ResearchPad - 70 https://www.researchpad.co Default RSS Feed en-us © 2020 Newgen KnowledgeWorks <![CDATA[The apparent exponential radiation of Phanerozoic land vertebrates is an artefact of spatial sampling biases]]> https://www.researchpad.co/article/Nc9e55dae-0ecc-4336-855c-b5ad1fdaf2ed There is no consensus about how terrestrial biodiversity was assembled through deep time, and in particular whether it has risen exponentially over the Phanerozoic. Using a database of 60 859 fossil occurrences, we show that the spatial extent of the worldwide terrestrial tetrapod fossil record itself expands exponentially through the Phanerozoic. Changes in spatial sampling explain up to 67% of the change in known fossil species counts, and these changes are decoupled from variation in habitable land area that existed through time. Spatial sampling therefore represents a real and profound sampling bias that cannot be explained as redundancy. To address this bias, we estimate terrestrial tetrapod diversity for palaeogeographical regions of approximately equal size. We find that regional-scale diversity was constrained over timespans of tens to hundreds of millions of years, and similar patterns are recovered for major subgroups, such as dinosaurs, mammals and squamates. Although the Cretaceous/Palaeogene mass extinction catalysed an abrupt two- to three-fold increase in regional diversity 66 million years ago, no further increases occurred, and recent levels of regional diversity do not exceed those of the Palaeogene. These results parallel those recovered in analyses of local community-level richness. Taken together, our findings strongly contradict past studies that suggested unbounded diversity increases at local and regional scales over the last 100 million years.

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<![CDATA[Genetic architecture of a key reproductive isolation trait differs between sympatric and non-sympatric sister species of Lake Victoria cichlids]]> https://www.researchpad.co/article/Nd141aa0e-3c78-4fd4-aac5-04dac3d58edc One hallmark of the East African cichlid radiations is the rapid evolution of reproductive isolation that is robust to full sympatry of many closely related species. Theory predicts that species persistence and speciation in sympatry with gene flow are facilitated if loci of large effect or physical linkage (or pleiotropy) underlie traits involved in reproductive isolation. Here, we investigate the genetic architecture of a key trait involved in behavioural isolation, male nuptial coloration, by crossing two sister species pairs of Lake Victoria cichlids of the genus Pundamilia and mapping nuptial coloration in the F2 hybrids. One is a young sympatric species pair, representative of an axis of colour motif differentiation, red-dorsum versus blue, that is highly recurrent in closely related sympatric species. The other is a species pair representative of colour motifs, red-chest versus blue, that are common in allopatric but uncommon in sympatric closely related species. We find significant quantitative trait loci (QTLs) with moderate to large effects (some overlapping) for red and yellow in the sympatric red-dorsum × blue cross, whereas we find no significant QTLs in the non-sympatric red-chest × blue cross. These findings are consistent with theory predicting that large effect loci or linkage/pleiotropy underlying mating trait differentiation could facilitate speciation and species persistence with gene flow in sympatry.

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<![CDATA[Structure–behaviour correlations between two genetically closely related snail species]]> https://www.researchpad.co/article/N34ae456a-4468-4991-abda-6f0c6f32bda7

Species, through their structure and composition, have evolved to respond to environmental constraints. Predator–prey interactions are among environmental pressures that can lead to speciation, but it remains unclear how this pressure can be related to the material structure and performance. Recently, two land snails, Karaftohelix editha and Karaftohelix gainesi, were found to exhibit divergent phenotypes and responses to predation despite sharing the same habitat and most of their genome. Indeed, under attack from a beetle, K. editha snails retract into their shell whereas K. gainesi snails swing their shell. In this paper, we looked at the microstructure, composition, morphology and mechanics of the shells of those two species and discuss potential relationships between material structure and the snail defence behaviour. The results of this study provide additional arguments for the role of predator–prey interactions on speciation, as well as an unusual approach for the design of biomimetic structures adapted to a particular function.

