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Sequencing the mitochondrial genome of the tunicate Oikopleura dioica is a challenging task due to the presence of long poly-A/T homopolymer stretches, which impair sequencing and assembly. Here, we report on the sequencing and annotation of the majority of the mitochondrial genome of O. dioica by means of combining several DNA and amplicon reads obtained by Illumina and MinIon Oxford Nanopore Technologies with public RNA sequences. We document extensive RNA editing, since all homopolymer stretches present in the mitochondrial DNA correspond to 6U-regions in the mitochondrial RNA. Out of the 13 canonical protein-coding genes, we were able to detect eight, plus an unassigned open reading frame that lacked sequence similarity to canonical mitochondrial protein-coding genes. We show that the nad3 gene has been transferred to the nucleus and acquired a mitochondria-targeting signal. In addition to two very short rRNAs, we could only identify a single tRNA (tRNA-Met), suggesting multiple losses of tRNA genes, supported by a corresponding loss of mitochondrial aminoacyl-tRNA synthetases in the nuclear genome. Based on the eight canonical protein-coding genes identified, we reconstructed maximum likelihood and Bayesian phylogenetic trees and inferred an extreme evolutionary rate of this mitochondrial genome. The phylogenetic position of appendicularians among tunicates, however, could not be accurately determined. [ABSTRACT FROM AUTHOR]

Understanding how phenotypic divergence arises among natural populations remains one of the major goals in evolutionary biology. As part of competitive exclusion experiment conducted in 1971, 10 individuals of Italian wall lizard (Podarcis siculus (Rafinesque‐Schmaltz, 1810)) were transplanted from Pod Kopište Island to the nearby island of Pod Mrčaru (Adriatic Sea). Merely 35 years after the introduction, the newly established population on Pod Mrčaru Island had shifted their diet from predominantly insectivorous towards omnivorous and changed significantly in a range of morphological, behavioural, physiological and ecological characteristics. Here, we combine genomic and quantitative genetic approaches to determine the relative roles of genetic adaptation and phenotypic plasticity in driving this rapid phenotypic shift. Our results show genome‐wide genetic differentiation between ancestral and transplanted population, with weak genetic erosion on Pod Mrčaru Island. Adaptive processes following the founder event are indicated by highly differentiated genomic loci associating with ecologically relevant phenotypic traits, and/or having a putatively adaptive role across multiple lizard populations. Diverged traits related to head size and shape or bite force showed moderate heritability in a crossing experiment, but between‐population differences in these traits did not persist in a common garden environment. Our results confirm the existence of sufficient additive genetic variance for traits to evolve under selection while also demonstrating that phenotypic plasticity and/or genotype by environment interactions are the main drivers of population differentiation at this early evolutionary stage. [ABSTRACT FROM AUTHOR]

Major migration events in Holocene Eurasia have been characterized genetically at broad regional scales1–4. However, insights into the population dynamics in the contact zones are hampered by a lack of ancient genomic data sampled at high spatiotemporal resolution5–7. Here, to address this, we analysed shotgun-sequenced genomes from 100 skeletons spanning 7,300 years of the Mesolithic period, Neolithic period and Early Bronze Age in Denmark and integrated these with proxies for diet (13C and 15N content), mobility (87Sr/86Sr ratio) and vegetation cover (pollen). We observe that Danish Mesolithic individuals of the Maglemose, Kongemose and Ertebølle cultures form a distinct genetic cluster related to other Western European hunter-gatherers. Despite shifts in material culture they displayed genetic homogeneity from around 10,500 to 5,900 calibrated years before present, when Neolithic farmers with Anatolian-derived ancestry arrived. Although the Neolithic transition was delayed by more than a millennium relative to Central Europe, it was very abrupt and resulted in a population turnover with limited genetic contribution from local hunter-gatherers. The succeeding Neolithic population, associated with the Funnel Beaker culture, persisted for only about 1,000 years before immigrants with eastern Steppe-derived ancestry arrived. This second and equally rapid population replacement gave rise to the Single Grave culture with an ancestry profile more similar to present-day Danes. In our multiproxy dataset, these major demographic events are manifested as parallel shifts in genotype, phenotype, diet and land use.Integrated data, including 100 human genomes from the Mesolithic, Neolithic and Early Bronze Age periods show that two major population turnovers occurred over just 1,000 years in Neolithic Denmark, resulting in dramatic changes in the genes, diet and physical appearance of the local people, as well as the landscape in which they lived. [ABSTRACT FROM AUTHOR]

