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Red listing isn’t all black and white: embracing the grey areas of a penguin conservation assessment

Blog written by Christina Hagen and Andrew de Blocq. Read the full paper here.

The International Union for the Conservation of Nature’s (IUCN) Red List of Threatened Species is a useful conservation tool for prioritising conservation and tracking the status of species. During a Red List assessment, a species’ extinction risk is given as one of nine categories ranging from Extinct to Least Concern. There are five criteria used to classify extinction risk which look at changes in population size or geographic range, quantitative analysis showing probability of extinction and the special cases of small populations. By far the mostly commonly used criterion examines the rate of decrease in the population over 10 years or three generations (whichever is longer).

While the criteria are quite clear-cut, the interpretation and analytical methods can differ between assessors and species. Some species are incredibly difficult to count (e.g. if they live in difficult-to-access areas or are cryptic) and this can lead to incomplete, inaccurate, or irregular population estimates. While there are different methods for filling missing data points, most consider the “true” population to follow a deterministic (without randomness) trend which is not realistic in terms of what we know about the real world.

JARA (Just Another Red List Assessment) is a new decision-support tool for assessments using the rate of population change criterion. JARA is notreally just another assessment tool, but rather one that takes uncertainty into account. Essentially, this algorithm considers the uncertainty in population estimates and plots the probability distribution of the population decline against the ICUN Red List categories. This means that a species can be classified as Endangered with 70% confidence, for instance, but with the likelihood that the assessment may have been too harsh (and should be Vulnerable) or too soft (and should be Critically Endangered). If for example, there was a 25% chance that the assessment should have been Critically Endangered, then more urgent action is needed, which may not be recognised without incorporating the uncertainty. Another useful way to use JARA is to plot these trends over time. This shows whether a species’ status is declining steadily or at an accelerating rate, stabilizing, or increasing either slowly or quickly. One can also use the JARA method on different sub-populations to see if the extinction risk differs spatially.

Penguins should normally make burrows in guano, but guano harvesting until the 1960s removed this insulating layer, forcing birds to nest on the surface, putting chicks at risk from predation and the elements. Photo: Andrew de Blocq

In our paper, we use JARA to analyse the decline in African Penguin numbers over the last 40 years. The African Penguin breeds only in South Africa and Namibia, with 32 colonies across the two countries. The colonies are clustered into three regions each separated by about 600 km: Namibia, South Africa’s Western Cape, and the Eastern Cape. Our results support the classification of this species as Endangered, with a high probability (97%). However, using the JARA framework also allowed us to deconstruct the trends over space and time, showing that the African Penguin has not decreased equally across its range nor over time. This is important as understanding the causes of the variation allows conservationists to prioritise different management strategies in each subpopulation.

The Namibian population has declined more slowly than the other regions, enough to allow it to be regionally classified as Vulnerable. However, this masks the fact that the population had decreased by over 70% prior to the start of our dataset in 1986. This is due to the collapse of the Namibian sardine stocks in the 1970s, and the species is at critically low levels compared to when fish stocks were healthy. The Namibian population also experienced an outbreak of avian influenza in 2018 which was much more lethal than a similar outbreak in the Western Cape colonies, so this again shows the importance of considering spatial differences in subpopulations when assessing risk.

The decreases in the South African population have been much more rapid over recent years. The decrease in penguin numbers has coincided with a decrease in sardine and anchovy biomass and the eastward displacement of spawning sardine and anchovy, which when combined with fishing pressure has decreased the availability of prey for penguins to the north of Cape Town. This region is changing the most rapidly, with decreases of 10% per year for the last 20 years. The Eastern Cape population, after decreases in the 2000s and late 2010s, has been relatively stable and now hosts the largest proportion of the global population.

