Cladistics最新文献

Here, we propose, prove mathematically and discuss maximum and minimum measures of maximum parsimony evolution across 12 discrete phylogenetic character types, classified across 4467 morphological and molecular datasets. Covered character types are: constant, binary symmetric, multistate unordered (non-additive) symmetric, multistate linear ordered symmetric, multistate non-linear ordered symmetric, binary irreversible, multistate irreversible, binary Dollo, multistate Dollo, multistate custom symmetric, binary custom asymmetric and multistate custom asymmetric characters. We summarize published solutions and provide and prove a range of new formulae for the algebraic calculation of minimum (m), maximum (g) and maximum possible (g_max) character cost for applicable character types. Algorithms for exhaustive calculation of m, g and g_max applicable to all classified character types (within computational limits on the numbers of taxa and states) are also provided. The general algorithmic solution for minimum steps (m) is identical to a minimum spanning tree on the state graph or minimum weight spanning arborescence on the state digraph. Algorithmic solutions for character g and g_max are based on matrix mathematics equivalent to optimization on the star tree, respectively for given state frequencies and all possible state frequencies meeting specified numbers of taxa and states. We show that maximizing possible cost (g_max) with given transition costs can be equivalent to maximizing, across all possible state frequency combinations, the lowest implied cost of state transitions if any one state is ancestral on the star tree, via the solution of systems of linear equations. The methods we present, implemented in the Claddis R package, extend to a comprehensive range, the fundamental character types for which homoplasy may be measured under parsimony using m, g and g_max, including extra cost (h), consistency index (ci), retention index (ri) or indices based thereon.

The Neotropical region is the most diverse on the planet, largely owing to its mosaic of tropical rainforests. Multiple tectonic and climatic processes have been hypothesized to contribute to generating this diversity, including Andean orogeny, the closure of the Isthmus of Panama, the GAARlandia land bridge and historical connections among currently isolated forests. Micrathena spiders are diverse and widespread in the region, and thus a complete phylogeny of this genus allows the testing of hypotheses at multiple scales. We estimated a complete, dated phylogeny using morphological data for 117 Micrathena species and molecular data of up to five genes for a subset of 79 species. Employing event-based approaches and biogeographic stochastic mapping while considering phylogenetic uncertainty, we estimated ancestral distributions, the timing and direction of dispersal events and diversification rates among areas. The phylogeny is generally robust, with uncertainty in the position of some of the species lacking sequences. Micrathena started diversifying around 25 Ma. Andean cloud forests show the highest in-situ speciation, while the Amazon is the major dispersal source for adjacent areas. The Dry Diagonal generated few species and is a sink of diversity. Species exchange between Central and South America involved approximately 23 dispersal events and started ~20 Ma, which is consistent with a Miocene age for the Isthmus of Panama closure. We inferred four dispersal events from Central America to the Antilles in the last 20 Myr, indicating the spiders did not reach the islands through the GAARlandia land bridge. We identified important species exchange routes among the Amazon, Andean cloud forests and Atlantic forests during the Plio-Pleistocene. Sampling all species of the genus was fundamental to the conclusions above, especially in identifying the Andean forests as the area that generated the majority of species. This highlights the importance of complete taxonomic sampling in biogeographic studies.

Sternorrhyncha, one of the four major suborders of Hemiptera, is a phytophagous taxon inclusive of nearly 18 000 described species. The phylogenetic relationships within the taxon and the earliest-branching lineage of its infraorders remain incompletely understood. This study attempted to illuminate the phylogenetic relationships within Sternorrhyncha through the use of maximum likelihood, Bayesian inference and maximum parsimony analyses, employing ultraconserved element (UCE) data from 39 genomic and 62 transcriptomic datasets and thereby representing most families within the taxon. The probe set Hemiptera 2.7Kv1 was used to recover a total of 2731 UCE loci: from 547 to 1699 (with an average of 1084) across all genomic datasets and from 108 to 849 (with an average of 329) across all transcriptomic datasets. All three types of phylogenetic analyses employed in this study produced robust statistical support for Sternorrhyncha being a monophyletic group. The different methods of phylogenetic analysis produced inconsistent descriptions of topological structure at the infraorder level: while maximum likelihood and Bayesian inference analyses produced strong statistical evidence (100%) indicating the clade Psylloidea + Aleyrodoidea to be a sister of the clade Aphidoidea (Aphidomorpha) + Coccoidea (Coccomorpha), the maximum parsimony analysis failed to recover a similar result. Our results also provide detail on the phylogenetic relationships within each infraorder. This study presents the first use of UCE data to investigate the phylogeny of Sternorrhyncha. It also shows the viability of amalgamating genomic and transcriptomic data in studies of phylogenetic relationships, potentially highlighting a resource-efficient approach for future inquiries into diverse taxa through the integration of varied data sources.

