Unit 3 Biodiversity BIOL 101

Biological diversity

the variety of all living things on Earth encompassing genetic differences, indivdidual species, and entire ecosystems

How many species inhabit Earth

2.16 million species measured (underestimate)

Estimates range from 5 million to 1 trillion

Why is measured species an underestimate of the total number of species

Lack of universally accepted definition for species

Largely unexplored regions of the planet (deep oceans, remote tropical canopies, etc.)

Microscopic organisms are difficult to isolate and ID and many species require expensive DNA testing to distinguish from lookalikes

There are new species constantly evolving

Too few taxonomists to name millions of species of unknown organisms before they face extinction

Levels of diversity

Genetic diversity, species diversity, and ecosystem diversity

Genetic diversity

Genetic variation (alleles) within a population (individuals not identical)

Helps populations adapt to changing environmental conditions

Makes it less likely that all individuals susceptible to the same disease

Preserves genetic variation needed to respond to future challenges

Maintains evolutionary potential

Species diversity

number of species and their relative abundances

Ecosystem biodiversity

the variety of habitats, biological communities, and ecological processes occurring across the biosphere

Carolus Linnaeus

1758

recognized species as fundamental unit of life

grouped similar species together in ever increasing hierarchy of classification

described Homo sapiens without designating a holotype

prior to 1959 was lectotype for Homo sapiens

remains in Sweden’s Uppsals Cathedral

Binomial nomenclature

unique two part name for every species

Important parts of measuring biodiversity

mathematical metics

geographic scale

sampling methods

How do we measure biodiversity

We count

Mathematical metrics for measuring diversity

Species richness (S) and Species evenness (E)

diversity indices: shannon index, and simpson diversity index

Species richness (S)

number of different species in an area

Species evenness (E)

how evenly individuals are distributed across species

Diversity indices

Combine species richness and evenness to calculate diversity

Simpson diversity index and shannon index

Simpson diversity index

emphasizes the dominance of common species

Shannon index

gives more weight to the diversity contributed by less common species

Geographic scales of diversity

Alpha, beta, and gamma diversity

Alpha (α) diversity

diversity within a single specific local area or ecosystem

e.g. the number of species in one pond

beta (β) diversity

difference in species composition between two different areas

based on concept measuring community composition change from place to place

Additive species turnover

Beta diversity calculated by counting the unique species

where S is total species at a site and c is the number of species shared between sites

Whittaker’s classic formula (ratio method)

it measures beta diversity by comparing regional diveristy to local diversity

where B is beta diveristy, Y is gamma diversity, and a is alpha diversity

Gamma (γ) diversity

Overall regional biodiversity across a landscape hosting multiple ecosystems

Number of unique species across entire ecosystem

Why does geographical diversity matter for conservation?

Sites with similar alpha diversity may contain different species

High beta diversity means that different sites contribute unique species to the region

Protecting multiple habitats can maintain a greater regional biodiversity

Conservation needs to consider the entire landscape not just individual sites but also genetic diversity

Sampling methods

Quadrants and transact sampling, canopy fogging and netting, environmental DNA (eDNA), and satellite and acoustic monitoring

Quadrant sampling

placing physical square frames across a habitat to count every plant, insect, or slow moving organism in that boundary

Transact sampling

running long lines across a habitat to count every plant, insect, or slow moving organism in that boundary

Canopy fogging

Using safe temporary knockdown mists to collect tree dwelling insects

Netting

Using fine mist nets to safely capture ,count, and release birds, bats, and aquatic life

Environmental DNA (eDNA)

Collecting water, soil, or snow samples and sequencing the genetic material left behind by local wildlife, revealing what organisms live nearby without ever needing to see them

Satellite imagery

Using satellite imagery to track changes in broad forest canopies

Acoustic monitoring

deploying microphone grids to record and identify bird calls, frog croaks, and bat clicks

why do sampling methods matter?

Different methods detect different species

sampling can favor certain species or habitats

consistent methods enable reliable comparisons between sites

rare or hidden species may be overlooked

accurate sampling helps identify biodiversity hotspots and prioritize conservation

Biodiversity hotspots

areas with exceptionally high biodiversity and many unique species

36 hotspots recognized worldwide support nearly 60% of the world’s plant, bird, mammal, reptile, and amphibian species

Ex. Brazil’s Atlantic Rainforest, and Africa’s Cape Floristic Region

How much have wildlife populations declined since 1970

73%

Criticisms of species decline metrics

analyses estimate an average decline of more than 50% driven by fewer than 3% of populations

extreme declines affect about 1% of populations and disproportionately involve larger animals

Global averages hide important differences among populations and regions

Extreme declines skew the average

Mass extinctions

when minimally 75% of species go extinct in a geologically short period of time

5 mass extinctions recognized in Earth’s history (End Ordovocian, Late Devonian, End Permian, End Triassic, End Cretaceous)

Systematics

the study of relationships of organisms

Taxonomy

classifying and categorizing organisms with the goal of communication and identification

in past 50 years has shifted towards a tool to describe evolution

Taxon (taxa pl.)

group of related organisms

How do you make a new species

be named according to the Code of Zoological Nomenclature

Taxon names must be unique and italicized

be published and illustrated with a diagnosis and description

designated one or more types

Principle of priority

The first validly published name has priority

Type

the representative or name bearer of the group

Each class has type order, each genus has type species, and each species must have one or more type individuals

Holotype

the single physical example of an organism used when a species was formally described

