Hierarchy Theory of Evolution and the Extended Evolutionary Synthesis: Some Epistemic Bridges,Some Conceptual Rifts

Contemporary evolutionary biology comprises a plural landscape of multiple co-existent conceptual frameworks and strenuous voices that disagree on the nature and scope of evolutionary theory. Since the mid-eighties, some of these conceptual frameworks have denounced the ontologies of the Modern Synthesis and of the updated Standard Theory of Evolution as unfinished or even flawed. In this paper, we analyze and compare two of those conceptual frameworks, namely Niles Eldredge’s Hierarchy Theory of Evolution (with its extended ontology of evolutionary entities) and the Extended Evolutionary Synthesis (with its proposal of an extended ontology of evolutionary processes), in an attempt to map some epistemic bridges (e.g. compatible views of causation; niche construction) and some conceptual rifts (e.g. extra-genetic inheritance; different perspectives on macroevolution; contrasting standpoints held in the “externalism–internalism” debate) that exist between them. This paper seeks to encourage theoretical, philosophical and historiographical discussions about pluralism or the possible unification of contemporary evolutionary biology.     

Evolutionary Lability of Integration in Cambrian Ptychoparioid Trilobites

Phenotypic integration can influence evolutionary rate and direction by channeling variation into few dimensions. The extent to which that channeling serves as a constraint over macroevolutionary timescales is determined in part by the evolutionary lability of phenotypic integration. Evolutionary change in patterns of pleiotropy, potentially reducing that constraint, is thought to be more readily achieved when pleiotropy is structured by variation arising in parallel along different developmental pathways rather than by variation arising from direct interactions within and between those pathways. Herein we test two predictions that follow from that hypothesis: (1) that clades undergoing dramatic diversification are characterized by integration that is weakly influenced by direct interactions; and (2) that the structure of integration arising from direct interactions is more conservative than that arising from parallel variation. We examine integration of the cranidium of two Cambrian ptychoparioid trilobites, Crassifimbra walcotti and Eokochaspis nodosa, comparing them to each other and to a previously studied species, C.? metalaspis. Shape variation is decomposed into components representing variation among individuals and variation due to direct interactions. In all three species, variation among individuals was only weakly influenced by direct interactions, suggesting that integration was unlikely to have been a long-term constraint on the Cambrian diversification of ptychoparioids. Phenotypic integration of E. nodosa is no more similar than expected by chance to either Crassifimbra species, but the component due to direct interactions is more similar than expected by chance to that of C.? metalaspis. Conversely, the two Crassifimbra species are generally similar (although not identical) in phenotypic integration, but markedly differ in their structure of direct interactions. Integration arising from direct interactions was therefore not immune to restructuring over even short evolutionary timescales, and was not always more conservative than that arising from parallel variation.     

Divergent Evolution of Symbiotic Bacteria: Rhizobia of the Relic Legume <Emphasis Type="Italic">Vavilovia formosa</Emphasis> Form an Isolated Group within <Emphasis Type="Italic">Rhizobium leguminosarum</Emphasis> bv. <Emphasis Type="Italic">viciae</Emphasis>

Comparative sequence analysis of symbiotic genes (nodA, nodC, nodD, nifH), which are elements of accessory component of the rhizobial genome, demonstrated that the strains of Rhizobium leguminosarum bv. viciae, isolated from the nodules of a relic legume, Vavilovia formosa, the closest relative of hypothetical common ancestor of the tribe Fabeae, represented a group separated from the strains of R. leguminosarum bv. viciae, isolated from other representatives of this tribe (Vicia, Lathyrus, Pisum, Lens). No isolation was observed relative to the genes representing the core component of the rhizobial genome (16S rDNA, ITS, glnII) or relative to host specificity of the rhizobia. The data obtained suggest that sequence divergence of symbiotic genes marks the initial stage of sympatric speciation, which can be classified as the isolation of the relic “vaviloviae” symbiotype, a possible evolutionary precursor of the “viciae” biotype.     

