How reticulated are species?

The biogeographic and genomic signatures of dynamic river networks for terrestrial species in Amazonia

Amazonia contains Earth's largest freshwater basin, largest contiguous stretch of tropical forest, and most species-rich terrestrial biota on Earth. Rivers are key geographic features that drive diversification of the Amazonian biota, but they are also dynamic, which challenges their role as long-term barriers to dispersal and gene flow. The impacts of such river dynamics on organismal evolution have only recently been explored in detail. Here I examine biodiversity patterns and processes in Amazonia to elucidate how taxa diversify in the context of river network dynamics. I borrow the River Capture Hypothesis from ichthyology, and draw on evidence from speciation genomics, hybrid zones, and community assembly to demonstrate the effects of river network evolution on biodiversification. The idea is simple: populations of organisms whose dispersal is restricted by rivers become semi-isolated by rivers. Drift and selection against introgression drive divergence, but as rivers move, previously isolated populations come into secondary contact, facilitating lineage fusions or the migration of hybrid zones to other rivers. The basin's unique macroecological patterns and rich biota thus may have resulted from repeated divergences, lineage fusions, and range expansions around a network of non-stationary extrinsic barriers with variable results depending on the degree of intrinsic reproductive isolation that accumulates during this process. The evolutionary consequences of dynamic landscapes extend beyond Amazonia as "fission-fusion-fission" cycles modulate the diversification and spatial patterning of life on Earth in general.

Towards the next generation of species delimitation methods: an overview of machine learning applications

Species delimitation is the process of distinguishing between populations of the same species and distinct species of a particular group of organisms. Various methods exist for inferring species limits, whether based on morphological, molecular, or other types of data. In the case of methods based on DNA sequences, most of them are rooted in the coalescent theory. However, coalescence-based models have limitations, for instance regarding complex evolutionary scenarios and large datasets. In this context, machine learning (ML) can be considered as a promising analytical tool, and provides an effective way to explore dataset structures when species-level divergences are hypothesized. In this review, we examine the use of ML in species delimitation and provide an overview and critical appraisal of existing workflows. We also provide simple explanations on how the main types of ML approaches operate, which should help uninitiated researchers and students interested in the field. Our review suggests that while current ML methods designed to infer species limits are analytically powerful, they also present specific limitations and should not be considered as definitive alternatives to coalescent methods for species delimitation. Future ML enterprises to delimit species should consider the constraints related to the use of simulated data, as in other model-based methods relying on simulations. Conversely, the flexibility of ML algorithms offers a significant advantage by enabling the analysis of diverse data types (e.g., genetic and phenotypic) and handling large datasets effectively. We also propose best practices for the use of ML methods in species delimitation, offering insights into potential future applications. We expect that the proposed guidelines will be useful for enhancing the accessibility, effectiveness, and objectivity of ML in species delimitation.

Repeated Mitochondrial Capture With Limited Genomic Introgression in a Lizard Group

Mitochondrial introgression is common among animals and is often first identified through mitonuclear discordance-discrepancies between evolutionary relationships inferred from mitochondrial DNA (mtDNA) and nuclear DNA (nuDNA). Over recent decades, genomic data have also revealed extensive nuclear introgression in many animal groups, with implications for genetic and phenotypic diversity. However, the extent to which mtDNA introgression corresponds to nuDNA introgression varies. Here, we investigated historical and recent introgression in the Gehyra nana-occidentalis clade, a complex group of Australian geckos with documented cases of mitonuclear discordance suggestive of repeated mtDNA introgression. We hypothesised that mitonuclear discordance in this clade reflects mtDNA introgression with substantial nuclear introgression. Despite evidence of repeated mtDNA introgression, however, we found little to no evidence of historical nuDNA introgression using exon capture and genome-wide single nucleotide polymorphism (SNP) data. We also found no evidence of gene flow at modern contact zones and detected only a single early generation hybrid. Unsurprisingly, given these results, we found no evidence of transgressive, intermediate, or more variable morphological phenotypes in taxa with introgressed mtDNA. These findings suggest that hybridisation in this system has, at least in some cases, resulted in repeated mitochondrial introgression with little or no nuclear introgression. This pattern aligns with other studies showing limited nuDNA introgression in taxa with mitonuclear discordance, highlighting a potentially broader trend in animal radiations.

Incomplete lineage sorting and introgression among genera and species of Liliaceae tribe Tulipeae: insights from phylogenomics

BACKGROUND

Phylogenetic research in Tulipa (Liliaceae), a genus of significant economic and horticultural value, has relied on limited nuclear (mostly nuclear ribosomal internal transcribed spacer, nrITS) and plastid DNA sequences, resulting in low-resolution phylogenetic trees and uncertain intrageneric classifications. The genus, noted for its large genome, presents discordant relationships among Amana, Erythronium, and Tulipa, likely due to incomplete lineage sorting (ILS) and/or reticulate evolution. Thus, phylogenomic approaches are needed to clarify these relationships and the conflicting signals within the tribe Tulipeae.

RESULTS

We newly sequenced 50 transcriptomes of 46 species of tribe Tulipeae (including multiple accessions of all four genera) and one outgroup species of the sister tribe Lilieae (Notholirion campanulatum), and downloaded 15 previously published transcriptomes of tribe Tulipeae to supplement the sampling. One plastid dataset (74 plastid protein-coding genes, PCGs) and one nuclear dataset (2594 nuclear orthologous genes, OGs) were constructed, with the latter used for species tree inference based on maximum likelihood (ML) and multi-species coalescent (MSC) methods. To investigate causes of gene tree discordance, "site con/discordance factors" (sCF and sDF1/sDF2) were calculated first, after which phylogenetic nodes displaying high or imbalanced sDF1/2 were selected for phylogenetic network analyses and polytomy tests to determine whether ILS or reticulate evolution best explain incongruence. Key relationships not resolved by this technique, especially those among Amana, Erythronium, and Tulipa, were further investigated by applying D-statistics and QuIBL.

CONCLUSIONS

We failed to reconstruct a reliable and unambiguous evolutionary history among Amana, Erythronium, and Tulipa due to especially pervasive ILS and reticulate evolution, likely caused either by obscured minority phylogenetic signal or differing signals among genomic compartments. However, within Tulipa we confirmed the monophyly of most subgenera, with the exception of two species in the small subgenus Orithyia, of which Tulipa heterophylla was recovered as sister to the remainder of the genus, whereas T. sinkiangensis clustered within subgenus Tulipa. In contrast, most traditional sections of Tulipa were found to be non-monophyletic.

Deforestation-induced Hybridization in Philippine Frogs Creates a Distinct Phenotype With an Inviable Genotype

Hybridization plays a major role in the evolutionary history of many taxa and can generate confounding patterns affecting many downstream applications. In this study, we empirically demonstrate how hybridization obfuscates phylogenetic inference (via the artefactual branch effect), species boundaries, and taxonomy in an adaptive radiation of frogs. Philippine narrow-mouthed frogs of the genus Kaloula exhibit a wide range of phenotypic and ecological adaptations but their evolutionary history and taxonomy remain poorly understood. In particular, the Kaloula conjuncta complex contains numerous subspecies with unresolved taxonomic boundaries and unclear evolutionary relationships. Within this complex, Kaloula conjuncta stickeli, until now was considered a rare, enigmatic, and phenotypically distinct subspecies that had not been encountered since its original description nearly 80 years ago. Here, we show that K. c. stickeli shares alleles with K. conjuncta meridionalis and another species outside the conjuncta group, K. picta. Using target-capture sequencing and a robust analytical framework, we show that despite having a unique phenotype, K. c. stickeli is likely an inviable F1 hybrid between K. c. meridionalis and K. picta and thus, does not warrant taxonomic recognition. Our results show how industry-standard approaches in systematic inference and integrative taxonomy-morphological, phylogenomic, clustering, and distance-based methods-can generate misleading results for identifying and understanding affinities of hybrids. In contrast, we demonstrate how network multispecies coalescent and population genetic approaches are more effective at accurately inferring reticulated evolutionary history. We also propose a rare phenomenon of deforestation-induced hybridization, which could have important consequences in light of large-scale Southeast Asian forest destruction.

