Systematic Biology最新文献

Eyes within the marine gastropod superfamily Stromboidea range widely in size, from 0.2 to 2.3 mm-the largest eyes known in any gastropod. Despite this interesting variation, the underlying evolutionary pressures remain unknown. Here, we use the wealth of material available in museum collections to explore the evolution of stromboid eye size and structure. Our results suggest that depth is a key light-limiting factor in stromboid eye evolution; here, increasing water depth is correlated with increasing aperture width relative to lens diameter, and therefore an increasing investment in sensitivity in dim light environments. In the major clade containing all large-eyed stromboid families, species observed active during the day and the night had wider eye apertures relative to lens sizes than species observed active during the day only, thereby prioritizing sensitivity over resolution. Species with no consistent diel activity pattern also had smaller body sizes than exclusively day-active species, which may suggest that smaller animals are more vulnerable to shell-crushing predators, and avoid the higher predation pressure experienced by animals active during the day. Within the same major clade, ancestral state reconstruction suggests that absolute eye size increased above 1 mm twice. The unresolved position of Varicospira, however, weakens this hypothesis and further work with additional markers is needed to confirm this result.

Popular comparative phylogenetic models such as Brownian Motion, Ornstein-Ulhenbeck, and their extensions assume that, at speciation, a trait value is inherited identically by 2 descendant species. This assumption contrasts with models of speciation at a micro-evolutionary scale where descendants' phenotypic distributions are sub-samples of the ancestral distribution. Different speciation mechanisms can lead to a displacement of the ancestral phenotypic mean among descendants and an asymmetric inheritance of the ancestral phenotypic variance. In contrast, even macro-evolutionary models that account for intraspecific variance assume symmetrically conserved inheritance of ancestral phenotypic distribution at speciation. Here, we develop an Asymmetric Brownian Motion model (ABM) that relaxes the assumption of symmetric and conserved inheritance of the ancestral distribution at the time of speciation. The ABM jointly models the evolution of both intra- and inter-specific phenotypic variation. It also infers the mode of phenotypic inheritance at speciation, which can range from a symmetric and conserved inheritance, where descendants inherit the ancestral distribution, to an asymmetric and displaced inheritance, where descendants inherit divergent phenotypic means and variances. To demonstrate this model, we analyze the evolution of beak morphology in Darwin finches, finding evidence of displacement at speciation. The ABM model helps to bridge micro- and macro-evolutionary models of trait evolution by providing a more robust framework for testing the effects of ecological speciation, character displacement, and niche partitioning on trait evolution at the macro-evolutionary scale.

Despite their extensive diversity and ecological importance, the history of diversification for most groups of parasitic organisms remains relatively understudied. Elucidating broad macroevolutionary patterns of parasites is challenging, often limited by the availability of samples, genetic resources, and knowledge about ecological relationships with their hosts. In this study, we explore the macroevolutionary history of parasites by focusing on parasitic body lice from doves. Building on extensive knowledge of ecological relationships and previous phylogenomic studies of their avian hosts, we tested specific questions about the evolutionary origins of the body lice of doves, leveraging whole genome data sets for phylogenomics. Specifically, we sequenced whole genomes from 68 samples of dove body lice, including representatives of all body louse genera from 51 host taxa. From these data, we assembled > 2300 nuclear genes to estimate dated phylogenetic relationships among body lice and several outgroup taxa. The resulting phylogeny of body lice was well supported, although some branches had conflicting signals across the genome. We then reconstructed ancestral biogeographic ranges of body lice and compared the body louse phylogeny to the phylogeny of doves, and also to a previously published phylogeny of the wing lice of doves. Divergence estimates placed the origin of body lice in the late Oligocene. Body lice likely originated in Australasia and dispersed with their hosts during the early Miocene, with subsequent codivergence and host switching throughout the world. Notably, this evolutionary history is very similar to that of dove wing lice, despite the stronger dispersal capabilities of wing lice compared to body lice. Our results highlight the central role of the biogeographic history of host organisms in driving the evolutionary history of their parasites across time and geographic space.

