Deep Genomic-Scale Analyses of the Metazoa Reject Coelomata: Evidence from Single- and Multigene Families Analyzed Under a Supertree and Supermatrix Paradigm

Solving the phylogeny of the animals with bilateral symmetry has proven difficult. Morphological studies have suggested a variety of alternative hypotheses, of which, Hyman’s Coelomata hypothesis has become the most established. Studies based on 18S rRNA have failed to endorse Coelomata, supporting instead the rearrangement of the protostomes into two new clades: the Lophotrochozoa (including, e.g., the molluscs and the annelids) and the Ecdysozoa (including the Panarthropoda and most pseudocoelomates, such as the nematodes and priapulids). Support for this new animal phylogeny has been attained from expressed sequence tag studies, although these generally have a limited gene sampling. In contrast, deep genomic-scale analyses have often supported Coelomata. However, these studies are problematic due to their limited taxonomic sampling, which could exacerbate tree reconstruction artifacts

Animal Evolution: Only Rocks Can Set the Clock

Molecular clocks have become the method of choice to date the tree of life. A new study demonstrates that there are limits to their precision, which may only be overcome by improving our knowledge of the fossil record

New Tardigrade Opsins and Differential Expression Analyses Show Ontogenic Variation in Light Perception

Abstract Opsins are light-sensitive proteins involved in many photoreceptive processes, including, but not limited to, vision and regulation of circadian rhythms. Arthropod (e.g., insects, spiders, centipedes, and crabs) opsins have been extensively researched, but the relationships and function of opsins found in lineages that are evolutionarily closely related to the arthropods remains unclear. Multiple, independent, opsin duplications are known in Tardigrada (the water bears), evidencing that protostome opsin duplications are not limited to the Arthropoda. However, the relationships, function, and expression of these new opsins are still unknown. Here, we use two tardigrade transcriptomes with deep coverage to greatly expand our knowledge of the diversity of tardigrade opsins. We reconstruct the phylogenetic relationships of the tardigrade opsins and investigate their ontogenetic expression. We found that while tardigrades have multiple opsins that evolved from lineage-specific duplications of well-understood arthropod opsins, their expression levels change during ontogeny such that most of these opsins are not co-temporally expressed. Co-temporal expression of multiple opsins underpins color vision in Arthropoda and Vertebrata. Our results clearly show duplications of both rhabdomeric and ciliary opsins within Tardigrada, forming clades specific to both the Heterotardigrada and Eutardigrada in addition to multiple independent duplications within genera. However, lack of co-temporal, ontogenetic, expression suggests that while tardigrades possess multiple opsins, they are unlikely to be able to distinguish color

Phylogenetic-Signal Dissection of Nuclear Housekeeping Genes Supports the Paraphyly of Sponges and the Monophyly of Eumetazoa

The relationships at the base of the metazoan tree have been difficult to robustly resolve, and there are several different hypotheses regarding the interrelationships among sponges, cnidarians, ctenophores, placozoans, and bilaterians, with each hypothesis having different implications for the body plan of the last common ancestor of animals and the paleoecology of the late Precambrian. We have sequenced seven nuclear housekeeping genes from 17 new sponges, bringing the total to 29 species analyzed, including multiple representatives of the Demospongiae, Calcarea, Hexactinellida, and Homoscleromorpha, and analyzed a data set also including six nonmetazoan outgroups and 36 eumetazoans using a variety of phylogenetic methods and evolutionary models. We used leaf stability to identify rogue taxa and investigate their effect on the support of the nodes in our trees, and we identified clades most likely to represent phylogenetic artifacts through the comparison of trees derived using different methods (and models) and through site-stripping analyses. Further, we investigated compositional heterogeneity and tested whether amino acid composition bias affected our results. Finally, we used Bayes factors to compare our results against previously published phylogenies. All our maximum likelihood (ML) and Bayesian analyses find sponges to be paraphyletic, with all analyses finding three extant paraphyletic sponge lineages, Demospongiae plus Hexactinellida, Calcarea, and Homoscleromorpha. All but one of our ML and Bayesian analyses support the monophyly of Eumetazoa (here Cnidaria þ Bilateria) and a sister group relationship between Placozoa (here Trichoplax adhaerens) and Eumetazoa. Bayes factors invariably provide decisive support in favor of poriferan paraphyly when compared against either a sister group relationship between Porifera and Cnidaria or with a monophyletic Porifera with respect to a monophyletic Eumetazoa. Although we were able to recover sponge monophyly using our data set, this was only possible under unrealistic evolutionary models, if poorly performing phylogenetic methods were used, or in situations where the potential for the generation of tree reconstruction artifacts was artificially exacerbated. Everything considered, our data set does not provide any support for a monophyletic Diploblastica (here Placozoa þ Cnidaria þ Porifera) and suggests that a monophyletic Porifera may be better seen as a phylogenetic artifact

Investigation on Modulation-Based Straightness Measurement

The concept of a novel non-contacting technique for measuring straightness and its practical realization in a mechanical device are presented in this article. The device, called InPlanT, is based on the acquisition of the luminous signal retroreflected by a spherical glass target and impinged on a photodiode after mechanical modulation. The received signal is reduced to the sought straightness profile using dedicated software. The system was characterized with a high-accuracy CMM and the maximum error of indication was derived

