Goodbye for now

Hello everyone - it's been a good ride. I intend to pick up this blog again in future when I have more time on my hands, but thank you for all your time and comments. I have thoroughly enjoyed writing here and I've learnt a lot, and I hope you all have as well (Or else I haven't done a very good job!). I'd like to leave you with one closing thought, or ramble as it may turn out to be.

Should we be optimistic? In writing this blog, I think I've definitely made more negative conclusions than I have positive. Whilst some of the facts and figures I, and many of my colleagues, have come across and written about are pretty sobering, I feel that it is important to maintain some kind of positive outlook, as hard as it may be. Yes, probably some things are set in stone from the emissions, chemicals and otherwise that are already in the earth systems but unless we try to fight to stop anything else being written off, the black list of species is going to be a lot longer. That fight is a hell of a lot easier if we don't give up, and that attitude needs to grow and extend beyond the reaches of academia.

As I've emphasised in many of my posts there is a relationship between society and the media and the sciences that we are wise not to ignore. Personally, I feel that there should be a dialogue between the public and academics and that those of us who have been privileged enough to learn have a responsibility to communicate some of these ideas to everyone else. In fact, I think this is an essential part of how we should approach global environmental issues such as climate change, mass extinctions and the rest of it. The interface between science and society is now more important than ever and I hope through this blog I have done (some of) my part in bridging that gap.

Thank you!

Thank you everyone!; Source.

Estimating Extinction

The extinction of a species can be a difficult thing to precisely pinpoint in the fossil record. Beyond recent history, extinction is not something we can directly observe. Some species may survive after our last known record of them, and we have no way of knowing how long. There might be instances where, for whatever reason, no remains of that species were preserved or simply instances where the remains have been lost through tectonic movements. Some remains might still be waiting for us to stumble upon them, given that there is a considerable geographic bias in palaeontological research. 

Extinction is actually something we have gotten wrong in the past. For years, it was thought that coelacanths went extinct in the End-Cretaceous mass extinction 65 million years ago. In 1938, a living coelacanth was found in the western Indian Ocean and although it was a distinct species from the fossil variants, it was anatomically very similar and what is called a "living fossil". "Living fossils" are species that are, mostly superficially, morphologically similar to their extinct ancestors and are thought (wrongly) to have undergone little to no evolutionary change. Whilst these species may retain the plesiomorphic phenotypical states, it does not mean they are not still evolving and palaeontologists dislike the misleading using of the term in pop-sci press. Another species of coelacanth was discovered in South East Asia in 1997, cementing the idea that we were wrong, both about its apparent extinction and also its static evolution. Whilst this doesn't happen very often, it begs the question, what if we're wrong about other organisms?

The Coelacanth, a "living fossil"; Source.

Two mockumentaries (fake documentaries) aired by the Discovery Channel over the last year or so attempt to answer exactly that question. The focus of the two programmes was the Megalodon, a gigantic shark which patrolled the seas between 15.9 - 2.6 million years ago. These are interesting programmes, but do have a tendency to spread misinformation, with 73% of viewers thinking that the Megalodon is still roaming our oceans. Many actual scientists, as oppose to the actors posing as scientists in the programme, were unhappy about the misrepresentation of palaeontological research, calling Discovery Channel "the rotting carcass of science on TV". Others, however, created a positive outcomes from the documentaries and worked on more robust mechanisms of estimating the extinction of the Megalodon, if only to put the rumours to bed once and for all. The authors, novelly, utilised a method that had previously been used to estimate the extinction of more modern species, such as the dodo. The method, a model called Optimal Linear Estimation (OLE), infers time to extinction from the temporal distribution of species sightings, or in the case, fossil instances. This method may not be applicable to all fossil taxa, but is an excellent step in out-of-the-box thinking towards a better extinction estimations.

I wasn't joking about them being big; Source.

Extinction is something we should be aware of and it can be a great tool to provoke changes in peoples outlook on human activity. Whilst "lazarus taxa", "living fossils" and the rest of it make for great sci-fi, their place in actual science should be profoundly separate from this.

Hunting - A Bear Necessity?

