Phylogenetic conflict-particularly hidden gene-tree discordance generated by incomplete lineage sorting (ILS)-is pervasive in multilocus and phylogenomic datasets, yet its consequences for nucleotide substitution model selection remain poorly understood. Modern molecular studies increasingly collect and concatenate large sets of independent loci sampled across distant and often poorly characterized regions of the genome, creating significant potential for heterogeneity when analyzed in combination. Here, we examine whether intra-alignment genealogical conflict can influence standard model selection procedures to favor parameter-rich substitution models even when sequences evolve under a simple substitution process. Through a series of in silico case studies, we simulated sequence evolution under the simplest rate-homogeneous Jukes-Cantor (JC69) model and generated concatenated alignments as mosaics of multiple loci, each evolving on its own gene tree drawn under the multispecies coalescent. Conflict was increased by manipulating conditions expected to elevate ILS and gene-tree heterogeneity and embedding progressively more hidden genealogies within alignments while holding total alignment length constant. Despite all data being generated under JC69, model selection frequently favored more complex models, with varying sensitivity depending on the number of taxa, the expected amount of conflict, and the specific selection criterion applied. A dominant pattern was frequent inclusion of among-site rate variation parameters (+ G4 and/or + I), and under extreme conflict, model selection increasingly favored richer substitution models (e.g., SYM, GTR). Broadly, our results showed that hidden conflict can manifest as substitutional and rate heterogeneity, driving selection procedures to compensate with additional parameters in concatenated analyses under high conflict. Broadly, our study contributes to a greater understanding and appreciation of the challenges in modeling molecular evolution in the era of multilocus phylogenetics.

Hemiplasy helps explain high rates of apparent morphological convergence in neoavian birds.

Australia has the world's most species-rich scincid lizard fauna (family Scincidae) with over 500 recognised species across three highly diverse radiations. One of these radiations is Tribe Sphenomorphini which comprises Australia's most species-rich endemic vertebrate radiation, with ∼280 recognised species plus considerable undescribed diversity. The varied ecomorphology and high species richness of Australian Sphenomorphini has been a focus of biogeographic and macroevolutionary analyses, however some relationships remain unresolved. Here, we combine a new phylogenomic dataset with weighted summary-coalescent tree inference and data filtering methods to produce a robust phylogeny spanning all Australian sphenomorphine genera and most recognised species-level taxa. Our results align with prior studies showing an early-burst signature of rapid speciation in the Miocene. Our phylogeny exhibits a deep split between lineages concentrated in arid (∼220 species, 3 genera) versus more mesic and temperate lineages (∼76 species, 18 genera) some 27.8-25.4Ma, implying early divergence and widespread niche conservatism within these relatively arid- versus mesic-biome associated lineages. Analyses also support most established genera and supra-generic clades but find some conflicting relationships that challenge monophyly and current systematics within the genera Concinnia and Saiphos and allied taxa. We provide generic reassignments to address these issues. Species delimitation analyses support previous work indicating Australian species diversity remains moderately underestimated by current taxonomy.

Schizaeaceae is a fern family with fossil records dating to the Early Cretaceous and currently comprise approximately 40 species. Although recent phylogenomic studies have revalidated Microschizaea to resolve paraphyly issues within the family, the genus Schizaea remains non-monophyletic due to the isolated phylogenetic position of the S. pusilla clade. To restore its monophyly, we describe a new genus, Neoschizaea. Our taxonomic conclusions are supported by an integrative approach combining phylogenomic, palynological, and morphological datasets. Neoschizaea is distinguished from all other genera by the combination of its linear, dimorphic fronds, large monolete spores (up to 105 µm) with coarsely reticulate and strongly perforate ornamentation, and a superficial, filamentous, and chlorophyllous gametophyte. We provide the new combination Neoschizaea pusilla, a formal description, and an updated identification key for the genera of Schizaeaceae.

