Forecasting Extinction

By Claire Asher, on 5 January 2015

Classifying a species as either extinct or extant is important if we are to quantify and monitor current rates of biodiversity loss, but it is rare that a biologist is handy to actually observe an extinction event. Finding the last member of a species is difficult, if not impossible, so extinction classifications are usually estimates based on the last recorded sightings of a species. Estimates always come with some inaccuracy, however, and recent research by GEE academics Dr Ben Collen and Professor Tim Blackburn aimed to investigate how accurate our best estimates of extinction really are.

Using data from experimental populations of the single-celled protist Loxocephalus, as well as wild populations of seven species of mammal, bird and amphibian, the authors tested six alternative estimation techniques to calculation the actual date of extinction. In particular, they were interested in whether the accuracy of these estimates is influenced by the rate of population decline, the search effort put in to find remaining individuals and the total number of sightings of the species. The dataset included very rapid declines (40% a year in the Common Mist frog) and much slower ones (16% per year in the Corncrake), and different sampling regimes.

Their results showed that the speed of decline was a crucial factor affecting the accuracy of extinction estimates – for experimental laboratory populations, estimates were most accurate for rapid population declines, however slow population declines in wild populations tended to produce more accurate results. The sampling regime was also important, with larger inaccuracies occurring when sampling effort decreased over time. This is probably a common situation for many species – close monitoring is common for species of high conservation priority, but interest may decrease as the species becomes closer and closer to extinction. The total number of sightings was also an important factor – a larger number of sightings overall tended to produce more accurate estimates.

Finally, the estimation technique also influenced accuracy, but only in interaction with the other variables mentioned above. Some methods fared best for rapid population declines, others for slower ones. Many of the methods fare poorly when sampling effort changes over time, particularly if it decreases, although they were relatively robust to sporadic, opportunistic sampling regimes. Overall, optimal linear estimation, a statistical method which makes fewer assumptions about the exact pattern of sightings, produced the most accurate results in cases where more than 10 sightings were recorded in total.

This study highlights the challenges faced by ecologists trying to determine whether a species has gone extinct or not. Sightings of rare species are often opportunistic, and only rarely are they part of a systematic, long-term monitoring program. Thus, methods that produce accurate results in the face of changing or sporadic search efforts are of key importance to conservationists. If the history of a species’ population declines and of the sampling effort are known, then statistical estimates can be selected which provide the best estimates for the particular situation. However, this information is rarely available and so using techniques that can provide accurate estimates for a range of different historical scenarios are likely to be of most use in predicting extinction status. Ultimately, it is extremely useful for conservationists to know whether a species is extinct or not, but estimates will always be subject to error except in rare cases (such as the passenger pigeon, for example) where the extinction event is observed first hand. There will always be cases of species turning up years after they were declared extinct, and no estimate will ever be perfect, but understanding the sources of error and the best methods to use to minimise it can be of great benefit in reducing the frequency with which that happens.

Original Article:

() Conservation Biology

This research was made possible by funding from the Natural Environment Research Council (NERC).

Dating Mammalian Evolution

By Claire Asher, on 28 March 2014

When the age of the dinosaurs ended around 65 million years ago, mammals stepped in to fill the gap, and the age of the placentals began. However, whether early placental mammals were already present on Earth before the demise of the dinosaurs has been the subject of a long standing debate. Recent research in GEE used genomic data, in combination with fossil evidence, to show that the earliest placental mammals were indeed scurrying between the feet of dinosaurs.

Shrew-like mammals scurry between the feet of dinosaursThe huge diversity of placental mammals on Earth today first appeared shortly after the mass extinction event that killed the dinosaurs. It is thought that the loss of the dinosaurs, along with much of life on Earth, freed up niches which placental mammals to evolved to fill. But were early placental mammals present, waiting in the wings, during the age of the dinosaurs, or did they appear rapidly after their demise? One recent study suggested that, based on fossil evidence, the placental mammals must have appeared after the cretaceous-tertiary boundary (KT) when dinosaurs and most life on Earth was wiped out. However, a recent paper by GEE’s Mario dos Reis and Ziheng Yang, in collaboration with Philip Donoghue from the University of Bristol, highlights flaws in the methods used in this study, and utilitsed a more thorough approach to show that early placental mammals likely predated the KT boundary.

Using genetic sequence data from over 14,000 genes, combined with fossil evidence, GEE researchers applied 3 alternative statistical methods to estimate the age of the earliest placental mammal; ancestor to all modern placental mammals. Although different statistical methods yielded slightly different estimates, and differed in their accuracy, they all agreed that placental mammals must have already been around before the dinosaurs went extinct. The adaptive radiation of mammals that occurred after the extinction of the dinosaurs was dramatic, but it was initiated by a few shrew-like species which had already evolved. This study highlights the importance of using statistical methods to estimate the true age of ancestral species; the age of the oldest fossils is not the same as the age of the ancestral species that gave rise to them, and statistical techniques must be employed to estimate this. Using both molecular and fossil evidence to inform estimates also provides more robust evidence for the true age of the first placental mammals, and the theory that the earliest ancestors of placentals predated the disappearance of the dinosaurs.

Original Article:

This research was made possible by funding from the Biotechnology and Biological Sciences Research Council (BBSRC).