---
title: "Extinctions of keystone species"
author: "Duncan Golicher"

output:
  slidy_presentation: default
  ioslides_presentation: default
  beamer_presentation: default
  powerpoint_presentation:
bibliography: [ecosystems1.bib, ecosystems2.bib,insects.bib]
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE, warning = FALSE,message = FALSE)

```

# Recent loss of keystone species

-   The current period has been termed the "anthropocene"

-   Many, if not all, ecosystems have been altered by human activities

-   Terrestrial ecosystems frequently lack populations of large mammals that may play a role as keystone species

-   However, although populations have been reduced in size or lost locally, how many keystone species have actually gone extinct in recent times?

# Are we witnessing the sixth mass extinction?

-   There have been five very large mass extinction events (and numerous smaller mass extinctions) in geological history
-   Species are continuously going extinct (and new species emerging) even in "normal" periods
-   This is known as the background rate of extinction
-   Why has the concept of the sixth mass extinction become popularised?

# How do we compare current extinction to the past?

-   A comparison with the background extinction rate is typically used
-   The fossil record is very incomplete
-   There is no direct record of the number of species that have ever lived
-   Many species are only slightly different from others (particularly plants)
-   Estimating the background rate of extinctions requires making assumptions [@lamkin2016]

# What is the background rate?

-   Estimated lifespans of species in the fossil record during non-mass extinction intervals.
-   Mean lifespans range from approximately 0.2 million to 16 million years depending on taxonomic group,
-   Average background longevity generally expressed as approximately 1 million to 10 million years [@pimm2014]
-   A rate of 1 extinction per million species years is quite widely used

# Recent extinctions

![](figs/extinctions1.png){width="800"}

# Which species are becoming extinct?

-   Most of the recently documented extinctions have been of endemic species on islands

-   Small islands have witnessed most extinctions

-   However, some large islands such as Madagascar have also lost many species

-   The populations of continental species have been reduced, but some remnant populations typically persist

-   As biodiversity is concentrated in the tropics more tropical species have been lost than temperate species

-   Many extinctions not recorded. Dark extinctions [@boehm2021]

# Why might extinctions on islands have a greater impact on their ecosystems?

-   Islands species tend to be endemic, but islands have fewer species overall

-   The loss of any species is more likely to disrupt trophic interactions

-   Introducing species to islands tends to have a major impact on ecosystem structure and function

-   Many island species went extinct as a result of European exploration and settlement beginning in the 15th century

- Polynesian colonisation and the introduction of rats, pigs and chickens may have caused even more.

# Extinctions on continents

-   Latitude and topography are important

-   Flat temperate areas -\> very low rates of extinction

-   Montane tropical areas -\> higher rates of extinction

-   Many extinctions (often dark extinctions) may be occurring as tropical montane forests are lost.

# Extinction of keystone species on continents

-   Habitat loss, fragmentation and hunting leads to local loss of large predators

-   May affect top down control

-   The UK has lost wolves, bears, lynx, large birds of prey (eagles) etc.

-   However, these species are still extant (not extinct) and could be reintroduced from continental remnants

-   As continents are large the complete eradication of an entire species is less likely

# When did the extinction of keystone species occur on continents?

-   Extensive extinctions of large mammals occurred in North and South America, Eurasia, Africa and Australia in the late Pleistocene between 50,000 and 10,000 years before present

-   Mammoths, Mastodons, Giant ground sloths, saber tooth cats, giant beaver

-   Coincided with the expansion of *Homo sapiens* populations

-   Modern humans reached Australia around 60 thousand years ago

-   "Great leap forward" in hunting techniques around the same time

# What caused the extinctions?

-   Three conflicting theories

    -   Climate change

    -   Hunting

    -   Disease

-   Probably involved some elements of all three, although disease less likely

# Arguments against climate change as main driver

-   Mammoths mastodons and other classic "ice age" herbivores evolved at least 1 million years ago
-   They therefore persisted through various interglacials
-   Even if climate changes some suitable habitat would always remain somewhere
-   Movement rather than extinction seems more likely on continents (no barriers to movement)

# Climate of last 5 million years

![](figs/extinctions2.png){width="600"}

# Arguments against disease hypothesis

-   Extinctions affected large mammals, but not many small mammals
-   No evidence that disease can completely eradicate populations of either
-   Disease is more likely to affect social mammals (extinctions were of non-social mammals)

# Arguments against hunting

-   Only limited evidence of human induced mortality in fossil record
-   Extinctions of non-prey species (carnivores)
-   Extant populations of large herbivores still found in Africa and Asia

# Ecological arguments in favour of hunting (overkill) hypothesis

-   Species that went extinct tended to be K selected
-   Slow growth rate
-   Long gestation periods
-   Potential keystone species (other extinctions the result of their loss)

# Hunted to extinction?

![](figs/hunters.png){width="500"}

# Large mammals became extinct

[@Lyons2004]

![](figs/extinctions3.png)

# Large mammals became extinct

![](figs/extinctions4.png)

# Carbon dioxide levels

![](figs/co2.png){width="500"}

# Low CO2 point 35 thousand years ago

-   Atmospheric C02 at the last glacial maximum may have been 75 ppm below the level at the beginning of the Holocene [@monnin2001]

-   Could have been a low point in net primary productivity

-   Large herbivores can digest low quality food in bulk

-   However, if net primary productivity was low they could have a negative energy balance

# Summary of late quaternary extinctions

-   During the Pleistocene, megaherbivores were more diverse and widespread than today on all continents.

-   By the early Holocene (c.11 700 kyr BP), hundreds of species of large herbivores and their predators had disappeared from the continents

-   The late quaternary extinctions were more selective than any event in the preceding 65 million yr of mammalian evolutionary history, disproportionately targeting large mammals (\>10 kg)

-   Could be due to disease (unlikely), climate change alone (why not previously?), hunting alone (why all the large mammals including equines .. hard to hunt) or reduced primary productivity (climate and low C02) + hunting (seems most likely)

# Consequences

-   Extinctions of large herbivores led to extinctions of their predators

-   Were large herbivores "landscape architects"?

![](figs/elephant.png){width="400"}

# Mastodon

![](figs/mastodon.png){width="400"}

# Evidence for vegetation change

![](figs/polen.png){width="500"}

# Evidence for increase in deciduous trees

[@gill2013]

![](figs/extinctions6.png){width="600"}

# Possible consequences

-   Reduced herbivory led to increase in trees

-   Increase in trees led to more fuel build up

-   More fires, thus more charcoal

# Possible consequences

![](figs/extinctions7.png){width="500"}

# The Vera hypothesis

![](figs/vera.png){width="500"}

[@hitchmough2002]

# References
