Evolutionary Occurrence Research Articles

The origin and loss of interferon regulatory factor 10 (IRF10) in different lineages of vertebrates

The vertebrate IFN regulatory factor (IRF) family consists of 11 members that exert distinct roles in a variety of biological processes, including antiviral defense, regulation of cell proliferation, differentiation and apoptosis. Of these, IRF10 is widely present in different vertebrate lineages, but appears to have been lost in primates and rodents. To understand the evolutionary occurrence of IRF10, we performed comparative analyses of currently available genomic data in a taxonomically diverse set of vertebrates, and found that IRF10 originated after the divergence of chondrichthyans from gnathostomes. Phylogenetically, vertebrate IRF10 is much more closely related to IRF4 than to IRF8 or IRF9, although these four IRFs may have a common ancestor. In addition, the loss of IRF10 in Euarchontoglires might be resulted from mutation accumulation, and the rate of mutations in rodents appears to be higher than in the primate lineage. In primates, the gene-disruptive mutations may have occurred at least prior to the separation of new world monkey and old world primates, roughly 40 million years ago. Overall, we propose a detailed evolutionary scenario for IRF10, which may help us understand the evolutionary mechanisms in the expansion and contraction of the IRF family.

Sacbrood Virus: A Growing Threat to Honeybees and Wild Pollinators.

Sacbrood virus (SBV) is one of the many viruses that infect both the Western honeybee (Apis mellifera) and the Eastern honeybee (Apis cerana). Recently, the interspecies transmission of SBV has been discovered, especially among wild pollinators. This newly discovered evolutionary occurrence regarding SBV indicates a much wider host range than previously believed, causing further concern about the future sustainability of agriculture and the resilience of ecosystems. Over the past few decades, vast numbers of studies have been undertaken concerning SBV infection in honeybees, and remarkable progress has been made in our understanding of the epidemiology, pathogenesis, transmission, and manifestations of SBV infection in honeybees and other pollinators. Meanwhile, some methods, including Chinese medicine, have been established to control and prevent sacbrood disease in A. cerana in Asian countries. In this review, we summarize the existing knowledge of SBV and address the gaps in the knowledge within the existing literature in the hope of providing future directions for the research and development of management strategies for controlling the spread of this deadly disease.

Species-specific tidal locomotion linked to a parasitic infection in sympatric sea snails

Parasites can play a critical role in mediating inter-species interactions. Potential effects induced by parasites can range from species-wide traits to functional alterations in host community structure. One of the most intriguing host–parasite interactions pertains to adaptative host manipulation, an evolutionary occurrence where parasites alter the phenotype of their host to increase their own fitness. This study aims to address this phenomenon in a marine setting by investigating the effect of a philophthalmid trematode, Parorchis sp., on the vertical upward movement and phototactic behaviour of their intermediate hosts whilst simultaneously addressing the host specificity of these effects. These behaviours could impact the odds of trematodes successfully transmitting from their intermediate snail host to their definitive shorebird host, a crucial step in the life cycle of these parasites. Most trematode species exhibit strong specificity for snail hosts, typically infecting only a single snail species. In this rare system, however, the trematode infects a pair of sympatric and congeneric littorinid sea snails found in the intertidal zone of New Zealand’s rocky shores: Austrolittorina cincta and A. antipodum. Precisely, experiments were conducted in a controlled, laboratory-based setting, extending over a period of six weeks, during which vertical displacement and response to light were measured. Our results demonstrate that vertical upward movement amongst infected snails increased for A. cincta, but not for A. antipodum. No difference in response to light between infected and uninfected groups was evident across either species. Our findings highlight the complex nature of parasitic infections, where trait-specific behavioural effects are dissimilar across even congeneric host taxa.

Spontaneous choices for insect-pollinated flower shapes by wild non-eusocial halictid bees.

