from Jamaica (C. collei), Cuba and Cayman Islands (C. nubila), and the eastern (C. rileyi) and western (C. cychlura) Lucayan Islands. Cyclura cychlura and C. rileyi form a clade whose sister taxon is C. nubila. Cyclura collei is the sister taxon to these three species combined.

opencc-zeroJun 2022View details →

Data from: Whole genome sequencing and phylogenomic analysis show support for the splitting of genus Pythium

The genus Pythium (nom. cons.) sensu lato (s.l.) is composed of many important species of plant pathogens. Early molecular phylogenetic studies suggested paraphyly of Pythium, which led to a formal proposal by Uzuhashi and colleagues in 2010 to split the genus into Pythium sensu stricto (s.s.), Elongisporangium, Globisporangium, Ovatisporangium (= Phytopythium), and Pilasporangium using morphological characters and phylogenies of the mt cytochrome c oxidase subunit 2 (cox2) and D1–D2 domains of nuc 28S rDNA. Although the split was fairly justified by the delineating morphological characters, there were weaknesses in the molecular analyses, which created reluctance in the scientific community to adopt these new genera for the description of new species. In this study, this issue was addressed using phylogenomics. Whole genomes of 109 strains of Pythium and close relatives were sequenced, assembled, and annotated. These data were combined with 10 genomes sequenced in previous studies. Phylogenomic analyses were performed with 148 single-copy genes represented in at least 90% of the taxa in the data set. The results showed support for the division of Pythium s.l. The status of alternative generic names that have been used for species of Pythium in the past (e.g., Artotrogus, Cystosiphon, Eupythium, Nematosporangium, Rheosporangium, Sphaerosporangium) was investigated. Based on our molecular analyses and review of the Pythium generic concepts, we urge the scientific community to adopt the generic names Pythium, Elongisporangium, Globisporangium, and their concepts as proposed by Uzuhashi and colleagues in 2010 in their work going forward. In order to consolidate the taxonomy of these genera, some of the recently described Pythium spp. are transferred to Elongisporangium and Globisporangium.

opencc-zeroOct 2019View details →

Data from: Phylogenomic resolution of the cetacean tree of life using target sequence capture

The evolution of the cetaceans, from their early transition to an aquatic lifestyle to their subsequent diversification, has been the subject of numerous studies. However, while the higher-level relationships among cetacean families have been largely settled, several aspects of the systematics within these groups remain unresolved. Problematic clades include the oceanic dolphins (37 spp.), which have experienced a recent rapid radiation, and the beaked whales (22 spp.), which have not been investigated in detail using nuclear loci. The combined application of high-throughput sequencing with techniques that target specific genomic sequences provide a powerful means of rapidly generating large volumes of orthologous sequence data for use in phylogenomic studies. To elucidate the phylogenetic relationships within the Cetacea, we combined sequence capture with Illumina sequencing to generate data for ~3200 protein-coding genes for 68 cetacean species and their close relatives including the pygmy hippopotamus. By combining data from >38,000 exons with existing sequences from 11 cetaceans and seven outgroup taxa, we produced the first comprehensive comparative genomic dataset for cetaceans, spanning 6,527,596 aligned base pairs and 89 taxa. Phylogenetic trees reconstructed with maximum likelihood and Bayesian inference of concatenated loci, as well as with coalescence analyses of individual gene trees, produced mostly concordant and well-supported trees. Our results completely resolve the relationships among beaked whales as well as the contentious relationships among ocean dolphins, especially the problematic subfamily Delphininae, which includes the common and bottlenose dolphins. We performed Bayesian estimation of species divergence times using MCMCtree, integrating recently described fossils as calibration points (e.g., Mystacodon selenensis) that have not been used before. Integration of new fossil dates in the context of autocorrelated rates indicate that the diversification of Crown Cetacea began before the Late Eocene and the divergence of Crown Delphinidae as early as the Middle Miocene.

