Issues and Perspectives in Species Delimitation using Phenotypic Data: Atlantean Evolution in Darwin's Finches

Integrative Taxonomy for Species Delimitation: A Case Study in Two Widely Accepted Yet Morphologically Confounding Rosa Species Within Sect. Pimpinellifoliae (Rosaceae)

The use of morphological traits as a practical approach for delimiting taxa at various ranks has long been regarded as a reliable basis for taxonomy. However, its efficacy has been increasingly called into question in many taxonomic groups due to its inherent limitations, such as failing to account for phenotypic plasticity, ecologically driven variation (e.g., ecotypes), and parallel evolution. These factors often introduce ambiguity or misleading similarities, thereby obscuring the true evolutionary relationships among taxa, particularly in the context of species delimitation. In the present study, we employ an integrated methodology that combines quantitative morphological analyses, whole-genome data, and ecological measurements to resolve the species boundaries of two morphologically similar roses, Rosa sericea and Rosa hugonis, which have long been considered as two distinct species but lack clear morphological boundaries. Our findings reveal that the unbiased analysis of morphological data based on a large and representative sample size was insufficient to identify effective diagnostic traits. However, when complemented with genome-wide population-level sequencing data or integrated with geographic and ecological niche assessments, the delineation of species boundaries was significantly improved. Furthermore, ecological data provide additional insight into the abiotic factors driving interspecific and intraspecific divergence. By integrating multiple lines of evidence-spanning genomic (intrinsic) and phenotypic (extrinsic) traits-and incorporating the interaction between species and their environments, species boundaries can be delineated with greater confidence. A well-defined species can thus be established through the mutual corroboration of diverse datasets, thereby ensuring a more rigorous and comprehensive taxonomic framework.

The role of leaf and root functional traits in the Espeletiinae (Asteraceae) radiation

PREMISE

Key innovations within a group result in ecological divergence. Those innovations involve functional traits that may reflect the species' adaptations to environmental conditions and to interactions within the community. The subtribe Espeletiinae is considered an adaptive radiation due to their exceptional diversity. In this study, we explored the role that functional traits have in this radiation.

METHODS

Nine functional traits (leaf and root) were measured in co-occurring species of five páramo complexes in Colombia. We used a principal component analysis to understand the climatic differences between complexes and to define the functional space of the species. Welch's ANOVA and t-test were used to unveil significant differences among co-occurring species. We also used normal mixture models (NMMs) to reassemble species based on the functional trait data.

RESULTS

Páramo complexes were partially separated in climatic conditions of temperature and precipitation. Leaf traits exhibited more significant differences among co-occurring species within each complex compared to root traits. Espeletia glandulosa was the only species that showed a species-specific combination of traits and formed a cluster in the NMM analysis.

CONCLUSIONS

There is a more pronounced variation in leaf traits among co-occurring species, suggesting a potential ecological diversity driver. We propose that there is convergence and stabilization of traits, given the colonization of similar habitats by species belonging to Espeletiinae. We highlight the need for studying the role of other functional traits in the ecological differentiation of species within this group to elucidate how they coexist and cope with environmental conditions of the páramo.

Tracing evolutionary trajectories in the presence of gene flow in South American temperate lizards (Squamata: Liolaemus kingii group)

Evolutionary processes behind lineage divergence often involve multidimensional differentiation. However, in the context of recent divergences, the signals exhibited by each dimension may not converge. In such scenarios, incomplete lineage sorting, gene flow, and scarce phenotypic differentiation are pervasive. Here, we integrated genomic (RAD loci of 90 individuals), phenotypic (linear and geometric traits of 823 and 411 individuals, respectively), spatial, and climatic data to reconstruct the evolutionary history of a speciation continuum of liolaemid lizards (Liolaemus kingii group). Specifically, we (a) inferred the population structure of the group and contrasted it with the phenotypic variability; (b) assessed the role of postdivergence gene flow in shaping phylogeographic and phenotypic patterns; and (c) explored ecogeographic drivers of diversification across time and space. We inferred eight genomic clusters exhibiting leaky genetic borders coincident with geographic transitions. We also found evidence of postdivergence gene flow resulting in transgressive phenotypic evolution in one species. Predicted ancestral niches unveiled suitable areas in southern and eastern Patagonia during glacial and interglacial periods. Our study underscores integrating different data and model-based approaches to determine the underlying causes of diversification, a challenge faced in the study of recently diverged groups. We also highlight Liolaemus as a model system for phylogeographic and broader evolutionary studies.