The majority of angiosperms require animal pollination for reproduction, and insects are the dominant group of animal pollinators. Bees are considered one of the most important and abundant insect pollinators. Research into bee behaviour and foraging decisions has typically centred on managed eusocial bee species, including Apis mellifera and Bombus terrestris. Non-eusocial bees are understudied with respect to foraging strategies and decision making, such as flower preferences. Understanding whether there are fundamental foraging strategies and preferences that are features of insect groups can provide key insights into the evolution of flower-pollinator co-evolution. In the current study, Lasioglossum (Chilalictus) lanarium and Lasioglossum (Parasphecodes) sp., two native Australian generalist halictid bees, were tested for flower shape preferences between native insect-pollinated and bird-pollinated flowers. Each bee was presented with achromatic images of either insect-pollinated or bird-pollinated flowers in a circular arena. Both native bee species demonstrated a significant preference for images of insect-pollinated flowers. These preferences are similar to those found in A. mellifera, suggesting that flower shape preference may be a deep-rooted evolutionary occurrence within bees. With growing interest in the sensory capabilities of non-eusocial bees as alternative pollinators, the current study also provides a valuable framework for further behavioural testing of such species.

Carboniferous ammonoid genozones

Abstract Considerable progress has been made by international teams in refining the traditional ammonoid zonation that remains the backbone of Carboniferous stratigraphy. The Carboniferous ammonoid genozones, with a few gaps, are now recognized throughout the entire system in most successions worldwide. Refined collecting and documentation of occurrences in Western Europe, North Africa, the Urals, China and North America aimed to establish the first evolutionary occurrences, and facilitated correlation with foraminiferal and conodont scales for most of the Carboniferous. From ten to eleven ammonoid genozones are now recognized in the Mississippian, and eight to nine genozones in the Pennsylvanian. Of these, the established lower boundaries of the subsystems are reasonably well correlated with the ammonoid zonation, whereas correlations with the ratified foraminiferal-based lower boundary of the Visean and other stage boundaries, currently under discussion, need further research. Future success in the ammonoid geochronology will also depend on accurate identification and re-illustration of the type material, including material described by pioneers of ammonoid biostratigraphy.

Juvenile hormone III skipped bisepoxide is widespread in true bugs (Hemiptera: Heteroptera).

Juvenile hormone (JH) plays important roles in almost every aspect of insect development and reproduction. JHs are a group of acyclic sesquiterpenoids, and their farnesol backbone has been chemically modified to generate a homologous series of hormones in some insect lineages. JH III (methyl farnesoate, 10,11-epoxide) is the most common JH in insects, but Lepidoptera (butterflies and moths) and ‘higher’ Diptera (suborder: Brachycera; flies) have developed their own unique JHs. Although JH was first proposed in the hemipteran suborder Heteroptera (true bugs), the chemical identity of the heteropteran JH was only recently determined. Furthermore, recent studies revealed the presence of a novel JH, JH III skipped bisepoxide (JHSB3), in some heteropterans, but its taxonomic distribution remains largely unknown. In the present study, we investigated JHSB3 production in 31 heteropteran species, covering almost all heteropteran lineages, through ultra-performance liquid chromatography coupled with tandem mass spectrometry. We found that all of the focal species produced JHSB3, indicating that JHSB3 is widespread in heteropteran bugs and the evolutionary occurrence of JHSB3 ascends to the common ancestor of Heteroptera.

Whispers from vestigial nubbins: Arrested development provokes trait loss in toads.

Despite the use of acoustic communication, many species of toads (family Bufonidae) have lost parts of the tympanic middle ear, representing at least 12 independent evolutionary occurrences of trait loss. The comparative development of the tympanic middle ear in toads is poorly understood. Here, we compared middle ear development among two pairs of closely related toad species in the genera Atelopus and Rhinella that have (eared) or lack (earless) middle ear structures. We bred toads in Peru and Ecuador, preserved developmental series from tadpoles to juveniles, and examined ontogenetic timing and volume of the otic capsule, oval window, operculum, opercularis muscle, columella (stapes), and extracolumella in three-dimensional histological reconstructions. All species had similar ontogenesis of the otic capsule, oval window, operculum, and opercularis muscle. Moreover, cell clusters of primordial columella in the oval window appeared just before metamorphosis in both eared and earless lineages. However, in earless lineages, the cell clusters either remained as small nubbins or cell buds in the location of the columella footplate within the oval window or disappeared by juvenile and adult stages. Thus, columella growth began around metamorphosis in all species but was truncated and/or degenerated after metamorphosis in earless species, leaving earless adults with morphology typical of metamorphic anurans. Shifts in the timing or expression of biochemical pathways that regulate the extension or differentiation of the columella after metamorphosis may be the developmental mechanism underlying convergent trait loss among toad lineages.

