Not plants or animals: a brief history of the origin of Kingdoms Protozoa, Protista and Protoctista.

In the wake of Darwin's evolutionary ideas, mid-nineteenth century naturalists realized the shortcomings of the long established two-kingdom system of organismal classification. Placement in a natural scheme of Protozoa, Protophyta, Phytozoa and Bacteria, microorganisms that exhibited plant-like and animal-like characteristics but obviously differed in organization from larger plants and animals, challenged traditional classification. The attempts of naturalists to classify these organisms outside the constraints of the plant and animal kingdoms led to concepts of additional kingdoms (Protozoa, Protista, Protoctista, etc.) to accommodate the nature of these organisms as not true plants or animals.     

The new higher level classification of eukaryotes with emphasis on the taxonomy of protists

This revision of the classification of unicellular eukaryotes updates that of Levine et al. (1980) for the protozoa and expands it to include other protists. Whereas the previous revision was primarily to incorporate the results of ultrastructural studies, this revision incorporates results from both ultrastructural research since 1980 and molecular phylogenetic studies. We propose a scheme that is based on nameless ranked systematics. The vocabulary of the taxonomy is updated, particularly to clarify the naming of groups that have been repositioned. We recognize six clusters of eukaryotes that may represent the basic groupings similar to traditional "kingdoms." The multicellular lineages emerged from within monophyletic protist lineages: animals and fungi from Opisthokonta, plants from Archaeplastida, and brown algae from Stramenopiles.     

Order amidst animalcules: the Protoctista kingdom and its undulipodiated cells

The eukaryotic microorganisms have always been studied and described in the context of Zoology (as 'tiny animals), Botany (as tiny plants), Mycology (as water molds) or Microbiology (as disease agents). Because their extent (as a group of about 200,000 species) and differences from the rest of life (worthy of Protoctista kingdom status) only recently has been recognized, their classification within the Plant and Animal kingdoms remains in scandalous disarray. Admitting this problem, this paper represents a step toward achieving nomenclatural order based on ultrastructural, biochemical and evolutionary considerations.     

Tetrahymena meiosis: Simple yet ingenious

The presence of meiosis, which is a conserved component of sexual reproduction, across organisms from all eukaryotic kingdoms, strongly argues that sex is a primordial feature of eukaryotes. However, extant meiotic structures and processes can vary considerably between organisms. The ciliated protist Tetrahymena thermophila, which diverged from animals, plants, and fungi early in evolution, provides one example of a rather unconventional meiosis. Tetrahymena has a simpler meiosis compared with most other organisms: It lacks both a synaptonemal complex (SC) and specialized meiotic machinery for chromosome cohesion and has a reduced capacity to regulate meiotic recombination. Despite this, it also features several unique mechanisms, including elongation of the nucleus to twice the cell length to promote homologous pairing and prevent recombination between sister chromatids. Comparison of the meiotic programs of Tetrahymena and higher multicellular organisms may reveal how extant meiosis evolved from proto-meiosis.     

Do early branching lineages signify ancestral traits?

A reverence for ancestors that has pre-occupied humans since time immemorial persists to the present. Reconstructing ancestry is the focus of many biological studies but failure to distinguish between present-day descendants and long-dead ancestors has led to incorrect interpretation of phylogenetic trees. This has resulted in erroneous reconstruction of traits such as morphology and ancestral areas. Misinterpretation becomes evident when authors use the terms 'basal' or 'early diverging' to refer to extant taxa. Here, we discuss the correct interpretation of trees and methods for reconstructing the ancestral features of organisms using recently developed statistical models. These models can be inaccurate unless they use information that is independent of phylogenies, such as genetics, molecular and developmental biology, functional morphology, geological and climatic processes, and the fossil record.     

Molecular phylogeny of the kingdoms Animalia, Plantae, and Fungi

The branching order of the kingdoms Animalia, Plantae, and Fungi has been a controversial issue. Using the transformed distance method and the maximum parsimony method, we investigated this problem by comparing the sequences of several kinds of macromolecules in organisms spanning all three kingdoms. The analysis was based on the large-subunit and small-subunit ribosomal RNAs, 10 isoacceptor transfer RNA families, and six highly conserved proteins. All three sets of sequences support the same phylogenetic tree: plants and animals are sibling kingdoms that have diverged more recently than the fungi. The ribosomal RNA and protein data sets are large enough so that in both cases the inferred phylogeny is statistically significant. The present report appears to be the first to provide statistically conclusive molecular evidence for the phylogeny of the three kingdoms. The determination of this phylogeny will help us to understand the evolution of various molecular, cellular, and developmental characters shared by any two of the three kingdoms. Noting that the large-subunit rRNA sequences have evolved at similar rates in the three kingdoms, we estimated the ratio of the time since the animal-plant split to the time since the fungal divergence to be 0.90.     