That's Not a Hybrid: How to Distinguish Patterns of Admixture and Isolation By Distance

Describing naturally occurring genetic variation is a fundamental goal of molecular phylogeography and population genetics. Popular methods for this task include STRUCTURE, a model-based algorithm that assigns individuals to genetic clusters, and principal component analysis (PCA), a parameter-free method. The ability of STRUCTURE to infer mixed ancestry makes it popular for documenting natural hybridisation, which is of considerable interest to evolutionary biologists, given that such systems provide a window into the speciation process. Yet, STRUCTURE can produce misleading results when its underlying assumptions are violated, like when genetic variation is distributed continuously across geographic space. To test the ability of STRUCTURE and PCA to accurately distinguish admixture from continuous variation, we use forward-time simulations to generate population genetic data under three demographic scenarios: two involving admixture and one with isolation by distance (IBD). STRUCTURE and PCA alone cannot distinguish admixture from IBD, but complementing these analyses with triangle plots, which visualise hybrid index against interclass heterozygosity, provides more accurate inference of demographic history, especially in cases of recent admixture. We demonstrate that triangle plots are robust to missing data, while STRUCTURE and PCA are not, and show that setting a low allele frequency difference threshold for ancestry-informative marker (AIM) identification can accurately characterise the relationship between hybrid index and interclass heterozygosity across demographic histories of admixture and range expansion. While STRUCTURE and PCA provide useful summaries of genetic variation, results should be paired with triangle plots before admixture is inferred.

Contact zones reveal restricted introgression despite frequent hybridization across a recent lizard radiation

Introgression-the exchange of genetic material through hybridization-is now recognized as common among animal species. The extent of introgression, however, can vary considerably even when it occurs: for example, introgression can be geographically restricted or so pervasive that populations merge. Such variation highlights the importance of understanding the factors mediating introgression. Here we used genome-wide SNP data to assess hybridization and introgression at 32 contact zones, comprising 21 phylogenetic independent contrasts across a recent lizard radiation (Heteronotia). We then tested the relationship between the extent of introgression (average admixture at contact zones) and genomic divergence across independent contrasts. Early-generation hybrids were detected at contact zones spanning the range of genomic divergence included here. Despite this, we found that introgression is remarkably rare and, when observed, geographically restricted. Only the two most genomically similar population pairs showed introgression beyond 5 km of the contact zone. Introgression dropped precipitously at only modest levels of genomic divergence, beyond which it was absent or extremely low. Our results contrast with the growing number of studies indicating that introgression is prevalent among animals, suggesting that animal groups will vary considerably in their propensity for introgression.

Fluctuating reproductive isolation and stable ancestry structure in a fine-scaled mosaic of hybridizing Mimulus monkeyflowers

Hybridization among taxa impacts a variety of evolutionary processes from adaptation to extinction. We seek to understand both patterns of hybridization across taxa and the evolutionary and ecological forces driving those patterns. To this end, we use whole-genome low-coverage sequencing of 458 wild-grown and 1565 offspring individuals to characterize the structure, stability, and mating dynamics of admixed populations of Mimulus guttatus and Mimulus nasutus across a decade of sampling. In three streams, admixed genomes are common and a M. nasutus organellar haplotype is fixed in M. guttatus, but new hybridization events are rare. Admixture is strongly unidirectional, but each stream has a unique distribution of ancestry proportions. In one stream, three distinct cohorts of admixed ancestry are spatially structured at ~20-50m resolution and stable across years. Mating system provides almost complete isolation of M. nasutus from both M. guttatus and admixed cohorts, and is a partial barrier between admixed and M. guttatus cohorts. Isolation due to phenology is near-complete between M. guttatus and M. nasutus. Phenological isolation is a strong barrier in some years between admixed and M. guttatus cohorts, but a much weaker barrier in other years, providing a potential bridge for gene flow. These fluctuations are associated with differences in water availability across years, supporting a role for climate in mediating the strength of reproductive isolation. Together, mating system and phenology accurately predict fluctuations in assortative mating across years, which we estimate directly using paired maternal and offspring genotypes. Climate-driven fluctuations in reproductive isolation may promote the longer-term stability of a complex mosaic of hybrid ancestry, preventing either complete isolation or complete collapse of species barriers.

Evolution, range formation and a revised taxonomy of the disjunctly distributed European members of Astragalus sect. Caprini, an intricate group including highly endangered species of dry grasslands

The Eurasian steppes are among the largest and most threatened biomes on Earth. During cold periods of the Pleistocene, the zonal Eurasian steppes had a much larger extent as compared to interglacial periods, and repeatedly expanded into large areas of present-day forested temperate Europe. Conversely, during warm periods, forest expansion recurrently forced Eurasian steppe biota into disjunct and small warm-stage refugia, i.e. today's extrazonal steppes. The rare, threatened and disjunctly distributed northwestern African and European members of Astragalus sect. Caprini constitute an ideal model for gaining insights into the evolutionary dynamics of typical steppe biota. Here, we reconstructed the spatiotemporal diversification of northwestern African and European members of Astragalus sect. Caprini based on a combination of RADseq data, single gene markers (internal transcribed spacer, plastid ycf1), genome size measurements and multivariate morphometrics. We outline an evolutionary scenario in which the group originated in the Irano-Turanian region and started to diversify shortly after the Mid-Pleistocene-Transition (ca. 0.5 to 0.7 Ma). While lineages occurring in (sub-)mediterranean mountain ranges diverged early, lineages occurring in northern lowland steppes are much younger (ca. 0.2 to 0.3 Ma), emphasizing the importance of southern European mountain ranges as long-term refugia. Recurrent colonization of the western Mediterranean region by eastern Mediterranean lineages and secondary contacts of currently spatially isolated lineages have significantly (co-)shaped the genetic structure within the group; we assume that these events may be a consequence of cold-stage range expansions. Based on combined genetic and morphometric data, we suggest treating the ten lineages introduced in this study as independent species, contrasting previous taxonomic treatments.

Genomic data support reticulate evolution in whiptail lizards from the Brazilian Caatinga

Species relationships have traditionally been represented by phylogenetic trees, but not all evolutionary histories fit into bifurcating divergence models. Introgressive hybridization challenges this assumption by sometimes [or maybe often] leading to mitochondrial introgression, wherein one species' mitochondrial genome is entirely replaced by another's (mitochondrial capture). Such processes result in mitonuclear discrepancies, complicating species delimitation and phylogenetic inference. In our study, we used ultraconserved elements (UCE) and mitogenomic data to investigate the evolutionary history of the Ameivula ocellifera complex, a group of South American whiptail lizards widely distributed in semiarid environments of the Caatinga Domain in Brazil. We examine mitonuclear discordances, assessing reticulate evolution, evaluating species limits, and testing for adaptive mitochondrial capture that could explain higher introgression in the mitochondrial genome compared to nuclear DNA. Our findings support the occurrence of an ancient reticulation event during the diversification of these lizards, driven by introgressive hybridization, leading to mitochondrial capture, and explaining mitonuclear discrepancies. Overall, we did not find clear evidence of positive selection across mitochondrial protein-coding genes suggesting adaptive mitochondrial capture of individuals with introgressed mtDNA. Thus, the genetic diversification and mitogenome evolution could be neutral, with selection against hybridization in the autosomal loci only, or even mediated by mitonuclear incompatibilities. Analyses of mtDNA genomes alongside network and species delimitation methods were crucial for identifying and validating individuals with introgressed mtDNA as a distinct species, demonstrating the potential of genome sampling, and using innovative analytical techniques for elucidating speciation processes in the presence of introgressive hybridization.