Phylogenomics resolves timing and patterns in the evolution of Australasian Cerambycinae (Coleoptera: Cerambycidae), and reveals new insights into the subfamily-level classification and historical biogeography of longhorn beetles

Cerambycinae is the second-largest subfamily of longhorn beetles in the Southern Hemisphere. The phylogeny of Cerambycinae is poorly known, resulting in a highly artificial tribal-level classification and a largely speculative evolutionary history. We reconstructed the phylogenetic relationships of Cerambycinae at the generic level using anchored hybrid enrichment data from hundreds of nuclear genes, with a primary focus on the extraordinarily diverse faunas of Australia and New Zealand. We also estimated divergence times by incorporating fossil calibrations in our analyses. We identified two main clades within Cerambycinae, which can also be separated morphologically by a distinct type of antennal foramen. We recovered a Late Jurassic origin of crown Cerambycinae. Dorcasominae, which was newly found to have representatives in Australia, was notably derived from within Cerambycinae. We recovered two independent origins of Australian Cerambycinae: one clade originated in the Early Cretaceous and is likely endemic to the Southern Hemisphere, while the other clade appears to have immigrated to Australia, perhaps from the Northern Hemisphere. Within the Australian lineages were multiple independent origins of New Zealand taxa, all of which are relative host-plant generalists. Tribal relationships and assignments are discussed and, based on our results, the following major nomenclatural acts were made: Dorcasominae Lacordaire, 1868, is downgraded to a tribe Dorcasomini of Cerambycinae Latreille, 1804; Neostenini Lacordaire, 1868 syn. nov. is treated as a junior synonym of Uracanthini Blanchard, 1851.

Data from: Phylogenomics and generic limits of Dypsidinae (Arecaceae), the largest palm radiation in Madagascar

With 178 species, the palm subtribe Dypsidinae is one of the largest plant radiations on Madagascar. A well-resolved species-level phylogeny is required not only to unpick the drivers of this spectacular radiation but also to define natural and useful generic limits in this taxonomically difficult group. The only recent taxonomic revision of Dypsidinae recognized just four genera, including the large genus Dypsis (currently with 172 species), which was considered impossible to divide further based on morphology alone. Here we describe the first comprehensively sampled species-level phylogeny of Dypsidinae, including 157 described species (88% of the subtribe) as well as 10 samples of uncertain taxonomic identity (potential new species). Our tree is based on target sequence capture data for 161 nuclear DNA loci. The phylogenetic relationships recovered render Dypsis s.l. paraphyletic, requiring the resurrection of two previously synonymised genera. In total, we recognize six genera in Dypsidinae (Dypsis Noronha ex Mart., Chrysalidocarpus H.Wendl., Marojejya Humbert, Vonitra Becc., Lemurophoenix J.Dransf., and Masoala Jum.), all of which are monophyletic and consistent with morphology.

Phylogenomics and biogeography of Castanea (chestnut) and Hamamelis (witch-hazel): Choosing between RAD-seq and Hyb-Seq approaches

Target enrichment and RAD-seq are well-established high throughput sequencing technologies that have been increasingly used for phylogenomic studies. Each method has its own pros and cons. The choice between them is a practical issue for plant systematists studying the evolutionary histories of biodiversity of relatively recent origins. However, few studies have compared the congruence and conflict between results from the two methods within the same group of organisms in plants. In this study, we employed RAD-seq and Hyb-Seq of Angiosperm 353 genes in phylogenomic and biogeographic studies of Hamamelis (the witch-hazels) and Castanea (chestnuts), two classic examples exhibiting the well-known eastern Asian (EA)-eastern North American (ENA) disjunct distribution, and compared them side by side. Our results showed congruences in phylogenetic inference and divergence time dating between the two data sets obtained through our customized procedures of library preparation and sequence trimming, although they differed in the number of loci and informative sites, the amount of missing data, and sampling within species. We suggest the selection of the two methods based on fund availability and sampling scale. Our phylogenetic analyses of RAD-seq and Hyb-Seq data resulted in well-resolved species relationships, and ancient introgressions were revealed in both genera by D-statistic test and PhyloNet. Biogeographic analyses including fossil data using total evidence-based dated tree and DEC model, applying specific inter-area dispersal probabilities, revealed a complicated history for each genus, indicating multiple intercontinental dispersals and local extinctions in areas outside of the taxa's modern ranges in both the Paleogene and Neogene. The study demonstrates the importance of including fossil taxa for a more accurate reconstruction of biogeographic histories of taxa to understand the EA and ENA floristic disjunction. Our results support an "out of western North America" migration of Castanea but an "out of Asia" migration of Hamamelis during their initial diversification, and the origins of the EA-ENA disjunction in both genera were results of vicariance.

