Molecular Phylogenetics and Evolution

The delineation of closely related species remains a persistent challenge in Zoantharia, where morphological plasticity and limited genetic differentiation complicate taxonomy. In this study, we investigated the phylogenetic relationship between the widely distributed sibling taxa Palythoa tuberculosa (Indo-Pacific) and Palythoa caribaeorum (Atlantic) using ultraconserved elements (UCEs) recovered from genome skimming. A dataset comprising 116 loci (35,699 bp) across 37 specimens from Brazil, the Red Sea, Okinawa, and New Caledonia was analysed using both concatenated maximum-likelihood and coalescent-based approaches. Phylogenetic reconstructions did not recover monophyletic relationships corresponding to either species or geographic origin, instead revealing intermixed lineages across the Indo-Pacific and Atlantic regions. Concordance factor analyses indicated low gene concordance and moderate site concordance, suggesting pervasive gene tree discordance rather than a lack of phylogenetic signal. These patterns are consistent with previous studies based on mitochondrial, nuclear, and reduced-representation datasets, indicating that increased marker resolution does not resolve species boundaries within this complex. The observed lack of differentiation may reflect ongoing or recent connectivity among populations, potentially facilitated by long-distance dispersal promoted by anthropogenic rafting or historical range expansion, biological invasion, or biological processes such as incomplete lineage sorting. The results support the hypothesis that P. tuberculosa and P. caribaeorum represent a species complex or a case of incipient speciation rather than fully distinct evolutionary lineages. These findings indicate that genome-scale data alone may be insufficient to resolve very recent divergences, supporting the need for integrative approaches to resolve complicated species boundaries in zoantharians.

The order Atheriniformes (silversides, rainbowfishes, and blue-eyes) is a globally distributed group of fishes with frequent evolutionary transitions between marine and freshwater ecosystems. However, understanding the tempo and mode of these transitions has been hampered by poor phylogenetic resolution and limited taxonomic sampling, particularly within the suborder Atherinoidei. We generated a phylogenomic dataset of 1,100 exon loci for 150 species to resolve interfamilial relationships and reconstruct the groups biogeographic history. We were also able to incorporate a large number of existing GenBank sequences, producing a phylogeny with 265 species sampled for at least some genetic data (67% of known species diversity). While the New World suborder Atherinopsidae is well-resolved, we found that the family Atherinidae is polyphyletic across all analyses. We propose a revised classification that restricts Atherinidae to the genus Atherina and recognizes Atherinomoridae and Craterocephalidae as separate families. Our biogeographic inferences using explicit geographic areas suggests more frequent marine-to-freshwater transitions than previously inferred with simplified binary (marine vs. freshwater) coding, and uncover habitat transitions where marine ancestors may have gone extinct. These results highlight how explicit geographic modeling can uncover marine ancestry erased by extinction, providing a robust phylogenetic framework for future evolutionary studies of Atheriniformes.

Macaws of the genus Ara comprise eight extant species distributed throughout the Neotropics. Among them, four have broad geographic ranges, yet little is known about the evolutionary history and demographic processes that shaped their genomic variation and present-day distributions. This is particularly relevant because, although these wide-ranging macaws are classified as Least Concern by the IUCN, many of their populations are declining due to habitat fragmentation, illegal trade, and climate change. Here, we used nuclear and mitochondrial genomic data to characterize the evolutionary relationships, population structure, genetic diversity, and demographic histories of three widely distributed species (A. ararauna, A. chloropterus, and A. severus) across their geographic distributions. We identified two main populations within Ara severus, and this species showed the highest heterozygosity levels among the three species. In A. ararauna and A. chloropterus, we observed four main genetic clusters corresponding to two populations in the Amazon rainforest biome and and two populations in the Cerrado savanna biome. Cerrado populations in both species exhibited markedly reduced heterozygosity and elevated inbreeding relative to Amazonian populations, consistent with smaller effective population sizes and increased isolation. Genome-wide scans suggested that genetic drift and divergent demographic histories played a predominant role in driving the strong differentiation between Amazon and Cerrado in these two species. Nevertheless, we detected two candidate genes, NALCN and RBBP6, with convergent selection signals across A. ararauna and A. chloropterus, suggesting possible local adaptation to the Cerrado biome.