African Penguins at the iconic Boulders Beach colony, a major tourist attraction but historically one of the smaller colonies that has remained relatively stable. Photo: Christina Hagen

The African Penguin is at serious risk as a species. However, it is also clear from our study that these declines are different for the three regional populations and that we cannot implement a one-size-fits-all conservation approach. Ongoing population monitoring is needed in Namibia to keep track of this vulnerable population. The Western Cape was traditionally seen as the stronghold for African Penguins, but with changing environmental conditions and the lack of food, the Eastern Cape has overtaken it as the new population stronghold. This mirrors the southwards and eastward shift shown by other marine species and raises the concern that the bulk of the penguin population is now on the edge of the species’ range. This should influence the priority of conservation action, especially with the colonies in Algoa Bay now facing novel threats from increased ship traffic and marine pollution related to ship-to-ship bunkering and the development of the local harbour.

The IUCN Red List is used extensively to inform scientific and conservation work, policies, and funding resource allocation. This means that assessment methods need to be as robust and transparent as possible, which includes an acknowledgement of the uncertainty that is inherent in each assessment and the breakdown of risk in space and time. The JARA method incorporates observation error (i.e. errors made during data collection or processing) and the variation that is part of any biological process.

Amid the current biodiversity crisis with many competing conservation priorities, we cannot afford for threatened species to be misclassified due to imperfect count data. We also need to make sure that conservation actions are appropriate and will address the correct threats at the correct sites and scales. JARA is a decision-support tool that can be applied to many taxa and can shed light on some of the inevitable uncertainty surrounding population trends.

Bat CATastrophe: the cause of many wing tears in UK bats

Blog written by Robyn Grant & Kirsty Shaw. Read the full paper here. Featured image of a common pipistrelle bat copyright Hugh Clark (bats.org.uk)

More than a quarter of all mammal species in the United Kingdom (UK) are bats, they also make up around 20% of all mammal species worldwide. Bats play important roles in many ecosystems, being pest controllers, pollinators and seed dispersers. Urbanisation is one of the most dramatic forms of land-use change and many bats, such as the Common pipistrelle (P. pipistrellus), exploit urban environments for roosting, water, and foraging under artificial lights. However, this also exposes them to urban risks, including collisions with man-made structures and predation from species that are concentrated in urban areas, such as cats.

In the UK, thousands of bats are found and rehabilitated by specialist bat carers every year, many of them for wing tear injuries. Indeed, when we surveyed bat carers around the UK, more than 2000 bats with wing tear injuries were reported to be taken to rescue centres annually. This is not a problem that is specific to the UK, wing tears are commonly found in bat populations worldwide. Tears are considered significant and severe injuries. Despite bat wings having resilient fibre structures and a good blood supply to encourage healing, rehabilitation in captivity can take a long time, which can significantly affect a bat’s health and welfare.

The causes of wing tears are not always clear, but may include collisions, fungal infections and predator attacks. We spoke to many bat carers around the UK, and they believed that the main cause of wing tears were cat attacks; however, positively identifying a cat attack can be difficult. In some cases cats can present a bat to their owners, or the tears “appear” to be made by claws. Previous studies have identified that 20-68% of bats admitted to rescue centres may be as a result of cat attacks; however, there is not yet an objective method to corroborate this.

We applied an objective, forensic DNA analysis method to identify the presence of cat DNA on bat wing tears. We asked bat carers to swab bats with wing tears and send us the swabs. We also asked them to take a photograph of the tear, and tell us what they think caused it. Overall, we collected 72 samples from bat carers, including 40 Common pipistrelles, 18 Soprano pipistrelles, 4 Whiskered bats, 4 brown long-eared bats, 2 Natterer’s bats and one Serotine, as well as 3 swabs from unknown species.

Bat wing swab sampling kit provided to bat rehabilitators

Our results showed that 48 out of 72 (67%) samples had cat DNA present. The presence of cat DNA appeared relatively equally across different bat genders, ages, and species, indicating that all bats may be targeted equally. While our method is a very sensitive technique for the detection of cat DNA, this value of two-thirds could still be an underestimation, due to bats not always being brought to carers, low amounts of DNA being transferred from the cat to the bat during the attack and variability in swabbing and storage techniques.

