Phylotypic stage

Last updated

In Embryology a phylotypic stage or phylotypic period is a particular developmental stage or developmental period during mid-embryogenesis where embryos of related species within a phylum express the highest degree of morphological and molecular resemblance. Recent molecular studies in various plant and animal species were able to quantify the expression of genes covering crucial stages of embryo development and found that during the morphologically defined phylotypic period the evolutionary oldest genes, genes with similar temporal expression patterns, and genes under strongest purifying selection are most active throughout the phylotypic period. [1]

Contents

Historical origins of concept

Haeckel's drawings, reproduced by G.J. Romanes in 1892. Early embryologists, including Haeckel and von Baer, noted that embryos of different animals pass through a similar stage in which they resemble one another very closely. Baer embryos.png
Haeckel's drawings, reproduced by G.J. Romanes in 1892. Early embryologists, including Haeckel and von Baer, noted that embryos of different animals pass through a similar stage in which they resemble one another very closely.
Karl Ernst von Baer, whose third law of embryology gave the basis for the idea of the phylotypic stage PGRS 2 015 Baer - crop.jpg
Karl Ernst von Baer, whose third law of embryology gave the basis for the idea of the phylotypic stage

The idea that embryos of different species have similar morphologies at some point during development can be traced back to Aristotle. Aristotle observed a number of developing vertebrate embryos, noting in his text The Generation of Animals that the morphological differences among the different embryos arose late in development. In 1828, Karl Ernst von Baer created his laws of embryology, which summarized the results of his comparative embryogenesis studies. [2] In his first law, he proposed that the more general characters of a group appear earlier in their embryos than the more special characters. [2] In 1866, Ernst Haeckel proposed that each developing organism passes through the evolutionary stages of its ancestors, i.e., ontogeny recapitulates phylogeny. [3] The hypothesis that different organisms pass through the developmental stages of closely related organisms is outdated. However, the idea that early stages of development are conserved among species, with increasing divergence as development progresses, has influenced modern evolutionary and developmental biology. [4] The early conservation or funnel model of development (see below) is closely tied to these historical origins.

Phylotypic period

The first formulation of the phylotypic period concept came in 1960 from Friedrich Seidel's Körpergrundgestalt, [5] which translates to “basic body shape.” In 1977, Cohen defined the phyletic stage as the first stage that reveals the general characters shared by all members of that phylum. [6] Klaus Sander revised this concept in 1983 and named it the phylotypic stage, [7] which is ‘‘the stage of greatest similarity between forms which, during evolution, have differently specialized both in their modes of adult life and with respect to the earliest stages of ontogenesis." Note that this definition demonstrates his support for the hourglass model (see below). Recent papers refer to the phylotypic period, or the phylotypic stage, as a period of maximal similarity between species within each animal phylum. [8]

While this concept was originally devised using morphological comparisons of developing embryos from different species, [7] the period of maximal similarity has recently been identified using molecular evidence. The phylotypic period has been identified using conservation of gene expression, [8] [9] estimates of gene age, [10] [11] [12] gene sequence conservation, [13] the expression of regulatory genes and transcription factors, [13] and the interconnectivity of genes and proteins. [14]

Funnel and hourglass models

The funnel model is the hypothesis that the most conserved stage of development (the phylotypic period) occurs at the beginning of embryogenesis, with increasing divergence as development progresses. This is also known as the early conservation model of development.

Evidence for an alternative model arose from careful comparisons of the temporal divergence in morphology of the embryos of different species. For example, Klaus Sander noticed that the “incredible variation in larvae and adults” of insects occurs after they "develop from nearly identical rudiments in the germ band stage". [7] The most conserved stage of development, the germ band stage, occurs near the middle of development rather than at the beginning, supporting a mid-developmental period of maximal similarity between species. This model, called the hourglass model, [15] [16] is the idea that early embryos of different species display divergent forms but their morphologies converge in the middle of development, followed by a period of increasing divergence.