Phylogenomic analyses re-evaluate the backbone of Corylus and unravel extensive signals of reticulate evolution

Phylogenomic analyses have shown that reticulate evolution greatly affects the accuracy of phylogenetic inferences, and thus may challenge the authority of bifurcating phylogenetic trees. In this study, we re-evaluated the phylogenetic backbone of the genus Corylus based on complete taxon sampling and genomic data. We assembled 581 single-copy nuclear genes and whole plastomes from 64 genome resequencing datasets to elucidate the reticulate relationships within Corylus. Nuclear coalescent and concatenation phylogenies revealed identical and fully supported backbone, clarifying the sisterhood between sect. Acanthochlamys and sect. Siphonochlamys as well as the phylogenetic position of C. fargesii and C. wangii, which have yet been addressed in previous phylogenetic studies. However, the monophyly of C. jacquemontii and C. kwechowensis and the distinction between C. ferox and C. ferox var. thibetica were not supported. Gene trees-species tree conflicts and cytonuclear discordance were identified, with multiple evidences supporting that hybridization/introgression, coupled with incomplete lineage sorting, have led to substantial phylogenetic incongruence in Corylus. Moreover, typical geographical clustering rather than strict monophyletic pattern in plastome phylogeny implies chloroplast capture within Corylus and offers evidence of cytoplasmic introgression. Overall, this study provides a robust phylogenomic backbone for Corylus and unravels that reticulate evolution can greatly shape taxonomic revision.

A straightforward workflow to explore species diversity using the Patagonian lizards of the Diplolaemus genus (Iguania: Leiosauridae) as a study case, with the description of a new species

Disputes over species descriptions, stemming from conceptual disparities and arbitrary species boundaries, are among the primary challenges of modern taxonomy. In this study, we introduce a straightforward workflow, grounded in evolutionary theory, designed to tackle these challenges. We exemplified this approach using Patagonian lizards from the Diplolaemus clade. This workflow involves assigning specimens to putative evolutionary lineages, conducting primary species delimitations, constructing a species tree, comparing lineages for evolutionary independence, and using post-hoc analyses to separate well-supported from ambiguous lineages. This approach aims to establish a reliable foundation for exploring the taxonomic and evolutionary diversity of challenging groups. Applying this workflow to the Diplolaemus clade, we used various analytical methods on genetic (mitochondrial and nuclear markers) and phenotypic data (meristic, linear, and geometric morphometrics). We identified ten lineages with varying degrees of evolutionary independence in a clade where only four species had been described. Among the newly identified lineages, two exhibited low support for evolutionary independence, three showed strong support but had non-conclusive information, and one was recognized and described as a new species. In summary, our hierarchical workflow not only facilitated comprehensive comparisons but also enabled us to draw robust conclusions.

Dollo's law of irreversibility in the post-genomic age

Dollo's law of irreversibility argues that evolution cannot revert to earlier states. It has remained controversial ever since its inception in the 19th century. Enabled by advances in phylogenomics and functional genomics, recent studies show that there are very likely some cases of 'breaking Dollo's law'. As post-genomic research grows from showing patterns to revealing processes, new emphasis is needed on the molecular mechanisms by which Dollo's law might be broken. Shifting the argument from 'if it happened' to 'how it happened' will provide richer understanding of organismal and evolutionary biology. Motivated by case studies and novel avenues to test trait loss and regain, we outline a set of alternative hypotheses to be evaluated and what the outcomes tell us about evolution.

Fine-Scale Variation in Soil Properties Promotes Local Taxonomic Diversity of Hybridizing Oak Species (Quercus spp.)

Although many tree species frequently hybridize and backcross, management decisions in forestry and nature conservation are usually concentrated on pure species. Therefore, understanding which environmental factors drive the distribution and admixture of tree species on a local stand scale is of great interest to support decision-making in the establishment and management of resilient forests. Here, we extensively sampled a mixed stand of hybridizing white oaks (Quercus petraea and Q. pubescens) near Lake Neuchâtel (Switzerland), where limestone and glacier moraine geologies coexist in proximity, to test whether micro-environmental conditions can predict taxonomic distribution and genetic admixture. We collected DNA from bud tissue, individual soil samples, and extracted high-resolution topographic data for 385 oak trees. We used 50 species-discriminatory single nucleotide polymorphism (SNP) markers to determine the taxonomic composition and admixture levels of individual trees and tested their association with micro-environmental conditions. We show that the trees' taxonomic distribution can be explained mainly by geographic position, soil pH, and potential rooting depth, a proxy for soil water availability. We found that admixed individuals tend to grow in habitats that are characteristic of the more drought-tolerant species Q. pubescens rather than in intermediate habitats. Using in situ measurements, we are the first to show that fine-scale variation in soil properties related to pH and water availability potentially drives the distribution of hybridizing tree species in a mixed stand. Microenvironmental variation therefore promotes local taxonomic diversity, facilitates admixture and adaptive introgression, and contributes to the resilience of forests under environmental change. Consequently, species such as white oaks should be managed and protected as a species complex rather than as pure species.

Phylogenomics reveal species limits and inter-relationships in the narrow-range endemic lycian salamanders

Salamanders of the genus Lyciasalamandra are represented by as many as 20 narrow-range endemic taxa inhabiting the Mediterranean coast of Turkey and a handful of Aegean Islands. Despite recent molecular phylogenetic studies, the genus is rife with uncertainty about the number of contained species and their phylogenetic relationships, both of which can interfere with needed conservation actions. To test species limits and infer interrelationships we generated as many as 113,176 RAD loci containing 229,427 single nucleotide polymorphisms (SNPs), for 110 specimens of Lyciasalamandra representing 19 of the 20 described taxa. Through a conservative species delimitation approach, we found support for eight species in the genus which broadly agree with currently described species-level diversity. We then use multiple coalescent-based species tree methods to resolve relationships in this relatively old, synchronous species radiation. We recommend synonymization of the largely over-split subspecific taxa, and the elevation of L. luschani finikensis to full species status as L. finikensis. Our hope is that this revised taxonomic framework provides a stable foundation for conservation management in these fragile, microendemic taxa.

Genomic Introgression Between Critically Endangered and Stable Species of Darwin's Tree Finches on the Galapagos Islands

Natural hybridisation among rare or endangered species and stable congenerics is increasingly topical for the conservation of species-level diversity under anthropogenic impacts. Evidence for beneficial genes being introgressed into or selected for in hybrids raises concurrent questions about its evolutionary significance. In Darwin's tree finches on the island of Floreana (Galapagos Islands, Ecuador), the Critically Endangered medium tree finch (Camarhynchus pauper) undergoes introgression with the stable small tree finch (Camarhynchus parvulus), and hybrids regularly backcross with C. parvulus. Earlier studies in 2005-2013 documented an increase in the frequency of Camarhynchus hybridisation on Floreana using field-based and microsatellite data. With single nucleotide polymorphism (SNP) data from the same Floreana tree finches sampled in 2005 and 2013 (n = 95), we examine genome-wide divergence across parental and hybrid birds and evidence for selection in hybrids. We found that just 18% of previously assigned hybrid birds based on microsatellites could be assigned to hybrids using SNPs. Over half of the previously assigned hybrids (63%) were reassigned to C. parvulus, though parental species showed concordance with prior assignments. Of 4869 private alleles found in hybrid birds, 348 were at a high frequency (≥ 0.30) that exceeded their parental species of origin 89%-96% of the time. For private alleles detected in both years (N = 536) between 11%-76% of alleles underwent a frequency increase and 13%-61% a frequency decrease between 2005 and 2013, which was sensitive to sampling effort. We identified 28 private alleles that were candidates under selection via local PCA and outlier tests. Alleles were annotated to genes associated with inflammation, immunity, brain function and development. We provide evidence that introgression among a critically endangered and stable species of Darwin's tree finch across years may aid in the retention of adaptive alleles and genetic diversity in birds threatened with extinction.

The Role of Hybridization in Species Formation and Persistence

Hybridization, or interbreeding between different taxa, was traditionally considered to be rare and to have a largely detrimental impact on biodiversity, sometimes leading to the breakdown of reproductive isolation and even to the reversal of speciation. However, modern genomic and analytical methods have shown that hybridization is common in some of the most diverse clades across the tree of life, sometimes leading to rapid increase of phenotypic variability, to introgression of adaptive alleles, to the formation of hybrid species, and even to entire species radiations. In this review, we identify consensus among diverse research programs to show how the field has progressed. Hybridization is a multifaceted evolutionary process that can strongly influence species formation and facilitate adaptation and persistence of species in a rapidly changing world. Progress on testing this hypothesis will require cooperation among different subdisciplines.

