Conservation Bio Midterm

Conservation Biology

a biological science with the focus on conserving species; the study of biodiversity; an integrated multidisciplinary scientific field developed in response to challenge of preserving species and ecosystems

• New synthetic discipline addressing dynamics and problems of perturbed species, communities, and ecosystems with goal of preserving biodiversity (Soule, 1985) 

• Response by the scientific community to the biodiversity crises. New synthetic field that applies principles of ecology, biogeography, population genetics, economics, sociology, and anthropology and philosophy to the maintenance of biological diversity

What encompasses conservation biology?

1. Highly disciplinary and collaborative brach on science  

• Developed as a field to address biodiversity loss (hence “synthetic”) 

  • Focus on long term preservation of biodiversity not just pure research or economics 

• Highly interdisciplinary: ecology, environmental law, sociology, biochemistry etc. 

2. It's the study of biodiversity 

• The number of species, genetic variation, ecosystems, and ecosystem-level interactions 

3. Created in response to biodiversity crisis 

• Holocene epoch ~12,000 years ago to now 

• Current extinction rate is up to 1,000x higher than background extinction rate (what we normally expect to occur) 

• Impacting human wellbeing 

Species diversity

all species in an area (bacteria, animals etc) and the relative abundance of those species 

What is biodiversity?

The defining issue of conservation bio; variety of genetic, ecosystem and species present in an area

Extinction

the elimination of species or taxon

Genetic diversity

genetic variability within a species or population

population

a group of species that have a high probability of interacting and reproducing with each other

Ecosystem Diversity

range of different ecosystems in an area, and the associations and interaction between and within them 

Problems with species diversity in con bio field

1. many unknown taxonomic synonyms - some species have been described more than once and therefore have more than one scientific name

2. most species have not yet been described - Number of described species in an underestimate of true biodiversity - Can estimate the number of undescribed species using species discovery rate; About 20,000 new species described each year - Can be completely new discoveries - Can be known species reanalyzed and divided into multiple species through DNA analysis 

Taxonomic synonyms

a species that has multiple scientific names

Biological Species Concept

A group of individuals that can interbreed or potentially interbreed in the wild; Interbreeding produces viable  and fertile offspring 

• biological species are maintained by reproductive isolating mechanism 

• most common theoretical approach; emphasizes species based on gene pool

Behavioral analytical or physiological mechanism that have evolved to either:

1. Prevent fertilization between species (prevent mating or prevent hybrid zygotes from forming); prezygotic barriers (ie. spatial isolation, gametic isolocation, behavioral isolation (like sounds/calls)) which can be useful in identification of species

2. Prevent hybrid zygotes from developing normally (postzygotic barriers) ex. Mating produces nonviable zygotes, sterile adults; reduces fitness of parents 

The biological species concept has complications such as:

• Organisms considered different species sometime interbreed successfully which then can produce viable and fertile hybrids which blurs the distinction between species; very common in coral reef fish 

• Ability to interbreed is difficult to demonstrate - mating is hard to observe in wild; hybrids often go undetected 

• Difficult to apply to organisms that reproduce asexually or with extensive self-fertilization 

• Does not apply to fossil species; important for comparison of modern extinction rates to historic extinction rates 

Morphological Species Concept

 group of individuals that is morphologically distinct from other groups in some important characteristic

• Ie. the clustering of phenotypes (hair color, number of teeth etc.) 

• Oldest method of differentiating species - Still widely used by biologists; s practical - used by most field biologists 

• Species defined by the morphological species concept are sometimes called morphospecies

• similar individuals can be different species

Cryptic Species

species that are difficult or impossible to tell apart using phenotypic differences; common problem with certain taxonomic groups 

Divergent Evolution

groups with common ancestors becoming increasingly different over time

Ecotype

genetically and phenotypically distinct forms of a species; adapted to different environments - may become subspecies but not recognized as such 

Polyphenism

Changing phenotype in different environmental conditions (ex. Seasonal forms of various butterflies) 

Metamorphosis

changing phenotype with life history (ex. reproductive status)

DNA-Based Species concepts

• Using DNA sequences has become gold standard of identifying species 

• Best to use molecular techniques combined with other evidence 

  • Taxonomy is always evolving and complicated 

  • Species is whatever a competent taxonomist says it is 

• Identifying species has massive legal, policy, public opinion and conservation consequences 

DNA-Barcoding

Analyzing a region of DNA to determine base-pair sequences that can be used for species-differentation and identification 