Support for hourglass model

Contrary to the early morphological work by von Baer and Haeckel, recent morphological studies have demonstrated the greatest divergence among closely related species both early in development (gastrulation) and late in development, [17] supporting the hourglass model. Further support for the hourglass model came from the discovery that Hox genes, a group of sequentially activated genes that regulate anterior-posterior body axis formation, are activated during the middle of development at the phylotypic stage. [18] Because these genes are highly conserved and are involved in body axis formation, the activation of Hox genes could be an important player in the heightened conservation among embryos of closely related species during mid-development. [15]

The advent of next-generation sequencing enabled scientists to use molecular methods to identify the period of development that has the most conserved gene expression patterns among different species. In 2010, two studies found molecular evidence that supports the hourglass model. [8] [10] Kalinka et al. [8] sequenced the transcriptome of six Drosophila species over developmental time, identifying the most conserved gene expression in mid-development during the arthropod germ band developmental stage. Genes that were enriched in the developing embryos at the germ band stage are involved in cellular and organismal development. Domazet-Lošo and Tautz [10] analyzed the transcriptome of zebrafish (Danio rerio) over developmental time, from unfertilized eggs to adults. They used a method called genomic phylostratigraphy to estimate the age of each gene during development. In zebrafish, as well as in additional transcriptomic datasets of Drosophila, the mosquito Anopheles and the nematode Caenorhabditis elegans , the authors found that genes expressed during mid-development are older than those expressed at the beginning and end of development, supporting the hourglass model.

Other recent genomic studies have supported a mid-developmental phylotypic stage in vertebrates [9] and in the plant Arabidopsis thaliana. [11] [12] [19] The temporal gene expression profiles for a developing mouse (Mus musculus), chicken (Gallus gallus), frog ( Xenopus laevis ) and zebrafish (Danio rerio) revealed that the most conserved gene expression in vertebrates occurs in mid-development at the pharyngular embryo stage. The pharyngula stage occurs when the four distinguishing features of vertebrates (notochord, dorsal hollow nerve cord, post-anal tail, and a series of paired branchial slits) have developed.

Support for early conservation (funnel) model

Recent molecular data also provide support for the early conservation model. For example, Piasecka et al. [13] re-analyzed the zebrafish dataset published by Domazet-Lošo and Tautz. [10] They found that applying a log-transformation to the gene expression data changed the results to support highest conservation in early development. Further, after clustering the zebrafish gene expression data into “transcription modules” reflecting each stage of development, they found multiple lines of evidence supporting the early conservation model (gene sequence, age, gene family size, and expression conservation) while only the analysis of gene regulatory regions supported the hourglass model. [13]

One hypothesis for the evolutionary conservation during the phylotypic period is that it is a period characterized by a high level of interactions as the body plan is being established. [14] In zebrafish, the interconnectivity of proteins over developmental time was found to be highest in early development, supporting the early conservation model. [14] Another way to examine the point in development at which developmental constraints are the strongest is through experimental gene loss, because the removal of a gene should be more deleterious when it is expressed at a developmental stage with stronger evolutionary constraints. [20] Gene knockout experiments from mice and zebrafish demonstrated that the ratio of essential genes to non-essential genes decreases over developmental time, suggesting that there are stronger constraints in early development that are relaxed over time. [20] Despite increasing evidence supporting the hourglass model, identifying the point in development that is most conserved among species with a phylum (the phylotypic period) is a controversy in the field of developmental biology.

Intra-phylum vs. inter-phylum phylotypic period

The phylotypic period is defined as a period of maximal similarity between species within a phylum, but a recent study compared the phylotypic period across different phyla to examine whether the same conserved periods during development have been maintained across deeper phylogenetic relationships. Levin et al. [21] compared the developmental gene expression patterns among ten individuals from ten different animal phyla and found evidence for an inverse hourglass model of gene expression divergence among different phyla. [21] This inverse hourglass model reflects the observation that gene expression was significantly more divergent among species at the mid-developmental transition, while gene expression was more conserved in early and late stages of development. [21] While this intriguing pattern could have implications for our definition of a phylum, [21] a follow-up paper argued that there are a few methodical issues that must be addressed to test the hypothesis that the timing of developmental constraints are different among phyla compared to within a phylum. First, the comparison of a single representative of ten different phyla could reflect differences between phyla as well as the deeper or shallower phylogenetic branches that fall between those ten individuals, so greater sampling within each phyla is necessary. [22] Second, pairwise comparisons treat each of the ten species as independent observations, but some species are more closely related than others. [22]

Related Research Articles

<span class="mw-page-title-main">Zebrafish</span> Species of fish

The zebrafish is a freshwater fish belonging to the minnow family (Cyprinidae) of the order Cypriniformes. Native to India and South Asia, it is a popular aquarium fish, frequently sold under the trade name zebra danio. It is also found in private ponds.