Polypodium hydriforme is an enigmatic parasite that belongs to the phylum Cnidaria. Its taxonomic position has been debated: whereas it was previously suggested to be part of Medusozoa, recent phylogenomic analyses based on nuclear genes support the view that P. hydriforme and Myxozoa form a clade called Endocnidozoa. Medusozoans have linear mitochondrial (mt) chromosomes, whereas myxozoans, as most metazoan species, have circular chromosomes. In this work, we determined the structure of the mt genome of P. hydriforme , using Illumina and Oxford Nanopore Technologies reads, and showed that it is circular. This suggests that P. hydriforme is not nested within Medusozoa, as this would entail linearization followed by recirculation. Instead, our results support the view that P. hydriforme is a sister clade to Myxozoa, and mt linearization in the lineage leading to medusozoans occurred after the divergence of Myxozoa +  P. hydriforme. Detailed analyses of the assembled P. hydriforme mt genome show that: (1) it is encoded on a single circular chromosome with an estimated size of ∼93,000 base pairs, making it one of the largest metazoan mt genomes; (2) around 78% of the genome encompasses a noncoding region composed of several repeat types; (3) similar to Myxozoa, no mt tRNAs were identified; (4) the codon TGA is a stop codon and does not encode for tryptophan as in other cnidarians; (5) similar to myxozoan mt genomes, it is extremely fast evolving. [ABSTRACT FROM AUTHOR]

The planktonic Oikopleura dioica belongs to Tunicata, the probable sister taxon to Craniota, and might show plesiomorphic characters, conserved from the common lineage of Tunicata and Craniota. In O. dioica a pericardium in a position similar to other chordates but also to the heart and pericardium of craniates is found. Surprisingly, little is known about the ultrastructure of the pericardium in O. dioica. Here, we show based on electron microscopy that the pericardium is completely lined by a single layer of 16 epithelial cells: 6 epithelial myocardial cells on the left side of the pericardium and 10 peritoneal cells constituting the right side. One of the peritoneal cells, situated at the ventral border between peritoneal cells and myocardial cells has an extension that anchors the pericardium to the basal lamina beneath the latero-ventral epidermis. The primary body cavity of O. dioica appears quite uniformly clear in electron microscopic aspect but several sheets, resembling the basal lamina of the pericardium cross the larger spaces of the body cavity and connect to the pericardial basal lamina. This is the first detailed description of two distinct cell types in the epithelial lining of the pericardium of O. dioica. In comparison with other chordates, we conclude that two cell types can be reconstructed for the last common ancestor of Chordata at least. The position of the pericardium at the intersection of trunk and tail in combination with the basal-lamina like sheets spanning the hemocoel is probably of importance for the function of the circulation of the hemocoelic fluid. Similar to the tail, the axis of the pericardium is shifted through 90 degrees to the left as compared to the main body axis of the trunk and we infer that this shift is an apomorphic character of Appendicularia. [ABSTRACT FROM AUTHOR]