• Tissue sample obtained from organism 

• Specific region of DNA is amplified using PCR 

• DNA is sequenced to determine specific nucleotides 

• Compared to reference different species in database 

Advantages of DNA barcoding

• Overcomes many limitations of biological and morphological species concepts like ones difficult to observe or identify using phenotypes 

• Can identify species using small tissue samples (ex. Biopsy, hair on wire, dart samples) 

• Identification of species from small samples and rapid analysis techniques has led to large increase in number of species identified 

  • Use of mass sampling techniques to look for new species and assess biodiversity = environmental DNA (eDNA) 

Complications of using DNA barcoding

• Using different regions of the genome can give different results 

• Uncertainty about how much genetic variation is needed to distinguish a group of species 

  • Intra and inter-specific sequence differentiation varies widely between taxa 

• Risk of taxonomic inflation = where everything can be distinguished becomes a species 

Latitudinal Diversity Gradient

the general increase in species diversity as you move further and closer to the equator 

• Observed in terrestrial, freshwater, and marine ecosystems 

• Occurs due to: (not exactly sure which drives it or why it occurs) 

Climatic stability hypothesis

tropical areas have more stable climates over both seasonal and geological time scales

• results in predictable resources, greater diversification through resource specialization (niche partitioning)

Diversification rate hypothesis

tropics have a faster speciation rate (eg. faster molecular processes leading to speciation)

Elevational Diversity Gradient

 terrestrial species diversity often increases with moderate increases in elevation then decreases with further elevation 

• Can be driven by climate, interspecific competition 

• Aquatic species diversity tends to decrease with increasing water depth 

  • Largely driven by light availability 

The Equilibrium Theory of Island Biogeography 

E.O Wilson and R. MacArthur studies species diversity on islands and made 2 important observations

1. Species diversity on islands is a factor of immigration rate and extinction rate 

2. Immigration and extinction rates are a factor island size and island isolation  (how far from continent or immigrant species it is) 

• One of the most important theories explaining patterns of species diversity 

• Also applies to insular habitats (parks in urban settings for example) 

• AKA Theory of Island Biogeography 

• Rate of species immigration is high at first then decreases as all possible species colonize the island 

• Rate of extinction is low at first but increases as mores species occupy the island due to competition for resources 

• Where the rates intersect, we find the number of species on the island at equilibrium 

  • Species immigration = species extinction 

Theory of Island Biogeography: 

1. Migrating species are more likely to encounter closer (less isolation) islands - Given random dispersal, closer islands are likely to receive more immigrant species (distance effect) - Given random dispersal, closer islands are more likely to receive additional members of a species - rescue effect 

2. Migrating species are more likely to encounter larger islands 

   1. Given random dispersal, larger islands will revive more immigrant species (target effect)  and individuals (rescue effect) 

3. Likely to be  more species present on larger islands (species-area relationship) 

   1. Larger habitats, more habitats, greater population sizes… 

   2. Extinction rate will be lower on larger islands 

• Island size and isolation affect species diversity 

Distance Effect

Immigration rate higher for closer islands

Species-area curve

Extinction rate lower for larger islands (species-area curve) 

Target Effect

Immigration rate also higher for large islands

Rescue effect

Extinction rate also lower for closer islands

(Where rates intersect, we can find the number of species for the system at equilibrium for different island size-distance scenarios)

Intermediate Disturbance Hypothesis

species diversity is maximized in areas with intermediate levels of disturbance 

• Supported by several studies especially benthic marine ecosystems 

• However, other studies do not support IDH - hypothesis is not universally accepted 

Species diversity is determined by: 

• Latitude, altitude. Size of habitat, level of disturbance 

• Primary production, level of species diversity in other taxonomic groups 

• Different theories and factors are more important depending on spatial scales and type of ecosystem 

What is Genetic Diversity? 

• Number of genetic characteristics (e.g. in a population) 

• Can be considered on several levels: 

1. Within an individual 

2. Within a population (a group of individuals that have high probability of mating) 

3. Between populations of a species 

4. Within the entire species    

Gene Pool

total array of genes and allele in a population, species, etc.

Genotype

particular combination of alleles that an individual possesses 

Phenotype

the morphological, physiological, and biochemical characteristics that result from an individual's genotype in that particular environment 

Allele Diversity: 

• Allele are the basic units of genetic diversity 

• Genetic diversity can be characterized as the diversity of allele present 

  • An individual can only have 2 alleles for a gene, but more than 2 alleles for a gene can be present in a population 

What are the two important factors in considering allele diversity?

