Development, evolution, and corroboration

Genome-Wide Identification and Expression Analysis of Cysteine-Rich Polycomb-like Protein (CPP) Gene Family in Tomato

The cysteine-rich polycomb-like protein (CPP) gene family is a class of transcription factors containing conserved cysteine-rich CRC structural domains that is involved in the regulation of plant growth and stress tolerance to adversity. Relative to other gene families, the CPP gene family has not received sufficient attention. In this study, six SlCPPs were identified for the first time using the most recent genome-wide identification data of tomato. Subsequently, a phylogenetic analysis classified SlCPPs into four subfamilies. The analysis of cis-acting elements in the promoter indicates that SlCPPs are involved in plant growth and development and also stress response. We present for the first time the prediction of the tertiary structure of these SlCPPs proteins using the AlphaFold2 artificial intelligence system developed by the DeepMind team. Transcriptome data analysis showed that SlCPPs were differentially expressed in different tissues. Gene expression profiling showed that all SlCPPs except SlCPP5 were up-regulated under drought stress; SlCPP2, SlCPP3 and SlCPP4 were up-regulated under cold stress; SlCPP2 and SlCPP5 were up-regulated under salt stress; all SlCPPs were up-regulated under inoculation with Cladosporium fulvum; and SlCPP1, SlCPP3, and SlCPP4 were up-regulated under inoculation with Stemphylium lycopersici. We performed a virus-induced gene silencing experiment on SlCPP3, and the results indicated that SlCPP3 was involved in the response to drought stress. Finally, we predicted the interaction network of the key gene SlCPP3, and there was an interaction relationship between SlCPP3 and 10 genes, such as RBR1 and MSI1. The positive outcome showed that SlCPPs responded to environmental stress. This study provides a theoretical and empirical basis for the response mechanisms of tomato in abiotic stresses.

Phylogeny and evo-devo: Characters, homology, and the historical analysis of the evolution of development

The concept of homology continues to attract more and more commentary. In systematic and evolutionary biology the meaning of homology as synapomorphic similarity inherited from a common ancestor has gained wide acceptance over the last three or four decades. In recent years, however, developmental biologists, in particular, have argued for a new approach to, and new definition for, homology that revolves around the desire to make it more process-oriented and more mechanistic. These efforts raise questions about the relationship between developmental and evolutionary biology as well as how the evolution of development is to be studied. It is argued in this paper that this new approach to homology seemingly decouples developmental biology from the study of the evolution of development rather than to facilitate that study. In contrast, applying the notion of historical, phylogenetic homology to developmental data is inherently comparative and therefore evolutionary.

Homology and ontogeny: pattern and process in comparative developmental biology

In this article the interface between development and homology is discussed. Development is here interpreted as a sequence of evolutionarily independent stages. Any approach stressing the importance of specific developmental stages is rejected. A homology definition is favoured which includes similarity, and complexity serves as a test for homology. Complexity is seen as the possibility of subdividing a character into evolutionarily independent corresponding substructures. Topology as a test for homology is critically discussed because corresponding positions are not necessarily indicative of homology. Complexity can be used twofold for homology assessments of development: either stages or processes of development are homologized. These two approaches must not be con-flated. This distinction leads to the conclusion that there is no ontogenetic homology "criterion".

Independence of alignment and tree search

I assert that similarity is the appropriate homology criterion for sequence alignment, as it is with morphology. Methods that select among alignments using parsimony-based tree lengths, as implemented in MALIGN and POY, arrange the data such that they are consistent with a minimum-evolution model. When combining data sets in phylogenetic analyses, we are not trying to reinforce our earlier hypotheses about relationships, but rather to test them. The severity of this test is compromised when congruence with other characters is favored when selecting among alignment parameters.

Resolving the evolutionary paradox of genetic instability: a cost-benefit analysis of DNA repair in changing environments

Loss of genetic stability is a critical phenomenon in cancer and antibiotic resistance, and the prevailing dogma is that unstable cells survive because instability provides adaptive mutations. Challenging this view, we have argued that genetic instability arises because DNA repair may be a counterproductive strategy in mutagenic environments. This paradoxical relationship has also been confirmed by explicit experiments, but the underlying evolutionary principles remain controversial. This paper aims to clarify the issue, and presents a model that explains genetic instability from the basic perspective of molecular evolution and information processing.

Latent homologues for the neural crest as an evolutionary novelty

The neural crest is a craniate synapomorphy and a bona fide evolutionary novelty. Recently, researchers considering intriguingly similar patterns of gene expression, cell behaviors, and embryogenetic processes in noncraniate deuterostomes have suggested that cephalochordates, urochordates, and echinoderms or their ancestors might have possessed cells that were precursors to the neural crest or its constituent cells. To emphasize the caution with which similarities at genetic, cellular, or embryological levels should be interpreted as substantiations for cell, germ layer, or tissue homologies, we present and evaluate additional tantalizing evidence that could be considered as documenting neural crest precursors in precraniates. Furthermore, we propose an evolutionary context--latent homologue--within which these data should be interpreted.

Current problems with the zootype and the early evolution of Hox genes

"Hox cluster type" genes have sparked intriguing attempts to unite all metazoan animals by a shared pattern of expression and genomic organization of a specific set of regulatory genes. The basic idea, the zootype concept, claims the conservation of a specific set of "Hox cluster type genes" in all metazoan animals, i.e., in the basal diploblasts as well as in the derived triploblastic animals. Depending on the data used and the type of analysis performed, different opposing views have been taken on this idea. We review here the sum of data currently available in a total evidence analysis, which includes morphological and the most recent molecular data. This analysis highlights several problems with the idea of a simple "Hox cluster type" synapomorphy between the diploblastic and triploblastic animals and suggests that the "zootype differentiation" of the Hox cluster most likely is an invention of the triploblasts. The view presented is compatible with the idea that early Hox gene evolution started with a single proto-Hox (possibly a paraHox) gene. J. Exp. Zool. (Mol. Dev. Evol.) 291:169-174, 2001.

Evolution of animal body plans: the role of metazoan phylogeny at the interface between pattern and process

Comprehensive integrative studies are the hallmark of evolutionary developmental biology. A properly defined phylogenetic framework takes a central place in such analyses as the meeting ground for observation and inference. Molecular phylogenies take this place in many current studies on animal body plan evolution. In particular, 18S rRNA/DNA sequence analyses have yielded a new view of animal evolution that is often contrasted with a presumed traditional or classical view. First, I expose this traditional view to be a simplified historical abstraction that became textbook dogma. Second, I discuss how two recent important studies of animal body plan evolution, examining the evolution of the platyhelminth body plan and the evolutionary significance of indirect development and set-aside cells, have actively incorporated two problematic aspects of the newly emerging molecular view of animal evolution: incomplete and unresolved phylogenies.