Evolutionary Biology: Phylogenetics and Gene Families

Phylogenetic Trees

• Phylogenetic trees represent hypotheses about evolutionary history supported by morphological and molecular data.
• Comparing outgroups and ingroups helps derive characters at specific branch points.
• Maximum parsimony favors the simplest explanation with minimal evolutionary events.
• Maximum likelihood identifies the tree most likely to produce a specific DNA set, based on probability.

Gene Duplications and Gene Families

• Gene duplications have produced homologous gene families, clusters of related genes.
• Orthologous genes form between species as a result of speciation, and their differences reflect speciation history.
• Paralogous genes form within a species from gene duplication and divergence.

Prokaryotic Relationships

• Prokaryotes typically form symbiotic relationships with larger organisms.
• Mutualism benefits both species.
• Commensalism benefits one species without affecting the other.
• Parasitism benefits one species while harming the other.
• Pathogens are disease-causing parasites.

Prokaryotes and Humans

• Mutualistic bacteria in the gut help digest food and break down waste.
• Pathogenic bacteria cause numerous human diseases.
• Some pathogens are transmitted by pests.
• Bacteria produce poisons classified as exotoxins (secreted proteins) and endotoxins (lipopolysaccharides).
• Through horizontal gene transfer, harmless bacteria can become pathogenic through antibiotic resistance.
• Antibiotic resistance is rapidly increasing due to bacterial reproduction and horizontal gene transfer.
• Prokaryotes produce fermented foods like cheese, yogurt, and sourdough bread.
• Prokaryotes are vital in biotechnology and genetic engineering.

Choanoflagellates and Animals

• Choanoflagellates share characteristics with animals, including the presence of similar proteins like cadherin.
• However, some key features like CCD domains distinguish them from animals.

The Neoproterozoic Era

• Macroscopic fossils of soft-bodied multicellular eukaryotes from the Ediacaran biota (around 560 mya) are linked to animal ancestry.
• Neoproterozoic rocks with microfossils exhibit the basic structure of an animal.

The Paleozoic Era

• The Cambrian explosion (535-525 mya) saw the emergence of ancestors of all modern phyla.
• Most Cambrian animals were bilaterians, characterized by bilateral symmetry, a complete digestive tract, and an efficient digestive system.
• The Ediacaran decline is linked to new predator-prey relationships, increased atmospheric oxygen, and development of new life forms.
• The Ordovician, Silurian, and Devonian periods witnessed increased animal diversity.
• Cambrian animals colonized the land, diversifying into amphibians and amniotes.

The Mesozoic Era

• Animal phyla from the Paleozoic continued to diversify into new habitats and traits.
• Dinosaurs and mammals emerged.
• Flight evolved in pterosaurs and birds.

The Cenozoic Era

• Marked by mass extinctions of dinosaurs and marine reptiles.
• Mammals occupied the available ecological niches.

Body Plans

• A body plan refers to a set of morphological and developmental traits organized into a whole organism.
• Symmetry is a key aspect of body plans, with animals possessing bilateral symmetry, radial symmetry, or no symmetry.

Protostome and Deuterostome Development

• Protostome and deuterostome development differ in cleavage, coelom formation, and blastopore fate.
• Protostome development involves spiral cleavage, coelom formation by splitting mesoderm, and blastopore becoming the mouth.
• Deuterostome development features radial cleavage, coelom formation by budding mesoderm from the archenteron, and blastopore becoming the anus.

Diversification of Animals

• The diversification of animals can be understood by examining their different clades and common characteristics.
• Arthropods are characterized by a segmented body, an exoskeleton, and jointed appendages.

Myriapods

• Myriapods, including centipedes and millipedes, share antennae and modified appendages.
• Millipedes are herbivorous with two pairs of legs per segment.
• Centipedes are carnivores with one pair of legs per segment.

Pancrustaceans

• Pancrustaceans include insects and crustaceans.
• Crustaceans have specialized appendages, gas exchange through a cuticle or gills, and diverse body sizes and forms
• Insects are characterized by a head, thorax, and post-gential region.
• Wings allowed insects to diversify and disperse.
• Insects exhibit metamorphosis, with incomplete metamorphosis involving nymphs that molt into adults and complete metamorphosis involving larval stages distinct from adults.
• Most insects reproduce sexually, with mate attraction mediated by coloration, sound, and odor.

Echinoderms and Chordates

• Echinoderms and chordates are closely related deuterostomes.

Echinoderms

• Echinoderms are slow-moving marine animals with a coelom.
• They possess a water vascular system, a network of hydraulic canals with extensions called tube feet, used in locomotion and feeding.
• Echinoderms exhibit bilateral symmetry in their larvae, but radial symmetry in their adults.
• They encompass five major clades.

Chordates

• Chordates exhibit five key characteristics at some point in their development.
• These include a notochord, a dorsal hollow nerve cord, pharyngeal slits, a post-anal tail, and an endostyle..
• Chordates are further divided into three subphyla:
  • Tunicates
  • Cephalochordates
  • Vertebrates
• Vertebrate innovations include a skull, a vertebral column, a well-developed brain, a closed circulatory system, and sensory organs.
• Vertebrates further diversified into amphibians, amniotes (reptiles, birds, mammals), and fish.

Explore the intricate concepts of phylogenetic trees and gene duplications in this quiz. Understand the relationships between prokaryotes and the impact of mutualism, commensalism, and parasitism. Test your knowledge on evolutionary history, gene families, and species relationships.