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The root system harbours complex bacterial communities, which are critical for plant growth and health. Significant differences exist between bacterial communities in the root compartments; however, limited reports have explored their phylogenetic composition and niche conservatism in the root system of sorghum. We used the sorghum Hongyingzi cultivar as test plant, and applied 16S rRNA high‐throughput sequencing and various statistical approaches. Phylogenetic composition of bacterial communities in root compartments were primarily driven by closely related species with similar environmental adaptations. We also found evidence of phylogenetic niche conservatism in bacterial communities for edaphic factors in the various root compartments, with pH and available N playing essential roles in shaping community composition. Environmental threshold analysis revealed threshold ranges of dominant taxa for pH and available N, indicating wider adaptive thresholds for more abundant taxa. Reconstruction of ancestral states suggested evolutionary changes in adaptability of certain bacterial taxa to edaphic factors, suggesting a shift towards slightly acidic, high N environments and reflecting the prolonged mutual interaction between bacteria and plants in cultivated soils. These findings enhance our understanding of environmental responses and evolutionary dynamics of root‐associated microbiota in young sorghum plants and provide novel insights into ecological adaptations, shedding light on their responses to environmental factors. Our study contributes to a better understanding of the ecological dynamics of root‐associated microbiota and offers analytical pathways for exploring the nutritional regulation of root microbiota. [ABSTRACT FROM AUTHOR]

The Hymenochaetales is an order with most species as wood-inhabiting fungi that have high phylogenetic complexity and morphological diversity. Species in this order play important roles in forest ecosystems and include wood decomposers, pathogens, and those that form ectomycorrhizal associations. However, we have limited knowledge of the patterns of large-scale evolutionary history of the order. In this study, using 171 genomes, including 113 newly assembled, we reconstructed the phylogenomic relationships, divergence times, biogeographic patterns, morphological evolution of basidiomata, and patterns of speciation/extinction in the Hymenochaetales. The phylogenomic relationships of 12 families within the Hymenochaetales suggested that 10 families can be accepted, and 2 families rejected. Molecular clock dating analyses suggested that the Hymenochaetales possibly started a rapid family-wide and genus-wide radiation during the early Cretaceous to late Jurassic and Cretaceous, respectively. Reconstruction of the ancestral state implied that Hymenochaetales probably originated from the temperate regions of Asia, with the basidiomata of the common ancestor likely being a corticioid species that rapidly transformed between the early Cretaceous and late Jurassic, coinciding with radiations at the family level. Furthermore, we detected a gradually increasing trend of speciation, extinction, and net diversification rates. We provided large-scale genomes of the Hymenochaetales and revealed evolutionary history patterns, which are key to understanding the evolution of fungi. [ABSTRACT FROM AUTHOR]

Litter size plays an essential role in mammalian evolution and is one of the most important factors determining whether an organism is deemed to have a 'slow' or 'fast' life history strategy. Humans are distinct in being classified as having slow life history yet bearing singletons who have completed relatively less growth than other ape neonates. Previous work has proposed that the ancestral primate gave birth to singletons. However, primate litter size has not yet been contextualized within a broad phylogenetic assessment of mammalian life history. We performed a comprehensive investigation of primate litter size using life history data for 155 primate species, and litter size data for an additional 791 boreoeutherian mammals. Litter size and life history traits have strong phylogenetic signal in primates (Pagel's lambda: 0.99, p < 0.001; Blomberg's K: 0.6311. p < 0.001), and litter size is significantly negatively correlated with gestation length (p < 0.001). Our data support that the last common ancestors of both primates and Haplorhini gave birth to multiples (litter size 1.7 and 1.6, respectively). We also find that singleton-bearing pregnancies evolved convergently in multiple primate lineages, including tarsiers and other haplorhines. This study contributes significantly to our understanding of life history and litter size in mammals, and we emphasize the utility of a callitrichid model for investigating the evolution of human reproduction. [ABSTRACT FROM AUTHOR]

The Hymenochaetales is an order with most species as wood-inhabiting fungi that have high phylogenetic complexity and morphological diversity. Species in this order play important roles in forest ecosystems and include wood decomposers, pathogens, and those that form ectomycorrhizal associations. However, we have limited knowledge of the patterns of large-scale evolutionary history of the order. In this study, using 171 genomes, including 113 newly assembled, we reconstructed the phylogenomic relationships, divergence times, biogeographic patterns, morphological evolution of basidiomata, and patterns of speciation/extinction in the Hymenochaetales. The phylogenomic relationships of 12 families within the Hymenochaetales suggested that 10 families can be accepted, and 2 families rejected. Molecular clock dating analyses suggested that the Hymenochaetales possibly started a rapid family-wide and genus-wide radiation during the early Cretaceous to late Jurassic and Cretaceous, respectively. Reconstruction of the ancestral state implied that Hymenochaetales probably originated from the temperate regions of Asia, with the basidiomata of the common ancestor likely being a corticioid species that rapidly transformed between the early Cretaceous and late Jurassic, coinciding with radiations at the family level. Furthermore, we detected a gradually increasing trend of speciation, extinction, and net diversification rates. We provided large-scale genomes of the Hymenochaetales and revealed evolutionary history patterns, which are key to understanding the evolution of fungi.

