Phylogenetic History Research Articles

O “organismo” na obra de B. F. Skinner: uma exploração contextual e quantitativa acerca de seu signficado


 
 
 Apesar de aparecer no título da obra primeira de B. F. Skinner, O comportamento dos organismos, está ausente, nessa e em outras obras do autor, uma de nição explícita de “organismo”, de modo que uma análise do termo em seus escritos se faz necessária para eluci- dar regularidades contextuais de sua ocorrência. Partindo do Procedimento de Interpretação Conceitual de Texto (PICT), analisamos o contexto de ocorrência do termo “organismo” em uma amostra de 8 obras de Skinner, abrangendo um período de 60 anos. Notamos que o termo ocorre em pelo menos 15 diferentes contextos, cada um deles consistindo em um nexo onde con uem diferentes discussões na literatura da analítico-comportamental. Ressaltamos algumas ambiguidades relativas ao critério de demarcação entre organismo e ambiente, ao papel da história logenética no desenvolvimento do organismo, e à extensão metafórica referente ao uso do termo para tratar da dimensão grupal ou social.
 
 

The complete mitogenome of the invasive Japanese mud snail Batillaria attramentaria (Gastropoda: Batillariidae) from Elkhorn Slough, California, USA

Genomic analysis of the invasive marine snail Batillaria attramentaria from Elkhorn Slough, Moss Landing, California, USA using 150 bp paired-end Illumina sequences resulted in the assembly of its complete mitogenome. The mitogenome is 16,095 bp in length and contains 2 rRNA, 13 protein-coding, and 22 tRNA genes (GenBank Accession MN557850). Gene content and organization of B. attramentaria are identical to the Turritellidae and Pachychilidae. The phylogenetic analysis of B. attramentaria resolves it in a fully supported clade with these same two families in the superfamily Cerithioidea. Nucleotide BLAST searches of the Elkhorn Slough cox1 gene of B. attramentaria yielded identical sequences from invasive populations from California and British Columbia, and native populations from northeastern and central Japan. These data show that mitogenome sequencing is a useful tool for studying the classification and phylogenetic history Cerithioidea.

Celebrating Research Devoted to Seed‐Free Land Plants

Celebrating Research Devoted to Seed‐Free Land Plants

Ecological trait evolution in amphibian phylogenetic relationships

Current biodiversity patterns of Neotropical amphibians are the result of their functional and phylogenetic relationships. Understanding the associations between ecological similarity and phylogenetic relatedness among species can provide a convincing statement on the role of evolutionary history in the filling of the niche space. Here, we assessed the ancestral character states of amphibian ecological traits and their evolutionary history in the Atlantic Forest Hotspot. We used 12 genes (11,906 bp) to reconstruct a phylogeny for 207 amphibian species and related it to eight ecological traits regarding their morphology, life-history and behavioural features. We revealed that closely related species can have similar ecological traits, suggesting that these traits are driven by phylogenetic history. Despite the high endemism rate of Atlantic Forest amphibians, our findings heavily rely on good studies on complete amphibian phylogenetic lineages to overcome potential biogeographical constraints. Using mechanisms of adaptive evolution in the context of phylogenetic diversification, we suggest that closely related species have different phylogenetic signals and ecological traits can evolve without relatedness.

Integrative Paleobotany: Affirming the Role of Fossils in Modern Plant Biology—Introduction and Dedication

Integrative Paleobotany: Affirming the Role of Fossils in Modern Plant Biology—Introduction and Dedication

Genetic analysis of Ghanaian G1P[8] and G9P[8] rotavirus A strains reveals the impact of P[8] VP4 gene polymorphism on P-genotyping.