Aim: Understanding the mechanisms determining species richness is a primary goal of biogeography. Richness patterns of sub‐groups within a taxon are usually assumed to be driven by similar processes. However, if richness of distinct ecological strategies respond differently to the same processes, inferences made for an entire taxon may be misleading. We deconstruct the global lizard assemblage into functional groups and examine the congruence among richness patterns between them. We further examine the species richness – functional richness relationship to elucidate the way functional diversity contributes to the overall species richness patterns. Location: Global. Methods: Using comprehensive biological trait databases we classified the global lizard assemblage into ecological strategies based on body size, diet, activity times and microhabitat preferences, using Archetypal Analysis. We then examined spatial gradients in the richness of each strategy at the one‐degree grid cell, biome, and realm scales. Results: We found that lizards can best be characterized by seven "ecological strategies": scansorial, terrestrial, nocturnal, herbivorous, fossorial, large, and semi‐aquatic. There are large differences among the global richness patterns of these strategies. While the major richness hotspot for lizards in general is in Australia, several strategies exhibit highest richness in the Amazon Basin. Importantly, the global maximum in lizard species richness is achieved at intermediate values of functional diversity and increasing functional diversity further result in a slow decline of species richness. Main conclusions: The deconstruction of the global lizard assemblage along multiple ecological axes offers a new way to conceive lizard diversity patterns. It suggests that local lizard richness mostly increases when species belonging to particular ecological strategies become hyper‐diverse there, and not because more ecological types are present in the most species rich localities. Thus maximum richness and maximum ecological diversity do not overlap. These results shed light on the global richness pattern of lizards, and highlight previously unidentified spatial patterns in understudied functional groups. [ABSTRACT FROM AUTHOR]

Insular species are predicted to broaden their niches, in response to having fewer competitors. They can thus exploit a greater proportion of the resource spectrum. In turn, broader niches are hypothesized to facilitate (or be a consequence of) increased population densities., We tested whether insular lizards have broader dietary niches than mainland species, how it relates to competitor and predator richness, and the nature of the relationship between population density and dietary niche breadth., We collected population density and dietary niche breadth data for 36 insular and 59 mainland lizard species, and estimated competitor and predator richness at the localities where diet data were collected. We estimated dietary niche shift by comparing island species to their mainland relatives. We controlled for phylogenetic relatedness, body mass and the size of the plots over which densities were estimated., We found that island and mainland species had similar niche breadths. Dietary niche breadth was unrelated to competitor and predator richness, on both islands and the mainland. Population density was unrelated to dietary niche breadth across island and mainland populations., Our results indicate that dietary generalism is not an effective way of increasing population density nor is it result of lower competitive pressure. A lower variety of resources on islands may prevent insular animals from increasing their niche breadths even in the face of few competitors. [ABSTRACT FROM AUTHOR]

Aim Lizards are ancestrally diurnal, and most of them remain so. Nocturnality is common among lizards, but the environmental factors associated with lizard nocturnal activity are still unknown. Here, we contrasted the ambient temperature and productivity hypotheses, where we predicted that cold temperatures will pose a stonger limit to nocturnal species richness than diurnal lizards. Moreover, we contrasted the relative importance of annual, day and night mean temperatures to pinpoint the drivers of nocturnal lizard richness. Location Mainland Eurasia. Methods We collected distribution range and activity time data for all 1,113 lizard species found throughout mainland Eurasia. This represents the largest geographical scope to date, for studies of lizard species richness. We examined the spatial patterns of nocturnal species richness in relationship to diurnal species richness across environmental gradients of ambient temperature and productivity. Results Nocturnal lizards are richest in the tropics and in deserts, and their richness decreases with latitude. However, nocturnal lizards are absent from the highest latitudes and coldest regions inhabited by lizards. Diurnal and nocturnal lizards respond in a similar manner to climatic factors. Ambient temperature has a strong influence on both, whereas productivity is more tightly related to the proportion of nocturnal species. Main conclusions Nocturnality is widespread among Eurasian lizards. However, nocturnal lizards are absent from invariably cold regions, and low temperatures seem to be a limiting factor for lizard activity period. We suggest that the year-round warm nights of the tropics reduce the cost of being active at night and open the nocturnal niche for many lizards. In hot deserts, the combination of hot days and aridity increases the cost of diurnal activity, whereas nocturnal activity provides a shelter from these extreme conditions. [ABSTRACT FROM AUTHOR]