Phytophagous insects have specialized on virtually every plant lineage. Parasitic plants, however, are uncommon hosts. Among insects, only a single lineage of weevils, the Smicronychini, has successfully radiated on both parasitic and non-parasitic plants in a large panel of distantly related Asterid families. This unusual pattern suggests that major host plant shifts have occurred over the course of their diversification. Through the analysis of a phylogenomic dataset, we reconstruct for the first time their evolutionary history and ancestral host-plant repertoire. Our results show that independent host plant shifts occurred both from parasitic to non-parasitic hosts and between distinct parasitic lineages. These results suggest that host shift mechanisms can be driven by ecological opportunities provided by plant-plant interactions. This first evidence of extreme insect host plant shifts, apparently mediated by parasitic plant-plant interactions, emphasizes the core importance of ecological interactions as driving forces behind insect host plant shifts.

Anthurium (Araceae) is one of the most species-rich Neotropical genera, yet its infrageneric classification remains unresolved. This study tests the monophyly of the morphologically defined Anthurium sect. Pachyneurium diagnosed by rosulate habit, involute prefoliation, and absence of a collective vein with a focus on Brazilian species. Using target capture sequencing (Angiosperms353 probe set), we generated a phylogenomic dataset for 35 Anthurium species (18 from sect. Pachyneurium) and conducted maximum likelihood and coalescent-based analyses. Our results demonstrate that sect. Pachyneurium is not monophyletic as traditionally circumscribed. Brazilian species previously assigned to the section are recovered in three geographically structured and strongly supported lineages: Amazonian, Atlantic Forest, and Caatinga/Cerrado. The Atlantic Forest lineage is unexpectedly resolved as sister to A. coriaceum (sect. Urospadix), revealing an evolutionary relationship not predicted by morphology. Divergence-time estimates place the origin of crown Anthurium in the Paleocene (~62 Ma), with diversification of the Brazilian lineages occurring during the Miocene (20-3 Ma), coinciding with major geoclimatic events in South America. Our findings indicate that key diagnostic morphological characters are homoplastic and provide a phylogenomic framework for revising the infrageneric classification of Anthurium. By identifying evolutionarily distinct lineages, this study also contributes to prioritizing conservation efforts in threatened Neotropical biomes.

Phylogenomics of Amazonian squirrel monkeys (Saimiri: Primates, Cebidae).

Phylogenomic datasets comprising hundreds of genes have become the standard for plant systematics and phylogenetics. However, large-scale phylogenomic studies often exclude polyploids and hybrids due to the challenges in assessing the origin of duplicated loci and incorporating them into tree reconstruction methods. Using a newly generated target enrichment dataset of 1081 genes from 452 samples from the Brassicaceae tribe Arabideae, including many hybrid and high ploidy taxa, we developed a novel approach to disentangle the evolutionary history of this phylogenetically and taxonomically challenging clade. Our approach extends beyond commonly used gene tree-species tree reconciliation techniques by using phylogenetic placement, a method adopted from metagenomics, of gene copies into a diploid tree. We show how it allows for the simultaneous assessment of the origins of ancient and recent hybrids and autopolyploids, and the detection of nested polyploidization events. Additionally, we demonstrate how synonymous substitution rates provide further evidence for the mode of polyploidization, specifically to distinguish between allo- and autopolyploidization, and to identify hybridization events involving a ghost lineage. Our approach can serve as an exploratory tool for large and complex phylogenomic datasets and can aid in identifying polyploid and hybrid clades for further analysis with specialized methods.

Rapid species radiations make hybridization among species more likely. Detecting and reconstructing hybridization is therefore critical for understanding species relationships in many cases. We explored the relative performance of two phylogenetic network methods, SNaQ, a gene tree-based method, and PhyNEST, a site pattern-based method, in evaluating the plausibility of proposed past hybridization hypotheses. As our study system, we used the New Zealand cicada genera Kikihia and Maoricicada. Previous phylogenomic work on these two species radiations suggested multiple hybridization events in response to changing landscapes and climate. We generated hypotheses for specific hybridization events based on observed hybrid mating songs and patterns of mito-nuclear discordance from previous studies. We tested our hypotheses using the D-statistic and a phylogenomic dataset of over 500 nuclear Anchored Hybrid Enrichment genes along with mitochondrial genomes. This larger dataset provided stronger support for some of our hybridization scenarios but not all. Using these same data we inferred phylogenetic networks using SNaQ and PhyNEST to determine whether the two methods recovered plausible network with respect to our hypothesized hybridization events. We found that both SNaQ and PhyNEST recovered an extensive history of reticulate evolution in New Zealand cicadas which broadly matched our predictions. We suggest that differences between networks inferred by the two network programs may result from using site patterns versus gene trees as input data or reflect other differences in the inference methods. Finally, we discuss considerations for users applying these methods to targeted enrichment data and suggest improvements for network method developers.

