1. Show a histogram of the population growth rate, and a separate histogram of the generation time of your subset of species. Describe the patterns. Do they make sense to you?

These plots were constructed using a subset of data from comadre composed of Reptilia. Histograms have then been plotted using lambda (calculated from the popbio package), and the generation time (calculated from the rage package)

In figure 1. the population growth rate is skewed to the right, this makes sense as we would expect populations to reach a dynamic equilibrium as time progresses. As the dynamic equilibrium is equivlent to a generation time of 1.0, we expect to see a skew around 1.

In figure 2. We also see a short generation time; this tells us that most species within the Reptilia clade a short amount of time is needed for a population to grow by a factor of its net reproductive rate. It also suggests a more R-selected life history. Within Reptilia there seems to be a few outlines that have a much longer generation time.

2. Fit a model to explore whether the generation time and population growth rate of your species’ populations are correlated. Would you have expected them to be correlated? Why?

## The Pearson correlation coefficient between the Population Growth Rate and Generation Time is: -0.12

Generation time and population growth rate have been cleaned of ‘na’ and molded in a Pearson correlation coefficient to be applied to it. The results of this model shows a little-to-no correlation between Population Growth Rate and Generation Time. Initially I thought there would be some correlation as populations that have a shorter generation time are able to reproduce more frequently, as such their population would grow at a quicker rate. This is not the case, which likely means demographic pressures are preventing this.

3. Using a different key to the one I provided you with in the computer practical, obtain the conservation status of these species from the IUCN Redlist site, and explore, using statistical models, whether generation time, on the one hand, and population growth rate, on the other hand, predict conservation status.

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## ✔  Found:  Caretta caretta
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## • Total: 1 
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## ✖  Not Found:  Chelodina expansa
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## ✔  Found:  Chelonia mydas
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## ✔  Found:  Chelydra serpentina
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## ✔  Found:  Chrysemys picta
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## • Total: 1 
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## ✔  Found:  Clemmys guttata
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## ✔  Found:  Crocodylus acutus
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## ✖  Not Found:  Crocodylus johnsoni
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## ✔  Found:  Cryptophis nigrescens
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## ✔  Found:  Drymarchon couperi
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## • Total: 1 
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## ✖  Not Found:  Emydura macquarii
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## ✔  Found:  Hoplocephalus bungaroides
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## ✔  Found:  Kinosternon flavescens
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## ✔  Found:  Kinosternon integrum
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## ✔  Found:  Kinosternon subrubrum
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## • Total: 1 
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## ✔  Found:  Malaclemys terrapin
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## • Total: 1 
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## ✔  Found:  Phrynosoma cornutum
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## ✔  Found:  Podocnemis expansa
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## ✔  Found:  Sceloporus arenicolus
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## ✔  Found:  Sceloporus grammicus
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## ✖  Not Found:  Sceloporus mucronatus mucronatus
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## ✔  Found:  Vipera aspis
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## ✔  Found:  Xenosaurus grandis
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## • Total: 1 
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## ✔  Found:  Xenosaurus platyceps
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## ✖  Not Found:  Xenosaurus sp.
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##             Df Sum Sq Mean Sq F value Pr(>F)
## IUCNstatus   3    714   238.1   1.037  0.398
## Residuals   20   4594   229.7               
## 1 observation deleted due to missingness

##             Df Sum Sq Mean Sq F value Pr(>F)
## IUCNstatus   3 0.5128  0.1709   1.483  0.249
## Residuals   20 2.3053  0.1153               
## 1 observation deleted due to missingness

The conservation status of each unique reptilia species, accessed via the IUCN database, was plotted against generation time and population growth rate. Additionally, an ANOVA was carried out. For both it is unclear to see any correlation. Population growth rate has a very flat trend; endangered species do have a higher mean generation time however error bars overlap and the box plot has a large range, so this does not seem significant; equally species that are ‘not assessed’ range across many different generation times — perhaps this is important data that is lost.  Both models show an F-Value of between 1 and 1.5, both of these are not particularly high, suggesting that the difference between groups is not that significant. With this being said, the p-values associated with each F-value are both > 0.05 by magnitudes of 10, as such this is not a statistically significant set of models.

4. Plot the values of generation time and of population growth rate of your species on the phylogeny provided to you. Is there any visual evidence of phylogenetic inertia in those traits? Why?

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To plot values of generation time and population growth rate for Reptilia on a phylogeny, the IUCNdata previously extracted was reformatted as a phylogeny and then used to filter a phylogeny from a wider tree of life. How lambda  and generation time changes over time was calculated and overlaid on this plot. From these phylogenies it is clear that population growth rate is not a highly conserved trait across the taxa, suggesting a low phylogenetic inertia (apart from one relatively recent clade that has been able to conserve it). Alternatively generation time is somewhat conserved with certain taxes having a higher phylogenetic inertia for it. This has seemed to increase over evolutionary time for some clades.

5. Create a new variable called “Population_performance”. Assign “Decline” or “Increase” to
those species whose unique population growth rate is <1 or >1, respectively. Then add another column to the phylogeny in such a way that you show the conservation status of those species.

Adapted from code accessed via (http://blog.phytools.org) this code plots a phylogeny with the population growth rate of each species represented as a binary ‘increasing’ or ‘decreasing’ along with the species IUCN status. This plot suggest quite an positive outcome as all species with an IUCN rank of ‘Endangered’ and ‘Vulnerable’ show an increasing population growth rate. However many species with a status of NA show a decreasing population growth rate; perhaps its decreasing population growth rate has played a role in the species lack of data. We also see ‘Endangered’ and ‘Vulnerable’ species grouping together on the phylogeny, to some extent — perhaps suggesting evolutionarily similar species are experiencing the same pressures resulting in their IUCN threat level (possibly the effects of anthropogenic activity).