Litter size plays an essential role in mammalian evolution and is one of the most important factors determining whether an organism is deemed to have a ‘slow’ or ‘fast’ life history strategy. Humans are distinct in being classified as having slow life history yet bearing singletons who have completed relatively less growth than other ape neonates. Previous work has proposed that the ancestral primate gave birth to singletons. However, primate litter size has not yet been contextualized within a broad phylogenetic assessment of mammalian life history. We performed a comprehensive investigation of primate litter size using life history data for 155 primate species, and litter size data for an additional 791 boreoeutherian mammals. Litter size and life history traits have strong phylogenetic signal in primates (Pagel’s lambda: 0.99, p < 0.001; Blomberg’s K: 0.6311. p < 0.001), and litter size is significantly negatively correlated with gestation length (p < 0.001). Our data support that the last common ancestors of both primates and Haplorhini gave birth to multiples (litter size 1.7 and 1.6, respectively). We also find that singleton-bearing pregnancies evolved convergently in multiple primate lineages, including tarsiers and other haplorhines. This study contributes significantly to our understanding of life history and litter size in mammals, and we emphasize the utility of a callitrichid model for investigating the evolution of human reproduction.

Agonistic displays are one of the most diverse social behaviors that have important functions in animal's life history. However, their origin and driving factors have largely been unexplored. Here, we evaluated agonistic displays of 71 bat species across 10 families and classified these displays into two categories: (a) boxing displays where a bat attacks its opponent with its wrist and thumb and (b) pushing displays where a bat uses its head or body to hit a rival. We estimated the strength of the phylogenetic signal of the agonistic displays, revealed their origin, and tested the potential evolutionary relationships between agonistic behaviors and body size or resting posture (free hanging vs. contact hanging where the bat is in contact with some surface). We found that agonistic displays were phylogenetically conserved and that boxing displays are the ancestral state. Moreover, we found that bats with a free-hanging resting posture were more likely to exhibit boxing displays than pushing displays. In addition, bats with longer forearms do not have a higher propensity for boxing displays. This study expands our limited knowledge of the evolution of agonistic displays and highlights the importance of resting posture as a driving force in the diversity of agonistic displays. [ABSTRACT FROM AUTHOR]

IntroductionEuchelicerata is a diverse group encompassing Xiphosura, Chasmataspidida, Eurypterida, and Arachnida. Xiphosura represents an extant group with a rich fossil record dating back to the Ordovician period. Xiphosurans are often referred to as “living fossils” due to their seemingly unchanged morphology over millions of years. Numerous studies have contributed to the understanding of xiphosuran development, revealing changes in the timing and rate of their growth. These changes have been mainly associated with the freshwater invasion of early xiphosuran forms. However, limited research has been conducted to compare the developmental patterns of xiphosurans with other euchelicerates inhabiting aquatic environments.MethodsThis study compares the developmental patterns of xiphosurans with that of the fossil clades of eurypterids and chasmataspidids. By incorporating environmental and phylogenetic information within ancestral state reconstruction analyses, and then testing different evolutionary scenarios, the influence of the environment on the evolution of developmental patterns of euchelicerates is examined.ResultsThe results confirm that the developmental changes in Xiphosura throughout their evolutionary history are correlated with the exploitation of different environments. However, the inclusion of eurypterids and chasmataspidids indicates that the entirety of changes seen for Xiphosura represent only a small portion of the total variability recovered for euchelicerates.DiscussionOur results emphasize the importance of considering phylogenetic relationships and outgroup comparisons to understand the evolutionary dynamics of Xiphosura.

Duetting, in which 2 or more individuals call in coordinated unison, is common in birds, yet most research investigating the function of avian duets has focused only on oscine passerines. However, we have discovered that duetting occurs in 61 species (59%) in the family Rallidae (rails), one of the highest known rates in any bird clade, and that rail duets are also significantly associated with year-round territoriality and habitat type. We applied a comparative approach to study the occurrence of duetting relative to socio-ecological traits and call properties in 103 rail species, with the prediction that duetting rails produce low-frequency calls that spread well over short distances in densely vegetated habitats. Using a model correcting for phylogenetic signal, we found that duetting is the ancestral state in Rallidae, and that duetting rails show a trending effect for being sedentary and nonmigratory. Contrary to our predictions, there was no significant correlation between rail duetting and social bond length, breeding system, breeding latitude from the equator, or sexual dimorphism, as year-round territoriality and forest or heterogeneous habitats were the strongest predictors of duets. Despite the prevalence of duetting in Rallidae, few studies have tested duet functions such as territory defense in this family, and our comparative phylogenetic study lays the groundwork for future research, as little remains known about the behavioral ecology and vocal interactions of many rails. [ABSTRACT FROM AUTHOR]

Female singing and coordinated male–female duetting are often but not always found in the same species. Both behaviors are more common in tropical than temperate songbirds, but few studies have differentiated between the factors selecting for each. Here we investigate the evolution of female vocal complexity and male–female vocal coordination in Carolina wrens (Thryothorus ludovicianus), one of the few non‐tropical members of a songbird family (Troglodytidae) that is well known for producing coordinated male–female duets. Female Carolina wrens are not known to sing; rather, they produce relatively simple, sex‐specific chatters, often during territorial encounters. We analyzed field recordings to show that females coordinate these chatters with male songs at rates similar to those observed in some tropical duetting wren species. We then used phylogenetic comparative methods to show that the evolutionary ancestors of Carolina wrens had female songs that were more acoustically complex than the vocalizations of current females, suggesting past selection against female vocal complexity. Levels of vocal coordination with males, in contrast, have changed relatively little from those of tropical ancestors. Our results suggest that these two aspects of female behavior, acoustic complexity and vocal coordination with males, have evolved independently and have different functions in communication. [ABSTRACT FROM AUTHOR]