The World Health Organisation rotavirus surveillance networks have documented and shown eclectic geographic and temporal diversity in circulating G- and P- genotypes identified in children <5 years of age. To effectively monitor vaccine performance and effectiveness, robust molecular and phylogenetic techniques are essential to detect novel strain variants that might emerge due to vaccine pressure. This study inferred the phylogenetic history of the VP7 and VP4 genes of previously non-typeable strains and provided insight into the diversity of P[8] VP4 sequences which impacted the outcome of our routine VP4 genotyping method. Near-full-length VP7 gene and the VP8* fragment of the VP4 gene were obtained by Sanger sequencing and genotypes were determined using RotaC v2.0 web-based genotyping tool. The genotypes of the 57 rotavirus-positive samples with sufficient stool was determined. Forty-eight of the 57 (84.2%) had the P[8] specificity, of which 43 (89.6%) were characterized as P[8]a subtype and 5 (10.4%) as the rare OP354-like subtype. The VP7 gene of 27 samples were successfully sequenced and their G-genotypes confirmed as G1 (18/27) and G9 (9/27). Phylogenetic analysis of the P[8]a sequences placed them in subcluster IIIc within lineage III together with contemporary G1P[8], G3P[8], G8P[8], and G9P[8] strains detected globally from 2006–2016. The G1 VP7 sequences of the study strains formed a monophyletic cluster with African G1P[8] strains, previously detected in Ghana and Mali during the RotaTeq vaccine trial as well as Togo. The G9 VP7 sequences of the study strains formed a monophyletic cluster with contemporary African G9 sequences from neighbouring Burkina Faso within the major sub-cluster of lineage III. Mutations identified in the primer binding region of the VP8* sequence of the Ghanaian P[8]a strains may have resulted in the genotyping failure since the newly designed primer successfully genotyped the previously non-typeable P[8] strains. In summary, the G1, G9, and P[8]a sequences were highly similar to contemporary African strains at the lineage level. The study also resolved the methodological challenges of the standard genotyping techniques and highlighted the need for regular evaluation of the multiplex PCR-typing method especially in the post-vaccination era. The study further highlights the need for regions to start using sequencing data from local rotavirus strains to design and update genotyping primers.

Pleistocene climate change and the formation of regional species pools.

Although the description of bioregions dates back to the origin of biogeography, the processes originating their associated species pools have been seldom studied. Ancient historical events are thought to play a fundamental role in configuring bioregions, but the effects of more recent events on these regional biotas are largely unknown. We used a network approach to identify regional and sub-regional faunas of European Carabus beetles and developed a method to explore the relative contribution of dispersal barriers, niche similarities and phylogenetic history on their configuration. We identify a transition zone matching the limit of the ice sheets at the Last Glacial Maximum. While southern species pools are mostly separated by dispersal barriers, in the north species are mainly sorted by their environmental niches. Strikingly, most phylogenetic structuration of Carabus faunas occurred during the Pleistocene. Our results show how extreme recent historical events-such as Pleistocene climate cooling, rather than just deep-time evolutionary processes-can profoundly modify the composition and structure of geographical species pools.

Evolution of Ceratozamia cycads: A proximate-ultimate approach

Evidence suggests that past climatic fluctuations affected speciation of extant cycads. However, empirical genetic and morphological evidence explaining patterns and processes of species diversification are scarce. There are some explanations for the origin and evolution of the genus Ceratozamia, but with inconclusive results. To elucidate the evolution of Ceratozamia, we used genetic and phenotypic sources as empirical data, which were applied in a ‘proximate-ultimate’ framework (ecological and evolutionary scale, respectively). Our results suggested that the evolutionary mechanisms of speciation were shaped by deterministic (natural selection-adaptation) driven by climatic conditions associated to water stress, and probably enhanced by stochastic processes (gene drift and inbreeding). In general terms, punctuated evolution models were those that best explained the patterns of speciation throughout the phylogenetic history of the lineages encompassed in the genus Ceratozamia. Finally, we provide empirical evidence on the tempo and mode of the evolution of a ‘living plant fossil’.