Developmental biology is the study of the process by which animals and plants grow and develop. Developmental biology also encompasses the biology of regeneration, asexual reproduction, metamorphosis, and the growth and differentiation of stem cells in the adult organism.

<span class="mw-page-title-main">Embryo drawing</span> Illustration of embryos in their developmental sequence

Embryo drawing is the illustration of embryos in their developmental sequence. In plants and animals, an embryo develops from a zygote, the single cell that results when an egg and sperm fuse during fertilization. In animals, the zygote divides repeatedly to form a ball of cells, which then forms a set of tissue layers that migrate and fold to form an early embryo. Images of embryos provide a means of comparing embryos of different ages, and species. To this day, embryo drawings are made in undergraduate developmental biology lessons.

The theory of recapitulation, also called the biogenetic law or embryological parallelism—often expressed using Ernst Haeckel's phrase "ontogeny recapitulates phylogeny"—is a historical hypothesis that the development of the embryo of an animal, from fertilization to gestation or hatching (ontogeny), goes through stages resembling or representing successive adult stages in the evolution of the animal's remote ancestors (phylogeny). It was formulated in the 1820s by Étienne Serres based on the work of Johann Friedrich Meckel, after whom it is also known as Meckel–Serres law.

<span class="mw-page-title-main">Evolutionary developmental biology</span> Comparison of organism developmental processes

Evolutionary developmental biology is a field of biological research that compares the developmental processes of different organisms to infer how developmental processes evolved.

Segmentation in biology is the division of some animal and plant body plans into a linear series of repetitive segments that may or may not be interconnected to each other. This article focuses on the segmentation of animal body plans, specifically using the examples of the taxa Arthropoda, Chordata, and Annelida. These three groups form segments by using a "growth zone" to direct and define the segments. While all three have a generally segmented body plan and use a growth zone, they use different mechanisms for generating this patterning. Even within these groups, different organisms have different mechanisms for segmenting the body. Segmentation of the body plan is important for allowing free movement and development of certain body parts. It also allows for regeneration in specific individuals.

<span class="mw-page-title-main">Somitogenesis</span>

Somitogenesis is the process by which somites form. Somites are bilaterally paired blocks of paraxial mesoderm that form along the anterior-posterior axis of the developing embryo in segmented animals. In vertebrates, somites give rise to skeletal muscle, cartilage, tendons, endothelium, and dermis.

Plant embryonic development, also plant embryogenesis is a process that occurs after the fertilization of an ovule to produce a fully developed plant embryo. This is a pertinent stage in the plant life cycle that is followed by dormancy and germination. The zygote produced after fertilization must undergo various cellular divisions and differentiations to become a mature embryo. An end stage embryo has five major components including the shoot apical meristem, hypocotyl, root meristem, root cap, and cotyledons. Unlike the embryonic development in animals, and specifically in humans, plant embryonic development results in an immature form of the plant, lacking most structures like leaves, stems, and reproductive structures. However, both plants and animals including humans, pass through a phylotypic stage that evolved independently and that causes a developmental constraint limiting morphological diversification.

Hox genes, a subset of homeobox genes, are a group of related genes that specify regions of the body plan of an embryo along the head-tail axis of animals. Hox proteins encode and specify the characteristics of 'position', ensuring that the correct structures form in the correct places of the body. For example, Hox genes in insects specify which appendages form on a segment, and Hox genes in vertebrates specify the types and shape of vertebrae that will form. In segmented animals, Hox proteins thus confer segmental or positional identity, but do not form the actual segments themselves.