A nasty note on which to start the new year, but the US Fish and Wildlife Service (FWS) has announced that their intend to remove protection from Yellowstone's grizzly bear population in the coming year. As someone who has had a grizzly bear themed calender for the last two years, my immediate reaction to this is one of shock and disgust. For a moment, however I will attempt to step back from my bear loving self and take a look at the reasons behind this decision.

Adorable animal which should clearly not be hunted; Source.

For the past 40 years, the bears of Yellowstone have been protected by hunting and have enjoyed population increases and range expansion under this protection from the Endangered Species Act (ESA). This protection was not undue, the grizzly population suffered huge losses from excessive hunting during the 1900s which earned them a place on the IUCN red list. The recovery of their population, however, has put pressure of the US FWS to revoke their special status, from state officials. The proposed new system would involve handing over the management of bear population to state level, after the delisting would remove federal protection. The agreement places no limit on the hunting of bears outside of the central Yellowstone management area, and within that splits the bears between the three states which share the region - Wyoming, Montana and Idaho. There are some loose pledges to maintain the bear population in the management area above 600, but nothing concrete except an apparent need to shoot at things.

Arguably, the new laws would promote, rather than limit the killing of bears. There are underlying societal and economic reasons why there is such animosity towards bears, and other large carnivores. Whilst states would plead that bears area threat to humans, the reasoning is more likely to do with their role as competitors for big game. However, the problems of hunting these animals also have multiple dimensions. Culturally, they hold high significance for many native people who also live in the Yellowstone management area and have not been consulted in the decision to delist bears. Ecologically, there are many issues in play. Bears are, arguably, still in a very vulnerable position in Yellowstone and are dying in disproportionate numbers each year even with the protection of the ESA. For example, climate change induced drought and invasive species have extirpated one of the bears main food sources, the cutthroat trout, as well as damaging other food sources including Whitebark pines and elk. Grizzlys have very low reproductive rates, with huge amounts of parental investment, meaning that they are very slow to react to changes in the environment and colonise new territories. This means that they will feel the pressures of climate change more than most, causing their population to suffer alongside hunting.

My personal bias aside, I feel that there is not a great case for delisting the grizzly bear from the ESA protection. There is a very real chance that hunting would lead to extirpation outside of the Yellowstone management area, where there are no limits in place. Isolating the population within Yellowstone, whilst hunting them as well, could have disastrous impacts on then stability of the population as their numbers dwindle and their genetic diversity lessens. Let me know your thoughts below, but I feel that there is no necessity behind this law change, simply a demand for blood.

Could the removal of the 'ESA Safety Net' mean extirpation for Yellowstone's grizzlys?; Source.

Paralleling Ocean Acidification to the Permian

The "evil twin of global warming", better known as ocean acidification, is considered an often overlooked but serious environmental impact from anthropogenic CO2 emissions. Ocean surface pH has been decreasing at an alarmingly rapid rate throughout the last 200 years, faster than at any point within the last 300 million years. In fact, as revealed by a study in April last year, the last time ocean acidification occurred this fast, it was a major contributing factor to the End-Permian mass extinction. The Permian, as a quick reminder from earlier posts, was the largest mass extinction event of the Big Five, with over 90% of species becoming extinct. The study found new evidence that extensive Siberian Trap volcanism triggered Ocean acidification during the end of the Permian era which drove the mass extinction and loss of 96% of marine life.

The study collected data using boron isotopes as a proxy for ocean pH and generated models based on this. They found the most likely scenario was two pulses of extinction in a setting where the Earth system began as "primed" for rapid increases in ocean acidity. The first pulse was a slow injection of CO2 into the atmosphere by ongoing volcanism over tens of thousands of years during which the extinctions were mostly terrestrial. The second phase there was a large and rapid injection of CO2, likely from a huge eruption, which caused abrupt acidification of the oceans and drove the loss of the many marine species that went extinct during the event.

An example of what ocean acidification can do to marine biota; Source. 

What does this mean for modern oceans? And why do we need to care? The quantity of CO2 injected into the atmosphere during the end of the Permian was probably greater than today's fossil fuel reserves, however, the rate of CO2 release and subsequent interactions with the oceans was likely similar to current emissions. The rate of release is crucial because it there is a correlation between rate of release and rate of absorption, meaning more CO2 absorbed by oceans ends up as H+ ions, as oceans cannot just hold all the CO2 being released. This means on the whole, more acidification than there otherwise would be. It also means that there is much less time for any species to adapt to changing conditions. 