Phylogenetic-Signal Dissection of Nuclear Housekeeping Genes Supports the Paraphyly of Sponges and the Monophyly of Eumetazoa

The relationships at the base of the metazoan tree have been difficult to robustly resolve, and there are several different hypotheses regarding the interrelationships among sponges, cnidarians, ctenophores, placozoans, and bilaterians, with each hypothesis having different implications for the body plan of the last common ancestor of animals and the paleoecology of the late Precambrian. We have sequenced seven nuclear housekeeping genes from 17 new sponges, bringing the total to 29 species analyzed, including multiple representatives of the Demospongiae, Calcarea, Hexactinellida, and Homoscleromorpha, and analyzed a data set also including six nonmetazoan outgroups and 36 eumetazoans using a variety of phylogenetic methods and evolutionary models. We used leaf stability to identify rogue taxa and investigate their effect on the support of the nodes in our trees, and we identified clades most likely to represent phylogenetic artifacts through the comparison of trees derived using different methods (and models) and through site-stripping analyses. Further, we investigated compositional heterogeneity and tested whether amino acid composition bias affected our results. Finally, we used Bayes factors to compare our results against previously published phylogenies. All our maximum likelihood (ML) and Bayesian analyses find sponges to be paraphyletic, with all analyses finding three extant paraphyletic sponge lineages, Demospongiae plus Hexactinellida, Calcarea, and Homoscleromorpha. All but one of our ML and Bayesian analyses support the monophyly of Eumetazoa (here Cnidaria þ Bilateria) and a sister group relationship between Placozoa (here Trichoplax adhaerens) and Eumetazoa. Bayes factors invariably provide decisive support in favor of poriferan paraphyly when compared against either a sister group relationship between Porifera and Cnidaria or with a monophyletic Porifera with respect to a monophyletic Eumetazoa. Although we were able to recover sponge monophyly using our data set, this was only possible under unrealistic evolutionary models, if poorly performing phylogenetic methods were used, or in situations where the potential for the generation of tree reconstruction artifacts was artificially exacerbated. Everything considered, our data set does not provide any support for a monophyletic Diploblastica (here Placozoa þ Cnidaria þ Porifera) and suggests that a monophyletic Porifera may be better seen as a phylogenetic artifact

Social and technological innovations in forestry

In Europe, when referring to innovation in forestry, the dominant discourses mostly deal with technological innovation based on large-scale industrial investments. \u201cInnovation is rather often used synonymously with technological innovation (Kubeczko et al. 2006:706)\u201d. This is supported by a biased (limited) interpretation of the bioeconomy strategies, where attention is almost completely focused on the development of bio-refineries, i.e. on innovative plants that produce power, heat, a potentially large set of bio-chemicals and in some cases pulp, normally using huge amounts of low-value biomasses from agriculture, forestry or organic wastes (McCormick and Kautto 2013; Scarlat et al. 2015; Fund et al. 2015.). Also in the case of plants producing just bio-energy, the needs for industrial scale economies are creating a demand for woody biomass that is frequently not covered by the potential local supply, so industrial plants are located in proximity to port facilities with a process of internationalization not only of the investment capital, but also wood procurement (P\ufclzl et al. 2017). Moreover, although it has been pointed out \u201cthe need to focus on innovation as a socially embedded phenomenon that should stretch across all economic sectors, [this concept] has mostly been applied in policy practice in high-tech fields, often with a technological focus or bias (EU 2003; von Tunzelmann and Acha 2003)\u201d, rather than in forestry (Rametsteiner and Weiss 2003: 692). Other emerging and innovative initiatives, like for example the creation of nature-based businesses connected with the establishment of payment schemes for ecosystem (or environmental) services (PES) that try to obtain value from the management of public goods such as water, biodiversity, human wellbeing and others (e.g., Wunder 2005), are often not considered as strategic choices to be invested in for the development of national economies , despite their potential in rural development (e.g., by means of income generation and employment creation) and innovation (Matilainen et al. 2011; Slee 2011; O\u2019Driscoll et al. 2017; Tyrv\ue4inen et al. 2017). However, it was recently stressed that a new policy narrative is needed, that \u201cshould emphasise a sustainable and socially inclusive forest-based bioeconomy (Winkel 2017:153)\u201d, i.e. a holistic bioeconomy [\u2026] \u201cthat recognises and mobilises the entire spectrum of ecosystem services that Europe\u2019s forests can provide for the benefit of Europe\u2019s societies (Winkel 2017)\u201d. This chapter introduces and discusses the various implications of social and technological innovation on the forestry sector, especially in Europe. In the first section, links are made with the various components of globalization. In the second, both approaches are presented based on commonly used definitions. In the third, the two approaches are illustrated by means of concrete examples, while their pros and cons (in terms of positive and negative consequences) are pointed out and briefly compared. In the fourth section, insights into how to integrate the two approaches are proposed and discussed in relation to the current perspectives of globalization and future development. The special role that information technologies can play in the two cases is highlighted