DryadLab Package: Extinction Risk

From Dryad wiki
Jump to: navigation, search


Datasets

This dataset is a version of that deposited in Dryad but with log10 values already calculated.

Text version of the file

Excel version of the file

Teacher Background

Background extinction and mass extinction
Extinctions of species have occurred gradually and continuously throughout the history of life, creating a turnover of species through time. This is background extinction. However, there are particular points in time when a very large number of species go extinct, this is a mass extinction. Historically we recognize 5 big events including the most recent event, which occurred approximately 65 million years ago at the K-T boundary when the non-avian dinosaurs went extinct. The causes of these past events are varied and still debated but include climate-change, volcanic activity and asteroid impacts.

Insert image about background vs mass extinctions from Understanding Evolution website -> evolution.berkeley.edu/evolibrary/search/imagedetail.php

Although estimates vary on the precise numbers of current extinctions, most scientists agree that we are very close to entering a sixth mass extinction event due to human actions such as habitat destruction, pollution and overexploitation. For example, the IUCN (an international union of scientists and conservation organizations) estimates that 20% of the world’s 5,494 livings mammals are currently threatened with extinction. Given their rates of decline, it is estimated that all threatened mammals may go extinct within 1000 years, which exceeds the rates of background extinction estimated from the fossil record.

Resources/Further reading
Barnosky et al. 2011 Has the Earth's sixth mass extinction already arrived? Nature 471, 51-57. doi:10.1038/nature09678


Non-random extinctions

It has long been recognized that extinctions appear to be non-random with respect to which species survive and which go extinct. For example, it has been shown that large carnivores that specialize on large vertebrate prey (known as hypercarnivores) evolve repeatedly but have far shorter durations within the fossil record than other mammalian species. One of the most extreme examples of repeated hypercarnivore evolution is the saber-tooth cat-like form, which has evolved multiple times within the history of mammals.

Insert image from Valkenburgh et al. 2007 Integrative and Comparative Biology 47(1), 147-163 showing skulls of two different sabertooth skulls from very different time periods

The hypothesized explanation for the short duration of these hypercarnivorous clades is that their large size and highly specialized diets, which required lots of morphological adaptations, means they are unable to switch to other prey types during environmental perturbations.

Many other traits that have been proposed to predispose species to extinction as well (see table below).

Trait
Hypothesized modes of action
Related traits in student dataset
Small populations
Experience increased demographic stochasticity and inbreeding, and so may be wiped out by a local catastrophe.
Geographic range area (km2)
Population density (per km2)
Slow reproductive rate
More likely to experience population decline when mortality is increased because they are less able to compensate with increased fecundity. This trait may be particularly important for hunted species because hunting directly increases mortality.
Gestation length (days)
Weaning age (days)
Age at sexual maturity (days)
Age at first birth (days)
Inter-birth interval (days)
Poor dispersal abilities
Are less able to move away from local threatening processes or to live in fragmented habitats. Poor dispersal may also be linked to small geographic range.

Ecological specialization
If availability of the specialist resource changes, may be unable to switch to other more common resources. Also, specialization is often linked to other traits such as low population density because specialized resources often have a patchy distribution.
Dietary specialization
Habitat breadth
Higher trophic levels
Are more vulnerable to disturbance of species lower down the food chain. Also, carnivory is often linked to other traits that may increase threat, such as low population densities and small population sizes.

Large group size
Means that the species may be preferred by hunters because they are more visible and easier to track.
Average group size
Large home range
Makes it harder for species to live in fragmented habitats. Large home ranges also mean that the species will have a low population density.
Home range (km2)
High human impacts
Humans are the cause of most, if not all, current threatening processes. Therefore species may experience more threatening processes if they live close to lots of humans or in countries that are less economically developed because this can force the citizens to exploit their natural resources unsustainably.
Mean human population density (per km2) across the species range
Minimum human population density (per km2) across the species range
Gross National Income (US $) across the species range
Large body size
Is often a composite trait linked to other traits that may increase threat level through other traits, such as slow reproductive rates and low population density. Also, hunters often prefer to hunt large specie

Body mass (g)





Some traits may only come into play during certain threatening processes. For example, the endangered Tibetan antelope (Pantholops hodgsonii) has incredibly soft hair. Consequently, it has been hunted close to extinction by humans. However, this trait would likely be irrelevant if the antelope were threatened by habitat loss! Insert image of Chiru here. In contrast, other traits may be agnostic with respect to the threatening process. For example, during previous mass extinction events, only one trait is consistently related to the probability of going extinct: narrow geographic range (the work of David Jablonski). If a species is widespread, it may persist in areas less affected by the threatening processes. More details about this can be found on the Understanding Evolution website http://evolution.berkeley.edu/evolibrary/article/jablonski_01.

Interestingly, despite many potential differences between the current extinction crisis and past mass-extinctions, small geographic range is the only consistent correlate of current extinction risk across different groups of mammals including primates, carnivores, rabbits and bats.

Because closely related organisms tend to inherit similar traits from their common ancestor, extinction selectivity can lead to extinction risk being clustered within families or genera. For example, over the last 200 million years extinctions in mollusks have been clustered within certain families. More details about this example can be found on the Understanding Evolution website http://evolution.berkeley.edu/evolibrary/news/090901_extinctionrisk

Insert image about phylogenetic clustering of extinction from Understanding Evolution website -> evolution.berkeley.edu/evolibrary/news/090901_extinctionrisk

Resources/Further reading

Van Valkenburgh, B. et al. (2004) Cope’s rule, hypercarnivory, and extinction in North American canids. Science 306(5693), 101-104.