Genetic analysis and evolutionary changes of Porcine circovirus 2

Porcine circovirus 2 (PCV2) has been increasingly isolated worldwide and represents one of the main causes of economic losses in the swine industry. During evolution, PCV2 has diverged into different genotypes and several recombinant strains have been identified. In this study, we performed thorough genetic, evolutionary and codon usage analyses using 1065 non-recombinant open reading frame 2 (ORF2) sequences from NCBI. Based on ML and Bayesian methods of the ORF2 gene, five main genotypes were defined including, PCV2a, PCV2b, PCV2c, PCV2d and PCV2e. The different genotypes displayed a variable degree of codon usage bias, mainly influenced by natural selection. Moreover, the host adaptation of these PCV2 genotypes to different hosts was analyzed for the first time showing that PCV2 is more adapted to swine than bats. Swine was especially relevant in shaping the PCV2b and PCV2d genomes according the Codon adaptation index (CAI) and Similarity index (SiD). When a broader range of circoviruses was considered, a certain incongruence between the phylogenetic history of these viruses and that of their hosts was observed, suggesting that cross-species transmission has played a major role during circoviruses evolution. Our study provides a new perspective of the evolution of Porcine circoviruses and may serve to aid future research on PCV2 origin and evolution patterns.

Phylogenomic interrogation resolves the backbone of the Pseudoscorpiones tree of life

Pseudoscorpiones, with nearly 3700 described species, are an ancient and globally distributed group of arachnids with a fossil record dating back to the Middle Devonian. Previous attempts to reconstruct their phylogenetic history have used morphology or a few amplicons, mostly of rRNAs and mitochondrial genes, which have not been able to completely resolve family-level relationships nor the earliest nodes in the pseudoscorpion tree—those which are most informative about the origins of key characters like venoms and silk. Here we undertake a phylogenetic approach using 41 pseudoscorpion transcriptomes and a series of analyses that account for many of the common pitfalls faced in large phylogenomic analyses. All analyses, using concatenation methods and coalescent approaches, supported monophyly of Iocheirata (the venomous pseudoscorpions), which diversified mostly during the Mesozoic, but paraphyly of Epiocheirata, with a sister group relationship of Feaelloidea to Iocheirata, with Chthonioidea as their sister group. These three main lineages were established during the mid-to-late Paleozoic. Our phylogenetic scheme is consistent with the prior hypothesis that the lack of venom in Pseudoscorpiones is plesiomorphic and not a synapomorphy of Epiocheirata. Based on the results of this study, a new classification is proposed for Pseudoscorpiones including the following new nomenclatural and taxonomic acts: the new suborders Palaeosphyronida Harvey and Atoposphyronida Harvey for Dracochelidae and Feaelloidea, respectively; the newly recognized superfamily Garypinoidea for Garypinidae and Larcidae; the revised rank for Lechytiidae and Tridenchthoniidae, which are regarded as subfamilies of Chthoniidae; the revised rank for Tridenchthoniini and Verrucadithini which are regarded as tribes of Tridenchthoniinae; and the elevation of Hesperolpiinae as a distinct family, Hesperolpiidae.

Two Coxsackievirus B3 outbreaks associated with hand, foot, and mouth disease in China and the evolutionary history worldwide

BackgroundCoxsackievirus B3 (CV-B3) is usually associated with aseptic meningitis and myocarditis; however, the association between CV-B3 and hand, foot, and mouth disease (HFMD) has not been clearly demonstrated, and the phylogenetic dynamics and transmission history of CV-B3 have not been well summarized.MethodTwo HFMD outbreaks caused by CV-B3 were described in Hebei Province in 2012 and in Shandong Province in 2016 in China. To analyze the epidemiological features of two CV-B3 outbreaks, a retrospective analysis was conducted. All clinical specimens from CV-B3 outbreaks were collected and disposed according to the standard procedures supported by the WHO Global Poliovirus Specialized Laboratory. EV genotyping and phylogenetic analysis were performed to illustrate the genetic characteristics of CV-B3 in China and worldwide.ResultsTwo transmissible lineages (lineage 2 and 3) were observed in Northern China, which acted as an important “reservoir” for the transmission of CV-B3. Sporadic exporting and importing of cases were observed in almost all regions. In addition, the global sequences of CV-B3 showed a tendency of geographic-specific clustering, indicating that geographic-driven adaptation plays a major role in the diversification and evolution of CV-B3.ConclusionsOverall, our study indicated that CV-B3 is a causative agent of HFMD outbreak and revealed the phylogenetic dynamics of CV-B3 worldwide, as well as provided an insight on CV-B3 outbreaks for effective intervention and countermeasures.