Since their discovery, the phylogenetic placement of the extremely halophilic, methanogenic Methanonatronarchaeia has remained controversial. Different studies have variably placed this lineage as sister to the archaeal class Halobacteria (haloarchaea) or as a deep-branching euryarchaeal group. These conflicting results may reflect methodological artefacts linked to the strong amino acid compositional bias characteristic of halophilic archaea and evolutionary model misspecification. Here, we reanalyse published phylogenomic datasets using site-heterogeneous mixture models that mitigate such biases. Our analyses consistently recover Methanonatronarchaeia as a deep-branching lineage basal to the Methanotecta, independent of the inclusion of the recently described Ordosarchaeia. We further show that Ordosarchaeia do not constitute a distinct lineage but fall within the previously described Halorutilales and Afararchaeaceae. Re-examination of the methyl-coenzyme M reductase phylogeny indicates that the placement of Methanonatronarchaeia mcr genes is best explained by vertical inheritance, without invoking horizontal gene transfer from unknown donors. Together, our results support ancestral methanogenesis within this lineage and its independent adaptation to extreme halophily.

Abstract The Cyperus margaritaceus–niveus complex (Cyperaceae) is a group of nine C4 Cyperus species ( C. karlschumanii , C. kibweanus , C. ledermannii , C. margaritaceus , C. nduru, C. niveus var. leucocephalus , C. somaliensis , C. sphaerocephalus , and C. tisserantii ) from Sub-Saharan Africa and Madagascar united by the combination of a capitate inflorescence, white–yellow glumes and swollen bulb-like bases. Previous molecular studies hinted that this complex forms a natural group within the C4 Cyperus Clade, although not all taxa were included. In this study, we used the Angiosperms353 bait kit to generate sequence data for all taxa in the complex. The species complex was resolved as monophyletic, while inter-species relationships produced differing results. Cyperus sphaerocephalus , C. kibweanus , C. ledermannii , C. somaliensis , and C. tisserantii were resolved as monophyletic, while C. karlschumannii appears monophyletic except for a moderately resolved isolated lineage that is positioned elsewhere. Cyperus niveus var. leucoephalus was resolved as paraphyletic. Cyperus nduru was resolved as polyphyletic even after rechecking determinations of the specimens. The latter result appears to show correlation with habitat in which one clade comprises specimens associated with Miombo woodland and another clade that comprising specimens associated with bowal grassland. This ecological difference correlates with differences in underground organ morphology. Cyperus margaritaceus requires further study to delimit since a specimen identified as this species is found in an unusual position in the phylogeny, possibly representing a new species to science. Combining this phylogenomic dataset with previous studies on morphometrics demonstrates how such integrative and iterative taxonomic methods can be the optimal approach in resolving species complexes in species-rich genera such as Cyperus , especially in the rapid diversifying C4 Cyperus Clade.