Modern oceans are estimated to have seen a 30% increase in the concentration of H+ ions since the late 18th Century, which corresponds in a fall in pH from 8.25 to 8.14. This is estimated to reach 7.75 by 2100 if there is not considerable intervention. We can see the impacts of ocean acidification in our oceans already, and many of them mirror the events of the End-Permian extinction event. For example, a group of snails known as pteropods have been identified in multiple studies as experiencing shell dissolution, sometimes as soon as they are born. It is thought that 50% of pteropods species are currently affected by acidification and that this has doubled since the 1800s, and will likely triple by 2050. In fact, all marine organisms which use calcareous materials are at risk of experiencing dissolution. This includes corals, crustaceans, echinoderms and foraminifera as well as the aforementioned molluscs. Additionally, we see coral reef bleaching as the symbiotic relationship between coral polyps and dinoflagellate algae is disrupted due to the algae having a narrow range of pH tolerance. Corals themselves, suffering from both dissolution and bleaching, are a massively important component of shallow water marine ecosystems - they provide habitat for 25% of marine species and drive fishing and tourist industries for many developing nations. (For more on this check out my colleagues blog on Tourism and the Environment).

Coral bleaching; Source.

This is likely what happened in the Permian extinction, the vast majority of marine life in that era had exoskeletal components composed of calcium which made them extremely vulnerable to rapid drops in ocean pH. Whilst modern marine biota is more morphologically diverse, there is still a large component of our ecosystems which is already suffering. Indeed, this component cannot be separated from the system just as it could not be in the Permian and any losses will have unavoidable trophic impacts on non-calcareous species. The "evil twin of global warming" cannot rationally be ignored any longer, and thankfully there was some recognition of that in the recent COP21 talks. Whilst they may not be the most spectacular or interesting of animals (to some), small molluscs, foraminifera and other calcareous micro-organisms form the basis of most, if not all, marine food webs and we need to truly recognise the importance of protecting them and reflect that in policy.

For a practical demonstration of the impacts of ocean acidification, check out this interesting video below!

Nocturnal Pollinators: A forgotten ecology?

In the post below I wanted to share what I have been working on in my independent study project. The project was about trying to establish a baseline for the diversity and importance of nocturnal pollinators, as they are a hugely under-researched group. Much of the focus of pollination research and media representation in recent years has been firmly on bees, and to a lesser extent butterflies, but the nocturnal component of the system remains unknown to many. I'll be giving a brief summary of the answers I found to my main research questions, and then talking about the relevance of this work in the context of this blog. I hope you find it as interesting as I did and, as always, please let me know if you have any questions in the comments!

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In the same train of thought as my earlier soil biota post, I feel that nocturnal pollination is another forgotten ecology - something critically important to both the ecosystem itself and to provision of ecosystem services but unappreciated as it isn't something we often see. The diversity of nocturnal pollinators and their importance within ecosystems are two questions to which current research does not provide a simple answer. Little is known about the scale and importance of nocturnal pollination services, largely due to the impracticalities of studying pollination in the dark. However, with the documented decline of known nocturnal pollinators throughout Europe and other continents (in particular, moths and bats), it is crucial that we reach a better understanding of their role in respective ecosystems. As some put it, we remain rather ‘in the dark’ about what happens after dusk.

Manduca sexta feeding from a Datura flower; Source. 

How many nocturnal pollinators are there and which taxonomic groups are they in?

Any number I gave you would be wildly innacurate. We can try to make estimations based on those species which have been observed, but a recurring issue throughout the research is the impracticality of observing things at night. Also there are taxonomic issues, particularly for invertebrates as I have discussed in previous posts. We don’t know what percentage of species we have described and many families, such as the Noctuidae moth family, are paraphyletic and contain genera not robustly assigned to subfamilies.

As for the taxonomic groups the pollinators belong to...