It is generally believed that marsupials are more primitive than placentals mammals and mainly solitary living, representing the ancestral form of social organization of all mammals. However, field studies have observed pair and group-living in marsupial species, but no comparative study about their social evolution was ever done. Here, we describe the results of primary literature research on marsupial social organization which indicates that most species can live in pairs or groups and many show intra-specific variation in social organization. Using Bayesian phylogenetic mixed-effects models with a weak phylogenetic signal of 0.18, we found that solitary living was the most likely ancestral form (35% posterior probability), but had high uncertainty, and the combined probability of a partly sociable marsupial ancestor (65%) should not be overlooked. For Australian marsupials, group-living species were less likely to be found in tropical rainforest, and species with a variable social organization were associated with low and unpredictable precipitation representing deserts. Our results suggest that modern marsupials are more sociable than previously believed and that there is no strong support that their ancestral state was strictly solitary living, such that the assumption of a solitary ancestral state of all mammals may also need reconsideration. [ABSTRACT FROM AUTHOR]

Although recent molecular phylogenetic analyses have greatly improved our understanding of the classification of the large liverwort family Lejeuneaceae, the frequent incongruencies between morphology‐based taxonomy and molecular phylogeny have hindered our understanding of evolutionary diversification within the group. Here we focus on Leptolejeunea (Spruce) Steph., a pantropical epiphyllous genus in Lejeuneaceae with 40 species. Phylogenetic studies on the genus have been hampered by insufficient taxon sampling, leaving the deep phylogenetic relationships within this group unresolved. We present the most comprehensive phylogenetic analysis of the genus to date with sampling of over 80% of species, including the enigmatic Leptolejeunea spinistipula (Mizut.) X.L.He endemic to Borneo. Based on data from three molecular markers with representatives of Leptolejeunea and its allies, Leptolejeunea appeared to be monophyletic following the exclusion of L. spinistipula and its transfer to Soella R.L.Zhu, L.Shu, Qiong He & Y.M.Wei. A total‐evidence approach was taken to resolve the backbone phylogeny of Leptolejeunea and a first infrageneric classification of Leptolejeunea, including a new subgenus and three new sections, is proposed based on integrated molecular and morphological evidence. Reconstruction of the evolutionary history showed a wide ancestral area of Leptolejeunea during the Paleogene that arose in mainland Asia, followed by an accelerated speciation rate. Across the biogeographical history of Leptolejeunea, long‐distance dispersal had profound effects on population expansion. Our findings suggest that Australasia is a source of biodiversity of Asian evergreen broad‐leaved forests that have been established since the Oligocene and rose after the early Miocene. [ABSTRACT FROM AUTHOR]

Abstract Actinopterygians (ray‐finned fishes) are the most diversified group of vertebrates and are characterized by a variety of protective structures covering their integument, the evolution of which has intrigued biologists for decades. Paleontological records showed that the first mineralized vertebrate skeleton was composed of dermal bony plates covering the body, including odontogenic and skeletogenic components. Later in evolution, the exoskeleton of actinopterygian's trunk was composed of scale structures. Although scales are nowadays a widespread integument cover, some contemporary lineages do not have scales but bony plates covering their trunk, whereas other lineages are devoid of any such structures. To understand the evolution of the integument coverage and particularly the transition between different structures, we investigated the pattern of scale loss events along with actinopterygian evolution and addressed the functional relationship between the scaleless phenotype and the ecology of fishes. Furthermore, we examined whether the emergence of trunk bony plates was dependent over the presence or absence of scales. To this aim, we used two recently published actinopterygian phylogenies, one including >11,600 species, and by using stochastic mapping and Bayesian methods, we inferred scale loss events and trunk bony plate acquisitions. Our results reveal that a scaled integument is the most frequent state in actinopterygians, but multiple independent scale loss events occurred along their phylogeny with essentially no scale re‐acquisition. Based on linear mixed models, we found evidence supporting that after a scale loss event, fishes tend to change their ecology and adopt a benthic lifestyle. Furthermore, we show that trunk bony plates appeared independently multiple times along the phylogeny. By using fitted likelihood models for character evolution, we show that trunk bony plate acquisitions were dependent on a previous scale loss event. Overall, our findings support the hypothesis that integument cover is a key evolutionary trait underlying actinopterygian radiation.

Abstract Background Bird mitogenomes differ from other vertebrates in gene rearrangement. The most common avian gene order, identified first in Gallus gallus, is considered ancestral for all Aves. However, other rearrangements including a duplicated control region and neighboring genes have been reported in many representatives of avian orders. The repeated regions can be easily overlooked due to inappropriate DNA amplification or genome sequencing. This raises a question about the actual prevalence of mitogenomic duplications and the validity of the current view on the avian mitogenome evolution. In this context, Palaeognathae is especially interesting because is sister to all other living birds, i.e. Neognathae. So far, a unique duplicated region has been found in one palaeognath mitogenome, that of Eudromia elegans. Results Therefore, we applied an appropriate PCR strategy to look for omitted duplications in other palaeognaths. The analyses revealed the duplicated control regions with adjacent genes in Crypturellus, Rhea and Struthio as well as ND6 pseudogene in three moas. The copies are very similar and were subjected to concerted evolution. Mapping the presence and absence of duplication onto the Palaeognathae phylogeny indicates that the duplication was an ancestral state for this avian group. This feature was inherited by early diverged lineages and lost two times in others. Comparison of incongruent phylogenetic trees based on mitochondrial and nuclear sequences showed that two variants of mitogenomes could exist in the evolution of palaeognaths. Data collected for other avian mitogenomes revealed that the last common ancestor of all birds and early diverging lineages of Neoaves could also possess the mitogenomic duplication. Conclusions The duplicated control regions with adjacent genes are more common in avian mitochondrial genomes than it was previously thought. These two regions could increase effectiveness of replication and transcription as well as the number of replicating mitogenomes per organelle. In consequence, energy production by mitochondria may be also more efficient. However, further physiological and molecular analyses are necessary to assess the potential selective advantages of the mitogenome duplications.