Bat carers tended to receive bats from a small working area within a 20 mile radius. The same bat carers sent us many samples, especially in Kent and East Dorset, so we also looked at using forensic DNA profiling to identify individual cats within these areas. We did not identify any of the same individuals. Other studies have suggested that there are likely to be “super predator cats” that repeatedly target bat roosts, so identifying any individuals that repeatedly predate on bats within a small area will be a useful thing to do in the future.

An example DNA profile which can be matched to an individual cat

Photographs of the tears showed that when cat DNA was present, these tears were often large, running from the internal membrane to the trailing edge, and tended to appear in the more proximal wing sections, close to the body. When bat carers supplied the suspected cause of the tear, they successfully identified a cat attack in all but one sample (in 93% of all cases). This confirms that bat carers are able to make strong, positive identifications of cat attacks.

An example of a bat wing tear close to the body, and an illustration of the most commonly affected areas of the bat wing

Free-roaming domestic cats cause a huge number of bird and mammal fatalities and, with the number of cats increasing annually, the effect of cat predation on wildlife is only likely to rise. Unfortunately, this means that the number of injured bats from cat attacks is also likely to increase in the future. As well as causing wing tears, cat attacks can also lead to bacterial diseases in bats. Cats may even receive a viral infection from the bats, such as Nipah virus and European bat lyssaviruses, which can lead to cat mortality. We would suggest that night-time curfews for cats, as well as anti-predator collars, will have beneficial impacts on the local bats as well as other nearby wildlife.

This is the first time that cat attacks on bats have been objectively identified using forensic DNA analysis techniques. Our results suggest that cat predation on bats, at least in the UK, is likely to be much higher than previously estimated. A better understanding of cat and bat interactions has implications for both cat and bat populations, as well as their health and welfare.

The Mystery of the Glacier Bear

Written by Tania Lewis and Neil Barten. Read the full paper here. Featured picture: Glacier Bear in Glacier Bay Alaska, by T. Hausler

There are few animals as elusive and mysterious as the glacier bear in Southeast Alaska and northwestern British Columbia, a region characterized by deep marine fjords left by the Pleistocene ice advances, steep rugged mountains from ongoing tectonism, and large glaciers and ice fields maintained by persistent cold precipitation. Glacier bears, also known as blue bears, are uncommon color variants of black bears (Ursus americanus) whose pelage ranges from white to grey to black with silver tipped guard hairs. The Alaskan Native Tlingit name for these bears was “siknoon” which translates into “a bear that disappears” in reference to their elusiveness and ability to blend in with snowfields (Lewis et al. 2020). These unique creatures are the subject of stories and books, and rare sightings are a once in a lifetime experience for a few lucky people. Glacier bears are also targeted and opportunistically harvested by sport hunters in some areas. Previously there was very little scientific knowledge regarding their range, the frequency, or the genetic basis of their unusual pelage color. This lack of knowledge has made it difficult to manage and predict the future survival of glacier bears.

A black bear mother with two glacier cubs in Glacier Bay, Alaska by C. Edwards

Neil Barten worked as a biologist for Alaska Department of Fish and Game (ADF&G) in Juneau in early 2000s, managing bear-human conflicts during a time when glacier bears were quite common in Alaska’s capital city. Bear problems in Juneau were increasing due to improperly stored trash and other attractants, and a few glacier bears were guilty of perpetuating this problem. Several glacier bears were hit by cars and up to six “nuisance” glacier bears were translocated, including a black mother bear with two glacier cubs and one black cub. Despite their prevalence in the capital city, Neil knew that glacier bears were uncommon in most areas, with only a couple harvested by hunters each year primarily near Yakutat over 100 miles to the northwest. Neil began collecting tissues from glacier bears captured or harvested to take advantage of recently developed genetic methods. As a management biologist, he recognized that genetics may be the key to answering basic questions about this little understood animal.

