Biodiversity & Classification

Biodiversity and Classification

• The Earth contains an astounding diversity of living organisms.
• A large number of species have already gone extinct.
• Biologists study the evolutionary relationships between organisms and develop classification systems to track evolutionary lineages.

Traditional Classification

• Traditionally, scientists defined species, then grouped them into successively more inclusive hierarchical categories.

Species and Genus

• A species is a group in which individuals are similar in structure, biochemistry, and behavior, allowing them to successfully interbreed.
• A genus is a group of similar species that share characteristics and a recent common ancestry.

Hierarchical Grouping

• Related genera are grouped into a family.
• Related families are grouped into an order.
• Related orders are grouped into a class.
• Related classes are grouped into a phylum.
• Related phyla are grouped into a kingdom.
• Domains were recently added and are the most inclusive grouping in biology.

Phylogenetic Trees

• Since the late 20th century, biologists started using DNA nucleotide sequences to determine evolutionary lineages.
• Phylogenetic trees illustrate evolutionary pathways.
• The newer techniques run parallel to the traditional hierarchical classification system.
• Phylogenetic trees provide more information than traditional hierarchical classification.
• Phylogenetic trees reveal when evolutionary events occurred.
• Phylogenetic trees show which ancestors gave rise to which descendants.

Tree of Life

• The phylogenetic tree that represents all life on earth is called the Tree of Life.
• The Tree of Life distinguishes 3 domains: Bacteria, Archaea, and Eukarya.

Historical Context

• Animals and Plants were recognized as two broad categories for thousands of years
• In the late 19th century Ernst Haeckel proposed to classify single-celled organisms separately as Protists.
• In the early 20th century, bacteria was recognized as a separate group, shortly followed by the fungi.
• By 1959, all living organisms were classified in five kingdoms.

Prokaryotes vs Eukaryotes

• A distinction was established between prokaryotes vs eukaryotes.
• In prokaryotes the DNA is suspended inside the cell (the nucleoid), without being separated from other cellular components, thus without a nuclear envelope.
• In eukaryotes the DNA is enclosed in a nucleus by a nuclear envelope, which is a separate structure inside the cell.
• Four of the five kingdoms were eukaryotic, and bacteria were classified as prokaryotes.

Molecular Data

• Determining phylogenetic relationships was impossible with just morphological characteristics as phylogenies were within kingdoms, but not between them.
• This changed when molecular sequence data became available.

Carl Woese's Contribution

• In 1977, Carl Woese published an analysis of rRNA sequences from all living organisms.
• Woese found another group of organisms that were prokaryotic, but their rRNA sequences were different than the bacteria; they were initially called archaeabacteria.
• In 1990, Woese and colleagues proposed a higher level of classification above kingdoms, called domains.

Domain Bacteria

• Bacteria are unicellular (one-celled) organisms.
• They are visible under a microscope.
• Bacteria are producers, consumers, or decomposers, and are found almost everywhere on Earth.
• These organisms have a relatively simple cellular organization in terms of internal structures and DNA.
• Bacteria are the most metabolically diverse group.
• Some groups of bacteria have unique structural molecules and mechanisms of photosynthesis.

Domain Archaea

• These organisms are similar to Bacteria because they are also unicellular and may live as producers or decomposers.
• Many Archaeans inhabit extreme environments, such as hot springs, extreme salty ponds, or habitats with little or no oxygen.
• Some Archaeans have distinctive structural molecules and a primitive form of photosynthesis (unique).
• Although they are prokaryotic, these organisms have some molecular and biochemical traits typical of eukaryotes, including DNA and RNA structure and protein synthesis (process).

Archaea vs Bacteria

• Archaea resemble bacteria by having circular chromosomes, operons, and being prokaryotic and small.
• Unlike bacteria, they have genes containing introns, DNA wrapped around proteins similar to eukaryotic histones, and RNA polymerases that resemble eukaryotic RNA polymerases.

Asgard Super-phylum

• More recently, further molecular studies suggest that the domain Eukarya is not a sister clade of the Archaea, but rather evolved from within the domain Archaea
• A new super phylum of Archaea was discovered/described in 2015 - the Asgard super-phylum, suggesting that the Eukarya evolved from within the Asgard super-phylum and is therefore now a secondary domain.
• The genomes of Asgard archaea contain genes related to eukaryotic genes whose protein products involved in cellular processes were thought to be unique to eukaryotes.

Domain Eukarya and Kingdoms

• The domains Bacteria and Archaea contain prokaryotic organisms.
• The domain Eukarya includes all eukaryotic organisms.
• The domain Eukarya is further divided into three kingdoms: Fungi, Animalia, and Plantae.
• There is also a group called the protists.
• The protists is not a kingdom because the organisms in this group do not share a common ancestor.

Protists

• Protists are a diverse group of single-celled and multi-cellular eukaryotes.
• This group is not a kingdom, because they do not share a unique common ancestry.
• The most common protists are the 'protozoans' are primarily uni-cellular, and the algae that vary from being unicellular to large multi-cellular seaweeds.
• Protozoans live as consumers and decomposers, while algae are photosynthetic producers.

Kingdom Plantae

• Plants are multi-cellular organisms.
• They carry out photosynthesis with very few exceptions.
• Plants are the producers in ecosystems.
• Plants are stationary organisms (except for their pollen and seeds).
• This kingdom includes the flowering plants, conifers, and mosses.

Kingdom Fungi

• This kingdom contains a highly varied group of uni- and multi-cellular species, including the yeasts and moulds.
• Most species of fungi live as decomposers and absorb nutrients from dead organisms.
• After absorption of the nutrients they break these complex molecules down into the raw materials again.
• Fungi do not carry out photosynthesis.
• Their cell walls contain chitin.

Kingdom Animalia

• These are multi-cellular organisms that live as consumers.
• They feed on protists and other organisms from all the other kingdoms.
• Animals can move from one place to another during some stage of their life cycle.
• This kingdom includes a great range of organisms such as sponges, worms, insects, fish, amphibians, reptiles, birds, and mammals.