Placentation refers to the mode of ovule attachment on the wall of the ovary. In multiovulate ovaries, placentation influences interactions among developing seeds with varying degrees of kinships. Placentation is a taxonomically informative character in flowering plants, yet little has been written about the origin and evolutionary trends of various placentation types in flowering plants since Puri’s and Stebbins’ work, over six decades and almost four decades ago, respectively. More recently, some authors have written about the evolution of placentation in certain groups, but an overall perspective for angiosperms is lacking. For 421 families of angiosperms, we collected data on placentation types and ovule number, and analyzed the data in the phylogenetic context using recent comprehensive phylogeny of angiosperms to test the hypotheses on the evolution of various placentation types and their association with ovule number. The distribution of placentation types across flowering plants suggests that axile placentation, followed by parietal and basal placentation, occurs more frequently than laminar and free central placentation that are very rare. Our results are more consistent with evolutionary trends proposed by Puri than by Stebbins and suggest that marginal placentation is the ancestral and most primitive placentation type, while axile is the most advanced. Placentation types show strong association with ovule number. Finally, our results on ovule number and placentation types indicate that most angiosperms may fall into two categories: one with one or few ovule(s) and basal placentation, and another with many ovules and parietal and axile placentation. Kin selection within ovaries may play a role in explaining the observed patterns. Overall, our results provide new insights into the evolution of placentation, particularly into the drivers underlying the diversification of various placentation types.

The rearrangement of 37 genes with one control region, firstly identified in Gallus gallus mitogenome, is believed to be ancestral for all Aves. However, mitogenomic sequences obtained in recent years revealed that many avian mitogenomes contain duplicated regions that were omitted in previous genomic versions. Their evolution and mechanism of duplication are still poorly understood. The order of Accipitriformes is especially interesting in this context because its representatives contain a duplicated control region in various stages of degeneration. Therefore, we applied an appropriate PCR strategy to look for duplications within the mitogenomes of the early diverged species Sagittarius serpentarius and Cathartiformes, which is a sister order to Accipitriformes. The analyses revealed the same duplicated gene order in all examined taxa and the common ancestor of these groups. The duplicated regions were subjected to gradual degeneration and homogenization during concerted evolution. The latter process occurred recently in the species of Cathartiformes as well as in the early diverged lineages of Accipitriformes, that is, Sagittarius serpentarius and Pandion haliaetus. However, in other lineages, that is, Pernis ptilorhynchus , as well as representatives of Aegypiinae, Aquilinae, and five related subfamilies of Accipitriformes (Accipitrinae, Circinae, Buteoninae, Haliaeetinae, and Milvinae), the duplications were evolving independently for at least 14–47 Myr. Different portions of control regions in Cathartiformes showed conflicting phylogenetic signals indicating that some sections of these regions were homogenized at a frequency higher than the rate of speciation, whereas others have still evolved separately. [ABSTRACT FROM AUTHOR]

Actinopterygians (ray‐finned fishes) are the most diversified group of vertebrates and are characterized by a variety of protective structures covering their integument, the evolution of which has intrigued biologists for decades. Paleontological records showed that the first mineralized vertebrate skeleton was composed of dermal bony plates covering the body, including odontogenic and skeletogenic components. Later in evolution, the exoskeleton of actinopterygian's trunk was composed of scale structures. Although scales are nowadays a widespread integument cover, some contemporary lineages do not have scales but bony plates covering their trunk, whereas other lineages are devoid of any such structures. To understand the evolution of the integument coverage and particularly the transition between different structures, we investigated the pattern of scale loss events along with actinopterygian evolution and addressed the functional relationship between the scaleless phenotype and the ecology of fishes. Furthermore, we examined whether the emergence of trunk bony plates was dependent over the presence or absence of scales. To this aim, we used two recently published actinopterygian phylogenies, one including >11,600 species, and by using stochastic mapping and Bayesian methods, we inferred scale loss events and trunk bony plate acquisitions. Our results reveal that a scaled integument is the most frequent state in actinopterygians, but multiple independent scale loss events occurred along their phylogeny with essentially no scale re‐acquisition. Based on linear mixed models, we found evidence supporting that after a scale loss event, fishes tend to change their ecology and adopt a benthic lifestyle. Furthermore, we show that trunk bony plates appeared independently multiple times along the phylogeny. By using fitted likelihood models for character evolution, we show that trunk bony plate acquisitions were dependent on a previous scale loss event. Overall, our findings support the hypothesis that integument cover is a key evolutionary trait underlying actinopterygian radiation. [ABSTRACT FROM AUTHOR]

Pollinators are often perceived as a primary selective agent influencing flower traits such as colour, size, and nectar properties. The genus Fritillaria L. (Liliaceae), comprising approximately 150 species, is described as generally insect pollinated. However, there are at least three exceptions: two hummingbird-pollinated North American species and one passerine-pollinated Asian species. Despite this variation in pollination, little is known about flower traits that may accompany this shift in fritillaries. In this study, we aimed to assess the attractiveness of the floral traits for (new) pollinators and track the evolution of flowers traits in the context of a shift in the principal pollinator. Therefore, we studied 14 flower traits related to the pollination in 60 Fritillaria species and traced the evolutionary trajectory of these traits. We used a phylogenetic tree of the genus, based on five DNA markers (matK, rpl16, and rbcL, 18S, and ITS) to reconstruct the ancestral state of studied flower traits. The results show that in bird-pollinated species several new traits evolved. For example, flower colouration, nectar sugar, and amino acid concentration and composition fulfil the criteria of ornithophilous flowers, although flower traits do not exclude insect pollinators in bird-pollinated fritillaries. Interestingly, we recorded potential reversals from bird to insect pollination. Our analysis, showing a broad study of flower traits among closely related species in the context of pollinator shift, serves as a starting point for future work exploring the genetic and physiological mechanisms controlling flower traits in the genus Fritillaria.