A glacier bear interacts with a police officer in Juneau, Alaska

Meanwhile Tania Lewis was hired to conduct bear research and management in Glacier Bay National Park and Preserve (GBNP&P), which lies halfway between Juneau and Yakutat. When Tania started digging into park archives to write the park’s first Bear Management Plan, she found a map of glacier bear sightings and harvest locations compiled by Linda Wiggins, wife of Canadian bear safety expert Steve Hererro. Linda had conducted visits to the region to attempt to determine the range of this rare color phase (Lewis et al. 2020). In 2009, at the Third International Human-Bear Conflicts Workshop in Canmore BC, Tania, Neil, Linda and others met for dinner to discuss glacier bears and the need for a collaborative research study to learn more about these mysterious creatures.

Glacier bear hide sealed and sampled by ADF&G

The team began collecting more genetic material of black bears across the range of the glacier bear color morph. GBNP&P and ADF&G staff collected DNA noninvasively from hair as well as tissue samples from harvested bears, noting the color of the pelage. Researchers used the DNA to examine genetic structure between populations of black bears within the geographic extent of glacier bears and explored how this structure related to pelage color and landscape features of a recently glaciated and highly fragmented landscape.

Glacier bear cub in Glacier Bay, Alaska, by E. Weiss

Ten populations of black bears were found in the study area divided largely by geographic features such as glaciers and marine fjords. Glacier bears were assigned to four of the ten populations found on opposite sides of two long fjords (Glacier Bay and Lynn Canal) with a curious absence in the non-glaciated peninsula between. Lack of genetic relatedness and geographic continuity between black bear populations containing glacier bears suggest a possible unsampled population and/or an association between glacier bears and large icefields, which would suggest a selective advantage for glacier bears in glacial environments. Such an association would increase the conservation risk of the color morph as glaciers recede suggesting further investigation is needed to determine the adaptive and evolutionary significance of the glacier bear color morph. Determining the genetic basis of the glacier bear color morph will also be necessary to determine the frequency of the gene(s) across black bear populations containing the rare phenotype. These results shed light on the distribution and population structure of the color morph across the region and may help focus conservation efforts to maximize and preserve genetic diversity of black bears as glaciation of the region decreases with climate change.

Lewis, T. M., Stanek, A. E. & Young, K. B. 2020. Bears in Glacier Bay National Park and Preserve: Sightings, human interactions, and research 2010–2017. Natural Resource Report NPS/GLBA/NRR—2020/2134. National Park Service, Fort Collins, Colorado.

Phylogenomics of endangered and threatened species of grasses reveal close phylogenetic relationships

Blog written by P. H. Pischl, S.V. Burke, E. M. Bach, and M. R. Duvall.  Read the full paper here.

Biodiversity is the variety of life forms on Earth, and includes the variation seen in animals, plants, fungi, and microorganisms.  A major cause for a decrease in biodiversity is loss of a species’ home or habitat.  Habitats are being lost by the conversion of natural areas to urban and agricultural lands by humans.  As habitats are lost, species and ecosystems (the community of living organisms and the place where they live) become threatened or endangered as their numbers and area decrease.

At The Nature Conservancy’s Nachusa Grasslands, grazing bison are partly obscured in the September tallgrass prairie.  Photo by P. H. Pischl.

One of the most endangered ecosystems in North America is the tallgrass prairie.  Illinois is nicknamed the “Prairie State” because it was once covered in tallgrass prairies.  However, since 1830 when European settlement began, 99.9% of Illinois’ original tallgrass prairies have been lost to agriculture, industry, and urbanization (Ellis, 2017).  The removal of the tallgrass prairie habitat has caused seventeen species of grasses to be listed as endangered and one species to be listed as threatened by the Illinois Environmental Species Protection Board.  Grasses provide many ecosystem services, such as erosion control, soil formation, habitat for wildlife and carbon storage.  Loss of these endangered and threatened species would result in a loss of ecosystem services as well as a loss of biodiversity.