The nine-banded armadillo (Dasypus novemcinctus) is the most widespread xenarthran species across the Americas. Recent studies have suggested it is composed of 4 morphologically and genetically distinct lineages of uncertain taxonomic status. To address this issue, we used a museomic approach to sequence 80 complete mitogenomes and capture 997 nuclear loci for 71 Dasypus individuals sampled across the entire distribution. We carefully cleaned up potential genotyping errors and cross-contaminations that could blur species boundaries by mimicking gene flow. Our results unambiguously support 4 distinct lineages within the D. novemcinctus complex. We found cases of mito-nuclear phylogenetic discordance but only limited contemporary gene flow confined to the margins of the lineage distributions. All available evidence including the restricted gene flow, phylogenetic reconstructions based on both mitogenomes and nuclear loci, and phylogenetic delimitation methods consistently supported the 4 lineages within D. novemcinctus as 4 distinct species. Comparable genetic differentiation values to other recognized Dasypus species further reinforced their status as valid species. Considering congruent morphological results from previous studies, we provide an integrative taxonomic view to recognize 4 species within the D. novemcinctus complex: D. novemcinctus, D. fenestratus, D. mexicanus, and D. guianensis sp. nov., a new species endemic of the Guiana Shield that we describe here. The 2 available individuals of D. mazzai and D. sabanicola were consistently nested within D. novemcinctus lineage and their status remains to be assessed. The present work offers a case study illustrating the power of museomics to reveal cryptic species diversity within a widely distributed and emblematic species of mammals.

Due to the hierarchical structure of the tree of life, closely related species often resemble each other more than distantly related species; a pattern termed phylogenetic signal. Numerous univariate statistics have been proposed as measures of phylogenetic signal for single phenotypic traits, but the study of phylogenetic signal for multivariate data, as is common in modern biology, remains challenging. Here, we introduce a new method to explore phylogenetic signal in multivariate phenotypes. Our approach decomposes the data into linear combinations with maximal (or minimal) phylogenetic signal, as measured by Blomberg's K. The loading vectors of these phylogenetic components or K-components can be biologically interpreted, and scatterplots of the scores can be used as a low-dimensional ordination of the data that maximally (or minimally) preserves phylogenetic signal. We present algebraic and statistical properties, along with 2 new summary statistics, KA and KG, of phylogenetic signal in multivariate data. Simulation studies showed that KA and KG have higher statistical power than the previously suggested statistic Km⁢u⁢l⁢t, especially if phylogenetic signal is low or concentrated in a few trait dimensions. In 2 empirical applications to vertebrate cranial shape (crocodyliforms and papionins), we found statistically significant phylogenetic signal concentrated in a few trait dimensions. The finding that phylogenetic signal can be highly variable across the dimensions of multivariate phenotypes has important implications for current maximum likelihood approaches to phylogenetic signal in multivariate data.

In Bayesian molecular-clock dating of species divergences, rate models are used to construct the prior on the molecular evolutionary rates for branches in the phylogeny, with independent and autocorrelated rate models being commonly used. The two classes of models, however, can result in markedly different divergence time estimates for the same data set, and thus selecting the best rate model appears important for obtaining reliable inferences of divergence times. However, the properties of Bayesian rate model selection are not well understood, in particular when the number of sequence partitions analyzed increases and when age calibrations (such as fossil calibrations) are misspecified. Furthermore, Bayesian rate model selection is computationally expensive as it requires the calculation of marginal likelihoods by Markov Chain Monte Carlo sampling, and therefore, methods that can speed up the model selection procedure without compromising its accuracy are desirable. In this study, we use a combination of computer simulations and real data analysis to investigate the statistical behavior of Bayesian rate model selection and we also explore approximations of the likelihood to improve computational efficiency in large phylogenomic data sets. Our simulations demonstrate that the posterior probability for the correct rate model converges to one as more molecular sequence partitions are analyzed and when no calibrations are used, as expected due to asymptotic Bayesian model selection theory. Furthermore, we also show the model selection procedure is robust to slight misspecification of calibrations, and reliable inference of the correct rate model is possible in this case. However, we show that when calibrations are seriously misspecified, calculated model probabilities are completely wrong and may converge to one for the wrong rate model. Finally, we demonstrate that approximating the phylogenetic likelihood under an arcsine branch-length transform can dramatically reduce the computational cost of rate model selection without compromising accuracy. We test the approximate procedure on two large phylogenies of primates (372 species) and flowering plants (644 species), replicating results obtained on smaller data sets using exact likelihood. Our findings and methodology can assist users in selecting the optimal rate model for estimating times and rates along the Tree of Life.