<span class="mw-page-title-main">Body plan</span> Set of morphological features common to members of a phylum of animals

A body plan, Bauplan, or ground plan is a set of morphological features common to many members of a phylum of animals. The vertebrates share one body plan, while invertebrates have many.

The pharyngula is a stage in the embryonic development of vertebrates. At this stage, the embryos of all vertebrates are similar, having developed features typical of vertebrates, such as the beginning of a spinal cord. Named by William Ballard, the pharyngula stage follows the blastula, gastrula and neurula stages.

<span class="mw-page-title-main">Otic vesicle</span> Two sac-like invaginations formed and subsequently closed off during embryonic development

Otic vesicle, or auditory vesicle, consists of either of the two sac-like invaginations formed and subsequently closed off during embryonic development. It is part of the neural ectoderm, which will develop into the membranous labyrinth of the inner ear. This labyrinth is a continuous epithelium, giving rise to the vestibular system and auditory components of the inner ear. During the earlier stages of embryogenesis, the otic placode invaginates to produce the otic cup. Thereafter, the otic cup closes off, creating the otic vesicle. Once formed, the otic vesicle will reside next to the neural tube medially, and on the lateral side will be paraxial mesoderm. Neural crest cells will migrate rostral and caudal to the placode.

Evolutionary developmental biology (evo-devo) is the study of developmental programs and patterns from an evolutionary perspective. It seeks to understand the various influences shaping the form and nature of life on the planet. Evo-devo arose as a separate branch of science rather recently. An early sign of this occurred in 1999.

Important structures in plant development are buds, shoots, roots, leaves, and flowers; plants produce these tissues and structures throughout their life from meristems located at the tips of organs, or between mature tissues. Thus, a living plant always has embryonic tissues. By contrast, an animal embryo will very early produce all of the body parts that it will ever have in its life. When the animal is born, it has all its body parts and from that point will only grow larger and more mature. However, both plants and animals pass through a phylotypic stage that evolved independently and that causes a developmental constraint limiting morphological diversification.

<span class="mw-page-title-main">Plant evolution</span> Subset of evolutionary phenomena that concern plants

Plant evolution is the subset of evolutionary phenomena that concern plants. Evolutionary phenomena are characteristics of populations that are described by averages, medians, distributions, and other statistical methods. This distinguishes plant evolution from plant development, a branch of developmental biology which concerns the changes that individuals go through in their lives. The study of plant evolution attempts to explain how the present diversity of plants arose over geologic time. It includes the study of genetic change and the consequent variation that often results in speciation, one of the most important types of radiation into taxonomic groups called clades. A description of radiation is called a phylogeny and is often represented by type of diagram called a phylogenetic tree.

Vasa is an RNA binding protein with an ATP-dependent RNA helicase that is a member of the DEAD box family of proteins. The vasa gene is essential for germ cell development and was first identified in Drosophila melanogaster, but has since been found to be conserved in a variety of vertebrates and invertebrates including humans. The Vasa protein is found primarily in germ cells in embryos and adults, where it is involved in germ cell determination and function, as well as in multipotent stem cells, where its exact function is unknown.

<span class="mw-page-title-main">Hox genes in amphibians and reptiles</span>

Hox genes play a massive role in some amphibians and reptiles in their ability to regenerate lost limbs, especially HoxA and HoxD genes.

von Baers laws (embryology) Foundational theory of embryonic development (published 1828)

In developmental biology, von Baer's laws of embryology are four rules proposed by Karl Ernst von Baer to explain the observed pattern of embryonic development in different species.

<span class="mw-page-title-main">Evo-devo gene toolkit</span>

The evo-devo gene toolkit is the small subset of genes in an organism's genome whose products control the organism's embryonic development. Toolkit genes are central to the synthesis of molecular genetics, palaeontology, evolution and developmental biology in the science of evolutionary developmental biology (evo-devo). Many of them are ancient and highly conserved among animal phyla.

