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Phenotypic covariation among suites of traits may constrain or promote diversification both within and between species, yet few studies have empirically tested this relationship. In this study, we investigate whether phenotypic covariation of craniofacial traits is associated with diversification in an adaptive radiation of pupfishes found only on San Salvador Island, Bahamas (SSI). The radiation includes generalist, durophagous, and lepidophagous species. We compared phenotypic variation and covariation (i.e., the P matrix) between (1) allopatric populations of generalist pupfish from neighboring islands and estuaries in the Caribbean, (2) SSI pupfish allopatric lake populations with only generalist pupfish, and (3) SSI lake populations containing the full radiation in sympatry. Additionally, we examine patterns observed in the P matrices of two independent lab-reared F2 hybrid crosses of the two most morphologically distinct members of the radiation to make inferences about the underlying mechanisms contributing to the variation in craniofacial traits in SSI pupfishes. We found that the P matrix of SSI allopatric generalist populations exhibited higher levels of mean trait correlation, constraints, and integration with simultaneously lower levels of flexibility compared to allopatric generalist populations on other Caribbean islands and sympatric populations of all three species on SSI. We also document that while many craniofacial traits appear to result from additive genetic effects, variation in key traits such as head depth, maxilla length, and lower jaw length may be produced via non-additive genetic mechanisms. Ultimately, this study suggests that differences in phenotypic covariation significantly contribute to producing and maintaining organismal diversity.

Environmental transitions, such as the salinity divide separating marine and fresh waters, shape biodiversity over both shallow and deep timescales, opening up new niches and creating opportunities for accelerated speciation and adaptive radiation. Understanding the genetics of environmental adaptation is central to understanding how organisms colonise and subsequently diversify in new habitats. We used time‐resolved transcriptomics to contrast the hyposalinity stress responses of two diatoms. Skeletonema marinoi has deep marine ancestry but has recently invaded brackish waters. Cyclotella cryptica has deep freshwater ancestry and can withstand a much broader salinity range. Skeletonema marinoi is less adept at mitigating even mild salinity stress compared to Cyclotella cryptica, which has distinct mechanisms for rapid mitigation of hyposaline stress and long‐term growth in low salinity. We show that the cellular mechanisms underlying low salinity tolerance, which has allowed diversification across freshwater habitats worldwide, includes elements that are both conserved and variable across the diatom lineage. The balance between ancestral and lineage‐specific environmental responses in phytoplankton have shaped marine–freshwater transitions on evolutionary timescales and, on contemporary timescales, will affect which lineages survive and adapt to changing ocean conditions. [ABSTRACT FROM AUTHOR]

The spider genus Dysdera has undergone a remarkable diversification in the oceanic archipelago of the Canary Islands, with ~60 endemic species having originated during the 20 million years since the origin of the archipelago. This evolutionary radiation has been accompanied by substantial dietary shifts, often characterised by phenotypic modifications encompassing morphological, metabolic and behavioural changes. Hence, these endemic spiders represent an excellent model for understanding the evolutionary drivers and to pinpoint the genomic determinants underlying adaptive radiations. Recently, we achieved the first chromosome‐level genome assembly of one of the endemic species, D. silvatica, providing a high‐quality reference sequence for evolutionary genomics studies. Here, we conducted a low coverage‐based resequencing study of a natural population of D. silvatica from La Gomera island. Taking advantage of the new high‐quality genome, we characterised genome‐wide levels of nucleotide polymorphism, divergence and linkage disequilibrium, and inferred the demographic history of this population. We also performed comprehensive genome‐wide scans for recent positive selection. Our findings uncovered exceptionally high levels of nucleotide diversity and recombination in this geographically restricted endemic species, indicative of large historical effective population sizes. We also identified several candidate genomic regions that are potentially under positive selection, highlighting relevant biological processes, such as vision and nitrogen extraction as potential adaptation targets. These processes may ultimately drive species diversification in this genus. This pioneering study of spiders that are endemic to an oceanic archipelago lays the groundwork for broader population genomics analyses aimed at understanding the genetic mechanisms driving adaptive radiation in island ecosystems. [ABSTRACT FROM AUTHOR]

Background: Echolocation was a key development in toothed whale evolution, enabling their adaptation and diversification across various environments. Previous bioacoustic and morphological studies suggest that environmental pressures have influenced the evolution of echolocation in toothed whales. This hypothesis demands further investigation, especially regarding the molecular mechanisms involved in the adaptive radiation of toothed whales across multiple habitats. Here we show that the coding sequences of four hearing genes involved in echolocation (CDH23, prestin, TMC1, and CLDN14) have different signatures of molecular evolution among riverine, coastal, and oceanic dolphins, suggesting that the evolutionary constraints of these habitats shaped the underlying genetic diversity of the toothed whale sonar. Results: Our comparative analysis across 37 odontocete species revealed patterns of accelerated evolution within coastal and riverine lineages, supporting the hypothesis that shallow habitats pose specific selective pressures to sonar propagation, which are not found in the deep ocean. All toothed whales with genes evolving under positive selection are shallow coastal species, including three species that have recently diverged from freshwater lineages (Cephalorhynchus commersonii, Sotalia guianensis, and Orcaella heinsohni - CDH23), and three species that operate specialized Narrow Band High Frequency (NBHF) Sonars (Phocoena sinus - prestin, Neophocaena phocaenoides - TMC1 and Cephalorhynchus commersonii - CDH23). For river dolphins and deep-diving toothed whales, we found signatures of positive selection and molecular convergence affecting specific sites on CDH23, TMC1, and prestin. Positively selected sites (PSS) were different in number, identity, and substitution rates (dN/dS) across riverine, coastal, and oceanic toothed whales. Conclusion: Here we shed light on potential molecular mechanisms underlying the diversification of toothed whale echolocation. Our results suggest that toothed whale hearing genes changed under different selective pressures in coastal, riverine, and oceanic environments. [ABSTRACT FROM AUTHOR]

Pterosaurs, the first true flying vertebrates, played a crucial role in Mesozoic terrestrial ecosystems. However, our understanding of their ability to move around on the ground and, more broadly, their terrestrial paleoecology remains limited. Here, we demonstrate an unexpectedly high degree of variation in the hands and feet of pterosaurs, comparable with that observed in extant birds. This suggests that pterosaurs were adapted to a remarkably broad range of non-aerial locomotor ecologies. Small, early, long-tailed pterosaurs (non-pterodactyliforms) exhibit extreme modifications in their hand and foot proportions indicative of climbing lifestyles. By contrast, the hands and feet of later, short-tailed pterosaurs (pterodactyliforms) typically exhibit morphologies consistent with more ground-based locomotor ecologies. These changes in proportions correlate with other modifications to pterosaur anatomy, critically, the separation along the midline of the flight membrane (cruropatagium) that linked the hindlimbs, enabling a much more effective locomotory ability on the ground. Together, these changes map a significant event in tetrapod evolution: a mid-Mesozoic colonization of terrestrial environments by short-tailed pterosaurs. This transition to predominantly ground-based locomotor ecologies did not occur as a single event coinciding with the origin of short-tailed forms but evolved independently within each of the four principal radiations: euctenochasmatians, ornithocheiroids, dsungaripteroids, and azhdarchoids. Invasion of terrestrial environments by pterosaurs facilitated the evolution of a wide range of novel feeding ecologies, while the freedom from limitations imposed by climbing permitted an increase in body size, ultimately enabling the evolution of gigantism in multiple lineages. • The hands and feet of pterosaurs were adapted to a broad range of locomotor ecologies • Early pterosaurs had a scansorial mode of life, which restricted maximum body size • Anatomical changes in later pterosaurs led to more effective terrestrial ability • Invasion of terrestrial habitats facilitated diverse feeding ecologies and gigantism Smyth et al. show that pterosaurs exhibit significant disparity in their hand and foot morphologies. This indicates that they occupied a broad range of locomotor ecologies. Early pterosaurs were adapted for climbing, while later forms evolved more effective terrestrial locomotion, which facilitated diversification and the evolution of gigantism. [ABSTRACT FROM AUTHOR]