Exon-based phylogenomics and the relationships of African cichlids: Tackling the challenges of reconstructing phylogenies with repeated rapid radiations

African cichlids (subfamily: Pseudocrenilabrinae) are among the most diverse vertebrates, and their propensity for repeated rapid radiation has made them a celebrated model system in evolutionary research. Nonetheless, despite numerous studies, phylogenetic uncertainty persists, and riverine lineages remain comparatively underrepresented in higher-level phylogenetic studies. Heterogeneous gene histories resulting from incomplete lineage sorting (ILS) and hybridization are likely sources of uncertainty, especially during episodes of rapid speciation. We investigate relationships of Pseudocrenilabrinae and its close relatives while accounting for multiple sources of genetic discordance using species tree and hybrid network analyses with hundreds of single-copy exons. We improve sequence recovery for distant relatives, thereby extending the taxonomic reach of our probes, with a hybrid reference guided/de novo assembly approach. Our analyses provide robust hypotheses for most higher-level relationships and reveal widespread gene heterogeneity, including in riverine taxa. ILS and past hybridization are identified as sources of genetic discordance in different lineages. Sampling of various Blenniiformes (formerly Ovalentaria) adds strong phylogenomic support for convict blennies (Pholidichthyidae) as sister to Cichlidae, and points to other potentially useful protein-coding markers across the order. A reliable phylogeny with representatives from diverse environments will support ongoing taxonomic and comparative evolutionary research in the cichlid model system.

opencc-zeroOct 2022View details →

Phylogenomics reveals deep relationships and diversification within phylactolaemate bryozoans

Bryozoans are mostly sessile colonial invertebrates that inhabit all kinds of aquatic ecosystems. Extant bryozoan species fall into two clades with one of them, Phylactolaemata, being the only exclusively freshwater clade. Phylogenetic relationships within the class Phylactolaemata have long been controversial owing to their limited distinguishable characteristics that reflect evolutionary relationships. Here, we present the first phylogenomic analysis of Phylactolaemata using transcriptomic data combined with dense taxon sampling of six families to better resolve the interrelationships and to estimate divergence time. Using maximum likelihood and Bayesian inference approaches, we recovered a robust phylogeny for Phylactolaemata in which the interfamilial relationships are fully resolved. We show Stephanellidae is the sister taxon of all other phylactolaemates and confirm that Lophopodidae represents the second offshoot within the phylactolaemate tree. Plumatella fruticosa clearly falls outside Plumatellidae as previous investigations have suggested, and instead clusters with Pectinatellidae and Cristatellidae as the sister taxon of Fredericellidae. Our results demonstrate that cryptic speciation is very likely in F. sultana and in two species of Plumatella (P. repens and P. casmiana). Divergence time estimates show that Phylactolaemata appeared at the end of the Ediacaran and started to diverge in the Silurian, although confidence intervals were large for most nodes. The radiation of most extant phylactolaemate families occurred mainly in the Paleogene and Neogene highlighting post-extinction diversification.

opennotspecifiedNov 2019View details →

Fig. 3 in Deep Instability in the Phylogenetic Backbone of Heteroptera is Only Partly Overcome by Transcriptome-Based Phylogenomics

Fig. 3. Metrics resulting from quartet sampling of the amino acid alignment over the phylogeny resulting from maximum likelihood analyses of amino acids. Clade support is depicted as: QC/QD/QI.

opennotspecifiedNov 2019View details →

Fig. 1 in Deep Instability in the Phylogenetic Backbone of Heteroptera is Only Partly Overcome by Transcriptome-Based Phylogenomics

Fig. 1. Phylogeny of Heteroptera resulting from partitioned analysis of concatenated nucleotides. Clade support is based on bootstrap replicates and the scale bar is average substitutions per site.

opennotspecifiedApr 2021View details →

Fig. 2 in Museomics: Phylogenomics of the Moth Family Epicopeiidae (Lepidoptera) Using Target Enrichment

Fig. 2. Number of raw loci recovered for each sample per year of collection. The dashed line is for reference and represents the trend. Plot made on R.

opennotspecifiedSep 2019View details →

Fig. 3 in Understanding UCEs: A Comprehensive Primer on Using Ultraconserved Elements for Arthropod Phylogenomics

Fig. 3. Breakdown of the phylogenetic programs used by arthropod UCE-based publications (as of July 2019).

opennotspecifiedSep 2019View details →

Fig. 1 in Understanding UCEs: A Comprehensive Primer on Using Ultraconserved Elements for Arthropod Phylogenomics

Fig. 1. Breakdown of the number of arthropod UCEs-based publications per year (as of July 2019) by taxonomic group and taxonomic hierarchy.

opennotspecifiedApr 2021View details →

Fig. 1 in Museomics: Phylogenomics of the Moth Family Epicopeiidae (Lepidoptera) Using Target Enrichment

Fig. 1. Simplified representation of Epicopeiidae phylogenetic relationships according to Minet (2002) (left) and Wei and Yen (2017) (right). Each genus has a specific color. Minet's alternative hypothesis about the position of Amana is represented by gray lines.