Abstract Previous phylogenomic analyses of Membracoidea have strongly supported the monophyly of most currently recognized subfamilies of leafhoppers (Cicadellidae) but suggested that some revisions to the higher classification are needed. However, the most taxon‐rich previous analysis included very few representatives of some family‐group taxa. Here, a dataset comprising sequences from 269 taxa, ca. twice as many loci and taxa as the largest previous phylogenomic dataset for Membracoidea and representing all extant families, subfamilies and over 96% of the extant tribes, was analysed using concatenated and coalescent methods to test previous results and provide a stronger basis for revisions to the higher classification. The following taxonomic changes are proposed based on the consistently strong branch support for several lineages in both concatenated maximum likelihood and coalescent gene tree analyses. Cicadellinae is expanded to include tribes Makilingiini and Tungurahualini, both previously included in Mileewinae. Mileewinae is therefore restricted to include the nominotypical tribe and Tinteromini. Errhomeninae, most recently treated as a tribe of Aphrodinae, is elevated to subfamily status and includes tribes Bathysmatophorini, Euacanthellini and Malmaemichungiini. Portanini is transferred from Aphrodinae to Neocoelidiinae. The concept of Aphrodinae is consequently narrowed to include only the nominotypical tribe, Sagmatiini and Xestocephalini. Neobalinae is expanded to include Equeefini, a tribe previously included in Coelidiinae. The morphologically aberrant soil‐dwelling genus Paulianiana from Madagascar, previously placed in Sagmatiini (Aphrodinae), is transferred to Ledrinae. The Australian endemic tribes Thymbrini and Stenocotini, most recently placed in Tartessinae, are transferred to Ledrinae. Tartessinae is restricted to include the nominotypical tribe, Neopsini and Tardrabassus (new placement, previously unplaced to a tribe within Iassinae). Although most leafhopper subfamilies, as currently defined, are consistently recovered as monophyletic with strong support, these major lineages are connected to each other by very short, deep internal branches and their relationships remain unstable. Aphrodinae, Eurymelinae, Iassinae, Mileewinae, Ledrinae and Tartessinae, as currently defined, were not consistently recovered as monophyletic, but support for their non‐monophyly was also low, so their current definitions are retained, pending further analyses. Keys to the families of Membracoidea and to the 19 currently recognized leafhopper subfamilies are provided. Divergence time estimates suggest that Cicadellidae originated during the Middle Triassic (~224 mya) and began to diverge at ~217 mya, with most modern leafhopper subfamilies arising during the Jurassic and Early Cretaceous periods.

Allopatric speciation is the predominant mode of speciation in riverine fishes. However, the relative importance of genetic drift versus natural selection in the allopatric speciation of these fishes remain uncertain. Here, we present a case study that demonstrates the role of ecology in the diversification of a group of imperiled freshwater fishes from the central United States. We integrate a phylogenomic dataset with analyses of streamwise distance, environmental variables, meristic and morphological traits, and diet to investigate the ecological context and outcomes of allopatric speciation within a species complex comprising the Slenderhead Darter Percina phoxocephala (Nelson), Ouachita Darter Percina brucethompsoni (Robison, Cashner, and Near), and Longnose Darter Percina nasuta (Bailey). We find that two of the species traditionally delimited based on disparity in snout length, P. phoxocephala and P. nasuta, are polyphyletic, revealing three instances of the parallel evolution of snout length disparity. We propose a revised taxonomy including the delimitation of six new species based on disparity in phenotypic traits and phylogenomic analyses. We find that morphological differences are not correlated with genetic divergence but are congruent with variations in diet and environmental niches, suggesting a role for ecological factors in allopatric speciation of riverine fishes.

Abstract Accounting for the estimated number of undescribed species, Gelechioidea are thought to be among the most species‐rich superfamilies of Lepidoptera, with 18,500 described species, including numerous pests of economically significant crops such as cotton, tomato and wheat. Family‐level topology of the superfamily and the extent and the number of accepted families have received important revisions throughout the previous phylogenetic work on the group. Here we extracted 1767 nuclear protein‐coding genes from genomic and transcriptomic data from 57 ingroup taxa, including Haplochrois buvati Baldizzone and Urodeta hibernella Staudinger, for which the whole‐genome sequences were generated in this study. We first analyse this phylogenomic dataset within a maximum likelihood framework to revisit the interfamilial relationships within Gelechioidea and then integrate it with the existing taxon‐rich, Sanger‐sequenced data from up to 24 genes to re‐evaluate the extent of the 20 currently accepted families by analysing this integrated dataset encompassing 381 ingroup taxa. Although we also recover some of the previously suggested multifamilial clades, the backbone topology we infer presents novel arrangements of families compared to previously published work: overall, we observe that Gelechioidea have diversified in four main lineages and find Stenomatinae (Depressariidae) to be sister to the rest of Gelechioidea. We therefore elevate it to family, Stenomatidae stat. nov . Moreover, we find the current circumscription of Elachistidae to be non‐monophyletic and propose a new delimitation to include the subfamilies Elachistinae, Parametriotinae, Cacochroinae (Depressariidae) and Ethmiinae stat. nov .