Background: The genus Robinsonia DC. (tribe Senecioneae, Asteraceae) endemic to the Juan Fernández Islands in Chile is one of the most conspicuous insular plant groups in the world. Unlike typical herbaceous Asteraceae plants, these plants demonstrate spectacular and unusual rosette tree growth forms as shown by the alpine giant senecios (genus Dendrosenecio, tribe Senecioneae) endemic to the East African mountains. However, monophyly of the genus and phylogenetic relationships among species of Robinsonia as well as their plastome evolution remain elusive. This study aims to explore their phylogeny, species diversification, and molecular evolution based on the complete plastome sequences in the context of adaptive radiation on oceanic islands. Results: The insular Robinsonia plastomes are highly conserved in their structures and organization of contents. Five divergence hotspots as potential chloroplast markers and five positively selected coding genes (accD, ndhF, rpoA, ycf1, and ycf2) are identified. Robinsonia plastomes has an overall nucleotide diversity higher than that of the sky island Dendrosenecio, but much lower than herbaceous Senecio. Phylogenetic analysis demonstrates the monophyly of Robinsonia and identifies two major infrageneric lineages. Both Robinsonia and Dendrosenecio are deeply nested within large genus Senecio. Conclusions: While plastid genomes of Robinsonia are highly conserved, their sequences strongly demonstrated the monophyly of the genus and inferred robust interspecific relationships, including herbaceous Senecio and woody Dendrosenecio. Different sets of positively selected chloroplast genes, five for Robinsonia and two for Dendrosenecio, may play an important role in the adaptation strategies of these fascinating woody species in insular and continental sky island habitats. Overall phylogenetic positions and sister lineages of Robinsonia and Dendrosenecio require additional study based on broader sampling of Senecio. [ABSTRACT FROM AUTHOR]

Efforts to reconcile development and evolution have demonstrated that development is biased, with phenotypic variation being more readily produced in certain directions. However, how this "developmental bias" can influence micro-and macroevolution is poorly understood. In this review, we demonstrate that defining features of adaptive radiations suggest a role for developmental bias in driving adaptive divergence. These features are i) common ancestry of developmental systems; ii) rapid evolution along evolutionary "lines of least resistance;" iii) the subsequent repeated and parallel evolution of ecotypes; and iv) evolutionary change "led" by biased phenotypic plasticity upon exposure to novel environments. Drawing on empirical and theoretical data, we highlight the reciprocal relationship between development and selection as a key driver of evolutionary change, with development biasing what variation is exposed to selection, and selection acting to mold these biases to align with the adaptive landscape. Our central thesis is that developmental biases are both the causes and consequences of adaptive radiation and divergence. We argue throughout that incorporating development and developmental bias into our thinking can help to explain the exaggerated rate and scale of evolutionary processes that characterize adaptive radiations, and that this can be best achieved by using an eco-evo-devo framework incorporating evolutionary biology, development, and ecology. Such a research program would demonstrate that development is not merely a force that imposes constraints on evolution, but rather directs and is directed by evolutionary forces. We round out this review by highlighting key gaps in our understanding and suggest further research programs that can help to resolve these issues. [ABSTRACT FROM AUTHOR]

ABSTRACT Studying niche evolution becomes central to understanding the processes driving species diversification along latitudinal gradients. Octodontoidea rodents serve as a model group for understanding how the colonisation of extratropical regions has shaped the climatic niche evolution of species. We analyse the time and mode of climatic niche evolution among different Octodontoidea lineages to understand how niche evolutionary processes operate across the spatial gradient of the Neotropical region. We constructed ecological niche models for living Octodontoidea species to assess the timing and mode of climatic niche evolution across tropical and extratropical lineages. We estimated niche similarity and correlated it with species divergence times, and estimated the rate of climatic niche diversification across lineages. Our results show a trend of greater niche overlap in more recent lineages and lower niche overlap in older lineages. However, extratropical lineages exhibit lower climatic niche overlaps. From diversification analysis, we detected that the Ctenomyidae group shows higher rates of niche diversification, whereas the tropical Echimyidae group exhibits the lowest rates of climatic niche diversification. Our results support the idea that the lineages restricted to tropical regions tend towards niche conservatism. However, some tropical lineages have successfully colonised extratropical regions, and this colonisation has been accompanied by strong selective pressures, leading to higher rates of niche diversification and lower climatic niche overlap among species. [ABSTRACT FROM AUTHOR]

Recent adaptive radiations provide experimental opportunities to parse the relationship between genomic variation and the origins of distinct phenotypes. Sympatric radiations of the charr complex (genus Salvelinus) present a trove for phylogenetic analyses as charrs have repeatedly diversified into multiple morphs with distinct feeding specializations. However, charr species flocks normally comprise only two to three lineages. Dolly Varden charr inhabiting Lake Kronotskoe represent the most extensive radiation described for the genus, containing at least seven lineages, each with defining morphological and ecological traits. Here, we perform the first genome-wide analysis of this species flock to parse the foundations of adaptive change. Our data support distinct, reproductively isolated lineages within the clade. We find that changes in genes associated with thyroid signaling and craniofacial development provided a foundational shift in evolution to the lake. The thyroid axis is further implicated in subsequent lineage partitioning events. These results delineate a genetic scenario for the diversification of specialized lineages and highlight a common axis of change biasing the generation of specific forms during adaptive radiation. [ABSTRACT FROM AUTHOR]

Melanogenesis, a natural responsive mechanism of human skin to harmful radiation, is a self-triggered defensive neural activity safeguarding the body from radiation exposure in advance. With the increasing significance of radiation shielding in diverse medical health care and wearable applications, a biomimetic neuromorphic optoelectronic system with adaptive radiation shielding capability is often needed. Here, we demonstrate a transparent and flexible metal oxide-based photovoltaic neuromorphic defensive system. By using a monolithically integrated ultraflexible optoelectronic circuitry and electrochromic device, seamless neural processing for ultraviolet (UV) radiation shielding including history-based sensing, memorizing, risk recognition, and blocking can be realized with piling the entire signal chain into the flexible devices. The UV shielding capability of the system can be evaluated as autonomous blocking up to 97% of UV radiation from 5 to 90 watts per square meter in less than 16.9 seconds, demonstrating autonomously modulated sensitivity and response time corresponding to UV environmental conditions and supplied bias. [ABSTRACT FROM AUTHOR]

The animal gut microbiome can have a strong influence on the health, fitness, and behavior of its hosts. The composition of the gut microbial community can be influenced by factors such as diet, environment, and evolutionary history (phylosymbiosis). However, the relative influence of these factors is unknown in most bird species. Furthermore, phylosymbiosis studies have largely focused on clades that diverged tens of millions of years ago, and little is known about the degree of gut microbiome divergence in more recent species radiations. This study explores the drivers of microbiome variation across the unique and recent Hawaiian honeycreeper radiation (Fringillidae: Drepanidinae). Fecal samples were collected from 14 extant species spanning the main islands of the Hawaiian archipelago and were sequenced using three metabarcoding markers to characterize the gut microbiome, invertebrate diet, and plant diet of Hawaiian honeycreepers. We then used these metabarcoding data and the honeycreeper host phylogeny to evaluate their relative roles in shaping the gut microbiome. Microbiome variation across birds was highly individualized; however, source island had a small but significant effect on microbiome structure. The microbiomes did not recapitulate the host phylogenetic tree, indicating that evolutionary history does not strongly influence microbiome structure in the honeycreeper clade. These results expand our understanding of the roles of diet, geography, and phylogeny on avian microbiome structure, while also providing important ecological information about the diet and gut microbiota of wild Hawaiian honeycreepers. [ABSTRACT FROM AUTHOR]

The connections between viruses and their hosts are complex and can arise from any combination of different evolutionary events including “codivergence”, “switching”, and “duplication” of the pathogen. Mycoviruses, a diverse virus group whose members specifically infect fungal hosts, are subject to similar evolutionary processes. In this study, we present the identification and complete genome characterization of the second isolate of a mitovirus, commonly known as Tuber excavatum mitovirus, officially named Triamitovirus tuex1. This mycovirus infects the hypogean, ectomyrrhizal fungus Tuber excavatum Vittad.. Both Triamitovirus tuex1 isolates, Tekirdağ (identified by us) and Lammspringe, were found in the fruiting bodies of T. excavatum isolates collected from Türkiye and Germany, respectively. Comparative genomic analyses revealed that the two virus isolates share 85.33% sequence similarity in their whole genomes, with their protein encompassing RNA-dependent RNA polymerase (RdRp) domain showing an identity rate of 94.60%. The most diverse part of the viral genomes was found to be the 5’ untranslated regions (UTRs), with a sequence similarity of 78.53%, while the 3’ UTRs were the most conserved, with 91.53% sequence similarity. Considering the shared host species, the emergence of these Triamitovirus tuex1 isolates appears to reflect a duplication pattern (intra-host divergence) resulting from adaptive radiation. [ABSTRACT FROM AUTHOR]