On Novelty,Heterochrony and Developmental Constraints in a Complex Morphological Theory of Recapitulation: The Genus <Emphasis Type="Italic">Trophon</Emphasis> as a Case Study

Darwin proposed natural selection as the main evolutionary mechanism in 1859. However, he did not think that this was the only process by which new species were generated. It was the so-called Modern Synthesis who established natural selection as the only mechanism responsible for evolution. Since then, the evolutionary process is explained by the pair mutation-adaptation: new species are generated by the appearance of new mutations, which in case of allowing new adaptations to the environment, they will be fixed and organisms will survive, therefore resulting in new species. An alternative view to the plasticity promoted by the adaptationist program is to think organisms as truly organized structures, having different levels of structural organization, which would mean that not every form is possible, but only those that correspond to a certain building plan. This would be reflected in the appearance of structural constraints, showing the limits imposed to the organism during its evolutionary development. In this work, I studied the ontogeny and development of three species of the genus Trophon by geometric morphometrics, in order to clarify important concepts in evolutionary developmental biology (Evo-Devo). Integrating theoretical and empirical investigations, I could propose a new conceptual framework for heterochrony in a context of a complex theory of recapitulation. Furthermore, I could detect a developmental constraint in Trophon, which provided an opportunity to reconstruct the concept of constraint and propose a synthesis between heterochrony and constraint that explained evolution as a process fueled by them, that is, as directive and driving force.     

Hypercalcified segmented sponges (“sphinctozoans”) from the Upper Triassic (Norian) reef boulders of Taurus Mountains (southern Turkey)

Upper Triassic Norian reef boulders, exposed in a locality near the fountain “Tavuk Cesme” (“Chicken Fountain”) in Taurus Mountains, southern Turkey yielded a large number of hypercalcified sponges, including “sphinctozoans”, “inozoans”, “spongiomorphids”, and “chaetetids”. The sphinctozoans from this locality are described in this paper. Geologically, this locality belongs to the Anamas-Akseki autochthonous. The reef boulders of this locality are exposed near the “Tavuk Cesme” fountain, located at the road, leading from the town of Aksu to Yenisarbademli. The following taxa are described: Amblysiphonella taurica nov. sp., Anthalythalamia riedeli Senowbari-Daryan, Calabrisiphonella sphaerica nov. sp., Calabrisiphonella cuifi nov. sp., Cinnabaria minima Senowbari-Daryan, Colospongia recta nov. sp., Colospongia sp. 1, Colospongia sp. 2, Colospongia sp. 3, Cryptocoelia compacta nov. sp., Cryptocoelia? sp., Deningeria crassireticulata Senowbari-Daryan, Zühlke, Bechstädt and Flügel, Discosiphonella minima Senowbari-Daryan and Link, Gigantothalamia ovoidalis Senowbari-Daryan, Hajarispongia dipoyrazensis nov. sp., Hajarispongia cortexifera nov. sp., Kashanella irregularis Senowbari-Daryan, Kashanella cylindrica nov. sp., Parauvanella ferdowsensis Senowbari-Daryan, Parastylothalamia cylindrica nov. gen., nov. sp., Asiphothalamia polyosculata nov. gen, nov. sp., Sollasia norica nov. sp., and Thaumastocoelia sphaeroida Senowbari-Daryan. The most abundant sponge is Amblysiphonella taurica nov. sp. followed by Hajarispongia dipoyrazensis nov. sp., Colospongia and Discosiphonella minima Senowbari-Daryan and Link are also relatively abundant. The stylothalamid sponge Parastylothalamia nov. gen. is an abundant sponge genus in other Norian reefs of the Taurus Mountains, but is rare at the “Tavuk Cesme” locality.     

