Phylogenetic Hypothesis Research Articles

Two new species of Thomasomys (Cricetidae: Sigmodontinae) from the western Andes of Ecuador and an updated phylogenetic hypothesis for the genus

Abstract The Andean cloud forests of Ecuador are home to numerous unique mammals. Rodents of the tribe Thomasomyini are particularly abundant in many Andean localities, with Thomasomys – the largest genus in the subfamily Sigmodontinae (51 species) – especially species-rich and diverse. Despite recent advances on the systematics of the genus, where seven species have been described in the last five years, there is tantalizing evidence that its true diversity remains completely understood. Over the course of approximately ten years of fieldwork in Ecuador, a significant number of Thomasomys specimens were collected from various localities in both, the eastern and western Andean ranges. Through an extensive genetic study of these specimens, augmented with what is available in public databases, we argue that there exist at least 20 undescribed species in the genus, with no less that twelve potential new species in Ecuador alone. In this paper, we describe two of these species belonging to the group cinereus, one recently collected and the other previously referred to as Thomasomys sp. 1; further, we present an updated cyt b gene tree of the genus. The gene tree includes at least 56 valid and putative species and supports the monophyly of the genus, while at the same time suggest a paraphyletic “aureus” group. Our findings suggest that the genus likely exhibits additional hidden diversity in significant portions of Colombia, Peru, and Bolivia which calls for the need for a comprehensive reassessment of the entire genus. The recognition of these two new species brings the total number of known Thomasomys to 53 species, 19 of which occur in Ecuador, including 17 that are endemic to this country.

Integrative systematics of Cheguevaria Kazantsev, 2007 (Coleoptera, Lampyridae, Cheguevariinae) identifies genetic stability in color-polymorphic individuals and a disjoint relationship with Amydetinae

Abstract The genus Cheguevaria (Kazantsev 2007) is currently comprised of three species which are endemic to the Greater Antilles: Cheguevaria angusta Kazantsev, 2007 (Hispaniola), Cheguevaria taino Kazantsev, 2007 and Cheguevaria montana Kazantsev, 2008 (both from Puerto Rico). Cheguevaria is the sole member of Cheguevariinae, and a previous morphology-based phylogenetic hypotheses suggested a close relationship with the subfamily Amydetinae. Recent collecting trips to Puerto Rico and the survey of other scientific collections allowed us to identify and locate more specimens of the genus, including several color morphs of specimens tentatively identified as C. montana. We used this material to revise the genus, and to describe Cheguevaria cubensisnew species, the first record of the genus from Cuba. We also produced DNA barcodes based on partial cytochrome c oxidase subunit 1 (COI), which were used to investigate the species limits within color morph species of C. montana. Our results showed a high level of genetic stability in those color morphs, indicating that all specimens belong to the same species. We present a discussion to explain possible scenarios leading to such variation in color patterns. We also generated amplicons for two specimens of Amydetinae, represented by two Amydetes Illiger, 1807 species, and we tested their relationship with Cheguevaria in a phylogenetic context based on a four gene dataset. Our analyzes indicated a disjoint relationship between Cheguevaria and Amydetes, corroborating previously published morphology-based phylogenies, and we maintained the status of Cheguevaria as an independent lineage within Lampyridae.

Phylogenetic analysis of the complete mitochondrial genome of the orange-winged sulphur butterfly Dercas nina Mell 1913 (Insecta: Lepidoptera: Pieridae: Coliadinae)