Reciprocal effects of adaptive radiations on the evolution of interspecific interactions, like parasitism, remain barely explored. We test whether the recent radiations of European whitefish (Coregonus spp.) across and within perialpine and subarctic lakes promote its parasite Proteocephalus fallax (Platyhelminthes: Cestoda) to undergo host repertoire expansion via opportunity and ecological fitting, or adaptive radiation by specialization. Using de novo genomic data, we examined P. fallax differentiation across lakes, within lakes across sympatric host species, and the contributions of host genetics versus host habitat use and trophic preferences. Whitefish intralake radiations prompted parasite host repertoire expansion in all lakes, whereas P. fallax differentiation remains incipient among sympatric fish hosts. Whitefish genetic differentiation per se did not explain the genetic differentiation among its parasite populations, ruling out codivergence with the host. Instead, incipient parasite differentiation was driven by whitefish phenotypic radiation in trophic preferences and habitat use in an arena of parasite opportunity and ecological fitting to utilize resources from emerging hosts. Whilst the whitefish radiation provides a substrate for the parasite to differentiate along the same water-depth ecological axis as Coregonus spp. the role of the intermediate hosts in parasite speciation may be overlooked. Parasite multiple-level ecological fitting to both fish and crustacean intermediate hosts resources may be responsible for parasite population substructure in Coregonus spp. We propose parasites' delayed arrival was key to the initial burst of postglacial intralake whitefish diversification, followed by opportunistic tapeworm host repertoire expansion and a delayed nonadaptive radiation cascade of incipient tapeworm differentiation. At the geographical scale, dispersal, founder events, and genetic drift following colonization of spatially heterogeneous landscapes drove strong parasite differentiation. We argue that these microevolutionary processes result in the mirroring of host–parasite phylogenies through phylogenetic tracking at macroevolutionary and geographical scales. [ABSTRACT FROM AUTHOR]

ABSTRACT Adaptive radiation is considered to be a major source of biodiversity in charrs of the genus Salvelinus. These fishes demonstrate numerous examples of diversification in postglacial lakes and rivers resulting in the emergence of different ecomorphs, including piscivorous. Usually, the number of fish feeders does not exceed two, suggesting the existence of ecological and/or internal factors that prevent further diversification. Under these circumstances, rare instances of increases in the number of piscivorous morphs are of particular interest. Here, we present a comprehensive study of the piscivorous charr assemblage in Lake Kronotskoe, residence of the most diverse species flock of Salvelinus fishes. To unravel the diversity and ecological relationships of piscivorous charrs, we analysed their morphology and microsatellite DNA polymorphism, distribution within the lake, trophic preferences and parasite load, as well as trace element accumulation, stable isotope and free fatty acid ratios. We revealed that, apart from a few strictly benthivorous morphs, the lake is inhabited by four closely related but morphologically and genetically distinct morphs that exhibit a range of piscivorous specialisation: from opportunistic secondary predation to ultra‐specialised primary piscivory. They effectively exploit the spatiotemporal structure of the ecosystem and experience diversifying selection due to niche discordance. Each piscivorous morph develops specific phenotypic, ecological and life history traits that allow it to terminate weakly overlapping branches of the trophic chain and share the energy flows of the lake ecosystem. Our data suggest that Lake Kronotskoe facilitates high level of ecological opportunity that favours niche expansion and allows the piscivorous lineage to simultaneously realise the archetypical modes of ecological diversification available to fishes in cold‐water freshwaters. [ABSTRACT FROM AUTHOR]

Here we describe a dataset of freely available, readily processed, whole-body μCT-scans of 56 species (116 specimens) of Lake Malawi cichlid fishes that captures a considerable majority of the morphological variation present in this remarkable adaptive radiation. We contextualise the scanned specimens within a discussion of their respective ecomorphological groupings and suggest possible macroevolutionary studies that could be conducted with these data. In addition, we describe a methodology to efficiently μCT-scan (on average) 23 specimens per hour, limiting scanning time and alleviating the financial cost whilst maintaining high resolution. We demonstrate the utility of this method by reconstructing 3D models of multiple bones from multiple specimens within the dataset. We hope this dataset will enable further morphological study of this fascinating system and permit wider-scale comparisons with other cichlid adaptive radiations. [ABSTRACT FROM AUTHOR]

Background: Hemiptera is the fifth species-rich order of insects and the most species-rich order of hemimetabolous insects, including numerous insect species that are of agricultural or medical significance. Despite much effort and recent advance in inferring the Hemiptera phylogeny, some high-level relationships among superfamilies remain controversial. Results: We sequenced the genomes of 64 hemipteran species from 15 superfamilies and the transcriptomes of two additional scale insect species, integrating them with existing genomic and transcriptomic data to conduct a comprehensive phylogenetic analysis of Hemiptera. Our datasets comprise an average of 1625 nuclear loci of 315 species across 27 superfamilies of Hemiptera. Our analyses supported Cicadoidea and Cercopoidea as sister groups, with Membracoidea typically positioned as the sister to Cicadoidea + Cercopoidea. In most analyses, Aleyrodoidea was recovered as the sister group of all other Sternorrhyncha. A sister-group relationship was supported between Coccoidea and Aphidoidea + Phylloxeroidea. These relationships were further supported by four-cluster likelihood mapping analyses across diverse datasets. Our ancestral state reconstruction indicates phytophagy as the primary feeding strategy for Hemiptera as a whole. However, predation likely represents an ancestral state for Heteroptera, with several phytophagous lineages having evolved from predatory ancestors. Certain lineages, like Lygaeoidea, have undergone a reversal transition from phytophagy to predation. Our divergence time estimation placed the diversification of hemipterans to be between 60 and 150 million years ago. Conclusions: By expanding phylogenomic taxon sampling, we clarified the superfamily relationships within the infraorder Cicadomorpha. Our phylogenetic analyses supported the sister-group relationship between the superfamilies Cicadoidea and Cercopoidea, and the superfamily Membracoidea as the sister to Cicadoidea + Cercopoidea. Our divergence time estimation supported the close association of hemipteran diversification with the evolutionary success and adaptive radiation of angiosperms during the Cretaceous period. [ABSTRACT FROM AUTHOR]

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 traits evolve during adaptive radiation. Here, we investigated the rate, pattern, and timing of morphological and physiological evolution in the anole lizard adaptive radiation from the Caribbean island of Hispaniola. Rates and patterns of morphological and physiological diversity are largely unaligned, corresponding to independent selective pressures associated with structural and thermal niches. Cold tolerance evolution reflects parapatric divergence across elevation, rather than niche partitioning within communities. Heat tolerance evolution and the preferred temperature evolve more slowly than cold tolerance, reflecting behavioral buffering, particularly in edge-habitat species (a pattern associated with the Bogert effect). In contrast to the nearby island of Puerto Rico, closely related anoles on Hispaniola do not sympatrically partition thermal niche space. Instead, allopatric and parapatric separation across biogeographic and environmental boundaries serves to keep morphologically similar close relatives apart. The phenotypic diversity of this island's adaptive radiation accumulated largely as a by-product of time, with surprisingly few exceptional pulses of trait evolution. A better understanding of the processes that guide multidimensional trait evolution (and nuance therein) will prove key in determining whether the stages model should be considered a common theme of adaptive radiation. [ABSTRACT FROM AUTHOR]

Summary: Callicarpa glabra Koidz., described from the Bonin Islands in 1918, is illustrated. Its ecology and evolution are discussed along with the adaptive radiation of Callicarpa in the Bonin Islands. Oceanic island biota offer fascinating examples of evolution, but are also vulnerable to disturbance, so further efforts are needed to conserve the biodiversity of the Bonin Islands. [ABSTRACT FROM AUTHOR]