Our study provides the first comprehensive karyotype evolution analysis of the insect order Zoraptera. We present karyotypic descriptions of seven species across two families: Zorotypidae (Usazoros hubbardi and two Zorotypus spp.) and Spiralizoridae (Centrozoros gurneyi, Spiralizoros magnicaudelli, and two Spiralizorose spp.). These results facilitate a critical evaluation of existing cytogenetic knowledge in Zoraptera and the evolution of karyotypic traits across Polyneoptera. Most notably, we refute the presence of holocentric chromosomes in Zoraptera. Also, we show that the XY sex chromosome system is prevalent and likely ancestral within the order. Furthermore, by integrating the chromosome numbers of the studied species with a dated molecular phylogeny of Zoraptera, we provide the first estimation of the mode of chromosome number evolution for this group. Finally, standard karyotypic features (2n, chromosome morphology, and size) and the distribution of 18S rDNA and (TTAGG) telomeric motif clusters--detected by fluorescence in situ hybridization--reveal highly differentiated karyotypes and genomic structures. This genetic diversity contrasts sharply with the recognized morphological uniformity of Zoraptera.

Chaetognathifera, a superphylum comprising Syndermata (Rotifera including Acanthocephala), Micrognathozoa, Gnathostomulida and Chaetognatha, is a complex grouping generally recovered as the sister to all other Lophotrochozoa. However, phylogenetic relationships within this group are controversial, in part due to poor sampling, resulting in two key questions. The first is whether Gnathostomulida or Chaetognatha represent the sister group to Syndermata+Micrognathozoa. The second is the phylogenetic position of the former phylum Acanthocephala within Syndermata. Here, we present the first study of the phylogenetic affinities of Chaetognathifera with genomic representation from all major phyla, and explore the potential of macrosynteny to better understand these relationships. For this latter aspect, we also developed a new jackknifing procedure to assess the robustness of linkage groups inferred by macrosyntenic analyses. We show that the phylogenetic relationships between these clades are corroborated through a variety of gene selection and analysis methodologies. This provides clear evidence of Acanthocephala as a derived clade within Syndermata as sister to Seisonidea, and that Gnathostomulida is sister to Syndermata+Micrognathozoa, with Chaetognatha as the earliest diverging clade within Chaetognathifera. On the other hand, we found that macrosyntenic patterns cannot resolve this question. Moreover, almost all possible linkage groups involving chaetognathiferan species lack robusticity and hence, should not be considered reliable. As a consequence so far, in Chaetognathifera none of the bilaterian ancestral linkage groups can be reliably found and independent massive chromosomal rearrangements occurred. We therefore strongly suggest that studies of macrosynteny should not only assess the significance of possible linkage groups, but also the robusticity of these linkage group inferences. Furthermore, we also present a script for this purpose, which can be found at: https://github.com/JFFleming/MacrosyntenicJackknife

The Hesperiine genus Atrytonopsis Godman, 1900, occurs broadly across the American Southwest. Atrytonopsis margarita (Skinner, 1913) and Atrytonopsis python (W. H. Edwards, 1882) have look-alike appearances, concurrent flights, and geographic distributions which converge in New Mexico. Their similar wing markings and intertwined taxonomic history has made it challenging to fully understand the identity and occurrence of each. Burns (2015) revealed differences in genitalia, clarifying that they are distinct species. Genomic DNA analysis of more than 100 specimens now illuminates their genetic uniqueness, phylogenetic relationship, field identification challenges and details of their geographic distributions.