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<![CDATA[Sexual frequency is associated with age of natural menopause: results from the Study of Women's Health Across the Nation]]> https://www.researchpad.co/article/N9ca572b3-18fc-4cfb-9e0f-7d2629bf6aa4

It is often observed that married women have a later age of natural menopause (ANM) than unmarried women; however, the reason for this association is unknown. We test an original hypothesis that sexual frequency acts as a bio-behavioural mediator between marital status and ANM. We hypothesize that there is a trade-off between continued ovulation and menopause based on the woman's chances of becoming pregnant. If a woman is sexually inactive, then pregnancy is impossible, and continued investment in ovulation would not be adaptive. In addition, we test an existing hypothesis that the observed relationship is because of the exposure to male pheromones. Data from 2936 women were drawn from 11 waves of the Study of Women's Health Across the Nation, which is a longitudinal study conducted in the United States. Using time-varying Cox regression, we found no evidence for the pheromone hypothesis. However, we did observe that women who reported to have sex weekly during the study period were 28% less likely to experience menopause than women who had sex less than monthly. This is an indication that ANM may be somewhat facultative in response to the likelihood of pregnancy.

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<![CDATA[What makes a pair bond in a Neotropical primate: female and male contributions]]> https://www.researchpad.co/article/N83ea953f-5c33-488f-a14d-34442f3aac35

Pair living and pair bonding are rare in mammals, and the mechanisms of their maintenance remain a puzzle. Titi monkeys, a ‘textbook example’ for ‘monogamous’ primates, have strong pair bonds and extensive male care. To investigate mechanisms of pair-bond maintenance, we studied seven wild groups of red titis (Plecturocebus cupreus) in Peruvian Amazonia over a period of 14 months. We analysed pair bonds by measuring proximity, grooming and approaches/leaves within pairs, and collected data on intergroup encounters. Females contributed to grooming more than males, especially during infant dependency, when most of the grooming within pairs was done by females. Females were also more active in controlling proximity between pair mates, making most of the approaches and leaves. Males, on the other hand, invested more in territorial defences. They participated in more intergroup encounters than females and were more active during these encounters. Our data is most consistent with the ‘male-services’ hypothesis for pair-bond maintenance, where a female contributes more to the proximity and affiliation maintenance while a male provides beneficial services.

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<![CDATA[Analysis of statistical correlations between properties of adaptive walks in fitness landscapes]]> https://www.researchpad.co/article/N2721638e-c6ac-41d4-8696-8dae5a7fc88a

The fitness landscape metaphor has been central in our way of thinking about adaptation. In this scenario, adaptive walks are idealized dynamics that mimic the uphill movement of an evolving population towards a fitness peak of the landscape. Recent works in experimental evolution have demonstrated that the constraints imposed by epistasis are responsible for reducing the number of accessible mutational pathways towards fitness peaks. Here, we exhaustively analyse the statistical properties of adaptive walks for two empirical fitness landscapes and theoretical NK landscapes. Some general conclusions can be drawn from our simulation study. Regardless of the dynamics, we observe that the shortest paths are more regularly used. Although the accessibility of a given fitness peak is reasonably correlated to the number of monotonic pathways towards it, the two quantities are not exactly proportional. A negative correlation between predictability and mean path divergence is established, and so the decrease of the number of effective mutational pathways ensures the convergence of the attraction basin of fitness peaks. On the other hand, other features are not conserved among fitness landscapes, such as the relationship between accessibility and predictability.

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<![CDATA[An atypical mating system in a neotropical manakin]]> https://www.researchpad.co/article/N3f9e6cbc-e8a0-42c4-bf6d-f36b51f0c46c

Most of the diversity in the mating systems of birds and other animals comes at higher taxonomic levels, such as across orders. Although divergent selective pressures should lead to animal mating systems that diverge sharply from those of close relatives, opportunities to examine the importance of such processes are scarce. We addressed this issue using the Araripe manakin (Antilophia bokermanni), a species endemic to a forest enclave surrounded by xeric shrublands in Brazil. Most manakins exhibit polygynous lekking mating systems that lack territoriality but exhibit strong sexual selection. In sharp contrast, we found that male Araripe manakins defended exclusive territories, and females nested within male territories. However, territoriality and offspring paternity were dissociated: males sired only 7% of nestlings from the nests within their territories and non-territorial males sired numerous nestlings. Moreover, female polyandry was widespread, with most broods exhibiting mixed paternity. Apparently, territories in this species function differently from both lekking arenas and resource-based territories of socially monogamous species. The unexpected territoriality of Araripe manakins and its dissociation from paternity is a unique evolutionary development within the manakin clade. Collectively, our findings underscore how divergences in mating systems might evolve based on selective pressures from novel environmental contexts.