Paleobiological Perspectives on Early Eukaryotic Evolution

Eukaryotic organisms radiated in Proterozoic oceans with oxygenated surface waters, but, commonly, anoxia at depth. Exceptionally preserved fossils of red algae favor crown group emergence more than 1200 million years ago, but older (up to 1600–1800 million years) microfossils could record stem group eukaryotes. Major eukaryotic diversification ∼800 million years ago is documented by the increase in the taxonomic richness of complex, organic-walled microfossils, including simple coenocytic and multicellular forms, as well as widespread tests comparable to those of extant testate amoebae and simple foraminiferans and diverse scales comparable to organic and siliceous scales formed today by protists in several clades. Mid-Neoproterozoic establishment or expansion of eukaryophagy provides a possible mechanism for accelerating eukaryotic diversification long after the origin of the domain. Protists continued to diversify along with animals in the more pervasively oxygenated oceans of the Phanerozoic Eon.Eukaryotic organisms have a long evolutionary history, recorded, in part, by conventional and molecular fossils. For the Phanerozoic Eon (the past 542 million years), eukaryotic evolution is richly documented by the skeletons (and, occasionally, nonskeletal remains) of animals, as well as the leaves, stems, roots, and reproductive organs of land plants. Phylogenetic logic, however, tells us that eukaryotes must have a deeper history, one that began long before the first plant and animal fossils formed. To what extent does the geological record preserve aspects of deep eukaryotic history, and can the chemistry of ancient sedimentary rocks elucidate the environmental conditions under which the eukaryotic cell took shape?     

ELECTROPHORESIS IS MODIFYING OUR CONCEPTS OF EVOLUTION IN HOMOSPOROUS PTERIDOPHYTES

Analyses of electrophoretically detectable enzyme variants in homosporous pteridophytes are facilitating the development of new insights into their genetics and evolution. The number of isozymes per enzyme indicates that homosporous pteridophytes are genetic diploids, in spite of the fact that they have high chromosome numbers. High levels of heterozygosity and genetic variability in sporophytic populations indicate that many diploid species are outcrossing with inbreeding representing a derived character state. Because the congeneric homosporous pteridophyte species analyzed to date have low genetic identities, allozymic characters are also proving to be useful as genomic markers for elucidating patterns of reticulate evolution. The accumulated data suggest that the genetic system of homosporous pteridophytes differs fundamentally from that of seed plants. The present genomic constitution of extant taxa may be the result of repeated cycles of allopolyploidy followed by gene silencing and extinction of progenitor taxa. Alternatively, the original homosporous pteridophytes may have had high chromosome numbers. Although current species probably evolved recently, their phylogenetic roots may be difficult to trace because even closely related pteridophytes are genetically distant and extinction has obliterated the ancestral intermediates between lineages. These hypotheses can and should be tested using a combination of molecular, phylogenetic, and population biology methods.     

Bodyplan diversification in crinoid-associated myzostomes (Myzostomida, Protostomia)

Abstract. When free-living organisms evolve into symbiotic organisms (parasites, commensals, or mutualists), their bodyplan is often dramatically modified as a consequence. The present work pertains to the study of this process in a group of marine obligate symbiotic worms, the Myzostomida. These are mainly ectocommensals and are only associated with echinoderms, mostly crinoids. Their usual textbook status as a class of the Annelida is generally accepted, although recent molecular phylogenetic studies have raised doubts on their relationships with other metazoans, and the question of their status remains open. Here, we reconstruct the evolution of their bodyplans by mapping 14 external morphological characters (analyzed using scanning electron microscopy) onto molecular phylogenies using maximum parsimony (MP) and maximum likelihood (ML) optimality criteria. Rooted MP, ML, and Bayesian phylogenetic trees were obtained by analyzing the nucleotide sequences of cytochrome oxidase subunit I, 18S rDNA, and 16S rDNA genes, separately and in combination. Representatives of 34 species distributed among seven extant genera were investigated. Our character evolution analyses, combined with recent ontogenetic and ultrastructural evidence, indicate that the organism at the base of the myzostome tree would have had six body segments and five pairs of polychaete-type parapodia, and that two lineages emerged from it: one comprising parasites, with large females and dwarf males, which gave rise to the extant Pulvinomyzostomum and Endomyzostoma species, and a second lineage comprising simultaneously hermaphroditic ectocommensals, from which all other extant myzostome taxa probably evolved.     