True lemmings (genus Lemmus) underwent substantial range shifts during the Late Pleistocene and the Pleistocene-Holocene transition, but the impact of these events on present-day diversity remains poorly understood. Here, we used whole-genome sequencing data from modern and ancient samples across the Palearctic range to address this knowledge gap. Reconstruction of autosomal phylogeny revealed that Palearctic true lemmings exhibit relatively shallow genetic structure, contrasting with the deep divergence inferred from mitochondrial genomes. Genetic variation largely follows an isolation-by-distance pattern, and no elevated nuclear divergence was detected between the major mitochondrial lineages. Window-based phylogenetic analyses identified several peripheral populations with high concordance factors, including Norway and Amur lemmings. The high degree of phylogenetic concordance along the genome in these populations is likely a consequence of postglacial bottlenecks and isolation, as indicated by reduced heterozygosity and the presence of runs of homozygosity in them. Overall, our results indicate that the modern genomic structure of Palearctic lemmings was shaped primarily by range fragmentation and population isolation following the broad distribution of the genus during the Last Glacial Maximum. Thus, the current genetic structure appears to represent only a fraction of the Late Pleistocene true lemming diversity. This is illustrated by a genetically distinct ancient specimen ([~]40 ka BP) from the Indigirka River basin that does not cluster with any modern lineage. From a taxonomic perspective, these findings do not support strong species-level differentiation among the major Palearctic lineages and highlight the discrepancy between mitochondrial and nuclear patterns of diversity within the genus.

Zingiberales includes eight morphologically distinctive families, but its family-level backbone has remained unstable, especially around Musaceae, Heliconiaceae, Lowiaceae, and Strelitziaceae. We analysed 1566 low-copy nuclear genes from 52 samples, representing all eight families and Pontederia crassipes as outgroup. Concatenated maximum likelihood and multispecies coalescent analyses recovered the same backbone: ((Zingiberaceae, Costaceae), (Cannaceae, Marantaceae)) is sister to (Musaceae, (Heliconiaceae, (Lowiaceae, Strelitziaceae))). Penalized-likelihood dating placed the sampled crown group in the Late Cretaceous, with several deep family-level divergences occurring on short internodes. Analysis of 1248 rerooted gene trees showed that conflict is concentrated on these deep branches and in several shallow clades. HyDe tests of empirical and simulated matrices, each including 62,475 triples, did not support widespread ancient hybridization among the major family-level lineages after filtering against the simulated null model. The nuclear data recover a stable Zingiberales backbone, and the long-standing instability of several deep nodes is best explained by rapid early divergence and extensive incomplete lineage sorting.

The global study of freshwater clams in the genus Corbicula is frequently confounded by invasive androgenetic lineages that experience mitochondrial DNA capture and clonal propagation. In contrast, the endemic Corbicula of Sulawesi's ancient lakes reproduce sexually, offering a uniquely reliable system for mitochondrial population genetics. This study provides the first population-genetic framework for two endemic species, Corbicula possoensis (Lake Poso) and C. linduensis (Lake Lindu), using the cytochrome c oxidase subunit I (COI) marker. We analysed 90 newly generated COI sequences from C. possoensis (six stations) and C. linduensis (three stations), integrated with reference sequences from GenBank, to assess genetic diversity, population structure, and phylogeographic patterns. Hierarchical AMOVA revealed deep divergence between the two lakes ({Phi}_CT = 0.607), consistent with prolonged independent isolation rather than a single shared vicariance event, as the two species do not form a sister pair in the phylogeny. Within Lake Poso, C. possoensis exhibited exceptionally high genetic diversity (24 haplotypes; h = 0.876; {pi} = 0.016) and pronounced micro-geographic structuring into three phylogeographic zones (North: Tentena and Siuri; East: Tando Nceppo and Busogo Beach; Southwest: Bancea and Pendolo), each characterised by distinct haplogroups. Remarkably, the maximum divergence between zones (K2P = 2.33%) approached the interspecific distance between C. possoensis and C. linduensis (K2P = 2.42%), indicating that within-lake mitochondrial divergence has reached near-interspecific levels. Conversely, C. linduensis displayed near-panmixia and extreme genetic depauperation (3 haplotypes; h = 0.246; {pi} = 0.0004), indicating long-term demographic stasis within a restricted habitat. The deep phylogeographic zonation in C. possoensis suggests that its discrete populations should be treated as separate Management Units (MUs) in conservation planning to preserve locally adapted gene complexes, whereas the severely depauperate gene pool of C. linduensis renders it critically vulnerable to environmental disturbance and invasive species, warranting urgent IUCN Red List assessment. To validate these mitochondrial boundaries and inform future conservation strategies, multi-marker and genome-wide reassessments are strongly recommended.