A new balaenopterid whale from the late Miocene of the Southern North Sea Basin and the evolution of balaenopterid diversity (Cetacea, Mysticeti).

BackgroundBalaenopterid mysticetes represent the most successful family-rank group of this clade. Their evolutionary history is characterized by a rich fossil record but the origin of the living genera is still largely not understood. Recent discoveries in the southern border of the North Sea revealed a number of well preserved fossil balaenopterid whales that may help resolving this problem. In particular, skull NMR 14035 shares morphological characters with the living humpback whale, Megaptera novaeangliae and, for this reason, its characteristics are investigated here.MethodsThe comparative anatomical analysis of the new specimen formed the basis of a new phylogenetic analysis of the Mysticeti based on a matrix including 350 morphological character states scored for 82 Operational Taxonomic Units. The stratigraphic age of the specimen was determined based on the analysis of the dinocyst assemblage recovered in the associated sediment. We assessed clade diversity in Balaenopteridae by counting the numbers of clades in given time intervals and then plotted the results.ResultsNehalaennia devossi n. gen. et sp. is described for the first time from the late Tortonian (8.7–8.1 Ma) of the Westerschelde (The Netherlands). This new taxon belongs to Balaenopteridae and shows a surprisingly high number of advanced characters in the skull morphology. Nehalaennia devossi is compared to a large sample of balaenopterid mysticetes and a phylogenetic analysis placed it as the sister group of a clade including the genus Archaebalaenoptera. The inclusion of this fossil allowed to propose a phylogenetic hypothesis for Balaenopteridae in which (1) Eschrichtiidae (gray whales) represents a family of its own, (2) Balaenopteridae + Eschrichtiidae form a monophyletic group (superfamily Balaenopteroidea), (3) Cetotheriidae is the sister group of Balaenopteroidea, (4) living Balaenoptera species form a monophyletic group and (5) living M. novaeangliae is the sister group of Balaenoptera. Our work reveals a complex phylogenetic history of Balaenopteridae and N. devossi informs us about the early morphological transformations in this family. Over time, this family experienced a number of diversity pulses suggesting that true evolutionary radiations had taken place. The paleoecological drivers of these pulses are then investigated.

Parasites and stable isotopes: a comparative analysis of isotopic discrimination in parasitic trophic interactions

Stable isotopes are widely used to identify trophic interactions and to determine trophic positions of organisms in food webs. Comparative studies have provided general insights into the variation in isotopic composition between consumers and their diet (discrimination factors) in predator–prey and herbivore–plant relationships while other major components of food webs such as host–parasite interactions have been largely overlooked. In this study, we conducted a literature‐based comparative analysis using phylogenetically‐controlled mixed effects models, accounting for both parasite and host phylogenies, to investigate patterns and potential drivers in Δ13C and Δ15N discrimination factors in metazoan parasitic trophic interactions. Our analysis of 101 parasite–host pairs revealed a large range in Δ13C (–8.2 to 6.5) and Δ15N (–6.7 to 9.0) among parasite species, with no significant overall depletion or enrichment of 13C and 15N in parasites. As previously found in other trophic interactions, we identified a scaling relationship between the host isotopic value and both discrimination factors with Δ13C and Δ15N decreasing with increasing host δ13C and δ15N, respectively. Furthermore, parasite phylogenetic history explained a large fraction (&gt;60%) of the observed variation in the Δ15N discrimination factor. Our findings suggest that the traditional isotope ecology framework (using an average Δ15N of 3.4‰) applies poorly to parasitic trophic interactions. They further indicate the need for a scaled rather than a fixed trophic discrimination factor framework along gradients of host δ15N. We also identified several conceptual and methodological issues which should to be considered in future research to help integrate parasitic interactions into a holistic isotope ecology framework across diverse trophic interactions.

Ecological contributions to body shape evolution in salamanders of the genus Eurycea (Plethodontidae).