Delimitation of evolutionary units in Cuvier’s dwarf caiman, <Emphasis Type="Italic">Paleosuchus palpebrosus</Emphasis> (Cuvier, 1807): insights from conservation of a broadly distributed species

An important goal of evolutionary and conservation biology is the identification of units below the species level, such as Evolutionarily Significant Units (ESUs), providing objectively delimited units for species conservation and management. In this study we tested the hypothesis that Cuvier’s dwarf caiman (Paleosuchus palpebrosus)—a species broadly distributed across several biomes and watersheds of South America—is comprised of different ESUs. We analyzed mitochondrial cytochrome b sequences of 206 individuals and 532 unlinked ddRAD loci of 20 individuals chosen from amongst the mitochondrial haplogroups. Analysis of the cytochrome b sequences revealed four mitochondrial clusters, while STRUCTURE analysis of ddRAD loci detected three genomic clusters with different levels of mixture between them. Using the Adaptive Evolutionary Conservation (AEC) framework we identified three ESUs: “Amazon”, “Madeira-Bolivia” and “Pantanal”; one of them composed of two different Management Units (MUs), “Madeira” and “Bolivia”. In general, based on the comparisons with other crocodilian species, genetic diversity of each lineage was moderate however, the Madeira MU showed fivefold lower genetic diversity than other geographic groups. Considering the particularities of each Paleosuchus palpebrosus conservation unit, we recommend that the conservation status of each is evaluated separately. Tropical biodiversity is largely underestimated and in this context the broadly distributed species are the most likely candidates to harbor distinct evolutionary lineages. Thus, we suggest that conservation research should not neglect species that are generally considered of Least Concern by IUCN due to the taxon’s broad geographic distribution.     

Complex adaptive traits between mating behaviour and post-copulatory sperm behaviour in squids

Emergence of male dimorphism within a species is the evolutionary process of disruptive selection. In squids, two types of male mating behaviour, known as alternative reproductive tactics (ARTs), are causally associated with adult body size. Males inseminate promiscuously with the same females; large “consort” males internally, and small “sneaker” males externally. Previously we found that in Heterololigo bleekeri, sneaker (but not consort) spermatozoa are able to swarm by sensing self-emitted CO₂. This suggests that a swarming trait might have arisen in sneakers as a “sperm cooperation” strategy among sibling sperm in order to compete with consort males, or as a consequence of adaptation to external fertilization. To address these possibilities, we examined six species where three patterns of insemination are present, namely, only internal, only external, or both ARTs. In three species that employ both ARTs (H. bleekeri, Loligo reynaudii and Uroteuthis edulis), sneaker spermatozoa always exhibited self-swarming capacity. In Idiosepius paradoxus and Todarodes pacificus, which use only external insemination, spermatozoa formed a swarm. However, in Euprymna morsei, which use only internal insemination, sperm were unable to swarm. These results suggest that the self-swarming trait is likely to be linked to the mode of insemination rather than the alternative strategy used by sneaker males. Thus we propose a new hypothesis in which cooperative sperm behaviour has evolved not only through kin selection against sperm competition risks, but also through adaptation to the insemination/fertilization environment.     

Experimental evidence that evolution by niche construction affects dissipative ecosystem dynamics

Evolution by niche construction occurs when organism-mediated modification of the environment causes an evolutionary response. Physicists have postulated that evolution in general, and evolution mediated via feedbacks between organisms and their environment in particular (i.e. evolution by niche construction), could increase the capacity of biological systems to dissipate free energy in an open thermodynamic system, and help them maintain a state far from thermodynamic equilibrium. Here, we propose using the bacterium Pseudomonas fluorescens (strain SBW25) as a model system to experimentally test theories in both evolutionary biology (e.g. niche construction) and physics (e.g. dissipative systems theory). P. fluorescens rapidly and predictably evolves multiple strategies for exploiting oxygen in unmixed culture flasks. This evolutionary dynamic is mediated by feedbacks between the modification of the oxygen gradient by P. fluorescens and the ecological and evolutionary responses of Pseudomonas to modified environmental conditions. To confirm this, we experimentally manipulated two aspects of the system that influence the strength of the feedback between P. fluorescens and oxygen gradients in the system. First, we inhibited the metabolism of the strain used to inoculate the cultures, and, second, we disturbed the formation of mats at the air–liquid interface. Overall, we found convincing experimental evidence of evolution by niche construction, and conclude that this study system is amenable to experimental investigations of both niche construction and dissipative systems theory.     