Pollinators are often perceived as a primary selective agent influencing flower traits such as colour, size, and nectar properties. The genus Fritillaria L. (Liliaceae), comprising approximately 150 species, is described as generally insect pollinated. However, there are at least three exceptions: two hummingbird-pollinated North American species and one passerine-pollinated Asian species. Despite this variation in pollination, little is known about flower traits that may accompany this shift in fritillaries. In this study, we aimed to assess the attractiveness of the floral traits for (new) pollinators and track the evolution of flowers traits in the context of a shift in the principal pollinator. Therefore, we studied 14 flower traits related to the pollination in 60 Fritillaria species and traced the evolutionary trajectory of these traits. We used a phylogenetic tree of the genus, based on five DNA markers (matK, rpl16 , and rbcL , 18S, and ITS) to reconstruct the ancestral state of studied flower traits. The results show that in bird-pollinated species several new traits evolved. For example, flower colouration, nectar sugar, and amino acid concentration and composition fulfil the criteria of ornithophilous flowers, although flower traits do not exclude insect pollinators in bird-pollinated fritillaries. Interestingly, we recorded potential reversals from bird to insect pollination. Our analysis, showing a broad study of flower traits among closely related species in the context of pollinator shift, serves as a starting point for future work exploring the genetic and physiological mechanisms controlling flower traits in the genus Fritillaria. [ABSTRACT FROM AUTHOR]

Background: Bird mitogenomes differ from other vertebrates in gene rearrangement. The most common avian gene order, identified first in Gallus gallus, is considered ancestral for all Aves. However, other rearrangements including a duplicated control region and neighboring genes have been reported in many representatives of avian orders. The repeated regions can be easily overlooked due to inappropriate DNA amplification or genome sequencing. This raises a question about the actual prevalence of mitogenomic duplications and the validity of the current view on the avian mitogenome evolution. In this context, Palaeognathae is especially interesting because is sister to all other living birds, i.e. Neognathae. So far, a unique duplicated region has been found in one palaeognath mitogenome, that of Eudromia elegans. Results: Therefore, we applied an appropriate PCR strategy to look for omitted duplications in other palaeognaths. The analyses revealed the duplicated control regions with adjacent genes in Crypturellus, Rhea and Struthio as well as ND6 pseudogene in three moas. The copies are very similar and were subjected to concerted evolution. Mapping the presence and absence of duplication onto the Palaeognathae phylogeny indicates that the duplication was an ancestral state for this avian group. This feature was inherited by early diverged lineages and lost two times in others. Comparison of incongruent phylogenetic trees based on mitochondrial and nuclear sequences showed that two variants of mitogenomes could exist in the evolution of palaeognaths. Data collected for other avian mitogenomes revealed that the last common ancestor of all birds and early diverging lineages of Neoaves could also possess the mitogenomic duplication. Conclusions: The duplicated control regions with adjacent genes are more common in avian mitochondrial genomes than it was previously thought. These two regions could increase effectiveness of replication and transcription as well as the number of replicating mitogenomes per organelle. In consequence, energy production by mitochondria may be also more efficient. However, further physiological and molecular analyses are necessary to assess the potential selective advantages of the mitogenome duplications. [ABSTRACT FROM AUTHOR]

Convergent morphology is a strong indication of an adaptive trait. Marine mussels (Mytilidae) have long been studied for their ecology and economic importance. However, variation in lifestyle and phenotype also make them suitable models for studies focused on ecomorphological correlation and adaptation. The present study investigates mantle margin diversity and ecological transitions in the Mytilidae to identify macroevolutionary patterns and test for convergent evolution. A fossil-calibrated phylogenetic hypothesis of Mytilidae is inferred based on five genes for 33 species (19 genera). Morphological variation in the mantle margin is examined in 43 preserved species (25 genera) and four focal species are examined for detailed anatomy. Trait evolution is investigated by ancestral state estimation and correlation tests. Our phylogeny recovers two main clades derived from an epifaunal ancestor. Subsequently, different lineages convergently shifted to other lifestyles: semi-infaunal or boring into hard substrate. Such transitions are correlated with the development of long siphons in the posterior mantle region. Two independent origins are reconstructed for the posterior lobules on the inner fold, which are associated with intense mucociliary transport, suggesting an important cleansing role in epifaunal mussels. Our results reveal new examples of convergent morphological evolution associated with lifestyle transitions in marine mussels. [ABSTRACT FROM AUTHOR]

The mitochondrial genome (mitogenome) of thrips is characterized by the presence of control region (CR) duplication. However, the evolution pattern of duplicated CRs in thrips is still unclear. In this study, the multiple independent origins of duplicated CR indicated that the CR duplication was not an ancestral state for Thysanoptera. The macroevolutionary pattern suggested that the earliest CR duplication event occurred in the middle Cretaceous (94.85 Ma) coincided with rearrangement events forming the ancestors of Aeolothripidae, but much later than that forming the ancestors of the suborder Terebrantia. The mitogenome with duplicated CRs showed a higher rate of gene rearrangement. The sequence similarity of the CR copies and divergence time were negatively correlated, indicating age-related deterioration of mitochondrial function. No significant differences were found in the mitochondrial DNA, the P 123 and P 4FD between the single and multiple-CR charactered mitogenomes, which suggested that the duplicated CRs may not affect the replication process in thrip mitogenome. The mitogenomes with duplicated CRs (mean: 0.0088 subs/s/my) show a significantly increased evolutionary rate than that with a single one (mean: 0.0058 subs/s/my). However, it seems that this higher evolutionary rate did not have adaptive mechanisms in Terebrantia. We speculated that the duplicated CRs may cause a more intense production of energy by mitochondria, and an accelerated mutation and substitution rate is expected in such mitogenomes. Our study provided new insights into the presence of CR duplications and their evolution in the mitogenomes of thrips., (© 2024 Wiley Periodicals LLC.)