Venus flytrap (Dionaea muscipula) is an insectivorous plant in the monotypic genus Dionaea, endemic to the Southeastern United States, and found in a small geographic range in North and South Carolina. Its unique morphology and natural history have intrigued biologists for centuries, yet the evolution of populations has not been adequately characterized. Population decline, driven primarily by disruptive land conversion, fire suppression, and illegal harvesting/poaching underscores the urgency of defining the genetic diversity in the present population to guide species conservation. We applied a genome-wide SNP dataset to analyze admixture and population structure and used coalescent modeling to trace the ancestry and migration of geographically distinct population clusters. Our population dynamics model supports four lineages, with the North Cape Fear Arch lineage as the ancestor of all lineages and two genetically distinct Sandhills lineages derived from the South Cape Fear Arch lineage independently at [~]13 Ma and [~]3 Ma, respectively, during peak climate optima periods and maximal sea level rise. Severe population decline events occurred among all lineages, with two ancient instant bottleneck population decline events in Sandhills lineages and two recent ones in the two Cape Fear Arch lineages, which contributed to the current genetic structure. Shorter peduncle lengths in Sandhills populations correspond with suspected local adaptation to Sandhills habitats.

Understanding how global biodiversity patterns arise is a central theme of biogeography, with contemporary theory recognising the roles of both dispersal and vicariance. Genera that are broadly distributed can provide important systems for disentangling the relative influence of these processes across evolutionary timescales. However, many lesser-studied groups, particularly those in the tropics, lack a densely sampled phylogeny which hinders robust inference of their evolutionary and biogeographic history. This study investigates the global diversification and systematics of the putative pantropical moth genus Parasa Moore (Lepidoptera: Limacodidae), with the aim of assessing the relative importance of dispersal and vicariance in shaping its distribution. Medium-coverage whole genome sequencing of specimens predominantly from museum collections were used to generate a globally sampled time-calibrated phylogeny of Parasa and associated genera (the Parasa-complex). Ancestral range estimation analyses were employed to infer geographical origins and possible dispersal times between bioregions. The Parasa-complex originated in Africa in the late Oligocene ([~]24 Ma) and, through a series of long-distance dispersal events during the early-mid Miocene, expanded into Asia ([~]23 Ma) and the Americas ([~]21 Ma). Across all regions, dispersal was the dominant process shaping present-day distributions, with a limited role of vicariance in some subregions. Phylogenetic analyses further demonstrated that Parasa is not monophyletic, with multiple independent lineages contributing to its apparent pantropical distribution. These findings highlight a central role of long-distance dispersal in generating certain global distributions. The results support a dynamic model of range evolution involving rapid Miocene dispersal and subsequent regional diversification. In addition, the non-monophyly of Parasa requires substantial taxonomic revision, underscoring the importance of robust phylogenetic frameworks for interpreting global biodiversity patterns.