Lemurs are often cited as an example of adaptive radiation, as more than 100 extant species have evolved and filled ecological niches on Madagascar. However, recent work suggests that lemurs lack a hallmark of other adaptive radiations: explosive speciation rates that decline over time. Thus, characterizing the tempo and mode of evolution in lemurs can reveal alternative ways that hyperdiverse clades arise over time, which might differ from traditional models. We explore lemur evolution using a phylogenomic dataset with broad taxonomic sampling that includes the lorisiforms of Asia and continental Africa. Our analyses reveal multiple bursts of diversification (without subsequent declines) that explain much of today’s lemur diversity. We also find higher rates of speciation in Madagascar’s lemurs compared to lorisiforms, and we demonstrate that the lemur clades with high diversification rates also have high rates of genomic introgression. This suggests that hybridization in these primates is not an evolutionary dead-end, but potential fuel for diversification. Considering the conservation crisis affecting strepsirrhine primates, with approximately 95% of species threatened with extinction, this study offers a perspective for explaining Madagascar’s primate diversity and reveals patterns of speciation, extinction, and gene flow that will help inform future conservation decisions.

Abstract The palm family (Arecaceae) has a rich history of phylogenetic research, including several recent phylogenomic studies. However, densely sampled phylogenomic datasets for larger palm clades – such as subfamilies – are still few in number. We used target sequence capture to obtain data for 971 nuclear genes across 421 (ca. 80%) species in the subfamily Coryphoideae. We inferred a robust phylogenetic tree to address systematic issues in the subfamily, specifically the relationships among tribes Cryosophileae, Sabaleae, Phoeniceae and Trachycarpeae, the affinities of seven genera in Trachycarpeae that are not currently assigned to any subtribe, and the monophyly of genera across the subfamily. We recovered relationships among tribes that are in accordance with other major nuclear phylogenomic datasets, but that are incongruent with trees derived from plastome sequences. Importantly, the placement of tribe Phoeniceae (the date palms) remains contentious. Our tree recovered with high support the relationship of all unplaced Trachycarpeae genera, paving the way for an updated classification. Most genera were resolved as monophyletic except for Livistona and all three genera of tribe Caryoteae, calling for a revision of generic limits. Our tree clarifies the relationships of many fan palm species for the first time, allowing for future studies of diversification, trait evolution or biogeography.

Theories of adaptive radiation propose predictable trajectories in which diversity accumulates rapidly in newly formed or colonized environments with underexploited niche space and few competing species, before slowing down as competition intensifies, and speciation and extinction rates approach equilibrium. This historical perspective on diversity may be more important than current environmental variation for explaining today's biodiversity, but this has been difficult to determine because of the complexity of diversification dynamics and the challenges of relating diversification processes to past environmental change. Here we unravel the complex and heterogenous diversification dynamics of Proteaceae (subfamily Grevilleoideae), a large Gondwanan plant clade, to investigate how the expansion and contraction of biomes since the Cretaceous has shaped its current megadiversity across the Sahul region (Australia and New Guinea). We modeled paleobiome dynamics over a 120 Ma period and produced a nuclear phylogenomic dataset of 458 loci for ~700 species (~74%) to show that historical diversification rates across the Grevilleoideae phylogeny are closely associated with ecological opportunity provided by emerging and expanding biomes. Diversification is rapid in emerging and expanding biomes, while long-occupied biomes tend to have higher species richness but lower diversification rates, as expected if these biomes have approached equilibrium diversity. Our results reveal a strong and heterogeneous legacy of climatic and geological history on today's floristic diversity and explain why diversity is often decoupled from expectations based on measures of ecological "carrying capacity" such as the area or climate of present-day biomes.