Functional Anatomy of the Forelimb of <Emphasis Type="Italic">Plesiotypotherium achirense</Emphasis> (Mammalia,Notoungulata, Mesotheriidae) and Evolutionary Insights at the Family Level

In the present work, we provide muscular reconstruction and we infer functional properties of the forelimb of Plesiotypotherium achirense, a fossil mesotheriid notoungulate from the late Miocene of Achiri (Bolivia). This locality has yielded the widest sample ever available for the forelimb of a mesotheriid. In addition, we propose a qualitative comparison of the forelimb (osteology and myology) at the family level, including the Miocene–Pleistocene mesotheriines Mesotherium cristatum, Plesiotypotherium achirense, Caraguatypotherium munozi, Plesiotypotherium casirense, and Pseudotypotherium sp, and the late Oligocene trachytheriine Trachytherus alloxus. Functional properties are consistent with a digging ability and a “scratch-digger” lifestyle for Mesotheriidae. In general, there are only slight differences among the comparison sample, except for Mesotherium cristatum, which reflect significant osteological modifications, likely to help increasing the moment arm while scratch-digging. These features are mainly observable on scapulae (distal border caudally displaced) and humeri (deltoid crest distally oriented and crista supracondylaris lateralis laterally projected).     

Natural genetic variation in <Emphasis Type="Italic">Brassica</Emphasis> homologs of <Emphasis Type="Italic">FLOWERING LOCUS T</Emphasis> and characterization of its expression domains

FLOWERING LOCUS T (FT), a major effect gene, regulates flowering time in Arabidopsis. We analyzed evolutionary changes distinguishing two FT homeologous loci in B. rapa, described genetic variation in homologs isolated and reported expression pattern of FT in B. juncea. Synteny analysis confirmed presence of two FT genomic copies in B. rapa ssp. pekinensis and resolved pre-existing anomalies regarding copy number in “AA” genome. Synteny analysis of B. rapa homeologous regions CR1 (129 kb) and CR2 (232 kb) revealed differential gene fractionation and wide-spread re-arrangements. Seven genomic DNA (gDNA) variants (2.1–2.2 kb) and 10 complementary DNA (cDNA) variants (528 bp) were isolated from 6 Brassica species. The gDNA variants shared 72–99 % similarity within Brassica and 58–60 % between Arabidopsis and Brassica. FT cDNA variants shared 92–100 % similarity within Brassica and 87 % between Arabidopsis and Brassica. Phylogenetic analysis of FT gDNA, cDNA and protein sequences revealed two major clades, differentiating homologs derived from species containing shared “BB” and “CC” genomes. Phylogram based on Brassica FT gDNA differentiated homeologs derived from AA-LF (Least fractioned) and AA-MF1 (Moderately fractioned) sub-genomes. Analysis of FT expression pattern in B. juncea revealed increasing levels correlating with attainment of physiological maturity; highest levels were detected in older leaves implying conservation in spatio-temporal expression pattern vis-à-vis Arabidopsis. In conclusion, our study reveals that polyploidy in Brassicas resulted in expansion of FT gene copies with homologs charting independent evolutionary course through accumulation of mutations. However, expression domains of FT remained conserved across Brassicaceae to preserve the critical function of FT in controlling flowering time.     

Snake fauna (Reptilia: Serpentes) from the Early/Middle Miocene of Sandelzhausen and Rothenstein 13 (Germany)

The Early/Middle Miocene (European Land Mammal Zone MN5) localities of Sandelzhausen and Rothenstein 13 in southern Germany have yielded remains of about 13 ophidian taxa: Eoanilius sp. (Aniliidae), Bavarioboa ultima (Boidae), “Coluber” sp., ?Telescopus sp., Natrix sp., cf. Natrix sp., cf. “Neonatrix” sp., unidentified “colubrines” and “natricines” (Colubridae), Naja sp., an unidentified elapid (Elapidae), Vipera sp. (“Oriental viper”), Vipera sp. (“aspis complex”) (Viperidae). Both faunas document a transitional phase from those reported from several late Early and Middle Miocene sites of Central and Western Europe. The climates of Sandelzhausen and Rothenstein 13, as indicated by ophidian fossils, were warm, although not tropical or subtropical.     