Dercas nina Mell 1913 (Pieridae) is a little-studied butterfly species endemic to China that flies primarily in the forest canopy. Genome skimming by Illumina sequencing allowed assembly of 146,702 reads for complete 1471.3-fold mean coverage of the circular 15,264 bp mitogenome from D. nina consisting of 82.1% AT nucleotides. A gene order typical of butterflies was recovered consisting of 13 protein-coding genes, 22 tRNAs, two rRNAs, and a predicted control region. The Dercas nina COX1 open reading frame begins with atypical start codon CGA. Six protein-coding genes (COX1, COX2, ND2, ND3, ND4, ND5) with single-nucleotide (T) stop codons, and two protein-coding genes (ATP6, ATP8) with two-nucleotide (TA) stop codons encoded in the DNA were inferred to be completed by adenine nucleotides from the Poly-A tail of the mRNA. Bayesian’s phylogenetic reconstruction places the D. nina and D. lycorias mitogenomes as sister clades. Dercas mitogenomes were sister to those from genus Colias in the monophyletic subfamily Coliadinae. The mitogenome phylogeny is consistent with previous molecular phylogenetic hypotheses based on other markers, but differs somewhat from a morphology-based hypothesis that suggested that Dercas was more closely related to genus Gonepteryx. This may falsify the hypothesis or may instead reflect mitochondrial-nuclear phylogenetic discordance.

Reconstructing host plant repertoire and timing of evolution of phyline plant bugs (Hemiptera, Miridae)

AbstractThe diversity of phytophagous insects is often attributed to the success of land plants in the framework of ecological speciation. Several hypotheses have been proposed to explain host plant driven insect diversification in a phylogenetic context and have mostly been explored using Lepidoptera. We posit that Miridae are a great system to examine these hypotheses because they are one of the largest primarily phytophagous insect families and include many species with narrow host repertoire. Focusing on the species‐rich Phylinae (>2700 spp.), we generate the most taxon‐rich phylogeny published to date and for the first time estimate divergence times and trace the evolution of host plant associations across the group. Focusing on two clades of oak‐associated phylines, we further examine if diversification in these insects and their hosts coincided or if the insects tracked their hosts. We find that Phylinae diverged from their orthotyline sister group before the end of the Cretaceous, tribal‐level taxa diversified throughout the Paleogene, and diversification within genera mostly occurred in the Neogene. Host plant repertoire reconstructions at the family level show transitions from stenophagy to polyphagy are more common than the reverse. We reconstructed the ancestral phyline host as ambiguous, followed by Asterales throughout most of the deep splits. Species‐level divergences in the two oak‐associated clades coincide with those in oaks, a pattern is that is consistent with the hypothesis that these plant bugs may have cospeciated with their hosts. Our study shows that Phylinae are a suitable system to further test hypotheses on ecological speciation of plants and insects but will require more robust phylogenetic hypotheses of the group.

Evidence for a Miocene pulse of diversification of the tropical American clade of the Brazil nut family (Lecythidaceae)

ABSTRACT The tropical American species of the Brazil nut family, Lecythidaceae, are abundant in the tree flora, with some economically important species. Yet, the phylogenetic relationships and pace of diversification within this family are understudied. Here, we used shotgun sequencing data for 86 of the 228 currently accepted species in the exclusively tropical American subfamily Lecythidoideae in a phylogenomic context. For each sampled species, we built the full plastid DNA sequence, and also extracted nuclear DNA for 571 regions using the new bioinformatics pipeline REFMAKER, which we used to produce a time-calibrated phylogenetic hypothesis. Our analysis shows that phylogenetic inference from plastid and nuclear DNA alignments resulted in different topologies. The nuclear DNA topology strongly suggests that genus Lecythis should be split into at least four genera. Samples of the genus Eschweilera formed a monophyletic group, with the exception of one sampled species (Eschweilera amazoniciformis S.A.Mori). The Bertholletia clade, which contains the majority of the Lecythidoideae species, and all Lecythis and Eschweilera species, started diversifying around 27.5 Ma, with an accelerated rate of diversification starting in the middle Miocene (c. 12 Ma). The clade sister to Bertholletia (including Corythophora, Eschweilera, and Corrugata, Chartacea and Poiteaui clades) includes at least 124 species and it has diversified less than 10 Ma. This time frame of diversification coincides with major changes in tropical American landscapes and climate associated with the Andean uplift.

Crocodylian diversity during the early Eocene climatic optimum in the Golden Valley Formation of North Dakota, U.S.A.