BackgroundBody shape can be both a consequence and cause of a species’ evolution and ecology. There are many examples of phenotypes associated with specific ecological niches, likely as a result of specific selective regimes. A classic example of this is the phenotypic change associated with colonization of caves, including body and limb elongation. However, studies explicitly testing for differences in body shape between cave-dwelling and non-cave-dwelling lineages have been limited and so the role of the cave environment in determining morphological characteristics is still not completely understood. Here we examine variation in body shape among 405 individuals representing 20 species in the salamander genus Eurycea (Plethodontidae) and select outgroups exhibiting great diversity in morphology, ecological niche, and life history.ResultsAfter analyzing morphometric data in a phylogenetic context using phylogenetic MANOVA and examination of the phylomorphospace, we found significant differences in body shape among cave-dwelling and non-cave-dwelling species and between aquatic and terrestrial species. Notably, limb elongation and reduced body and tail size characterized cave-dwelling species. Terrestrial species also exhibited elongation of the limbs and digits. We also observed differences in shape variance among paedomorphic and biphasic species. Our results suggest that the functional limitations imposed by habitat and life history played a key role in the evolution of body shape in this group in the context of their phylogenetic history.

Evolution of phytochemical diversity in Pilocarpus (Rutaceae)

The evolution of phytochemical diversity and biosynthetic pathways in plants can be evaluated from a phylogenetic and environmental perspective. Pilocarpus Vahl (Rutaceae), an economically important medicinal plant in the family Rutaceae, has a great diversity of imidazole alkaloids and coumarins. In this study, we used phylogenetic comparative methods to determine whether there is a phylogenetic signal for chemical traits across the genus Pilocarpus; this included ancestral reconstructions of continuous and discrete chemical traits. Bioclimatic variables found to be associated with the distribution of this genus were used to perform OLS regressions between chemical traits and bioclimatic variables. Next, these regression models were evaluated to test whether bioclimatic traits could significantly predict compound concentrations. Our study found that in terms of compound concentration, variation is most significantly associated with adaptive environmental convergence rather than phylogenetic relationships. The best predictive model of chemical traits was the OLS regression that modeled the relationship between coumarin and precipitation in the coldest quarter. However, we also found one chemical trait was dependent on phylogenetic history and bioclimatic factors. These findings emphasize that consideration of both environmental and phylogenetic factors is essential to tease out the intricate processes in the evolution of chemical diversity in plants. These methods can benefit fields such as conservation management, ecology, and evolutionary biology.

Taxonomy, phylogeny and biogeography of African spurfowls Galliformes, Phasianidae, Phasianinae, Coturnicini: Pternistis spp.

Afro-Asiatic perdicine galliform birds, commonly and inconsistently referred to as francolins, spurfowls and partridges, have contentious taxonomic and phylogenetic histories. In a widely followed monograph, Hall combined two putative monophyletic, but taxonomically unnamed, clades comprising 28 perdicine species known as ‘francolins’ or fisante in South Africa and 13 additional quail-like species (partridges or patryse) into a single genus, Francolinus, which was the largest genus within the Galliformes. Furthermore, she partitioned fisante + patryse into eight, also formally unnamed, putative monophyletic ‘Groups’ and speculated on the phylogenetic affinities of four ‘Unplaced’ species. We investigate fisante using combined morphological, vocalisation and DNA-based evidence and produce a comprehensive revision of fisante taxonomy and phylogeny, a stable classification system and common terminology, and hypotheses vis-à-vis eco-biogeographical processes that promoted their speciation and cladogenesis. Three of Hall’s four Groups of fisante sensu stricto (Montane, Scaly and Vermiculated) are para- or polyphyletic evolutionary grades. Only her Bare-throated Group emerges as monophyletic. We recommend the recognition of only one genus, Pternistis, and the use of ‘spurfowl’ as its collective common name. The proposed new system recognises 25 species, elevating two of Hall’s subspecies (schuetti and cranchii) to species level and reduces the number of subspecies taxa from 59 to 16. Several species pairs of spurfowls, most notably P. afer and P. cranchii, hybridise in para/sympatry. At least one Bare-throated spurfowl, P. rufopictus, may be the product of stabilised hybridisation between P. afer and/or P. cranchii and P. leucoscepus, and hybridisation between proto-taxa in the Montane and Scaly grades may undermine nodal support for basal spurfowl clades.