The Neotropical genus Atelopus has experienced a drastic population decline in recent decades. Despite this, a knowledge gap remains regarding the conservation genetic status, phylogeography, and demographic history of most of its species, especially those endemic to areas with limited access like the Sierra Nevada de Santa Marta in Colombia. In this genomic study, we inferred phylogenetic relationships, demographic history, and gene flow among four endemic Atelopus morphospecies in the Sierra Nevada de Santa Marta-SNSM. Additionally, we compared the effective population size (Ne) estimates with the available population census data. NextRAD was used to obtain genomic data from 95 individuals collected at five sites in the SNSM and two in the Colombian Pacific (outgroup). The morphospecies recently diverged in a scenario without gene flow and were recovered as monophyletic. Their phylogenetic relationships were discordant, which is attributed to the presence of incomplete lineage sorting-ILS, which would also explain their shared ancestry among them. The lack of gene flow as well as the recent divergence times given by demography suggests a recent and rapid speciation. However, the reproductive isolation mechanisms that promote or maintain the species boundaries in this group remain unknown and require further investigation. We suggest that this process may have been influenced by the complex topography of the SNSM, traits such as high philopatry, low dispersal ability, and behavioral factors such as habitat preference or to factors related to genetic architecture that influenced the rapid formation of reproductive barriers among populations. Additionally, a pattern of population decline was observed around 200.000 years ago, with recent increases in three morphospecies. Despite the reduction in effective population size, no signs of inbreeding were detected. However, for A. laetissimus, the only species surveyed, the estimated value of Ne and its implications should be interpreted with caution. Ultimately, our findings reveal an evolutionary history shaped by a burst of diversification and abrupt reproductive isolation, highlighting how the resulting endemism and restricted genetic connectivity shape the unique evolutionary trajectory and vulnerability of this threatened montane species. Significance StatementThe mechanisms driving rapid speciation in montane ecosystems remain a central question in evolutionary biology. This study provides crucial genomic insights into the diversification of four endemic Atelopus species in an isolated Neotropical massif. We reveal a compelling evolutionary scenario where species diverge rapidly in absence of gene flow. This rapid speciation was likely facilitated by complex topography, environmental heterogeneity, and ecological and behavioral differences among species. Nevertheless, the evolutionary processes that limited gene flow among SNSM species have not yet been identified.

Among Neotropical cichlids the tribe Heroini exhibits substantial ecological diversity and is one of the dominant fish groups across northern Neotropical riverscapes. The majority of studies on heroine cichlids have focused on macroevolutionary patterns but the role of geological and ecological factors shaping lineage diversification within the tribe remains poorly understood. Here we used ultraconserved elements (UCEs) to infer a taxonomically complete and geographically comprehensive phylogenomic framework of the early-diverging herichthyine sister genera Thorichthys and Trichromis and to comparatively investigate their evolutionary and biogeographic histories. All our phylogenomic hypotheses support the monophyly of both genera and two species subgroups within Thorichthys. Our results provide evidence of a) unrecognized diversity within Trichromis salvini, b) uncertainty in species boundaries in Thorichthys, and c) the first report of ghost introgression in fishes of the northern Neotropics. Additionally, our results demonstrate the importance of the Papaloapan and Coatzacoalcos watersheds for fish diversification in the region. Finally, we show patterns consistent with ecological divergence during the evolution of this group, particularly among sympatric species. Altogether, these patterns suggest that lineage diversification in northern Neotropical cichlids has been driven by the interaction of geological restructuring, climatic and sea-level oscillations, and heterogeneous ecological pressures.

The tribe Spermacoceae (Rubiaceae) comprises a morphologically diverse assemblage of approximately 1,400 species distributed across the Neotropics, Africa, Asia, Australia, and Pacific region. It remains one of the most taxonomically intractable groups in the family, with generic limits repeatedly redefined for more than two centuries. Previous phylogenetic studies based on a limited number of plastid and nuclear markers left numerous relationships unresolved and provided sparse representation of Neotropical lineages. Here, we present the first phylogenomic study of the tribe based on plastome-scale data and expanded sampling of Neotropical taxa. We sampled 121 species representing 55 genera spanning all major clades and generated 123 new plastomes, including 25 species incorporated into a molecular phylogenetic framework for the first time. Maximum-likelihood and Bayesian analyses recovered a highly resolved and strongly supported phylogeny, with uncertainty restricted to a small number of deep backbone nodes. Pollen and seed micromorphology provided additional evidence for evaluating phylogenetic relationships. The resulting phylogenetic framework clarifies generic boundaries across several problematic lineages and supports multiple taxonomic changes. Pervasive homoplasy in seed and floral characters rendered several traditionally recognized genera non-monophyletic, warranting new combinations, including Edrastima oxycoccoides, Stenotis alexanderae, and S. prostrata, and a reassessment of taxa such as Terrellianthus serpyllaceus and Oldenlandia dusenii. We further identify genera requiring additional study and provide an updated key to the 82 recognized genera of Spermacoceae. Together, these results provide the most robust phylogenetic framework yet available for the tribe and establish a foundation for future systematic, biogeographic, and evolutionary research.