ABSTRACT Rich bone beds from the lower Eocene strata of the Golden Valley Formation of Stark County, North Dakota reveal a speciose sympatric crocodylian fauna. However, analyses demonstrate limited phylogenetic diversity among these co-occurring taxa, and of the four species known for the locality, three are alligatorids and one is a crocodyloid. Phylogenetic hypotheses recover Chrysochampsa mylnarskii as a late lived member of Brachychampsini—a stem-based clade including Brachychampsa montana and all alligatorids more closely related to it than to Caiman crocodilus or Alligator mississippiensis—and a new genus and species, Ahdeskatanka russlanddeutsche groups with species of Allognathosuchus. The crocodylians, partitioned by body size and plan, would have occupied an array of ecological niches and feeding strategies. Whereas the large-bodied alligatorid Chrysochampsa mylnarskii preserves a generalist morphology, Ahdeskatanka russlanddeutsche bears a short, broad snout and globular distal teeth. Contemporaneous with a peak in alligatoroid diversity during this interval, Ahdeskatanka russlanddeutsche is an exemplar of a radiation of small-bodied alligatorids with crushing dentition and preserves the ancestral alligatorid feeding strategy. Trophic dynamics of the locality diverge from modern environments and the abundant crocodylians may have filled the ecological niche of large mammalian carnivores conspicuously absent here. This alligatorid-rich crocodylian fauna evolved in swampy lowlands and meandering streams flanked by subtropical forests during one of the hottest sustained intervals in Earth history. The lush, highly productive ecosystems preserved in the Golden Valley Formation inform the evolutionary history of North American alligatorids and preserve significant biodiversity following the Paleocene–Eocene Thermal Maximum.

A step in the deep evolution of Alvinellidae (Annelida: Polychaeta): A phylogenomic comparative approach based on transcriptomes

The Alvinellidae are a family of worms that are endemic to deep-sea hydrothermal vents in the Pacific and Indian Oceans. These annelid worms, a sister group to the Ampharetidae, occupy a wide range of thermal habitats. The family includes the most thermotolerant marine animals described to date such as the Pompeii worm Alvinella pompejana, and other species living at much lower temperatures such as Paralvinella grasslei or Paralvinella pandorae. The phylogeny of this family has not been studied extensively. It is, however, a complex case where molecular phylogenies have given conflicting results, especially concerning the monophyletic or polyphyletic nature of the genus Paralvinella.We carried out a comprehensive study of the phylogeny of this family using the best molecular data currently available from RNAseq datasets, leading to several hundred orthologous transcripts for 11 of the 14 species currently described or in description. The results obtained by the two most popular phylogenetic inference models (using either gene concatenation with maximum likelihood, or a coalescent-based model from gene trees) were compared using a series of ampharetid and terebellid outgroups.Our study shows that the global phylogenetic signal favors the hypothesis of paraphyly for the Paralvinella genus, with P. pandorae being sister species of the other Alvinellidae.However, a high number of gene trees also supports the hypothesis of alternative trees in which the monophyly of the Paralvinella genus, as initially proposed by Desbruyères and Laubier, is valid with the species P. pandorae and Paralvinella unidentata being sister species. According to molecular dating, the radiation of the Alvinellidae was rapid and took place in a short period of time between 80 and 110 million years ago. This is reflected at the genomic scale by gene trees equally separated between different phylogenetic hypothesis, showing high rates of incomplete lineage sorting between the first lineages of the Alvinellidae and probable gene transfers. Although different genomic regions seem to have different phylogenetic stories in the early step of the alvinellid radiation, our study supports the view that the two P. pandorae species can be grouped into a separate genus (possibly Nautalvinella) and that the Miralvinella subgenus, defined by Desbruyères and Laubier, is not valid anymore.