Van Valkenburgh, B. et al. (2007) Déjà vu: the evolution of feeding morphologies in the Carnivora. Integrative and Comparative Biology 47(1), 147-163.

Purvis et al. (2000) Predicting extinction risk in decline species. Proceedings of the Royal Society London, B. 267, 1947-1952.

Jones et al. (2003) Biological correlates of extinction risk in bats. American Naturalist 161, 601-614.

Extinction in Artiodactyla

Artiodactyls are even-toed hoofed mammals. The group includes cows, sheep, antelope, deer, giraffes, pronghorn, hippos, pigs, peccaries and camels. On an interesting side note, recent phylogenetic work has actually placed whales and dolphins (Cetacea) within this clade closely related to hippos, however they are not included in the dataset as terrestrial and aquatic extinction risk factors may be very different. According to the IUCN Red List of threatened species (www.iucnredlist.org), around half of all artiodactyls are threatened with extinction, and the primary threatening processes are overexploitation (hunting) and habitat loss. The IUCN uses scientists and other experts to assess the threat of extinction of each species using quantitative criteria such as the percent decline in population size or in geographic range. Each species is then categorized as Least Concern (0), Near Threatened (1), Vulnerable (2), Endangered (3), Critically Endangered (4), Extinct in Wild or Extinction (5). The details of the assessment criteria can be found here: www.iucnredlist.org/technical-documents/categories-and-criteria/2001-categories-criteria. Species are considered threatened with extinction if they are classified as Vulnerable, Endangered or Critically Endangered. Please be aware the red list classification in the dataset is from 2006 and so a species’ threat status may have changed since then – we will actually take advantage of this for the homework exercise.

The dataset contains average size, reproductive, population density and range data for 212 species of artiodactyl from across the globe. The dataset was generated by synthesizing data from scientific papers and books published on the biology and natural history of these species. Data for Gross National Income across the species range was taken from the GEO data portal part of the United Nations Environment Program (UNEP) and was added as an indicator of the socioeconomic conditions experienced by the species. This dataset was generated as part of a larger collaborative project known as panTHERIA, which is a database of life-history, geographical and ecological traits of all living mammals (see Jones et al. Ecology 90(9), 2648 www.esajournals.org/doi/abs/10.1890/08-1494.1). Species were identified as experiencing unregulated hunting by searching the conservation and anthropologic literature for documentation of species caught by hunters or available in markets. Species that were not found to be hunted are likely primarily threatened by habitat loss as according to the IUCN habitat loss is the second biggest threat facing artiodactyls today.

In the paper that this module is based upon (Price & Gittleman, 2007), the relationship between IUCN threat level and a variety of biological and socioeconomic factors (listed in the table above) was determined to see if any were associated with an elevated extinction risk. Globally, artiodactyls at greatest risk live in economically less developed areas and have smaller geographic ranges and older weaning ages. However, it is important to take into account the type of threatening process. In artiodactyls, the two major threats are overexploitation (hunting) and habitat loss. Species that experience unregulated hunting live in significantly less economically developed areas than those that are not hunted; however, hunted species are more susceptible to extinction if they have slower reproductive rates (older weaning ages). In contrast, risk in non-hunted artiodactyls is unrelated to reproductive rate and is more closely associated with the economic development of the region in which they live. The students will be using simple scatter plots and regression analyses to investigate their own hypotheses using these data. The methods of the original paper incorporated a phylogenetic framework to ensure that each association between the trait and threat-level was independent of shared-ancestry. Of course, students are not likely to complete an analysis of this complexity, and therefore may not obtain the same results as the original study. That is fine. They will still be able to observe important patterns in the data as they investigate their own hypotheses.

Resources/Further reading

Article: Price, S. A. & Gittleman, J. L. (2007) Hunting to extinction: biology and regional economy influence extinction risk and the impact of hunting in artiodactyls. Proceedings of the Royal Society B 274: 1845-1851 http://dx.doi.org/10.1098/rspb.2007.0505

Data: Price SA, Gittleman JL (2007) Data from: Hunting to extinction: biology and regional economy influence extinction risk and the impact of hunting in artiodactyls. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.82





Links to include

IUCN Red List of Threatened Species

Other articles and resources on extinction:

  • including jablonski and stuff on UE
  • Paper on body size and extinction risk:

Johnson, C. N. 2002 Determinants of loss of mammal species during the Late Quaternary ‘megafauna’ extinctions: life history and ecology, but not body size. Proc. R. Soc. B 269, 2221–2227. http://dx.doi.org/10.1098/rspb.2002.2130


Images to include

  • This figure would require permission from the publisher:

Media:Integr._Comp._Biol._2007_Jul_47(1)_147-63,_Fig._7.ppt

Fig. 7 from: Van Valkenburgh, B. et al. (2007) Déjà vu: the evolution of feeding morphologies in the Carnivora. Integrative and Comparative Biology 47(1), 147-163 doi: 10.1093/icb/icm016

  • This image of chiru, Pantholops hodgsonii, is from Flickr user yun dan carries the CC-BY license:

Chiru


  • These additional chiru images appear on the web without any copyright statement; they may be freely available:

Chiru1

Chiru2

Chiru3