The use of historical analogues for interpreting fossil pollen records

Modern vegetational analogues of palaeo-landscapes, which could be useful for interpreting fossil pollen assemblages, are often not available, because increased human impact all over the world has altered the vegetation, and the way in which vegetation is recorded by pollen assemblages, including changes in species composition, pollen production, dispersal and sedimentation. Historical maps, survey records and other sources may, however, provide vegetation data for periods prior to this increased human impact, and these may be compared with pollen assemblages from the same period to provide historical analogue data sets. In this paper we review the use of historical analogues in pollen analysis to describe past vegetation patterns in relation to soil properties, climate and fire regimes, and to reconstruct past land use changes, forest composition and species range limits. The methods used include qualitative interpretations, analogue matching, ordination techniques and regression. Because the historical data sources were originally created for other purposes, they may lack the precision or detail needed for quantitative analysis.      

A nomenclature for the radula of the Cephalopoda (Mollusca)–living and fossil

A nomenclature for the teeth of the radula of fossil and living Cephalopoda is proposed. The names suggested can be used for the 13 elements (teeth and plates) across each transverse row of the radula of Nautiloidea (fossil and extant), and, by retaining the names for all except the two outer elements on either side, for the nine elements in Ammonoidea (fossil) and Coleoidea (fossil and extant). One transverse row of the radula has a central rhachidian tooth, and on either side lateral tooth 1, lateral tooth 2, marginal tooth 1, marginal plate 1, marginal tooth 2, marginal plate 2, the last two being present only in the Nautiloidea.     

The use of cranial variables for the estimation of body mass in fossil hominins

Estimating body mass/size/weight remains a crucial precursor to the evaluation of relative brain size and to achieving an understanding of brain evolution in fossil species. Despite the obvious close association between the metrics of postcranial elements and body mass a number of factors combine to reduce their utility. This study examines the feasibility of cranial variables for predicting body mass. The use of traditional regression procedures, independent contrasts analysis, and variance partitioning all support the hypothesis that cranial variables are correlated with body mass even when taking phylogeny into account, with r values typically ranging between 0.52 and 0.98. Body mass estimates derived for fossil hominins using cranial variables are similar to those obtained from previous studies using either cranial or postcranial elements. In particular, upper facial breadth and orbital height display strong predictive capability. Average body masses derived from Least Squares Regression (LSR) equations were used to calculate estimates of body mass for three hominin species. This resulted in estimates of between 30 kg and 47 kg for Australopithecus africanus, 48 kg and 52 kg for Paranthropus robustus, and 75 kg for Homo neanderthalensis. It is proposed that regression equations derived for the order primates are used to estimate body mass for archaic hominins, while hominoid based equations are most suited for Homo.     

The mosasaur fossil record through the lens of fossil completeness

The quality of the fossil record affects our understanding of macroevolutionary patterns. Palaeodiversity is filtered through geological and human processes; efforts to correct for these biases are part of a debate concerning the role of sampling proxies and standardization in biodiversity models. We analyse the fossil record of mosasaurs in terms of fossil completeness as a measure of fossil quality, using three novel, correlating metrics of fossil completeness and 4083 specimens. A new qualitative measure of character completeness (QCM) correlates with the phylogenetic character completeness metric. Mean completeness by species decreases with specimen count; average completeness by substage varies significantly. Mean specimen completeness is higher for species‐named fossils than those identified to genus and family. We consider the effect of tooth‐only specimens. Importantly, we find that completeness of species does not correlate with completeness of specimens. Completeness varies by palaeogeography: North American specimens show higher completeness than those from Eurasia and Gondwana. These metrics can be used to identify exceptional preservation; specimen completeness varies significantly by both formation and lithology. The Belgian Ciply Formation displays the highest completeness; clay lithologies show higher completeness values. Neither species diversity nor sea level correlates significantly with fossil completeness. A generalized least squares (GLS) analysis using multiple variables agrees with this result, but reveals two variables with significant predictive value for modelling averaged diversity: sea level, and mosasaur and plesiosaur‐bearing formations (the latter is redundant with diversity). Mosasaur completeness is not driven by sea level, nor does completeness limit the mosasaur diversity signal.     