Phylogenomic insights into the worldwide evolutionary relationships of the stingless bees (Apidae, Meliponini)

Stingless bees (tribe Meliponini) are remarkable for their characteristically large social colonies, their capacity to produce honey and other useful products, and their morphological and behavioral diversity. They have a disjunct pan-tropical distribution, primarily occurring in warm and humid environments in the Neotropical, Afrotropical, and Indo-Australasian regions. Even though phylogenetic hypotheses have been proposed for Meliponini based on morphology and molecular data, many questions are still unsolved regarding the evolutionary relationships and systematics of the tribe. In this contribution, we present a large phylogenomic dataset comprising over 2,500 ultra-conserved element (UCE) loci sequenced for 153 species of Meliponini, representing all known genera of stingless bees. The genera Camargoia, Paratrigonoides, Plectoplebeia, Cleptotrigona, Ebaiotrigona, Papuatrigona, Pariotrigona, Platytrigona, and Sahulotrigona were included in molecular phylogenetic analyses for the first time. Concatenated and species-tree analyses were performed using different partitioning strategies and summary methods. We performed gene-genealogy interrogation (GGI) on several recalcitrant nodes to resolve discordances among recovered tree topologies. Results were mostly consistent among analyses, recovering three main lineages of Meliponini congruent with the biogeographic domains to which they are associated. Within major clades, discordances were found in relation to previous works. The genus Frieseomelitta was recovered as paraphyletic in relation to Trichotrigona, and the genus Lepidotrigona was revealed to be composed of two independent lineages. Even though concatenated and weighted ASTRAL analyses were mostly effective in recovering the relationships favored by GGI, they retrieved different results in relation to the phylogenetic placements of Oxytrigona and Cephalotrigona. The most favored hypothesis in GGI analyses was not found in any other analyses, being more congruent with morphological evidence and highlighting the relevance of exploring the support given to alternative hypotheses through topological tests. Recent advances in our capacity to generate molecular sequences from old specimens using modern sequencing methods allowed for unparalleled sampling across genera, yielding a backbone for the phylogenetic relationships of stingless bees, which will further investigations into their systematics and evolution.

Plastome phylogenomics and new fossil evidence from Dominican amber shed light on the evolutionary history of the Neotropical fern genus Pecluma.

Molecular studies based on chloroplast markers have questioned the monophyly of the fern genus Pecluma (Polypodioideae, Polypodiaceae), which has several species of Polypodium nested within it. We explored the delimitation of Pecluma and its biogeographic pattern by evaluating the phylogenetic position of four Polypodium species not sequenced thus far and integrating the first fossil evidence of Pecluma. Using herbarium material, we applied a genome-skimming approach to obtain a phylogenetic hypothesis of Polypodioideae; assessed the combination of character states observed in the fossil from Miocene Dominican amber using a previously published phylogeny of Polypodioideae based on four plastid markers as framework; calculated divergence times; and conducted an ancestral area estimation. Within Polypodioideae, Pecluma was recovered as sister to Phlebodium. Three of the newly sequenced species-Polypodium otites, P. pinnatissimum, and P. ursipes-were recovered with maximum support within the Pecluma clade, whereas P. christensenii remained within Polypodium. The closest combination of character states of the fossil was found within Pecluma. Our biogeographic analyses suggest an Eocene origin of the genus in South America, with several subsequent Oligocene and Miocene colonization events to Mexico-Central America and to the West Indies. Although the circumscription of Pecluma is still challenging, our results elucidate the origin and age of the genus. The newly described fossil, Pecluma hispaniolae sp. nov., supports the hypothesis that the epiphytic communities of the Greater Antilles exhibit a constant generic composition since the Miocene. We propose new combinations (Pecluma otites, Pecluma pinnatissima, and Pecluma ursipes) to accommodate three species previously classified in Polypodium.

Phylogeny of the Neotropical Hypoctonine Whip-Scorpions (Thelyphonida, Thelyphonidae), with Descriptions of Two New Genera and Species.

