Ecological opportunity and the origin of adaptive radiations

Macroevolution of the plant-hummingbird pollination system

Plant-hummingbird interactions are considered a classic example of coevolution, a process in which mutually dependent species influence each other's evolution. Plants depend on hummingbirds for pollination, whereas hummingbirds rely on nectar for food. As a step towards understanding coevolution, this review focuses on the macroevolutionary consequences of plant-hummingbird interactions, a relatively underexplored area in the current literature. We synthesize prior studies, illustrating the origins and dynamics of hummingbird pollination across different angiosperm clades previously pollinated by insects (mostly bees), bats, and passerine birds. In some cases, the crown age of hummingbirds pre-dates the plants they pollinate. In other cases, plant groups transitioned to hummingbird pollination early in the establishment of this bird group in the Americas, with the build-up of both diversities coinciding temporally, and hence suggesting co-diversification. Determining what triggers shifts to and away from hummingbird pollination remains a major open challenge. The impact of hummingbirds on plant diversification is complex, with many tropical plant lineages experiencing increased diversification after acquiring flowers that attract hummingbirds, and others experiencing no change or even a decrease in diversification rates. This mixed evidence suggests that other extrinsic or intrinsic factors, such as local climate and isolation, are important covariables driving the diversification of plants adapted to hummingbird pollination. To guide future studies, we discuss the mechanisms and contexts under which hummingbirds, as a clade and as individual species (e.g. traits, foraging behaviour, degree of specialization), could influence plant evolution. We conclude by commenting on how macroevolutionary signals of the mutualism could relate to coevolution, highlighting the unbalanced focus on the plant side of the interaction, and advocating for the use of species-level interaction data in macroevolutionary studies.

Key innovations and niche variation promoted rapid diversification of the widespread Juniperus (Cupressaceae)

The processes of forming lineages undergoing widespread radiations remain a knowledge gap that is fundamental to our understanding of the geographic distributions of species. Although early studies emphasized the importance of dispersal ability and historical migration events, key innovations that promote rapid diversification and/or adaptation to new habitats may also strongly influence distribution ranges. Juniperus is the second largest genus of conifers and is widely distributed throughout the Northern Hemisphere. Here, we used phylogenetic, phenotypic, and climatic data to investigate the contributions of these processes to the wide distribution and rapid diversification of Juniperus. Combining a time-scaled phylogeny and macroevolutionary theory, we show that the key innovations of berry-like seed cones and dioecy promoted the rapid diversification of Juniperus and that increased dispersal ability promoted allopatric speciation. Ecological niches had significant divergence among different clades of Juniperus. Biogeographic results supported multiple long-distance dispersal events and niche variation that contributed to the modern range of Juniperus, while both phenotypic adaptation and ecological opportunity probably drove its distribution range. Our findings suggest that the current widespread distribution is likely the result of significant divergence driven by niche variation in which ecological opportunities from key innovation and phenotypic divergence.

Pelagic zone is an evolutionary catalyst, but an ecological dead end, for North American minnows

The colonization of a novel geographic area is a classic source of ecological opportunity. Likewise, complex microhabitats are thought to promote biodiversity. We sought to reconcile these two predictions when they are naturally opposing outcomes. We assess the macroevolutionary consequences of an ancestral shift from benthic to pelagic microhabitat zones on rates of speciation and phenotypic evolution in North American minnows. Pelagic species have more similar phenotypes and slower rates of phenotypic evolution, but faster speciation rates, than benthic species. These are likely two independent, opposing responses to specialization along the benthic-pelagic axis, as rates of phenotypic evolution and speciation are not directly correlated. The pelagic zone is more structurally homogenous and offers less ecological opportunity, acting as an ecological dead end for minnows. In contrast, pelagic species may be more mobile and prone to dispersal and subsequent geographic isolation and, consequently, experience elevated instances of allopatric speciation. Microhabitat shifts can have decoupled effects on different dimensions of biodiversity, highlighting the need for nuance when interpreting the macroevolutionary consequences of ecological opportunity.

Sequential trait evolution did not drive deep-time diversification in sharks

Estimating how traits evolved and impacted diversification across the tree of life represents a critical topic in ecology and evolution. Although there has been considerable research in comparative biology, large parts of the tree of life remain underexplored. Sharks are an iconic clade of marine vertebrates, and key components of marine ecosystems since the early Mesozoic. However, few studies have addressed how traits evolved or whether they impacted their extant diversity patterns. Our study aimed to fill this gap by reconstructing the largest time-calibrated species-level phylogeny of sharks and compiling an exhaustive database for ecological (diet, habitat) and biological (reproduction, maximum body length) traits. Using state-of-the-art models of evolution and diversification, we outlined the major character shifts and modes of trait evolution across shark species. We found support for sequential models of trait evolution and estimated a small to medium-sized lecithotrophic and coastal-dwelling most recent common ancestor for extant sharks. However, our exhaustive hidden traits analyses do not support trait-dependent diversification for any examined traits, challenging previous works. This suggests that the role of traits in shaping sharks' diversification dynamics might have been previously overestimated and should motivate future macroevolutionary studies to investigate other drivers of diversification in this clade.

Dispersal evolution alters evolution-mediated priority effects in a metacommunity

Biologists have long sought to predict the distribution of species across landscapes to understand biodiversity patterns and dynamics. These efforts usually integrate ecological niche and dispersal dynamics, but evolution can also mediate these ecological dynamics. Species that disperse well and arrive early might adapt to local conditions, which creates an evolution-mediated priority effect that alters biodiversity patterns. Yet, dispersal is also a trait that can evolve and affect evolution-mediated priority effects. We developed an individual-based model where populations of competing species can adapt not only to local environments but also to different dispersal probabilities. We found that lower regional species diversity selects for populations with higher dispersal probabilities and stronger evolution-mediated priority effects. When all species evolved dispersal, they monopolized fewer patches and did so at the same rates. When only one of the species evolved dispersal, it evolved lower dispersal than highly dispersive species and monopolized habitats once freed from maladaptive gene flow. Overall, we demonstrate that dispersal evolution can shape evolution-mediated priority effects when provided with a greater ecological opportunity in species-poor communities. Dispersal- and evolution-mediated priority effects probably play greater roles in species-poor regions like the upper latitudes, isolated islands and in changing environments. This article is part of the theme issue 'Diversity-dependence of dispersal: interspecific interactions determine spatial dynamics'.

Urban landscape as a determinant of sarcosaprophagous fly assemblages of sanitary interest: a comparative field study between larviparous and oviparous reproductive strategies

In Diptera, reproductive strategies vary according to the stage of development of the newly deposited offspring and their abundance. The aim of our study is to establish connections between the reproductive strategies of flies (larviparous or oviparous) and the prevailing local conditions (sun or shade) as well as landscape attributes (low or high urbanization) in an urban setting. We collected flies using 2 baited traps (in the sun or shade) at each of the 13 study sites with varying levels of urbanization. We used generalized linear mixed models to examine the impact of landscape and local characteristics on the diversity (abundance and richness of larviparous and oviparous Diptera) of sarcosaprophagous flies. Our findings indicate that while the abundance and diversity of both larviparous and oviparous flies are affected by urbanization, larviparous flies would be less sensitive to more urbanized environments. Larviparous also exhibit a preference for resources under sun exposure, while the responses of oviparous seem more species-dependent. The observed patterns can be explained by the known biology of the studied groups.

The succession of ecological divergence and reproductive isolation in adaptive radiations

Adaptive radiation is a major source of biodiversity but the way in which known components of ecological opportunity, ecological differentiation, and reproductive isolation underpin such biodiversity patterns remains elusive. Much is known about the evolution of ecological differentiation and reproductive isolation during single speciation events, but exactly how those processes scale up to complete adaptive radiations is less understood. Do we expect complete reproductive barriers between newly formed species before the ecological differentiation continues, or does proper species formation occur much later, long after the ecological diversification? Our goal is to improve our mechanistic understanding of adaptive radiations by analyzing an individual-based model that includes a suite of mechanisms that are known to contribute to biodiversity. The model includes variable biogeographic settings, ecological opportunities, and types of mate choice, which makes several different scenarios of an adaptive radiation possible. We find that evolving clades tend to exploit ecological opportunities early whereas reproductive barriers evolve later, demonstrating a decoupling of ecological differentiation and species formation. In many cases, we also find a long-term trend where assortative mating associated with ecological traits is replaced by sexual selection of neutral display traits as the primary mechanism for reproductive isolation. Our results propose that reticulate phylogenies are likely common and stem from initially low reproductive barriers, rather than the previously suggested idea of repeated hybridization events between well-separated species.