A cerebellar substrate for cognition evolved multiple times independently in mammals.

Given that complex behavior evolved multiple times independently in different lineages, a crucial question is whether these independent evolutionary events coincided with modifications to common neural systems. To test this question in mammals, we investigate the lateral cerebellum, a neurobiological system that is novel to mammals, and is associated with higher cognitive functions. We map the evolutionary diversification of the mammalian cerebellum and find that relative volumetric changes of the lateral cerebellar hemispheres (independent of cerebellar size) are correlated with measures of domain-general cognition in primates, and are characterized by a combination of parallel and convergent shifts towards similar levels of expansion in distantly related mammalian lineages. Results suggest that multiple independent evolutionary occurrences of increased behavioral complexity in mammals may at least partly be explained by selection on a common neural system, the cerebellum, which may have been subject to multiple independent neurodevelopmental remodeling events during mammalian evolution.

A threshold model for polydactyly

We present a cellular automaton-based model for threshold behaviors in vertebrate digit patterning and polydactyly formation. The rules of the model follow classical reactor-diffusion algorithms. Yet it is not physical diffusion that is taken as the required natural agent but the propagation of cellular states, which can be represented by the same differential equations. The bistable cellular states in the model correspond to mesenchymal limb bud cells that can be either "on" or "off" for the cartilage differentiation pathway. Simulation runs demonstrate that reaction rate and cell number have the most decisive influence on the number of digit-like cell activation patterns. Threshold-based effects can generate supernumerary activation stripes via de novo condensation, stabilized bifurcation, and free floaters. All three behaviors are consistent with processes in natural polydactyly formation. It is argued that these effects are rooted in cell-based behaviors, not in gene regulation or globally diffusing morphogens. Our model suggests that the origin of discrete character states, such as individual digits, is a consequence of an additive cell state variable with a normal distribution that is transformed by a growth function with Turing behaviors into discontinuous phenotypic units. We discuss the application of this type of autopod patterning to the mutational, developmental, experimental, and evolutionary occurrences of polydactyly. The model provides a refinement of the previous Hemingway model for digit novelty and supports Turing type pattern formation in the vertebrate limb.

Taxonomy, Stratigraphy and Phylogeny of the Middle Miocene Fohsella Lineage: Geometric Morphometric Evidence

Abstract The taxonomy and phylogeny of the planktonic foraminifera Fohsella lineage has been controversial for nearly 50 years, despite its widespread application in Middle Miocene stratigraphy. We have re-examined type specimens of this lineage together with specimens from a continuous deep-sea record (Ocean Drilling Program Site 806, Ontong Java Plateau, western equatorial Pacific Ocean) with an astronomic chronology. Landmark-based geometric morphometry is employed to visualize and quantify morphologic variation within this lineage. Combined morphologic and stratigraphic data help clarify the evolutionary occurrence of diagnostic traits that characterize two problematic taxa, F. praefohsi and F. “praefohsi”, resulting in a revised taxonomy and phylogeny of the lineage. We emphasize the importance of biometric studies of populations from continuous geologic records in establishing taxonomy and phylogeny of planktonic foraminifera. In the past, over-emphasis on the importance of type specimens as reference points in delineating various evolutionary stages of the Fohsella lineage has resulted in inaccurate phylogenetic reconstructions.