<span class="mw-page-title-main">Grainyhead-like gene family</span> Family of highly conserved genes for transcription factors in animals

Grainyhead-like genes are a family of highly conserved transcription factors that are functionally and structurally homologous across a large number of vertebrate and invertebrate species. For an estimated 100 million years or more, this genetic family has been evolving alongside life to fine tune the regulation of epithelial barrier integrity during development, fine-tuning epithelial barrier establishment, maintenance and subsequent homeostasis. The three main orthologues, Grainyhead-like 1, 2 and 3, regulate numerous genetic pathways within different organisms and perform analogous roles between them, ranging from neural tube closure, wound healing, establishment of the craniofacial skeleton and repair of the epithelium. When Grainyhead-like genes are impaired, due to genetic mutations in embryogenesis, it will cause the organism to present with developmental defects that largely affect ectodermal tissues in which they are expressed. These subsequent congenital disorders, including cleft lip and exencephaly, vary greatly in their severity and impact on the quality of life for the affected individual. There is much still to learn about the function of these genes and the more complex roles of Grainyhead-like genes are yet to be discovered.

References

  1. Drost, Hajk-Georg; Janitza, Philipp; Grosse, Ivo; Quint, Marcel (2017). "Cross-kingdom comparison of the developmental hourglass". Current Opinion in Genetics & Development. 45: 69–75. doi: 10.1016/j.gde.2017.03.003 . PMID   28347942.
  2. 1 2 von Baer, Karl Ernst (1828). Über Entwickelungsgeschichte der Thiere. Beobachtung und Reflexion. Königsberg: Bornträger.
  3. Haeckel, Ernst (1866). Generelle Morphologie der Organismen. Berlin: Georg Reimer.
  4. Sander, Klaus; Schmidt-Ott, Urs (2004). "Evo-Devo Aspects of Classical and Molecular Data in a Historical Perspective". Journal of Experimental Zoology Part B: Molecular and Developmental Evolution. 302B (1): 69–91. doi: 10.1002/jez.b.20003 . PMID   14760654.
  5. Seidel, F. (1960). "Körpergrundgestalt und Keimstruktur. Eine Erörterung über die Grundlagen der vergleichenden und experimentellen Embryologie und deren Gültigkeit bei phylogenetischen Berlegungen". Zoologischer Anzeiger. 164: 245–305.
  6. Cohen, J. (1977). Reproduction. London: Butterworth.
  7. 1 2 3 Sander, K. (1983). In Development and Evolution: the sixth Symposium of the British Society for Developmental Biology. Cambridge University Press.
  8. 1 2 3 4 Kalinka, Alex T.; Varga, Karolina M.; Gerrard, Dave T.; Preibisch, Stephan; Corcoran, David L.; Jarrells, Julia; Ohler, Uwe; Bergman, Casey M.; Tomancak, Pavel (2010-12-09). "Gene expression divergence recapitulates the developmental hourglass model". Nature. 468 (7325): 811–814. Bibcode:2010Natur.468..811K. doi:10.1038/nature09634. ISSN   0028-0836. PMID   21150996. S2CID   4416340.
  9. 1 2 Irie, Naoki; Kuratani, Shigeru (2011-03-22). "Comparative transcriptome analysis reveals vertebrate phylotypic period during organogenesis". Nature Communications. 2: 248. Bibcode:2011NatCo...2..248I. doi:10.1038/ncomms1248. ISSN   2041-1723. PMC   3109953 . PMID   21427719.
  10. 1 2 3 4 Domazet-Lošo, Tomislav; Tautz, Diethard (2010-12-09). "A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns". Nature. 468 (7325): 815–818. Bibcode:2010Natur.468..815D. doi:10.1038/nature09632. ISSN   0028-0836. PMID   21150997. S2CID   1417664.