Some East Asian rivers experienced repeated rearrangements due to Indian–Asian Plates' collisions and an uplift of the Tibetan Plateau. For the upper Changjiang (Yangtze/Jinsha River), its ancient south-flowing course and subsequent capture by the middle Changjiang at the First Bend (FB) remained controversial. The DNA of freshwater fishes possess novel evolutionary signals of these tectonic events. In this study, mtDNA Cyt b sequences of endemic Schizopygopsis fish belonging to a highly specialized grade of the Schizothoracinae from the eastern Tibetan Plateau were used to infer the palaeo-drainages connectivity history of the upper Changjiang system. Through phylogenetic reconstruction, a new clade D of Schizopygopsis with three genetic clusters and subclusters (DI, DII, DIIIa, and DIIIb) were identified from the upper Yalong, Changjiang, and Yellow Rivers; the Shuiluo River; the FB-upper Changjiang; and the Litang River; respectively. Ancient drainage connections and capture signals were indicated based on these cladogenesis events and ancestral origin inference: (1) the upper Yalong River likely acted as a dispersal origin of Schizopygopsis fish to the adjacent upper Yellow and Changjiang Rivers at ca. 0.34 Ma; (2) the Litang River seemed to have directly drained into the upper Changjiang/Yangtze/Jinsha River before its capture by the Yalong River at ca. 0.90 Ma; (3) the Shuiluo River likely flowed south along a course parallel to the upper Changjiang before their connection through Hutiao Gorge; (4) a palaeo-lake across the contemporary Shuiluo, Litang, and Yalong Rivers was inferred to have served as an ancestral origin of clade D of Schizopygopsis at 1.56 Ma. Therefore, this study sheds light on disentangling ambiguous palaeo-drainage history through integrating biological and geological evidence. [ABSTRACT FROM AUTHOR]

During the present study, the phylogeography of the wetland specialist, freshwater crab, Potamonautes flavusjo, was investigated and compared to that of the ubiquitous, generalist, P. sidneyi, using DNA sequence data from the mitochondrial cytochrome oxidase subunit one (COI). We inferred the evolutionary history of each species and compared their population‐level genetic structure by constructing haplotype networks and using an analysis of molecular variation. Additionally, we explored the evolutionary relationship between southern African lentic and lotic freshwater crab species by examining the usefulness of carapace attributes in relation to genetic indices and a species' assumed dispersal capacity. In the lentic species, P. flavusjo, a single interconnected haplocluster characterized by shared haplotypes was observed, suggesting marked maternal dispersal, a result corroborated by the low FST values. In contrast, for the lotic species, P. sidneyi two distinct haploclusters and marked genetic differentiation was observed indicating the absence of maternal dispersal, a result corroborated by the high FST values. The phylogenetic relationship in P. sidneyi was further investigated using a maximum likelihood and Bayesian inference analyses with the addition of sequence data from the mitochondrial 16S rRNA locus to estimate divergence times. Three species delimitation methods (ASAP, PTP, and bGMYC) were used to explore the presence of distinct lineages in P. sidneyi. The phylogenetic results indicated that within P. sidneyi two clades were present, while divergence time estimates suggest cladogenesis during the middle to late Pleistocene. The species delimitation methods used showed moderate congruence, however all oversplit the number of putative lineages. Our results indicated that P. sidneyi is a species complex comprised of two cryptic lineages, occurring in sympatry contemporarily possibly alluding to secondary contact. Carapace height was found to have no discernible influence on the genetic indices and presumed dispersal capabilities of mainland southern African freshwater crab species. The importance of our results are discussed in terms of conservation of freshwater habitats. [ABSTRACT FROM AUTHOR]

Meristic traits are often treated as distinct phenotypes that can be used to differentiate and delineate recently diverged species. For instance, the number of lateral line scales and vertebrae, two traits that vary substantially among Neotropical Heroine cichlid species, have been previously suggested to co‐evolve. These meristic traits could co‐evolve due to shared adaptive, developmental, or genetic factors. If they were found to be genetically or developmentally non‐independent, this might require a more general re‐evaluation of their role in evolutionary or taxonomic studies. We expanded a previous analysis of correlated evolution of meristic traits (lateral line scales and vertebrae counts) in these fishes to include a range of phylogenetic reconstructions as well as the analyses of 13 Nicaraguan Midas cichlid species (Amphilophus spp.). Additionally, we performed qualitative traits locus (QTL) mapping in a F2 laboratory‐reared hybrid population from two ecologically divergent Midas cichlid fish species to discover and evaluate whether genomic co‐segregation might explain the observed patterns of meristic co‐evolution. Meristic values for these traits were found to morphologically differentiate some species of the Midas cichlid adaptive radiation. Our QTL analysis pinpointed several genomic regions associated with divergence in these traits and highlighted the potential for genomic co‐segregation of the lateral line and vertebrae numbers on two chromosomes. Further, our phylogenetic comparative analyses consistently recovered a significant positive evolutionary correlation between the counts of lateral line scale and vertebrae numbers in Neotropical cichlids. Hence, the findings of genomic co‐segregation could partially explain the co‐evolution of these two meristic traits in these species. Continuing to unravel the genetic architecture governing meristic divergence helps to better understand both trait correlations and the utility of meristic traits in taxonomic diagnoses and how traits in phenotypes might be expected to co‐evolve. [ABSTRACT FROM AUTHOR]

The Bonin Islands, comprised of the Mukojima, Chichijima, and Hahajima Islands, are known for their isolated and distinctive habitats, hosting a diverse array of endemic flora and fauna. In these islands, adaptive radiation has played a remarkable role in speciation, particularly evident in the Callicarpa genus that is represented by three species: Callicarpa parvifolia and C. glabra exclusive to the Chichijima Islands, and Callicarpa subpubescens, distributed across the entire Bonin Islands. Notably, C. subpubescens exhibits multiple ecotypes, differing in leaf hair density, flowering time, and tree size. In this study, we aimed to investigate species and ecotype diversification patterns, estimate divergence times, and explore cryptic species within Callicarpa in the Bonin Islands using phenotypic and genetic data (double‐digest restriction site‐associated DNA sequencing). Genetic analysis revealed that C. parvifolia and C. glabra both formed single, distinct genetic groups. Conversely, C. subpubescens consisted of six genetic groups corresponding to different ecotypes and regions, and a hybrid group resulting from the hybridization between two of these genetic groups. Population demography analysis focusing on six Chichijima and Hahajima Islands‐based species/ecotypes indicated that all species and ecotypes except one ecotype diverged simultaneously around 73–77 kya. The star‐shaped neighbor‐net tree also suggests the simultaneous divergence of species and ecotypes. The species and ecotypes that simultaneously diverged adapted to dry environments and understory forests, suggesting that aridification may have contributed to this process of adaptive radiation. Moreover, leaf morphology, flowering time, and genetic analyses suggested the presence of two cryptic species and one hybrid species within C. subpubescens. [ABSTRACT FROM AUTHOR]

Adaptive radiations highlight the mechanisms by which species and traits diversify and the extent to which these patterns are predictable. We used 1,110 high-speed videos of suction feeding to study functional and morphological diversification in 300 cichlid species from three African Great Lake radiations of varying ages (Victoria, Malawi, and Tanganyika) and an older, spatially dispersed continental radiation in the Neotropics. Among African radiations, standing diversity was reflective of time. Morphological and functional variance in Lake Victoria, the youngest radiation, was a subset of that within Lake Malawi, which itself was nested within the older Tanganyikan radiation. However, functional diversity in Neotropical cichlids was often lower than that in Lake Tanganyika, despite being much older. These two radiations broadly overlapped, but each diversified into novel trait spaces not found in the youngest lake radiations. Evolutionary rates across radiations were inversely related to age, suggesting extremely rapid trait evolution at early stages, particularly in lake radiations. Despite this support for early bursts, other patterns of trait diversity were inconsistent with expectations of adaptive radiations. This work suggests that cichlid functional evolution has played out in strikingly similar fashion in different radiations, with contingencies eventually resulting in lineage-specific novelties. [ABSTRACT FROM AUTHOR]