Thelyphonida Blanchard, 1852, also known as vinegaroons or whip-scorpions, is a small arachnid order with 140 described species contained in a single family, Thelyphonidae Lucas, 1835. Despite being conspicuous and widely distributed across the tropics and subtropics on four continents, knowledge of the order has been slow to advance. Hypoctoninae Pocock, 1899, one of four subfamilies currently recognized and one of two represented in the New World, comprises five genera. Since its inception, Thelyphonellus Pocock, 1894 has remained the only hypoctonine genus occurring in South America, with only four species described prior to the present contribution. The first detailed morphological study and phylogenetic analysis of Thelyphonellus is presented herein. The morphological phylogenetic analysis-the first for Thelyphonida-includes all except one of the previously described species of Thelyphonellus in addition to two new species described herein; the species of Ravilops Víquez and Armas, 2005 (from the Caribbean island of Hispaniola); and the monotypic Old World genus Etienneus Heurtault, 1984 (from West Africa) scored for 45 morphological characters. A single, most parsimonious phylogenetic hypothesis revealed that Thelyphonellus is paraphyletic with respect to Ravilops. The New World Hypoctoninae comprises four clades with disjunct distributions and well supported by a combination of morphological characteristics, on the basis of which four genera, two of which are new, are recognized: Ravilops, with two species, endemic to Hispaniola; Thelyphonellus, herein restricted to Thelyphonellus amazonicus (Butler, 1872) and Thelyphonellus ruschii Weygoldt, 1979, occurring in Guyana, Suriname, French Guiana, and northern Brazil; Wounaan, gen. n., containing Wounaan vanegasae (Giupponi and Vasconcelos, 2008), comb. n. and Wounaan yarigui, sp. n. from Colombia; and Yekuana, gen. n., containing Yekuana venezolensis (Haupt, 2009), comb. n. and Yekuana wanadi, sp. n. from Venezuela. The two new species are described and illustrated. A key to the identification of the Neotropical genera of Hypoctoninae and a map plotting the known distribution of its species are also presented.

Skink systematics inside out: Comparative cranial osteology of the New World Mabuyinae.

The Mabuyinae subfamily exhibits remarkable diversity, encompassing 26 genera and 236 currently recognized species. Traditionally, the entire range of the group was attributed to the single genus Mabuya, which had a wide distribution along tropical regions of the Planet. In recent studies, phylogenetic hypotheses based on molecular data have identified four major groups, which have been further divided into geographically distinct clades. At least two phylogenetically distinct lineages of Mabuyinae are distributed in the Neotropical Region: Trachylepis atlantica and the remaining 16 genera within the Mabuyinae clade from the mainland and the Caribbean islands. Our understanding of Mabuyinae osteology is still quite limited, particularly concerning interspecific variation. This lack of information hinders our ability to make strong contributions to the phylogenetic relationships within this group or even to confirm the existence of certain new taxa considering their relatively conserved external morphology. This work provides a comprehensive anatomical reference for the adult skull of Neotropical Mabuyinae lizards, highlighting osteological features that might be useful for delimiting each genus. This descriptive guide includes illustrations and employs multiple techniques, such as dry preparation, clearing and staining, and high-resolution computerized microtomography. Our results provide additional diagnostic characteristics that include specific cranial bone arrangements, dental patterns, and cranial adaptations, such as dorsoventral head flattening, and their functional implications for bite force and cranial biomechanics. This study reinforces the importance of cranial morphology in understanding the phylogenetic relationships and evolutionary trajectories of New World Mabuyinae lizards, advocating for broader morphological sampling to enrich our understanding of these diverse reptiles.

Phylogenomics of the major lineages of Bembidion and related ground beetles (Coleoptera: Carabidae: Bembidiini)

Abstract Bembidion Latreille (Coleoptera: Carabidae) is a genus of small ground beetles containing about 1,380 species. To test previous phylogenetic hypotheses about deeper lineages of Bembidion and near relatives, we recover and examine over 1,800 nuclear protein-coding loci from 33 species representing the main lineages of Bembidion, 10 species of other bembidiine genera, and 7 outgroups. We find that Bembidion exclusive of subgenus Phyla Motschulsky is monophyletic, and we reclassify Phyla as a separate genus. Within Bembidion we find 2 dominant clades, the Bembidion superseries (containing about 490 species in the subgenera Eupetedromus Netolitzky and Lindrochthus Maddison, the Philochthus Stephens complex, and the Bembidion series), and the Ocydromus Clairville superseries (containing almost all other Bembidion representing about 840 species). The only known lineages within Bembidion outside of these superseries are subgenus Hoquedela Müller-Motzfeld and the Desarmatocillenus Netolitzky complex, which combined contain less than 30 species. Most clades are insensitive to variations in analyses and hold up under different sets of taxa and loci, analyses at the nucleotide or amino acid levels, and different analytical methods (maximum likelihood, including posterior mean site frequency analyses, Bayesian analyses, invariant-based methods, and those that consider incomplete lineage sorting). Despite the clarity achieved in most aspects of the phylogeny, there are several unresolved regions, notably the relationships of Desarmatocillenus, Hoquedela, and Phyla to other bembidiines. A divergence dating analysis suggests that crown Bembidion is about 48 million years old (95% confidence intervals 40–58 Ma), and that the 2 large superseries are about 38 million years old (95% confidence intervals about 29–47 Ma).