Arabidopsis thaliana, one of the most important model plants, has played an essential role in every biological field including evolutionary biology. Recent population genomic studies have gradually clarified the origin and evolution of this species. Nevertheless, incongruent patterns among gene trees based on cytogenetic data have highlighted the importance of understanding the life history evolution and landscape biogeography of extant A. thaliana populations. Here, we focus on the maternally inherited chloroplast genome in A. thaliana and carry out phylogeographic analyses and coalescent time estimations. The maternal lineage of A. thaliana originated in the European to West and Central Asian regions in the Early Pleistocene. Relicts, the ancient lineages suggested by population genomic data, are not ancestral maternal lineages, but are derived from the European population. Part of the European population then dispersed eastward and spread to the Indian region, and finally extended to the Yangtze River region. The branching patterns and evolutionary time scales of the maternal genealogy are significantly different from those estimated from analyses of autosomal genes, and these cannot be explained by incomplete lineage sorting of the ancestral polymorphisms during the coalescent process due to large differences in the evolutionary time scale involved. [ABSTRACT FROM AUTHOR]

ABSTRACT The recent emergence of novel tick-borne RNA viruses has complicated the epidemiological landscape of tick-borne infectious diseases, posing a significant challenge to public health systems that seek to counteract tick-borne diseases. The identification of two novel tick-borne phleboviruses (TBPVs), severe fever with thrombocytopenia syndrome virus (SFTSV) and Heartland virus (HRTV), as causative agents of severe illness in humans has accelerated the investigation and discoveries of novel TBPVs. In the present study, we isolated a novel TBPV designated Mukawa virus (MKWV) from host-questing Ixodes persulcatus females captured in Japan. Genetic characterization revealed that MKWV is a member of the genus Phlebovirus in the family Phenuiviridae. Interestingly, MKWV is genetically distinct from other known TBPVs and shares a most recent common ancestor with mosquito/sandfly-borne (insect-borne) phleboviruses. Despite its genetic similarity to insect-borne phleboviruses, the molecular footprints of its viral proteins and its biological characteristics define MKWV as a tick-borne virus that can be transmitted to mammals. A phylogenetic ancestral-state reconstruction for arthropod vectors of phleboviruses including MKWV based on viral L segment sequences indicated that ticks likely harbored ancestral phleboviruses that evolved into both the tick-borne and MKWV/insect-borne phlebovirus lineages. Overall, our findings suggest that most of the phlebovirus evolution has occurred in hard ticks to generate divergent viruses, which may provide a seminal foundation for understanding the mechanisms underlying the evolution and emergence of pathogenic phleboviruses, such as Rift Valley fever virus and SFTSV/HRTV. IMPORTANCE The emergence of novel tick-borne RNA viruses causing severe illness in humans has complicated the epidemiological landscape of tick-borne diseases, requiring further investigation to safeguard public health. In the present study, we discovered a novel tick-borne phlebovirus from Ixodes persulcatus ticks in Japan. While its viral RNA genome sequences were similar to those of mosquito/sandfly-borne viruses, molecular and biological footprints confirmed that this is a tick-borne virus. The unique evolutionary position of the virus allowed us to estimate the ancestral phlebovirus vector, which was likely a hard tick. Our findings may provide a better understanding of the evolution and emergence of phleboviruses associated with emerging infectious diseases, such as severe fever with thrombocytopenia syndrome (SFTS) and Heartland virus disease.

Amongst the Australasian kangaroos and wallabies (Macropodidae) one anomalous genus, the tree-kangaroos, Dendrolagus , has secondarily returned to arboreality. Modern tree-kangaroos are confined to the wet tropical forests of north Queensland, Australia (2 species) and New Guinea (8 species). Due to their behavior, distribution and habitat most species are poorly known and our understanding of the evolutionary history and systematics of the genus is limited and controversial. We obtained tissue samples from 36 individual Dendrolagus including representatives from 14 of the 17 currently recognised or proposed subspecies and generated DNA sequence data from three mitochondrial (3116 bp) and five nuclear (4097 bp) loci. Phylogenetic analysis of these multi-locus data resolved long-standing questions regarding inter-relationships within Dendrolagus. The presence of a paraphyletic ancestral long-footed and derived monophyletic short-footed group was confirmed. Six major lineages were identified: one in Australia ( D. lumholtzi, D. bennettianus ) and five in New Guinea ( D. inustus , D. ursinus , a Goodfellow’s group, D. mbaiso and a Doria’s group). Two major episodes of diversification within Dendrolagus were identified: the first during the late Miocene/early Pliocene associated with orogenic processes in New Guinea and the second mostly during the early Pleistocene associated with the intensification of climatic cycling. All sampled subspecies showed high levels of genetic divergence and currently recognized species within both the Doria’s and Goodfellow’s groups were paraphyletic indicating that adjustments to current taxonomy are warranted. [ABSTRACT FROM AUTHOR]