Gondwanan dinosaur faunae during the 20 Myr preceding the Cretaceous–Palaeogene (K/Pg) extinction included several lineages that were absent or poorly represented in Laurasian landmasses. Among these, the South American fossil record contains diverse abelisaurids, arguably the most successful groups of carnivorous dinosaurs from Gondwana in the Cretaceous, reaching their highest diversity towards the end of this period. Here we describe Koleken inakayali gen. et sp. n., a new abelisaurid from the La Colonia Formation (Maastrichtian, Upper Cretaceous) of Patagonia. Koleken inakayali is known from several skull bones, an almost complete dorsal series, complete sacrum, several caudal vertebrae, pelvic girdle and almost complete hind limbs. The new abelisaurid shows a unique set of features in the skull and several anatomical differences from Carnotaurus sastrei (the only other abelisaurid known from the La Colonia Formation). Koleken inakayali is retrieved as a brachyrostran abelisaurid, clustered with other South American abelisaurids from the latest Cretaceous (Campanian–Maastrichtian), such as Aucasaurus, Niebla and Carnotaurus. Leveraging our phylogeny estimates, we explore rates of morphological evolution across ceratosaurian lineages, finding them to be particularly high for elaphrosaurine noasaurids and around the base of Abelisauridae, before the Early Cretaceous radiation of the latter clade. The Noasauridae and their sister clade show contrasting patterns of morphological evolution, with noasaurids undergoing an early phase of accelerated evolution of the axial and hind limb skeleton in the Jurassic, and the abelisaurids exhibiting sustained high rates of cranial evolution during the Early Cretaceous. These results provide much needed context for the evolutionary dynamics of ceratosaurian theropods, contributing to broader understanding of macroevolutionary patterns across dinosaurs.

The water-lily clade represents the second earliest-diverging branch of angiosperms. Most of its species belong to Nymphaeaceae, of which the “core Nymphaeaceae”—comprising the genera Euryale, Nymphaea and Victoria—is the most diverse clade. Despite previous molecular phylogenetic studies on the core Nymphaeaceae, various aspects of their evolutionary relationships have remained unresolved. The length-variable introns and intergenic spacers are known to contain most of the sequence variability within the water-lily plastomes. Despite the challenges with multiple sequence alignment, any new molecular phylogenetic investigation on the core Nymphaeaceae should focus on these noncoding plastome regions. For example, a new plastid phylogenomic study on the core Nymphaeaceae should generate DNA sequence alignments of all plastid introns and intergenic spacers based on the principle of conserved sequence motifs. In this investigation, we revisit the phylogenetic history of the core Nymphaeaceae by employing such an approach. Specifically, we use a plastid phylogenomic analysis strategy in which all coding and noncoding partitions are separated and then undergo software-driven DNA sequence alignment, followed by a motif-based alignment inspection and adjustment. This approach allows us to increase the reliability of the character base compared to the default practice of aligning complete plastomes through software algorithms alone. Our approach produces significantly different phylogenetic tree reconstructions for several of the plastome regions under study. The results of these reconstructions underscore that Nymphaea is paraphyletic in its current circumscription, that each of the five subgenera of Nymphaea is monophyletic, and that the subgenus Nymphaea is sister to all other subgenera of Nymphaea. Our results also clarify many evolutionary relationships within the Nymphaea subgenera Brachyceras, Hydrocallis and Nymphaea. In closing, we discuss whether the phylogenetic reconstructions obtained through our motif-based alignment adjustments are in line with morphological evidence on water-lily evolution.

Although simulations have shown that implied weighting (IW) outperforms equal weighting (EW) in phylogenetic parsimony analyses, weighting against homoplasy lacks extensive usage in palaeontology. Iterative modifications of several phylogenetic matrices in the last decades resulted in extensive genealogies of datasets that allow the evaluation of differences in the stability of results for alternative character weighting methods directly on empirical data. Each generation was compared against the most recent generation in each genealogy because it is assumed that it is the most comprehensive (higher sampling), revised (fewer misscorings) and complete (lower amount of missing data) matrix of the genealogy. The analyses were conducted on six different genealogies under EW and IW and extended implied weighting (EIW) with a range of concavity constant values (k) between 3 and 30. Pairwise comparisons between trees were conducted using Robinson–Foulds distances normalized by the total number of groups, distortion coefficient, subtree pruning and regrafting moves, and the proportional sum of group dissimilarities. The results consistently show that IW and EIW produce results more similar to those of the last dataset than EW in the vast majority of genealogies and for all comparative measures. This is significant because almost all of these matrices were originally analysed only under EW. Implied weighting and EIW do not outperform each other unambiguously. Euclidean distances based on a principal components analysis of the comparative measures show that different ranges of k-values retrieve the most similar results to the last generation in different genealogies. There is a significant positive linear correlation between the optimal k-values and the number of terminals of the last generations. This could be employed to inform about the range of k-values to be used in phylogenetic analyses based on matrix size but with the caveat that this emergent relationship still relies on a low sample size of genealogies.