Historical biogeography and the evolution of habitat preference in the North American camel spider family, Eremobatidae (Arachnida:Solifugae)

Abiotic variables can influence species distributions, often restricting taxa to an acquired climatic signature or conversely, related species are conserved in the same ecological space over millions of years. An investigation into how abiotic change has shaped geographic distributions of taxa may be key to understanding diversification of lineages, and in the absence of reliable morphological characteristics, such information may support taxonomic units at multiple scales.Here, we examine the historical biogeography and patterns of habitat preference within the North American solifuge family, Eremobatidae. A previous study demonstrated that a major taxonomic revision of Eremobatidae is warranted, however recent studies demonstrate high levels of morphological convergence within the group, thus a re-classification of generic boundaries using additional information must be prioritized before we can formally begin solid revisionary efforts. In this study, we aimed to reconstruct a well-resolved phylogenetic hypothesis of Eremobatidae by filtering UCE loci based on informativeness, by mitigating the effect of cogenic UCE on phylogenetic estimation, and by supplementing our curated UCE loci with mitochondrial information. Using our preferred topology, in conjunction with published estimated divergence dates for Eremobatidae, we inferred a time-calibrated phylogenetic hypothesis to inform the historical biogeography and patterns of habitat preference. The two major habitat types that were observed for Eremobatidae were warm deserts for early diverging taxa and a subsequent evolution to cold deserts and Mediterranean California ecoregions for later diverging taxa. Eremobatid niche space, determined by temperature and precipitation, has been conserved for at least 25 million years in North America, supporting a warm desert origin, and thus supporting high species richness in the Sonoran and Mexican Plateau. Overall, our study provides support for new generic level designations within Eremobatidae.

Orthoptera-specific target enrichment (OR-TE) probes resolve relationships over broad phylogenetic scales

Phylogenomic data are revolutionizing the field of insect phylogenetics. One of the most tenable and cost-effective methods of generating phylogenomic data is target enrichment, which has resulted in novel phylogenetic hypotheses and revealed new insights into insect evolution. Orthoptera is the most diverse insect order within polyneoptera and includes many evolutionarily and ecologically interesting species. Still, the order as a whole has lagged behind other major insect orders in terms of transitioning to phylogenomics. In this study, we developed an Orthoptera-specific target enrichment (OR-TE) probe set from 80 transcriptomes across Orthoptera. The probe set targets 1828 loci from genes exhibiting a wide range of evolutionary rates. The utility of this new probe set was validated by generating phylogenomic data from 36 orthopteran species that had not previously been subjected to phylogenomic studies. The OR-TE probe set captured an average of 1037 loci across the tested taxa, resolving relationships across broad phylogenetic scales. Our detailed documentation of the probe design and bioinformatics process is intended to facilitate the widespread adoption of this tool.

Phylogeny of the Chinese species groups of the subgenus Homoneura Wulp, 1891 (Diptera, Lauxaniidae, Homoneurinae) based on morphological characters

