Understanding Of Animal Evolution Research Articles

Ancient gene linkages support ctenophores as sister to other animals

A central question in evolutionary biology is whether sponges or ctenophores (comb jellies) are the sister group to all other animals. These alternative phylogenetic hypotheses imply different scenarios for the evolution of complex neural systems and other animal-specific traits1–6. Conventional phylogenetic approaches based on morphological characters and increasingly extensive gene sequence collections have not been able to definitively answer this question7–11. Here we develop chromosome-scale gene linkage, also known as synteny, as a phylogenetic character for resolving this question12. We report new chromosome-scale genomes for a ctenophore and two marine sponges, and for three unicellular relatives of animals (a choanoflagellate, a filasterean amoeba and an ichthyosporean) that serve as outgroups for phylogenetic analysis. We find ancient syntenies that are conserved between animals and their close unicellular relatives. Ctenophores and unicellular eukaryotes share ancestral metazoan patterns, whereas sponges, bilaterians, and cnidarians share derived chromosomal rearrangements. Conserved syntenic characters unite sponges with bilaterians, cnidarians, and placozoans in a monophyletic clade to the exclusion of ctenophores, placing ctenophores as the sister group to all other animals. The patterns of synteny shared by sponges, bilaterians, and cnidarians are the result of rare and irreversible chromosome fusion-and-mixing events that provide robust and unambiguous phylogenetic support for the ctenophore-sister hypothesis. These findings provide a new framework for resolving deep, recalcitrant phylogenetic problems and have implications for our understanding of animal evolution.

A Middle Ordovician Burgess Shale-type fauna from Castle Bank, Wales (UK).

Burgess Shale-type faunas are critical to our understanding of animal evolution during the Cambrian, giving an unrivalled view of the morphology of ancient organisms and the ecology of the earliest animal-dominated communities. Rare examples in Lower Ordovician strata such as the Fezouata Biota illustrate the subsequent evolution of ecosystems but only from before the main phase of the Great Ordovician Biodiversification Event. Later Ordovician Konservat-Lagerstätten are not directly comparable with the Burgess Shale-type faunas as they do not represent diverse, open-shelf communities, limiting our ability to track ecological development through the critical Ordovician biodiversification interval. Here we present the Castle Bank fauna: a highly diverse Middle Ordovician Burgess Shale-type fauna from Wales (UK) that is directly comparable with the Burgess Shale and Chengjiang biotas in palaeoenvironment and preservational style. The deposit includes animals with morphologies similar to the iconic Cambrian taxa Opabinia, Yohoia and Wiwaxia, combined with early examples of more derived groups such as barnacles. Many taxa such as kinorhynchs show the small sizes typical of modern faunas, illustrating post-Cambrian miniaturization. Castle Bank provides a new perspective on early animal evolution, revealing the next chapter in ecosystem development following the Chengjiang, Burgess Shale and Fezouata biotas.

Breakthrough in Marine Invertebrate Cell Culture: Sponge Cells Divide Rapidly in Improved Nutrient Medium

Sponges (Phylum Porifera) are among the oldest Metazoa and considered critical to understanding animal evolution and development. They are also the most prolific source of marine-derived chemicals with pharmaceutical relevance. Cell lines are important tools for research in many disciplines, and have been established for many organisms, including freshwater and terrestrial invertebrates. Despite many efforts over multiple decades, there are still no cell lines for marine invertebrates. In this study, we report a breakthrough: we demonstrate that an amino acid-optimized nutrient medium stimulates rapid cell division in 9 sponge species. The fastest dividing cells doubled in less than 1 hour. Cultures of 3 species were subcultured from 3 to 5 times, with an average of 5.99 population doublings after subculturing, and a lifespan from 21 to 35 days. Our results form the basis for developing marine invertebrate cell models to better understand early animal evolution, determine the role of secondary metabolites, and predict the impact of climate change to coral reef community ecology. Furthermore, sponge cell lines can be used to scale-up production of sponge-derived chemicals for clinical trials and develop new drugs to combat cancer and other diseases.

Разнообразие клеточных типов у гаплотипа H4 Placozoa sp.