Whole-genome analysis reveals phylogenetic and demographic history of Eurasian perch

The contemporary diversity and distribution of species are shaped by their evolutionary and ecological history. This can be deciphered with the help of phylogenetic and demographic analysis methods, ideally combining and supplementing information from mitochondrial and nuclear genomes. In this study, we investigated the demographic history of Eurasian perch (Perca fluviatilis), a highly adaptable teleost with a distribution range across Eurasia. We combined whole-genome resequencing data with available genomic resources to analyse the phylogeny, phylogeography, and demographic history of P. fluviatilis populations from Europe and Siberia. We identified five highly diverged evolutionary mtDNA lineages, three of which show a strong signal of admixture in the Baltic Sea region. The estimated mean divergence time between these lineages ranged from 0.24 to 1.42 million years. Based on nuclear genomes, two distinct demographic trajectories were observed in European and Siberian samples reflecting contrasting demographic histories ca. 30,000-100,000 years before the present. A comparison of mtDNA and nuclear DNA evolutionary trees and AMOVA revealed concordances, as well as incongruences, between the two types of data, most likely reflecting recent postglacial colonization and hybridization events. Overall, our findings demonstrate the power and usefulness of genome-wide information for delineating historical processes that have shaped the genome of P. fluviatilis. We also highlight the added value of data-mining existing transcriptomic resources to complement novel sequence data, helping to shed light on putative glacial refugia and postglacial recolonization routes.

Viviparity imparts a macroevolutionary signature of ecological opportunity in the body size of female Liolaemus lizards

Viviparity evolved ~115 times across squamate reptiles, facilitating the colonization of cold habitats, where oviparous species are scarce or absent. Whether the ecological opportunity furnished by such colonization reconfigures phenotypic diversity and accelerates evolution is unclear. We investigated the association between viviparity and patterns and rates of body size evolution in female Liolaemus lizards, the most species-rich tetrapod genus from temperate regions. Here, we discover that viviparous species evolve ~20% larger optimal body sizes than their oviparous relatives, but exhibit similar rates of body size evolution. Through a causal modeling approach, we find that viviparity indirectly influences body size evolution through shifts in thermal environment. Accordingly, the colonization of cold habitats favors larger body sizes in viviparous species, reconfiguring body size diversity in Liolaemus. The catalyzing influence of viviparity on phenotypic evolution arises because it unlocks access to otherwise inaccessible sources of ecological opportunity, an outcome potentially repeated across the tree of life.

Climatic niche shift after range expansion of Eustachys (Poaceae)

Eustachys presents lower diversity in the Old World than in the Neotropics and it occurs disjunctly between main tropical regions. This qualifies Eustachys as a good model to test whether lineages expand their niches during the process of range expansion. We performed ancestral range reconstruction, compared environmental spaces of the different geographic areas and assessed bioclimatic trait evolution. Ancestral range reconstruction indicated that most speciation in Eustachys occurred in the South America. Ancestral climatic niches of the New World are different from those of African and Australasia lineages. Our results show that Eustachys experienced niche expansion when it reached the New World. Evolutionary history of Eustachys illustrates how the range expansion promoted climatic niche shifts, which could drive unbalanced species richness of the genus among different tropical regions.

Situating physiology within evolutionary theory

Traditionally defined as the science of the living, or as the field that beyond anatomical structure and bodily form studies functional organization and behaviour, physiology has long been excluded from evolutionary research. The main reason for this exclusion is that physiology has a presential and futuristic outlook on life, while evolutionary theory is traditionally defined as the study of natural history. In this paper, I re-evaluate these classic science divisions and situate physiology within the history of the evolutionary sciences, as well as within debates on the Extended Evolutionary Synthesis and the need for a Third Way of Evolution. I then briefly point out how evolutionary physiology in particular contributes to research on function, causation, teleonomy, agency and cognition.

Which contributes more to the relict flora distribution pattern in East Asia, geographical processes or climate change? New evidence from the phylogeography of Rehderodendron kwangtungense

BACKGROUND

Relict species are important for enhancing the understanding of modern biogeographic distribution patterns. Although both geological and climatic changes since the Cenozoic have affected the relict flora in East Asia, the contributions of geographical processes remain unclear. In this study, we employed restriction-site associated DNA sequencing (RAD-seq) and shallow genome sequencing data, in conjunction with ecological niche modeling (ENM), to investigate the spatial genetic patterns and population differentiation history of the relict species Rehderodendron kwangtungense Chun.

RESULTS

A total of 138 individuals from 16 populations were collected, largely covering the natural distribution of R. kwangtungense. The genetic diversity within the R. kwangtungense populations was extremely low (HO = 0.048 ± 0.019; HE = 0.033 ± 0.011). Mantel tests revealed isolation-by-distance pattern (R2 = 0.38, P < 0.001), and AMOVA analysis showed that the genetic variation of R. kwangtungense occurs mainly between populations (86.88%, K = 7). Between 23 and 21 Ma, R. kwangtungense underwent a period of rapid differentiation that coincided with the rise of the Himalayas and the establishment of the East Asian monsoon. According to ENM and population demographic history, the suitable area and effective population size of R. kwangtungense decreased sharply during the glacial period and expanded after the last glacial maximum (LGM).

CONCLUSION

Our study shows that the distribution pattern of southern China mountain relict flora may have developed during the panplain stage between the middle Oligocene and the early Miocene. Then, the flora later fragmented under the force of orogenesis, including intermittent uplift during the Cenozoic Himalayan orogeny and the formation of abundant rainfall associated with the East Asian monsoon. The findings emphasized the predominant role of geographical processes in shaping relict plant distribution patterns.

A chromosome-level genome assembly of an avivorous bat species (Nyctalus aviator)

Currently, three carnivorous bat species, namely Ia io, Nyctalus lasiopterus, and Nyctalus aviator, are known to actively prey on seasonal migratory birds (hereinafter referred to as "avivorous bats"). However, the absence of reference genomes impedes a thorough comprehension of the molecular adaptations of avivorous bat species. Herein, we present the high-quality chromosome-scale reference genome of N. aviator based on PacBio subreads, DNBSEQ short-reads and Hi-C sequencing data. The genome assembly size of N. aviator is 1.77 Gb, with a scaffold N50 of 102 Mb, of which 99.8% assembly was anchored into 21 pseudo-chromosomes. After masking 635.1 Mb repetitive sequences, a total of 19,412 protein-coding genes were identified, of which 99.3% were functionally annotated. The genome assembly and gene prediction reached 96.1% and 96.1% completeness of Benchmarking Universal Single-Copy Orthologs (BUSCO), respectively. This chromosome-level reference genome of N. aviator fills a gap in the existing information on the genomes of carnivorous bats, especially avivorous ones, and will be valuable for mechanism of adaptations to dietary niche expansion in bat species.