Edward D. Cope

Proposed Homo sapien type specimen in 1990s by Louie Psihoyos and Robert Bakker

Due to degenrative veneral disease was anatomically unsuitable to serve as ideal baseline benchmark for humanity

Ernst Mayr Species definition

An array of populations which are actually or potentially interbreeding and which are reproductively isolated from other such arrays under natural conditions (1942)

Limitations of biological species concept

asexual reproduction, fossil record, natural hybridization, geographic isolation, and horizontal gene transfer

Biological species concept issue: Asexual reproduction

in bacteria, archaea, and self replicating plants interbreeeding never occurs

Biological species concept issue: fossil record

no behavioral data or reproduction

Biological species concept issue: natural hybridization

fertile hybrid zones (coywolves)

Biological species concept issue: geographic isolation

populations separated by immense distance aren’t naturally tested, introducing guesswork into species assignment

Biological species concept issue: horizontal gene transfer

transfer of genetic material between organisms besides reproduction

Methods to group organisms

phenetic taxonomy, cladistic approach

Phenetic taxonomy

measuring, plotting and statistically grouping species based on morphology

Cladistic approach

classifying by branching points and shared derived traits

Cladistic categories

monophyletic clade, paraphyletic group, polyphyletic group

Monophyletic clade

A taxonomic group descendant from one ancestor containing all its descendants

Paraphyletic group

groups in a taxonomic group of descendants from one ancestor but not including all descendants

Polyphyletic

a taxonomic group of descendants from more than one ancestor

phylogeny

evolutionary history and relationships among organisms

all phylogenies are hypotheses

Homologous structures

structures that may have different function but derive from common ancestry

useful for reconstructing phylogeny

Analogous structures

structures in different organisms that may have the same function but different ancestral origin

result of evolutionary convergence

useless in reconstructing phylogenies

Cladistics

a method of reconstructing phylogenetic relationships using shared derived traits

clade (monophyletic group)

the common ancestor and all its descendants

synapomorphy

a homologous trait that evolved in a common ancestor and is shared by its descendants

cladogram

a simplified phylogenetic tree that lacks a scale of time

Branches

at the ends of which we list groups

nodes

where one branch splits into two groups due to evolution of new characters/traits

sister taxa

share an immediate common ancestor

polytomy

when three or more taxonomic groups arise from one node

shows unclear evolutionary history among descendant taxa

Root

base of tree that represents last common ancestor of all taxa in tree

What does cladistic analysis rely on

correctly distinguishing inherited characters from derived characters across all taxa in study

Pleisomorphic characters

inherited characters

apomorphic characters

derived characters

synapomorphies

apomorphic characters that are inherited

The principle of parsimony

simplest hypothesis most likely to be true (Occam’s razor)

cladogram with fewest steps most likely to be correct

Limits of phylogenetic trees

we cannot assume that branch sequence indicates actual ages of particular species (unless tree is calibrated to time or genetic change)

E.g can only say most recent common ancestor of wolf and otter lived before most recent common ancestor of wolf and coyote

Relative dating

Three domain system

Bacteria, Archaea, and Eukarya

baseline standard in biology

Horizontal Gene Transfer

Transfer of genes between organisms other than through parent to offspring inheritance

common in bacteria and archaea but also occurs in Eukarya

Can occur across evolutionary lineages making “tree” of life more like web

transformation, transduction, conjugation

Eukaryote evolution

evolved from a community of prokaryotes rather than one ancestor

Prokaryote contributions to Eukarya

bacterial ancestors became mitochondria and cyanobacterial ancestors became chloroplasts

Prokaryotes

10,500 species published (<1% of what’s out there)

unicellular

small cells (.5-5 μm in diameter)

lack membrane-bound nucleus, mitochondria, and chloroplasts

typically have a circular chromosome and reproduce asexually through binary fission

Why are prokaryotes so successful

small size

rapid reproduction (ex. E. coli divide approximately every 20 minutes)

long evolutionary history (3.5 billion years)

large population means high mutation potential

diverse adaptation enables them to live in many different environments

rapid evolution gives them diverse metabolic and structural adaptations

Bacterial shapes

cocci, bacilli, spirilla, and spirochetes

Cocci

spherical or round

Bacillia

rod shaped

spirilla

rigid spiral shaped

Spirochete

thin flexible spiral shaped

capsule

sticky outer layer of polysaccharides or proteins surrounding the cell wall

helps cells adhere to surfaces and to one another creating colonies or biofilms

protects against dehydration

Appendages

Fimbriae, pili, and flagella

Fimbriae

numerous short hair-like structures used for attachment

pili

help bring bacterial cells together for gene transfer

Flagella

used for movement

Bacterial species

a group of closely related bacteria defined primarily through genetic and evolutionary similarity

Bacterial strain

A particular genetic variant within a bacterial species

Different strains of the same species may differ in genes, characteristics and ability to cause disease

ex. E. coli variants some live harmlessly in gut while others cause disease

Transformation

The uptake of naked foreign DNA from the environment

living cells bind cell free DNA released from dead donor cells then specialized surface proteins pull foreign DNA inside

DNA segments are incorporated into hosts DNA

Natural competence

naturally competent species can take up extracellular DNA under certain conditions

Regulated competence

develops only at a particular growth stage or in response to environmental signals

Noncompetent species

lack the natural ability for DNA uptake

Artificial competence

induced competence in a lab setting (chemical treatment or electroporation)