Reliable species delimitation underpins biodiversity assessment but remains difficult for organisms with plastic morphology and few diagnostic characters. Multispecies coalescent (MSC) methods can delimit species from genomic data, yet they are rarely tested in taxonomically complex, marine invertebrate groups where they are arguably most needed. We used the three Mediterranean species of the genus Tethya, a rare, well-characterised system within the otherwise taxonomically difficult phylum Porifera-distinguished by multiple independent morphological and ecological characters-to evaluate how robust MSC-based delimitation is in such groups. Analysing 64 single-copy nuclear loci in BEAST2 and BPP, we compared constrained, hypothesis-testing approaches (BFD*, BFdriver, A10) with freer, heuristic ones (SPEEDEMON, A11), and examined their sensitivity to data type, clock model, priors, and the species-collapse threshold. All methods recovered the three recognised Mediterranean species, but the resolution of within-lineage structure was method-dependent. The hypothesis-testing approaches consistently supported six lineages, robustly across data types and model assumptions, whereas the heuristic approaches proved less stable. Configurations without a priori species hypotheses often failed to converge or were computationally intractable, a problem compounded by the relaxed clock. In SPEEDEMON the outcome changed with the collapse threshold. Because our system lacks an independent reference point to calibrate this threshold, any delimitation based on it is poorly constrained. We conclude that constrained, hypothesis-testing delimitation is the most robust and reproducible MSC approach, yielding a quantitative, model-based hypothesis that can be weighed against other lines of evidence to inform taxonomic decisions. By clarifying how these methods behave and how their outcomes should be interpreted, our study offers a practical guide for researchers working on comparably complex systems.

The Dinaric karst of Croatia encompasses a network of over 10,000 caves and represents one of the worlds most important subterranean biodiversity hotspots. It is inhabited by remarkably diverse and often endemic species, including planarian flatworms, which are among the rarest macroinvertebrates encountered in cave habitats. Although the presence of cave planarians has long been known, no integrative research on this group has been conducted to date, and the evolutionary relationships between these animals and their surface water counterparts are currently unresolved. To address these gaps, we combined field sampling, phylogenetic analysis based on COI and 18S genes, and phenotypic characterization. Our results show that cave planariids in Croatia belong to at least three genera and are more widespread and diverse across both Croatia, and the broader Dinaric karst, than previously assumed. We increased the number of cave records in the Dinaric karst from 26 to 37 and documented cf. Atrioplanaria and Phagocata in Croatian caves for the first time. Phylogenetic reconstructions suggest numerous independent cave colonization events, including multiple instances within the genera Crenobia and cf. Atrioplanaria. Variation in pigmentation and eye reduction, both within and between populations, further reveal heterogeneous evolutionary trajectories of cave-associated phenotypes. The biogeographical patterns and high genetic diversity we report here point to a complex evolutionary history of planariids in the Dinarides. Our newly generated molecular phylogenies and systematic documentation of trait variability establish Planariidae as a valuable model for studying mechanisms underlying convergent evolution of pigment loss and eye reduction in cave environments.

This investigation aimed at compiling all phylogenetic lineages within and around genus Cyanoboletus. The evolutionary inference obtained from the nuclear ribosomal genes internal transcribed spacer region (ITS) suggests that part of the species currently classified in Cyanoboletus belong in lineages separate from the genus, thus suggesting a narrower boundary that includes only the species that develop a strong staining reaction to touch and to air exposure of the context. The separate lineages are the monotypic Cupreoboletus genus and a few species that do not develop such reaction, which are part of a clade together with genera Cacaoporus and Acyanoboletus, thus broadening the concept of Cacaoporus to encompass all of them. The emerging 3C perspective of Cupreoboletus, Cacaoporus and Cyanoboletus offers a remarkably consistent morphological diagnosis, overcoming the problems of a too broad concept for Cyanoboletus. This work reveals that Boletus neotropicus, B. novae-zelandiae and B. sensibilis belong respectively in Cyanoboletus, Cacaoporus and Lanmaoa, and by studying multigene alignment concatenates it identifies lineages that probably represent undescribed species: at least four in Cacaoporus and at least five in Cyanoboletus. Diagnostic tables and dichotomic keys are presented by geographic region. The present work also includes a study of the phylogenetic position of Neoboletus flavosanguineus, a species once classified in Cyanoboletus. The complexity of assigning species epithets in some lineages is addressed, namely for the boundaries between Cacaoporus instabilis and Ca. fagaceophilus as well as the diversity under the names Cyanoboletus sinopulverulentus and Cy. pulverulentus. The overall picture of evolutionary lineages sets a framework for the choice of reference data that can provide, in future phylogenetic studies that involve the 3C, a balanced and efficient coverage. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=197 SRC="FIGDIR/small/724631v1_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@7f618corg.highwire.dtl.DTLVardef@dd6a14org.highwire.dtl.DTLVardef@5f7399org.highwire.dtl.DTLVardef@9e7443_HPS_FORMAT_FIGEXP M_FIG C_FIG