Species characterized by undetermined clade affiliations, limited research coverage, and deficient systematic investigation serve as enigmatic entities in plant and animal taxonomy, yet hold critical significance for exploring phylogenetic relationships and evolutionary trajectories. Subgenus Cyathophora (Allium, Amayllidaceae), a small taxon comprising approximately five species distributed in the Qinghai-Tibet Plateau (QTP) and adjacent regions might contain an enigmatic species that has long remained unexplored. In this study, we collected data on species from subgenus Cyathophora and its close relatives in subgenus Rhizirideum, as well as the enigmatic species Allium siphonanthum. Combining phylogenomic datasets and morphological evidence, we investigated species relationships and the underlying mechanism of phylogenetic discordance. A total of 1662 single-copy genes (SCGs) and 150 plastid loci were filtered and used for phylogenetic analyses based on concatenated and coalescent-based methods. Furthermore, to systematically evaluate phylogenetic discordance and decipher its underlying drivers, we implemented integrative analyses using multiple approaches, such as coalescent simulation, Quartet Sampling (QS), and MSCquartets. Our phylogenetic analyses robustly resolve A. siphonanthum as a member of subg. Cyathophora, forming a sister clade with A. spicatum. This relationship was further corroborated by their shared morphological characteristics. Despite the robust phylogenies inferred, extensive phylogenetic conflicts were detected not only among gene trees but also between SCGs and plastid-derived species trees. These significant phylogenetic incongruences in subg. Cyathophora predominantly stem from incomplete lineage sorting (ILS) and reticulate evolutionary processes, with historical hybridization events likely correlated with the past orogenic dynamics and paleoclimatic oscillations in the QTP and adjacent regions. Our findings not only provide new insights into the phylogeny of subg. Cyathophora but also significantly enhance our understanding of the evolution of species in this subgenus.

While ontogenetic habitat shifts are a widely appreciated phenomenon across fishes, the macroevolutionary implications of habitat shifts and subsequent ecological opportunity have mainly focused on adult organisms, largely overlooking juvenile life history diversification. The snappers and fusiliers (Lutjanidae) represent a successful tropical teleost radiation exhibiting complex ontogenetic shifts and use of diverse nursery and adult habitats across the marine–freshwater interface. Lutjanids collectively occupy a broad range of environments within the seascape mosaic, including freshwater rivers, estuaries, reefs, and deep offshore slopes. Using an extensive phylogenomic dataset of ~ 110 species, we test models of juvenile and adult habitat evolution across seascape gradients. Evolutionary model fitting and ancestral state reconstructions, conducted independently for juvenile nurseries and adult habitats, both support an ordered, stepwise pattern of habitat transitions, with low-salinity associations evolving only via intermediate coastal habitats. This ‘stepping stone’ model of marine–freshwater macroevolution saw adoption of low salinity habitats preceded by adaptation to intermediate brackish habitats, rather than random jumps between widely separated seascape components. While our results highlight that ontogenetic shifts have been central to lutjanid diversification, more consistent and transferable research frameworks are required to clarify the ecological and evolutionary implications of lutjanid life history diversity.

An understanding of Branchiopoda’s evolutionary history is crucial for a comprehensive knowledge of the Pancrustacea tree of life, given their close evolutionary relationship with Hexapoda. Despite significant advances in molecular and morphological phylogenetics that have resolved much of the branchiopod backbone topology, a reliable temporal framework remains elusive. Key challenges include a sparse fossil record, long-term morphological stasis, and past topological inconsistencies. Leveraging a Bayesian Inference approach and the most extensive phylogenomic dataset for branchiopod to date, encompassing 46 species and over 130 genes, we inferred a time-calibrated phylogenetic tree. Furthermore, to strengthen the confidence in our divergence times estimation, we assessed the impact of age priors, topological uncertainties, and gene trees which are discordant from the species trees. Our results are largely consistent with the fossil record and with previous studies, indicating that Branchiopoda originated between 400 and 500 million years ago, and the orders of large branchiopods diversified during the Mesozoic. Concerning Cladocera, results remain problematic, with a sharper uncertainty in the diversification time with respect to the fossil record. Though, the jackknife resampling of fossils and the other sensitivity analyses proved our calibration method to be robust, suggesting that the difficulties in obtaining a paleontological-consistent time tree may be hindered by the variability in branchiopod substitution rates and topological instability within certain clades.