Systematics and evolutionary dynamics of insect-fern interactions in the specialized fern-spore feeding Cuprininae (Lepidoptera, Stathmopodidae)

Fern-spore-feeding (FSF) is rare and found in only four families of Lepidoptera. Stathmopodidae is the most speciose family that contains FSF species, and its subfamily Cuprininae exclusively specializes on FSF. However, three species of Stathmopodinae also specialize on FSF. To better understand the evolutionary history of FSF and, more generally, the significance of specialization on a peculiar host, a phylogenetic and taxonomic revision for this group is necessary. We reconstructed the most comprehensive molecular phylogeny, including one mitochondrial and four nuclear genes, of Stathmopodidae to date, including 137 samples representing 62 species, with a particular focus on the FSF subfamily, Cuprininae, including 33 species (41% of named species) from 6 of the 7 Cuprininae genera. Species from two other subfamilies, Stathmopodinae and Atkinsoniinae, were also included. We found that FSF evolved only once in Stathmopodidae and that the previous hypothesis of multiple origins of FSF was misled by inadequate taxonomy. Moreover, we showed that (1) speciation/extinction rates do not differ significantly between FSF and non-FSF groups and that (2) oligophage is the ancestral character state in Cuprininae. We further revealed that a faster rate of accumulating specialists over time, and thus a higher number of specialists, was achieved by a higher transition rate from oligophagages to specialists compared to the transition rate in the opposite direction. We finish by describing three new genera, Trigonodagen. nov., Petalagen. nov., and Pediformisgen. nov., and revalidating five genera: Cuprina, Calicotis, Thylacosceles, Actinoscelis, Thylacosceloides in Cuprininae, and we provide an updated taxonomic key to genera and a revised global checklist of Cuprininae.

Emergence and maintenance of stable coexistence during a long-term multicellular evolution experiment

The evolution of multicellular life spurred evolutionary radiations, fundamentally changing many of Earth's ecosystems. Yet little is known about how early steps in the evolution of multicellularity affect eco-evolutionary dynamics. Through long-term experimental evolution, we observed niche partitioning and the adaptive divergence of two specialized lineages from a single multicellular ancestor. Over 715 daily transfers, snowflake yeast were subjected to selection for rapid growth, followed by selection favouring larger group size. Small and large cluster-forming lineages evolved from a monomorphic ancestor, coexisting for over ~4,300 generations, specializing on divergent aspects of a trade-off between growth rate and survival. Through modelling and experimentation, we demonstrate that coexistence is maintained by a trade-off between organismal size and competitiveness for dissolved oxygen. Taken together, this work shows how the evolution of a new level of biological individuality can rapidly drive adaptive diversification and the expansion of a nascent multicellular niche, one of the most historically impactful emergent properties of this evolutionary transition.

Complexity of avian evolution revealed by family-level genomes

Despite tremendous efforts in the past decades, relationships among main avian lineages remain heavily debated without a clear resolution. Discrepancies have been attributed to diversity of species sampled, phylogenetic method and the choice of genomic regions1-3. Here we address these issues by analysing the genomes of 363 bird species4 (218 taxonomic families, 92% of total). Using intergenic regions and coalescent methods, we present a well-supported tree but also a marked degree of discordance. The tree confirms that Neoaves experienced rapid radiation at or near the Cretaceous-Palaeogene boundary. Sufficient loci rather than extensive taxon sampling were more effective in resolving difficult nodes. Remaining recalcitrant nodes involve species that are a challenge to model due to either extreme DNA composition, variable substitution rates, incomplete lineage sorting or complex evolutionary events such as ancient hybridization. Assessment of the effects of different genomic partitions showed high heterogeneity across the genome. We discovered sharp increases in effective population size, substitution rates and relative brain size following the Cretaceous-Palaeogene extinction event, supporting the hypothesis that emerging ecological opportunities catalysed the diversification of modern birds. The resulting phylogenetic estimate offers fresh insights into the rapid radiation of modern birds and provides a taxon-rich backbone tree for future comparative studies.

Microgeographic variation in demography and thermal regimes stabilize regional abundance of a widespread freshwater fish

Predicting the persistence of species under climate change is an increasingly important objective in ecological research and management. However, biotic and abiotic heterogeneity can drive asynchrony in population responses at small spatial scales, complicating species-level assessments. For widely distributed species consisting of many fragmented populations, such as brook trout (Salvelinus fontinalis), understanding the drivers of asynchrony in population dynamics can improve the predictions of range-wide climate impacts. We analyzed the demographic time series from mark-recapture surveys of 11 natural brook trout populations in eastern Canada over 13 years to examine the extent, drivers, and consequences of fine-scale population variation. The focal populations were genetically differentiated, occupied a small area (~25 km2 ) with few human impacts, and experienced similar climate conditions. Recruitment was highly asynchronous, weakly related to climate variables and showed population-specific relationships with other demographic processes, generating diverse population dynamics. In contrast, individual growth was mostly synchronized among populations and driven by a shared positive relationship with stream temperature. Outputs from population-specific models were unrelated to four of the five hypothesized drivers (recruitment, growth, reproductive success, phylogenetic distance), but variation in groundwater inputs strongly influenced stream temperature regimes and stock-recruitment relationships. Finally, population asynchrony generated a portfolio effect that stabilized regional species abundance. Our results demonstrated that population demographics and habitat diversity at microgeographic scales can play a significant role in moderating species responses to climate change. Moreover, we suggest that the absence of human activities within study streams preserved natural habitat variation and contributed to asynchrony in brook trout abundance, while the small study area eased monitoring and increased the likelihood of detecting asynchrony. Therefore, anthropogenic habitat degradation, landscape context, and spatial scale must be considered when developing management strategies to monitor and maintain populations that are diverse, stable, and resilient to climate change.

The evolution of ectomycorrhizal symbiosis in the Late Cretaceous is a key driver of explosive diversification in Agaricomycetes

Ectomycorrhizal (EcM) symbiosis, a ubiquitous plant-fungus interaction in forests, evolved in parallel in fungi. Why the evolution of EcM fungi did not necessarily increase ecological opportunities for explosive diversification remains unclear. This study aimed to reveal the driving mechanism of the evolutionary diversification in the fungal class Agaricomycetes, specifically by testing whether the evolution of EcM symbiosis in the Late Cretaceous increased ecological opportunities. The historical character transitions of trophic state and fruitbody form were estimated based on phylogenies inferred from fragments of 89 single-copy genes. Moreover, five analyses were used to estimate the net diversification rates (speciation rate minus extinction rate). The results indicate that the unidirectional evolution of EcM symbiosis occurred 27 times, ranging in date from the Early Triassic to the Early Paleogene. The increased diversification rates appeared to occur intensively at the stem of EcM fungal clades diverging in the Late Cretaceous, coinciding with the rapid diversification of EcM angiosperms. By contrast, the evolution of fruitbody form was not strongly linked with the increased diversification rates. These findings suggest that the evolution of EcM symbiosis in the Late Cretaceous, supposedly with coevolving EcM angiosperms, was the key drive of the explosive diversification in Agaricomycetes.

Impact of the climatic changes in the Pliocene-Pleistocene transition on Irano-Turanian species. The radiation of genus Jurinea (Compositae)

The Irano-Turanian region is one of the world's richest floristic regions and the centre of diversity for numerous xerophytic plant lineages. However, we still have limited knowledge on the timing of evolution and biogeographic history of its flora, and potential drivers of diversification remain underexplored. To fill this knowledge gap, we focus on the Eurasian genus Jurinea (ca. 200 species), one of the largest plant radiations that diversified in the region. We applied a macroevolutionary integrative approach to explicitly test diversification hypotheses and investigate the relative roles of geography vs. ecology and niche conservatism vs. niche lability in speciation processes. To do so, we gathered a sample comprising 77% of total genus richness and obtained data about (1) its phylogenetic history, recovering 502 nuclear loci sequences; (2) growth forms; (3) ecological niche, compiling data of 21 variables for more than 2500 occurrences; and (4) paleoclimatic conditions, to estimate climatic stability. Our results revealed that climate was a key factor in the evolutionary dynamics of Jurinea. The main diversification and biogeographic events that occurred during past climate changes, which led to colder and drier conditions, are the following: (1) the origin of the genus (10.7 Ma); (2) long-distance dispersals from the Iranian Plateau to adjacent regions (∼7-4 Ma); and (3) the diversification shift during Pliocene-Pleistocene Transition (ca. 3 Ma), when net diversification rate almost doubled. Our results supported the pre-adaptation hypothesis, i.e., the evolutionary success of Jurinea was linked to the retention of the ancestral niche adapted to aridity. Interestingly, the paleoclimatic analyses revealed that in the Iranian Plateau long-term climatic stability favoured old-lineage persistence, resulting in current high species richness of semi-arid and cold adapted clades; whereas moderate climate oscillations stimulated allopatric diversification in the lineages distributed in the Circumboreal region. In contrast, growth form lability and high niche disparity among closely related species in the Central Asian clade suggest adaptive radiation to mountain habitats. In sum, the radiation of Jurinea is the result of both adaptive and non-adaptive processes influenced by climatic, orogenic and ecological factors.