Aim The species population density-range size relationship posits that locally abundant species are widely distributed. However, this proposed pattern has been insufficiently tested. The few tests conducted were usually limited in scale and gave conflicting results. We tested the generality of the positive population density-range size relationship. We then studied whether similar environmental niche requirements are correlated with range size and with population density to search for mechanisms driving the hypothesized link between population density and range size. Location Worldwide. Methods We collected data on population density, range size and environmental niche for a global dataset of 192 lizard, 893 bird and 350 mammal species. Assessing the relationship between population density and range size and environmental niche parameters, we corrected for phylogenetic relationships, body mass, diet and study area. Results Our findings reveal that density had a weak negative correlation with bird range size and was unrelated to lizard and mammal range size. These trends were consistent at the global scale and across the biogeographical realms. Range size was related to relatively similar environmental niche parameters in all groups. Population density, however, was explained by taxon-specific factors and was therefore unrelated to range size by common causation. Main conclusions We suggest that the positive relationship between population density and range size identified in previous studies might be an artefact arising through incomplete sampling of range sizes. Our results indicate that the mechanisms shaping population density and range size may be independent. [ABSTRACT FROM AUTHOR]

Aim To map and assess the richness patterns of reptiles (and included groups: amphisbaenians, crocodiles, lizards, snakes and turtles) in Africa, quantify the overlap in species richness of reptiles (and included groups) with the other terrestrial vertebrate classes, investigate the environmental correlates underlying these patterns, and evaluate the role of range size on richness patterns. Location Africa. Methods We assembled a data set of distributions of all African reptile species. We tested the spatial congruence of reptile richness with that of amphibians, birds and mammals. We further tested the relative importance of temperature, precipitation, elevation range and net primary productivity for species richness over two spatial scales (ecoregions and 1° grids). We arranged reptile and vertebrate groups into range-size quartiles in order to evaluate the role of range size in producing richness patterns. Results Reptile, amphibian, bird and mammal richness are largely congruent ( r = 0.79-0.86) and respond similarly to environmental variables (mainly productivity and precipitation). Ecoregion size accounts for more variation in the richness of reptiles than in that of other groups. Lizard distributions are distinct with several areas of high species richness where other vertebrate groups (including snakes) are species-poor, especially in arid ecoregions. Habitat heterogeneity is the best predictor of narrow-ranging species, but remains relatively important in explaining lizard richness even for species with large range sizes. Main conclusions Reptile richness varies with similar environmental variables as the other vertebrates in Africa, reflecting the disproportionate influence of snakes on reptile richness, a result of their large ranges. Richness gradients of narrow-ranged vertebrates differ from those of widespread taxa, which may demonstrate different centres of endemism for reptile subclades in Africa. Lizard richness varies mostly with habitat heterogeneity independent of range size, which suggests that the difference in response of lizards is due to their ecological characteristics. These results, over two spatial scales and multiple range-size quartiles, allow us to reliably interpret the influence of environmental variables on patterns of reptile richness and congruency. [ABSTRACT FROM AUTHOR]

Aim Islands organisms usually have fewer predator and competitor species than mainland ones. This is thought to result in high population densities on islands. We hypothesize that insular lizards have denser populations than mainland species and that density, in general, is negatively correlated with competitor and predator richness. Location Global. Methods We compared densities of 346 lizard species on islands and the mainland while examining the relationship between density and, predator and competitor richness, primary productivity, seasonality and island area. We controlled for phylogenetic non-independence, body mass and study area, which are known to strongly affect population density. Results Insular populations (especially on snake-free islands) are denser than mainland ones. Mainland populations of lizard species that also inhabit islands were denser than those of species that do not inhabit islands. Population density was the highest on islands with low net primary productivity and was not significantly affected by competitor or predator richness. Moreover, insular populations show high density regardless of island area. Main conclusions We conclude that the ability of mainland species to reach high population densities may increase their chances in reaching and successfully colonizing islands. We postulate that population density may be affected by predator and competitor density rather than by their richness. Density increase on islands may result not from the environmental simplicity of island faunas but through propagule sorting or pressure. [ABSTRACT FROM AUTHOR]

