Phylogenies, the Comparative Method, and the Conflation of Tempo and Mode

The comparison of mathematical models that represent alternative hypotheses about the tempo and mode of evolutionary change is a common approach for assessing the evolutionary processes underlying phenotypic diversification. However, because model parameters are estimated simultaneously, they are inextricably linked, such that changes in tempo, the pace of evolution, and mode, the manner in which evolution occurs, may be difficult to assess separately. This may potentially complicate biological interpretation, but the extent to which this occurs has not yet been determined. In this study, we examined 160 phylogeny × trait empirical datasets, and conducted extensive numerical phylogenetic simulations, to investigate the efficacy of phylogenetic comparative methods to distinguish between models that represent different evolutionary processes in a phylogenetic context. We observed that, in some circumstances, a high uncertainty exists when attempting to distinguish between alternative evolutionary scenarios underlying phenotypic variation. When examining datasets simulated under known conditions, we found that evolutionary inference is straightforward when phenotypic patterns are generated by simple evolutionary processes that are represented by modifying a single model parameter at a time. However, inferring the exact nature of the evolutionary process that has yielded phenotypic variation when facing complex, potentially more realistic, mechanisms is more problematic. A detailed investigation of the influence of different model parameters showed that changes in evolutionary rates, marked changes in phylogenetic means, or the existence of a strong selective pull on the data, are all readily recovered by phenotypic model comparison. However, under evolutionary processes with a milder restraining pull acting on trait values, alternative models representing very different evolutionary processes may exhibit similar goodness-of-fit to the data, potentially leading to the conflation of interpretations that emphasize tempo and mode during empirical evolutionary inference. This is a mathematical and conceptual property of the considered models that, while not prohibitive for studying phenotypic evolution, should be taken into account and addressed when appropriate

Comparing multiple criteria for species identification in two recently diverged seabirds

Correct species identification is a crucial issue in systematics with key implications for prioritising conservation effort. However, it can be particularly challenging in recently diverged species due to their strong similarity and relatedness. In such cases, species identification requires multiple and integrative approaches. In this study we used multiple criteria, namely plumage colouration, biometric measurements, geometric morphometrics, stable isotopes analysis (SIA) and genetics (mtDNA), to identify the species of 107 bycatch birds from two closely related seabird species, the Balearic (Puffinus mauretanicus) and Yelkouan (P. yelkouan) shearwaters. Biometric measurements, stable isotopes and genetic data produced two stable clusters of bycatch birds matching the two study species, as indicated by reference birds of known origin. Geometric morphometrics was excluded as a species identification criterion since the two clusters were not stable. The combination of plumage colouration, linear biometrics, stable isotope and genetic criteria was crucial to infer the species of 103 of the bycatch specimens. In the present study, particularly SIA emerged as a powerful criterion for species identification, but temporal stability of the isotopic values is critical for this purpose. Indeed, we found some variability in stable isotope values over the years within each species, but species differences explained most of the variance in the isotopic data. Yet this result pinpoints the importance of examining sources of variability in the isotopic data in a case-by-case basis prior to the cross-application of the SIA approach to other species. Our findings illustrate how the integration of several methodological approaches can help to correctly identify individuals from recently diverged species, as each criterion measures different biological phenomena and species divergence is not expressed simultaneously in all biological traits

Local segregation of realised niches in lizards

Species can occupy different realised niches when sharing the space with other congeneric species or when living in allopatry. Ecological niche models are powerful tools to analyse species niches and their changes over time and space. Analysing how species’ realised niches shift is paramount in ecology. Here, we examine the ecological realised niche of three species of wall lizards in six study areas: three areas where each species occurs alone; and three areas where they occur together in pairs. We compared the species’ realised niches and how they vary depending on species’ coexistence, by quantifying niche overlap between pairs of species or populations with the R package ecospat. For this, we considered three environmental variables (temperature, humidity, and wind speed) recorded at each lizard re-sighting location. Realised niches were very similar when comparing syntopic species occurring in the same study area. However, realised niches differed when comparing conspecific populations across areas. In each of the three areas of syntopy, the less abundant species shift its realised niche. Our study demonstrates that sympatry may shift species’ realised niche

Hybridization patterns between two marine snails, Littorina fabalis and L. obtusata

