Animal diversity I

What are monophyletic and paraphyletic groups?

Monophyletic groups = a lineage with a common ancestor and all of its descendants

Paraphyletic group = groups that included a common ancestor and some of its descendants (they don’t provide information about evolutionary relationships or history)

What is taxonomy?

Taxonomy = how scientists name and organise living things

Linnaean taxonomy

• This groups species by physical traits (kingdom, phylum, class, order, family, genus, species)

• This system doesn’t always show evolutionary relationships

Phylogenetic taxonomy

• This organises species based on their actual evolutionary history, recognising groups with an ancestor and all its descendants

• Node-based = includes taxa, their common ancestor, and all its descendants e.g. a crown group - both main branches include at least one living species

• Stem-based = extinct species that are more closely related to a certain crown group than to any other crown group

• Total clade = a crown group plus its fossil stem relatives

What is homology and homoplasy?

Homology = traits shared by different species because they come from a common ancestor

• Historical homology = traits inherited from a common ancestor e.g. similar bones in a human arm and a bird wing

• Deep homology = different structures that evolved independently but share the same underlying genetic mechanisms e.g. the eyes of vertebrates and insects look very different, but they used similar genes to develop

• Serial homology = repeated structures within the same organism that are controlled by the same genes e.g. arms and legs (which are patterened by the same Hox genes), and jaws and gill arches in cartilaginous fishes (patterned by the same Dlx genes)

Homoplasy = the independent evolution of similar traits

What is Animalia?

A diverse clade of multicellular organisms, which is within a eukaryote clade and is a sister-taxon to Choanoflagellata

Bilateria = a diverse animal clade that is diagnosed by a single plane of symmetry (bilateral) along the body

Nephorozoa = diagnosed by having digestive tracts and organs for excreting waste

Protostomia = early formation of an opening in the embryo forms the mouth (Lophotrochozoa and Ecdysozoa)

Deuterostomia = early formation of an opening in the embryo forms the anus (Ambulacraria and Chordata)

What is adaptation and exaptation?

Adaptation = a trait which improves or maintains fitness and is maintained by selection

Exaptation = the evolutionary shift in traits from one function to another
E.g. the evolution of features associated with flight - feathers, hollow bones, unidirectional lungs (feathers provided the primary surface area for wings to generate lift, pneumatisation of bones reduces their weight, unidirectional air flow allows for efficient respiration which is necessary for the high metabolic rates associated with flying), feathers originally functioned as body insulation, pneumatised bones helped with breathing and made the body lighter

What are the origins of animal multicellularity?

Multicellular animals evolved by using traits that their single-celled ancestors (choanoflagellates) already had, but for different purposes
E.g. chaonoflagellates had cadherins (genes for producing adhesion proteins), but multicellular organisms exapted these to help their cells stick together and to develop different cell types

Division of labour model = animal cell diversity comes from splitting the role of one multifunctional cell into different, specialised cells e.g. the eye likely evolved by dividing a single type of cell into three different cells for detecting different aspects of light
We previously though that animal multicellularity evolved through these mechanisms (choanocyte cells were the ancestral cell type)

The choanoflagellate-poriferan model of animal origins

• Porifera have an inner layer of choanocyte cells with a flagellum and a microvilli collar to capture food particles, and a gelatinous layer with specialised cells (pinacocytes and archaeocytes - archaeocytes are totipotent)

• We would assume that choanoflagellates are most similar to choanocytes, but they are actually most similar to archaeocytes - they likely evolved by having individual cells that could turn into many different types of cells
  ^This was shown due the greatest mRNA overlap between choanoflagellates and archaeocytes (the common ancestor was not a specialised choanocyte, but multicellularity evolved through the division of labour from totipotent cells)

What is the fossil evidence for animal origins?

Fossils = evidence of past life

Many fossils are thought to be stem animals (they are more closely related to living animals than choanoflagellates)

One fossil of Dickinsonia is bilateral (a trait found in modern animals), which indicates that the crown group of animals existed before 555 million years ago

Prokaryotic bacteria were the primary producers (produced solid organic compounds and energy from photosynthesis and chemosynthesis) - this has been shown from carbon-13 isotope records

Several major glaciation events led to algae becoming the dominant primary producer (a shift from prokaryotic primary producers to eukaryotic primary producers) and the first animal fossils appearing (major environmental changes influenced the development of early life

What is ontogeny?

Ontogeny = how an organism grows and develops from an embryo into an adult

Ontogeny can impact evolution by leading to new body forms and even the formation of new species (these changes often occur due to changes in regulatory genes)

What are Homeobox genes?

Regulatory genes that encode a family of transcription factors (they have a homeodomain - a DNA binding domain)
^These genes have more types in animals due to gene duplication events

They specify cell types and specify the geography of the body, with similar genes doing similar jobs in distantly related organisms

Homeotic mutation = a mutation in which part of the body thinks it’s a different part of the body - this results in a large effect due to a small mutation (Homeobox genes can cause rapid evolution)

What are Hox genes?

A subfamily of Homeobox genes that are specific to animals (front-to-back)

During development, different Hox genes will turn on in different parts of the body

• Different body segment arrangements (tagmosis) in arthropods result from different patterns of Hox gene activity
  E.g. one of the Hox proteins expressed in the abdomen of insects has acquired the ability to repress genes needed to make limbs (so crustaceans often have limbs on their abdomen, while insects don’t)

• Tardigrades have shorter bodies with fewer segments with limbs
  They only express Hox genes for the front and back of their bodies, so they lost the middle segments of their bodies during development because some Hox genes were lost

• The Hox10 genes in mammals prevent the development of dorsal ribs

Hox genes lead to very quick changes (because it changes many genes at once due to one change to a transcription factor), but they can impact adaptive traits

What are Dlx genes?