Эволюционная ветвь Пластинчатых (Placozoa) имеет большое значение для понимания происхождения и эволюции Metazoa. Представители типа Placozoa обладают простым строением тела, однако полное отсутствие органов, нервной системы и мышечных клеток резко контрастирует с достаточно сложными поведенческими реакциями, в том числе динамическими изменениями формы тела. Известно 19 гаплотипов Placozoa, включающих два вида — Trichoplax adhaerens (H1) и Hoilungia hongkongensis (H13) — и пока ещё малоисследованные штаммы, обозначаемые как H2–H19 Placozoa sp. Хотя все Placozoa имеют похожий фенотип (пластинчатую дископодобную форму тела), анализ клеточной организации был сделан только для H1 (Trichoplax adhaerens) с идентификацией шести типов клеток. В этой работе мы, используя конфокальную и электронную микроскопию, исследовали организацию штамма H4, который близок к новому роду — Hoilungia. У H4 обнаружены все шесть основных типов клеток, идентифицированных ранее у H1. Между тем мы выявили у штамма H4 большее разнообразие клеток по форме, плотности и, впервые, по мембранному потенциалу митохондрий, чем ранее было описано для H1. Это позволяет нам подчеркнуть важность объединения методов молекулярно-генетических исследований и микроскопии для уточнения клеточной систематики, включая параметры митохондриальной активности для классификации клеток и их состояний. Сравнительно-эволюционное изучение клеточных типов у разных экологических групп Placozoa и их сопоставление с функциями расширяют понимание того, как относительно простой организм формирует сложное поведение и как типы клеток эволюционируют.

Understanding Animal Evolution: The Added Value of Sponge Transcriptomics and Genomics: The disconnect between gene content and body plan evolution.

Sponges are important but often-neglected organisms. The absence of classical animal traits (nerves, digestive tract, and muscles) makes sponges challenging for non-specialists to work with and has delayed getting high quality genomic data compared to other invertebrates. Yet analyses of sponge genomes and transcriptomes currently available have radically changed our understanding of animal evolution. Sponges are of prime evolutionary importance as one of the best candidates to form the sister group of all other animals, and genomic data are essential to understand the mechanisms that control animal evolution and diversity. Here we review the most significant outcomes of current genomic and transcriptomic analyses of sponges, and discuss limitations and future directions of sponge transcriptomic and genomic studies.

Myoanatomy of the velvet worm leg revealed by laboratory-based nanofocus X-ray source tomography

X-ray computed tomography (CT) is a powerful noninvasive technique for investigating the inner structure of objects and organisms. However, the resolution of laboratory CT systems is typically limited to the micrometer range. In this paper, we present a table-top nanoCT system in conjunction with standard processing tools that is able to routinely reach resolutions down to 100 nm without using X-ray optics. We demonstrate its potential for biological investigations by imaging a walking appendage of Euperipatoides rowelli, a representative of Onychophora-an invertebrate group pivotal for understanding animal evolution. Comparative analyses proved that the nanoCT can depict the external morphology of the limb with an image quality similar to scanning electron microscopy, while simultaneously visualizing internal muscular structures at higher resolutions than confocal laser scanning microscopy. The obtained nanoCT data revealed hitherto unknown aspects of the onychophoran limb musculature, enabling the 3D reconstruction of individual muscle fibers, which was previously impossible using any laboratory-based imaging technique.

The phylogenetic position of dicyemid mesozoans offers insights into spiralian evolution

BackgroundObtaining phylogenomic data for enigmatic taxa is essential to achieve a better understanding of animal evolution. Dicyemids have long fascinated biologists because of their highly simplified body organization, but their life-cycles remain poorly known. Based on the discovery of the dicyemid DoxC gene, which encodes a spiralian peptide, it has been proposed that dicyemids are members of the Spiralia. Other studies have suggested that dicyemids may have closer affinities to mollusks and annelids. However, the phylogenetic position of dicyemids has remained a matter of debate, leading to an ambiguous picture of spiralian evolution.ResultsIn the present study, newly sequenced transcriptomic data from Dicyema japonicum were complemented with published transcriptomic data or predicted gene models from 29 spiralian, ecdysozoan, and deuterostome species, generating a dataset (Dataset 1) for phylogenomic analyses, which contains 348 orthologs and 58,124 amino acids. In addition to this dataset, to eliminate systematic errors, two additional sub-datasets were created by removing compositionally heterogeneous or rapidly evolving sites and orthologs from Dataset 1, which may cause compositional heterogeneity and long-branch attraction artifacts. Maximum likelihood and Bayesian inference analyses both placed Dicyema japonicum (Dicyemida) in a clade with Intoshia linei (Orthonectida) with strong statistical support. Furthermore, maximum likelihood analyses placed the Dicyemida + Orthonectida clade within the Gastrotricha, while in Bayesian inference analyses, this clade is sister group to the clade of Gastrotricha + Platyhelminthes.ConclusionsWhichever the case, in all analyses, Dicyemida, Orthonectida, Gastrotricha, and Platyhelminthes constitute a monophyletic group that is a sister group to the clade of Mollusca + Annelida. Based on present phylogenomic analyses, dicyemids display close affinity to orthonectids, and they may share a common ancestor with gastrotrichs and platyhelminths, rather than with mollusks and annelids. Regarding spiralian phylogeny, the Gnathifera forms the sister group to the Rouphozoa and Lophotrochozoa, as has been suggested by previous studies; thus our analysis supports the traditional acoeloid–planuloid hypothesis of a nearly microscopic, non-coelomate common ancestor of spiralians.