Morphological variability or inter-observer bias? A methodological toolkit to improve data quality of multi-researcher datasets for the analysis of morphological variation

OBJECTIVES

The investigation of morphological variation in animals is widely used in taxonomy, ecology, and evolution. Using large datasets for meta-analyses has dramatically increased, raising concerns about dataset compatibilities and biases introduced by contributions of multiple researchers.

MATERIALS AND METHODS

We compiled morphological data on 13 variables for 3073 individual mouse lemurs (Cheirogaleidae, Microcebus spp.) from 25 taxa and 153 different sampling locations, measured by 48 different researchers. We introduced and applied a filtering pipeline and quantified improvements in data quality (Shapiro-Francia statistic, skewness, and excess kurtosis). The filtered dataset was then used to test for genus-wide sexual size dimorphism and the applicability of Rensch's, Allen's, and Bergmann's rules.

RESULTS

Our pipeline reduced inter-observer bias (i.e., increased normality of data distributions). Inter-observer reliability of measurements was notably variable, highlighting the need to reduce data collection biases. Although subtle, we found a consistent pattern of sexual size dimorphism across Microcebus, with females being the larger (but not heavier) sex. Sexual size dimorphism was isometric, providing no support for Rensch's rule. Variations in tail length but not in ear size were consistent with the predictions of Allen's rule. Body mass and length followed a pattern contrary to predictions of Bergmann's rule.

DISCUSSION

We highlighted the usefulness of large multi-researcher datasets for testing ecological hypotheses after correcting for inter-observer biases. Using genus-wide tests, we outlined generalizable patterns of morphological variability across all mouse lemurs. This new methodological toolkit aims to facilitate future large-scale morphological comparisons for a wide range of taxa and applications.

Speciation-by-Extinction

Extinction is a dominant force shaping patterns of biodiversity through time; however its role as a catalyst of speciation through its interaction with intraspecific variation has been overlooked. Here, we synthesize ideas alluded to by Darwin and others into the model of "speciation-by-extinction" in which speciation results from the extinction of intermediate populations within a single geographically variable species. We explore the properties and distinguishing features of speciation-by-extinction with respect to other established speciation models. We demonstrate its plausibility by showing that the experimental extinction of populations within variable species can result in speciation. The prerequisites for speciation-by-extinction, geographically structured intraspecific variation and local extinction, are ubiquitous in nature. We propose that speciation-by-extinction may be a prevalent, but underappreciated, speciation mechanism.

Biogeography and the evolution of acoustic communication in the polyploid North American grey treefrog complex

After polyploid species are formed, interactions between diploid and polyploid lineages may generate additional diversity in novel cytotypes and phenotypes. In anurans, mate choice by acoustic communication is the primary method by which individuals identify their own species and assess suitable mates. As such, the evolution of acoustic signals is an important mechanism for contributing to reproductive isolation and diversification in this group. Here, we estimate the biogeographical history of the North American grey treefrog complex, consisting of the diploid Hyla chrysoscelis and the tetraploid Hyla versicolor, focusing specifically on the geographical origin of whole genome duplication and the expansion of lineages out of glacial refugia. We then test for lineage-specific differences in mating signals by applying comparative methods to a large acoustic data set collected over 52 years that includes >1500 individual frogs. Along with describing the overall biogeographical history and call diversity, we found evidence that the geographical origin of H. versicolor and the formation of the midwestern polyploid lineage are both associated with glacial limits, and that the southwestern polyploid lineage is associated with a shift in acoustic phenotype relative to the diploid lineage with which they share a mitochondrial lineage. In H. chrysoscelis, we see that acoustic signals are largely split by Eastern and Western lineages, but that northward expansion along either side of the Appalachian Mountains is associated with further acoustic diversification. Overall, results of this study provide substantial clarity on the evolution of grey treefrogs as it relates to their biogeography and acoustic communication.

