Species: A History of the Idea

Our ability to investigate processes shaping the evolutionary diversification of corals (Cnidaria: Anthozoa) is limited by a lack of understanding of species boundaries. Discerning species of corals has been challenging due to a multitude of factors, including homoplasious and plastic morphological characters and the use of molecular markers that are either not informative or have not completely sorted. Hybridization can also blur species boundaries by leading to incongruence between morphology and genetics. We used traditional DNA barcoding and restriction-site associated DNA sequencing combined with coalescence-based and allele-frequency methods to elucidate species boundaries and simultaneously examine the potential role of hybridization in a speciose genus of octocoral, Sinularia. Species delimitations using two widely used DNA barcode markers, mtMutS and 28S rDNA, were incongruent with one another and with the morphospecies identifications. When mtMutS and 28S were concatenated, a 0.3% genetic distance threshold delimited the majority of morphospecies. In contrast, 12 of the 15 examined morphospecies formed well-supported monophyletic clades in both concatenated RAxML phylogenies and SNAPP species trees of > 6000 RADSeq loci. DAPC and Structure analyses also supported morphospecies assignments, but indicated the potential for two additional cryptic species. Three morphologically distinct species pairs could not, however, be distinguished genetically. ABBA-BABA tests demonstrated significant admixture between some of those species, suggesting that hybridization may confound species delimitation in Sinularia. A genomic approach can help to guide species delimitation while simultaneously elucidating the processes generating coral diversity. Results support the hypothesis that hybridization is an important mechanism in the evolution of Anthozoa, including octocorals, and future research should examine the contribution of this mechanism in generating diversity across the coral tree of life.

/pdf/a-next-generation-approach-to-species-delimitation-reveals-x3sa05tdui.pdf

A next generation approach to species delimitation reveals the role of hybridization in a cryptic species complex of corals.

Careful investigation of the form of animal signals can offer novel insights into their function. Here, we deconstruct the face patterns of a tribe of primates, the guenons (Cercopithecini), and examine the information that is potentially available in the perceptual dimensions of their multicomponent displays. Using standardized colour-calibrated images of guenon faces, we measure variation in appearance both within and between species. Overall face pattern was quantified using the computer vision ‘eigenface’ technique, and eyebrow and nose-spot focal traits were described using computational image segmentation and shape analysis. Discriminant function analyses established whether these perceptual dimensions could be used to reliably classify species identity, individual identity, age and sex, and, if so, identify the dimensions that carry this information. Across the 12 species studied, we found that both overall face pattern and focal trait differences could be used to categorize species and individuals reliably, whereas correct classification of age category and sex was not possible. This pattern makes sense, as guenons often form mixed-species groups in which familiar conspecifics develop complex differentiated social relationships but where the presence of heterospecifics creates hybridization risk. Our approach should be broadly applicable to the investigation of visual signal function across the animal kingdom.

/pdf/assessing-the-potential-information-content-of-3r740odc9f.pdf

Assessing the potential information content of multicomponent visual signals: a machine learning approach.

A study of Late Woodland projectile point typology in New York using elliptical Fourier outline analysis

Non-intrusive load monitoring methods aim to disaggregate the total power consumption of a household into individual appliances by analysing changes in the voltage and current measured at the grid connection point of the household. The goal is to identify the active appliances, based on their unique fingerprint. This information can be communicated to the electricity provider and the end-user enabling the potential of smart grids. An informative characteristic to attain the appliance classification is the voltage-current trajectory. In this paper, this trajectory is represented as a binary image from which the contours are extracted. From these contours, the elliptic Fourier descriptors are calculated and used as input for several classification algorithms outputting the appliance name. Benchmarking this method on the PLAID dataset shows that the descriptors can yield a prediction accuracy up to 79%, comparable to the state-of-the-art, based on only a very compact representation (12 numbers).

/pdf/automated-classification-of-appliances-using-elliptical-19gjzgemvb.pdf

Automated classification of appliances using elliptical fourier descriptors

Species descriptions of most alcyonacean oc- tocorals rely heavily on the morphology of sclerites, the calcium carbonate spicules embedded in the soft tissue. Sclerites provide taxonomic characters for species delinea- tion but require qualitative descriptions, which introduce ambiguities in recognizing morphological features. Ellipti- cal Fourier analysis of the outline of sclerites was used to quantify the morphology of eight species of gorgoniid oc- tocoral in the genus Pseudopterogorgia. Sclerites from one to seven colonies of each species were compared. Scaphoids and spindles were examined separately; rods and octoradi- ates were excluded from the analyses because of their morphologic similarity across all species. Discriminant analysis of elliptical Fourier descriptors (EFDs) was used to determine whether the elliptical Fourier analysis could be used to identify the specimens. Sclerites were highly vari- able even within a single colony. Correct species assign- ments of individual sclerites were greater than 50% for both scaphoids and spindles. Species assignments based on av- erages of the EFDs for each colony approached 90%. El- liptical Fourier analysis quantifies morphological differ- ences between species and measures colony variance in sclerite size and shape among colonies and species. Phylo- genetic analysis based on EFDs did not capture monophy- letic groups. The quantification of complex shapes such as sclerites provides an important tool in alpha taxonomy but may be less useful in phylogenetic analyses.

https://www.jstor.org/stable/info/23046947

Quantifying Complex Shapes: Elliptical Fourier Analysis of Octocoral Sclerites

Species level identification of octocorals is often based on the form of skeletal elements, the sclerites. Morphological variation in sclerites across and within habitats complicates both species delineation and the identification of specimens, both of which are essential for characterizing and understanding octocoral diversity. In order to quantify the effects of environmental plasticity on sclerite morphology, branches from the Caribbean gorgonian Antillogorgia bipinnata were removed from colonies at depths of 18 and 23 m and reciprocally transplanted between those sites and transplanted to an 8 m depth site for 7 months. Images of sclerites from those colonies were compared using elliptical Fourier analyses (EFA) of the sclerite outline. The length of scaphoids produced after transplantation was larger than those in older tissue, suggesting length was affected by the process of transplantation. Shape of scaphoids as detected in the EFA, differed between sites, and the reciprocal crosses suggest some of the difference was a plastic response to the environment. The results demonstrate the presence of some environmental plasticity in sclerite form. However, while detectable using EFA, the differences in form were not apparent in microscopical observations of the sclerites and thus would not affect identification of specimens nor traditional species delineation.

Joseph M. Carlo

Papers

Quantifying Complex Shapes: Elliptical Fourier Analysis of Octocoral Sclerites

Plasticity and conservatism in sclerites of a Caribbean octocoral