Horizontal gene transfer (HGT) from one organism to another, according to some researchers, can be abundant in the evolution of species. A phylogenetic network is a network structure that describes the HGTs among species. Several studies have proposed methods to construct phylogenetic networks to predict HGTs based on parsimony values. Existing definitions of parsimony values for a phylogenetic network are based on the assumption that each gene site or segment evolves independently along different trees in the network. However, in the current study, we define a novel parsimony value, denoted the p definition, for phylogenetic networks, considering that a gene as a whole typically evolves along a tree. Using Simulated Annealing, a new method called the Phylogeny with Simulated Annealing (PSA) algorithm is proposed to search for an optimal network based on the p definition. The PSA method is tested on the simulated data. The results reveal that the parsimonious networks constructed using PSA can better represent the evolutionary relationships of species involving HGTs. Additionally, the HGTs predicted using PSA are more accurate than those predicted using other methods. The PSA algorithm is publicly accessible at http://github.com/imustu/sap.

Insects have evolved complex sensory systems that are important for feeding, defence and reproduction. Parasitoid wasps often spend much time and effort in searching for concealed hosts with the help of specialized sensilla. However, the early evolution of such behaviour and sensilla is poorly known. We describe two fossil female wasps, †Tichostephanus kachinensis sp. nov. and †Tichostephanus longus sp. nov., from mid-Cretaceous Kachin amber. Phylogenetic analyses based on morphological data retrieved †Tichostephanus as deeply nested within Evanioidea and closely related to extant Gasteruptiidae and Evaniidae. Both of these Cretaceous wasps possess features, e.g. coronal tubercles and flexible ovipositor sheaths, that indicate that they might have laid eggs in wood where their larvae possibly parasitized insect larvae. They have a peculiar and unique ‘bottle brush’ of sensilla close to the apex of their ovipositor sheaths, which has not been observed in any extant parasitoid wasps. These sensilla comprise many regularly arranged plate-shaped setae, attached in relatively large sockets and with rows of longitudinal ridges. Such specialized sensilla perhaps served to enhance the ability to detect hosts inside wood.

Biogeographic studies have generally relied on methods that use a few, large predefined areas, which may overlook fine-scale patterns. Here we test previous hypotheses about the biogeographic history of a diverse bat clade regarding its association with major Neotropical geological formations, particularly the Antilles, the South American Dry Diagonal, the Andes and the Panamanian land bridge, by applying a recently available method that uses actual distributions instead of predefined areas. We compiled and curated spatially explicit, georeferenced data of 173 bat species (Mammalia: Chiroptera: Noctilionoidea) from the online database Global Biodiversity Information Facility. By taking a previous comprehensive phylogeny as an evolutionary framework, we performed computationally intensive analyses using the Geographically-explicit Event Model. This method uses the observed species distributions to reconstruct the ancestral areas and biogeographic events at each phylogeny node. We found that sympatric speciation was the most frequently reconstructed event, and involved mainly the Panamanian Isthmus and northern South America (SA), but all sympatry reconstructions were different and specific to each node. Allopatric events were important in the Andes; vicariance caused both west/east and north/south disjunctions that went unnoticed previously. Founder events indicated bidirectional dispersal between the mainland and the Antilles since the Miocene, and across the incomplete Panamanian bridge and the SA Dry Diagonal since the early Pliocene. Overall, we found support for previous hypotheses on the influence of major Neotropical paleogeographic events in the diversification of the group, but additionally revealed multi-scale patterns that are embedded within the mainland and were previously overlooked. Our results highlight a trans-isthmian centre of diversification in the biogeographic history of Noctilionoidea including the Panamanian Isthmus and Northern SA.

In the last decade, the Fossilized Birth–Death (FBD) process has yielded interesting clues about the evolution of biodiversity through time. To facilitate such studies, we extend our method to compute the probability density of phylogenetic trees of extant and extinct taxa in which the only temporal information is provided by the fossil ages (i.e. without the divergence times) in order to deal with the piecewise constant FBD process, known as the “skyline FBD”, which allows rates to change between pre-defined time intervals, as well as modelling extinction events at the bounds of these intervals. We develop approaches based on this method to assess hypotheses about the diversification process and to answer questions such as “Does a mass extinction occur at this time?” or “Is there a change in the fossilization rate between two given periods?”. Our software can also yield Bayesian and maximum-likelihood estimates of the parameters of the skyline FBD model under various constraints. These approaches are applied to a simulated dataset in order to test their ability to answer the questions above. Finally, we study an updated dataset of Permo-Carboniferous synapsids to get additional insights into the dynamics of biodiversity change in three clades (Ophiacodontidae, Edaphosauridae and Sphenacodontidae) in the Pennsylvanian (Late Carboniferous) and Cisuralian (Early Permian), and to assess support for end-Sakmarian (or Artinskian) and end-Cisuralian mass extinction events discussed in previous studies.