Tangled banks, braided rivers, and complex hierarchies: beyond microevolution and macroevolution

Ever since the Modern Synthesis, a debate about the relationship between microevolution and macroevolution has persisted-specifically, whether they are equivalent, distinct, or explain one another. How one answers these questions has become shorthand for a much broader set of theoretical debates in evolutionary biology. Here, we examine microevolution and macroevolution in the context of the vast proliferation of data, knowledge, and theory since the advent of the Modern Synthesis. We suggest that traditional views on microevolution and macroevolution are too binary and reductive given current empirical and theoretical advances in biology. For example, patterns and processes are interconnected at various temporal and spatial scales and among hierarchical entities, rather than defining micro- or macro-domains. Further, biological entities have variably fuzzy boundaries, resulting in complex evolutionary processes that influence macroevolution occuring at both micro- and macro-levels. In addition, conceptual advances in phylodynamics have yet to be fully integrated with contemporary macroevolutionary approaches. Finally, holding microevolution and macroevolution as distinct domains thwarts synthesis and collaboration on important research questions. Instead, we propose that the focal entities and processes considered by evolutionary studies be contextualized within the complexity of the multidimensional, multimodal, multilevel phylogenetic system.

The interplay of local adaptation and gene flow may lead to the formation of supergenes

Supergenes are genetic architectures resulting in the segregation of alternative combinations of alleles underlying complex phenotypes. The co-segregation of alleles at linked loci is often facilitated by polymorphic chromosomal rearrangements suppressing recombination locally. Supergenes are involved in many complex polymorphisms, including sexual, colour or behavioural polymorphisms in numerous plants, fungi, mammals, fish, and insects. Despite a long history of empirical and theoretical research, the formation of supergenes remains poorly understood. Here, using a two-island population genetic model, we explore how gene flow and the evolution of overdominant chromosomal inversions may jointly lead to the formation of supergenes. We show that the evolution of inversions in differentiated populations, both under disruptive selection, leads to an increase in frequency of poorly adapted, immigrant haplotypes. Indeed, rare allelic combinations, such as immigrant haplotypes, are more frequently reshuffled by recombination than common allelic combinations, and therefore benefit from the recombination suppression generated by inversions. When an inversion capturing a locally adapted haplotype spreads but is associated with a fitness cost hampering its fixation (e.g. a recessive mutation load), the maintenance of a non-inverted haplotype in the population is enhanced; under certain conditions, the immigrant haplotype persists alongside the inverted local haplotype, while the standard local haplotype disappears. This establishes a stable, local polymorphism with two non-recombining haplotypes encoding alternative adaptive strategies, that is, a supergene. These results bring new light to the importance of local adaptation, overdominance, and gene flow in the formation of supergenes and inversion polymorphisms in general.

Prezygotic barriers effectively limit hybridization in a rapid evolutionary radiation

Hybridization is increasingly recognized as an important evolutionary process across the tree of life. In many clades, phylogenomic approaches have permitted unparalleled insight into the extent and frequency of hybridization. However, we continue to lack a deep understanding of the factors that limit and shape patterns of hybridization, especially in evolutionary radiations. In this study, we characterized patterns of introgression across Costus (Costaceae), a young evolutionary radiation of tropical understory plants that maintain widespread interfertility despite exhibiting strong prezygotic reproductive isolation. We analyzed a phylogenomic dataset of 756 genes from 54 Costus species using multiple complementary approaches - D-statistics, gene-tree-based tests, and phylogenetic network analyses - to detect and characterize introgression events throughout the evolutionary history of the radiation. Our results identified a moderate number of introgression events, including a particularly ancient, well-supported event spanning one of the deepest divergences in the clade. Most introgression events occurred between taxa or ancestral lineages that shared the same pollination syndrome (bee-pollinated or hummingbird-pollinated). These findings suggest that prezygotic barriers, including pollinator specialization, have been key to the balance between introgression and reproductive isolation in Costus.

Reticulate evolution: Detection and utility in the phylogenomics era

Phylogenomics has enriched our understanding that the Tree of Life can have network-like or reticulate structures among some taxa and genes. Two non-vertical modes of evolution - hybridization/introgression and horizontal gene transfer - deviate from a strictly bifurcating tree model, causing non-treelike patterns. However, these reticulate processes can produce similar patterns to incomplete lineage sorting or recombination, potentially leading to ambiguity. Here, we present a brief overview of a phylogenomic workflow for inferring organismal histories and compare methods for distinguishing modes of reticulate evolution. We discuss how the timing of coalescent events can help disentangle introgression from incomplete lineage sorting and how horizontal gene transfer events can help determine the relative timing of speciation events. In doing so, we identify pitfalls of certain methods and discuss how to extend their utility across the Tree of Life. Workflows, methods, and future directions discussed herein underscore the need to embrace reticulate evolutionary patterns for understanding the timing and rates of evolutionary events, providing a clearer view of life's history.

Unravelling the role of mitochondrial DNA in hybrid incompatibility within species of the Anopheles gambiae complex

Isolation mechanisms between mosquito species of the Anopheles gambiae complex, which includes major malaria vectors, remain poorly understood. In some cases, pre-zygotic barriers have been shown to limit gene flow between species of the complex, leading to a low level of hybridisation in nature. Post-zygotic mechanisms manifest with F1 hybrid males fully sterile and F1 hybrid females with reduced fertility. Genetic approaches combined with DNA sequencing techniques have highlighted the involvement of genomic regions in hybrid incompatibility with a predominant role of the X chromosome. In addition, differences in the phenotype of F1 hybrid males have been identified depending on the directionality of the parental cross used to generate them. All these studies have focused on the interaction of nuclear DNA elements in hybrid individuals. Given the role that mitochondrial DNA plays in genetic incompatibilities within other organisms and its unique inheritance pattern, commonly maternal, we conducted a genetic study that relied on the introgression of mitochondrial DNA between Anopheles gambiae and Anopheles arabiensis. The findings indicate that the mitochondrial switch does not appear to restore the fertility of F1 hybrid males, suggesting that mitochondrial DNA may not play a role in hybrid incompatibilities in these Anopheles species.

Cas9/guide RNA-based gene-drive dynamics following introduction and introgression into diverse anopheline mosquito genetic backgrounds

BACKGROUND

Novel technologies are needed to combat anopheline vectors of malaria parasites as the reductions in worldwide disease incidence has stalled in recent years. Gene drive-based approaches utilizing Cas9/guide RNA (gRNA) systems are being developed to suppress anopheline populations or modify them by increasing their refractoriness to the parasites. These systems rely on the successful cleavage of a chromosomal DNA target site followed by homology-directed repair (HDR) in germline cells to bias inheritance of the drive system. An optimal drive system should be highly efficient for HDR-mediated gene conversion with minimal error rates. A gene-drive system, AgNosCd-1, with these attributes has been developed in the Anopheles gambiae G3 strain and serves as a framework for further development of population modification strains. To validate AgNosCd-1 as a versatile platform, it must perform well in a variety of genetic backgrounds.

RESULTS

We introduced or introgressed AgNosCd-1 into different genetic backgrounds, three in geographically-diverse Anopheles gambiae strains, and one each in an An. coluzzii and An. arabiensis strain. The overall drive inheritance, determined by presence of a dominant marker gene in the F2 hybrids, far exceeded Mendelian inheritance ratios in all genetic backgrounds that produced viable progeny. Haldane's rule was confirmed for AgNosCd-1 introgression into the An. arabiensis Dongola strain and sterility of the F1 hybrid males prevented production of F2 hybrid offspring. Back-crosses of F1 hybrid females were not performed to keep the experimental design consistent across all the genetic backgrounds and to avoid maternally-generated mutant alleles that might confound the drive dynamics. DNA sequencing of the target site in F1 and F2 mosquitoes with exceptional phenotypes revealed drive system-generated mutations resulting from non-homologous end joining events (NHEJ), which formed at rates similar to AgNosCd-1 in the G3 genetic background and were generated via the same maternal-effect mechanism.

CONCLUSIONS

These findings support the conclusion that the AgNosCd-1 drive system is robust and has high drive inheritance and gene conversion efficiency accompanied by low NHEJ mutation rates in diverse An. gambiae s.l. laboratory strains.