Lepidoptera: We know of 21 families of moths involved in nocturnal pollination. but from these some of the most important are the Noctuidae and Geometridae families which land on the flowers the same was as butterflies do but also the Sphingidae or 'hawk moths' which hover and reach the nectar with their extremely long tongues. Moths and the other insects I will discuss typically pick up pollen on their legs and wings when they visit flowers by accident and deposit it on subsequent floral visits. A few species of moth, however, are the only known insects to do this purposefully.

Hymenoptera: The family containing bees, wasps and ants. Bees are commonly thought of as diurnal pollinators but there are nocturnal bees which play an important role in desert environments. Wasps and ants are not well studied as pollinators, but we know that some species are involved in nocturnal pollination.

Coleoptera: Beetles are one of the most neglected groups in literature despite being among the first animals involved in pollination. There are several families of small beetles which are fairly well studied but we also know that large beetles, particularly scarabs, act as pollinators. Most beetle pollination is found in tropics and linked with commercially important palm trees.

Diptera: We know that flies are important pollinators and often considered second only to bees, but again they are neglected in a nocturnal context. They are particularly important in regions where bees aren't as capable, such as high altitude areas and alpine environments. The Syrphid family is considered most important among diurnal pollinators and likely there are members of this which act as nocturnal pollinators as well. Mosquitoes are actually important nocturnal pollinators, and are well studied in desert environments.

A cross section of  a cactus flower, showing how the bat pollinates it; Source.

Chiroptera: Although well known as nocturnal mammals, it is not often known that bats act as crucial pollinators. Over 500 plant species, including many tropical fruits, rely on bats. Similar to hawk moths, they hover in front of the flower, and stick their head and long tongues into the flower to reach the nectar reward – their heads get covered in pollen and they look very cute but are then effective vectors to carry this pollen to the next plant they visit.

Non-Flying Mammals: There are also mammals other than bats involved. Mostly within marsupial, rodent and primate families, these mammals make big contributions to pollination in Australia and South Africa. These nectarivorous mammals are very cute as well, with obvious nocturnal adaptations in terms of big eyes and ears. Similarly to bats, pollen gets stuck in their fur and they transfer it between flowers they feed on.

Squamata: : Lizards! There are 3 known nocturnal pollinators in this group, and all of them are geckos. Nectivory is quite well established among geckos so there is a huge potential for nocturnal that may have been missed. Research also suggests that nocturnality is ancestral state for geckos, so this further hints that these guys could be important nocturnal pollinators.

How effective are nocturnal pollinators in comparison to diurnal?

This graph is from data I collected and shows the number of studies which considered a certain pollinator more or less effective than the diurnal counterparts. The data was sorted into three categories: more effective, less effective and those which were unclear or considered equal. There isn't a straightforward answer – there is a fairly even spread between the three columns, and no one category is significantly larger than the other two. There is a potential for bats to be strong pollinators, as they have larger amounts of effective studies, but moths are seem equal in all categories despite some papers being written about biological reasons for their effectiveness. Other groups did not yield not enough data to make any sensible inferences, again highlighting bias issues within nocturnal research. What is clear, however, is that in many instances nocturnal pollinators are highly important components of the system.

How many plants are pollinated by nocturnal pollinators? Are they commercially important?

Again, this is a very difficult question. Perhaps the most sensible approach would be to consider pollination syndromes and make the assumption that if a plant displays adaptations for nocturnal pollination then it is nocturnally pollinated. However, the validity of pollination syndromes has been in question a lot incurrent literature, and is largely seen as outdated, so perhaps this isn't best approach. Alternatively, we could make the assumption that all plants with nocturnal anthesis are nocturnally pollinated, but again we know this isn't true, as some of these plants will self pollinate. In addition, there are some plants which have nocturnal-diurnal anthesis and are pollinated by a mix of daytime and night-time pollinators, so for most of we don’t know which of these are primarily reliant on nocturnal pollinators, if at all.

There is potential for nocturnal pollinators to make significant contributions to a limited set of agricultural plants. Many essential staple food crops do not rely on biological pollination whatsoever, such as corn, wheat, and rice which are all wind pollinated and  need no insect help at all. Other staple food crops, such as bananas and plantains, are propagated from cuttings meaning that they require no pollination of any form. Where we see nocturnal pollinations evidenced is mostly in tropical fruit crops including species of mango, banana, cocoa, palm, durian, guava and agave (used to make tequila). Bats and beetles are, of all groups, the most likely to be responsible for pollinating these crops. So, next time you eat some chocolate, say thanks to the bats!

