The Inference of the Evolution of Immune Traits as Constrained by Phylogeny: Insight into the Immune System of the Basal Diapsid.

Among vertebrates, some of the most vulnerable taxa to emergent fungal pathogens are members of Reptilia. In light of the growing threat of emergent fungal pathogens affecting wildlife, it is important to broaden the current understanding of immune system function, development, and evolution. The homologous condition of a trait is necessary in order to study its evolution, as such, homology is necessary in the study of immunological evolution.

Empirical and philosophical problems with the subspecies rank.

Species-level taxonomy derives from empirical sources (data and techniques) that assess the existence of spatiotemporal evolutionary lineages via various species "concepts." These concepts determine if observed lineages are independent given a particular methodology and ontology, which relates the metaphysical species concept to what "kind" of thing a species is in reality. Often, species concepts fail to link epistemology back to ontology.

The evolution of crocodilian nesting ecology and behavior.

Crocodilians comprise an ancient and successful lineage of archosaurs that repeatedly raises questions on how they survived a mass extinction and remained relatively unchanged for ~100 million years. Was their success due to the change-resistant retention of a specific set of traits over time (phylogenetic conservatism) or due to flexible, generalist capabilities (e.g.

Squamate areas of endemism in Cuba as determined by parsimony analysis of endemicity.

Cuba, the largest island in the Greater Antilles, hosts a high diversity of native squamate reptiles and is characterized by a complex geological history. The island has undergone repeated submergence and emergence, positioned on the dynamic border between the Caribbean and North American tectonic plates. Here, we infer current areas of endemism on Cuba based on squamate distributions using standard parsimony analysis of endemism under the "areas of endemism as individuals" hypothesis.

Early usage and meaning of evolvability.

Evolvability has become an enormously popular concept in evolutionary biology and in machine learning software architecture. While it is claimed that the term was coined in 1988 by Richard Dawkins, it was used as early as 1931 as a characteristic of life by John A. Thomson.

Translating a clade based classification into one that is valid under the international code of zoological nomenclature: the case of the lizards of the family Dactyloidae (Order Squamata).

In a tour-de-force for anole biology, Poe et al. (2017) provide the most complete phylogenetic analysis of members of the family Dactyloidae yet attempted. The contribution is remarkable in the completeness of sampled taxa and breath of included characters.

Skin glands of an aquatic salamander vary in size and distribution and release antimicrobial secretions effective against chytrid fungal pathogens.

Amphibian skin is unique among vertebrate classes, containing a large number of multicellular exocrine glands that vary among species and have diverse functions. The secretions of skin glands contain a rich array of bioactive compounds including antimicrobial peptides (AMPs). Such compounds are important for amphibian innate immune responses and may protect some species from chytridiomycosis, a lethal skin disease caused by the fungal pathogens (Bd) and (Bsal).

Testable but not falsifiable?

We are puzzled by a recent comment that suggested that historical hypotheses can be tested but are unfalsifiable. We argue that phylogenetic hypotheses are falsifiable without the aid of a time machine and that they are like any other hypothesis: they are tentative knowledge propositions capable of falsification with character evidence.

Entities on a Temporal Scale.

Ontological understanding of biological units (i.e. what kinds of things are they) is crucial to their use in experimental design, analysis, and interpretation.

Evolution of the germ line-soma relationship in vertebrate embryos.

The germ line and soma together maintain genetic lineages from generation to generation: the germ line passes genetic information between generations; the soma is the vehicle for germ line transmission, and is shaped by natural selection. The germ line and somatic lineages arise simultaneously in early embryos, but how their development is related depends on how primordial germ cells (PGC) are specified. PGCs are specified by one of two means.

Evolution of germ cell development in tetrapods: comparison of urodeles and amniotes.

The embryonic development of germ cells in tetrapods is described, focusing on groups with the inductive mode of germ cell specification. In mammals PGCs are induced early in the gastrulation process, they are internalized with future extraembryonic mesoderm in the early posterior primitive streak, and specified soon thereafter. Strong evidence indicates that a similar process occurs in turtles and some other reptiles.

Expression of Dazl and Vasa in turtle embryos and ovaries: evidence for inductive specification of germ cells.

In bilaterian animals, germ cells are specified by the inductive/regulative mode or the predetermined (germ plasm) mode. Among tetrapods, mammals and urodeles use the inductive mode, whereas birds and anurans use the predetermined mode. From histological data it has been predicted that some reptiles including turtles use the inductive mode.

Inferring developmental constraint and constraint release: primordial germ cell determination mechanisms as examples.

Developmental constraint and its converse constraint release are significant concepts in understanding pattern and process in macroevolution. The purpose of this paper is to propose a two-step method for identifying constraints and constraint release. The first step is a phylogenetic optimization procedure to identify which trait/process is primitive and which is derived.

Evolution of predetermined germ cells in vertebrate embryos: implications for macroevolution.

The germ line is established in animal embryos with the formation of primordial germ cells (PGCs), which give rise to gametes. Therefore, the need to form PGCs can act as a developmental constraint by inhibiting the evolution of embryonic patterning mechanisms that compromise their development. Conversely, events that stabilize the PGCs may liberate these constraints.

Is the PTP Test Useful?

We show empirically that the PTP test has very little discriminatory power, with highly significant PTP test probabilities often being associated with parsimony data that produce trees with low confidence (as measured by bootstrapping) and resolution. Because of this, we argue that the PTP test is useful only in the following, very limited way: if a data set fails the PTP test, it should not be used in a phylogenetic analysis. More conservative methods of measuring confidence such as the bootstrap or decay index are preferable.