Past climate cooling and orogenesis of the Hengduan Mountains have influenced the evolution of Impatiens sect. Impatiens (Balsaminaceae) in the Northern Hemisphere

BACKGROUND

Impatiens sect. Impatiens is distributed across the Northern Hemisphere and has diversified considerably, particularly within the Hengduan Mountains (HDM) in southwest China. Yet, the infra-sectional phylogenetic relationships are not well resolved, largely due to limited taxon sampling and an insufficient number of molecular markers. The evolutionary history of its diversification is also poorly understood. In this study, plastome data and the most complete sampling to date were used to reconstruct a robust phylogenetic framework for this section. The phylogeny was then used to investigate its biogeographical history and diversification patterns, specifically with the aim of understanding the role played by the HDM and past climatic changes in its diversification.

RESULTS

A stable phylogeny was reconstructed that strongly supported both the monophyly of the section and its division into seven major clades (Clades I-VII). Molecular dating and ancestral area reconstruction suggest that sect. Impatiens originated in the HDM and Southeast China around 11.76 Ma, after which different lineages dispersed to Northwest China, temperate Eurasia, and North America, mainly during the Pliocene and Pleistocene. An intercontinental dispersal event from East Asia to western North America may have occurred via the Bering Land Bridge or Aleutian Islands. The diversification rate was high during its early history, especially with the HDM, but gradually decreased over time both within and outside the HDM. Multiple linear regression analysis showed that the distribution pattern of species richness was strongly associated with elevation range, elevation, and mean annual temperature. Finally, ancestral niche analysis indicated that sect. Impatiens originated in a relatively cool, middle-elevation area.

CONCLUSIONS

We inferred the evolutionary history of sect. Impatiens based on a solid phylogenetic framework. The HDM was the primary source or pump of its diversity in the Northern Hemisphere. Orogeny and climate change may have also shaped its diversification rates, as a steady decrease in the diversification rate coincided with the uplift of the HDM and climate cooling. These findings provide insights into the distribution pattern of sect. Impatiens and other plants in the Northern Hemisphere.

Dispersal modes affect Rhamnaceae diversification rates in a differentiated manner

The evolution of dispersal modes has been proposed to promote the diversification of angiosperms. However, little is known about the relative impact of different dispersal modes on plant diversification. We test the association between dispersal modes and diversification rates using Rhamnaceae, the cosmopolitan buckthorn family, as a model. We found that species with diplochory have the highest diversification rates followed by those with myrmecochory and ballistic dispersal, while lineages dispersed by vertebrates and wind have relatively low diversification rates. The difference in diversification rates may be closely linked to the difference in dispersal distance and ecological interactions implied by each dispersal mode. Species which disperse over larger geographical distances may have much higher speciation rates due to the increased chance of establishing isolated populations due to geological barriers or habitat fragmentation. However, long-distance dispersal may also increase the chance of extinction. By contrast, species with short-distance dispersal modes may have low speciation rates. Complex interactions with the surrounding environment may, however, impact diversification rates positively by increasing plant survival and reproductive success.

Phenotypic rate and state are decoupled in response to river-to-lake transitions in cichlid fishes

Geographic access to isolated ecosystems is an important catalyst of adaptive radiation. Cichlid fishes repeatedly colonized rift, crater, and volcanic lakes from surrounding rivers. We test the "lake effect" on the phenotypic rate and state across 253 cichlid species. The rate of evolution was consistently higher (~10-fold) in lakes, and consistent across different dimensions of the phenotype. Rate shifts tended to occur coincident with or immediately following river-to-lake transitions, generally resulting in 2- to 5-fold faster rates than in the founding riverine lineage. By contrast, river- and lake-dwelling cichlids exhibit considerable overlap in phenotypes, generally with less disparity in lakes, but often different evolutionary optima. Taken together, these results suggest that lake radiations rapidly expand into niches largely already represented by ancestral riverine lineages, albeit in different frequencies. Lakes may provide ecological opportunity via ecological release (e.g., from predators/competitors) but need not be coupled with access to novel ecological niches.

The macroevolutionary dynamics of activity pattern in mammals: Primates in context

Activity pattern has played a prominent role in discussions of primate evolutionary history. Most primates are either diurnal or nocturnal, but a small number are active both diurnally and nocturnally. This pattern-cathemerality-also occurs at low frequency across mammals. Using a large sample of mammalian species, this study evaluates two macroevolutionary hypotheses proposed to explain why cathemerality is less common than diurnality and nocturnality: 1) that cathemeral lineages have higher extinction probabilities (differential diversification) and 2) that transitions out of cathemerality are more frequent, making it a less persistent state (differential state persistence). Rates of speciation, extinction, and transition between character states were estimated using hidden-rates models applied to a phylogenetic tree containing 3013 mammals classified by activity pattern. The models failed to detect consistent differences in diversification dynamics among activity patterns, but there is strong support for differential state persistence. Transition rates out of cathemerality tend to be much higher than transition rates out of nocturnality. Transition rates out of diurnality are similar to those for cathemerality in most clades, with two important exceptions: diurnality is unusually persistent in anthropoid primates and sciurid rodents. These two groups combine very low rates of transition out of diurnality with high speciation rates. This combination has no parallels among cathemeral lineages, explaining why diurnality has become more common than cathemerality in mammals. Similarly, the combination of rates found in anthropoids is sufficient to explain the low relative frequency of cathemerality in primates, making it unnecessary to appeal to high extinction probabilities in cathemeral lineages in this clade. These findings support the hypothesis that the distribution of activity patterns across mammals has been influenced primarily by differential state persistence, whereas the effect of differential diversification appears to have been more idiosyncratic.

Genetic and morphological concordance and discordance within the Cyrtodactylus brevipalmatus group (Squamata: Gekkonidae)

We use data sets from the Cyrtodactylus brevipalmatus group with limited genetic and morphological sampling to demonstrate that not accounting for sampling error may adversely influence decisions regarding species delimitation and diagnosis. Lack of geographic sampling between the endpoints of a species range may recover notable interpopulational genetic differentiation consistent with species-level differentiation. Additionally, small population sample sizes may fail recover statistically different diagnostic morphological differences. Combined, these types of sampling error can produce results seemingly consistent with the recognition of cryptic speciesgenetically delimited populations lacking diagnostic morphological characters. This is the current situation within some lineages of the C. brevipalmatus group whereas in others, sampling error is less problematic and does not jeopardize their taxonomy. We note the potential negative effects for comparative biology as a whole if sampling error is not taken into consideration prior to constructing taxonomies.

A continuous fish fossil record reveals key insights into adaptive radiation

Adaptive radiations have been instrumental in generating a considerable amount of life's diversity. Ecological opportunity is thought to be a prerequisite for adaptive radiation1, but little is known about the relative importance of species' ecological versatility versus effects of arrival order in determining which lineage radiates2. Palaeontological records that could help answer this are scarce. In Lake Victoria, a large adaptive radiation of cichlid fishes evolved in an exceptionally short and recent time interval3. We present a rich continuous fossil record extracted from a series of long sediment cores along an onshore-offshore gradient. We reconstruct the temporal sequence of events in the assembly of the fish community from thousands of tooth fossils. We reveal arrival order, relative abundance and habitat occupation of all major fish lineages in the system. We show that all major taxa arrived simultaneously as soon as the modern lake began to form. There is no evidence of the radiating haplochromine cichlid lineage arriving before others, nor of their numerical dominance upon colonization; therefore, there is no support for ecological priority effects. However, although many taxa colonized the lake early and several became abundant, only cichlids persisted in the new deep and open-water habitats once these emerged. Because these habitat gradients are also known to have played a major role in speciation, our findings are consistent with the hypothesis that ecological versatility was key to adaptive radiation, not priority by arrival order nor initial numerical dominance.