Ecologists and conservation biologists work to preserve biodiversity by conserving the various species in a region or an ecosystem.  They not only look at the number of species, but also consider the phylogenetic diversity between the species in the ecosystem.  The phylogenetic diversity compares the DNA of the species in the ecosystem to better understand the variation in genetic background of the species.  This genetic variation is seen in the traits the species have or do not have in common.  Plant communities with greater genetic variation are considered to have higher phylogenetic diversity.  Plant communities with higher phylogenetic diversity have been shown to be more productive and resistant to invasion by nonnative species (Barak, 2017).  Plant communities that are more closely related and exhibit less phylogenetic diversity may share traits that make them more vulnerable to the same threat.  These species are considered to be at a higher risk of extirpation from the ecosystem by habitat loss or changes in environmental conditions.

Leaf tissue was obtained from preserved herbarium specimens for DNA extraction.  Photo by M. R. Duvall.

In our article in Ecology and Evolution, we study the phylogenetic diversity of the endangered and threatened species of grasses from Illinois.  However, in order to study phylogenetic diversity, it is necessary to extract DNA from the species of interest.  Since these species are endangered and threatened, we were able to refine our methods to use preserved grass tissue from herbarium specimens.  The use of herbarium specimens avoided the disturbance of living populations of the endangered or threatened grasses.  From the extracted DNA, we were able to use Next Generation Sequencing techniques to sequence the complete plastid genomes for the endangered and threatened species of grass.  Our use of the complete plastid genome in our analysis leads to phylogenetic trees with greater support than studies using gene coding sequences alone.  We then analyzed these phylogenetic trees with three phylogenetic diversity metrics to relate the evolutionary history of the species to their ecological characteristics.  All of these phylogenetic diversity metric values show that the endangered and threatened species are phylogenetically clustered at evolutionary points in both past and more recent events.  Phylogenetic clustering means that these species may be more closely related than expected by chance and share traits that make them vulnerable to the same threats.  Phylogenetic clustering is indicative of phylogenetic niche conservatism.  Should these species be lost from the landscape, several small groups of native grass diversity would be lost. 

In our study, we have shown how herbarium material is useful for ecological research, allowing the study of endangered and threatened species without disturbing the few remaining populations.  DNA extracted from the herbarium material was used to produce complete plastid genome sequences using Next Generation Sequencing techniques.  The complete plastomes from species of grasses known to grow in Illinois provided a robust and strongly supported phylogeny.  Communities of grasses in Illinois were evaluated using three phylogenetic diversity metrics.  The three phylogenetic diversity metrics all led to the same result; the endangered and threatened species are phylogenetically clustered, which can be interpreted as phylogenetic niche conservatism of these grasses.  The loss of the endangered and threatened species and the genetic biodiversity they supply would also lead to changes in ecosystem services and protection from invasive species.  The niches occupied by the endangered and threatened grasses should be considered as priority conservation sites to protect these species, the biodiversity, and ecosystem services they provide.  Maintaining healthy native plant communities is essential.  Not only for organisms that share these habitats and rely on these plants for shelter and forage, but for humans and the ecosystem services that are provided to maintain a healthy environment.

Barak, R. S., Williams, E. W., Hipp, A. L., Bowles, M. L., Carr, G. M., Sherman, R., & Larkin, D. J. (2017). Restored tallgrass prairies have reduced phylogenetic diversity compared with remnants. Journal of Applied Ecology, 54(4), 1080-1090.

Ellis, J. L. (2017). Ecosystem Conservation and Management in an Era of Global Climate Change. Science & Ecological Policy Paper. Retrieved January 7, 2018, from http://www.inhs.illinois.edu/research/ctap

Barriers facing early career researchers from minority groups

Written by Klara M Wanelik, Joanne S Griffin, Megan L Head, Fiona C Ingleby and Zenobia Lewis.

Read the full article here.