Apoptotic cell death is a type of eukaryotic cell death. In animals, it regulates development, is involved in cancer suppression, and causes cell death during pathological aging of neuronal cells in neurodegenerative diseases such as Alzheimer's. Mitochondrial apoptotic-like cell death, a form of primordial apoptosis, also occurs in unicellular organisms. Here, we ask the question why the apoptosis machinery has been acquired and maintained in unicellular organisms and attempt to answer it by performing ancestral state reconstruction. We found indications of an ancient evolutionary arms race between protomitochondria and host cells, leading to the establishment of the currently existing apoptotic pathways. According to this reconstruction, the ancestral protomitochondrial apoptosis machinery contained both caspases and metacaspases, four types of apoptosis induction factors (AIFs), both fungal and animal OMI/HTR proteases, and various apoptotic DNases. This leads to the prediction that in extant unicellular eukaryotes, the apoptotic factors are involved in mitochondrial respiration and their activity is needed exclusively in aerobic conditions. We test this prediction experimentally using yeast and find that a loss of the main apoptotic factors is beneficial under anaerobic conditions yet deleterious under aerobic conditions in the absence of lethal stimuli. We also point out potential medical implications of these findings. [ABSTRACT FROM AUTHOR]

Species traits have been hypothesized by one of us (Ponge, 2013) to evolve in a correlated manner as species colonize stable, undisturbed habitats, shifting from 'ancestral' to 'derived' strategies. We predicted that generalism, r-selection, sexual monomorphism, and migration/gregariousness are the ancestral states (collectively called strategy A) and evolved correlatively toward specialism, K-selection, sexual dimorphism, and residence/territoriality as habitat stabilized (collectively called B strategy). We analyzed the correlated evolution of four syndromes, summarizing the covariation between 53 traits, respectively, involved in ecological specialization, r-K gradient, sexual selection, and dispersal/social behaviors in 81 species representative of Fringillidae, a bird family with available natural history information and that shows variability for all these traits. The ancestrality of strategy A was supported for three of the four syndromes, the ancestrality of generalism having a weaker support, except for the core group Carduelinae (69 species). It appeared that two different B-strategies evolved from the ancestral state A, both associated with highly predictable environments: one in poorly seasonal environments, called B1, with species living permanently in lowland tropics, with 'slow pace of life' and weak sexual dimorphism, and one in highly seasonal environments, called B2, with species breeding out-of-the-tropics, migratory, with a 'fast pace of life' and high sexual dimorphism. [ABSTRACT FROM AUTHOR]

The origins of novel traits are often studied using species trees and modeling phenotypes as different states of the same character, an approach that cannot always distinguish multiple origins from fewer origins followed by reversals. We address this issue by studying the origins of C4 photosynthesis, an adaptation to warm and dry conditions, in the grass Alloteropsis. We dissect the C4 trait into its components, and show two independent origins of the C4 phenotype via different anatomical modifications, and the use of distinct sets of genes. Further, inference of enzyme adaptation suggests that one of the two groups encompasses two transitions to a full C4 state from a common ancestor with an intermediate phenotype that had some C4 anatomical and biochemical components. Molecular dating of C4 genes confirms the introgression of two key C4 components between species, while the inheritance of all others matches the species tree. The number of origins consequently varies among C4 components, a scenario that could not have been inferred from analyses of the species tree alone. Our results highlight the power of studying individual components of complex traits to reconstruct trajectories toward novel adaptations. [ABSTRACT FROM AUTHOR]

RAG1 and RAG2 are essential subunits of the V(D)J recombinase required for the generation of the variability of antibodies and T cell receptors in jawed vertebrates. It was demonstrated that the amphioxus homologue of RAG1-RAG2 is encoded in an active transposon, belonging to the transposase DDE superfamily. The data provided support the possibility that the RAG transposon has been active through the deuterostome evolution and is still active in several lineages. The RAG transposon corresponds to several families present in deuterostomes. RAG1-RAG2 V(D)J recombinase evolved from one of them, partially due to the new ability of the transposon to interact with the cellular reparation machinery. Considering the fact that the RAG transposon survived millions of years in many different lineages, in multiple copies, and that DDE transposases evolved their association with proteins involved in repair mechanisms, we propose that the apparition of V(D)J recombination machinery could be a predictable genetic event. [ABSTRACT FROM AUTHOR]

We provide an integrative view of the evolution of dispersal strategies in modern conifers, by characterizing and examining the phylogenetic distribution of diaspore functional morphotypes, diaspore structural compositions, seed coat modifications, and dispersal syndromes using the phylogeny of Leslie et al. (2012). We first classified diaspores into nine functional morphotypes, which represent overall dispersal strategies that encompass the multiple phases of dispersal. We mapped these morphotypes, the eight different structural compositions of diaspores, two types of seed coat modifications, and the four recognized dispersal vectors onto the phylogeny and used maximum parsimony and maximum likelihood to infer ancestral states and assess shifts in dispersal characteristics. We found that structural traits (diaspore composition and seed coat modifications) are more conserved than ecological traits (functional morphotype and dispersal vector/syndrome). Almost all diaspore functional morphotypes have multiple independent origins, with several instances of parallelism (using the same structures to generate a morphotype) within families, but generally functional convergence (using different structures to generate a morphotype) between families. Within extant conifer families, shifts in the dispersal syndrome occur most frequently with simultaneous shifts in both diaspore morphotype and composition. Shifts from winged wind-dispersed to fleshy animal-dispersed diaspores are infrequent and occur only in the direction from wind to animal dispersal. Shifts to gravity or water dispersal occur from both wind and animal dispersed diaspores, concurrent with the loss of dispersal structures from the diaspore. Within both wind and animal-dispersed syndromes, shifts between functional morphotypes represent further differentiation of overall dispersal strategies, and occur most frequently without corresponding changes in the structural composition of the diaspore. The recurrent evolution of distinct functional morphologies suggests that there are local adaptive maxima that balance tradeoffs in traits related to both transport and establishment, within developmental limitations. Overall, our results suggest that the ancestral diaspore type for all modern conifers consisted only of a seed. Conifers diversified in their dispersal strategies through seed coat modifications or by the incorporation of various parts of the seed cone into the diaspore, with the modern conifer families independently evolving their characteristic diaspore compositions. Almost all functional morphotypes were present prior to the Cenozoic in at least one lineage, with more recent shifts in morphotypes representing functional convergence or parallel evolution rather than ecological novelties. [ABSTRACT FROM AUTHOR]