Genome-wide comparative analysis of H3K4me3 profiles between diploid and allotetraploid cotton to refine genome annotation

Polyploidy is a common evolutionary occurrence in plants. Recently, published genomes of allotetraploid G. hirsutum and its donors G. arboreum and G. raimondii make cotton an accessible polyploid model. This study used chromatin immunoprecipitation with high-throughput sequencing (ChIP-Seq) to investigate the genome-wide distribution of H3K4me3 in G. arboreum and G. hirsutum, and explore the conservation and variation of genome structures between diploid and allotetraploid cotton. Our results showed that H3K4me3 modifications were associated with active transcription in both cottons. The H3K4me3 histone markers appeared mainly in genic regions and were enriched around the transcription start sites (TSSs) of genes. We integrated the ChIP-seq data of H3K4me3 with RNA-seq and ESTs data to refine the genic structure annotation. There were 6,773 and 12,773 new transcripts discovered in G. arboreum and G. hirsutum, respectively. Furthermore, co-expression networks were linked with histone modification and modularized in an attempt to explain differential H3K4me3 enrichment correlated with changes in gene transcription during cotton development and evolution. Taken together, we have combined epigenomic and transcriptomic datasets to systematically discover functional genes and compare them between G. arboreum and G. hirsutum, which may be beneficial for studying diploid and allotetraploid plants with large genomes and complicated evolution.

Evolution of the patellar sesamoid bone in mammals.

The patella is a sesamoid bone located in the major extensor tendon of the knee joint, in the hindlimb of many tetrapods. Although numerous aspects of knee morphology are ancient and conserved among most tetrapods, the evolutionary occurrence of an ossified patella is highly variable. Among extant (crown clade) groups it is found in most birds, most lizards, the monotreme mammals and almost all placental mammals, but it is absent in most marsupial mammals as well as many reptiles. Here, we integrate data from the literature and first-hand studies of fossil and recent skeletal remains to reconstruct the evolution of the mammalian patella. We infer that bony patellae most likely evolved between four and six times in crown group Mammalia: in monotremes, in the extinct multituberculates, in one or more stem-mammal genera outside of therian or eutherian mammals and up to three times in therian mammals. Furthermore, an ossified patella was lost several times in mammals, not including those with absent hindlimbs: once or more in marsupials (with some re-acquisition) and at least once in bats. Our inferences about patellar evolution in mammals are reciprocally informed by the existence of several human genetic conditions in which the patella is either absent or severely reduced. Clearly, development of the patella is under close genomic control, although its responsiveness to its mechanical environment is also important (and perhaps variable among taxa). Where a bony patella is present it plays an important role in hindlimb function, especially in resisting gravity by providing an enhanced lever system for the knee joint. Yet the evolutionary origins, persistence and modifications of a patella in diverse groups with widely varying habits and habitats—from digging to running to aquatic, small or large body sizes, bipeds or quadrupeds—remain complex and perplexing, impeding a conclusive synthesis of form, function, development and genetics across mammalian evolution. This meta-analysis takes an initial step toward such a synthesis by collating available data and elucidating areas of promising future inquiry.

Retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs) in fish: current knowledge and future perspectives.

Retinoic acid-inducible gene I (RIG-I) -like receptors (RLRs) are found conservatively present in teleost fish. All three members, RIG-I, MDA5 and LGP2, together with the downstream molecules such as MITA, TRAF3 and TBK1, have been identified in a range of fish species. However, it is unexpected that RIG-I has not been reported in fish of Acanthopterygii, and it would be important to clarify the presence and role of the RIG-I gene in a broad range of taxa in Teleostei. RLRs in fish can be induced invivo and invitro by viral pathogens as well as synthetic dsRNA, poly(I:C), leading to the production of type I interferons (IFNs) and the expression of IFN-stimulated genes (ISGs). Bacterial pathogens, such as Edwardsiella tarda, and their components, such as lipopolysaccharide are also found to induce the expression of RLRs, and whether such induction was mediated through the direct recognition by RLRs or through crosstalk with other pattern recognition receptors recognizing directly bacterial pathogen-associated molecular patterns awaits to be investigated. On the other hand, RLR-activated type I IFN production can be negatively regulated in fish by molecules, such as TBK-1-like protein and IRF10, which are found to negatively regulate RIG-I and MAVS-activated type I IFN production, and to block MITA or bind ISRE motifs, respectively. It is considered that the evolutionary occurrence of RLRs in fish, and their recognized ligands, especially those from their fish pathogens, as well as the mechanisms involved in the RLR signalling pathways, are of significant interest for further investigation.

CcNET: Database of co-expression networks with functional modules for diploid and polyploid Gossypium.