Advances in genomics have greatly enhanced our understanding of mountain biodiversity, providing new insights into the complex and dynamic mechanisms that drive the formation of mountain biotas. These span from broad biogeographic patterns to population dynamics and adaptations to these environments. However, significant challenges remain in integrating large-scale and fine-scale findings to develop a comprehensive understanding of mountain biodiversity. One significant challenge is the lack of genomic data, especially in historically understudied arid regions where reptiles are a particularly diverse vertebrate group. In the present study, we assembled a de novo genome-wide SNP dataset for the complete endemic reptile fauna of a mountain range (19 described species with more than 600 specimens sequenced), and integrated state-of-the-art biogeographic analyses at the population, species, and community level. Thus, we provide a holistic integration of how a whole endemic reptile community has originated, diversified and dispersed through a mountain system. Our results show that reptiles independently colonized the Hajar Mountains of southeastern Arabia 11 times. After colonization, species delimitation methods suggest high levels of within-mountain diversification, supporting up to 49 deep lineages. This diversity is strongly structured following local topography, with the highest peaks acting as a broad barrier to gene flow among the entire community. Interestingly, orogenic events do not seem key drivers of the biogeographic history of reptiles in this system. Instead, past climatic events seem to have had a major role in this community assemblage. We observe an increase of vicariant events from Late Pliocene onwards, coinciding with an unstable climatic period of rapid shifts between hyper-arid and semiarid conditions that led to the ongoing desertification of Arabia. We conclude that paleoclimate, and particularly extreme aridification, acted as a main driver of diversification in arid mountain systems which is tangled with the generation of highly adapted endemicity. Overall, our study does not only provide a valuable contribution to understanding the evolution of mountain biodiversity, but also offers a flexible and scalable approach that can be reproduced into any taxonomic group and at any discrete environment.

The total number of species on earth and the rate at which new species are created are fundamental questions for ecology, evolution and conservation. These questions have typically been approached separately, despite their obvious interconnection. In this study, we approach both questions in conjunction, for all terrestrial animals. To do this, we combine two previously unconnected bodies of theory: general ecosystem models and individual-based ecological neutral theory. General ecosystem models provide us with estimated numbers of individual organisms, separated by functional group and body size. Neutral theory, applied within a guild of functionally similar individuals, connects species richness, speciation rate, and number of individual organisms. In combination, for terrestrial endotherms where species numbers are known, they provide us with estimates for speciation rates as a function of body size and diet class. Extrapolating the same rates to guilds of ectotherms enables us to estimate the species richness of those groups, including species yet to be described. We find that speciation rates per species per million years decrease with increasing body size. Rates are also higher for carnivores compared to omnivores or herbivores of the same body size. Our estimate for the total number of terrestrial species of animals is in the range 1.03-2.92 million species, a value consistent with estimates from previous studies, despite having used a fundamentally new approach. Perhaps what is most remarkable about these results is that they have been obtained using only limited data from larger endotherms and their speciation rates, with the predictive process being based on mechanistic theory. This work illustrates the potential of a new approach to classic eco-evolutionary questions, while also adding weight to existing predictions. As we now face an era of dramatic biological change, new methods will be needed to mechanistically model global biodiversity at the species and individual organism level. This will be a huge challenge but the combination of general ecosystem models and neutral theory that we introduce here is a way to tractably achieve it.

Phylogenomic analyses of closely related species allow important glimpses into their evolutionary history. Although recent studies have demonstrated that interspecies hybridization has occurred in several groups, incorporating this process in phylogenetic reconstruction remains challenging. Specifically, the most predominant topology across the genome is often assumed to reflect the speciation tree, but rampant hybridization might overwhelm the genomes, causing that assumption to be violoated. The notoriously challenging phylogeny of the five extant Panthera species (specifically jaguar [P. onca], lion [P. leo], and leopard [P. pardus]) is an interesting system to address this problem. Here we employed a Panthera-wide whole-genome-sequence dataset incorporating three jaguar genomes and two representatives of lions and leopards to dissect the relationships among these three species. Maximum-likelihood trees reconstructed from non-overlapping genomic fragments of four different sizes strongly supported the monophyly of all three species. The most frequent topology (76-95%) united lion+leopard as sister-species (topology 1), followed by lion+jaguar (topology 2: 4-8%) and leopard+jaguar (topology 3: 0-6%). Topology 1 was dominant across the genome, especially in high-recombination regions. Topologies 2 and 3 were enriched in low-recombination segments, likely reflecting the species tree in the face of hybridization. Divergence times between sister-species of each topology, corrected for local recombination rate effects, indicated that the lion-leopard divergence was significantly younger than the alternatives, likely driven by post-speciation admixture. Introgression analyses detected pervasive hybridization between lions and leopards, regardless of the assumed species tree. This inference was strongly supported by multi-species-coalescence-with-introgression (MSci) analyses, which rejected topology 1 or any model without introgression. Interestingly, topologies 2 and 3 with extensive lion-leopard introgression were unidentifiable, highlighting the complexity of this phylogenetic problem. Our results suggest that the dominant genome-wide tree topology is not the true species tree but rather a consequence of overwhelming post-speciation admixture between lion and leopard.