BIOL 30115 – Evolutionary Biology Mapanao & Reboa EXERCISE NO. 3 BASES OF CLADISTICS PROCEDURE Taxonomic ranking based on cladistics In this activity, you will create a taxonomic ranking based on the given proposed cladogram of chordates proposed below. Free answers are given below as your starting point. Image from Wikipedia (2021) – Phylum Chordata cladogram Phylum: Chordata Subphylum: Cephalocohordata Clade: Olfactores Genus: Haikouella (extinct) Subphylum: Tunicata Class: Appendicularia Class: Thaliacea Class: Ascidiacea Clade: Craniata Superclass: Cyclostomata (undetermined linkage) Class: Myxini Class: Hyperoartia Clade: ????? (undetermined linkage) Class: Conodonta (extinct) Class: Pteraspidomorphi (extinct) Class: Cephalaspidomorphi (extinct) Infraphylum: Gnathostomata Class: Placodermi (extinct) Clade: Eugnathostomata (crown gnathostomata) ___________________________________________________________________________________________________________________________________________________________________________________________ Polytechnic University of the Philippines Page|1 BIOL 30115 – Evolutionary Biology Mapanao & Reboa Phylum: Chordata Subphylum: Cephalocohordata Class: Amphioxus Clade: Olfactores Genus: Haikouella (extinct) Subphylum: Tunicata Class: Appendicularia Class: Thaliacea Class: Ascidiacea Clade: Craniata Superclass: Cyclostomata (undetermined linkage) Class: Myxini Class: Hyperoartia Clade: ????? (undetermined linkage) Class: Conodonta (extinct) Class: Pteraspidomorphi (extinct) Class: Cephalaspidomorphi (extinct) Infraphylum: Gnathostomata Class: Placodermi (extinct) Clade: Eugnathostomata (crown gnathostomata) Class: Acanlhodii (extinct) Class: Aclinopterygii Clade: Osteichthyes Class: Actinopterygii Clade: Sarcopterygii Super Class: Actinistia Clade: ????? (undetermined linkage) Class: Dipnoi Infraphylum: Tetrapoda Class: Amphibia Clade: Amniotes Class: Mammalia Clade: Sauropsida Class: Archosauromorpha Class: Lepidosauromorpha ___________________________________________________________________________________________________________________________________________________________________________________________ Polytechnic University of the Philippines Page|2 BIOL 30115 – Evolutionary Biology Mapanao & Reboa https://natmus.humboldt.edu/exhibits/plants-history/evolution-land-plants Note: - Land plants – clade Embryophyta Vascular plants – clade Tracheophyta Seed plants – clade Spermatophytes Gymnosperms – clade Acrogymnospermae Angiosperms – clade Angiospermae o ANA grade or basal angiosperms (paraphyletic) o Clade Mesangiospermae - core angiosperms Group: Algae (paraphyletic) Clade: Embryophyta (land plants) _______________________________________ _______________________________________ ___________________________________________________________________________________________________________________________________________________________________________________________ Polytechnic University of the Philippines Page|3 BIOL 30115 – Evolutionary Biology Mapanao & Reboa Group: Algae (paraphyletic) Clade: Embryophyta (Land Plants w/ Cuticle), (~420MYA) Class: (Liverworts) • Haplomitriopsida • Marchantiopsida • Jungermanniopsida Class: (Hornworts) • Leiosporocerotopsida • Anthocerotopsida Class: (Mosses) • • • • • • • • Takakiopsida Sphagnopsida Andreaeopsida Andreaeobryopsida Oedipodiopsida Polytrichopsida Tetraphidopsida Bryopsida Clade: Tracheophyta (Vascular Plants w/ Xylem and Phloem), (~410-375 MYA) Class: (Lycopods) • Lycopodiopsida • Zosterophyllopsida (extinct) Class: (Ferns and Horsetails) • Cladoxylopsida (extinct) • Polypodiopsida Clade: Spermatophytes (Seed Plants w/ Woody Tissue and Seeds) Clade: Acrogymnospermae (~300 MYA) Class: Cycadopsida (Cycads) Class: Ginkgoopsida (Ginkgo) Class: Pinopsida (Conifers) Clade: Angiosperm (w/ Flowers and Carpel), (~120 MYA) *MYA – Million Years Ago ___________________________________________________________________________________________________________________________________________________________________________________________ Polytechnic University of the Philippines Page|4 BIOL 30115 – Evolutionary Biology Mapanao & Reboa https://theoneandonlybioproject.weebly.com/eubacteria.html Domain: Bacteria _______________________________________ _______________________________________ ___________________________________________________________________________________________________________________________________________________________________________________________ Polytechnic University of the Philippines Page|5 BIOL 30115 – Evolutionary Biology Mapanao & Reboa Domain: Bacteria Phylum: Firmicutes Genus: Mycoplasma Phylum: Actinobacteria Genus: Actinomycetes Genus: Clostridium Phylum: Spirochaetota Order: Spirochetes Phylum: Chlorobi Order: Rhodospirillales (Green Sulfur) Order: Cyanobacteriales (Cyanobacteria) Order: Prochlorales (Prochlorophytes) Order: Chromatiales (Purple Sulfur) Phylum: Pseudomonadota Genus: Rhodopseudomonas Family: Rhodospirillaceae (Purple nonsulfur) Genus: Desulfovibrios Order: Rikettsia Phylum: Myxococcota Order: Myxococcales ___________________________________________________________________________________________________________________________________________________________________________________________ Polytechnic University of the Philippines Page|6 BIOL 30115 – Evolutionary Biology Mapanao & Reboa Creating your own monophyletic groupings based on the organisms features In this activity, you will create a cladogram with the indicated features (refer to the cladograms above) that will make as much as possible a monophyletic grouping. You can omit traits that seem to be not relevant to the monophyly. Otherwise, you can give additional traits not indicated below based on what you know or have researched that will make the monophyly. Also, you can sort traits given which is applicable to the taxa given, assuming that those taxa have those traits. Enjoy! The Three (3) Domains of Life Key characteristics - Eukaryotic cell with two (2) flagella (or at least have existed once during its lifecycle) - Single gene encoding a single protein enzyme with two separate functions essential in thymine nucleotide metabolism - Plastids (like chloroplastids, leukoplastids, chromoplastids, apicoplastids etc.) Unique flagella structures - Almost all doesn‟t have plastids - Having highly modified mitochondria to no mitochondria at all - Cellular structures to support cellular ingestion of nutrients - Phagocytic ingestion of foods - Many have one (1) flagella (or at least have existed once during its lifecycle) - Membrane-cytoplasmic structures to support cytoplasmic extensions (pseudopodia, filopodia etc.) Clades Bikonta • • Archaeplastida-Hacrobia-SAR supergroup Archaeplastida • • Chromista Excavata supergroup • Discoba • • Loukozoa • • • Archaeplastida-Hacrobia-SAR supergroup Archaeplastida Chromista • • • Excavata supergroup Discoba Loukozoa • • CRuMs supergroup Amorphea ___________________________________________________________________________________________________________________________________________________________________________________________ Polytechnic University of the Philippines Page|7 BIOL 30115 – Evolutionary Biology Mapanao & Reboa - Chromosomes are linear and found in the nucleus Nucleus, endoplasmic reticulum, and other membrane-bounded organelles Endosymbionts (mitochondria and plastids) Phospholipids chains of the cell membrane is linear with glycerol having ester linkages to a fatty acid Has many form of RNA polymerase Methionine is used for the initiation of protein synthesis Cell wall constitution can be diverse from organic to mineral origin • • • • • • • • • Loukozoa Bikonta Archaeplastida-Hacrobia-SAR supergroup Archaeplastida Discoba Chromista Eukarya Excavata supergroup CRuMs supergroup • Amorphea - Their chloroplasts have chlorophyll “a” and “b” as the main photosynthesis pigments - Main photosynthesis product is made up of starch - Almost all are autotrophic • Archaeplastida - Have variety of photosynthetic and non-photosynthetic plastids with diverse pigments different from archaeplastids - Many are autotrophic while some are heterotrophic • Chromista - Flagellates and some amoeboid protists Distinct “discoid” (disc) shape cristae of the mitochondria Most are heterotrophic • Discoba - - All are heterotrophic - Flagellate protists with pronounced cellular “groove” used for feeding - Many are anaerobic having no mitochondria, while others have special organelles acting like a mitochondria or highly modified mitochondria • Loukozoa - Heterotrophic flagellates and amoeboid - Protists with high nuclear genomic similarity • CRuMs ___________________________________________________________________________________________________________________________________________________________________________________________ Polytechnic University of the Philippines Page|8 BIOL 30115 – Evolutionary Biology Mapanao & Reboa - “free-form” cells leading to variety of observed and possible cellular morphologies of these organisms, if any external structures (like cell wall, test casing, lorica etc.) covering the cells are absent Heterotrophic • Amorphea (Unikonta) Prokaryotic unicellular organisms - Circular chromosome found in the nucleoid region - Cell membrane phospholipid chain is linear with its glycerol having ester linkages to a fatty acid - Cell wall has peptidoglycan - Only one kind of RNA polymerase - Formylmethionine is used for the initiation of protein synthesis • Bacteria - - Prokaryotic unicellular organisms Circular chromosome found in the nucleoid region Cell membrane is made of special phospholipid where instead of a fatty acid, a branched phytanyl (isoprene) • Archaea chain is ether linked to the glycerol Cell wall is made up of crystalline-like layers of proteins or glycoproteins Has many form of RNA polymerase Methionine is used for the initiation of protein synthesis ___________________________________________________________________________________________________________________________________________________________________________________________ Polytechnic University of the Philippines Page|9 BIOL 30115 – Evolutionary Biology Mapanao & Reboa ___________________________________________________________________________________________________________________________________________________________________________________________ Polytechnic University of the Philippines Page|10 BIOL 30115 – Evolutionary Biology Mapanao & Reboa Guide Questions 1) What is the importance of doing cladistics monophyletic groupings instead of other approaches in taxonomic and evolutionary studies of different organisms? Explain comprehensively. - Cladistics is the study and interpretation of evolutionary relationships between species based on shared or derived traits. Cladistics is regarded as an important strategy in taxonomy and evolutionary studies since it allows scientists to categorize organisms based on common ancestry rather than merely physical similarities. The use of monophyletic groups in cladistics is important since they reflect the most closely related creatures and are based on common ancestry (Templeton, 2010). This signifies that all members of a monophyletic group have a common ancestor and are more closely related to one another than to organisms outside the group. In contrast, some techniques, such as paraphyletic groups, may contain some, but not all, offspring of a common ancestor. Scientists can better comprehend the evolutionary links between various creatures and appropriately reflect these ties in taxonomy classifications by using monophyletic groupings in cladistics. It also contributes to ensuring that taxonomy classifications are based on evolutionary history rather than physical similarities (Fristrup, 2001). 2) Explain the problems or difficulties you have encountered in interpretation and creation of cladograms and use of cladistics as basis of taxonomic ranking. - When characters with multiple states are used, the method has a circularity that makes it biased. Coding of such features can only be done using prior criteria, and this is normally done using an established phylogenetic system. The way that character state coding handles diversity among species is another issue. Although paleoanthropologists typically neglect this type of variation, when characteristics are acknowledged as fluctuating, their presentation as a distinct state adds a significant amount of inaccuracy to cladograms. Cladistics is the favored approach for taxonomic "splitters," according to certain experts who are against its usage and who assert that it has revived typology. Regardless of the adoption or use of cladistics, typology continues to be an element of research on the evolution of humans. 3) Choose one of the cladograms (including the one you have made) and analyze some inconsistencies (taxon problems) you have found based on recent findings. Explain comprehensively only one taxon problem and your given possible solution to it. Identifying which character states are derived and which are primitive is the goal of cladistic analysis. Hennig (1966) and others developed a number of techniques for achieving this, but the outgroup comparison - ___________________________________________________________________________________________________________________________________________________________________________________________ Polytechnic University of the Philippines Page|11 BIOL 30115 – Evolutionary Biology Mapanao & Reboa technique is the most popular one now in use. In outgroup comparison, if a taxon that is not a part of the group of organisms being classed has a character state that is the same as some of the creatures in the group, then that character state might be deemed to be plesiomorphic. The organisms being classed are the ingroup, while the outside taxon is referred to as the outgroup. Two arguments can be made to justify using this method: one based on what we believe about evolutionary process and the other on logic: 1. The only way a homologous feature could be present in both an ingroup and an outgroup, would be for it to have been inherited by both from an ancestor older than the ancestor of just the ingroup 2. Consider the following example in which a character has states a and b. When a character only has two states, it is very easy to distinguish between primitive and derived states: the state that is found in the outgroup is primitive, while the one that is exclusively found in the ingroup is derived. Polytechnic University of the Philippines Page|12 BIOL 30115 – Evolutionary Biology Mapanao & Reboa REFERENCES Bremer K. (1990). COMBINABLE COMPONENT CONSENSUS. Cladistics : the international journal of the Willi Hennig Society, 6(4), 369–372. https://doi.org/10.1111/j.1096-0031.1990.tb00551.x Curnoe D. (2003). Problems with the use of cladistic analysis in palaeoanthropology. Homo : internationale Zeitschrift fur die vergleichende Forschung am Menschen, 53(3), 225–234. https://doi.org/10.1078/0018-442x-00048 Fristrup, K. M. (2001). A History of Character Concepts in Evolutionary Biology. The Character Concept in Evolutionary Biology, 13–35. https://doi.org/10.1016/b978-012730055-9/50010-0 Templeton, A. (2010). The Diverse Applications of Cladistic Analysis of Molecular Evolution, with Special Reference to Nested Clade Analysis. International Journal of Molecular Sciences, https://doi.org/10.3390/ijms11010124 11(1), 124–139.