Plant genera with both diploid and polyploid species are a common evolutionary occurrence. Polyploids, especially allopolyploids such as cotton and wheat, are a great model system for heterosis research. Here, we have integrated genome sequences and transcriptome data of Gossypium species to construct co-expression networks and identified functional modules from different cotton species, including 1155 and 1884 modules in G. arboreum and G. hirsutum, respectively. We overlayed the gene expression results onto the co-expression network. We further provided network comparison analysis for orthologous genes across the diploid and allotetraploid Gossypium We also constructed miRNA-target networks and predicted PPI networks for both cotton species. Furthermore, we integrated in-house ChIP-seq data of histone modification (H3K4me3) together with cis-element analysis and gene sets enrichment analysis tools for studying possible gene regulatory mechanism in Gossypium species. Finally, we have constructed an online ccNET database (http://structuralbiology.cau.edu.cn/gossypium) for comparative gene functional analyses at a multi-dimensional network and epigenomic level across diploid and polyploid Gossypium species. The ccNET database will be beneficial for community to yield novel insights into gene/module functions during cotton development and stress response, and might be useful for studying conservation and diversity in other polyploid plants, such as T. aestivum and Brassica napus.

CcNET: Database of co-expression networks with functional modules for diploid and polyploid Gossypium.

Plant genera with both diploid and polyploid species are a common evolutionary occurrence. Polyploids, especially allopolyploids such as cotton and wheat, are a great model system for heterosis research. Here, we have integrated genome sequences and transcriptome data of Gossypium species to construct co-expression networks and identified functional modules from different cotton species, including 1155 and 1884 modules in G. arboreum and G. hirsutum, respectively. We overlayed the gene expression results onto the co-expression network. We further provided network comparison analysis for orthologous genes across the diploid and allotetraploid Gossypium. We also constructed miRNA-target networks and predicted PPI networks for both cotton species. Furthermore, we integrated in-house ChIP-seq data of histone modification (H3K4me3) together with cis-element analysis and gene sets enrichment analysis tools for studying possible gene regulatory mechanism in Gossypium species. Finally, we have constructed an online ccNET database (http://structuralbiology.cau.edu.cn/gossypium) for comparative gene functional analyses at a multi-dimensional network and epigenomic level across diploid and polyploid Gossypium species. The ccNET database will be beneficial for community to yield novel insights into gene/module functions during cotton development and stress response, and might be useful for studying conservation and diversity in other polyploid plants, such as T. aestivum and Brassica napus.

How fish evolved an abyssal glow

Evolution![Figure][1] Bioluminescence, as seen in this moray eel, has evolved many times. PHOTO: ©WATERFRAME/ALAMY STOCK PHOTO The darkness of the deep sea presents a particular challenge for fish wanting to mate or eat. Rising to this selective challenge, fish inhabiting these deep waters have evolved—very many times, it turns out—an extraordinary array of luminescent appendages. Davis et al. amassed sequence data from almost 300 fish genera (representing about 1500 bioluminescent species) to determine the evolutionary origins, age, and patterns of diversity of this phenomenon. Bioluminescence in fish is due to either intrinsic biochemistry or symbiotic relationships with luminescent bacteria. Starting in the Early Cretaceous, intrinsic bioluminescence evolved eight times, and relationships with glowing bacterial symbionts have evolved on at least 17 occasions. This work substantially adds to the tally of independent evolutionary occurrences of bioluminescence. PLOS ONE 10.1371/journal.pone.0155154 (2016). [1]: pending:yes

Mitochondrial poly(A) polymerase is involved in tRNA repair.