The contribution of evolvability to the eco-evolutionary dynamics of competing species

Evolvability is the capacity of a population to generate heritable variation that can be acted upon by natural selection. This ability influences the adaptations and fitness of individual organisms. By viewing this capacity as a trait, evolvability is subject to natural selection and thus plays a critical role in eco-evolutionary dynamics. Understanding this role provides insight into how species respond to changes in their environment and how species coexistence can arise and be maintained. Here, we create a G-function model of competing species, each with a different evolvability. We analyze population and strategy (= heritable phenotype) dynamics of the two populations under clade initiation (when species are introduced into a population), evolutionary tracking (constant, small changes in the environment), adaptive radiation (availability of multiple ecological niches), and evolutionary rescue (extreme environmental disturbances). We find that when species are far from an eco-evolutionary equilibrium, faster-evolving species reach higher population sizes, and when species are close to an equilibrium, slower-evolving species are more successful. Frequent, minor environmental changes promote the extinction of species with small population sizes, regardless of their evolvability. When several niches are available for a species to occupy, coexistence is possible, though slower-evolving species perform slightly better than faster-evolving ones due to the well-recognized inherent cost of evolvability. Finally, disrupting the environment at intermediate frequencies can result in coexistence with cyclical population dynamics of species with different rates of evolution.

Ecological correlates of cranial evolution in the megaradiation of dipsadine snakes

BACKGROUND

Dipsadine snakes represent one of the most spectacular vertebrate radiations that have occurred in any continental setting, with over 800 species in South and Central America. Their species richness is paralleled by stunning ecological diversity, ranging from arboreal snail-eating and aquatic eel-eating specialists to terrestrial generalists. Despite the ecological importance of this clade, little is known about the extent to which ecological specialization shapes broader patterns of phenotypic diversity within the group. Here, we test how habitat use and diet have influenced morphological diversification in skull shape across 160 dipsadine species using micro-CT and 3-D geometric morphometrics, and we use a phylogenetic comparative approach to test the contributions of habitat use and diet composition to variation in skull shape among species.

RESULTS

We demonstrate that while both habitat use and diet are significant predictors of shape in many regions of the skull, habitat use significantly predicts shape in a greater number of skull regions when compared to diet. We also find that across ecological groupings, fossorial and aquatic behaviors result in the strongest deviations in morphospace for several skull regions. We use simulations to address the robustness of our results and describe statistical anomalies that can arise from the application of phylogenetic generalized least squares to complex shape data.

CONCLUSIONS

Both habitat and dietary ecology are significantly correlated with skull shape in dipsadines; the strongest relationships involved skull shape in snakes with aquatic and fossorial lifestyles. This association between skull morphology and multiple ecological axes is consistent with a classic model of adaptive radiation and suggests that ecological factors were an important component in driving morphological diversification in the dipsadine megaradiation.

Reed bamboos drive skull shape evolution in bush frogs of the Western Ghats, Peninsular India

Reed bamboo is a major ecological and economic resource for many animals, including humans. Nonetheless, the influence of this plant's evolutionary role on the morphology of animal species remains unexplored. Here, we investigated the significance of bamboo habitats as ecological opportunities in shaping the skull morphology of bush frogs (Raorchestes) from the Western Ghats, Peninsular India. We applied a three-dimensional (3D) geometric morphometric approach to capture the skull shape of 55 species of bush frogs. We visualized the skull shape variables in phylomorphospace with principal component analysis and performed phylogenetic generalized least-squares analysis to assess the impact of cranial size (evolutionary allometry) and habitat (bamboo or non-bamboo) on cranial shape. We quantified the morphological disparity between bamboo and non-bamboo bush frogs' skull shape, and employed RRphylo, a phylogenetic ridge regression method, to access the evolutionary rate and rate shifts of skull shape change. The phylomorphospace delineated bamboo and non-bamboo bush frogs. While cranial shape exhibited a significant but smaller association with size, its association with habitat type was non-significant. We detected, however, significant differences in skull shape between the two frog groups, with bamboo frogs showing higher morphological disparity and a remarkable shift in the evolutionary rate of skull shape diversification. These findings underscore the role of reed bamboo in the evolution of skull shape in the radiation of frogs, endemic to the Western Ghats. We demonstrate that the association between the members of two distinct endemic clades (bamboo reeds and bamboo frogs) is the outcome of a deep-time ecological opportunity that dates back to the Miocene.

Beaks promote rapid morphological diversification along distinct evolutionary trajectories in labrid fishes (Eupercaria: Labridae)

The upper and lower jaws of some wrasses (Eupercaria: Labridae) possess teeth that have been coalesced into a strong durable beak that they use to graze on hard coral skeletons, hard-shelled prey, and algae, allowing many of these species to function as important ecosystem engineers in their respective marine habitats. While the ecological impact of the beak is well understood, questions remain about its evolutionary history and the effects of this innovation on the downstream patterns of morphological evolution. Here we analyze 3D cranial shape data in a phylogenetic comparative framework and use paleoclimate modeling to reconstruct the evolution of the labrid beak across 205 species. We find that wrasses evolved beaks three times independently, once within odacines and twice within parrotfishes in the Pacific and Atlantic Oceans. We find an increase in the rate of shape evolution in the Scarus+Chlorurus+Hipposcarus (SCH) clade of parrotfishes likely driven by the evolution of the intramandibular joint. Paleoclimate modeling shows that the SCH clade of parrotfishes rapidly morphologically diversified during the middle Miocene. We hypothesize that possession of a beak in the SCH clade coupled with favorable environmental conditions allowed these species to rapidly morphologically diversify.

Trait-based species richness: ecology and macroevolution

Understanding the origins of species richness patterns is a fundamental goal in ecology and evolutionary biology. Much research has focused on explaining two kinds of species richness patterns: (i) spatial species richness patterns (e.g. the latitudinal diversity gradient), and (ii) clade-based species richness patterns (e.g. the predominance of angiosperm species among plants). Here, I highlight a third kind of richness pattern: trait-based species richness (e.g. the number of species with each state of a character, such as diet or body size). Trait-based richness patterns are relevant to many topics in ecology and evolution, from ecosystem function to adaptive radiation to the paradox of sex. Although many studies have described particular trait-based richness patterns, the origins of these patterns remain far less understood, and trait-based richness has not been emphasised as a general category of richness patterns. Here, I describe a conceptual framework for how trait-based richness patterns arise compared to other richness patterns. A systematic review suggests that trait-based richness patterns are most often explained by when each state originates within a group (i.e. older states generally have higher richness), and not by differences in transition rates among states or faster diversification of species with certain states. This latter result contrasts with the widespread emphasis on diversification rates in species-richness research. I show that many recent studies of spatial richness patterns are actually studies of trait-based richness patterns, potentially confounding the causes of these patterns. Finally, I describe a plethora of unanswered questions related to trait-based richness patterns.

Genomic data provide a robust phylogeny backbone for Rhodiola L. (Crassulaceae) and reveal extensive reticulate evolution during its rapid radiation

The Tibetan Plateau and adjacent mountain regions (TP; including the Tibetan Plateau, Himalaya, Hengduan Mountains and Mountains of Central Asia) harbor great biodiversity, some lineages on which may have undergone rapid radiations. However, only a few studies have investigated the evolutionary pattern of such diversification in depth using genomic data. In this study, we reconstructed a robust phylogeny backbone of Rhodiola, a lineage that may have undergone rapid radiation in the TP, using Genotyping-by-sequencing data, and conducted a series of gene flow and diversification analyses. The concatenation and coalescent-based methods yield similar tree topologies, and five well-supported clades were revealed. Potential gene flow and introgression events were detected, both between species from different major clades and closely related species, suggesting pervasive hybridization and introgression. An initial rapid and later slowdown of the diversification rate was revealed, indicating niche filling. Molecular dating and correlation analyses showed that the uplift of TP and global cooling in the mid-Miocene might have played an important role in promoting the rapid radiation of Rhodiola. Our work demonstrates that gene flow and introgression might be an important contributor to rapid radiation possibly by quickly reassembling old genetic variation into new combinations.