Luxuriant, bushy antlers, bizarre crests, and huge, twisting horns and tusks are conventionally understood as products of sexual selection. This view stems from both direct observation and from the empirical finding that the size of these structures grows faster than body size (i.e., ornament size shows positive allometry).We contend that the familiar evolutionary increase in the complexity of ornaments over time in many animal clades is decoupled from ornament size evolution. Increased body size comes with extended growth. Since growth scales to the quarter power of body size, we predicted that ornament complexity should scale according to the quarter power law as well, irrespective of the role of sexual selection in the evolution and function of the ornament. To test this hypothesis, we selected three clades (ammonites, deer, and ceratopsian dinosaurs) whose species bore ornaments that differ in terms of the importance of sexual selection to their evolution.We found that the exponent of the regression of ornament complexity to body size is the same for the three groups and is statistically indistinguishable from0.25.We suggest that the evolution of ornament complexity is a by-product of Cope's rule. We argue that although sexual selection may control size in most ornaments, it does not influence their shape. [ABSTRACT FROM AUTHOR]

Aim Longevity is an important life-history trait, directly linked to the core attributes of fitness (reproduction and survival), yet large-scale comparative studies quantifying its implications for the ecology and life history of ectotherms are scarce. We tested the allometry of longevity in squamates and the tuatara, and determined how longevity is related to key environmental characteristics and life-history traits. Predictions based on life-history theory are expected to hold true for ectotherms, similarly to mammals and birds. Location World-wide. Methods We assembled from the literature a dataset of the maximum longevities of more than a thousand squamate species, representing c. 10% of their known species diversity, their phylogenetic relationships and multiple life-history and ecological variables. Correcting for phylogeny, we modelled the link between squamate longevity and both key life-history traits, such as body mass and age at first reproduction, and important environmental factors, such as latitude and primary productivity within species distributional ranges. Results Large-bodied species live for longer than small ones, but body size explains far less of the variance in longevity than it does in mammals and birds. Accounting for body size, squamate brood frequency is negatively correlated with longevity, while age at first reproduction is positively correlated with longevity. This points to a continuum of slow-to-fast life-history strategies. Squamates in high latitudes and cold regions live for longer, probably because a shorter season of activity translates to slower development, older age at first reproduction and hence to increased longevity. Individuals live longer in captivity than in the wild. Herbivorous and omnivorous squamates live for longer than carnivorous ones. We postulate that low-quality nutrition reduces growth rates, promotes a relative decline in reproductive rates and thus prolongs life. Main conclusions Our results support key predictions from life-history theory and suggest that reproducing more slowly and at older ages, being herbivorous and, plausibly, lowering metabolism, result in increased longevity. [ABSTRACT FROM AUTHOR]

Sexual size dimorphism ( SSD) can allow males and females of the same species to specialize on different sized food items and therefore minimize intraspecific competition., Interspecific competition, however, is thought to limit sexual dimorphism, as larger competitors in the community will prevent the larger sex from evolving larger size, and smaller species may prevent the smaller sex from becoming even smaller., We tested this prediction using data on the sexual size dimorphism of lizards, and mammalian carnivores, on islands world-wide., Because insular communities are depauperate, and guilds are species-poor, it is often assumed that enhanced sexual size dimorphism is common on islands. The intensity of interspecific competition, hindering enhanced dimorphism, is thought to increase with competitor richness., We tested whether intraspecific sexual size dimorphism of mammalian carnivores and lizards decreases with increasing island species richness. We further computed the average sexual dimorphism of species on islands and tested whether species-rich islands are inhabited by relatively monomorphic species. Within families and guilds across carnivores and lizards, and with both intraspecific and interspecific approaches, we consistently failed to find support for the notion that species-poor islands harbour more sexually dimorphic individuals or species., We conclude that either interspecific competition does not affect the sexual size dimorphism of insular lizards and carnivores (i.e. character displacement and species sorting are rare in these taxa), or that the number of species in an assemblage or guild is a poor proxy for the intensity of interspecific competition in insular assemblages. [ABSTRACT FROM AUTHOR]