Comparative Phylogeography of Two Specialist Rodents in Forest Fragments in Kenya

The fragmented forests of the Kenya highlands, known for their exceptional species richness and endemism, are among the world's most important biodiversity hotspots. However, detailed studies on the fauna of these ecosystems-especially specialist species that depend on moist forests, which are particularly threatened by habitat fragmentation-are still limited. In this study, we used mitochondrial genes (cytochrome b and the displacement loop) and a nuclear marker (retinol-binding protein 3) to investigate genetic and morphological diversity, phylogenetic associations, historical divergence, population dynamics, and phylogeographic patterns in two rodent species-the soft-furred mouse (Praomys jacksoni) and the African wood mouse (Hylomyscus endorobae)-across Kenya's forest landscapes. We found a complex genetic structure, with P. jacksoni exhibiting greater genetic diversity than H. endorobae. The Mt. Kenya P. jacksoni populations are significantly genetically different from those in southwestern forests (Mau Forest, Kakamega Forest, and Loita Hills). In contrast, H. endorobae presented no observable biogeographic structuring across its range. The genetic diversity and geographic structuring patterns highlighted selectively strong effects of forest fragmentation and differing species' ecological and evolutionary responses to these landscape changes. Our findings further underscore the need for expanded sampling across Kenya's highland forests to better understand species' changing diversity and distribution patterns in response to the impacts of human-mediated habitat changes. These insights are critical for informing conservation strategies to preserve biodiversity better in this globally important region.

LINgroups as a Robust Principled Approach to Compare and Integrate Multiple Bacterial Taxonomies

As a central organizing principle of biology, bacteria and archaea are classified into a hierarchical structure across taxonomic ranks from kingdom to subspecies. Traditionally, this organization was based on observable characteristics of form and chemistry but recently, bacterial taxonomy has been robustly quantified using comparisons of sequenced genomes, as exemplified in the Genome Taxonomy Database (GTDB). Such genome-based taxonomies resolve genomes down to genera and species and are useful in many contexts yet lack the flexibility and resolution of a fine-grained approach. The Life Identification Number (LIN) approach is a common, quantitative framework to tie existing (and future) bacterial taxonomies together, increase the resolution of genome-based discrimination of taxa, and extend taxonomic identification below the species level in a principled way. Utilizing LINgroup as an organizational concept helps resolve some of the confusion and unforeseen negative effects resulting from nomenclature changes of microorganisms that are closely related by overall genomic similarity (often due to genome-based reclassification). Our experimental results demonstrate the value of LINs and LINgroups in mapping between taxonomies, translating between different nomenclatures, and integrating them into a single taxonomic framework. They also reveal the robustness of LIN assignment to hyper-parameter changes when considering within-species taxonomic groups.

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.

Whole Genomes Reveal Evolutionary Relationships and Mechanisms Underlying Gene-Tree Discordance in Neodiprion Sawflies

Rapidly evolving taxa are excellent models for understanding the mechanisms that give rise to biodiversity. However, developing an accurate historical framework for comparative analysis of such lineages remains a challenge due to ubiquitous incomplete lineage sorting (ILS) and introgression. Here, we use a whole-genome alignment, multiple locus-sampling strategies, and summary-tree and single nucleotide polymorphism-based species-tree methods to infer a species tree for eastern North American Neodiprion species, a clade of pine-feeding sawflies (Order: Hymenopteran; Family: Diprionidae). We recovered a well-supported species tree that-except for three uncertain relationships-was robust to different strategies for analyzing whole-genome data. Nevertheless, underlying gene-tree discordance was high. To understand this genealogical variation, we used multiple linear regression to model site concordance factors estimated in 50-kb windows as a function of several genomic predictor variables. We found that site concordance factors tended to be higher in regions of the genome with more parsimony-informative sites, fewer singletons, less missing data, lower GC content, more genes, lower recombination rates, and lower D-statistics (less introgression). Together, these results suggest that ILS, introgression, and genotyping error all shape the genomic landscape of gene-tree discordance in Neodiprion. More generally, our findings demonstrate how combining phylogenomic analysis with knowledge of local genomic features can reveal mechanisms that produce topological heterogeneity across genomes.

Common misconceptions of speciation

Speciation is a complex process that can unfold in many different ways. Speciation researchers sometimes simplify core principles in their writing in a way that implies misconceptions about the speciation process. While we think that these misconceptions are usually inadvertently implied (and not actively believed) by the researchers, they nonetheless risk warping how external readers understand speciation. Here we highlight six misconceptions of speciation that are especially widespread. First, species are implied to be clearly and consistently defined entities in nature, whereas in reality species boundaries are often fuzzy and semipermeable. Second, speciation is often implied to be 'good', which is two-fold problematic because it implies both that evolution has a goal and that speciation universally increases the chances of lineage persistence. Third, species-poor clades with species-rich sister clades are considered 'primitive' or 'basal', falsely implying a ladder of progress. Fourth, the evolution of species is assumed to be strictly tree-like, but genomic findings show widespread hybridization more consistent with network-like evolution. Fifth, a lack of association between a trait and elevated speciation rates in macroevolutionary studies is often interpreted as evidence against its relevance in speciation-even if microevolutionary case studies show that it is relevant. Sixth, obvious trait differences between species are sometimes too readily assumed to be (i) barriers to reproduction, (ii) a stepping-stone to inevitable speciation, or (iii) reflective of the species' whole divergence history. In conclusion, we call for caution, particularly when communicating science, because miscommunication of these ideas provides fertile ground for misconceptions to spread.

Inferring phylogenetic networks from multifurcating trees via cherry picking and machine learning

The Hybridization problem asks to reconcile a set of conflicting phylogenetic trees into a single phylogenetic network with the smallest possible number of reticulation nodes. This problem is computationally hard and previous solutions are limited to small and/or severely restricted data sets, for example, a set of binary trees with the same taxon set or only two non-binary trees with non-equal taxon sets. Building on our previous work on binary trees, we present FHyNCH, the first algorithmic framework to heuristically solve the Hybridization problem for large sets of multifurcating trees whose sets of taxa may differ. Our heuristics combine the cherry-picking technique, recently proposed to solve the same problem for binary trees, with two carefully designed machine-learning models. We demonstrate that our methods are practical and produce qualitatively good solutions through experiments on both synthetic and real data sets.

Museum Skins Enable Identification of Introgression Associated with Cytonuclear Discordance

Increased sampling of genomes and populations across closely related species has revealed that levels of genetic exchange during and after speciation are higher than previously thought. One obvious manifestation of such exchange is strong cytonuclear discordance, where the divergence in mitochondrial DNA (mtDNA) differs from that for nuclear genes more (or less) than expected from differences between mtDNA and nuclear DNA (nDNA) in population size and mutation rate. Given genome-scale data sets and coalescent modeling, we can now confidently identify cases of strong discordance and test specifically for historical or recent introgression as the cause. Using population sampling, combining exon capture data from historical museum specimens and recently collected tissues we showcase how genomic tools can resolve complex evolutionary histories in the brachyotis group of rock-wallabies (Petrogale). In particular, applying population and phylogenomic approaches we can assess the role of demographic processes in driving complex evolutionary patterns and assess a role of ancient introgression and hybridization. We find that described species are well supported as monophyletic taxa for nDNA genes, but not for mtDNA, with cytonuclear discordance involving at least 4 operational taxonomic units across 4 species which diverged 183-278 kya. ABC modeling of nDNA gene trees supports introgression during or after speciation for some taxon pairs with cytonuclear discordance. Given substantial differences in body size between the species involved, this evidence for gene flow is surprising. Heterogenous patterns of introgression were identified but do not appear to be associated with chromosome differences between species. These and previous results suggest that dynamic past climates across the monsoonal tropics could have promoted reticulation among related species.

Incomplete lineage sorting and hybridization underlie tree discordance in Petunia and related genera (Petunieae, Solanaceae)

Despite the overarching history of species divergence, phylogenetic studies often reveal distinct topologies across regions of the genome. The sources of these gene tree discordances are variable, but incomplete lineage sorting (ILS) and hybridization are among those with the most biological importance. Petunia serves as a classic system for studying hybridization in the wild. While field studies suggest that hybridization is frequent, the extent of reticulation within Petunia and its closely related genera has never been examined from a phylogenetic perspective. In this study, we used transcriptomic data from 11 Petunia, 16 Calibrachoa, and 10 Fabiana species to illuminate the relationships between these species and investigate whether hybridization played a significant role in the diversification of the clade. We inferred that gene tree discordance within genera is linked to hybridization events along with high levels of ILS due to their rapid diversification. Moreover, network analyses estimated deeper hybridization events between Petunia and Calibrachoa, genera that have different chromosome numbers. Although these genera cannot hybridize at the present time, ancestral hybridization could have played a role in their parallel radiations, as they share the same habitat and life history.