Bats making their home in palm tree, which they also pollinate; Source.

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So, we've established that this is an extremely diverse group that is likely highly important commercially and ecologically. Therefore, the threats that they are currently under should be taken seriously. Unfortunately, due to the lack of research in general about nocturnal pollinators, there is an equal lack of literature considering threats and appropriate conservation measures. Whilst there are likely many more threats than this, and indeed many we are unaware of, I'll discuss one of the main, unrecognised, threats to nocturnal pollinators.

Light pollution
Artificial lighting has become a huge component of many urban areas, and has established effects on a lot of nocturnal wildlife. Moths are famously attracted to bright lighting, and whilst we use this to our advantage when using light-trapping to survey them, there is also evidence that urban lighting is effecting moths negatively. MacGregor et al. suggested that artificial night lighting could potentially limit reproduction and make moths more vulnerable to predation. Both of these impacts are quite well established with evidential backing, but there may also be impacts of their ability to see properly. Moth population declines are likely linked to artificial lighting in some capacity, though MacGregor et al. suggest that the risk goes beyond decline, but to species loss and changes in community assemblages. Other research has linked artificial lighting to declines in bat populations and disruption to ecosystem services.

Alongside other threats such as habitat loss, global warming and invasive species - many species of nocturnal pollinator, both in the UK and around the world are at risk. In the tropics, where bats and beetles provide crucial pollination services, the impacts deforestation and climate change have been felt severely and I don't doubt we will have already seen extirpations of pollinating species. It is an unfortunate situation where a combination of under-researched fields meet at a crossroads and we are probably losing pollinators before we have identified them, let alone studied their importance.

Moths below a streetlight; Source.

Merry Christmas from the "Santa Spider"

Merry Christmas to all my readers! I hope you're all enjoying a good festive break from work, university and life. Whilst I'm sure you all have better things to do today than read my blog, I thought I would bring some ecology in to your day if you're up to it! The spider below is colloquially known as the ladybird spider or 'Father Christmas' spider, which as you can probably guess, is due to the bright red, white and black markings found on the males. It's one of the UK's rarest and smallest spiders and suffered from habitat degradation throughout the 20th Century.

Eresus sandaliatus, apparently trying to sniff out a female with organs on his legs; Source.

The spider is somewhat of a conservation "Christmas miracle" and has been brought back from the brink of extirpation in the UK to a now thriving population. The spider went from an estimated 50 individuals remaining in Britain in 1993 to well over 600 in 2000. The spider makes its home in heathland, which is one of the UKs most threatened habitats, and over 90% of it has been lost to development and agriculture since 1800. In Dorset, there has been concerted conservation efforts to restore the spider populations as well as protect heathland habitats. At one site there were only 7 spiders left, but there are now thriving and have been released from this site into other areas, where they have successfully colonised. Workers from the RSPB used plastic water battles filled with moss and heather to create houses for the spiders where they could breed safely.

A cute and inspiring conservation story - I try not to be too pessimistic on this blog!

 Merry Christmas!

Tiny spider is tiny; Source.

Plastic water bottle houses, Source.

De-Extinction: Return of the Endlings?

This blog has looked at the extinction and extirpation of many species and admittedly, has been fairly pessimistic. However, it has yet to consider the growing phenomenon of 'de-extinction', perhaps there is room for a little optimism? Is this a realistic approach to conservation or is it a load of Jurassic Park wannabe nonsense? The idea based on using preserved or "ancient" DNA from several individuals of an extinct species and creating clones of each of them, we would be able to create a new and viable population of that species. There are cryo-zoos, such as the one in San Diego, which store frozen DNA of extinct species with the potential to form these clones. Much of the attention given to, and work within, de-extinction focuses on this cloning aspect, but other researchers have attempted to work through selectively back breeding a species from its genetically similar living descendants.