The illogical basis of phylogenetic nomenclature

The current advocacy for the so-called PhyloCode has a history rooted in twentieth-century arguments among biologists and philosophers regarding a putative distinction between classes and individuals. From this seemingly simple and innocuous discussion have come supposed distinctions between definitions and diagnosis, classification and systematization, and now Linnaean and “phylogenetic” nomenclature. Nevertheless, the metaphysical dichotomy of class versus individual, insofar as its standard applications to the issue of biological taxonomy are concerned, is an outdated remnant of early logical positivist thinking. Current views on natural kinds and their definitions under a scientific realist perspective provide grounds for rejecting the class versus individual dichotomy altogether insofar as biological entities are concerned. We review the role of natural kinds in scientific practice and the nature of definitions and scientific classifications. Although inherent instabilities of the PhyloCode are clearly sufficient to argue against the general application of this nominally phylogenetic system, our goal here is to address serious and fundamental flaws in its very foundation by exposing the unsubstantiated philosophical assumptions preceding and subtending it.

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Resumen  Las propuestas actuales en favor del llamado Código de Nomenclatura Filogenética (Phylo-Code) tienen una historia basada en argumentos desarrollados, durante el siglo veinte, por biólogos y filósofos sobre una distinción putativa entre clases e individuos. De esta simple y aparentemente inocua discusión han surgido supuestas distinciones entre definición y diagnosis, clasificación y sistematización, y ahora entre nomenclatura Lineana y “filogenética.” Sin embargo, la dicotomía metafísica clase contra individuo, al menos en lo concerniente a su aplicación estándar al tema de taxonomía biológica, es un remanente obsoleto del pensamiento positivista lógico. Opiniones actuales sobre categorías naturales y sus definiciones bajo la perspectiva del realismo científico proveen bases para rechazar por completo dicha dicotomía, al menos en lo que concierne a las entidades biológicas. En este artículo se revisa el papel de las categorías naturales en la práctica científica, y la naturaleza de las definiciones y la clasificación científica. Aún cuando la inestabilidad inherente en el Código de Nomenclatura Filogenética es claramente suficiente para argumentar contra la aplicación general de este sistema nominal filogenético, el objetivo de este artículo es mostrar las serias y fundamentales deficiencias en sus propias bases al exponer las suposiciones filosóficas sin fundamento que le preceden y sustentan.

     

The grapevine gene nomenclature system

Background

Grapevine (Vitis vinifera L.) is one of the most important fruit crops in the world and serves as a valuable model for fruit development in woody species. A major breakthrough in grapevine genomics was achieved in 2007 with the sequencing of the Vitis vinifera cv. PN40024 genome. Subsequently, data on structural and functional characterization of grape genes accumulated exponentially. To better exploit the results obtained by the international community, we think that a coordinated nomenclature for gene naming in species with sequenced genomes is essential. It will pave the way for the accumulation of functional data that will enable effective scientific discussion and discovery. The exploitation of data that were generated independently of the genome release is hampered by their heterogeneous nature and by often incompatible and decentralized storage. Classically, large amounts of data describing gene functions are only available in printed articles and therefore remain hardly accessible for automatic text mining. On the other hand, high throughput “Omics” data are typically stored in public repositories, but should be arranged in compendia to better contribute to the annotation and functional characterization of the genes.

Results

With the objective of providing a high quality and highly accessible annotation of grapevine genes, the International Grapevine Genome Project (IGGP) commissioned an international Super-Nomenclature Committee for Grape Gene Annotation (sNCGGa) to coordinate the effort of experts to annotate the grapevine genes. The goal of the committee is to provide a standard nomenclature for locus identifiers and to define conventions for a gene naming system in this paper.

Conclusions

Learning from similar initiatives in other plant species such as Arabidopsis, rice and tomato, a versatile nomenclature system has been developed in anticipation of future genomic developments and annotation issues. The sNCGGa’s first outreach to the grape community has been focused on implementing recommended guidelines for the expert annotators by: (i) providing a common annotation platform that enables community-based gene curation, (ii) developing a gene nomenclature scheme reflecting the biological features of gene products that is consistent with that used in other organisms in order to facilitate comparative analyses.     

The colour of fossil feathers

Feathers are complex integumentary appendages of birds and some other theropod dinosaurs. They are frequently coloured and function in camouflage and display. Previous investigations have concluded that fossil feathers are preserved as carbonized traces composed of feather-degrading bacteria. Here, an investigation of a colour-banded feather from the Lower Cretaceous Crato Formation of Brazil revealed that the dark bands are preserved as elongate, oblate carbonaceous bodies 1-2mum long, whereas the light bands retain only relief traces on the rock matrix. Energy dispersive X-ray analysis showed that the dark bands preserve a substantial amount of carbon, whereas the light bands show no carbon residue. Comparison of these oblate fossil bodies with the structure of black feathers from a living bird indicates that they are the eumelanin-containing melanosomes. We conclude that most fossil feathers are preserved as melanosomes, and that the distribution of these structures in fossil feathers can preserve the colour pattern in the original feather. The discovery of preserved melanosomes opens up the possibility of interpreting the colour of extinct birds and other dinosaurs.