Insect herbivores frequently cospeciate with symbionts that enable them to survive on nutritionally unbalanced diets. While ancient symbiont gain and loss events have been pivotal for insect diversification and feeding niche specialization, evidence of recent events is scarce. We examine the recent loss of nutritional symbionts (in as little as 1 MY) in sap-feeding Pariaconus , an endemic Hawaiian insect genus that has undergone adaptive radiation, evolving various galling and free-living ecologies on a single host-plant species, Metrosideros polymorpha within the last ∼5 MY. Using 16S rRNA sequencing, we investigated the bacterial microbiomes of 19 Pariaconus species and identified distinct symbiont profiles associated with specific host-plant ecologies. Phylogenetic analyses and metagenomic reconstructions revealed significant differences in microbial diversity and functions among psyllids with different host-plant ecologies. Within a few millions of years, Pariaconus species convergently evolved the closed-gall habit twice. This shift to enclosed galls coincided with the loss of the Morganella -like symbiont that provides the essential amino acid arginine to free-living and open-gall sister species. After the Pariaconus lineage left Kauai and colonized younger islands, both open- and closed-gall species lost the Dickeya -like symbiont. This symbiont is crucial for synthesizing essential amino acids (phenylalanine, tyrosine, and lysine) as well as B vitamins in free-living species. The recurrent loss of these symbionts in galling species reinforces evidence that galls are nutrient sinks and, combined with the rapidity of the evolutionary timeline, highlights the dynamic role of insect–symbiont relationships during the diversification of feeding ecologies. We propose new Candidatus names for the novel Morganella -like and Dickeya -like symbionts. [ABSTRACT FROM AUTHOR]

Abstract Background The genus Robinsonia DC. (tribe Senecioneae, Asteraceae) endemic to the Juan Fernández Islands in Chile is one of the most conspicuous insular plant groups in the world. Unlike typical herbaceous Asteraceae plants, these plants demonstrate spectacular and unusual rosette tree growth forms as shown by the alpine giant senecios (genus Dendrosenecio, tribe Senecioneae) endemic to the East African mountains. However, monophyly of the genus and phylogenetic relationships among species of Robinsonia as well as their plastome evolution remain elusive. This study aims to explore their phylogeny, species diversification, and molecular evolution based on the complete plastome sequences in the context of adaptive radiation on oceanic islands. Results The insular Robinsonia plastomes are highly conserved in their structures and organization of contents. Five divergence hotspots as potential chloroplast markers and five positively selected coding genes (accD, ndhF, rpoA, ycf1, and ycf2) are identified. Robinsonia plastomes has an overall nucleotide diversity higher than that of the sky island Dendrosenecio, but much lower than herbaceous Senecio. Phylogenetic analysis demonstrates the monophyly of Robinsonia and identifies two major infrageneric lineages. Both Robinsonia and Dendrosenecio are deeply nested within large genus Senecio. Conclusions While plastid genomes of Robinsonia are highly conserved, their sequences strongly demonstrated the monophyly of the genus and inferred robust interspecific relationships, including herbaceous Senecio and woody Dendrosenecio. Different sets of positively selected chloroplast genes, five for Robinsonia and two for Dendrosenecio, may play an important role in the adaptation strategies of these fascinating woody species in insular and continental sky island habitats. Overall phylogenetic positions and sister lineages of Robinsonia and Dendrosenecio require additional study based on broader sampling of Senecio.

Understanding the genetic basis of novel adaptations in new species is a fundamental question in biology. Here we demonstrate a new role for galr2 in vertebrate craniofacial development using an adaptive radiation of trophic specialist pupfishes endemic to San Salvador Island, Bahamas. We confirmed the loss of a putative Sry transcription factor binding site upstream of galr2 in scale-eating pupfish and found significant spatial differences in galr2 expression among pupfish species in Meckel's cartilage using in situ hybridization chain reaction (HCR). We then experimentally demonstrated a novel role for Galr2 in craniofacial development by exposing embryos to Garl2-inhibiting drugs. Galr2-inhibition reduced Meckel's cartilage length and increased chondrocyte density in both trophic specialists but not in the generalist genetic background. We propose a mechanism for jaw elongation in scale-eaters based on the reduced expression of galr2 due to the loss of a putative Sry binding site. Fewer Galr2 receptors in the scale-eater Meckel's cartilage may result in their enlarged jaw lengths as adults by limiting opportunities for a circulating Galr2 agonist to bind to these receptors during development. Our findings illustrate the growing utility of linking candidate adaptive SNPs in non-model systems with highly divergent phenotypes to novel vertebrate gene functions.

The family Dysderidae is a highly diverse group of nocturnal ground‐dwelling and active‐hunter spiders. Dysderids are mostly restricted to the Western Palearctic, and particularly rich and abundant around the Mediterranean region. Interestingly, the distribution of species richness among its 24 genera and three subfamilies is highly biased—80% of its 644 documented species belong to just two genera, Dysdera (326) and Harpactea (211). Dysderidae provides an excellent study case for evolutionary and ecological research. It includes cases of trophic specialization, which are uncommon among spiders, and exhibit other remarkable biological (e.g. holocentric chromosomes), behavioural (e.g. cryptic female choice), evolutionary (e.g. adaptive radiation) and ecological features (e.g. recurrent colonization of the subterranean environment). The lack of a quantitative hypothesis on its phylogenetic structure has hampered its potential as a testing ground for evolutionary, biogeographical and ecological hypotheses. Here, we present the results of a target, multi‐locus phylogenetic analysis, using mitochondrial (cox1, 16s and 12s) and nuclear genes (h3, 28s and 18s), of the most exhaustive taxonomic sample within Dysderidae (104 spp.) to date and across related families (Synspermiata) (83 spp.). We estimate divergence times using a combination of fossil and biogeographic node calibrations and use this timeline to identify shifts in diversification rates. Our results support the monophyly of the Dysderidae subfamilies Rhodinae and Dysderinae but reject Harpacteinae as currently defined. Moreover, the clades recovered within Harpacteinae do not support its current taxonomy. The origin of the family most likely post‐dated the break‐up of Pangea, and cave colonization may be older than previously considered. After correcting for the taxonomic artefacts, we identified a significant shift in diversification rates at the base of the genus Dysdera. Although the unique coexistence of specialist and generalist diets within the lineage could be suggested as the potential driver for the rate acceleration, further quantitative analyses would be necessary to test this hypothesis. [ABSTRACT FROM AUTHOR]

Constraint is a fundamental concept in evolutionary theory. Morphology and ecology both are limited by functional, historical and developmental factors to a subset of the theoretical range species could occupy. Cat-like carnivorans (Feliformia) offer a unique opportunity to investigate phenotypic constraint, as several feliform clades are purported to be limited to generalized ecomorphological roles, while others possess extremely specialized durophagous (bone-crushing) and sabretooth morphology. We investigated the evolutionary history of feliforms by considering their phylogeny, morphological disparity and rates of evolution. We recover results that show a mosaic pattern exists in the degree of morphological disparity per anatomical region per clade and ecology. Non-hypercarnivores, such as viverrids (civets and genets), Malagasy euplerids and lophocyonids (extinct hypocarnivores), have the greatest dental disparity, while hypercarnivores (felids, nimravids, many hyaenids) have the lowest dental disparity but highest cranial and mandibular disparity (excluding dentition). However, high disparity is not necessarily associated with high rates of evolution, but instead with ecological radiations. We reveal that relationships between specialization and disparity are not as simple as past research has concluded. Instead, morphological disparity results from an anatomical mosaic of evolution, where different ecologies correlate with and likely channel unique patterns/combinations of disparity per anatomical partition. [ABSTRACT FROM AUTHOR]

Speciation events often occur with adaptive radiation. The factors that promote these adaptive radiating species diversity patterns have intrigued biologists for more than a century. In the present study, we used the adaptive radiated genus Ligustrum to evaluate the relative contributions of the environment, species interactions, phylogenetic diversity, and diversification rates in generating extant species diversity patterns. Using complete chloroplast genome data, we reconstructed the highly supported and dated backbone phylogenetic relationships of Ligustrum. Biogeographic results indicated that Ligustrum originated in Southwest China during the Oligocene and spread to suitable areas that were warm and humid via 18 dispersal events. For the overlapping ranges of species pairs, a smaller phylogenetic distance was detected in high species overlap than in low species overlap, which is consistent with no significant difference in niche among the different species. We found that the phylogenetic diversity and interspecies competition induced by insignificant niche divergence shaped the global pattern of Ligustrum diversity. [ABSTRACT FROM AUTHOR]