  11. 1 2 Quint, Marcel; Drost, Hajk-Georg; Gabel, Alexander; Ullrich, Kristian Karsten; Bönn, Markus; Grosse, Ivo (2012-10-04). "A transcriptomic hourglass in plant embryogenesis". Nature. 490 (7418): 98–101. Bibcode:2012Natur.490...98Q. doi:10.1038/nature11394. ISSN   0028-0836. PMID   22951968. S2CID   4404460.
  12. 1 2 Drost, Hajk-Georg; Gabel, Alexander; Grosse, Ivo; Quint, Marcel (2015-05-01). "Evidence for Active Maintenance of Phylotranscriptomic Hourglass Patterns in Animal and Plant Embryogenesis". Molecular Biology and Evolution. 32 (5): 1221–1231. doi:10.1093/molbev/msv012. ISSN   0737-4038. PMC   4408408 . PMID   25631928.
  13. 1 2 3 4 Piasecka, Barbara; Lichocki, Paweł; Moretti, Sébastien; Bergmann, Sven; Robinson-Rechavi, Marc (2013-04-25). "The Hourglass and the Early Conservation Models—Co-Existing Patterns of Developmental Constraints in Vertebrates". PLOS Genetics. 9 (4): e1003476. doi: 10.1371/journal.pgen.1003476 . ISSN   1553-7404. PMC   3636041 . PMID   23637639.
  14. 1 2 3 Comte, Aurélie; Roux, Julien; Robinson-Rechavi, Marc (2010-03-01). "Molecular signaling in zebrafish development and the vertebrate phylotypic period". Evolution & Development. 12 (2): 144–156. doi:10.1111/j.1525-142X.2010.00400.x. ISSN   1525-142X. PMC   2855863 . PMID   20433455.
  15. 1 2 Duboule, D. (1994-01-01). "Temporal colinearity and the phylotypic progression: a basis for the stability of a vertebrate Bauplan and the evolution of morphologies through heterochrony". Development. Supplement: 135–142. PMID   7579514.
  16. Raff, Rudolf A. (1996). The Shape of Life: Genes, Development, and the Evolution of Animal Form. University of Chicago Press. ISBN   9780226256573.
  17. Schmidt, Kai; Starck, J. Matthias (2004-09-15). "Developmental variability during early embryonic development of zebra fish, Danio rerio". Journal of Experimental Zoology Part B: Molecular and Developmental Evolution. 302B (5): 446–457. doi:10.1002/jez.b.21010. ISSN   1552-5015. PMID   15580642.
  18. Slack, J. M. W.; Holland, P. W. H.; Graham, C. F. (1993-02-11). "The zootype and the phylotypic stage". Nature. 361 (6412): 490–492. Bibcode:1993Natur.361..490S. doi:10.1038/361490a0. PMID   8094230. S2CID   4362531.
  19. Drost, Hajk-Georg; Bellstaedt, Julia; Ó'Maoiléidigh, Diarmuid S.; Silva, Anderson T.; Gabel, Alexander; Weinholdt, Claus; Ryan, Patrick T.; Dekkers, Bas J.W.; Bentsink, Leónie; Hilhorst, Henk W.M.; Ligterink, Wilco; Wellmer, Frank; Grosse, Ivo; Quint, Marcel (2016-02-23). "Post-embryonic Hourglass Patterns Mark Ontogenetic Transitions in Plant Development". Molecular Biology and Evolution. 33 (5): 1158–1163. doi: 10.1093/molbev/msw039 . PMC   4839224 . PMID   26912813.
  20. 1 2 Roux, Julien; Robinson-Rechavi, Marc (2008-12-19). "Developmental Constraints on Vertebrate Genome Evolution". PLOS Genetics. 4 (12): e1000311. doi: 10.1371/journal.pgen.1000311 . ISSN   1553-7404. PMC   2600815 . PMID   19096706.
  21. 1 2 3 4 Levin, Michal; Anavy, Leon; Cole, Alison G.; Winter, Eitan; Mostov, Natalia; Khair, Sally; Senderovich, Naftalie; Kovalev, Ekaterina; Silver, David H. (2016-03-31). "The mid-developmental transition and the evolution of animal body plans". Nature. 531 (7596): 637–641. Bibcode:2016Natur.531..637L. doi:10.1038/nature16994. ISSN   0028-0836. PMC   4817236 . PMID   26886793.
  22. 1 2 Hejnol, Andreas; Dunn, Casey W. (2016). "Animal Evolution: Are Phyla Real?". Current Biology. 26 (10): R424–R426. doi: 10.1016/j.cub.2016.03.058 . PMID   27218852.