Walking with hominins: from the reconstruction of a plausible anatomical model to gait energetics in Neandertals. Methodological aspects

Bipedalism as preferential locomotor mode is considered essential in the hominins’ phylogenetic history (e.g., Darwin 1871; Harcourt-Smith and Aiello 2004; Fleagle and Lieberman 2015). However, sim...

Gazprom Neft, Omsk sign investment contract for oil refining catalyst plant

Cyanobacteria are an ancient lineage with an extraordinary history of symbiotic associations with a wide variety of organisms. We focus on the cyanobacteria’s ability to fix atmospheric nitrogen and provide an overview of the conditions in which symbioses are formed, and the genes used to facilitate the uptake of nitrogen, with an emphasis on nitrogenases. We provide a brief overview of the genome changes in obligate interactions in inherited symbionts, captured symbionts, and in facultative symbionts. Many of the traits that differentiate symbiotic cyanobacteria from their free-living counterparts can be traced back to their genomes and in some cases, the phylogenetic history of a group. We hope to generate a guideline for comparative studies in cyanobacteria centered in their ability to fix nitrogen and be symbionts, and to aid in our understanding of their evolutionary history.

Tracing the phylogenetic history of the Crl regulon through the Bacteria and Archaea genomes

BackgroundCrl, identified for curli production, is a small transcription factor that stimulates the association of the σS factor (RpoS) with the RNA polymerase core through direct and specific interactions, increasing the transcription rate of genes during the transition from exponential to stationary phase at low temperatures, using indole as an effector molecule. The lack of a comprehensive collection of information on the Crl regulon makes it difficult to identify a dominant function of Crl and to generate any hypotheses concerning its taxonomical distribution in archaeal and bacterial organisms.ResultsIn this work, based on a systematic literature review, we identified the first comprehensive dataset of 86 genes under the control of Crl in the bacterium Escherichia coli K-12; those genes correspond to 40% of the σS regulon in this bacterium. Based on an analysis of orthologs in 18 archaeal and 69 bacterial taxonomical divisions and using E. coli K-12 as a framework, we suggest three main events that resulted in this regulon’s actual form: (i) in a first step, rpoS, a gene widely distributed in bacteria and archaea cellular domains, was recruited to regulate genes involved in ancient metabolic processes, such as those associated with glycolysis and the tricarboxylic acid cycle; (ii) in a second step, the regulon recruited those genes involved in metabolic processes, which are mainly taxonomically constrained to Proteobacteria, with some secondary losses, such as those genes involved in responses to stress or starvation and cell adhesion, among others; and (iii) in a posterior step, Crl might have been recruited in Enterobacteriaceae; because its taxonomical pattern constrained to this bacterial order, however further analysis are necessary.ConclusionsTherefore, we suggest that the regulon Crl is highly flexible for phenotypic adaptation, probably as consequence of the diverse growth environments associated with all organisms in which members of this regulatory network are present.

Unveiling patterns of genetic variation in parasite-host associations: an example with pinworms and Neotropical primates - CORRIGENDUM.

Patterns of genetic variation among populations can reveal the evolutionary history of species. Pinworm parasites are highly host specific and form strong co-evolutionary associations with their primate hosts. Here, we describe the genetic variation observed in four Trypanoxyuris species infecting different howler and spider monkey subspecies in Central America to determine if historical dispersal processes and speciation in the host could explain the genetic patterns observed in the parasites. Mitochondrial (cox1) and ribosomal (28S) DNA were analysed to assess genetic divergence and phylogenetic history of these parasites. Sequences of the 28S gene were identical within pinworms species regardless of host subspecies. However, phylogenetic analyses, haplotype relationships and genetic divergence with cox1 showed differentiation between pinworm populations according to host subspecies in three of the four Trypanoxyuris species analysed. Haplotype separation between host subspecies was not observed in Trypanoxyuris minutus, nor in Trypanoxyuris atelis from Ateles geoffoyi vellerosus and Ateles geoffoyi yucatanensis. Levels of genetic diversity and divergence in these parasites relate with such estimates reported for their hosts. This study shows how genetic patterns uncovered in parasitic organisms can reflect the host phylogenetic and biogeographic histories.