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<![CDATA[Evolutionary dynamics in the dispersal of sign languages]]> https://www.researchpad.co/article/N0c6dfb45-274e-40b3-bb09-8523fd161d97

The evolution of spoken languages has been studied since the mid-nineteenth century using traditional historical comparative methods and, more recently, computational phylogenetic methods. By contrast, evolutionary processes resulting in the diversity of contemporary sign languages (SLs) have received much less attention, and scholars have been largely unsuccessful in grouping SLs into monophyletic language families using traditional methods. To date, no published studies have attempted to use language data to infer relationships among SLs on a large scale. Here, we report the results of a phylogenetic analysis of 40 contemporary and 36 historical SL manual alphabets coded for morphological similarity. Our results support grouping SLs in the sample into six main European lineages, with three larger groups of Austrian, British and French origin, as well as three smaller groups centring around Russian, Spanish and Swedish. The British and Swedish lineages support current knowledge of relationships among SLs based on extra-linguistic historical sources. With respect to other lineages, our results diverge from current hypotheses by indicating (i) independent evolution of Austrian, French and Spanish from Spanish sources; (ii) an internal Danish subgroup within the Austrian lineage; and (iii) evolution of Russian from Austrian sources.

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<![CDATA[Parasite diversity and ecology in a model species, the guppy (Poecilia reticulata) in Trinidad]]> https://www.researchpad.co/article/N5822ac7a-9048-4d5a-bf46-3a73d89eebf9

The guppy (Poecilia reticulata) is a model species in ecology and evolution. Many studies have examined effects of predators on guppy behaviour, reproduction, survival strategies, feeding and other life-history traits, but few have studied variation in their parasite diversity. We surveyed parasites of 18 Trinidadian populations of guppy, to provide insight on the geographical mosaic of parasite variability, which may act as a source of natural selection acting on guppies. We found 21 parasite species, including five new records for Trinidad. Spatial variation in parasite diversity was significantly higher than that of piscine predators, and significant variation in parasite richness among individuals and populations was correlated with: (i) host size, (ii) snail species richness, and (iii) the distance between populations. Differences in parasite species richness are likely to play an important, yet underestimated role in the biology of this model species of vertebrate ecology and evolution.

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<![CDATA[Evolution in the Debian GNU/Linux software network: analogies and differences with gene regulatory networks]]> https://www.researchpad.co/article/N36ed7a4d-f37c-42e3-b0e5-334f53109fd2

Biological networks exhibit intricate architectures deemed to be crucial for their functionality. In particular, gene regulatory networks, which play a key role in information processing in the cell, display non-trivial architectural features such as scale-free degree distributions, high modularity and low average distance between connected genes. Such networks result from complex evolutionary and adaptive processes difficult to track down empirically. On the other hand, there exists detailed information on the developmental (or evolutionary) stages of open-software networks that result from self-organized growth across versions. Here, we study the evolution of the Debian GNU/Linux software network, focusing on the changes of key structural and statistical features over time. Our results show that evolution has led to a network structure in which the out-degree distribution is scale-free and the in-degree distribution is a stretched exponential. In addition, while modularity, directionality of information flow, and average distance between elements grew, vulnerability decreased over time. These features resemble closely those currently shown by gene regulatory networks, suggesting the existence of common adaptive pathways for the architectural design of information-processing networks. Differences in other hierarchical aspects point to system-specific solutions to similar evolutionary challenges.

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<![CDATA[Disentangling the interplay of positive and negative selection forces that shaped mitochondrial genomes of Gammarus pisinnus and Gammarus lacustris]]> https://www.researchpad.co/article/Nc05398be-3540-47ad-8119-eb6b26a443fa

