Maximum Likelihood (ML) based phylogenetic inference constitutes a challenging optimization problem. Given a set of aligned input sequences, phylogenetic inference tools strive to determine the tree topology, the branch-lengths, and the evolutionary model parameters that maximize the phylogenetic likelihood function. However, there exist compelling reasons to not push optimization to its limits, by

Studying rates of species diversification is one of the key themes in macroevolution. In particular, we are interested in if some clades in a phylogeny diversify more rapidly/slowly than others due to branch-specific diversification rates. A common approach in neontological studies is to use a phylogenetic birth-death process to model species diversification. Specifically, the birth-death-shift process

Analysis of genomic data in the past two decades has highlighted the prevalence of introgression as an important evolutionary force in both plants and animals. The genus Drosophila has received much attention recently, with an analysis of genomic sequence data revealing widespread introgression across the species phylogeny for the genus. However, the methods used in the study are based on data summaries

Name-bearing type specimens have a fundamental role in characterising biodiversity, as these objects represent the physical link between a scientific name and the biological organism. Type specimens are usually deposited in natural history collections, which provide key infrastructure for research on essential biological structures and processes, while preserving records of biodiversity for future

Batesian mimicry is an impressive example of convergent evolution driven by predation. However, the observation that many mimics only superficially resemble their models despite strong selective pressures is an apparent paradox. Here, we tested the ‘perfecting hypothesis’, that posits that inaccurate mimicry may represent a transitional stage at the macro-evolutionary scale by performing the hereto

Models used in likelihood-based morphological phylogenetics often adapt molecular phylogenetics models to the specificities of morphological data. Such is the case for the widely used Mkv model—which introduces an acquisition bias correction for sampling only characters that are observed to be variable—and for models of among-character rate variation (ACRV), routinely applied by researchers to relax

Phylogenies contain a wealth of information about the evolutionary history and process that gave rise to the diversity of life. This information can be extracted by fitting phylogenetic models to trees. However, many realistic phylogenetic models lack tractable likelihood functions, prohibiting their use with standard inference methods. We present phyddle, pipeline-based software for performing phylogenetic

Understanding the ecological drivers and limitations of adaptive convergence is a fundamental challenge. Here, we explore how adaptive convergence of planktivorous fishes has been influenced by multiple ecological factors, evolutionary history, and chance. Using ecomorphological data for over 1600 marine species, we integrate pattern-based metrics of convergence with evolutionary model fitting to test

Understanding the drivers of diversification is a central goal in evolutionary biology but can be challenging when lineages radiate quickly and/or hybridize frequently. Cichlids in the tribe Lamprologini, an exceptionally diverse clade found in the Congo basin, exemplify these issues: their evolutionary history has been difficult to untangle with previous datasets, particularly with regard to river-dwelling

Phenotypic convergence is found across the tree of life, and morphological similarities in distantly related species are often presumed to have evolved independently. However, clarifying the origins of traits has recently highlighted the complex nature of evolution, as apparent convergent features often share similar genetic foundations. Hence, the tree topology of genes that underlie such traits frequently

Genomic analyses of hybrid zones provide excellent opportunities to investigate the consequences of introgression in nature. In combination with phylogenomics analyses, hybrid zone studies may illuminate the role of ancient and contemporary gene flow in shaping variation of phylogenetic signals across the genome, but this avenue has not been explored yet. We combined phylogenomic and geographic cline

Methods for rapidly inferring the evolutionary history of species or populations with, genome-wide data are progressing, but computational constraints still limit our abilities in, this area. We developed an alignment-free method to infer genome-wide phylogenies and, implemented it in the Python package TopicContml. The method uses probabilistic, topic modeling (specifically, Latent Dirichlet Allocation

After collecting large data sets for phylogenomics studies, researchers must decide which, genes or samples to include when reconstructing a species tree. Incomplete or unreliable, data sets make the empiricist’s decision more difficult. Researchers rely on ad hoc, strategies to maximize sampling while ensuring sufficient data for accurate inferences. An, algorithm called PickMe formalizes the sample

A relationship between the rate of molecular change and diversification has long been, discussed, on both theoretical and empirical grounds. However, the effect on our, understanding of evolutionary patterns is yet to be fully explored. Here we develop a new, model, the Covariant Evolutionary Tempo (CET) model, with the aim of integrating, patterns of diversification and molecular evolution within

Evolutionary radiations underlie much of the species diversity of life on Earth, particularly within the world’s most species-rich tree flora – that of the Amazon rainforest. Hybridisation occurs in many radiations, with effects ranging from homogenisation of divergent species to the generation of genetic and phenotypic novelty that fuels speciation. However, the influence of hybridisation on Amazonian