Improving species delimitation for effective conservation: a case study in the endemic maple-leaf oak (Quercus acerifolia)

Species delimitation is challenging in lineages that exhibit both high plasticity and introgression. This challenge can be compounded by collection biases, which may downweight specimens morphologically intermediate between traditional species. Additionally, mismatch between named species and observable phenotypes can compromise species conservation. We studied the species boundaries of Quercus acerifolia, a tree endemic to Arkansas, U.S. We performed morphometric analyses of leaves and acorns from 527 field and 138 herbarium samples of Q. acerifolia and its close relatives, Q. shumardii and Q. rubra. We employed two novel approaches: sampling ex situ collections to detect phenotypic plasticity caused by environmental variation and comparing random field samples with historical herbarium samples to identify collection biases that might undermine species delimitation. To provide genetic evidence, we also performed molecular analyses on genome-wide SNPs. Quercus acerifolia shows distinctive morphological, ecological, and genomic characteristics, rejecting the hypothesis that Q. acerifolia is a phenotypic variant of Q. shumardii. We found mismatches between traditional taxonomy and phenotypic clusters. We detected underrepresentation of morphological intermediates in herbarium collections, which may bias species discovery and recognition. Rare species conservation requires considering and addressing taxonomic problems related to phenotypic plasticity, mismatch between taxonomy and morphological clusters, and collection biases.

Sniffing out Stingray Noses: The Functional Morphology of Batoid Olfaction

Batoid fishes (rays, skates, sawfishes, and guitarfishes) are macrosmatic, meaning they rely on their sense of smell as one of the primary senses for survival and reproduction. Olfaction is important for long-distance tracking and navigation, predator and prey recognition, and conspecific signaling. However, the mechanisms by which batoids harness odorants is unknown. Without a direct pump-like system, it is hypothesized that batoids irrigate their nostrils via one or a combination of the following: the motion pump, buccopharyngeal pump, pressure (ex. pitot-like mechanism), or a shearing force (ex. viscous entrainment). These mechanisms rely on the size, shape, and position of the nostrils with respect to the head and to each other. Batoids are united as a group by their dorsoventrally compressed body plans, with nostrils on the ventral side of their body. This position presents several challenges for odor capture and likely limits the effectivity of the motion pump. Batoid fishes display an expansive nasal morphology, with inlet nostrils ranging from thin, vertical slits to wide, horizontal ovals to protruding, tube-like funnels, and more. In this paper, a morphometric model is developed to quantify the vast diversity in batoid nose shapes, sizes, and positions on the head in an ecological and functional framework. Specifically, swimming mode, lifestyle, habitat, and diet are examined for correlations with observed nasal morphotypes. Morphometric measurements were taken on all 4 orders present in Batoidea to broadly encompass batoid nasal diversity (Rhinopristiformes 4/5 families; Rajiformes 2/4 families; Torpediniformes 4/4 families; Myliobatiformes 8/11 families). All batoid external nasal diversity was found to be categorized into 5 major morphological groups and were termed: flush nare [circle, comma, intermediate], open nare, and protruding nare. Several morphometric traits remained significant when accounting for shared ancestry, including the position and angle of the nostril on the head, the width of the inlet hole, and the spacing of the nostrils from each other. These measurements were found to be closely correlated and statistically significant with the swimming mode of the animal. This study provides the first crucial step in understanding batoid olfaction, by understanding the diversity of the morphology of the system. Because odor capture is a strictly hydrodynamic process, it may be that factors relating more directly to the fluid dynamics (i.e., swimming mode, velocity, Reynolds number) may be more important in shaping the evolution of the diversity of batoid noses than other ecological factors like habitat and diet.