Phylogenomic analyses revealed widely occurring hybridization events across Elsholtzieae (Lamiaceae)

Obtaining a robust phylogeny proves challenging due to the intricate evolutionary history of species, where processes such as hybridization and incomplete lineage sorting can introduce conflicting signals, thereby complicating phylogenetic inference. In this study, we conducted comprehensive sampling of Elsholtzieae, with a particular focus on its largest genus, Elsholtzia. We utilized 503 nuclear loci and complete plastome sequences obtained from 99 whole-genome sequencing datasets to elucidate the interspecific relationships within the Elsholtzieae. Additionally, we explored various sources of conflicts between gene trees and species trees. Fully supported backbone phylogenies were recovered, and the monophyly of Elsholtzia and Keiskea was not supported. Significant gene tree heterogeneity was observed at numerous nodes, particularly regarding the placement of Vuhuangia and the E. densa clade. Further investigations into potential causes of this discordance revealed that incomplete lineage sorting (ILS), coupled with hybridization events, has given rise to substantial gene tree discordance. Several species, represented by multiple samples, exhibited a closer association with geographical distribution rather than following a strictly monophyletic pattern in plastid trees, suggesting chloroplast capture within Elsholtzieae and providing evidence of hybridization. In conclusion, this study provides phylogenomic insights to untangle taxonomic problems in the tribe Elsholtzieae, especially the genus Elsholtzia.

Selection leads to false inferences of introgression using popular methods

Detecting introgression between closely related populations or species is a fundamental objective in evolutionary biology. Existing methods for detecting migration and inferring migration rates from population genetic data often assume a neutral model of evolution. Growing evidence of the pervasive impact of selection on large portions of the genome across diverse taxa suggests that this assumption is unrealistic in most empirical systems. Further, ignoring selection has previously been shown to negatively impact demographic inferences (e.g. of population size histories). However, the impacts of biologically realistic selection on inferences of migration remain poorly explored. Here, we simulate data under models of background selection, selective sweeps, balancing selection, and adaptive introgression. We show that ignoring selection sometimes leads to false inferences of migration in popularly used methods that rely on the site frequency spectrum. Specifically, balancing selection and some models of background selection result in the rejection of isolation-only models in favor of isolation-with-migration models and lead to elevated estimates of migration rates. BPP, a method that analyzes sequence data directly, showed false positives for all conditions at recent divergence times, but balancing selection also led to false positives at medium-divergence times. Our results suggest that such methods may be unreliable in some empirical systems, such that new methods that are robust to selection need to be developed.

The role of deep hybridization in fern speciation: Examples from the Thelypteridaceae

PREMISE

Hybridization is recognized as an important mechanism in fern speciation, with many allopolyploids known among congeners, as well as evidence of ancient genome duplications. Several contemporary instances of deep (intergeneric) hybridization have been noted, invariably resulting in sterile progeny. We chose the christelloid lineage of the family Thelypteridaceae, recognized for its high frequency of both intra- and intergeneric hybrids, to investigate recent hybrid speciation between deeply diverged lineages. We also seek to understand the ecological and evolutionary outcomes of resulting lineages across the landscape.

METHODS

By phasing captured reads within a phylogenomic data set of GoFlag 408 nuclear loci using HybPhaser, we investigated candidate hybrids to identify parental lineages. We estimated divergence ages by inferring a dated phylogeny using fossil calibrations with treePL. We investigated ecological niche conservatism between one confirmed intergeneric allotetraploid and its diploid progenitors using the centroid, overlap, unfilling, and expansion (COUE) framework.

RESULTS

We provide evidence for at least six instances of intergeneric hybrid speciation within the christelloid clade and estimate up to 45 million years of divergence between progenitors. The niche quantification analysis showed moderate niche overlap between an allopolyploid species and its progenitors, with significant divergence from the niche of one progenitor and conservatism to the other.

CONCLUSIONS

The examples provided here highlight the overlooked role that allopolyploidization following intergeneric hybridization may play in fern diversification and range and niche expansions. Applying this approach to other fern taxa may reveal a similar pattern of deep hybridization resulting in highly successful novel lineages.

Complex Polyploids: Origins, Genomic Composition, and Role of Introgressed Alleles

Introgression allows polyploid species to acquire new genomic content from diploid progenitors or from other unrelated diploid or polyploid lineages, contributing to genetic diversity and facilitating adaptive allele discovery. In some cases, high levels of introgression elicit the replacement of large numbers of alleles inherited from the polyploid's ancestral species, profoundly reshaping the polyploid's genomic composition. In such complex polyploids, it is often difficult to determine which taxa were the progenitor species and which taxa provided additional introgressive blocks through subsequent hybridization. Here, we use population-level genomic data to reconstruct the phylogenetic history of Betula pubescens (downy birch), a tetraploid species often assumed to be of allopolyploid origin and which is known to hybridize with at least four other birch species. This was achieved by modeling polyploidization and introgression events under the multispecies coalescent and then using an approximate Bayesian computation rejection algorithm to evaluate and compare competing polyploidization models. We provide evidence that B. pubescens is the outcome of an autoploid genome doubling event in the common ancestor of B. pendula and its extant sister species, B. platyphylla, that took place approximately 178,000-188,000 generations ago. Extensive hybridization with B. pendula, B. nana, and B. humilis followed in the aftermath of autopolyploidization, with the relative contribution of each of these species to the B. pubescens genome varying markedly across the species' range. Functional analysis of B. pubescens loci containing alleles introgressed from B. nana identified multiple genes involved in climate adaptation, while loci containing alleles derived from B. humilis revealed several genes involved in the regulation of meiotic stability and pollen viability in plant species.

A roadmap of phylogenomic methods for studying polyploid plant genera

Phylogenetic inference of polyploid species is the first step towards understanding their patterns of diversification. In this paper, we review the challenges and limitations of inferring species relationships of polyploid plants using traditional phylogenetic sequencing approaches, as well as the mischaracterization of the species tree from single or multiple gene trees. We provide a roadmap to infer interspecific relationships among polyploid lineages by comparing and evaluating the application of current phylogenetic, phylogenomic, transcriptomic, and whole-genome approaches using different sequencing platforms. For polyploid species tree reconstruction, we assess the following criteria: (1) the amount of prior information or tools required to capture the genetic region(s) of interest; (2) the probability of recovering homeologs for polyploid species; and (3) the time efficiency of downstream data analysis. Moreover, we discuss bioinformatic pipelines that can reconstruct networks of polyploid species relationships. In summary, although current phylogenomic approaches have improved our understanding of reticulate species relationships in polyploid-rich genera, the difficulties of recovering reliable orthologous genes and sorting all homeologous copies for allopolyploids remain a challenge. In the future, assembled long-read sequencing data will assist the recovery and identification of multiple gene copies, which can be particularly useful for reconstructing the multiple independent origins of polyploids.

Evolutionary déjà vu? A case of convergent evolution in an ant-plant association

Obligatory ant-plant symbioses often appear to be single evolutionary shifts within particular ant lineages; however, convergence can be revealed once natural history observations are complemented with molecular phylogenetics. Here, we describe a remarkable example of convergent evolution in an ant-plant symbiotic system. Exclusively arboreal, Myrmelachista species can be generalized opportunists nesting in several plant species or obligately symbiotic, live-stem nesters of a narrow set of plant species. Instances of specialization within Myrmelachista are known from northern South America and throughout Middle America. In Middle America, a diverse radiation of specialists occupies understory treelets of lowland rainforests. The morphological and behavioural uniformity of specialists suggests that they form a monophyletic assemblage, diversifying after a single origin of specialization. Using ultraconserved element phylogenomics and ancestral state reconstructions, we show that shifts from opportunistic to obligately symbiotic evolved independently in South and Middle America. Furthermore, our analyses support a remarkable case of convergence within the Middle American radiation, with two independently evolved specialist clades, arising nearly simultaneously from putative opportunistic ancestors during the late Pliocene. This repeated evolution of a complex phenotype suggests similar mechanisms behind trait shifts from opportunists to specialists, generating further questions about the selective forces driving specialization.