Inferring the ancestral state at the root of a phylogenetic tree from states observed at the leaves is a problem arising in evolutionary biology. The simplest technique – majority rule – estimates the root state by the most frequently occurring state at the leaves. Alternative methods – such as maximum parsimony - explicitly take the tree structure into account. Since either method can outperform the other on particular trees, it is useful to consider the accuracy of the methods on trees generated under some evolutionary null model, such as a Yule pure-birth model. In this short note, we answer a recently posed question concerning the performance of majority rule on Yule trees under a symmetric 2-state Markovian substitution model of character state change. We show that majority rule is accurate precisely when the ratio of the birth (speciation) rate of the Yule process to the substitution rate exceeds the value 4. By contrast, maximum parsimony has been shown to be accurate only when this ratio is at least 6. Our proof relies on a second moment calculation, coupling, and a novel application of a reflection principle. [ABSTRACT FROM AUTHOR]

Since the occurrence of giant genomes in angiosperms is restricted to just a few lineages, identifying where shifts towards genome obesity have occurred is essential for understanding the evolutionary mechanisms triggering this process., Genome sizes were assessed using flow cytometry in 79 species and new chromosome numbers were obtained. Phylogenetically based statistical methods were applied to infer ancestral character reconstructions of chromosome numbers and nuclear DNA contents., Melanthiaceae are the most diverse family in terms of genome size, with C-values ranging more than 230-fold. Our data confirmed that giant genomes are restricted to tribe Parideae, with most extant species in the family characterized by small genomes. Ancestral genome size reconstruction revealed that the most recent common ancestor ( MRCA) for the family had a relatively small genome (1C = 5.37 pg). Chromosome losses and polyploidy are recovered as the main evolutionary mechanisms generating chromosome number change., Genome evolution in Melanthiaceae has been characterized by a trend towards genome size reduction, with just one episode of dramatic DNA accumulation in Parideae. Such extreme contrasting profiles of genome size evolution illustrate the key role of transposable elements and chromosome rearrangements in driving the evolution of plant genomes. [ABSTRACT FROM AUTHOR]

Coloration of the egg sacs of spiders varies widely to the human eye, both across and within taxonomic groups. These differences in coloration are expected with differences in the biology and ecology of different species. Here we measure the spectral properties of the egg sacs of 15 species in six families. Ultraviolet chroma, red chroma, and particularly overall brightness vary widely across and within taxonomic groups. We discuss the spectral properties of the silk of the egg sacs in the context of the physical characteristics of the silk, the reflective properties of the background, the environmental illumination, and the natural history and behavior of the spider species. In most cases, the spectral characteristics of the egg sacs seem to reduce their conspicuousness against the background and in those cases in which the coloration does not reduce the contrast in relation to the background, the low environmental light available may help to camouflage the egg sacs. [ABSTRACT FROM AUTHOR]

Abstract: The Entomophthoromycota is a ubiquitous group of fungi best known as pathogens of a wide variety of economically important insect pests, and other soil invertebrates. This group of fungi also includes a small number of parasites of reptiles, vertebrates (including humans), macromycetes, fern gametophytes, and desmid algae, as well as some saprobic species. Here we report on recent studies to resolve the phylogenetic relationships within the Entomophthoromycota and to reliably place this group among other basal fungal lineages. Bayesian Interference (BI) and Maximum Likelihood (ML) analyses of three genes (nuclear 18S and 28S rDNA, mitochondrial 16S, and the protein-coding RPB2) as well as non-molecular data consistently and unambiguously identify 31 taxa of Entomophthoromycota as a monophyletic group distinct from other Zygomycota and flagellated fungi. Using the constraints of our multi-gene dataset we constructed the most comprehensive rDNA phylogeny yet available for Entomophthoromycota. The taxa studied here belong to five distinct, well-supported lineages. The Basidiobolus clade is the earliest diverging lineage, comprised of saprobe species of Basidiobolus and the undescribed snake parasite Schizangiella serpentis nom. prov. The Conidiobolus lineage is represented by a paraphyletic grade of trophically diverse species that include saprobes, insect pathogens, and facultative human pathogens. Three well supported and exclusively entomopathogenic lineages in the Entomophthoraceae center around the genera Batkoa, Entomophthora and Zoophthora, although several genera within this crown clade are resolved as non-monophyletic. Ancestral state reconstruction suggests that the ancestor of all Entomophthoromycota was morphologically similar to species of Conidiobolus. Analyses using strict, relaxed, and local molecular clock models documented highly variable DNA substitution rates among lineages of Entomophthoromycota. Despite the complications caused by different rates of molecular evolution among lineages, our dating analysis indicates that the Entomophthoromycota originated 405±90million years ago. We suggest that entomopathogenic lineages in Entomophthoraceae probably evolved from saprobic or facultatively pathogenic ancestors during or shortly after the evolutionary radiation of the arthropods. [Copyright &y& Elsevier]

The article presents a study that deals with phylogenetic approaches to inferring ancestral character states. The authors evaluated inferences of ancestral limb morphology in the scincid lizard clade Lerista using the consistency of ancestral states inferred for two or more characters. They highlighted the role of a suboptimal model for the pes in yielding accurate ancestral state estimates.