We use synchrotron x-ray tomography of annual growth increments in the dental cementum of mammaliaforms (stem and crown fossil mammals) from three faunas across the Jurassic to map the origin of patterns of mammalian growth patterns, which are intrinsically related to mammalian endothermy. Although all fossils studied exhibited slower growth rates, longer life spans, and delayed sexual maturity relative to comparably sized extant mammals, the earliest crown mammals developed significantly faster growth rates in early life that reduced at sexual maturity, compared to stem mammaliaforms. Estimation of basal metabolic rates (BMRs) suggests that some fossil crown mammals had BMRs approaching the lowest rates of extant mammals. We suggest that mammalian growth patterns first evolved during their mid-Jurassic adaptive radiation, although growth remained slower than in extant mammals. [ABSTRACT FROM AUTHOR]

As the world becomes warmer and precipitation patterns less predictable, organisms will experience greater heat and water stress. It is crucial to understand the factors that predict variation in thermal and hydric physiology among species. This study focuses on investigating the relationships between thermal and hydric diversity and their environmental predictors in a clade of Hispaniolan anole lizards, which are part of a broader Caribbean adaptive radiation. This clade, the "cybotoid" anoles, occupies a wide range of thermal habitats (from sea level to several kilometers above it) and hydric habitats (such as xeric scrub, broadleaf forest, and pine forest), setting up the possibility for ecophysiological specialization among species. Among the thermal traits, only cold tolerance is correlated with environmental temperature, and none of our climate variables are correlated with hydric physiology. Nevertheless, we found a negative relationship between heat tolerance (critical thermal maximum) and evaporative water loss at higher temperatures, such that more heat-tolerant lizards are also more desiccation-tolerant at higher temperatures. This finding hints at shared thermal and hydric specialization at higher temperatures, underscoring the importance of considering the interactive effects of temperature and water balance in ecophysiological studies. While ecophysiological differentiation is a core feature of the anole adaptive radiation, our results suggest that close relatives in this lineage do not diverge in hydric physiology and only diverge partially in thermal physiology. [ABSTRACT FROM AUTHOR]

The sub-Antarctic terrestrial ecosystems survive on isolated oceanic islands in the path of circumpolar currents and winds that have raged for more than 30 million years and are shaped by climatic cycles that surpass the tolerance limits of many species. Surprisingly little is known about how these ecosystems assembled their native terrestrial fauna and how such processes have changed over time. Here, we demonstrate the patterns and timing of colonization and speciation in the largest and dominant arthropod predators in the eastern sub-Antarctic: spiders of the genus Myro. Our results indicate that this lineage originated from Australia before the Plio-Pleistocenic glacial cycles and underwent an adaptive radiation on the Crozet archipelago, from where one native species colonized multiple remote archipelagos via the Antarctic circumpolar current across thousands of kilometers. The results indicate limited natural connectivity between terrestrial macroinvertebrate faunas in the eastern sub-Antarctic and partial survival of repeated glaciations in the Plio-Pleistocene. Furthermore, our findings highlight that by integrating arthropod taxa from multiple continents, the climatically more stable volcanic Crozet archipelago played a critical role in the evolution and distribution of arthropod life in the sub-Antarctic. [ABSTRACT FROM AUTHOR]

The Cenozoic topographic development of the Himalaya‐Tibet orogen (HTO) substantially affected the paleoenvironment and biodiversity patterns of High Asia. However, concepts on the evolution and paleoenvironmental history of the HTO differ massively in timing, elevational increase and sequence of surface uplift of the different elements of the orogen. Using target enrichment of a large set of transcriptome‐derived markers, ancestral range estimation and paleoclimatic niche modelling, we assess a recently proposed concept of a warm temperate paleo‐Tibet in Asian spiny frogs of the tribe Paini and reconstruct their historical biogeography. That concept was previously developed in invertebrates. Because of their early evolutionary origin, low dispersal capacity, high degree of local endemism, and strict dependence on temperature and humidity, the cladogenesis of spiny frogs may echo the evolution of the HTO paleoenvironment. We show that diversification of main lineages occurred during the early to Mid‐Miocene, while the evolution of alpine taxa started during the late Miocene/early Pliocene. Our distribution and niche modelling results indicate range shifts and niche stability that may explain the modern disjunct distributions of spiny frogs. They probably maintained their (sub)tropical or (warm)temperate preferences and moved out of the ancestral paleo‐Tibetan area into the Himalaya as the climate shifted, as opposed to adapting in situ. Based on ancestral range estimation, we assume the existence of low‐elevation, climatically suitable corridors across paleo‐Tibet during the Miocene along the Kunlun, Qiangtang and/or Gangdese Shan. Our results contribute to a deeper understanding of the mechanisms and processes of faunal evolution in the HTO. [ABSTRACT FROM AUTHOR]

Recent studies have demonstrated that evolution can be observed in a few dozen generations, especially when species occupy a new ecological opportunity due to environmental changes. There are several factors that induce this rapid evolution and are related to the phenotype and its response to the environment. This response is then determined by phenotypic variation, because if patterns of diversity in a population produce a rapid response to an environmental change, then rapid adaptation to the new environment can occur. This paper aims to investigate patterns of evolution of species in an artificial ecosystem, and to highlight some patterns that promote rapid evolution. Understanding how rapid evolution occurs is not only of fundamental importance in understanding evolutionary processes and species conservation, but also to provide support for improving the resolution of certain types of problems, especially those in which the solution is time-variant. To achieve the objectives of this paper, a computational model of Adaptive Radiation was designed using the concepts of Biogeographic Computing, an area of knowledge that studies ecosystems as information processors, a fundamental principle of Natural Computing. Habitats are represented by adaptive surfaces, which in turn are composed of different ecological opportunities. The results show, for example, that dramatic changes in ecosystems can lead to a rapid response and a rapid adaptation to new ecological opportunities, mainly because of the emergent and self-sustaining behaviour promoted by the continuous speciation, extinction and adaptation of species. This emergent dynamic supports the thesis that rapid environmental changes can lead to rapid evolution. This behaviour, in turn, is highly desired when considering time-varying problem solving. If solutions to a problem are changing over time, sometimes it is necessary to rapidly find new solutions. [ABSTRACT FROM AUTHOR]

Sex chromosomes are evolutionarily labile in many animals and sometimes fuse with autosomes, creating so-called neo-sex chromosomes. Fusions between sex chromosomes and autosomes have been proposed to reduce sexual conflict and to promote adaptation and reproductive isolation among species. Recently, advances in genomics have fuelled the discovery of such fusions across the tree of life. Here, we discovered multiple fusions leading to neo-sex chromosomes in the sapho subclade of the classical adaptive radiation of Heliconius butterflies. Heliconius butterflies generally have 21 chromosomes with very high synteny. However, the five Heliconius species in the sapho subclade show large variation in chromosome number ranging from 21 to 60. We find that the W chromosome is fused with chromosome 4 in all of them. Two sister species pairs show subsequent fusions between the W and chromosomes 9 or 14, respectively. These fusions between autosomes and sex chromosomes make Heliconius butterflies an ideal system for studying the role of neo-sex chromosomes in adaptive radiations and the degeneration of sex chromosomes over time. Our findings emphasize the capability of short-read resequencing to detect genomic signatures of fusion events between sex chromosomes and autosomes even when sex chromosomes are not explicitly assembled. Author summary: Fusions between sex chromosomes and autosomes are thought to have the potential to resolve sexual conflict and enhance local adaptation or reproductive isolation between species. Here, we discovered such fusions in Heliconius butterflies. These butterflies mostly have a very stable karyotype with 21 chromosomes and high synteny across species. However, the five species in the sapho subclade have up to 60 chromosomes, suggesting that they have undergone many chromosomal fissions. We document that in addition to the fissions, the sapho subclade also shows multiple fusions between the female-specific sex chromosome W and autosomes. We found an ancestral W-4 fusion shared by all five species and additional W fusions with chromosomes 9 and 14 shared by two species each. Even though in many sapho subclade species the autosomes have undergone fissions, the chromosomes fused with the W did not undergo fissions. Our study reveals the power of short-read sequencing to detect the genomic signatures of Sex-A fusions and shows Heliconius butterflies as a promising system for studying the causes and consequences of sex chromosome evolution. [ABSTRACT FROM AUTHOR]