Are Viruses Taxonomic Units? A Protein Domain and Loop-Centric Phylogenomic Assessment

Virus taxonomy uses a Linnaean-like subsumption hierarchy to classify viruses into taxonomic units at species and higher rank levels. Virus species are considered monophyletic groups of mobile genetic elements (MGEs) often delimited by the phylogenetic analysis of aligned genomic or metagenomic sequences. Taxonomic units are assumed to be independent organizational, functional and evolutionary units that follow a 'natural history' rationale. Here, I use phylogenomic and other arguments to show that viruses are not self-standing genetically-driven systems acting as evolutionary units. Instead, they are crucial components of holobionts, which are units of biological organization that dynamically integrate the genetics, epigenetic, physiological and functional properties of their co-evolving members. Remarkably, phylogenomic analyses show that viruses share protein domains and loops with cells throughout history via massive processes of reticulate evolution, helping spread evolutionary innovations across a wider taxonomic spectrum. Thus, viruses are not merely MGEs or microbes. Instead, their genomes and proteomes conduct cellularly integrated processes akin to those cataloged by the GO Consortium. This prompts the generation of compositional hierarchies that replace the 'is-a-kind-of' by a 'is-a-part-of' logic to better describe the mereology of integrated cellular and viral makeup. My analysis demands a new paradigm that integrates virus taxonomy into a modern evolutionarily centered taxonomy of organisms.

Toward telomere-to-telomere cat genomes for precision medicine and conservation biology

Genomic data from species of the cat family Felidae promise to stimulate veterinary and human medical advances, and clarify the coherence of genome organization. We describe how interspecies hybrids have been instrumental in the genetic analysis of cats, from the first genetic maps to propelling cat genomes toward the T2T standard set by the human genome project. Genotype-to-phenotype mapping in cat models has revealed dozens of health-related genetic variants, the molecular basis for mammalian pigmentation and patterning, and species-specific adaptations. Improved genomic surveillance of natural and captive populations across the cat family tree will increase our understanding of the genetic architecture of traits, population dynamics, and guide a future of genome-enabled biodiversity conservation.

The Andes as a semi-permeable geographical barrier: Genetic connectivity between structured populations in a widespread spider

Geographical barriers like mountain ranges impede genetic exchange among populations, promoting diversification. The effectiveness of these barriers in limiting gene flow varies between lineages due to each species' dispersal modes and capacities. Our understanding of how the Andes orogeny contributes to species diversification comes from well-studied vertebrates and a few arthropods and plants, neglecting organisms unable to fly or walk long distances. Some arachnids, such as Gasteracantha cancriformis, have been hypothesized to disperse long distances via ballooning (i.e. using their silk to interact with the wind). Yet, we do not know how the environment and geography shape its genetic diversity. Therefore, we tested whether the Andes contributed to the diversification of G. cancriformis acting as an absolute or semi-permeable barrier to genetic connectivity between populations of this spider at opposite sides of the mountain range. We sampled thousands of loci across the distribution of the species and implemented population genetics, phylogenetic, and landscape genetic analyses. We identified two genetically distinct groups structured by the Central Andes, and a third less structured group in the Northern Andes that shares ancestry with the previous two. This structure is largely explained by the altitude along the Andes, which decreases in some regions, possibly facilitating cross-Andean dispersal and gene flow. Our findings support that altitude in the Andes plays a major role in structuring populations in South America, but the strength of this barrier can be overcome by organisms with long-distance dispersal modes together with altitudinal depressions.

Detection of Ghost Introgression Requires Exploiting Topological and Branch Length Information

In recent years, the study of hybridization and introgression has made significant progress, with ghost introgression-the transfer of genetic material from extinct or unsampled lineages to extant species-emerging as a key area for research. Accurately identifying ghost introgression, however, presents a challenge. To address this issue, we focused on simple cases involving 3 species with a known phylogenetic tree. Using mathematical analyses and simulations, we evaluated the performance of popular phylogenetic methods, including HyDe and PhyloNet/MPL, and the full-likelihood method, Bayesian Phylogenetics and Phylogeography (BPP), in detecting ghost introgression. Our findings suggest that heuristic approaches relying on site-pattern counts or gene-tree topologies struggle to differentiate ghost introgression from introgression between sampled non-sister species, frequently leading to incorrect identification of donor and recipient species. The full-likelihood method BPP uses multilocus sequence alignments directly-hence taking into account both gene-tree topologies and branch lengths, by contrast, is capable of detecting ghost introgression in phylogenomic datasets. We analyzed a real-world phylogenomic dataset of 14 species of Jaltomata (Solanaceae) to showcase the potential of full-likelihood methods for accurate inference of introgression.

Geogenomic Predictors of Genetree Heterogeneity Explain Phylogeographic and Introgression History: A Case Study in an Amazonian Bird (Thamnophilus aethiops)

Can knowledge about genome architecture inform biogeographic and phylogenetic inference? Selection, drift, recombination, and gene flow interact to produce a genomic landscape of divergence wherein patterns of differentiation and genealogy vary nonrandomly across the genomes of diverging populations. For instance, genealogical patterns that arise due to gene flow should be more likely to occur on smaller chromosomes, which experience high recombination, whereas those tracking histories of geographic isolation (reduced gene flow caused by a barrier) and divergence should be more likely to occur on larger and sex chromosomes. In Amazonia, populations of many bird species diverge and introgress across rivers, resulting in reticulated genomic signals. Herein, we used reduced representation genomic data to disentangle the evolutionary history of 4 populations of an Amazonian antbird, Thamnophilus aethiops, whose biogeographic history was associated with the dynamic evolution of the Madeira River Basin. Specifically, we evaluate whether a large river capture event ca. 200 Ka, gave rise to reticulated genealogies in the genome by making spatially explicit predictions about isolation and gene flow based on knowledge about genomic processes. We first estimated chromosome-level phylogenies and recovered 2 primary topologies across the genome. The first topology (T1) was most consistent with predictions about population divergence and was recovered for the Z-chromosome. The second (T2), was consistent with predictions about gene flow upon secondary contact. To evaluate support for these topologies, we trained a convolutional neural network to classify our data into alternative diversification models and estimate demographic parameters. The best-fit model was concordant with T1 and included gene flow between non-sister taxa. Finally, we modeled levels of divergence and introgression as functions of chromosome length and found that smaller chromosomes experienced higher gene flow. Given that (1) genetrees supporting T2 were more likely to occur on smaller chromosomes and (2) we found lower levels of introgression on larger chromosomes (and especially the Z-chromosome), we argue that T1 represents the history of population divergence across rivers and T2 the history of secondary contact due to barrier loss. Our results suggest that a significant portion of genomic heterogeneity arises due to extrinsic biogeographic processes such as river capture interacting with intrinsic processes associated with genome architecture. Future phylogeographic studies would benefit from accounting for genomic processes, as different parts of the genome reveal contrasting, albeit complementary histories, all of which are relevant for disentangling the intricate geogenomic mechanisms of biotic diversification. [Amazonia; biogeography; demographic modeling; gene flow; gene tree; genome architecture; geogenomics; introgression; linked selection; neural network; phylogenomic; phylogeography; reproductive isolation; speciation; species tree.].

Divergence and reticulation in the Mexican white oaks: ecological and phylogenomic evidence on species limits and phylogenetic networks in the Quercus laeta complex (Fagaceae)

BACKGROUND AND AIMS

Introgressive hybridization poses a challenge to taxonomic and phylogenetic understanding of taxa, particularly when there are high numbers of co-occurring, intercrossable species. The genus Quercus exemplifies this situation. Oaks are highly diverse in sympatry and cross freely, creating syngameons of interfertile species. Although a well-resolved, dated phylogeny is available for the American oak clade, evolutionary relationships within many of the more recently derived clades remain to be defined, particularly for the young and exceptionally diverse Mexican white oak clade. Here, we adopted an approach bridging micro- and macroevolutionary scales to resolve evolutionary relationships in a rapidly diversifying clade endemic to Mexico.