The subgenus Homoneura Wulp, 1891 (Diptera, Lauxaniidae, Homoneurinae) is highly diverse with more than 220 species known from China, representing more than 80% of the Chinese genus Homoneura Wulp, 1891. These species were assigned into 21 species groups in studies mainly focusing on the classification and description of species. The phylogenetic relationships of each subgenus of Homoneura and the phylogenetic relationship of the species groups are still not well understood. We investigated the male morphology to provide the basis to further revise the species groups of this subgenus. In this survey, 230 species were examined and 117 morphological characters obtained, a phylogenetic analysis was conducted using the maximum parsimony analysis with TNT and WinClada. The analyses yielded 45 most parsimonious trees and one strict consensus tree. A phylogenetic hypothesis is proposed dividing the subgenus Homoneura into 12 species groups: H. (H.) nigrifacies, H. (H.) pallida, H. (H.) patella, H. (H.) beckeri, H. (H.) formosae, H. (H.) henanensis, H. (H.) nigra, H. (H.) notostigma, H. (H.) ornatifrons, and H. (H.) trispina, H. (H.) laticosta, and H. (H.) quinquenotata. This research provides valuable contributions towards a better understanding of the phylogenetic relationships within the subgenus Homoneura. However, the monophyly of the genus and subgenus was not supported.

Phylogenomics resolves the backbone of Poales and identifies signals of hybridization and polyploidy

Poales, as one of the largest orders of angiosperm, holds crucial economic and ecological importance. Nevertheless, achieving a consensus topology has been challenging in previous studies due to limited molecular data and sparse taxon sampling. The uneven distribution of species diversity among families and the factors leading to elevated species richness in certain lineages have also been subjects of ongoing discussion and investigation. In this study, we conducted a comprehensive sampling, including representatives from all 14 families and 85 taxa of Poales, along with five additional outgroups. To reconstruct the phylogeny of Poales, we employed a combination of coalescent and concatenation methods on three nuclear gene sets (1093, 491, 143) and one plastid gene set (53), which were inferenced from genomic data. We also conducted phylogenetic hypothesis analyses to evaluate two major conflicting nodes detected in phylogenetic analyses. As a result, we successfully resolved the backbone of Poales and provided a timeline for its evolutionary history. We recovered the sister relationship between Typhaceae and Bromeliaceae as the earliest diverging families within Poales. The clade consisting of Ecdeiocoleaceae and Joinvilleaceae was recovered as the sister group of Poaceae. Within the xyrid clade, Mayacaceae and Erioaculaceae + Xyridaceae successively diverged along the backbone of Poales. The topology of [Aristidoideae, ((Micrairoideae, Panicoideae), (Arundinoideae, (Chloridoideae, Danthonioideae)))] within the PACMAD clade has received strong support from multiple findings. We also delved into the underlying biological factors that contributed to the conflicting nodes observed in the phylogenetic analysis. Apart from the uncertainty regarding the sister group of Poaceae caused by cytonuclear discordance, frequent hybridization and polyploidy may have contributed to other conflicting nodes. We identified 26 putative whole-genome duplication (WGD) events within Poales. However, apart from the σ-WGD and the ρ-WGD, we did not observe any potential polyploid events that could be directly linked to the species diversification in specific lineages. Furthermore, there was a significant increase in the net diversification rate of Poales following the K-Pg boundary.

The monophyly of Magelona F. Müller, 1858 (Polychaeta, Magelonidae): Comments on Meißner et al.’s (2023) reinstatement of Octomagelona Aguirrezabalaga, Ceberio & Fiege, 2001

The first published phylogenetic hypotheses involving members of the polychaete taxon Magelonidae Cunningham & Ramage, 1888, were reported by Mortimer et al. (2021), wherein results showed that for the two genera in the family, Magelona F. Müller, 1858, was paraphyletic relative to Octomagelona Aguirrezabalaga, Ceberio & Fiege, 2001. The only option to formally name at least some of the resultant phylogenetic hypotheses was to place Octomagelona into synonymy with Magelona, leaving the definition of Magelonidae redundant with that of a monophyletic Magelona. Meißner et al. (2023) subsequently described specimens as members of new species, Octomagelona borowskii Fiege, Knebelsberger & Meißner, 2023, and O. sp. cf. O. borowskii, with the view that Octomagelona should be maintained as distinct from Magelona. We present reasons why reestablishing the paraphyly of Magelona is scientifically unwarranted.

