PartitionFinder 2 is a program for automatically selecting best-fit partitioning schemes and models of evolution phylogenetic analyses. substantially faster more efficient than version 1, incorporates many new methods features. These include the ability to analyze morphological datasets, genome-scale output formats facilitate interoperability with downstream software, molecular evolution. freely available under an open source license works on Windows, OSX, Linux operating systems. It can be...

Despite the introduction of likelihood-based methods for estimating phylogenetic trees from phenotypic data, parsimony remains most widely-used optimality criterion building discrete morphological data. However, it has been known decades that there are regions solution space in which is a poor estimator tree topology. Numerous software implementations models estimation phylogeny data exist, especially Mk model character evolution. Here we explore efficacy Bayesian phylogeny, using model,...

The Mk model was developed for estimating phylogenetic trees from discrete morphological data, whether living or fossil taxa. Like any model, the makes a number of assumptions. One assumption is that transitions between character states are symmetric (i.e., probability changing 0 to 1 same as 0). However, some characters in data matrix may not satisfy this assumption. Here, we test methods relaxing Bayesian context. Using empirical sets, perform fitting illustrate cases which modeling...

Tip-dating methods are becoming popular alternatives to traditional node calibration approaches for building time-scaled phylogenetic trees, but questions remain about their application empirical datasets. We compared the performance of most against a dated tree fossil Canidae derived from previously published monographs. Using canid morphology dataset, we performed tip-dating using BEAST v. 2.1.3 and M r B ayes 3.2.5. find that key nodes ( Canis, approx. 3.2 Ma, Caninae 11.7 Ma)...

Groundwater-dependent species are among the least-known components of global biodiversity, as well some most vulnerable because rapid groundwater depletion at regional and scales. The karstic Edwards-Trinity aquifer system west-central Texas is one species-rich systems in world, represented by dozens endemic groundwater-obligate with narrow, naturally fragmented distributions. Here, we examine how geomorphological hydrogeological processes have driven population divergence speciation a...

Abstract The rapid shift to online teaching in spring 2020 meant most of us were panic mode. As we move forward with course planning for fall and beyond, can invest more time energy into improving the experience our students. We advocate that instructors use inclusive practices, specifically through active learning, their classes. Incorporating pedagogical practices work maximize concepts will be beneficial all students, especially those from minoritized or underserved groups. Like many STEM...

To elucidate fungicultural specializations contributing to ecological dominance of leafcutter ants, we estimate the phylogeny fungi cultivated by fungus-growing (attine) including fungal cultivars from (i) entire range southern South America North America, (ii) all higher-attine ant lineages (leafcutting genera Atta, Acromyrmex; nonleafcutting Trachymyrmex, Sericomyrmex) and (iii) lower-attine lineages. Higher-attine form two clades, Clade-A (Leucocoprinus gongylophorus, formerly Attamyces)...

Over the past decade, a new set of methods for estimating dated trees has emerged. Originally referred to as fossilized birth–death (FBD) process, this single model expanded family models that allows researchers coestimate evolutionary parameters (e.g., diversification, sampling) and patterns alongside divergence times variety applications from paleobiology real-time epidemiology. We provide an overview models. explore ways in which these correspond quantitative paleobiology, FBD process...

The partitioning of global biodiversity into biogeographic regions is critical for understanding the impacts global-scale ecological and evolutionary processes on species assemblages as well prioritizing areas conservation. However, lack globally comprehensive data distributions precludes fine-scale estimation biogeographical regionalization numerous taxa ecological, economic conservation interest. Using a recently published phylogeny novel curated native range maps over 10 000 butterflies...

Changes in parity mode between egg-laying (oviparity) and live-bearing (viviparity) have occurred repeatedly throughout vertebrate evolution. Oviparity is the ancestral amniote state, viviparity has evolved many times independently within amniotes (especially lizards snakes), with possibly a few reversions to oviparity. In amniotes, shelled egg considered complex structure that unlikely re-evolve if lost (i.e., it an example of Dollo's Principle). However, recent state reconstruction...