Evolutionary radiations are considered key processes underlying the origin of biodiversity. Notably, the mechanisms driving these radiations can vary across organisms and often involve a complex interplay of abiotic and biotic factors. Empirical studies on evolutionary history are crucial for validation of multiple hypothesis regarding the mode of evolutionary radiations. Within the aquatic insect

In previous studies, we presented our site-specific Stability Constrained substitution models of Protein Evolution (Stab-CPE) that define fitness as the probability of finding a protein folded in its native state but ignore changes in the native structure. Stab-CPE models can be used to predict a more realistic evolutionary variability across protein sites, nevertheless they still qualitatively differ

In recent years, there has been a growing interest in using morphology to establish the placement of species on phylogenetic trees derived from molecular data. This is relevant in the case of recently extinct or fossil species, which are usually represented only by fragmentary morphology. In the latter case, constrained analyses using backbone trees have also proven helpful in evaluating the placement

Ants are a globally distributed and highly diverse group of eusocial animals, playing key ecological roles in most of the world’s terrestrial ecosystems. Our understanding of the processes involved in the evolution of this diverse family is contingent upon our knowledge of the phylogeny of the ants. While relationships among most subfamilies have come into resolution recently, several of the tribal

Phylogenomic analyses of closely related species allow important glimpses into their evolutionary history. Although recent studies have demonstrated that interspecies hybridization has occurred in several groups, incorporating this process in phylogenetic reconstruction remains challenging. Specifically, the most predominant topology across the genome is often assumed to reflect the speciation tree

Explaining global species richness patterns is a major goal of evolution, ecology, and biogeography. These richness patterns are often attributed to spatial variation in diversification rates (speciation minus extinction). Surprisingly, prominent studies of birds, fish, and plants have reported higher speciation and/or diversification rates at higher latitudes, where species richness is lower. We hypothesize

Tropical insular systems have long attracted biologists, stimulating some important controversies in ecology and evolution. Eustatic fluctuations during the Pleistocene have been invoked to explain species dispersal and proliferation in these fragmented systems by controlling the extent of landmasses and their temporary connections. In ancient archipelagos, the Pleistocene represents only a small slice

Genome-scale datasets are resolving challenging nodes across the tree of life. These datasets however, characterized by inherent heterogeneity, often push traditional phylogenetic reconstruction methods to their limits. By integrating multiple phylogenomic approaches, we can identify the causes of topological discordance within genomic partitions while accounting for various sources of heterogeneity

Summary methods are widely used to reconstruct species trees from gene tres while accommodating discordance from incomplete lineage sorting; however, it is increasingly recognized that their accuracy can be negatively impacted by incomplete and/or error-ridden gene trees. To address the latter, Zhang and Mirarab (2022) updated the popular summary method ASTRAL so that it weights quartets based on gene

The interplay of key innovation and ecological opportunity is commonly recognized to be the catalyst for rapid radiation. Underground storage organs (USOs), as a vital ecological trait, are advantageous for adaptation of plants to extreme environments, but receive less attention compared to aboveground organs. Repeated evolution of various USOs has occurred across the plant tree of life. However, whether

Accurate estimates of species diversity are essential for all biodiversity research. Delimiting species and understanding the underlying processes of speciation are also central components of systematic biology that frame our comprehension of the evolutionary mechanisms generating biodiversity. The South American tree squirrels (genus Guerlinguetus) are keystone mammals, widely distributed, that are

Over two million species have been named so far, but many will be invalidated due to redundant descriptions. Undetected invalid species (i.e., synonyms) can impair inferences we make in biodiversity research and hamper the implementation of effective conservation strategies. However, the processes leading to the accumulation of invalid names remain largely unknown. Using multi-model inferences, we

The subphylum Pezizomycotina (filamentous ascomycetes) is the largest clade within Ascomycota. Despite the importance of this group of fungi, our understanding of their evolution is still limited due to insufficient taxon sampling. Although next-generation sequencing technology allows us to obtain complete genomes for phylogenetic analyses, generating complete genomes of fungal species can be challenging

Paleobiologists have long sought to explain how alternative modes of speciation, including budding and bifurcating cladogenesis, shape patterns of evolution. Methods introduced over the past decade have paved the way for a renewed enthusiasm for exploring modes of speciation in the fossil record. However, the field does not yet have a strong intuition for how ancestor-descendant relationships, especially

Different species concepts and their associated criteria have been used to delimit species boundaries, such as the absence of gene flow for the biological species concept and the presence of morphological distinction for the morphological species concept. The need for different delimitation criteria largely reflects the fact that species are generated under various speciation mechanisms. A key question