METHODS

Ecological data and sequences of 155 low-copy nuclear genes were used to identify distinct lineages within the Quercus laeta complex. Concatenated and coalescent approaches were used to assess the phylogenetic placement of these lineages relative to the Mexican white oak clade. Phylogenetic network methods were applied to evaluate the timing and genomic significance of recent or historical introgression among lineages.

KEY RESULTS

The Q. laeta complex comprises six well-supported lineages, each restricted geographically and with mostly divergent climatic niches. Species trees corroborated that the different lineages are more closely related to other species of Mexican white oaks than to each other, suggesting that this complex is polyphyletic. Phylogenetic networks estimated events of ancient introgression that involved the ancestors of three present-day Q. laeta lineages.

CONCLUSIONS

The Q. laeta complex is a morphologically and ecologically related group of species rather than a clade. Currently, oak phylogenetics is at a turning point, at which it is necessary to integrate phylogenetics and ecology in broad regional samples to figure out species boundaries. Our study illuminates one of the more complicated of the Mexican white oak groups and lays groundwork for further taxonomic study.

Homoplastic versus xenoplastic evolution: exploring the emergence of key intrinsic and extrinsic traits in the montane genus Soldanella (Primulaceae)

Specific ecological conditions in the high mountain environment exert a selective pressure that often leads to convergent trait evolution. Reticulations induced by incomplete lineage sorting and introgression can lead to discordant trait patterns among gene and species trees (hemiplasy/xenoplasy), providing a false illusion that the traits under study are homoplastic. Using phylogenetic species networks, we explored the effect of gene exchange on trait evolution in Soldanella, a genus profoundly influenced by historical introgression. At least three features evolved independently multiple times: the single-flowered dwarf phenotype, dysploid cytotype, and ecological generalism. The present analyses also indicated that the recurring occurrence of stoloniferous growth might have been prompted by an introgression event between an ancestral lineage and a still extant species, although its emergence via convergent evolution cannot be completely ruled out. Phylogenetic regression suggested that the independent evolution of larger genomes in snowbells is most likely a result of the interplay between hybridization events of dysploid and euploid taxa and hostile environments at the range margins of the genus. The emergence of key intrinsic and extrinsic traits in snowbells has been significantly impacted not only by convergent evolution but also by historical and recent introgression events.

The contours of evolution: In defence of Darwin's tree of life paradigm

Both the concept of a Darwinian tree of life (TOL) and the possibility of its accurate reconstruction have been much criticized. Criticisms mostly revolve around the extensive occurrence of lateral gene transfer (LGT), instances of uptake of complete organisms to become organelles (with the associated subsequent gene transfer to the nucleus), as well as the implications of more subtle aspects of the biological species concept. Here we argue that none of these criticisms are sufficient to abandon the valuable TOL concept and the biological realities it captures. Especially important is the need to conceptually distinguish between organismal trees and gene trees, which necessitates incorporating insights of widely occurring LGT into modern evolutionary theory. We demonstrate that all criticisms, while based on important new findings, do not invalidate the TOL. After considering the implications of these new insights, we find that the contours of evolution are best represented by a TOL.

Deep genome skimming reveals the hybrid origin of Pseudosasa gracilis (Poaceae: Bambusoideae)

Pseudosasa gracilis (Poaceae: Bambusoideae) is a temperate woody bamboo species endemic to South-central China with a narrow distribution. Previous phylogenetic studies revealed an unexpected, isolated phylogenetic position of Ps. gracilis. Here we conducted phylogenomic analysis by sampling populations of Ps. gracilis and its sympatric species Ps. nanunica and Sinosasa polytricha reflecting different genomic signals, by deep genome skimming. Integrating molecular evidence from chloroplast genes and genome-wide SNPs, we deciphered the phylogenetic relationships of Ps. gracilis. Both plastid and nuclear data indicate that Ps. gracilis is more closely related to Sinosasa, which is discordant with the taxonomic treatment. To further explore this molecular-morphological conflict, we screened 411 "perfect-copy" syntenic genes to reconstruct phylogenies using both the concatenation and coalescent methods. We observed extensive discordance between gene trees and the putative species tree. A significant hybridization event was detected based on 411 genes from the D subgenome, showing Ps. gracilis was a hybrid descendant between Sinosasa longiligulata and Ps. nanunica, with 63.56% and 36.44% inheritance probabilities of each parent. Moreover, introgression events were detected in the C subgenome between Ps. gracilis and S. polytricha in the same distribution region. Our findings suggest that sympatric hybridization and introgression play a crucial role in the origin of Ps. gracilis. By providing an empirical example of bamboo of hybrid origin using comprehensive analyses based on genomic data from different inheritance systems and morphological characters, our study represents a step forward in understanding of reticulate evolution of bamboos.

Hybrids as mirrors of the past: genomic footprints reveal spatio-temporal dynamics and extinction risk of alpine extremophytes in the mountains of Central Asia

Hybridization is one of the key processes shaping lineage diversification, particularly in regions that experienced strong climate oscillations. The alpine biome with its rich history of glacial-interglacial cycles and complex patterns of species distribution shifts offers an excellent system to investigate the impact of gene flow on population dynamics and speciation, important issues for evolutionary biology and biodiversity conservation. In this study, we combined genomic data (DArTseq), chloroplast markers, and morphology to examine phylogenetic relationships and the permeability of species boundaries and their evolutionary outcomes among the alpine extremophilic species of Puccinellia (Poaceae) in the Pamir Mountains, a part of the Mountains of Central Asia biodiversity hotspot. We determined the occurrence of interspecific hybrids between P. himalaica and P. pamirica, which demonstrated almost symmetric ancestry from their parental species and did not show signals of introgression. According to our integrative revision, the natural hybrids between P. himalaica and P. pamirica should be classified as Puccinellia ×vachanica (pro species). Using approximate Bayesian computation for population history inference, we uncovered that P. himalaica hybridized with P. pamirica independently in multiple localities over the Holocene. Hybrids inherited the fine-scale genetic structure from their parental species, which developed these patterns earlier, during the Late Pleistocene. Hybridization had different consequences for the involved parental lineages, likely playing an important role in a continuing decline of P. himalaica in the Pamir Mountains over the Holocene. Our results show that P. himalaica should be considered a critically endangered species in the Pamir Mountains and could also be retreating across its entire range of distribution in High Mountain Asia. Using a comparative phylogeographic framework, we revealed the risk of extinction of a cold-adapted alpine species in a global biodiversity hotspot. This study highlights that genomics could unravel diversity trends under climate change and provides valuable evidence for conservation management.

Giraffe lineages are shaped by major ancient admixture events

Strong genetic structure has prompted discussion regarding giraffe taxonomy,1,2,3 including a suggestion to split the giraffe into four species: Northern (Giraffa c. camelopardalis), Reticulated (G. c. reticulata), Masai (G. c. tippelskirchi), and Southern giraffes (G. c. giraffa).4,5,6 However, their evolutionary history is not yet fully resolved, as previous studies used a simple bifurcating model and did not explore the presence or extent of gene flow between lineages. We therefore inferred a model that incorporates various evolutionary processes to assess the drivers of contemporary giraffe diversity. We analyzed whole-genome sequencing data from 90 wild giraffes from 29 localities across their current distribution. The most basal divergence was dated to 280 kya. Genetic differentiation, FST, among major lineages ranged between 0.28 and 0.62, and we found significant levels of ancient gene flow between them. In particular, several analyses suggested that the Reticulated lineage evolved through admixture, with almost equal contribution from the Northern lineage and an ancestral lineage related to Masai and Southern giraffes. These new results highlight a scenario of strong differentiation despite gene flow, providing further context for the interpretation of giraffe diversity and the process of speciation in general. They also illustrate that conservation measures need to target various lineages and sublineages and that separate management strategies are needed to conserve giraffe diversity effectively. Given local extinctions and recent dramatic declines in many giraffe populations, this improved understanding of giraffe evolutionary history is relevant for conservation interventions, including reintroductions and reinforcements of existing populations.