The classification of genus Anopheles (Diptera: Culicidae): a working hypothesis of phylogenetic relationships

The internal classification of genus Anopheles is updated to reflect taxonomic actions published since the classification was last reviewed in 1994. Both formal and informal taxa are included. The classification is intended to aid researchers and students who are interested in analysing species relationships, making group comparisons and testing phylogenetic hypotheses. The genus includes 444 formally named and 40 provisionally designated extant species divided between six subgenera: Anopheles, Cellia, Kerteszia, Lophopodomyia, Nyssorhynchus and Stethomyia. Subgenera Anopheles, Cellia and Nyssorhynchus are subdivided hierarchically into nested informal groups of morphologically similar species that are believed to represent monophyletic lineages based on morphological similarity. Changes to the classification include additional species, eliminated species and changes to the hierarchical organization and composition of supraspecific groups, some as a result of molecular studies.     

Stochastic models for phylogenetic trees on higher-order taxa

Simple stochastic models for phylogenetic trees on species have been well studied. But much paleontology data concerns time series or trees on higher-order taxa, and any broad picture of relationships between extant groups requires use of higher-order taxa. A coherent model for trees on (say) genera should involve both a species-level model and a model for the classification scheme by which species are assigned to genera. We present a general framework for such models, and describe three alternate classification schemes. Combining with the species-level model of Aldous and Popovic (Adv Appl Probab 37:1094–1115, 2005), one gets models for higher-order trees, and we initiate analytic study of such models. In particular we derive formulas for the lifetime of genera, for the distribution of number of species per genus, and for the offspring structure of the tree on genera. David Aldous’s research was supported by NSF Grant DMS-0704159.     

Living genera of sea pens (Goelenterata: Octocorallia: Pennatulacea): illustrated key and synopses

An illustrated dichotomous key and synopses of the 32 genera of living pennatulacean octocorals are presented, which incorporate new morphological and distributional data from the examination of recendy collected material. In addition, a key to the 15 extant families, lists of valid genera, synonyms, and a table of comparative characters are also included. Lasdy, a revised classification and phylogenetic considerations are presented. Preliminary investigations indicate that the traditional higher classification scheme of the Pennatulacea is inadequate for reasons of paraphyly and intermediate taxa, that tend to negate precise distinctions between some of the nominal higher taxa. Of the approximately 436 described species of sea pens worldwide, only 186 (or 43%) are estimated to be valid. In addition, several undescribed species have recently been discovered, and others will no doubt be discovered in the future. It is therefore estimated that the extant pennatulacean fauna of the world comprises approximately 200 species in 32 genera.     

SUMMARY OF GREEN PLANT PHYLOGENY AND CLASSIFICATION

Abstract— A cladogram of green plants involving all major extant groups of green algae, bryophytes, pteridophytes, and seed plants is presented. It is partly based on contributions by B. Mishler and S. Churchill, H. Wagner, and P. Crane. The relationships of green plants to other green organisms ( Prochloron , euglenophytes) are discussed. The characters and subclades of the cladogram are briefly discussed, with an attempt to indicate weak points. The possibility of including some major extinct groups is considered. A cladistic classification consistent with the cladogram is presented. Grades are abandoned as taxa and major clades like the division Chlorophyta (green algae excluding micro-monadophytes and charophytes sensu Mattox and Stewart), the division Streptophyta (charophytes + embryophytes), the subdivision Embryophytina (land plants or embryophytes), the superclass Tracheidatae (tracheophytes), and the class Spermatopsida (seed plants) are recognized.     

获取生物物种名录信息的R程序包SP2000

物种名录为衡量区域和全球生物多样性提供了数据基础。随着互联网的兴起与发展, 人们将地球上已知的动物、植物、微生物等类群的物种名录信息存储到公共数据平台中, 并对物种名录进行快速及时地更新, 这极大地促进了分类学、保护生物学和宏观生态学等学科的发展, 成为政府或国际组织开展物种保育现状评估、红色名录编撰和生物多样性保护的重要依据。物种2000中国节点(http://www.sp2000.org.cn)和Catalogue of Life网站(http://www.catalogueoflife.org)分别是中国和全球最大的生物物种名录数据平台, 截至2020年6月4日, 其收录的物种数分别为122,280种和1,829,672种。然而这些数据平台仅提供物种查询、检索、下载等基本功能, 难以满足使用者准确、快速地批量获取所需生物物种名录数据信息的需求, 制约了这些大数据平台在生物多样性研究和保护中的作用。因此, 我们选取R语言开发了程序包SP2000, 旨在帮助用户批量获取中国或全球生物物种名录信息。该程序包具有跨Windows、MacOS、Linux等多个系统运行、操作便捷、代码开源等特点。为了方便用户使用, 本文详细介绍了SP2000的基本原理、特点及使用指南, 包括程序包的下载、安装、运行和参数设置等。     