Adaptation to replicated environmental conditions can be remarkably predictable, suggesting that parallel evolution may be a common feature of adaptive radiation. An open question, however, is how phenotypic variation itself evolves during repeated adaptation. Here, we use a dataset of morphological measurements from 35 populations of threespine stickleback, consisting of 16 parapatric lake-stream pairs and three marine populations, to understand how phenotypic variation has evolved during transitions from marine to freshwater environments and during subsequent diversification across the lake-stream boundary. We find statistical support for divergent phenotypic covariance (P) across populations, with most diversification of P occurring among freshwater populations. Despite a close correspondence between within-population phenotypic variation and among-population divergence, we find that variation in P is unrelated to total variation in population means across the set of populations. For lake-stream pairs, we find that theoretical predictions for microevolutionary change can explain more than 30% of divergence in P matrices across the habitat boundary. Together, our results indicate that divergence in variance structure occurs primarily in dimensions of trait space with low phenotypic integration, correlated with disparate lake and stream environments. Our findings illustrate how conserved and divergent features of multivariate variation can underlie adaptive radiation. [ABSTRACT FROM AUTHOR]

Understanding phenotype variation is among the central topics in biology. We revise and reanalyze studies of the amphipod genus Niphargus to confront two potential mechanisms driving its phenotype variation, namely, cladogenesis and adaptive evolution. We found evidence for both mechanisms. Reanalysis of a subset of traits using molecular phylogeny showed moderate phylogenetic signal, consistent with the hypothesis that overall phylogenetic variation increases with phylogeny. The phylogenetic signal in Niphargus traits seems to be stronger at the tips of the phylogeny than at basal splits. Indirect evidence suggests that much of the phenotype variation can be attributed to adaptive evolution. Both lines of evidence are consistent with the hypothesis that Niphargus evolved in several adaptive radiations, where theory predicts that most of the phenotype variation evolves early, when ecological niches are vacant. As the niches fill up, the rate of phenotype variation slows down and becomes associated with cladogenetic events. This hypothesis can explain the high level of trait-convergence and unresolved taxonomy above the species level. The main caveats to these hypotheses comprise lack of experimental evidence for trait function and nonquantified heritable component of trait variation. Promising venues towards better understanding of phenotypic variation include studies of ontogenetic variation, functional interactions between traits, and genome–phenotype associations. [ABSTRACT FROM AUTHOR]

The entanglement of population dynamics, evolution, and adaptive radiation for species competing for resources is studied. For resource harvesting, we modify the model used in Tikhonov and Monasson (Phys. Rev. Lett. 118:048103, 2017), and introduce new resource contest principles. We realistically implement the effects of beneficial and deleterious mutations on the coefficients in the equations governing the population dynamics and consider the emergence of reproductive isolation. The proposed model is shown to be in agreement with the competitive exclusion principle and no vacant niche principle. We establish a mechanism that contributes to preventing the accumulation of irreversible deleterious mutations: competition between recently diverged species/subpopulations. The proposed model is applicable for descriptions of more complex systems. In case of many constants in time resources, one observes very rapid specialization, a feature not reproducible by the common model. [ABSTRACT FROM AUTHOR]

We describe a high‐diversity silicified assemblage of marine molluscs (Pelsa‐Vazzoler Lagerstätte) from the upper Ladinian of the Agordo Dolomites (northeastern Italy). New data on the Triassic rebound, after the end‐Permian mass extinction, constrain it to an interval of relatively stable climatic conditions. This Lagerstätte, in the Sciliar Formation, yields a structure comparable to the famous lower Carnian San Cassiano Lagerstätte and suggests that the radiation of benthic molluscs may have occurred as early as the late Middle Triassic. We classified more than 4800 Cassian‐type molluscs, measuring abundance distributions of 109 species, including one new family (Rhaetidiidae), three new genera (Pelsia, Gaetania, Agordozyga) and 21 new species: Grammatodon egortinus, Modiolus friesenbichlerae, Myoconcha busattae, Schizogonium letiziae, Predazzella? monarii, Eucycloscala nitida, Tricolnaticopsis elongatus, Cortinella stricta, Triadoskenea alpicornu, Trachynerita tenuicostata, Coelostylina civettae, Gaetania coronata, Agordozyga caprina, Euthystylus dincae, Zygopleura elongata, Diatrypesis agordina, Cryptaulax pelsae, Pseudoscalites karapunari, Promathildia gracile, Camponaxis ladinica and Striactaeonina ingens. In this fauna, associated with tropical carbonate platforms, epifaunal filter‐feeding bivalves adopted new antipredatory features and gastropods conquered new ecospace, including parasitism and microcarnivory on sponges and scleractinian corals. Small size was an advantage in an ecosystem of small, isolated patch reefs. This is how, where and when caenogastropod and heterobranch snails (groups that today dominate global marine diversity) began their rise in the marine benthos. The origins of some evolutionary innovations that are key to our understanding of the time and place of the Mesozoic Marine Revolution, are therefore pushed back to the Middle Triassic. [ABSTRACT FROM AUTHOR]

El'gygytgyn is the only ancient lake in the Arctic that avoided continental-scale glaciations. This lake is located on an arid mountain plateau, far from the main routes of post-glacial freshwater fish dispersal, and it is therefore challenging to consider the local fauna in a historical context. Here we present a study of the ecology and evolutionary history of the local charr complex (genus Salvelinus). We found that the endemic charrs exhibit extreme longevity, contrasting lifestyles and phenotypes. Salvelinus svetovidovi is a relic benthivorous species. The remaining charrs are descendants of Salvelinus taranetzi. Mitochondrial and microsatellite DNA polymorphisms analyzed in them and in charrs from surrounding basins indicate that S. taranetzi invaded the lake from Arctic Chukotka in the late Pleistocene as two distinct, previously diverged lineages. Descendants of both lineages occupied the pelagic food chain. The first lineage has flourished as a monomorphic planktivorous population since colonization. The second represents an example of a recent in-lake adaptive divergence, in which a deepwater piscivore specialist formed a new epilimnetic ecomorph of an impressive size (up to 9.0 kg). We suggest that this diversification was triggered by modern warming in the Arctic, which led to the formation of a productive littoral ecosystem. [ABSTRACT FROM AUTHOR]

The article offers information on Catocala moths in the U.S., and exploring their diversity, historical interest and field observations. Topics discussed include the discovery of new species in Kentucky, U.S.; historical techniques like 'sugaring' for moth attraction; and also mentions about the comparison of moth populations between North America and Europe.

Clownfish (subfamily Amphiprioninae) are an iconic group of coral reef fish that evolved a mutualistic interaction with sea anemones, which triggered the adaptive radiation of the clade. Within clownfishes, the "skunk complex" is particularly interesting. Besides ecological speciation, interspecific gene flow and hybrid speciation are thought to have shaped the evolution of the group. We investigated the mechanisms characterizing the diversification of this complex. By taking advantage of their disjunct geographical distribution, we obtained whole‐genome data of sympatric and allopatric populations of the three main species of the complex (Amphiprion akallopisos, A. perideraion and A. sandaracinos). We examined population structure, genomic divergence and introgression signals and performed demographic modelling to identify the most realistic diversification scenario. We excluded scenarios of strict isolation or hybrid origin of A. sandaracinos. We discovered moderate gene flow from A. perideraion to the ancestor of A. akallopisos + A. sandaracinos and weak gene flow between the species in the Indo‐Australian Archipelago throughout the diversification of the group. We identified introgressed regions in A. sandaracinos and detected in A. perideraion two large regions of high divergence from the two other species. While we found that gene flow has occurred throughout the species' diversification, we also observed that recent admixture was less pervasive than initially thought, suggesting a role of host repartition or behavioural barriers in maintaining the genetic identity of the species in sympatry. [ABSTRACT FROM AUTHOR]

Since recolonizing the seas, most teleosts evolved as pelagophils, producing highly hydrated pelagic (buoyant) eggs. Osmotic drive for oocyte hydration is mainly generated through differential proteolysis of vitellogenin-Aa-derived yolk proteins. Teleost-specific water channels are selectively retained in pelagophils and coevolved with 14-3-3ζ-like binding proteins to co-operatively regulate channel trafficking in a manner that avoids competitive membrane space occupancy and accelerates oocyte water influx. Gonadotropinergic and vasopressinergic systemic and paracrine signaling systems converge to activate meiosis resumption and oocyte hydration. Developmental downregulation of dominant-negative inhibitory aquaporin variants maximizes oocyte hydration. These innovative genetic adaptations are highly conserved in modern marine teleosts, contributing to the success of their eggs in the oceans. Genetic adaptations of organisms living in extreme environments are fundamental to our understanding of where life can evolve. Water is the single limiting parameter in this regard, yet when released in the oceans, the single-celled eggs of marine bony fishes (teleosts) have no means of acquiring it. They are strongly hyposmotic to seawater and lack osmoregulatory systems. Paradoxically, modern teleosts successfully release vast quantities of eggs in the extreme saline environment and recorded the most explosive radiation in vertebrate history. Here, we highlight key genetic adaptations that evolved to solve this paradox by filling the pre-ovulated eggs with water. The degree of water acquisition is uniquely prevalent to marine teleosts, permitting the survival and oceanic dispersal of their eggs. [ABSTRACT FROM AUTHOR]