We sequenced the nearly complete mitochondrial genome of the hammerhead flatworm Bipalium nobile Kawakatsu and Makino, 1982 using short-read sequencing technology, yielding a 16,018 bp genome comprising 12 protein-coding genes, 22 tRNA genes, and 2 rRNA genes. The composition and order of genes were consistent with those observed in the closely related species Bipalium kewense and Diversibipalium multilineatum, except for the position of tRNA-Glu. Phylogenetic analysis based on all mitochondrial proteins from species within the family Geoplanidae supports the monophyly of a clade comprising B. nobile, B. kewense, and D. multilineatum. The mitochondrial genome sequence obtained in this study provides a valuable resource for investigating the genetic diversity and population structure of B. nobile, a soil-dwelling predator with the potential for global spread as an invasive organism.

Forest trees pose numerous potential challenges to phylogenomic inference. Their large effective population sizes and relatively long generation times lead to deep allele coalescence and consequently incomplete lineage sorting (ILS), which biases inferences of divergence times toward older ages and introduces gene tree discordance. Deep phylogenetic divergences, reaching back into the Paleocene, introduce reference-mapping biases. Introgression--the movement of genes between lineages--may result in different phylogenies being inferred depending on which individuals are included in analysis, even if the plurality of the genome favors the divergence history unaffected by introgression. These factors influence phylogenetic inference across the Tree of Life but are particularly prevalent in forest trees. Oaks (Quercus) are notable for all three influences. In addition, our knowledge of the oak phylogeny is currently based strongly on restriction site associated DNA sequencing (RADseq) datasets published over the past decade, which may introduce additional sources of uncertainty. In this chapter, we analyze a 322-species RADseq dataset and genome resequencing data from across the genus to address sources of uncertainty in our understanding of the global oak phylogeny, which we hope will serve as a model for other research groups working on comparable woody plant groups.

The potential for hybridization to act as a driver of genetic diversity and adaptation in harmful algal bloom-forming species has received scarce attention, despite growing recognition of its occurrence in diverse protist and algal lineages. Prymnesium parvum s.l. (Haptophyta), is a cryptic species complex whose members form ecosystem-disruptive toxic algal blooms around the world. A prior genome analysis showed that UTEX2797, a widely used laboratory strain, originated via hybridization between clade A1 and clade A2 of this species complex. To assess the extent of A1xA2 hybridization in P. parvum s.l., we screened the genomes of 28 strains and identified 16 additional A1xA2 hybrid strains isolated from inland Texas or the eastern United States between 2001 and 2020. Chloroplast haplotypes indicated that hybridization between A1 and A2 may have occurred multiple times, and hybrids with different chloroplast haplotypes have been co-isolated from blooms in Texas in 2013 and 2020. Additionally, strain NIES1812 from Okinawa, Japan was sufficiently divergent from A1 and A2 to warrant designation as a separate clade, which we name A3. These results provide evidence for a facultative sexual life cycle in P. parvum s.l. and expand our understanding of the extensive cryptic genetic diversity present in the species complex. The frequent isolation of hybrid strains from North American blooms suggests that hybridization is common and represents a significant source of adaptive potential in these economically and ecologically damaging organisms.