Shape outline extraction software (DiaOutline) for elliptic Fourier analysis application in morphometric studies

Morphometrics and Phylogenomics of Coca (Erythroxylum spp.) Illuminate Its Reticulate Evolution, With Implications for Taxonomy

South American coca (Erythroxylum coca and E. novogranatense) has been a keystone crop for many Andean and Amazonian communities for at least 8,000 years. However, over the last half-century, global demand for its alkaloid cocaine has driven intensive agriculture of this plant and placed it in the center of armed conflict and deforestation. To monitor the changing landscape of coca plantations, the United Nations Office on Drugs and Crime collects annual data on their areas of cultivation. However, attempts to delineate areas in which different varieties are grown have failed due to limitations around identification. In the absence of flowers, identification relies on leaf morphology, yet the extent to which this is reflected in taxonomy is uncertain. Here, we analyze the consistency of the current naming system of coca and its four closest wild relatives (the "coca clade"), using morphometrics, phylogenomics, molecular clocks, and population genomics. We include name-bearing type specimens of coca's closest wild relatives E. gracilipes and E. cataractarum. Morphometrics of 342 digitized herbarium specimens show that leaf shape and size fail to reliably discriminate between species and varieties. However, the statistical analyses illuminate that rounder and more obovate leaves of certain varieties could be associated with the subtle domestication syndrome of coca. Our phylogenomic data indicate extensive gene flow involving E. gracilipes which, combined with morphometrics, supports E. gracilipes being retained as a single species. Establishing a robust evolutionary-taxonomic framework for the coca clade will facilitate the development of cost-effective genotyping methods to support reliable identification.

A pre-Campanian Ignimbrite techno-cultural shift in the Aurignacian sequence of Grotta di Castelcivita, southern Italy

The Aurignacian is the first European technocomplex assigned to Homo sapiens recognized across a wide geographic extent. Although archaeologists have identified marked chrono-cultural shifts within the Aurignacian mostly by examining the techno-typological variations of stone and osseous tools, unraveling the underlying processes driving these changes remains a significant scientific challenge. Scholars have, for instance, hypothesized that the Campanian Ignimbrite (CI) super-eruption and the climatic deterioration associated with the onset of Heinrich Event 4 had a substantial impact on European foraging groups. The technological shift from the Protoaurignacian to the Early Aurignacian is regarded as an archaeological manifestation of adaptation to changing environments. However, some of the most crucial regions and stratigraphic sequences for testing these scenarios have been overlooked. In this study, we delve into the high-resolution stratigraphic sequence of Grotta di Castelcivita in southern Italy. Here, the Uluzzian is followed by three Aurignacian layers, sealed by the eruptive units of the CI. Employing a comprehensive range of quantitative methods-encompassing attribute analysis, 3D model analysis, and geometric morphometrics-we demonstrate that the key technological feature commonly associated with the Early Aurignacian developed well before the deposition of the CI tephra. Our study provides thus the first direct evidence that the volcanic super-eruption played no role in this cultural process. Furthermore, we show that local paleo-environmental proxies do not correlate with the identified patterns of cultural continuity and discontinuity. Consequently, we propose alternative research paths to explore the role of demography and regional trajectories in the development of the Upper Paleolithic.

Phylotranscriptomics reveals the reticulate evolutionary history of a widespread diatom species complex

In contrast to surveys based on a few genes that often provide limited taxonomic resolution, transcriptomes provide a wealth of genomic loci that can resolve relationships among taxonomically challenging lineages. Diatoms are a diverse group of aquatic microalgae that includes important bioindicator species and many such lineages. One example is Nitzschia palea, a widespread species complex with several morphologically defined taxonomic varieties, some of which are critical pollution indicators. Morphological differences among the varieties are subtle and phylogenetic studies based on a few genes fail to resolve their evolutionary relationships. We conducted morphometric and transcriptome analyses of 10 Nitzschia palea strains to resolve the relationships among strains and taxonomic varieties. Nitzschia palea was resolved into three clades, one of which corresponds to a group of strains with narrow linear-lanceolate valves. The other morphological group recovered in the shape outline analysis was not monophyletic and consisted of two clades. Gene-tree concordance analyses and phylogenetic network estimations revealed patterns of incomplete lineage sorting and gene flow between intraspecific lineages. We detected reticulated evolutionary patterns among lineages with different morphologies, resulting in a putative recent hybrid. Our study shows that phylogenomic analyses of unlinked nuclear loci, complemented with morphometrics, can resolve complex evolutionary histories of recently diverged species complexes.

