Biodiversity and Conservation Biology

Definition and Levels of Biodiversity

• Biodiversity Defined: A measure of the number of lineages in a defined area. It is not a single value but is assessed at multiple levels.

• Five Major Levels of Biodiversity:     - Genetic Diversity: The number and relative frequency of all alleles present in a species or group of species.     - Species Diversity: A measure incorporating both the number of species (richness) and their relative abundance (evenness).     - Phylogenetic Diversity: The measure of independent evolutionary lineages present in a phylogeny.     - Functional Diversity: The variety of functional traits related to ecosystem processes like primary production or nitrogen fixation.     - Ecosystem Diversity: The variety of distinct ecosystems within a geographic area.

Genetic Diversity and Conservation Goal #1

• Mechanisms of Diversity: Distinct populations often exhibit unique alleles due to mutation occurring without gene flow, or because different selection pressures act on separate populations.

• Measuring Genetic Diversity: Advanced sequencing techniques make measurement easier:     - Genome sequencing: Provides a full genetic blueprint.     - Environmental sequencing: Allows assessment of diversity in a whole community sample.

• Goal #1: Preserve as much genetic variation as possible.     - Reasoning: Genetic diversity is the raw material for evolution. It represents the adaptive capacity of a group, allowing it to persist despite changes in the environment.

• Cheetah Case Study: The cheetah genome is composed of $93\%$ homozygous stretches. They retain only $0.1\text{--}4\%$ of the overall genetic variation seen in most living species.

• Haplotypes: A combination of genes that are closely linked and typically inherited together. Differences in haplotypes indicate different alleles within a section of DNA.

Species Diversity and DNA Barcoding

• Key Terms:     - Species Richness: The literal count of species in a particular area.     - Species Diversity: A weighted number incorporating richness and evenness (relative abundance). For example, if a few species dominate an area while others are rare, diversity is considered low, even if richness is high.

• Goal #2: Preserve as many species as possible.

• DNA Barcoding: Biologists use a well-characterized gene sequence to identify distinct species. It operates on the principle that genetic variation should be higher between species than within them. Tens of thousands of species have been barcoded in reference libraries.

Phylogenetic Diversity and Lineages

• Definition: The number of independent evolutionary lineages present, measured using branch lengths among species in a phylogeny.

• Lineage Richness Examples:     - African Cichlids: Lineage with $1300\text{--}3000$ species.     - Sturgeon: Lineage with approximately $26$ species.     - Red Panda: Only $1$ species in its group compared to Weasels ($38$), Dogs ($43$), or Seals ($36$).

• Evolutionary Distinctiveness: High phylogenetic diversity means species are distantly related (branches are long and spread out); low diversity means species are closely related.

• Goal #3: Preserve as many independent lineages as possible.

Functional and Ecosystem Diversity

• Functional Diversity: Diversity in traits playing important roles in the ecosystem, such as primary production, decomposition, predation, and nitrogen fixation.

• Ecosystem Diversity: The count of distinct ecosystems. Goal #4 is to preserve as many ecosystems as possible because different ecosystems house unique communities (e.g., Glacier Creek Prairie Preserve).

Evolutionary Significant Units (ESUs) and Conservation Priorities

• Definition: ESUs are genetically distinct populations, species, or lineages identified by conservation biologists to maximize preservation goals.     - Typically includes all species.     - Includes varieties or subspecies with local adaptation or geographic separation.     - Includes populations with high genetic differentiation.

• Resource Allocation: Because money, time, and energy are limited, biologists must choose where to invest. Choices are based on the chance for success and the value of the organism.

• Case Study: Kemp’s Ridley Sea Turtle:     - Background: Numbers declined from $40,000$ nesting females in 1947 to < 1,000 in 1985. Taxonomic status was uncertain (possible subspecies of Olive ridley).     - Analysis: Mitochondrial DNA analysis by Bowen et al. (1991) proved genetic differentiation.     - Outcome: Justified as an ESU; conservation plans implemented. Despite > 100 dying in the 2010 Deepwater Horizon Oil Spill, numbers are rising, though it remains critically endangered.

• Case Study: Dusky Seaside Sparrow:     - Background: Subspecies of the seaside sparrow; extinct in the wild by 1987.     - Analysis: DNA showed it was almost identical to the seaside sparrow.     - Outcome: Not declared an ESU; no reintroduction; declared officially extinct in 1990.

Global Biodiversity Patterns and Hotspots

• Distribution: Species richness is not even. Tropical rainforests occupy only $7\%$ of Earth's land area but contain an estimated $50\%$ of all species.

• Endemic Species: Species present in only one area and nowhere else.

• Biological Hotspots Criteria:     - Contain at least $1500$ endemic vascular plant species.     - Have lost at least $70\%$ of primary vegetation.

• Hotspot Statistics: They cover $17\%$ of land (excluding Antarctica) but are home to:     - $50\%$ of known plant species.     - $77\%$ of known terrestrial vertebrate species.     - $42\%$ of endemic terrestrial vertebrate species.