An integrative genomic and phenomic analysis to investigate the nature of plant species in Escallonia (Escalloniaceae)

What we mean by species and whether they have any biological reality has been debated since the early days of evolutionary biology. Some biologists even suggest that plant species are created by taxonomists as a subjective, artificial division of nature. However, the nature of plant species has been rarely tested critically with data while ignoring taxonomy. We integrate phenomic and genomic data collected across hundreds of individuals at a continental scale to investigate this question in Escallonia (Escalloniaceae), a group of plants which includes 40 taxonomic species (the species proposed by taxonomists). We first show that taxonomic species may be questionable as they match poorly to patterns of phenotypic and genetic variation displayed by individuals collected in nature. We then use explicit statistical methods for species delimitation designed for phenotypic and genomic data, and show that plant species do exist in Escallonia as an objective, discrete property of nature independent of taxonomy. We show that such species correspond poorly to current taxonomic species (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$< 20\%$$\end{document}<20%) and that phenomic and genomic data seldom delimit congruent entities (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$< 20\%$$\end{document}<20%). These discrepancies suggest that evolutionary forces additional to gene flow can maintain the cohesion of species. We propose that phenomic and genomic data analyzed on an equal footing build a broader perspective on the nature of plant species by helping delineate different ‘types of species’. Our results caution studies which take the accuracy of taxonomic species for granted and challenge the notion of plant species without empirical evidence. Note: A version of the complete manuscript in Spanish is available in the Supplemental Materials.

Revisiting the hyperdominance of Neotropical tree species under a taxonomic, functional and evolutionary perspective

Recent studies have leveraged large datasets from plot-inventory networks to report a phenomenon of hyperdominance in Amazonian tree communities, concluding that few species are common and many are rare. However, taxonomic hypotheses may not be consistent across these large plot networks, potentially masking cryptic diversity and threatened rare taxa. In the current study, we have reviewed one of the most abundant putatively hyperdominant taxa, Protium heptaphyllum (Aubl.) Marchand (Burseraceae), long considered to be a taxonomically difficult species complex. Using morphological, genomic, and functional data, we present evidence that P. heptaphyllum sensu lato may represent eight separately evolving lineages, each warranting species status. Most of these lineages are geographically restricted, and few if any of them could be considered hyperdominant on their own. In addition, functional trait data are consistent with the hypothesis that trees from each lineage are adapted to distinct soil and climate conditions. Moreover, some of the newly discovered species are rare, with habitats currently experiencing rapid deforestation. We highlight an urgent need to improve sampling and methods for species discovery in order to avoid oversimplified assumptions regarding diversity and rarity in the tropics and the implications for ecosystem functioning and conservation.

Speciation and gene flow across an elevational gradient in New Guinea kingfishers

Closely related species with parapatric elevational ranges are ubiquitous in tropical mountains worldwide. The gradient speciation hypothesis proposes that these series are the result of in situ ecological speciation driven by divergent selection across elevation. Direct tests of this scenario have been hampered by the difficulty inferring the geographic arrangement of populations at the time of divergence. In cichlids, sticklebacks and Timema stick insects, support for ecological speciation driven by other selective pressures has come from demonstrating parallel speciation, where divergence proceeds independently across replicated environmental gradients. Here, we take advantage of the unique geography of the island of New Guinea to test for parallel gradient speciation in replicated populations of Syma kingfishers that show extremely subtle differentiation across elevation and between historically isolated mountain ranges. We find that currently described high-elevation and low-elevation species have reciprocally monophyletic gene trees and form nuclear DNA clusters, rejecting this hypothesis. However, demographic modelling suggests selection has likely maintained species boundaries in the face of gene flow following secondary contact. We compile evidence from the published literature to show that although in situ gradient speciation in labile organisms such as birds appears rare, divergent selection and post-speciation gene flow may be an underappreciated force in the origin of elevational series and tropical beta diversity along mountain slopes.

Species delimitation in the cyanolichen genus Rostania

Background

In this study, we investigate species limits in the cyanobacterial lichen genus Rostania (Collemataceae, Peltigerales, Lecanoromycetes). Four molecular markers (mtSSU rDNA, β-tubulin, MCM7, RPB2) were sequenced and analysed with two coalescent-based species delimitation methods: the Generalized Mixed Yule Coalescent model (GMYC) and a Bayesian species delimitation method (BPP) using a multispecies coalescence model (MSC), the latter with or without an a priori defined guide tree.

Results

Species delimitation analyses indicate the presence of eight strongly supported candidate species. Conclusive correlation between morphological/ecological characters and genetic delimitation could be found for six of these. Of the two additional candidate species, one is represented by a single sterile specimen and the other currently lacks morphological or ecological supporting evidence.