Evolution and systematics of Green Bush-crickets (Orthoptera: Tettigoniidae: <Emphasis Type="Italic">Tettigonia</Emphasis>) in the Western Palaearctic: testing concordance between molecular,acoustic, and morphological data

The genus Tettigonia includes 26 species distributed in the Palaearctic region. Though the Green Bush-crickets are widespread in Europe and common in a variety of habitats throughout the Palaearctic ecozone, the genus is still in need of scientific attention due to the presence of a multitude of poorly explored taxa. In the present study, we sought to clarify the evolutionary relationships of Green Bush-crickets and the composition of taxa occurring in the Western Palaearctic. Based on populations from 24 disjunct localities, the phylogeny of the group was estimated using sequences of the cytochrome oxidase subunit I (COI) and the internal transcribed spacers 1 and 2 (ITS1 and ITS2). Morphological and acoustic variation documented for the examined populations and taxa was interpreted in the context of phylogenetic relationships inferred from our genetic analyses. The trees generated in the present study supported the existence of three main lineages: “A”—composed of all sampled populations of Tettigonia viridissima and the Tettigonia vaucheriana complex, “B”—comprising Tettigonia caudata, Tettigonia uvarovi, and the Tettigonia armeniaca complex, and “C”—consisting of Tettigonia cantans. The present study provides the first phylogenetic foundation for reviewing the systematics of Tettigonia (currently classified mostly according to morphological characteristics), proposing seven new synonymies.     

High-throughput sequencing of <Emphasis Type="Italic">Prunus ferganensis</Emphasis> indicates that it is a geographical population of <Emphasis Type="Italic">P. persica</Emphasis>

Peach belongs to the genus Prunus, which includes Prunus persica and its relative species, P. mira, P. davidiana, P. kansuensis, and P. ferganensis. Of these, P. ferganensis have been classified as a species, subspecies, or geographical population of P. persica. To explore the genetic difference between P. ferganensis and P. persica, high-throughput sequencing was used in different peach accessions belonging to different species. First, low-depth sequencing data of peach accessions belonging to four categories revealed that similarity between P. ferganensis and P. persica was similar to that between P. persica accessions from different geographical populations. Then, to further detect the genomic variation in P. ferganensis, the P. ferganensis accession “Xinjiang Pan Tao 1” and the P. persica accession “Xia Miao 1” were sequenced with high depth, and sequence reads were assembled. The results showed that the collinearity of “Xinjiang Pan Tao 1” with the reference genome “Lovell” was higher than that of “Xia Miao 1” and “Lovell” peach. Additionally, the number of genetic variants, including single nucleotide polymorphisms (SNPs), structural variations (SVs), and the specific genes annotated from unmapped sequence in “Xia Miao 1” was higher than that in “Xinjiang Pan Tao 1” peach. The data showed that there was a close distance between “Xinjiang Pan Tao 1” (P. ferganensis) and reference genome which belong to P. persica, comparing “Xia Miao 1” (P. persica) and reference ones. The results accompany with phylogenetic tree and structure analysis confirmed that P. ferganensis should be considered as a geographic population of P. persica rather than a subspecies or a distinct species. Furthermore, gene ontology analysis was performed using the gene comprising large-effect variation to understand the phenotypic difference between two accessions. The result revealed that the pathways of gene function affected by SVs but SNPs and insertion-deletions markedly differed between the two peach accessions.     

The Creativity of Natural Selection? Part I: Darwin,Darwinism, and the Mutationists

This is the first of a two-part essay on the history of debates concerning the creativity of natural selection, from Darwin through the evolutionary synthesis and up to the present. Here I focus on the mid-late nineteenth century to the early twentieth, with special emphasis on early Darwinism and its critics, the self-styled “mutationists.” The second part focuses on the evolutionary synthesis and some of its critics, especially the “neutralists” and “neo-mutationists.” Like Stephen Gould, I consider the creativity of natural selection to be a key component of what has traditionally counted as “Darwinism.” I argue that the creativity of natural selection is best understood in terms of (1) selection initiating evolutionary change, and (2) selection being responsible for the presence of the variation it acts upon, for example by directing the course of variation. I consider the respects in which both of these claims sound non-Darwinian, even though they have long been understood by supporters and critics alike to be virtually constitutive of Darwinism.     