• Limitation: The definition does not account for the current rate of loss; regions like the Amazon do not count until they reach the $70\%$ loss threshold.

Documenting Biodiversity: Taxa Surveys

• Methods:     - Taxa Surveys: Group-specific inventories (Floras, etc.).     - BioBlitz: Short-term events to catalog all species in an area (e.g., a weekend).     - All Taxa Biological Inventory (ATBI): Labor-intensive efforts often involving the public.

• Great Smoky Mountains National Park (ATBI initiated 1998):     - Select Results (as of Nov 2019): Total species new to science: $1021$; total species new to the park: $9605$.     - Groups (New to Park / New to Science):         - Algae: $566$ / $78$         - Bacteria: $212$ / $270$         - Coleoptera: $1984$ / $73$         - Fungi: $583$ / $66$         - Vertebrates: $30$ / $0$

• Census of Marine Life: International effort involving $2700$ scientists and $540$ expeditions. Collected $30,000,000$ records and $6000$ potentially new species. Marine species count estimated at $250,000$.

The Sixth Major Extinction

• Extinction Rates: Currently $100\text{--}1000$ times greater than the geological average.

• Drivers: Unlike previous events (climate, volcanic activity, asteroid impact), this is caused directly and indirectly by human activity.

• IUCN Red List: Categorizes risk as Vulnerable, Endangered, or Critically Endangered.     - $41\%$ of Amphibians are threatened.     - $27\%$ of Mammals are threatened.     - $13\%$ of Birds are threatened.

Major Threats to Biodiversity

• 1. Habitat Destruction: Leading factor for $90\%$ of terrestrial endangered species. Includes deforestation, logging, and infrastructure. If rates continue, half of the Brazilian Amazon will be gone within a lifetime.

• 2. Habitat Fragmentation: Habitats broken into isolated metapopulations.     - Fragments are more susceptible to disease, fire, and storms.     - Limits gene flow, leading to inbreeding depression and genetic drift.

• 3. Overexploitation: Leading threat in marine environments. $70\%$ of fisheries are fully/over-exploited or depleted. Some predict total fishery collapse by $2048$.

• 4. Invasive Species: Second leading threat. Species multiply rapidly and threaten natives (e.g., Burmese python in Everglades; Zebra mussels in the US).

• 5. Pollution: Includes chemical pollutants and garbage. The Great Pacific Garbage Patch features plastic outweighing zooplankton $6:1$.

• 6. Climate Change: Targets specific species; e.g., coral bleaching due to warming waters.

Conservation Strategies

• Corridors: Man-made paths to connect fragmented habitats. Data shows increased species richness in connected vs. unconnected plots over time ($2001\text{--}2005$).

• Introduction of New Members: Used to counteract genetic drift/inbreeding (e.g., introducing new sheep to Montana refuges).

• Population Viability Analysis (PVA): Estimating the likelihood of survival using demographic data and migration scenarios (e.g., Leadbeater’s possum).

• Sustainable Practices: Managed use of resources replaced as fast as they are consumed (biopolymers, sustainable agriculture).

• Ex Situ Conservation: Preservation in artificial settings (Zoos like Henry Doorly, Seed Banks, Botanical Gardens, Aquaria).

• Ecosystem Restoration: Assisting the recovery of degraded ecosystems. Steps include reducing human impact, reintroducing species, removing unwanted species (predator-proof fences), and restoring disturbance regimes (e.g., controlled burns).

• Consumer Behavior: Using tools like "Seafood WATCH" to make ocean-friendly choices.

The Importance of Biodiversity: Ecosystem Function

• Productivity: Experiments (e.g., planting $289$ plots with varying richness and functional groups) show that Net Primary Productivity (NPP) increases with species richness and functional diversity.

• Stability:     - Resistance: Extent to which a community remains unchanged after disturbance.     - Resilience: Speed of recovery following disturbance.

• Ecosystem Services:     - Provisioning: Food, fuel, fiber, medicine, water.     - Regulating: Climate moderation, erosion control, water purification.     - Cultural: Aesthetics, recreation, mental/physical health.     - Supporting: Primary productivity, nutrient cycling, pollination.

Historical Perspective and Ethics

• Shifting Baseline Syndrome: The tendency to accept the current state of nature as "normal," forgetting historical abundance.     - Bison: Once spanning North America, nearly exterminated by 1889.     - Passenger Pigeon: Once existing in "countless multitudes" (John James Audubon description in 1827); extinct by 1914.     - Key West Trophy Fish: Photos from 1950s show giant groupers; by the 2000s, the average catch was only a foot long.

• Ethical Arguments for Preservation:     - Organisms have intrinsic worth.     - Industrialized nations hold responsibility for harm; must not inflict hardship on poor nations.     - Depriving future generations of ecosystem services is unethical.

• Take-Home Message: Biology provides the tools for change. As William Shatner noted after his trip to space, the beauty and nurturing "harmony of the universe" is found on Earth, and it is mankind's responsibility to protect it from further destruction.