Scallop genome provides insights into evolution of bilaterian karyotype and development

Reconstructing the genomes of bilaterian ancestors is central to our understanding of animal evolution, where knowledge from ancient and/or slow-evolving bilaterian lineages is critical. Here we report a high-quality, chromosome-anchored reference genome for the scallop Patinopecten yessoensis, a bivalve mollusc that has a slow-evolving genome with many ancestral features. Chromosome-based macrosynteny analysis reveals a striking correspondence between the 19 scallop chromosomes and the 17 presumed ancestral bilaterian linkage groups at a level of conservation previously unseen, suggesting that the scallop may have a karyotype close to that of the bilaterian ancestor. Scallop Hox gene expression follows a new mode of subcluster temporal co-linearity that is possibly ancestral and may provide great potential in supporting diverse bilaterian body plans. Transcriptome analysis of scallop mantle eyes finds unexpected diversity in phototransduction cascades and a potentially ancient Pax2/5/8-dependent pathway for noncephalic eyes. The outstanding preservation of ancestral karyotype and developmental control makes the scallop genome a valuable resource for understanding early bilaterian evolution and biology.

Animal Evolution: Last Word on Sponges-First?

A major problem in understanding animal evolution is where early branching phyla, especially sponges and comb jellies (sea gooseberries), sit in the tree of life. A new study seeks to overcome this problem by sampling more species and data cleansing.

New Ediacara fossils preserved in marine limestone and their ecological implications

Ediacara fossils are central to our understanding of animal evolution on the eve of the Cambrian explosion, because some of them likely represent stem-group marine animals. However, some of the iconic Ediacara fossils have also been interpreted as terrestrial lichens or microbial colonies. Our ability to test these hypotheses is limited by a taphonomic bias that most Ediacara fossils are preserved in sandstones and siltstones. Here we report several iconic Ediacara fossils and an annulated tubular fossil (reconstructed as an erect epibenthic organism with uniserial arranged modular units), from marine limestone of the 551–541 Ma Dengying Formation in South China. These fossils significantly expand the ecological ranges of several key Ediacara taxa and support that they are marine organisms rather than terrestrial lichens or microbial colonies. Their close association with abundant bilaterian burrows also indicates that they could tolerate and may have survived moderate levels of bioturbation.

Ctenophores

Ctenophores

Ctenophore Whole-Mount Antibody Staining

INTRODUCTIONCtenophores, or comb jellies, are a group of marine animals whose unique biological features and phylogenetic placement make them a key taxon for understanding animal evolution. Some characteristics are present in nearly all ctenophores, including biradial symmetry, comb rows composed of linked cilia, an apical sensory organ, and two tentacles bearing specialized adhesive cells. All ctenophores studied thus far have the same stereotyped cleavage program and go through a specific stage of development known as the cydippid larva, after which adult structures develop and diverge greatly among species; this is particularly useful for comparative studies. Because of the ease of embryo collection, their size (up to 1 mm in some species), and their rapid development, ctenophores have been attractive animals for experimental embryologists. This protocol describes how to fix ctenophore embryos and their cydippid larvae for antibody staining. Once the samples have been fixed, tissues are incubated with an antibody to the epitope of interest. A secondary antibody conjugated to a fluorescent molecule then reveals the expression pattern of the epitope. Fluorescent microscopy is used to visualize and document the signal. The protocol also includes methods for staining or counterstaining with a fluorescent derivative of phalloidin, which reveals F-actin in muscles and cell borders. Although the protocol focuses on embryonic and larval samples, the technique can also be applied to adult tissues.