1 Abstract Reconstructing the evolutionary history of different groups organisms provides insight into how life originated and diversified on Earth. Phylogenetic trees are commonly used to estimate this history, providing a hypothesis events. Within Bayesian phylogenetics major step in estimating tree is choosing an appropriate model character evolution. In case most extinct species, our only source information decipher their phylogenetic relationships through morphology fossils. We...

Most previous studies of morphological and molecular data have consistently supported the monophyly true water bugs (Hemiptera: Nepomorpha). An exception is a recent study by Hua et al. (BMC Evol Biol 9: 134, 2009) based on nine nepomorphan mitochondrial genomes. In analysis 2009), in group Pleoidea formed sister to clade that consisted Nepomorpha (the remaining bugs) + Leptopodomorpha (shore Cimicomorpha (assassin relatives) Pentatomomorpha (stink relatives), thereby suggesting fully...

Abstract Logical character dependency is a major conceptual and methodological problem in phylogenetic inference of morphological data sets, as it violates the assumption independence that common to all methods. It more frequently observed higher-level phylogenies or sets characterizing evolutionary transitions, these represent parts tree life where (primary) anatomical characters either originate disappear entirely. As result, secondary traits related primary become “inapplicable” across...

Abstract Phylogenetic trees establish a historical context for the study of organismal form and function. Most phylogenetic are estimated using model evolution. For molecular data, modeling evolution is often based on biochemical observations about changes between character states. example, there 4 nucleotides, we can make assumptions probability transitions them. By contrast, morphological characters, may not know priori how many characters states per character, as both extant sampling...

Continuous characters have received comparatively little attention in Bayesian phylogenetic estima- tion. This is predominantly because they cannot be modeled by a standard Q-matrix approach due to their non-discrete nature. In this manuscript, we explore the use of continuous traits under two Brownian Motion models estimate tree for Dicynodontia, well-studied group early synapsids (stem mammals) which been extensively used parsimony-based reconstruction. We examine differences signal...

Fungus-gardening (attine) ants grow fungus for food in protected gardens, which contain beneficial, auxiliary microbes, but also microbes harmful to gardens. Among these potentially pathogenic microorganisms, the most consistently isolated are fungi genus Escovopsis , thought co-evolve with and their cultivar a tripartite model. To test clade-to-clade correspondence between higher attine symbiosis (including leaf-cutting non-leaf-cutting ants), we amassed geographically comprehensive...

Abstract Establishing hypotheses of relationships is a critical prerequisite for any macroevolutionary analysis, but different approaches exist achieving this goal. Amongst palaeontologists using morphological data the Bayesian approach increasingly preferred over parsimony, shift also alters way we think about samples trees. Here revisit stratigraphic congruence as comparator between and parsimony samples, in new visual context: treespace. Such spaces represent an ordination unique...

Abstract Simulations are playing an increasingly important role in paleobiology. When designing a simulation study, many decisions have to be made and common challenges will encountered along the way. Here, we outline seven rules for executing good study. We cover topics including choice of study question, empirical data used as basis statistical methodological concerns, how validate ensure it can reproduced extended by others. hope that these accompanying examples guide paleobiologists when...

Phylogenetic estimation is, and has always been, a complex endeavor. Estimating phylogenetic tree involves evaluating many possible solutions evolutionary histories that could explain set of observed data, typically by using model evolution. Values for all parameters need to be evaluated as well. Modern statistical methods involve not just the tree, but also more models involving fossil record information other data sources. Markov chain Monte Carlo (MCMC) is leading method approximating...

Abstract Reconstructing the evolutionary history of different groups organisms provides insight into how life originated and diversified on Earth. Phylogenetic trees are commonly used to estimate this history. Within Bayesian phylogenetics a major step in estimating tree is choosing an appropriate model character evolution. While most common data molecular sequence data, morphological remains vital source information. The use characters allows for incorporation fossil taxa, despite advances...

<ns4:p>Many biologists are interested in teaching computing skills or using the classroom, despite not being formally trained these themselves. Thus may find themselves researching how to teach skills, and therefore many individuals individually attempting discover resources methods do so. Recent years have seen an expansion of new technologies assist delivering course content interactively. Educational research provides insights into learners absorb process information during interactive...