The contribution of integrated 3D model analysis to Protoaurignacian stone tool design

Protoaurignacian foragers relied heavily on the production and use of bladelets. Techno-typological studies of these implements have provided insights into crucial aspects of cultural variability. However, new technologies have seldom been used to quantify patterns of stone tool design. Taking advantage of a new scanning protocol and open-source software, we conduct the first 3D analysis of a Protoaurignacian assemblage, focusing on the selection and modification of blades and bladelets. We study a large dataset of complete blanks and retouched tools from the early Protoaurignacian assemblage at Fumane Cave in northeastern Italy. Our main goal is to validate and refine previous techno-typological considerations employing a 3D geometric morphometrics approach complemented by 2D analysis of cross-section outlines and computation of retouch angle. The encouraging results show the merits of the proposed integrated approach and confirm that bladelets were the main focus of stone knapping at the site. Among modified bladelets, various retouching techniques were applied to achieve specific shape objectives. We suggest that the variability observed among retouched bladelets relates to the design of multi-part artifacts that need to be further explored via renewed experimental and functional studies.

Geometric Morphometrics of Bilateral Asymmetry in Eunotia bilunaris (Eunotiales, Bacillariophyceae) as a Tool for the Quantitative Assessment of Teratogenic Deviations in Frustule Shapes

A number of pennate diatom genera typically have teratogenic deformations of their siliceous frustules due to the effects of environmental stress, such as high concentrations of heavy metals and low pH. However, the quantitative assessment of these deformations has rarely been applied. One species in which aberrations have frequently been reported is Eunotia bilunaris, which typically has bilaterally symmetric frustules with dorso-ventral differentiation. In this study, we aimed to illustrate the geometric morphometric analysis of symmetry as a tool for assessing the severity of teratogenic deformations. These were quantified by Procrustes superimposition of equidistant points placed along the valvar outlines in pairs of configurations based on their bilateral reflection symmetry. The shape deformations were mostly confined to central parts of the ventral outlines and were captured both by the symmetric and asymmetric subspaces of the variation. The amount of bilateral asymmetry in individual cells was negatively related to frustule size via the allometric power law relationship, illustrating that asymmetry increased in the asexual diminution series. The presented analysis provides a framework for the quantitative assessment of frustule deformations in eunotioid diatoms that can be used for the comparative scoring of teratogenic deviations among cells, populations, or species.

Geometric morphometric analysis of spore shapes improves identification of fungi

Morphology of organisms is an essential source of evidence for taxonomic decisions and understanding of ecology and evolutionary history. The geometric structure (i.e., numeric description of shape) provides richer and mathematically different information about an organism's morphology than linear measurements. A little is known on how these two sources of morphological information (shape vs. size) contribute to the identification of organisms when implied simultaneously. This study hypothesized that combining geometric information on the outline with linear measurements results in better species identification than either evidence alone can provide. As a test system for our research, we used the microscopic spores of fungi from the genus Subulicystidium (Agaricomycetes, Basidiomycota). We analyzed 2D spore shape data via elliptic Fourier and principal component analyses. Using flexible discriminant analysis, we achieved the highest species identification success rate for a combination of shape and size descriptors (64.7%). The shape descriptors alone predicted species slightly better than size descriptors (61.5% vs. 59.1%). We conclude that adding geometric information on the outline to linear measurements improves the identification of the organisms. Despite the high relevance of spore traits for the taxonomy of fungi, they were previously rarely analyzed with the tools of geometric morphometrics. Therefore, we supplement our study with an open access protocol for digitizing and summarizing fungal spores' shape and size information. We propagate a broader use of geometric morphometric analysis for microscopic propagules of fungi and other organisms.

Morphological Analysis of Size and Shape (MASS): An integrative software program for morphometric analyses of leaves

PREMISE

Morphometric analysis is a common approach for comparing and categorizing botanical samples; however, completing a suite of analyses using existing tools may require a multi-stage, multi-program process. To facilitate streamlined analysis within a single program, Morphological Analysis of Size and Shape (MASS) for leaves was developed. Its utility is demonstrated using exemplar leaf samples from Acer saccharum, Malus domestica, and Lithospermum.

METHODS

Exemplar samples were obtained from across a single tree (Acer saccharum), three trees in the same species (Malus domestica), and online, digitized herbarium specimens (Lithospermum). MASS was used to complete simple geometric measurements of samples, such as length and area, as well as geometric morphological analyses including elliptical Fourier and Procrustes analyses. Principal component analysis (PCA) of data was also completed within the same program.

RESULTS

MASS is capable of making desired measurements and analyzing traditional morphometric data as well as landmark and outline data.

DISCUSSION

Using MASS, differences were observed among leaves of the three studied taxa, but only in Malus domestica were differences statistically significant or correlated with other morphological features. In the future, MASS could be applied for analysis of other two-dimensional organs and structures. MASS is available for download at https://github.com/gillianlynnryan/MASS.