Over the course of the past ten years, Science Technology Engineering and Maths (STEM) academia has recognised that it has a diversity problem. The ‘leaky pipeline’, as it is often called, represents the shrinking pool of women in academia through the career stages from undergraduate students, through tenured staff, and then into more senior positions. Although the numbers vary between fields and countries, the overall trend is similar. Figures from the UK show that while over half of postgraduate biosciences students are women, only 15% are at professorial level. Aside from the moral argument for careers in academia being accessible to all those who want a place at the table, studies from corporate sectors have shown that diversity is beneficial in terms of productivity, outputs, and financial gains.

National schemes to improve the representation of women in STEM academia, such as Athena SWAN in the UK and Australia, have made some progress. And yet, the picture for non-gender minority groups is even more stark. Black, Asian, and Minority Ethnic (BAME), disabled, and LGBT+ people are even more poorly represented in academia, compared to in the general population, and are more likely to experience institutional and cultural barriers to career progression.

Back in 2017, we held a symposium for graduate students and postdocs at the University of Liverpool, showcasing the experiences of staff from minority backgrounds. Feedback from respondents suggested there was an appetite for more open discussion regarding the challenges associated with being in a minority group in academia, and from this, the Breaking Barriers project was born.

We surveyed early career researchers in the ecology and evolution community. We asked respondents for data regarding their personal characteristics, for example, which gender they identified with, whether they identified as LGBT+, and whether they were from an ethnic minority background. We also asked whether they had come from a lower socioeconomic background, as we predicted that socioeconomic background could prove to be a barrier to career progression. We asked respondents to provide information on their career to date, and finally, we asked respondents for information on whether they had experienced any barriers to their career progression and, if so, whether they had overcome them.

Our results were upsetting to say the least. Of the 188 individuals that responded to the survey, 54% reported having faced a barrier or multiple barriers to their career progression. Of these, almost a third reported that they had not overcome stated barriers and/or had left academia as a result of them. If anything, we believe this could be an underestimate, since people who had since left academia would have been less likely to engage with a study on an academic issue. We also found that BAME and Latino-Hispanic respondents reported having few publications on finishing their PhD, and having fewer publications translated into having to apply for more positions before obtaining a job. Respondents from lower socioeconomic backgrounds were more likely to be in a research and teaching role, as opposed to a research only role. They were also more likely, along with women, and LGBT+ individuals, to report having experienced a barrier to their career progression.

What does all this mean? It seems that in the field of ecology and evolution there is a significant pool of the workforce who are struggling to access, retain, and succeed in an academic career. Our study suggests that multiple interacting individual characteristics should be considered in combination when we try to understand diversity issues in academia. In particular we would like to highlight that, while barriers related to sex were cited most frequently in the free-text questions, it was not significant in predicting the measures of career progression that we examined. This could suggest that gender is still viewed as an obstacle, despite efforts to improve female representation. Alternatively, the wider discourse with respect to gender diversity in recent years may have helped people feel more comfortable to voice these concerns (rather than concerns they may have about other diversity issues). Worryingly, the relative lack of discourse around other diversity issues, for instance with respect to ethnic minority groups or people from lower socioeconomic backgrounds, may mean that these issues are more likely to be overlooked and underestimated. Until we have more open discussion and understanding of diversity as an intersectional issue, we might not see as much improvement in the field as we’d like to.

But it’s not all doom and gloom. Over two thirds of individuals who said they had faced a barrier (or multiple barriers) to their career progression reported that they had overcome stated barriers. We were able to draw on these individuals’ rich experience, asking them about how they had done this. Two main themes emerged in these individuals’ responses: the importance of people (including mentoring, networking and associating with senior allies) and opportunities (including taking up as well as actively asking for opportunities).

In light of this, we suggest some routes towards improvement in our paper, including more emphasis on mentoring schemes, as well as broadening accessibility of networking opportunities by creating more online spaces for this purpose (which might be something positive we could take forward from the current Covid-related working circumstances!). We also comment on the somewhat grander aim of overall institutional cultural change. This will be crucial in order to see major improvements, particularly with regards to ensuring that opportunities are made accessible to all early-career researchers. We hope that through further research into intersectional diversity issues in academia, we might open up the discussion a little more, and move towards creating a culture where diversity can be fully appreciated.

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