Transcription of the mitochondrial genome results in polycistronic precursors, which are processed mainly by the release of tRNAs interspersed between rRNAs and mRNAs. In many metazoan mitochondrial genomes some tRNA genes overlap with downstream genes; in the case of human mitochondria the genes for tRNATyr and tRNACys overlap by one nucleotide. It has previously been shown that processing of the common precursor releases an incomplete tRNATyr lacking the 3′-adenosine. The 3′-terminal adenosine has to be added before addition of the CCA end and subsequent aminoacylation. We show that the mitochondrial poly(A) polymerase (mtPAP) is responsible for this A addition. In vitro, a tRNATyr lacking the discriminator is a substrate for mtPAP. In vivo, an altered mtPAP protein level affected tRNATyr maturation, as shown by sequencing the 3′ ends of mitochondrial tRNAs. Complete repair could be reconstituted in vitro with three enzymes: mtPAP frequently added more than one A to the 3′ end of the truncated tRNA, and either the mitochondrial deadenylase PDE12 or the endonuclease RNase Z trimmed the oligo(A) tail to a single A before CCA addition. An enzyme machinery that evolved primarily for other purposes thus allows to tolerate the frequent evolutionary occurrence of gene overlaps.

Experimentally induced innovations lead to persistent culture via conformity in wild birds.

In human societies, cultural norms arise when behaviours are transmitted with high-fidelity social learning through social networks1. However a paucity of experimental studies has meant that there is no comparable understanding of the process by which socially transmitted behaviours may spread and persist in animal populations2,3. Here, we introduce alternative novel foraging techniques into replicated wild sub-populations of great tits (Parus major), and employ automated tracking to map the diffusion, establishment and long-term persistence of seeded behaviours. We further use social network analysis to examine social factors influencing diffusion dynamics. From just two trained birds in each sub-population, information spread rapidly through social network ties to reach an average of 75% of individuals, with 508 knowledgeable individuals performing 58,975 solutions. Sub-populations were heavily biased towards the technique originally introduced, resulting in established local arbitrary traditions that were stable over two generations, despite high population turnover. Finally, we demonstrate a strong effect of social conformity, with individuals disproportionately adopting the most frequent local variant when first learning, but then also continuing to favour social over personal information by matching their technique to the majority variant. Cultural conformity is thought to be a key factor in the evolution of complex culture in humans4-7. In providing the first experimental demonstration of conformity in a wild non-primate, and of cultural norms in foraging techniques in any wild animal, our results suggest a much wider evolutionary occurrence of such apparently complex cultural behaviour.

Chordate evolution and the three-phylum system.

Traditional metazoan phylogeny classifies the Vertebrata as a subphylum of the phylum Chordata, together with two other subphyla, the Urochordata (Tunicata) and the Cephalochordata. The Chordata, together with the phyla Echinodermata and Hemichordata, comprise a major group, the Deuterostomia. Chordates invariably possess a notochord and a dorsal neural tube. Although the origin and evolution of chordates has been studied for more than a century, few authors have intimately discussed taxonomic ranking of the three chordate groups themselves. Accumulating evidence shows that echinoderms and hemichordates form a clade (the Ambulacraria), and that within the Chordata, cephalochordates diverged first, with tunicates and vertebrates forming a sister group. Chordates share tadpole-type larvae containing a notochord and hollow nerve cord, whereas ambulacrarians have dipleurula-type larvae containing a hydrocoel. We propose that an evolutionary occurrence of tadpole-type larvae is fundamental to understanding mechanisms of chordate origin. Protostomes have now been reclassified into two major taxa, the Ecdysozoa and Lophotrochozoa, whose developmental pathways are characterized by ecdysis and trochophore larvae, respectively. Consistent with this classification, the profound dipleurula versus tadpole larval differences merit a category higher than the phylum. Thus, it is recommended that the Ecdysozoa, Lophotrochozoa, Ambulacraria and Chordata be classified at the superphylum level, with the Chordata further subdivided into three phyla, on the basis of their distinctive characteristics.

THE FRIENDS OF MY FRIENDS

Relations between humans and animals occur under myriad forms and with profound richness. However, taking account of these relations often poses a considerable difficulty. That humans have a strong interest in many other animals, and that humans give rise to a reciprocal interest among many animals, is an important cultural and evolutionary occurrence. Common living and the sharing (or co-constitution) of territory often give rise to social ties between humans and animals. It is important to study the material dimensions that render possible friendship between species. Distance often complicates the material proximity of these relations. The human voice and music are significant conduits of communication between species. Excessive focus on formal symbolic communication has often occluded the significant affective exchange that takes place between species by means of human voice and language. Music, as explored by Jim Nollman, constitutes a “privileged vector” of interspecies communication.