De-extinction efforts have already been made for many species that we have seen recent endlings of, such as the passenger pigeon, the Pyrenean ibex and the Tasmanian tiger, whereas some scientists are working on much older animals such as the woolly mammoth. However, 60,000 years is effectively the age limit for use of DNA, so dinosaurs won't be happening any time soon. The first de-extinction in history was the Pyrenean ibex, which was done in 2009 by creating a clone egg using the DNA of Celia, the (formerly) last ibex, which was taken shortly before she died in 2000. Unfortunately, the ibex was short lived and died within 10 minutes but scientists are planning to reattempt when cloning techniques have improved. This attempt, in itself, was an improvement on previous attempts in 2003 which had failed to produce an egg capable of surviving the full gestation period. Significant progress has also been made for the passenger pigeon, where DNA has been preserved in museum specimens. Unfortunately the DNA of these specimens is contaminated and fragmented due to the way they have been preserved and kept, as oppose to the ibex DNA which was stored in liquid nitrogen. However, it is still possible to reconstruct the genome by synthetic hybridisation of the DNA fragments with the genome of its closest living relative, the band tailed pigeon, which scientists are currently working on. This would then be used to create cells which contain passenger pigeon genes, which would then be injected into band-pigeon embryo with the goal to create a band pigeon which lays passenger pigeon eggs and acts a surrogate parent for it.

National Geographic cover of de-extinction issue; Source.

Since 2013, a team of scientists from South Korea and Russia have been working on the de-extinction of woolly mammoths.  There have been difficulties as although mammoths have been found well preserved, their DNA has not been intact enough to produce viable embryos for a clone based de-extinction. Alternatively, a second method has been investigated which involves the artificial insemination of elephant eggs with preserved woolly mammoth sperm. The elephant-mammoth hybrid offspring would be able to be cross-bred over several generations to produce near pure mammoths. Again, this has been unsuccessfully due to mammal sperm cells lose their potency after over 15 years in freezing. The major problem has been finding usable DNA, blood recovered from the 2013 carcass provides an apparently good chance of successful cloning - we will have to wait and see. Others are pursuing different routes to restoring the mammoth, Harvard geneticists are working on migrating components of the mammoth genome into the Asian elephant genome in order to create viable hybrids. Adrian Lister, a renowned mammoth expert, highlighted that there is a lack of suitable habitat remaining for any resurrected mammoths and that, as highly social animals, they would suffer from existing in very small numbers. However, a Pleistocene rewilding experiment known as 'Pleistocene Park' (not joking), could provide refuge for the mammoths and would also benefit from the grazing herd behaviours in recreation of steppe. Interestingly, Pleistocene Park also aims to prove that it was not climate change but over-hunting and other human interferences that lead to the disappearances of these grasslands and associated species during the Pleistocene. This could be a exciting new evidence in the debate surrounding the Pleistocene megafaunal extinctions.

Pleistocene Park in Siberia; Source.

As mentioned earlier, selective back-breeding from the closest living relatives of animals is another option for potential de-extinctions. This is being done for aurochs in Europe, based on genetic material taken from bone and teeth fragements. The last European aurochs were lost in 1627 after a long history of over-hunting and exploitation, but their descendants (most modern cattle breeds) are abundant throughout Europe. The genetic material provides a goal, so that cattle can be bred to try and reach as close to the original aurochs as possible, both phenotypically and genotypically. Early attempts resulted in the created of a new breed, Heck cattle, which are at best vague-lookalikes. Currently there are two projects, the TaurOs Project and the Uruz Project, which are competing to resurrect a true, or atleast very close to, aurochs within the next 20 years. Earlier this year, it was proposed that there could be the potential to bring back Lonesome George, or at least a genetically very similar species, by a breeding programme rather than cloning. Even if the animals themselves are clones, captive breeding, which has proved successful in many conservation efforts, will be a major part of de-extinction.

So, whilst it seems that de-extinction is scientifically possible, the bigger question is rather, should we actually be doing this? Proponents of de-extinction such as Stewart Brand would argue that we have the ability and the moral obligation to repair the damage we have done, so there is no excuse not to. Others such as Adrian Lister would say that efforts and resources should be focused on conserving currently endangered extant species. The lack of suitable habitat is also a concern for many species. I feel that whilst there is certainly value and appeal in resurrecting species and "righting our wrongs", it must be done carefully and must not detract the need for conservation efforts to currently endangered species. This is not an alternative to conservation. This is an unfortunate second best to not having lost the species in the first place.