The Phylogenomic and Biogeographic History of the Gartersnakes, Watersnakes, and Allies (Natricidae: Thamnophiini)

North American Thamnophiini (gartersnakes, watersnakes, brownsnakes, and swampsnakes) are an ecologically and phenotypically diverse temperate clade of snakes representing 61 species across 10 genera. In this study, we estimate phylogenetic trees using ∼3,700 ultraconserved elements (UCEs) for 76 specimens representing 75% of all Thamnophiini species. We infer phylogenies using multispecies coalescent methods and time calibrate them using the fossil record. We also conducted ancestral area estimation to identify how major biogeographic boundaries in North America affect broadscale diversification in the group. While most nodes exhibited strong statistical support, analysis of concordant data across gene trees reveals substantial heterogeneity. Ancestral area estimation demonstrated that the genus Thamnophis was the only taxon in this subfamily to cross the Western Continental Divide, even as other taxa dispersed southward toward the tropics. Additionally, levels of gene tree discordance are overall higher in transition zones between bioregions, including the Rocky Mountains. Therefore, the Western Continental Divide may be a significant transition zone structuring the diversification of Thamnophiini during the Neogene and Pleistocene. Here we show that despite high levels of discordance across gene trees, we were able to infer a highly resolved and well-supported phylogeny for Thamnophiini, which allows us to understand broadscale patterns of diversity and biogeography.

Camera Traps Uncover the Behavioral Ecology of an Endemic, Cryptic Monkey Species in the Congo Basin

Guenons are the most diverse clade of African primates, and many species living within the core of the Congo Basin rainforest are still understudied. The recently described guenon species, Cercopithecus lomamiensis, known as lesula, is a cryptic, semi-terrestrial species endemic to the central Congo Basin in the Democratic Republic of the Congo. The recent IUCN Red List Assessment recognizes lesula's risk of extinction in the wild as Vulnerable. The objective of our study was to use camera traps to expand knowledge on the behavioral ecology of lesula. We conducted three systematic, terrestrial camera trap (CT) surveys within Lomami National Park and buffer zone (Okulu: 2013; Losekola: 2014; E15: 2015). We accumulated 598 independent events of lesula over 5960 CT days from 92 CTs. Typical of Cercopithecus species, camera trap videos reveal that lesula has a diurnal activity pattern, birth seasonality, a group size of up to 32 individuals, and social organization with female philopatry and male dispersal. Results also suggest that lesula are highly terrestrial, distinguishing them from other Cercopithecus species, which are mostly arboreal. Our study provides new information about the behavioral ecology of this little-studied primate, generating species-specific knowledge of a threatened species for successful conservation planning.

Emergence and maintenance of stable coexistence during a long-term multicellular evolution experiment

The evolution of multicellular life spurred evolutionary radiations, fundamentally changing many of Earth’s ecosystems. Yet little is known about how early steps in the evolution of multicellularity transform eco-evolutionary dynamics, e.g., via niche expansion processes that may facilitate coexistence. Using long-term experimental evolution in the snowflake yeast model system, we show that the evolution of multicellularity drove niche partitioning and the adaptive divergence of two distinct, specialized lineages from a single multicellular ancestor. Over 715 daily transfers, snowflake yeast were subject to selection for rapid growth in rich media, followed by selection favoring larger group size. Both small and large cluster-forming lineages evolved from a monomorphic ancestor, coexisting for over ~4,300 generations. These small and large sized snowflake yeast lineages specialized on divergent aspects of a trade-off between growth rate and survival, mirroring predictions from ecological theory. Through modeling and experimentation, we demonstrate that coexistence is maintained by a trade-off between organismal size and competitiveness for dissolved oxygen. Taken together, this work shows how the evolution of a new level of biological individuality can rapidly drive adaptive diversification and the expansion of a nascent multicellular niche, one of the most historically-impactful emergent properties of this evolutionary transition.

Blowin' in the wind: Dispersal of Glossy Ibis Plegadis falcinellus in the West Mediterranean basin

The movement of organisms is a central process in ecology and evolution, and understanding the selective forces shaping the spatial structure of populations is essential to conservation. Known as a trans-Saharan migrant capable of long-distance flights, the Glossy Ibis Plegadis falcinellus' dispersal remains poorly known. We started a ringing scheme in 2008, the first of its kind in North Africa, and ringed 1121 fledglings over 10 years, of which 265 (23.6%) were resighted. Circular statistics and finite mixture models of natal dispersal indicated: (1) a strong West/Northwest-East/Southeast flight orientation; (2) Glossy Ibis colonies from North Africa and Southern Europe (particularly on the Iberian Peninsula) are closely linked through partial exchanges of juvenile and immature birds; (3) unlike birds from Eastern Europe, North African Glossy Ibis disperse to but do not seem to undergo regular round-trip migration to the Sahel; (4) young adults (>2-years-old) have a higher probability of dispersing further than individuals in their first calendar year (<1-year-old); and (5) dispersal distance is not influenced by sex or morphometric traits. Together, these results enhance our knowledge of the dispersal and metapopulation dynamics of Glossy Ibis, revealing large-scale connectivity between the Iberian Peninsula and Algeria, likely driven by the spatial heterogeneity of the landscape in these two regions and the prevailing winds in the Western Mediterranean.

Unraveling the macroevolution of horseshoe bats (Chiroptera: Rhinolophidae: Rhinolophus)

Unraveling the diversification mechanisms of organisms is a fundamental and important macroevolutionary question regarding the diversity, ecological niche, and morphological divergence of life. However, many studies have only explored diversification mechanisms via isolated factors. Here, based on comparative phylogenetic analysis, we performed a macroevolutionary examination of horseshoe bats (Chiroptera: Rhinolophidae: Rhinolophus), to reveal the inter-relationships among diversification, intrinsic/extrinsic factors, and climatic ecological niche characteristics. Results showed a general slowing trajectory during diversification, with two dispersal events from Asia into Southeast Asia and Africa playing key roles in shaping regional heterogeneous diversity. Morphospace expansions of the investigated traits (e.g., body size, echolocation, and climate niche) revealed a decoupled pattern between diversification trajectory and trait divergence, suggesting that other factors (e.g., biotic interactions) potentially played a key role in recent diversification. Based on ancestral traits and pathway analyses, most Rhinolophus lineages belonging to the same region overlapped with each other geographically and were positively associated with the diversification rate, implying a competitive prelude to speciation. Overall, our study showed that multiple approaches need to be integrated to address diversification history. Rather than a single factor, the joint effects of multiple factors (biogeography, environmental drivers, and competition) are responsible for the current diversity patterns in horseshoe bats, and a corresponding multifaceted strategy is recommended to study these patterns in the future.

TE, Solari S, Colmenares-Pinzon J, Nivelo C, Rodríguez Herrera B, Merino W, Medina CE, Murillo-García O, Pardiñas UF. Systematics and diversification of the Ichthyomyini (Cricetidae, Sigmodontinae) revisited: evidence from molecular, morphological, and combined approaches

Ichthyomyini, a morphologically distinctive group of Neotropical cricetid rodents, lacks an integrative study of its systematics and biogeography. Since this tribe is a crucial element of the Sigmodontinae, the most speciose subfamily of the Cricetidae, we conducted a study that includes most of its recognized diversity (five genera and 19 species distributed from southern Mexico to northern Bolivia). For this report we analyzed a combined matrix composed of four molecular markers (RBP3, GHR, RAG1, Cytb) and 56 morphological traits, the latter including 15 external, 14 cranial, 19 dental, five soft-anatomical and three postcranial features. A variety of results were obtained, some of which are inconsistent with the currently accepted classification and understanding of the tribe. Ichthyomyini is retrieved as monophyletic, and it is divided into two main clades that are here recognized as subtribes: one to contain the genus Anotomys and the other composed by the remaining genera. Neusticomys (as currently recognized) was found to consist of two well supported clades, one of which corresponds to the original concept of Daptomys. Accordingly, we propose the resurrection of the latter as a valid genus to include several species from low to middle elevations and restrict Neusticomys to several highland forms. Numerous other revisions are necessary to reconcile the alpha taxonomy of ichthyomyines with our phylogenetic results, including placement of the Cajas Plateau water rat (formerly Chibchanomys orcesi) in the genus Neusticomys (sensu stricto), and the recognition of at least two new species (one in Neusticomys, one in Daptomys). Additional work is necessary to confirm other unanticipated results, such as the non-monophyletic nature of Rheomys and the presence of a possible new genus and species from Peru. Our results also suggest that ichthyomyines are one of the main Andean radiations of sigmodontine cricetids, with an evolutionary history dating to the Late Miocene and subsequent cladogenesis during the Pleistocene.