We hypothesized that the mitogenome of Gammarus lacustris (GL), native to the Qinghai-Tibet Plateau, might exhibit genetic adaptations to the extreme environmental conditions associated with high altitudes (greater than 3000 m). To test this, we also sequenced the mitogenome of Gammarus pisinnus (GP), whose native range is close to the Tibetan plateau, but at a much lower altitude (200–1500 m). The two mitogenomes exhibited conserved mitochondrial architecture, but low identity between genes (55% atp8 to 76.1% cox1). Standard (homogeneous) phylogenetic models resolved Gammaridae as paraphyletic, but ‘heterogeneous’ CAT-GTR model as monophyletic. In indirect support of our working hypothesis, GL, GP and Gammarus fossarum exhibit evidence of episodic diversifying selection within the studied Gammaroidea dataset. The mitogenome of GL generally evolves under a strong purifying selection, whereas GP evolves under directional (especially pronounced in atp8) and/or relaxed selection. This is surprising, as GP does not inhabit a unique ecological niche compared to other gammarids. We propose that this rapid evolution of the GP mitogenome may be a reflection of its relatively recent speciation and heightened non-adaptive (putatively metabolic rate-driven) mutational pressures. To test these hypotheses, we urge sequencing mitogenomes of remaining Gammarus species populating the same geographical range as GP.

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<![CDATA[Hidden patterns of codon usage bias across kingdoms]]> https://www.researchpad.co/article/N34680f65-51e7-4171-99d0-45d58d6a7774

The genetic code is necessarily degenerate with 64 possible nucleotide triplets being translated into 20 amino acids. Eighteen out of the 20 amino acids are encoded by multiple synonymous codons. While synonymous codons are clearly equivalent in terms of the information they carry, it is now well established that they are used in a biased fashion. There is currently no consensus as to the origin of this bias. Drawing on ideas from stochastic thermodynamics we derive from first principles a mathematical model describing the statistics of codon usage bias. We show that the model accurately describes the distribution of codon usage bias of genomes in the fungal and bacterial kingdoms. Based on it, we derive a new computational measure of codon usage bias—the distance D capturing two aspects of codon usage bias: (i) differences in the genome-wide frequency of codons and (ii) apparent non-random distributions of codons across mRNAs. By means of large scale computational analysis of over 900 species across two kingdoms of life, we demonstrate that our measure provides novel biological insights. Specifically, we show that while codon usage bias is clearly based on heritable traits and closely related species show similar degrees of bias, there is considerable variation in the magnitude of D within taxonomic classes suggesting that the contribution of sequence-level selection to codon bias varies substantially within relatively confined taxonomic groups. Interestingly, commonly used model organisms are near the median for values of D for their taxonomic class, suggesting that they may not be good representative models for species with more extreme D, which comprise organisms of medical and agricultural interest. We also demonstrate that amino acid specific patterns of codon usage are themselves quite variable between branches of the tree of life, and that some of this variability correlates with organismal tRNA content.

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<![CDATA[Exploring the visual world of fossilized and modern fungus gnat eyes (Diptera: Keroplatidae) with X-ray microtomography]]> https://www.researchpad.co/article/N174fb572-c9b0-44b0-8e7a-973b8d8c76c9

Animal eyes typically possess specialized regions for guiding different behavioural tasks within their specific visual habitat. These specializations, and evolutionary changes to them, can be crucial for understanding an animal's ecology. Here, we explore how the visual systems of some of the smallest flying insects, fungus gnats, have adapted to different types of forest habitat over time (approx. 30 Myr to today). Unravelling how behavioural, environmental and phylogenetic factors influence the evolution of visual specializations is difficult, however, because standard quantitative techniques often require fresh tissue and/or provide data in eye-centric coordinates that prevent reliable comparisons between species with different eye morphologies. Here, we quantify the visual world of three gnats from different time periods and habitats using X-ray microtomography to create high-resolution three-dimensional models of the compound eyes of specimens in different preservation states—fossilized in amber, dried or stored in ethanol. We present a method for analysing the geometric details of individual corneal facets and for estimating and comparing the sensitivity, spatial resolution and field of view of species across geographical space and evolutionary time. Our results indicate that, despite their miniature size, fungus gnats do have variations in visual properties across their eyes. We also find some indication that these visual specializations vary across species and may represent adaptations to their different forest habitats. Overall, the findings demonstrate how such investigations can be used to study the evolution of visual specializations—and sensory ecology in general—across a range of insect taxa from different geographical locations and across time.