Characterizing the patterns of hybridization between closely related species is crucial to understand the role of gene flow in speciation. In particular, systems comprising multiple contacts between sister species offer an outstanding opportunity to investigate how reproductive isolation varies with environmental conditions, demography and geographic contexts of divergence. The flat periwinkles, Littorina obtusata and L. fabalis (Gastropoda), are two intertidal sister species with marked ecological differences compatible with late stages of speciation. Although hybridization between the two was previously suggested, its extent across the Atlantic shores of Europe remained largely unknown. Here, we combined genetic (microsatellites and mtDNA) and morphological data (shell and male genital morphology) from multiple populations of flat periwinkles in north‐western Iberia to assess the extent of current and past hybridization between L. obtusata and L. fabalis under two contrasting geographic settings of divergence (sympatry and allopatry). Hybridization signatures based on both mtDNA and microsatellites were stronger in sympatric sites, although evidence for recent extensive admixture was found in a single location. Misidentification of individuals into species based on shell morphology was higher in sympatric than in allopatric sites. However, despite hybridization, species distinctiveness based on this phenotypic trait together with male genital morphology remained relatively high. The observed variation in the extent of hybridization among locations provides a rare opportunity for future studies on the consequences of different levels of gene flow for reinforcement, thus informing about the mechanisms underlying the completion of speciation

Unravelling the phylogenetic and ecological drivers of beak shape variability in cephalopods

19 pages, 5 figures, 4 tables, supplementary Information https://doi.org/10.1007/s11160-022-09744-5.-- Data availability: Genetic data underlying this article are available in the GenBank Nucleotide Database at https://www.ncbi.nlm.nih.gov/genbank/ and can be accessed with the GenBank accession numbers OP151115-OP151122, OP161136-OP161143, OP235417-OP235424. The FastQ files can be accessed within the GenBank Nucleotide Database with the BioProject accession number PRJNA866317. Stable isotope and geometric morphometric data are available upon request from the corresponding author. Additional material is available in Supplementary files 1–3Cephalopod beaks are essential for prey acquisition and fragmentation during feeding. Thus, it is expected that ecological pressures affect cephalopod beak shape. From a practical perspective, these structures are also used to identify gut contents of marine megafauna, such as toothed whales, sharks, seabirds, and large pelagic fishes. Here, we investigated the relative importance of ecological pressures and phylogenetic relatedness in the evolution of beak shape using a wide range of Mediterranean cephalopod species. Phylogenetic analyses based on complete mitogenomes and nuclear ribosomal genes provided a well-supported phylogeny among the 18 included cephalopods. Geometric morphometric and stable isotope methods were implemented to describe interspecific beak shape and trophic niche variability, respectively. Phylogenetic signal was detected in the shape of both parts of the beak (upper and lower). However, lower beak shape was more distinct among closely related species, in line with the empirical notion that lower beak morphology is more useful as an identification tool in cephalopods. Interestingly, no association between beak shape and trophic niche (stable isotope values) was found. These results suggest that the evolution of cephalopod beak shape as quantified here is mainly driven by phylogenetic relationships, while feeding habits play a minor roleWe are thankful to the crew of the projects SAP (ARP029/18/00003, Departament d'Acció Climàtica, Alimentació i Agenda Rural, Generalitat de Catalunya), to BITER, OCTOSET and ECOPHYN (PID2020-114732RB-C31, RTI2018-097908-B-I00 and PID2021-126824NB-C32 respectively, Ministerio de Ciencia e Innovación, Gobierno de España) for granting the access to the samples and to Núria Lombarte Recasens for the illustrations provided of the beaks and major taxonomic groups. This study is part of the Master thesis of A.S.-M., who was supported by a JAE-Intro grant of CSIC (JAEIntro2020-ICM-2). F.Á.F.-Á. was supported by an Irish Research Council–Government of Ireland Postdoctoral Fellowship Award (ref. GOIPD/2019/460) and a JdC-I Postdoctoral Fellowship Grant (ref. IJC2020-043170-I) awarded by MCIN/AEI/10.13039/501100011033 and the European Union NextGenerationEU/PRTR. A.K. is supported by a Ramón y Cajal research grant co-funded by the Spanish State Research Agency and the European Social Fund (RYC2019-026688-I/AEI/10.13039/501100011033). M.T. was funded by a Ph.D. fellowship from the Irish Research Council (GOIPG/2017/1740) and was supported by the Dr. Tony Ryan Research Fund. This research was supported by the Spanish government through the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S). [...] Open Access funding provided thanks to the CRUE-CSIC agreement with Springer NaturePeer reviewe

Evaluating taxonomic inflation: towards evidence-based species delimitation in Eurasian vipers (Serpentes: Viperinae)