1. Number of polymorphic genes = genes that have more than one allele 

   1. Polymorphic = some individuals 

2. Number of alleles that exist for these polymorphic genes 

   1. Polymorphic genes have at least 2 alleles but can have more 

   2. Ex. rabbit color has four alleles with complex dominance 

What are the Factors that influence genetic diversity: 

• Population size 

  • Most significant factor 

  • Smaller populations generally have less genetic diversity 

  • Effective population size (Ne) is more important than observed population size (N) 

    • Size of an Idealized population (constant size, random matiting, etc.) which has the same loss of genetic diversity as the observed population 

• Life history patterns, behavior 

  • E.g. species with small home ranges/low rates of dispersal 

    • Can be due to lack of mobility, dependence on isolated habitat, etc. 

    • Reduces gene flow = exchange of alleles between populations

-Historic changes in population 

- populations increasing from low numbers tend to have less genetic diversity 

- population/genetic bottlenecks  

- Mutation Rate 

- source of all genetic variation 

- varies between species but tends to be low 

Genetic Drift

Loss of alleles due to non-selective processes (random loss of alleles) 

- in large stable populations theoretically balance mutation rate (mutation drift equilibrium) 

Polymorphism

the proportion of genes in a population that are polymorphic (have multiple alleles)

Mean heterozygosity

proportion of genes for which the average individual is heterozygous 

• Other molecular techniques require tissue samples

Measuring Polymorphism (P) 

• The proportion of genes in a population that are polymorphic 

• Common to consider a gene as polymorphic if the proportion of the most common allele is less than 0.95 (95%) 

• Consider a population that has two alleles for a gene (check lecture) 

  • P = # genes polymorphic / # genes sampled 

• Higher levels of polymorphism = higher proportion of genes that have different version of alleles (good) 

Measuring heterozygosity (H0) 

• Proportion of genes for which the average individual is heterozygous for 

• For each gene: individuals heterozygous / total individuals 

• Also expressed as mean homozygosity 

• Higher levels of mean heterozygosity = higher proportion of genes that the average individual has different versions of alleles for  

Ecosystems

defined by the specific pathways of energy and organic material transfer 

• Pathways can be summarized as a food web (who eats who) 

• Species can be categorized into trophic levels based on where they are in the food web

  • Trophic levels shown in trophic pyramid which represents distribution of biomass 

Bottom-up Control 

• Population level and activity of primary producers regular overall activity of ecosystem

• Abundance of organisms at each trophic level is determined by the abundance of resources for those organisms

• Ex. seasonal changes bring various nutrients and phytoplankton bloom 

Top-down Ecosystem Control: 

• When a species suppresses or controls the population of one or more species lower in the food web 

• Removal or drastic reduction of a species that has a top-down control function in the food web can be detrimental 

  • Resulting in changes in population so father species in food web 

  • Reduction in species diversity 

  • Loss of ecosystem function 

  • Mesopredator release

• When involving three or more levels; known as trophic cascades 

  • When predators limit the density and or behavior of their prey, which increases survival of next trophic level

  • Can affect entire ecosystems 

Mesopredator release

population increase in mesopredators due to decreased predation from higher-order predators  

Density Mediated Control

 predators directly reduce the number of prey by consuming them

Trait mediated control

predators indirectly reduce number of prey 

• Risk cues - prey can detect presence of predators through cues (chemical, acoustic, etc) 

• Spend less time foraging, mating etc.

Insurance Hypothesis

high species diversity is insurance against ecosystem collapse 

• More connections there are, less important any given connection is 

  • Few species are highly dependent on a single species 

  • Fewer redundant pathways 

    • Fewer connections there are, the more important a given connection is 

    • If a single species is removed, there are not as many species that could potentially do the same job in the ecosystem

Hypothesis 2 - Diversity-Stability Paradox

Based on mathematical ecosystem simulations using random, linear pairwise interactions between species (increased species diversity doesn’t lead to increased ecosystem stability)

• More complex systems less likely to recover from perturbations than simple ones 

• Biological logic: Ecosystems can only support so many species and individuals

  • › Additional species = lower populations

  • › Additional trophic levels = less energy transfer through food web

  • Widely (but reluctantly) accepted as ecological theory

Ecosystem Service

any benefit that an ecosystem provides to society; the greater the ecosystem function, the greater quantity or quality of the ecosystem services provided

Millenium Ecosystem Assessment

UN Sanctioned assessment of human impact on the environment with 4 categories

Provisioning Services

• Obtaining products from the environment 

• Extractive - taking something from the environment (ex. Food, water, wood, genetic resources, medicinal, ornamental, minerals) 