A subgroup of homeobox genes (top-to-bottom in the head region) - they will help form different plarts of the face and throat, like the upper and lower jaws and the gill arches

Because Dlx genes regulate both jaw and gill arches, this suggests that jaws evolved from modified gill arches in jawless ancestors (serial homologs)

Dlx genes control the development of the bones in the middle of the ears (tapes, incus, malleus)
^These bones also evolved from the bones of the jaw joint in other vertebrates

What is heterochrony?

Evolutionary change in the timing of character development in organisms (it can be caused by genes turning on and off during development)

• Paedomorphosis = development slows down or stops early so there’s retention of juvenile traits e.g. axolotls keep their gills even as adults

• Peramorphosis = development speeds up or starts earlier so there’s acceleration of growth rate e.g. moles start making cartilage for digging claws earlier

We can study heterochrony by comparing related species (using evolutionary trees) to see how development timing has changed between them

Heterochrony also shows how changing development can greatly impact evolution

What are bilaterians?

They have three germ layers (tripoblasty) instead of two (dipoblasty)

• Ectoderm = forms outer body layers and nervous system tissues

• Endoderm = forms gut tube / digestive tract

• Mesoderm = forms muscle, nephritic tissues, and reproductive tissues

During gastriculation, the mesoderm forms the coelom (internal cavity that houses organs, such as the heart and intestines) - this structure supports more complex body plans

What is biomineralisation?

The formation of minerals within cells and tissues

Bilaterians show the greatest variety in biomieral type (support for the body, protection, insulation, ion storage)

Biomineralisation gave animals key advantages which helped them diversify and evolve (this evolution was driven by changes in the environment e.g. increased ocean calcium)

What are the main clades of bilaterians?

Protostomia = the blastopore forms the mouth end of the gut tube

• Lophotrochozoa

  • Annelida = include chetae (bundles of hair-like chitin bristles that function for locomotion, body stabilisation, and defense) and an internal coelom

  • Mollusca = mantle (for locomotion), radula (tongue-like structureth multiple teeth)

• Ecdysozoa = they grow with periodic moults of the skin or cuticle (ecdysis)

  • Arthropoda = segmented (adaptation of arthropods to different different lifestyles has been achieved by varying the number of segments (includes chelicerata, myriapoda, crustacea, insecta)

  • Nematodes

Deuterostomia = the blastopore forms the anus

What are evolutionary constraints?

Factors that prohibit or limit evolutionary changes

E.g. the cuticle in arthropods which limits arthropods from receiving large body sizes  
^They grow by moulting, and after moulting their body expands by taking in air, but once the new exoskeleton hardens, growth stops until the next moult 

Physical and developmental constraints can shape the path of evolution

What are the deuterostomes?

Deuterostomes have pharyngeal slits and their blastopore forms the anus

Chordata = the presence of a notochord (dorsal hollow nerve chord)

• Cephalochordata

• Urochordata

• Vertebrata = neural crest and duplicated Hox genes

  • Cyclostomata = lakc jaws and many of the sensory specialisations of jaws vertebrates (these are likely secondary losses)

  • Gnathostomata = origin of paired appendages as fins, and jaws

Ambulacraria

• Echinodermata = water vascular system, radial symmetry as adults

• Hemichordata

What are the vertebrate germ layers and tissues?

The evolution of these features demonstrate the diversification of vertebrates

Bone = a living mineralised tissue reshapes by resorption and growth

• It is composed of osteocytes

• Endochronal bone = replaces cartilages in ontogeny (it forms limb bones and vertebrae)

• Intramembranous bone = condenses directly from mesenchyme (forms most of the skull)

• Bone first evolved as an external armour in early jawed vertebrates (stem gnathostomes) for protection
  Later, endochronal bone evolved, which enabled larger body sizes and more complex movement

Neural crest = a specialised form of ectoderm unique to vertebrates

• This forms during development and gives rise to a wide range of specialised structures (such as facial bones and cartilage)

• This is essential for forming the facial skeleton and jaws in vertebrates

Neuogenic placodes = thickened sections of ectoderm cells that form above the neural tube and then sink into the ectoderm (positioned on either side of the developing nervous system)

• With neural crest cells, they enabled the evolution of complex sensory systems in vertebrates

What are adaptive radiations?

Diversification events in which species or trait richness increases as a result of one of several environmental opportunities

To qualify as an adaptive radiation, a lineage must be monophyletic, show a link between traits and environment, demonstrate trait-based fitness differences, and evolve rapidly

Radiations are often driven by geographic colonisation, extinction of competitors, appearance of new resources, or key innovations that provide ecological advantages

What are the hypotheses of adaptive radiation?

Extinction = the permanent cessation of reproduction in species

• Background extinction = the independent extinction of individual species through evolutionary processes (gradual)

• Mass extinction = the extinction of multiple species due to a common cause (faster)

• Adaptive radiations follow mass extinctions via ecological opportunity for extinction survivors (the sudden availability of ecological niches)

• They act as evolutionary bottlenecks (wiping out vast numbers of species) and they create ecological opportunities by vacating niches

What are the causes of mass extinctions?

Temperature

• Can push conditions beyond biological limits of organisms

• Associated sea level changes can disrupt habitats

Chemistry

• Alterations in water pH

• Volcanic releases of gasses can result in short term greenhouse effects

• Ocean stratification

What can the fossil record and mass extinctions show us?

It can help us predict how modern biodiversity might respond to human-driven environmental changes (shifts in climate, habitat loss, and pollution today an resemble past conditions that led to mass extinctions)

We can compare ancient extinctions with current biodiversity declines

The rapid in increase in threatened species suggests we could be heading towards similar extinctions if current trends continue