Why is the beautyberry so colourful? Evolution, biogeography, and diversification of fruit colours in Callicarpa (Lamiaceae)

Fruit colour is essential to seed dispersal, speciation, and biological diversity in global ecosystems. The relationship between fruit-colour variation and species diversification has long been of interest in evolutionary biology, but remains poorly understood at the genus level. Here, we used Callicarpa, a typical representative of pantropical angiosperm, to analyse whether fruit colours are correlated with biogeographic distribution, dispersal events, and diversification rate. We estimated a time-calibrated phylogeny for Callicarpa and reconstructed ancestral fruit colour. Utilizing phylogenetic methods, we estimated the major dispersal events across the phylogenetic tree and the most likely fruit colours related to each dispersal event, and tested whether the dispersal frequencies and distances of the four fruit colours between major biogeographical areas were equal. We then tested whether fruit colours are correlated with latitude, elevation, and diversification rate. Biogeographical reconstructions showed that Callicarpa originated in the East Asia and Southeast Asia during the Eocene (∼35.53 Ma) and diverse species diverged mainly in the Miocene and lasted into the Pleistocene. Large-scale dispersal events were significantly associated with violet-fruited lineages. Furthermore, different fruit colours were markedly correlated with different latitudes and elevations (e.g., violet fruits were correlated with higher latitudes and elevations; red fruits and black fruits with lower latitudes; white fruits with higher elevations). Notably, violet fruits were statistically associated with highest diversification rates, driving fruit colour variation among different regions globally. Our results contribute to further understanding why fruit colour is so variable at the genus level of angiosperms in different areas around the world.

Evolutionary models demonstrate rapid and adaptive diversification of Australo-Papuan pythons

Lineages may diversify when they encounter available ecological niches. Adaptive divergence by ecological opportunity often appears to follow the invasion of a new environment with open ecological space. This evolutionary process is hypothesized to explain the explosive diversification of numerous Australian vertebrate groups following the collision of the Eurasian and Australian plates 25 Mya. One of these groups is the pythons, which demonstrate their greatest phenotypic and ecological diversity in Australo-Papua (Australia and New Guinea). Here, using an updated and near complete time-calibrated phylogenomic hypothesis of the group, we show that following invasion of this region, pythons experienced a sudden burst of speciation rates coupled with multiple instances of accelerated phenotypic evolution in head and body shape and body size. These results are consistent with adaptive radiation theory with an initial rapid niche-filling phase and later slow-down approaching niche saturation. We discuss these findings in the context of other Australo-Papuan adaptive radiations and the importance of incorporating adaptive diversification systems that are not extraordinarily species-rich but ecomorphologically diverse to understand how biodiversity is generated.

Global patterns and rates of habitat transitions across the eukaryotic tree of life

The successful colonization of new habitats has played a fundamental role during the evolution of life. Salinity is one of the strongest barriers for organisms to cross, which has resulted in the evolution of distinct marine and non-marine (including both freshwater and soil) communities. Although microbes represent by far the vast majority of eukaryote diversity, the role of the salt barrier in shaping the diversity across the eukaryotic tree is poorly known. Traditional views suggest rare and ancient marine/non-marine transitions but this view is being challenged by the discovery of several recently transitioned lineages. Here, we investigate habitat evolution across the tree of eukaryotes using a unique set of taxon-rich phylogenies inferred from a combination of long-read and short-read environmental metabarcoding data spanning the ribosomal DNA operon. Our results show that, overall, marine and non-marine microbial communities are phylogenetically distinct but transitions have occurred in both directions in almost all major eukaryotic lineages, with hundreds of transition events detected. Some groups have experienced relatively high rates of transitions, most notably fungi for which crossing the salt barrier has probably been an important aspect of their successful diversification. At the deepest phylogenetic levels, ancestral habitat reconstruction analyses suggest that eukaryotes may have first evolved in non-marine habitats and that the two largest known eukaryotic assemblages (TSAR and Amorphea) arose in different habitats. Overall, our findings indicate that the salt barrier has played an important role during eukaryote evolution and provide a global perspective on habitat transitions in this domain of life.

Songbirds of the Americas show uniform morphological evolution despite heterogeneous diversification

Studying the relationship between diversification and functional trait evolution among broadly co-occurring clades can shed light on interactions between ecology and evolutionary history. However, evidence from many studies is compromised because of their focus on overly broad geographic or narrow phylogenetic scales. We addressed these limitations by studying 46 independent, biogeographically delimited clades of songbirds that dispersed from the Eastern Hemisphere into the Americas and assessed (1) whether diversification has varied through time and/or among clades within this assemblage, (2) the extent of heterogeneity in clade-specific morphological trait disparity and (3) whether morphological disparity among these clades is consistent with a uniform diversification model. We found equivalent support for constant rates birth-death and density-dependent speciation processes, with notable outliers having significantly fewer or more species than expected given their age. We also found substantial variation in morphological disparity among these clades, but that variation was broadly consistent with uniform evolutionary rates, despite the existence of diversification outliers. These findings indicate relatively continuous, ongoing morphological diversification, arguing against conceptual models of adaptive radiation in these continental clades. Additionally, they suggest surprisingly consistent diversification among the majority of these clades, despite tremendous variance in colonization history, habitat valences and trophic specializations that exist among continental clades of birds.

Geometric Morphometrics Reveal Shape Differences in the Toes of Urban Lizards

Urbanization, despite its destructive effects on natural habitats, offers species an opportunity to colonize novel niches. Previous research found that urban Anolis lizards in Puerto Rico had increased adhesive toepad area and more ventral toepad scales, traits that are likely adaptive and genetically based. We further investigated these phenotypic changes using geometric morphometrics to measure differences in toe shape, toepad shape, and lamellar morphology. Our results indicate that the increased toepad area of urban Anolis cristatellus lizards in Puerto Rico is not simply an isometric increase in toe size. Toes of urban populations exhibit multiple disproportional changes compared to forest lizards, with a larger proportion of the toe length covered in adhesive toepad. In addition, the toepads of urban lizards increase more in length than width. Lastly, lizards in urban populations exhibit both increased number of lamellae as well as increased spacing between individual lamellae. We also observed regional variation, with urban specimens having significantly more disparity, suggesting similar processes of urban adaptation are likely happening in parallel across the island, yet with region-specific idiosyncrasies, possibly generating more variation in toepad morphology across urban specimens as compared to forest specimens. Considering the use of geometric morphometrics, we found that specimen preparation, specifically how flat and straight toes are during imaging, to be an important factor affecting our data, more so than specimen size or any other meaningful morphological variation. In addition, we found that landmark and semilandmark data can be used to directly estimate toepad area, offering the opportunity to streamline future studies. In conclusion, our results highlight the value of considering toepad morphology in more detail beyond adhesive pad area or number of lamellae. Geometric morphometrics tools may be employed to elucidate subtle differences in shape to better allow researchers to connect changes in morphology to ecology and adhesive performance.