Regulating Services

1. Services that regulate the natural environment for the betterment of society 

2. All non-extractive (ex. Climate moderation and air quality, carbon sequestration and storage, eroding prevention and prevention of flooding, waste treatment, pollination, pest control

Cultural Services

1. Services that provide enjoyment, recreation, spiritual or cognitive benefits

2. All non-extractive (ex. Tourism, science and education, aesthetic appreciation, mental and physical health, and recreation (like fishing)) 

Supporting Services

1. Necessary for the existence of all other ecosystem services 

2. Non-extractive (ex. Nutrient cycling, primary production, biodiversity)

Species Richness (s) 

• Number of species in an area 

• Simplest measure of species diversity; Easy to understand - useful way of reporting species diversity to the public (websites, public service announcements etc) 

• R.H. Whittaker used species richness to develop the concepts of alpha, gamma, and beta diversity 

Alpha Diversity (a)

• species diversity measured as species richness at a local scale (e.g. a lake) 

  • Higher alpha diversity (more species) = good

Gamma Diversity (y)

• number of species in a landscape (usually interpreted as larger geographic scale that includes different ecosystems (e.g. watershed) 

  • Higher gamma diversity (more species) = good 

Beta Diversity

difference in species composition between local areas 

• Ratio between regional special diversity (y) and mean local species diversity (mean a) 

• High beta diversity indicates less similarly in species composition between local areas within a region 

• Beta = gamma/alpha

Diversity Indices

Better measurements of species diversity than simple species richness 

• Take into account relative abundances of the species → evenness 

• Better indicator of ecosystem function and community structure 

• Increasing species richness and increasing species evenness affect diversity indices

Shannon’s Diversity Index (H’)

Information index

• based on information theory

• most common used

• measures amount of disorder observed in a system

Simpson’s Diversity Index (Ds)

Dominance index

• gives more weight to common or numerically dominant species

• rare species will not affect the diversity index much or at all

• relates to the probability of any 2 individuals drawn at random belonging to the same species

• ranges 0 to 1 (1 = infininte diversity, 0 = no diversity)

Rank Abundance Curves

Graphical way to describe patterns of  species richness and evenness

1. Change species survey data to rank order abundance (most to least abundant) 

   1. Species abundances arranged from highest to lowest (omit zeros) 

   2. Can ignore what species the abundances correspond with 

2. Plot abundance (y-axis) against species rank number (x-axis) 

   1. Data may be better represented using log 

Species accumulation curve 

Used to estimate proportion of species found

• Number of total species found vs. survey effort (e.g. distanced surveyed or time surveyed 

• As curve approaches an asymptote you are approaching the survey effort necessary to discover all species present 

• The exact shape of the curve is highly dependent on community structure, patchiness etc. 

• Related to the species area curve of insular biogeography (increased species with increased habitat area) 

Assumptions of species diversity analysis

1. All observations were obtained randomly; especially important in shannon diversity index, least important with species richness 

2. Assumes all species in area are detected 

   1. Not detecting all species is the most significant error 

   2. How do you know if you've found all (or majority) of species? 

• Proportion of species found can be estimated by making a species accumulation curve 

  • Number of total species found vs. survey effort (e.g. distanced surveyed or time surveyed 

Edge Effect

Transition zone between destroyed habitat and natural habitat 

• Characterized by increased anthropogenic disturbances like air pollution; changes in physical properties of habitat (hotter, drier); changes in biological community (increased presence of disturbance-tolerant species) 

  • Width of Edge Effect: 

    • Complex - different for different types of threats, different types of habitats 

• As total area of habitat decreases, the proportion of edge effect increases 

Habitat Fragmentation

Caused when a habitat is divided into two or more smaller areas by disturbances such as habitat destruction 

• Ex. roads, power lines, dams

• Often overlooked as threat to biodiversity since habitat destruction can be small 

• Even narrow discontinuities in habitat can be problematic 

• Adding to edge effect 

Ecological Extinction

When a species in found at such low numbers that it no longer performs its ecological role

Invasive Species

• Highly adaptable, generalists

• Tolerant to human and can live in disturbed habitats 

• High rate of dispersal 

• Able to physically modify habitat 

Able to overcome colonization bottleneck (founder effect)

Colonization bottleneck (founder effect)

The reduction in genetic diversity when a small number of individuals colonize an area

r-selected species

Early sexual maturity, produce many offspring, low parental investment

• a population can be described by the logisitc growth equation and curve

  • describes the population size with respect to time

K-selected species

have few offspring and invest heaviliy in them (careful reproduction)