Molecular classification of living organisms

Recent studies in molecular evolution have generated strong conflicts in opinion as to how world living organisms should be classified. The traditional classification of life into five kingdoms has been challenged by the molecular analysis carried out mostly on rRNA sequences, which supported the division of the extant living organisms into three major groups: Archaebacteria, Eubacteria, and Eukaryota. As to the problem of placing the root of the tree of life, the analysis carried out on a few genes has provided discrepant results. In order to measure the genetic distances between species, we have carried out an evolutionary analysis of the glutamine synthetase genes, which previously have been revealed to be good molecular clocks, and of the small and large rRNA genes. All data demonstrate that archaebacteria are more closely related to eubacteria than to eukaryota, thus supporting the classical division of living organisms into two main superkingdoms, Prokaryota and Eukaryota.Abbreviations Mya million years ago - GS glutamine synthetase - Isu large subunit - ssu small subunit - SMC Stationary Markov clock Correspondence to: G. Pesole     

Developmental system drift and flexibility in evolutionary trajectories

SUMMARY The comparative analysis of homologous characters is a staple of evolutionary developmental biology and often involves extrapolating from experimental data in model organisms to infer developmental events in non-model organisms. In order to determine the general importance of data obtained in model organisms, it is critical to know how often and to what degree similar phenotypes expressed in different taxa are formed by divergent developmental processes. Both comparative studies of distantly related species and genetic analysis of closely related species indicate that many characters known to be homologous between taxa have diverged in their morphogenetic or gene regulatory underpinnings. This process, which we call "developmental system drift" (DSD), is apparently ubiquitous and has significant implications for the flexibility of developmental evolution of both conserved and evolving characters. Current data on the population genetics and molecular mechanisms of DSD illustrate how the details of developmental processes are constantly changing within evolutionary lineages, indicating that developmental systems may possess a great deal of plasticity in their responses to natural selection.     

Generalized fire response strategies in plants and animals

Despite the existing large body of research on plant–animal interactions, plant research and animal research are still relatively independent and asymmetrical in relation to disturbance. Animals and plants are likely to have different fire responses, yet biodiversity studies in relation to disturbance may benefit from a more integrated functional approach across kingdoms. This would also force us to go deeper into the biological mechanisms and scales for persistence than a taxonomic‐based classification. An integrated view of plant and animal responses would enable us to learn from a great variety of life forms and benefit from expertise in complementary disciplines. To achieve this integrated view, I propose a functional classification for both plants and animals in relation to their fire response strategy. This classification includes the following strategies: resistance, refugia, avoidance, dormancy, recolonization, crypsis and intolerance. Given the limited knowledge of fire responses for many organisms, and especially for many animals, this classification may require further development. However, it provides a framework that facilitates finding knowledge gaps and directing future research for gaining a better understanding of the role of fire on biodiversity.     

ABA in bryophytes: how a universal growth regulator in life became a plant hormone?

Abscisic acid (ABA) is not a plant-specific compound but one found in organisms across kingdoms from bacteria to animals, suggesting that it is a ubiquitous and versatile substance that can modulate physiological functions of various organisms. Recent studies have shown that plants developed an elegant system for ABA sensing and early signal transduction mechanisms to modulate responses to environmental stresses for survival in terrestrial conditions. ABA-induced increase in stress tolerance has been reported not only in vascular plants but also in non-vascular bryophytes. Since bryophytes are the key group of organisms in the context of plant evolution, clarification of their ABA-dependent processes is important for understanding evolutionary adaptation of land plants. Molecular approaches using Physcomitrella patens have revealed that ABA plays a role in dehydration stress tolerance in mosses, which comprise a major group of bryophytes. Furthermore, we recently reported that signaling machinery for ABA responses is also conserved in liverworts, representing the most basal members of extant land plant lineage. Conservation of the mechanism for ABA sensing and responses in angiosperms and basal land plants suggests that acquisition of this mechanism for stress tolerance in vegetative tissues was one of the critical evolutionary events for adaptation to the land. This review describes the role of ABA in basal land plants as well as non-land plant organisms and further elaborates on recent progress in molecular studies of model bryophytes by comparative and functional genomic approaches.