Obtaining a timescale for bacterial evolution is crucial to understand early life evolution but is difficult owing to the scarcity of bacterial fossils. Here, we introduce multiple new time constraints to calibrate bacterial evolution based on ancient symbiosis. This idea is implemented using a bacterial tree constructed with genes found in the mitochondrial lineages phylogenetically embedded within

Deep learning has previously shown success in automatically generating morphological traits which carry a phylogenetic signal. In this paper we explore combining molecular data with deep learning derived morphological traits from images of pinned insects to generate total-evidence phylogenies and we reveal challenges. Deep learning derived morphological traits, while informative, underperform when

The vast majority of pathogen phylogenetic studies do not consider the possibility of multiple merger events being present, where a single node of the tree leads to more than two descendent branches. These events are however likely to occur when studying a relatively small population or if there is high variability in the reproductive chances. Here we consider the problem of detecting the presence

As lineages become separated in time, they are expected to accumulate mutational (or developmental-genetic) differences that influence the macroevolutionary trajectories of those lineages even under similar environmental conditions. Here, we compare the dynamics of phenotypic evolution in radiations of scincid lizards from Australia and Madagascar that are separated by more than 100 million years of

While some relationships in phylogenomic studies have remained stable since the Sanger sequencing era, many challenging nodes remain, even with genome-scale data. Incongruence or lack of resolution in the phylogenomic era is frequently attributed to inadequate data modeling and analytical issues that lead to systematic biases. However, few studies investigate the potential for random error or establish

The phylum Nematoda represents one of the most cosmopolitan and abundant metazoan groups on Earth. In this study, we reconstructed the phylogenomic tree for phylum Nematoda. A total of 60 genomes, belonging to eight nematode orders, were newly sequenced, providing the first low-coverage genomes for the orders Dorylaimida, Mononchida, Monhysterida, Chromadorida, Triplonchida, and Enoplida. The resulting

Comparative research on the evolution of parental care has followed a general trend in recent years, with researchers gathering data on clutch size or egg size and correlating these traits with ecological variables across a phylogeny. The goal of these studies is to shed light on how and why certain strategies evolve. However, results vary across studies, and we rarely have results explaining why the

Orchid mycorrhizal fungi (OMF) associations in the Orchidaceae are thought to have been a major driver of diversification in the family. In the terrestrial orchid tribe Diurideae, it has long been hypothesised that OMF symbiont associations may reflect evolutionary relationships among orchid hosts. Given that recent phylogenomic efforts have been unable to fully resolve relationships among subtribes

Evolutionary novelties are commonly identified as drivers of lineage diversification, with key innovations potentially triggering adaptive radiation. Nevertheless, testing hypotheses on the role of evolutionary novelties in promoting diversification through deep time has proven challenging. Here we unravel the role of the raptorial appendages, with evolutionary novelties for predation, in the macroevolution

Comparisons of extant and extinct biodiversity are often dependent on objective morphology-based identifications of fossils and assume a well-established and comparable taxonomy for both fossil and modern taxa. However, since many modern (cryptic) species are delimitated mainly via external morphology and/or molecular data, it is often unclear to what degree fossilized (osteological) remains allow

In Bayesian molecular-clock dating of species divergences, rate models are used to construct the prior on the molecular evolutionary rates for branches in the phylogeny, with independent and autocorrelated rate models being commonly used. The two classes of models, however, can result in markedly different divergence time estimates for the same data set, and thus selecting the best rate model appears

The spatial and environmental features of regions where clades are evolving are expected to impact biogeographic processes such as speciation, extinction, and dispersal. Any number of regional features (such as elevation, distance, area, etc.) may be directly or indirectly related to these processes. For example, it may be that distances or differences in elevation or both may limit dispersal rates

Genomic data have become ubiquitous in phylogenomic studies, including divergence time estimation, but provide new challenges. These challenges include, among others, biological gene tree discordance, methodological gene tree estimation error, and computational limitations on performing full Bayesian inference under complex models. In this study, we use a recently published firefly (Coleoptera: Lampyridae)

Biology has become a highly mathematical discipline in which probabilistic models play a central role. As a result, research in the biological sciences is now dependent on computational tools capable of carrying out complex analyses. These tools must be validated before they can be used, but what is understood as validation varies widely among methodological contributions. This may be a consequence

Eyes within the marine gastropod superfamily Stromboidea range widely in size, from 0.2 to 2.3 mm—the largest eyes known in any gastropod. Despite this interesting variation, the underlying evolutionary pressures remain unknown. Here, we use the wealth of material available in museum collections to explore the evolution of stromboid eye size and structure. Our results suggest that depth is a key light-limiting