Aim The origins of islands influence island colonization and radiation dynamics, thus exerting differential selection pressures on the species that inhabit them. The occurrence of lower numbers of predator and competitor species on islands than the mainland selects for 'slow' life-history attributes (the 'island syndrome'). Animals colonizing, and radiating on, oceanic islands probably face more novel environments than do those inhabiting continental fragment and land-bridge islands. We hypothesized that oceanic island endemics will show the slowest life histories, whereas land-bridge island species will resemble mainland species the most. We predicted that species on old, small and isolated islands will also have slow life histories. Location World-wide. Methods We assembled life-history data for 540 mainland and 319 insular endemic lizard species. We tested whether clutch size, brood frequency, hatchling mass and productivity differed between islands of different origin and between islands and the mainland. We controlled for female size, for latitude and for phylogenetic relationship using the R package caper. In addition, we tested the influences of island age, area and isolation on species life histories. Results Oceanic island endemics have the smallest clutches and the largest offspring, and, together with continental fragment island endemics, lay most frequently. Clutch size, brood frequency and productivity increase with increasing island age. Isolation and area have little effect on lizard life history. Main conclusions Our findings support the proposition that selection pressure differs across island type. The predator-poor environments on oceanic islands select for few, large offspring, while the predator-rich environments of the mainland and land-bridge islands select for many, small offspring. Island geological origin creates the environment within which evolution takes place, and thus plays a major role in life-history evolution. As islands grow older, lizards adapt by increasing their yearly reproductive effort. [ABSTRACT FROM AUTHOR]

Aim Temperature influences most components of animal ecology and life history - but what kind of temperature? Physiologists usually examine the influence of body temperatures, while biogeographers and macroecologists tend to focus on environmental temperatures. We aim to examine the relationship between these two measures, to determine the factors that affect lizard body temperatures and to test the effect of both temperature measures on lizard life history. Location World-wide. Methods We used a large (861 species) global dataset of lizard body temperatures, and the mean annual temperatures across their geographic ranges to examine the relationships between body and mean annual temperatures. We then examined factors influencing body temperatures, and tested for the influence of both on ecological and life-history traits while accounting for the influence of shared ancestry. Results Body temperatures and mean annual temperatures are uncorrelated. However, accounting for activity time (nocturnal species have low body temperatures), use of space (fossorial and semi-aquatic species are 'colder'), insularity (mainland species are 'hotter') and phylogeny, the two temperatures are positively correlated. High body temperatures are only associated with larger hatchlings and increased rates of biomass production. Annual temperatures are positively correlated with clutch frequency and annual longevity, and negatively correlated with clutch size, age at first reproduction and longevity. Main conclusions Lizards with low body temperatures do not seem to have 'slower' life-history attributes than species with high body temperatures. The longer seasons prevalent in warm regions, and physiological processes that operate while lizards are inactive (but warm enough), make environmental temperatures better predictors of lizard life-history variation than body temperatures. This surprisingly greater effect of environmental temperatures on lizard life histories hints that global warming may have a profound influence on lizard ecology and evolution. [ABSTRACT FROM AUTHOR]

Aim Islands are thought to promote correlated ecological and life-history shifts in species, including increased population density, and an infrequent production of few, large, offspring. These patterns are collectively termed 'the island syndrome'. We present here the first, phylogenetically informed, global test of the 'island syndrome' hypothesis, using lizards as our model organisms. Location World-wide. Methods We assembled a database containing 641 lizard species, their phylogenetic relationships, geographic ranges and the following life-history traits: female mass, clutch size, brood frequency, hatchling body mass and population density. We tested for life-history differences between insular and mainland forms in light of the island syndrome, controlling for mass and latitude, and for phylogenetic non-independence. We also examined the effects of population density and, in insular endemics, of island area, on lizard reproductive traits. Results We found that insular endemic lizards lay smaller clutches of larger hatchlings than closely related mainland lizards of similar size, as was expected by the island syndrome. In general, however, insular endemics lay more frequently than mainland ones. Species endemic to small islands lay as frequently as mainland species. Continental and insular lizards have similar productivity rates overall. Island area had little effect on lizard reproductive traits. No trait showed association with population density. Main conclusions Island endemic lizards mainly follow the island syndrome. We hypothesize that large offspring are favoured on islands because of increased intra-specific aggression and cannibalism by adults. Stable populations on islands lacking predators may likewise lead to increased intra-specific competition, and hence select for larger hatchlings that will quickly grow to adult size. This view is supported by the fact that lizard populations are denser on islands - although population density per se was uncorrelated with any of the traits we examined. [ABSTRACT FROM AUTHOR]