Comb Jellies (Ctenophora): A Model for Basal Metazoan Evolution and Development

INTRODUCTIONCtenophores, or comb jellies, are a group of marine organisms whose unique biological features and phylogenetic placement make them a key taxon for understanding animal evolution. These gelatinous creatures are clearly distinct from cnidarian medusae (i.e., jellyfish). Key features present in the ctenophore body plan include biradial symmetry, an oral-aboral axis delimited by a mouth and an apical sensory organ, two tentacles, eight comb rows composed of interconnected cilia, and thick mesoglea. Other morphological features include definitive muscle cells, a nerve net, basal lamina, a sperm acrosome, and light-producing photocytes. Aspects of their development made them attractive to experimental embryologists as early as the 19th century. Recently, because of their role as an invasive species, studies on their role in ecology and fisheries-related fields have increased. Although the phylogenetic placement of ctenophores with respect to other animals has proven difficult, it is clear that, along with poriferans, placozoans, and cnidarians, ctenophores are one of the earliest diverging extant animal groups. It is important to determine if some of the complex features of ctenophores are examples of convergence or if they were lost in other animal branches. Because ctenophores are amenable to modern technical approaches, they could prove to be a highly useful emerging model.

Mnemiopsis leidyi Spawning and Embryo Collection

INTRODUCTIONCtenophores, or comb jellies, are a group of marine animals whose unique biological features and phylogenetic placement make them a key taxon for understanding animal evolution. Because of its large size, fecundity, abundance in coastal areas, and recent introduction to European waters, Mnemiopsis leidyi (commonly called "sea walnuts") is the most highly studied ctenophore. Under optimal conditions, these self-fertile hermaphrodites are capable of reproduction at 2 wk of age and can release up to 10,000 eggs per day. Adults can be maintained in large aquaria with gentle aeration as long as they are well fed and can be spawned daily; multiple generations can be raised in the laboratory. This protocol describes how to collect embryos from M. leidyi. Under natural conditions, spawning normally occurs ~8 h after sunset, such that eggs are released under the cover of darkness. Because spawning is triggered by the onset of darkness, keeping animals under an artificial light regimen in the laboratory can alter the time of spawning. This protocol is designed to induce animal spawning at approximately 11:00 a.m.; however, it can be adjusted for other times. The duration from spawning to hatching of larvae is 18-24 h.

Ctenophore Tissue Preparation and Extraction of RNA

INTRODUCTIONCtenophores, or comb jellies, are a group of marine animals whose unique biological features and phylogenetic placement make them a key taxon for understanding animal evolution. Some characteristics are present in nearly all ctenophores, including biradial symmetry, comb rows composed of linked cilia, an apical sensory organ, and two tentacles bearing specialized adhesive cells. All ctenophores studied thus far have the same stereotyped cleavage program and go through a specific stage of development known as the cydippid larva, after which adult structures develop and diverge greatly among species; this is particularly useful for comparative studies. In some cases, gene expression patterns appear to be conserved. Of particular interest is the finding that some genes are expressed in regions of the ctenophore body that are not morphologically distinct from the adjacent areas. However, it has proven difficult to determine the orthology of some genes, possibly because of the extreme divergence of ctenophore representatives. This protocol describes how to isolate total RNA from ctenophore embryos and larvae. After the specimens are sorted, cleaned, and concentrated, they are placed into TRI Reagent, a solution containing phenol and guanidine thiocyanate that allows for the effective isolation of total RNA. The resulting RNA can be used for various applications (e.g., to generate cDNA for reverse transcriptase-polymerase chain reactions). Although the protocol focuses on embryonic and larval samples, the technique can also be applied to adult tissues.

Ctenophore Tissue Preparation and Extraction of DNA

INTRODUCTIONCtenophores, or comb jellies, are a group of marine animals whose unique biological features and phylogenetic placement make them a key taxon for understanding animal evolution. Some characteristics are present in nearly all ctenophores, including biradial symmetry, comb rows composed of linked cilia, an apical sensory organ, and two tentacles bearing specialized adhesive cells. All ctenophores studied thus far have the same stereotyped cleavage program and go through a specific stage of development known as the cydippid larva, after which adult structures develop and diverge greatly among species; this is particularly useful for comparative studies. In some cases, gene expression patterns appear to be conserved. Of particular interest is the finding that some genes are expressed in regions of the ctenophore body that are not morphologically distinct from the adjacent areas. However, it has proven difficult to determine the orthology of some genes, possibly because of the extreme divergence of ctenophore representatives. This protocol describes how to isolate genomic DNA from ctenophores. The procedure can be applied to adult tissues, but it is best to use embryos and larvae. After washing and concentrating the embryos or larvae, DNA is extracted using DNAzol reagent, a guanidine-detergent lysing solution. The resulting DNA can be used for polymerase chain reaction (PCR) or other applications.