The genus Cortinarius should not (yet) be split

The genus Cortinarius (Agaricales, Basidiomycota) is one of the most species-rich fungal genera, with thousands of species reported. Cortinarius species are important ectomycorrhizal fungi and form associations with many vascular plants globally. Until recently Cortinarius was the single genus of the family Cortinariaceae, despite several attempts to provide a workable, lower-rank hierarchical structure based on subgenera and sections. The first phylogenomic study for this group elevated the old genus Cortinarius to family level and the family was split into ten genera, of which seven were described as new. Here, by careful re-examination of the recently published phylogenomic dataset, we detected extensive gene-tree/species-tree conflicts using both concatenation and multispecies coalescent approaches. Our analyses demonstrate that the Cortinarius phylogeny remains unresolved and the resulting phylogenomic hypotheses suffer from very short and unsupported branches in the backbone. We can confirm monophyly of only four out of ten suggested new genera, leaving uncertain the relationships between each other and the general branching order. Thorough exploration of the tree space demonstrated that the topology on which Cortinarius revised classification relies on does not represent the best phylogenetic hypothesis and should not be used as constrained topology to include additional species. For this reason, we argue that based on available evidence the genus Cortinarius should not (yet) be split. Moreover, considering that phylogenetic uncertainty translates to taxonomic uncertainty, we advise for careful evaluation of phylogenomic datasets before proposing radical taxonomic and nomenclatural changes.

Fossils indicate marine dispersal in osteoglossid fishes, a classic example of continental vicariance.

The separation of closely related terrestrial or freshwater species by vast marine barriers represents a biogeographical riddle. Such cases can provide evidence for vicariance, a process whereby ancient geological events like continental rifting divided ancestral geographical ranges. With an evolutionary history extending tens of millions of years, freshwater ecology, and distribution encompassing widely separated southern landmasses, osteoglossid bonytongue fishes are a textbook case of vicariance attributed to Mesozoic fragmentation of the Gondwanan supercontinent. Largely overlooked fossils complicate the clean narrative invoked for extant species by recording occurrences on additional continents and in marine settings. Here, we present a new total-evidence phylogenetic hypothesis for bonytongue fishes combined with quantitative models of range evolution and show that the last common ancestor of extant osteoglossids was likely marine, and that the group colonized freshwater settings at least four times when both extant and extinct lineages are considered. The correspondence between extant osteoglossid relationships and patterns of continental fragmentation therefore represents a striking example of biogeographical pseudocongruence. Contrary to arguments against vicariance hypotheses that rely only on temporal or phylogenetic evidence, these results provide direct palaeontological support for enhanced dispersal ability early in the history of a group with widely separated distributions in the modern day.

Phylogenomics of Phengodidae (Coleoptera: Elateroidea): towards a natural classification of a bioluminescent and paedomorphic beetle lineage, with recognition of a new subfamily

Abstract Phengodidae (Coleoptera: Elateroidea), commonly known as glowworm beetles, are a small family of bioluminescent and paedomorphic beetles. There are few phylogenetic studies of Phengodidae, and these are mostly discordant, especially when comparing morphology-based and molecular-based phylogenetic hypotheses. Here, we used the anchored hybrid enrichment approach to undertake the first phylogenomic analysis of Phengodidae (≤358 loci and 39 taxa) and evaluate the higher-level classification of the group. In agreement with previous molecular studies, we recovered Phengodidae as sister to Rhagophthalmidae, and the Old World Cydistinae as sister to all New World Phengodidae. In contrast to previous hypotheses, both Phengodinae and Mastinocerinae were each recovered as monophyletic. Cenophengus was found to be sister to Mastinocerinae, in contrast to some previous hypotheses that placed it as sister to all New World Phengodidae. Considering its morphological divergence, we here establish Cenophenginae subfam. nov. Despite the largest and most comprehensive sampling of Phengodidae in any molecular-based study to date, we had only limited success in revealing the relationships among genera within the most species-rich subfamily, Mastinocerinae. Further studies should focus on the phylogeny and classification of this taxonomically neglected subfamily, on the phylogenetic placement of enigmatic Penicillophorinae, and on seeking morphological support for the main clades of Phengodidae.