International audienceThe designation of taxonomic units has important implications for the understanding and conservation ofbiodiversity. Eurasian vipers are a monophyletic group of viperid snakes (Serpentes, Viperinae), currently comprising fourgenera (Daboia, Macrovipera, Montivipera and Vipera) and up to 40 species. Taxonomic units have been described usinga wide variety of methods and criteria, and consequently, considerable controversy still surrounds the validity of somecurrently listed species. In order to promote a consensus- and evidence-based taxonomy of Eurasian vipers, we analysedpublished mitochondrial and nuclear DNA sequences for this group to reconstruct phylogenetic relationships among currentlyrecognized viper species.We also compiled information on external morphology to assess their morphological distinctiveness.Phylogenetic inference based on mtDNA sequences shows contrasting levels of divergence across genera and species andidentifies several instances of non-monophyly in described species. Nuclear DNA sequences show extremely low levels ofgenetic variation, with a widespread pattern of allele sharing among distant species, and even among genera. Revision ofmorphological data shows that most species designations rely on scalation traits that overlap extensively among species ofthe same genus. Based on our combined assessment, we recognize 15 taxa as valid species, three taxa which likely representspecies complexes, 17 taxa of doubtful validity as species, and five taxa for which species status is maintained but furtherresearch is highly recommended to assess taxonomic arrangements. We stress the need to implement integrative taxonomicapproaches for the recognition of evidence-based taxonomic units in Eurasian viper

Reacquisition of the lower temporal bar in sexually dimorphic fossil lizards provides a rare case of convergent evolution

Temporal fenestration has long been considered a key character to understand relationships amongst reptiles. In particular, the absence of the lower temporal bar (LTB) is considered one of the defining features of squamates (lizards and snakes). In a re-assessment of the borioteiioid lizard Polyglyphanodon sternbergi (Cretaceous, North America), we detected a heretofore unrecognized ontogenetic series, sexual dimorphism (a rare instance for Mesozoic reptiles), and a complete LTB, a feature only recently recognized for another borioteiioid, Tianyusaurus zhengi (Cretaceous, China). A new phylogenetic analysis (with updates on a quarter of the scorings for P. sternbergi) indicates not only that the LTB was reacquired in squamates, but it happened independently at least twice. An analysis of the functional significance of the LTB using proxies indicates that, unlike for T. zhengi, this structure had no apparent functional advantage in P. sternbergi, and it is better explained as the result of structural constraint release. The observed canalization against a LTB in squamates was broken at some point in the evolution of borioteiioids, whereas never re-occuring in other squamate lineages. This case of convergent evolution involves a mix of both adaptationist and structuralist causes, which is unusual for both living and extinct vertebrates

Molecular phylogeny and timing of diversification in Alpine Rhithrogena (Ephemeroptera: Heptageniidae).

BACKGROUND: Larvae of the Holarctic mayfly genus Rhithrogena Eaton, 1881 (Ephemeroptera, Heptageniidae) are a diverse and abundant member of stream and river communities and are routinely used as bio-indicators of water quality. Rhithrogena is well diversified in the European Alps, with a number of locally endemic species, and several cryptic species have been recently detected. While several informal species groups are morphologically well defined, a lack of reliable characters for species identification considerably hampers their study. Their relationships, origin, timing of speciation and mechanisms promoting their diversification in the Alps are unknown. RESULTS: Here we present a species-level phylogeny of Rhithrogena in Europe using two mitochondrial and three nuclear gene regions. To improve sampling in a genus with many cryptic species, individuals were selected for analysis according to a recent DNA-based taxonomy rather than traditional nomenclature. A coalescent-based species tree and a reconstruction based on a supermatrix approach supported five of the species groups as monophyletic. A molecular clock, mapped on the most resolved phylogeny and calibrated using published mitochondrial evolution rates for insects, suggested an origin of Alpine Rhithrogena in the Oligocene/Miocene boundary. A diversification analysis that included simulation of missing species indicated a constant speciation rate over time, rather than any pronounced periods of rapid speciation. Ancestral state reconstructions provided evidence for downstream diversification in at least two species groups. CONCLUSIONS: Our species-level analyses of five gene regions provide clearer definitions of species groups within European Rhithrogena. A constant speciation rate over time suggests that the paleoclimatic fluctuations, including the Pleistocene glaciations, did not significantly influence the tempo of diversification of Alpine species. A downstream diversification trend in the hybrida and alpestris species groups supports a previously proposed headwater origin hypothesis for aquatic insects