Ctenophore Whole-Mount In Situ Hybridization

INTRODUCTIONCtenophores, or comb jellies, are a group of marine animals whose unique biological features and phylogenetic placement make them a key taxon for understanding animal evolution. Some characteristics are present in nearly all ctenophores, including biradial symmetry, comb rows composed of linked cilia, an apical sensory organ, and two tentacles bearing specialized adhesive cells. All ctenophores studied thus far have the same stereotyped cleavage program and go through a specific stage of development known as the cydippid larva, after which adult structures develop and diverge greatly among species; this is particularly useful for comparative studies. In some cases, gene expression patterns appear to be conserved. Of particular interest is the finding that some genes are expressed in regions of the ctenophore body that are not morphologically distinct from the adjacent areas. However, it has proven difficult to determine the orthology of some genes, possibly because of the extreme divergence of ctenophore representatives. This protocol describes how to fix, prepare, and hybridize antisense RNA probes in ctenophore embryos and cydippid larvae, as well as how to detect the probes using an alkaline phosphatase-conjugated antibody and colorimetric substrates. Using these techniques, it is possible to determine which cells or tissues express the gene of interest. Although the protocol focuses on embryonic and larval samples, the technique can also be applied to adult tissues.

Recent advances in crustacean genomics

Crustaceans are a diverse and ancient group of arthropods that have long been studied as interesting model systems in biology, especially for understanding animal evolution and physiology and for environmentally relevant studies. Like many model systems, advances in DNA-sequencing methodologies have led to a large amount of genomics-related projects. The purpose of this article is to highlight the genome projects and functional genomics (transcriptomics) projects that are currently underway in crustacean biology. Specifically, we have surveyed the amount of publicly available DNA sequence data (both genomic and EST data) across all crustacean taxa for which a significant number of DNA sequences have been generated. Several ongoing projects are presented including the ecology of invasive species, thermal physiology, ion and water balance, ecology and evolutionary biology, and developmental biology.

The evolution of the animals: introduction to a Linnean tercentenary celebration

Celebrating 300 years since the birth of Carl Linnaeus (1707-1778), a meeting was held in June 2007 to review recent progress made in understanding the origins and evolutionary radiation of the animals. The year 2008 celebrates the 250th anniversary of the publication of the 10th edition of Linnaeus' Systema Naturae, generally considered to be the starting point of zoological nomenclature. With subsequent advances in comparative taxonomic and systematic studies, Darwin's discovery of evolution by natural selection, the birth of phylogenetic systematics, and the wider interest in biodiversity, it is salutary to consider that many of the major advances in our understanding of animal evolution have been made in recent years. Phylogenetic systematics, drawing from evidence provided by genotype, phenotype and an understanding of the link between them through comparative embryological and evolutionary developmental studies, has provided a wide consensus of the major branching patterns of the tree of life. More importantly, the integrated approaches discussed in the 16 contributions to this volume highlight the identity and nature of problematic taxa, the missing data, errors in existing analytical procedures and the promise of a wealth of additional characters from genomes that need to be accumulated and assessed in providing a definitive Systema Naturae.

Unleashing the Force of Cladistics? Metazoan Phylogenetics and Hypothesis Testing

The accumulation of multiple phylogenetic hypotheses for the Metazoa invites an evaluation of current progress in the field. I discuss three case studies from the recent literature to assess how cladistic analyses of metazoan morphology have contributed to our understanding of animal evolution. The first case study on cleavage cross patterns examines whether a decade of unanimous character scoring across different cladistic studies can be considered a reliable indicator of accumulated wisdom. The two remaining case studies illustrate how the unique strength of cladistic analyses to arbitrate between competing hypotheses can be crippled when insufficient attention is directed towards the construction of the data matrix. The second case study discusses a recent morphological cladistic analysis aimed at providing insight into the evolution of larval ciliary bands (prototrochs) in the Spiralia, and the third case study evaluates how four subsequent morphological cladistic analyses have contributed to our understanding of the phylogenetic placement of a problematicum, the Myzostomida. I conclude that current phylogenetic analyses of the Metazoa have not fully exploited the power of cladistics to test available alternative hypotheses. If our goal is to generate genuine progress in understanding rather than stochastic variation of opinions through time, we have to shift our attention from using cladistics as an easy tool to generate "novel" hypotheses of metazoan relationships, towards employing cladistics more critically as an effective instrument to test the relative merit of available multiple alternative hypotheses.