Exploitation of an ancestral pheromone biosynthetic pathway contributes to diversification in Heliconius butterflies

During courtship, male butterflies of many species produce androconial secretions containing male sex pheromones (MSPs) that communicate species identity and affect female choice. MSPs are thus likely candidates as reproductive barriers, yet their role in speciation remains poorly studied. Although Heliconius butterflies are a model system in speciation, their MSPs have not been investigated from a macroevolutionary perspective. We use GC/MS to characterize male androconial secretions in 33 of the 69 species in the Heliconiini tribe. We found these blends to be species-specific, consistent with a role in reproductive isolation. We detected a burst in blend diversification rate at the most speciose genus, Heliconius; a consequence of Heliconius and Eueides species using a fatty acid (FA) metabolic pathway to unlock more complex blends than basal Heliconiini species, whose secretions are dominated by plant-like metabolites. A comparison of 10 sister species pairs demonstrates a striking positive correlation between blend dissimilarity and range overlap, consistent with character displacement or reinforcement in sympatry. These results demonstrate for the first time that MSP diversification can promote reproductive isolation across this group of butterflies, showcasing how implementation of an ancestral trait, the co-option of the FA metabolic pathway for pheromone production, can facilitate rapid speciation.

Environmental correlates of phenotypic evolution in ecologically diverse Liolaemus lizards

Evolutionary correlations between phenotypic and environmental traits characterize adaptive radiations. However, the lizard genus Liolaemus, one of the most ecologically diverse terrestrial vertebrate radiations on earth, has so far shown limited or mixed evidence of adaptive diversification in phenotype. Restricted use of comprehensive environmental data, incomplete taxonomic representation and not considering phylogenetic uncertainty may have led to contradictory evidence. We compiled a 26-taxon dataset for the Liolaemus gracilis species group, representing much of the ecological diversity represented within Liolaemus and used environmental data to characterize how environments occupied by species' relate to phenotypic evolution. Our analyses, explicitly accounting for phylogenetic uncertainty, suggest diversification in phenotypic traits toward the present, with body shape evolution rapidly evolving in this group. Body shape evolution correlates with the occupation of different structural habitats indicated by vegetation axes suggesting species have adapted for maximal locomotory performance in these habitats. Our results also imply that the effects of phylogenetic uncertainty and model misspecification may be more extensive on univariate, relative to multivariate analyses of evolutionary correlations, which is an important consideration in analyzing data from rapidly radiating adaptive radiations.

Maintenance of local adaptation despite gene flow in a coastal songbird

Adaptation to local environments is common in widespread species and the basis of ecological speciation. The song sparrow (Melospiza melodia) is a widespread, polytypic passerine that occurs in shrubland habitats throughout North America. We examined the population structure of two parapatric subspecies that inhabit different environments: the Atlantic song sparrow (M. m. atlantica), a coastal specialist, and the eastern song sparrow (M. m. melodia), a shrubland generalist. These populations lacked clear mitochondrial population structure, yet coastal birds formed a distinct nuclear genetic cluster. We found weak overall genomic differentiation between these subspecies, suggesting either recent divergence, extensive gene flow, or a combination thereof. There was a steep genetic cline at the transition to coastal habitats, consistent with isolation by environment, not isolation by distance. A phenotype under divergent selection, bill size, varied with the amount of coastal ancestry in transitional areas, but larger bill size was maintained in coastal habitats regardless of ancestry, further supporting a role for selection in the maintenance of these subspecies. Demographic modeling suggested a divergence history of limited gene flow followed by secondary contact, which has emerged as a common theme in adaptive divergence across taxa.

Macroevolutionary Analyses Provide New Evidence of Phasmid Wings Evolution as a Reversible Process

The concept that complex ancestral traits can never be recovered after their loss is still widely accepted, despite phylogenetic and molecular approaches suggest instances where phenotypes may have been lost throughout the evolutionary history of a clade and subsequently reverted back in derived lineages. One of the first and most notable examples of such a process is wing evolution in phasmids; this polyneopteran order of insects, which comprises stick and leaf insects, has played a central role in initiating a long-standing debate on the topic. In this study, a novel and comprehensive time tree including over 300 Phasmatodea species is used as a framework for investigating wing evolutionary patterns in the clade. Despite accounting for several possible biases and sources of uncertainty, macroevolutionary analyses consistently revealed multiple reversals to winged states taking place after their loss, and reversibility is coupled with higher species diversification rates. Our findings support a loss of or reduction in wings that occurred in the lineage leading to the extant phasmid most recent common ancestor, and brachyptery is inferred to be an unstable state unless co-opted for nonaerodynamic adaptations. We also explored how different assumptions of wing reversals probability could impact their inference: we found that until reversals are assumed to be over 30 times more unlikely than losses, they are consistently inferred despite uncertainty in tree and model parameters. Our findings demonstrate that wing evolution is a reversible and dynamic process in phasmids and contribute to our understanding of complex trait evolution.

Patterns of Phenotypic Evolution Associated with Marine/Freshwater Transitions in Fishes

Evolutionary transitions between marine and freshwater ecosystems have occurred repeatedly throughout the phylogenetic history of fishes. The theory of ecological opportunity predicts that lineages that colonize species-poor regions will have greater potential for phenotypic diversification than lineages invading species-rich regions. Thus, transitions between marine and freshwaters may promote phenotypic diversification in trans-marine/freshwater fish clades. We used phylogenetic comparative methods to analyze body size data in nine major fish clades that have crossed the marine/freshwater boundary. We explored how habitat transitions, ecological opportunity, and community interactions influenced patterns of phenotypic diversity. Our analyses indicated that transitions between marine and freshwater habitats did not drive body size evolution, and there are few differences in body size between marine and freshwater lineages. We found that body size disparity in freshwater lineages is not correlated with the number of independent transitions to freshwaters. We found a positive correlation between body size disparity and overall species richness of a given area, and a negative correlation between body size disparity and diversity of closely related species. Our results indicate that the diversity of incumbent freshwater species does not restrict phenotypic diversification, but the diversity of closely related taxa can limit body size diversification. Ecological opportunity arising from colonization of novel habitats does not seem to have a major effect in the trajectory of body size evolution in trans-marine/freshwater clades. Moreover, competition with closely related taxa in freshwaters has a greater effect than competition with distantly related incumbent species.

Evolutionary transitions in diet influence the exceptional diversification of a lizard adaptive radiation

Background

Diet is a key component of a species ecological niche and plays critical roles in guiding the trajectories of evolutionary change. Previous studies suggest that dietary evolution can influence the rates and patterns of species diversification, with omnivorous (animal and plant, ‘generalist’) diets slowing down diversification compared to more restricted (‘specialist’) herbivorous and carnivorous diets. This hypothesis, here termed the “dietary macroevolutionary sink” hypothesis (DMS), predicts that transitions to omnivorous diets occur at higher rates than into any specialist diet, and omnivores are expected to have the lowest diversification rates, causing an evolutionary sink into a single type of diet. However, evidence for the DMS hypothesis remains conflicting. Here, we present the first test of the DMS hypothesis in a lineage of ectothermic tetrapods—the prolific Liolaemidae lizard radiation from South America.

Results

Ancestral reconstructions suggest that the stem ancestor was probably insectivorous. The best supported trait model is a diet-dependent speciation rate, with independent extinction rates. Herbivory has the highest net diversification rate, omnivory ranks second, and insectivory has the lowest. The extinction rate is the same for all three diet types and is much lower than the speciation rates. The highest transition rate was from omnivory to insectivory, and the lowest transition rates were between insectivory and herbivory.

Conclusions

Our findings challenge the core prediction of the DMS hypothesis that generalist diets represent an ‘evolutionary sink’. Interestingly, liolaemid lizards have rapidly and successfully proliferated across some of the world’s coldest climates (at high elevations and latitudes), where species have evolved mixed arthropod-plant (omnivore) or predominantly herbivore diets. This longstanding observation is consistent with the higher net diversification rates found in both herbivory and omnivory. Collectively, just like the evolution of viviparity has been regarded as a ‘key adaptation’ during the liolaemid radiation across cold climates, our findings suggest that transitions from insectivory to herbivory (bridged by omnivory) are likely to have played a role as an additional key adaptation underlying the exceptional diversification of these reptiles across extreme climates.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-022-02028-3.