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<![CDATA[New theropod remains and implications for megaraptorid diversity in the Winton Formation (lower Upper Cretaceous), Queensland, Australia]]> https://www.researchpad.co/article/N54f0ac06-7dd3-4132-a1ec-8c71ec345581

The holotype specimen of the megaraptorid Australovenator wintonensis, from the Upper Cretaceous Winton Formation (Rolling Downs Group, Eromanga Basin) of central Queensland, is the most complete non-avian theropod found in Australia to date. In fact, the holotype of A. wintonensis and isolated megaraptorid teeth (possibly referable to Australovenator) constitute the only theropod body fossils reported from the Winton Formation. Herein, we describe a new fragmentary megaraptorid specimen from the Winton Formation, found near the type locality of A. wintonensis. The new specimen comprises parts of two vertebrae, two metatarsals, a pedal phalanx and multiple unidentifiable bone fragments. Although the new megaraptorid specimen is poorly preserved, it includes the only megaraptorid vertebrae known from Queensland. The presence of pleurocoels and highly pneumatic caudal centra with camerate and camellate internal structures permit the assignment of these remains to Megaraptora gen. et sp. indet. A morphological comparison revealed that the distal end of metatarsal II and the partial pedal phalanx II-1 of the new specimen are morphologically divergent from Australovenator. This might indicate the presence of a second megaraptorid taxon in the Winton Formation, or possibly intraspecific variation.

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<![CDATA[Transposable elements as a potent source of diverse cis-regulatory sequences in mammalian genomes]]> https://www.researchpad.co/article/N9ea8f7a1-a170-48c2-8302-884abaa3d683

Eukaryotic gene regulation is mediated by cis-regulatory elements, which are embedded within the vast non-coding genomic space and recognized by the transcription factors in a sequence- and context-dependent manner. A large proportion of eukaryotic genomes, including at least half of the human genome, are composed of transposable elements (TEs), which in their ancestral form carried their own cis-regulatory sequences able to exploit the host trans environment to promote TE transcription and facilitate transposition. Although not all present-day TE copies have retained this regulatory function, the preexisting regulatory potential of TEs can provide a rich source of cis-regulatory innovation for the host. Here, we review recent evidence documenting diverse contributions of TE sequences to gene regulation by functioning as enhancers, promoters, silencers and boundary elements. We discuss how TE-derived enhancer sequences can rapidly facilitate changes in existing gene regulatory networks and mediate species- and cell-type-specific regulatory innovations, and we postulate a unique contribution of TEs to species-specific gene expression divergence in pluripotency and early embryogenesis. With advances in genome-wide technologies and analyses, systematic investigation of TEs' cis-regulatory potential is now possible and our understanding of the biological impact of genomic TEs is increasing.

This article is part of a discussion meeting issue ‘Crossroads between transposons and gene regulation’.

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<![CDATA[Transposable elements contribute to the genomic response to insecticides in Drosophila melanogaster]]> https://www.researchpad.co/article/Ne908036a-4276-474f-be67-a2c9f2c36fca

Most of the genotype–phenotype analyses to date have largely centred attention on single nucleotide polymorphisms. However, transposable element (TE) insertions have arisen as a plausible addition to the study of the genotypic–phenotypic link because of to their role in genome function and evolution. In this work, we investigate the contribution of TE insertions to the regulation of gene expression in response to insecticides. We exposed four Drosophila melanogaster strains to malathion, a commonly used organophosphate insecticide. By combining information from different approaches, including RNA-seq and ATAC-seq, we found that TEs can contribute to the regulation of gene expression under insecticide exposure by rewiring cis-regulatory networks.

This article is part of a discussion meeting issue ‘Crossroads between transposons and gene regulation’.

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<![CDATA[Beauty in artistic expressions through the eyes of networks and physics]]> https://www.researchpad.co/article/N034345df-04aa-4302-808a-d26b534fce2a

Beauty is subjective, and as such it, of course, cannot be defined in absolute terms. But we all know or feel when something is beautiful to us personally. And in such instances, methods of statistical physics and network science can be used to quantify and to better understand what it is that evokes that pleasant feeling, be it when reading a book or looking at a painting. Indeed, recent large-scale explorations of digital data have lifted the veil on many aspects of our artistic expressions that would remain forever hidden in smaller samples. From the determination of complexity and entropy of art paintings to the creation of the flavour network and the principles of food pairing, fascinating research at the interface of art, physics and network science abounds. We here review the existing literature, focusing in particular on culinary, visual, musical and literary arts. We also touch upon cultural history and culturomics, as well as on the connections between physics and the social sciences in general. The review shows that the synergies between these fields yield highly entertaining results that can often be enjoyed by layman and experts alike. In addition to its wider appeal, the reviewed research also has many applications, ranging from improved recommendation to the detection of plagiarism.