Conclusions

We conclude that Rostania includes a minimum of six species: R. ceranisca, R. multipunctata, R. occultata 1, R. occultata 2, R. occultata 3, and R. occultata 4,5,6. Three distinct Nostoc morphotypes occur in Rostania, and there is substantial correlation between these morphotypes and Rostania thallus morphology.

A morphometric assessment of species boundaries in a widespread anole lizard (Squamata: Dactyloidae)

Cryptic species – genetically distinct species that are morphologically difficult to distinguish – present challenges to systematists. Operationally, cryptic species are very difficult to identify and sole use of genetic data or morphological data can fail to recognize evolutionarily isolated lineages. We use morphometric data to test species boundaries hypothesized with genetic data in the North Caribbean bark anole (Anolis distichus), a suspected species complex. We use univariate and multivariate analyses to test if candidate species based on genetic data can be accurately diagnosed. We also test alternative species delimitation scenarios with a model fitting approach that evaluates normal mixture models capable of identifying morphological clusters. Our analyses reject the hypothesis that the candidate species are diagnosable. Neither uni- nor multivariate morphometric data distinguish candidate species. The best-supported model included two morphological clusters; however, these clusters were uneven and did not align with a plausible species divergence scenario. After removing two related traits driving this result, only one cluster was supported. Despite substantial differentiation revealed by genetic data, we recover no new evidence to delimit species and refrain from taxonomic revision. This study highlights the importance of considering other types of data along with molecular data when delimiting species.

Interdependent Phenotypic and Biogeographic Evolution Driven by Biotic Interactions

Biotic interactions are hypothesized to be one of the main processes shaping trait and biogeographic evolution during lineage diversification. Theoretical and empirical evidence suggests that species with similar ecological requirements either spatially exclude each other, by preventing the colonization of competitors or by driving coexisting populations to extinction, or show niche divergence when in sympatry. However, the extent and generality of the effect of interspecific competition in trait and biogeographic evolution has been limited by a dearth of appropriate process-generating models to directly test the effect of biotic interactions. Here, we formulate a phylogenetic parametric model that allows interdependence between trait and biogeographic evolution, thus enabling a direct test of central hypotheses on how biotic interactions shape these evolutionary processes. We adopt a Bayesian data augmentation approach to estimate the joint posterior distribution of trait histories, range histories, and coevolutionary process parameters under this analytically intractable model. Through simulations, we show that our model is capable of distinguishing alternative scenarios of biotic interactions. We apply our model to the radiation of Darwin’s finches—a classic example of adaptive divergence—and find limited support for in situ trait divergence in beak size, but stronger evidence for convergence in traits such as beak shape and tarsus length and for competitive exclusion throughout their evolutionary history. These findings are more consistent with presympatric, rather than postsympatric, niche divergence. Our modeling framework opens new possibilities for testing more complex hypotheses about the processes underlying lineage diversification. More generally, it provides a robust probabilistic methodology to model correlated evolution of continuous and discrete characters. [Bayesian; biotic interactions; competition; data augmentation; historical biogeography; trait evolution.]

Species boundaries in the human pathogen Paracoccidioides

The use of molecular taxonomy for identifying recently diverged species has transformed the study of speciation in fungi. The pathogenic fungus Paracoccidioides spp has been hypothesized to be composed of five phylogenetic species, four of which compose the brasiliensis species complex. Nuclear gene genealogies support this divergence scenario, but mitochondrial loci do not; while all species from the brasiliensis complex are differentiated at nuclear coding loci, they are not at mitochondrial loci. We addressed the source of this incongruity using 11 previously published gene fragments, 10 newly-sequenced nuclear non-coding loci, and 10 microsatellites. We hypothesized and further demonstrated that the mito-nuclear incongruence in the brasiliensis species complex results from interspecific hybridization and mitochondrial introgression, a common phenomenon in eukaryotes. Additional population genetic analyses revealed possible nuclear introgression but much less than that seen in the mitochondrion. Our results are consistent with a divergence scenario of secondary contact and subsequent mitochondrial introgression despite the continued persistence of species boundaries. We also suggest that yeast morphology slightly-but significantly-differs across all five Paracoccidioides species and propose to elevate four of these phylogenetic species to formally described taxonomic species.