Within 15,000 years, the explosive adaptive radiation of haplochromine cichlids in Lake Victoria, East Africa, generated 500 endemic species. In the 1980s, the upsurge of Nile perch, a carnivorous fish artificially introduced to the lake, drove the extinction of more than 200 endemic cichlids. The Nile perch predation particularly harmed piscivorous cichlids, including paedophages, cichlids eat eggs and fries, which is an example of the unique trophic adaptation seen in African cichlids. Here, aiming to investigate past demographic events possibly triggered by the invasion of Nile perch and the subsequent impacts on the genetic structure of cichlids, we conducted large-scale comparative genomics. We discovered evidence of recent bottleneck events in 4 species, including 2 paedophages, which began during the 1970s to 1980s, and population size rebounded during the 1990s to 2000s. The timing of the bottleneck corresponded to the historical records of endemic haplochromines" disappearance and later resurgence, which is likely associated with the introduction of Nile perch by commercial demand to Lake Victoria in the 1950s. Interestingly, among the 4 species that likely experienced bottleneck, Haplochromis sp. "matumbi hunter," a paedophagous cichlid, showed the most severe bottleneck signatures. The components of shared ancestry inferred by ADMIXTURE suggested a high genetic differentiation between matumbi hunter and other species. In contrast, our phylogenetic analyses highly supported the monophyly of the 5 paedophages, consistent with the results of previous studies. We conclude that high genetic differentiation of matumbi hunter occurred due to the loss of shared genetic components among haplochromines in Lake Victoria caused by the recent severe bottleneck. [ABSTRACT FROM AUTHOR]

ABSTRACT The animal gut microbiome can have a strong influence on the health, fitness, and behavior of its hosts. The composition of the gut microbial community can be influenced by factors such as diet, environment, and evolutionary history (phylosymbiosis). However, the relative influence of these factors is unknown in most bird species. Furthermore, phylosymbiosis studies have largely focused on clades that diverged tens of millions of years ago, and little is known about the degree of gut microbiome divergence in more recent species radiations. This study explores the drivers of microbiome variation across the unique and recent Hawaiian honeycreeper radiation (Fringillidae: Drepanidinae). Fecal samples were collected from 14 extant species spanning the main islands of the Hawaiian archipelago and were sequenced using three metabarcoding markers to characterize the gut microbiome, invertebrate diet, and plant diet of Hawaiian honeycreepers. We then used these metabarcoding data and the honeycreeper host phylogeny to evaluate their relative roles in shaping the gut microbiome. Microbiome variation across birds was highly individualized; however, source island had a small but significant effect on microbiome structure. The microbiomes did not recapitulate the host phylogenetic tree, indicating that evolutionary history does not strongly influence microbiome structure in the honeycreeper clade. These results expand our understanding of the roles of diet, geography, and phylogeny on avian microbiome structure, while also providing important ecological information about the diet and gut microbiota of wild Hawaiian honeycreepers.

Madagascar is one of the world’s foremost biodiversity hotspots with more than 90% of its species endemic to the island. Malagasy carnivorans are one of only four extant terrestrial mammalian clades endemic to Madagascar. Although there are only eight extant species, these carnivorans exhibit remarkable phenotypic and ecological diversity that is often hypothesized to have diversified through an adaptive radiation. Here, we investigated the evolution of skull diversity in Malagasy carnivorans and tested if they exhibited characteristics of convergence and an adaptive radiation. We found that their skull disparity exceeds that of any other feliform family, as their skulls vary widely and strikingly capture a large amount of the morphological variation found across all feliforms. We also found evidence of shared adaptive zones in cranial shape between euplerid subclades and felids, herpestids and viverrids. Lastly, contrary to predictions of adaptive radiation, we found that Malagasy carnivorans do not exhibit rapid lineage diversification and only marginally faster rates of mandibular shape evolution and to a lesser extent cranial shape evolution, compared to other feliforms. These results reveal that exceptional diversification rates are not necessary to generate the striking phenotypic diversity that evolved in carnivorans after their dispersal to and isolation on Madagascar.

Background: Hypersaline environments (> 40 practical salinity units [PSU]) represent some of the most extreme conditions on Earth, supporting a variety of halophilic and halotolerant bacteria, archaea, and protists. The taxon Heterolobosea includes numerous halophilic protists, making it a valuable model for studying eukaryotic adaptation to high salinity. Particularly, the genus Pharyngomonas, a deep-branching lineage within Heterolobosea, comprises mainly obligate halophiles, providing insights into early protist adaptations in hypersaline environments. Additionally, these protozoa play crucial ecological roles as grazers of bacteria and archaea, and are prey for higher trophic levels in hypersaline environments. Results: In the present study, two previously reported amoeboflagellates were isolated for the first time from hypersaline waters (~300 PSU) in two solar salterns in the Republic of Korea. Microscopic observations revealed that both strains exhibited the characteristic morphologies of Pharyngomonas, including amoeboid, flagellate, and cyst forms. Molecular phylogenetic analysis of their 18S rRNA gene sequences confirmed their close relationship to known Pharyngomonas kirbyi strains. The two strains demonstrated growth within a salinity range of 75–200 PSU, with optimal growth observed at 75–100 PSU, confirming their status as true halophiles. All known P. kirbyi strains are obligate halophiles, exhibiting a clear instance of adaptive radiation of halophilic eukaryotes. Additionally, the genus Pharyngomonas has been found in hypersaline environments across multiple continents (Asia, Europe, North America, Australia, and Africa), suggesting that it plays an ecologically significant role as a grazer of prokaryotes or prey for higher trophic levels in these habitats. Conclusions: On the bases of morphological and molecular analyses, two strains identified as P. kirbyi were isolated and characterized for the first time from solar salterns in the Republic of Korea. This discovery highlights the presence and adaptation of halophilic eukaryotes in such extreme environments. The confirmation of these strains as obligate halophiles provides additional evidence for the adaptive radiation of halophilic eukaryotes. Furthermore, the ecological role of Pharyngomonas species underscores their importance as trophic regulators in hypersaline ecosystems. These findings contribute to a deeper understanding of the diversity, adaptation, and ecological functions of halophilic eukaryotes in extreme environments.

Abstract Meristic traits are often treated as distinct phenotypes that can be used to differentiate and delineate recently diverged species. For instance, the number of lateral line scales and vertebrae, two traits that vary substantially among Neotropical Heroine cichlid species, have been previously suggested to co‐evolve. These meristic traits could co‐evolve due to shared adaptive, developmental, or genetic factors. If they were found to be genetically or developmentally non‐independent, this might require a more general re‐evaluation of their role in evolutionary or taxonomic studies. We expanded a previous analysis of correlated evolution of meristic traits (lateral line scales and vertebrae counts) in these fishes to include a range of phylogenetic reconstructions as well as the analyses of 13 Nicaraguan Midas cichlid species (Amphilophus spp.). Additionally, we performed qualitative traits locus (QTL) mapping in a F2 laboratory‐reared hybrid population from two ecologically divergent Midas cichlid fish species to discover and evaluate whether genomic co‐segregation might explain the observed patterns of meristic co‐evolution. Meristic values for these traits were found to morphologically differentiate some species of the Midas cichlid adaptive radiation. Our QTL analysis pinpointed several genomic regions associated with divergence in these traits and highlighted the potential for genomic co‐segregation of the lateral line and vertebrae numbers on two chromosomes. Further, our phylogenetic comparative analyses consistently recovered a significant positive evolutionary correlation between the counts of lateral line scale and vertebrae numbers in Neotropical cichlids. Hence, the findings of genomic co‐segregation could partially explain the co‐evolution of these two meristic traits in these species. Continuing to unravel the genetic architecture governing meristic divergence helps to better understand both trait correlations and the utility of meristic traits in taxonomic diagnoses and how traits in phenotypes might be expected to co‐evolve.