Evolutionary changes in geographic distribution and larval host plants may promote the rapid diversification of montane insects, but this scenario has been rarely investigated. We studied the rapid radiation of the butterfly genus Colias, which has diversified in mountain ecosystems in Eurasia, Africa, and the Americas. Based on a data set of 150 nuclear protein-coding genetic loci and mitochondrial

Reticulation between radiating lineages is a common feature of diversification. We examine these phenomena in the Pisgah clade of Desmognathus salamanders from the southern Appalachian Mountains of the eastern United States. The group contains 4–7 species exhibiting 2 discrete phenotypes, aquatic “shovel-nosed” and semi-aquatic “black-bellied” forms. These ecomorphologies are ancient and have apparently

Online phylogenetic inference methods add sequentially arriving sequences to an inferred phylogeny without the need to recompute the entire tree from scratch. Some online method implementations exist already, but there remains concern that additional sequences may change the topological relationship among the original set of taxa. We call such a change in tree topology a lack of stability for the inferred

Xenacoelomorpha are mostly microscopic, morphologically simple worms, lacking many structures typical of other bilaterians. Xenacoelomorphs –which include three main groups: Acoela, Nemertodermatida, and Xenoturbella– have been proposed to be an early diverging Bilateria, sister to protostomes and deuterostomes, but other phylogenomic analyses have recovered this clade nested within the deuterostomes

Time-dependent birth-death sampling models have been used in numerous studies for inferring past evolutionary dynamics in different biological contexts, e.g. speciation and extinction rates in macroevolutionary studies, or effective reproductive number in epidemiological studies. These models are branching processes where lineages can bifurcate, die, or be sampled with time-dependent birth, death,

Variation in gene tree estimates is widely observed in empirical phylogenomic data and is often assumed to be the result of biological processes. However, a recent study using tetrapod mitochondrial genomes to control for biological sources of variation due to their haploid, uniparentally inherited, and non-recombining nature found that levels of discordance among mitochondrial gene trees were comparable

While phylogenies have been essential in understanding how species evolve, they do not adequately describe some evolutionary processes. For instance, hybridization, a common phenomenon where interbreeding between 2 species leads to formation of a new species, must be depicted by a phylogenetic network, a structure that modifies a phylogenetic tree by allowing 2 branches to merge into 1, resulting in

Reconstructing the evolutionary history of different groups of organisms provides insight into how life originated and diversified on Earth. Phylogenetic trees are commonly used to estimate this evolutionary history. Within Bayesian phylogenetics a major step in estimating a tree is in choosing an appropriate model of character evolution. While the most common character data used is molecular sequence

Despite significant advances in phylogenetics over the past decades, the deep relationships within Bivalvia (phylum Mollusca) remain inconclusive. Previous efforts based on morphology or several genes have failed to resolve many key nodes in the phylogeny of Bivalvia. Advances have been made recently using transcriptome data, but the phylogenetic relationships within Bivalvia historically lacked consensus

In vicariant species formation, divergence results primarily from periods of allopatry and restricted gene flow. Widespread species harboring differentiated, geographically distinct sublineages offer a window into what may be a common mode of species formation, whereby a species originates, spreads across the landscape, then fragments into multiple units. However, incipient lineages usually lack reproductive

To model distribution ranges, the most popular methods of phylogenetic biogeography divide Earth into a handful of predefined areas. Other methods use explicit geographic ranges, but unfortunately, these methods assume a static Earth, ignoring the effects of plate tectonics and the changes in the landscape. To address this limitation, I propose a method that uses explicit geographic ranges and incorporates

The multispecies coalescent (MSC) model accommodates genealogical fluctuations across the genome and provides a natural framework for comparative analysis of genomic sequence data from closely related species to infer the history of species divergence and gene flow. Given a set of populations, hypotheses of species delimitation (and species phylogeny) may be formulated as instances of MSC models (e

Phylogenomics has the power to uncover complex phylogenetic scenarios across the genome. In most cases, no single topology is reflected across the entire genome as the phylogenetic signal differs among genomic regions due to processes, such as introgression and incomplete lineage sorting. Baleen whales are among the largest vertebrates on Earth with a high dispersal potential in a relatively unrestricted

African antelope diversity is a globally unique vestige of a much richer world-wide Pleistocene megafauna. Despite this, the evolutionary processes leading to the prolific radiation of African antelopes are not well understood. Here, we sequenced 145 whole genomes from both subspecies of the waterbuck (Kobus ellipsiprymnus), an African antelope believed to be in the process of speciation. We investigated

Adaptive radiation involves diversification along multiple trait axes, producing phenotypically diverse, species-rich lineages. Theory generally predicts that multi-trait evolution occurs via a “stages” model, with some traits saturating early in a lineage’s history, and others diversifying later. Despite its multidimensional nature, however, we know surprisingly little about how different suites of