The genusSaccharomyces (Meyen) Reess

The authors submit a taxonomic evaluation of an intermediate group of strains between the speciesSaccharomyces carlsbergensis Hansen andSaccharomyces cerevisiae Hansen. The material consisted of atypical strains of “bottom” brewer’s yeasts and the synonymous strainsSaccharomyces monacensis Hansen andSaccharomyces mandshuricus Saito. It was found that there were two different serological types in the speciesSaccharomyces carlsbergensis, one of which was characterized by the presence of antigen “C” and was typical for this species, while the other possessed antigen “M” and was grouped roundSaccharomyces monacensis. This second serological type merges with a group of strains which gives only one third fermentation of raffinose, so that it is actually an intermediate betweenSaccharomyces cerevisiae Hansen andSaccharomyces carlsbergensis Hansen and indicates the course of progressive development from the former species to the latter. No close similarity was found betweenSaccharomyces mandshuricus Saito and some of the strains of the transitional group or typical representatives of the two main species, and the authors therefore consider that there is some obscurity as to its synonymity withSaccharomyces carlsbergensis.     

Letting the Air Out: <Emphasis Type="Italic">Aire</Emphasis> as an Empty Signifier in Oaxacan Understandings of Illness

“Air (aire, also aigre) in the body” is a frequent explanation of illness according to the traditional medical beliefs in Mexico. Anthropologists have generally scrutinized aire in the context of other common folk illnesses treated by traditional healers (curanderas). However, drawing on my research in the communities of Northern Oaxaca I suggest that aire occupies a more distinct position in the folk medical cosmology than it has usually been credited with. This distinction rests on the notion’s exceptional ambivalence and openness to multiple interpretations. “Air” is recurred to as the cause of illness mainly in situations where every other explanation, either “traditional” or “biomedical,” seems to be inadequate. The physical properties of air—its transparency, invisibility, apparent immateriality, near omnipresence, and virtual “nothingness”—render it a suitable explanation of the last resort. Local understandings of what aire “is” are often vague and elusive, and in many respects the term functions in folk medical discourse as an “empty signifier.”     

On new Jurassic Rissooidea and Zygopleuroidea convergently similar to them (Gastropoda: Pectinibranchia)

A new genus, Boreomica gen. nov., is established; it comprises small-sized gastropods widespread in the Jurassic of the Russian Plate, the taxonomic position of which was ambiguously treated by previous authors. The new genus is assigned to the family Rissoidae. The species composition and stratigraphical and geographical distribution of the genus and its species are discussed. From the Jurassic of the Russian Plate, Callovian Boreomica exigua (Gerasimov, 1992), the type species of the genus, and Kimmeridgian–Volgian Boreomica undulata (Tullberg, 1881), and members of the genus without species status from the Bathonian and Upper Oxfordian are described. Conchological polymorphism of species connected with their eurybiontic characteristics is discussed. Based on the study of samples of the species B. exigua from different types of facies, two subspecies are recognized, B. exigua exigua and B. exigua arenosa subsp. nov. Finds of gastropods morphologically similar to Boreomica are discussed: Katosira? sp. from Mitta et al., 2004, “Procerithium?” volgense Gerasimov, 1955, “Eulima” pusilla Tullberg, 1881, and “Hudlestonella” caleptra sensu Gerasimov, 1992 are considered. It is concluded that E. pusilla and H. caleptra are unknown zygopleurids, Katosira? sp. is likely a poorly preserved Katosira, and “Procerithium?” volgense is represented by a mixture of several species belonging to different genera: several zygopleurid species, the rissoids Boreomica undulata and Bralitzia. Shells of P. volgense in the P.A. Gerasimov’s collection from the Craspedites nodiger Zone are described as Laevipleura sp.