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<![CDATA[Does kin discrimination promote cooperation?]]> https://www.researchpad.co/article/N01b835c1-9d43-4386-b6c3-65c57bb08a49

Genetic relatedness is a key driver of the evolution of cooperation. One mechanism that may ensure social partners are genetically related is kin discrimination, in which individuals are able to distinguish kin from non-kin and adjust their behaviour accordingly. However, the impact of kin discrimination upon the overall level of cooperation remains obscure. Specifically, while kin discrimination allows an individual to help more-related social partners over less-related social partners, it is unclear whether and how the population average level of cooperation that is evolutionarily favoured should differ under kin discrimination versus indiscriminate social behaviour. Here, we perform a general mathematical analysis in order to assess whether, when and in which direction kin discrimination changes the average level of cooperation in an evolving population. We find that kin discrimination may increase, decrease or leave unchanged the average level of cooperation, depending upon whether the optimal level of cooperation is a convex, concave or linear function of genetic relatedness. We develop an extension of the classic ‘tragedy of the commons' model of cooperation in order to provide an illustration of these results. Our analysis provides a method to guide future research on the evolutionary consequences of kin discrimination.

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<![CDATA[Architectural instability, inverted skews and mitochondrial phylogenomics of Isopoda: outgroup choice affects the long-branch attraction artefacts]]> https://www.researchpad.co/article/N4fc92d9b-b731-41c3-b4d4-2b148fc7b862

The majority strand of mitochondrial genomes of crustaceans usually exhibits negative GC skews. Most isopods exhibit an inversed strand asymmetry, believed to be a consequence of an inversion of the replication origin (ROI). Recently, we proposed that an additional ROI event in the common ancestor of Cymothoidae and Corallanidae families resulted in a double-inverted skew (negative GC), and that taxa with homoplastic skews cluster together in phylogenetic analyses (long-branch attraction, LBA). Herein, we further explore these hypotheses, for which we sequenced the mitogenome of Asotana magnifica (Cymothoidae), and tested whether our conclusions were biased by poor taxon sampling and inclusion of outgroups. (1) The new mitogenome also exhibits a double-inverted skew, which supports the hypothesis of an additional ROI event in the common ancestor of Cymothoidae and Corallanidae families. (2) It exhibits a unique gene order, which corroborates that isopods possess exceptionally destabilized mitogenomic architecture. (3) Improved taxonomic sampling failed to resolve skew-driven phylogenetic artefacts. (4) The use of a single outgroup exacerbated the LBA, whereas both the use of a large number of outgroups and complete exclusion of outgroups ameliorated it.

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<![CDATA[Revisiting the hypothesis of an energetic barrier to genome complexity between eukaryotes and prokaryotes]]> https://www.researchpad.co/article/N0bd3f347-f06c-4152-b53d-fbf3e5c05574

The absence of genome complexity in prokaryotes, being the evolutionary precursors to eukaryotic cells comprising all complex life (the prokaryote–eukaryote divide), is a long-standing question in evolutionary biology. A previous study hypothesized that the divide exists because prokaryotic genome size is constrained by bioenergetics (prokaryotic power per gene or genome being significantly lower than eukaryotic ones). However, this hypothesis was evaluated using a relatively small dataset due to lack of data availability at the time, and is therefore controversial. Accordingly, we constructed a larger dataset of genomes, metabolic rates, cell sizes and ploidy levels to investigate whether an energetic barrier to genome complexity exists between eukaryotes and prokaryotes while statistically controlling for the confounding effects of cell size and phylogenetic signals. Notably, we showed that the differences in bioenergetics between prokaryotes and eukaryotes were less significant than those previously reported. More importantly, we found a limited contribution of power per genome and power per gene to the prokaryote–eukaryote dichotomy. Our findings indicate that the prokaryote–eukaryote divide is hard to explain from the energetic perspective. However, our findings may not entirely discount the traditional hypothesis; in contrast, they indicate the need for more careful examination.

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