Martijn van de Pol

Today our new R package hiphop (developed together with my colleagues Lyanne Brouwer & Andrew Cockburn) was published online by CRAN.

No, my music taste is not developing, I still stick to my good-old rock music preference. Instead, this package contains several functions to easily perform parentage analysis using bi-allelic genetic markers such as SNPs. It outperforms conventional methods where closely related individuals occur in the pool of possible parents. The method compares the genotypes of offspring with any combination of potentials parents and scores the number of genetic mismatches of these individuals at different loci. It elaborates on a prior exclusion method based on the Homozygous Opposite Test (HOT; Huisman 2017) by introducing the additional exclusion criterion HIPHOP (Homozygous Identical Parents, Heterozygous Offspring are Precluded; Cockburn et al., in revision). Potential parents are excluded if they have more mismatches than can be expected due to genotyping error and mutation, and thereby one can identify the true genetic parents and detect situations where one (or both) of the true parents is not sampled. Package ‘hiphop’ can deal with (a) the case where there is contextual information about parentage of the mother (i.e. a female has been seen to be involved in reproductive tasks such as nest building), but paternity is unknown (e.g. due to promiscuity), (b) where both parents need to be assigned, because there is no contextual information on which female laid eggs and which male fertilized them (e.g. polygynandrous mating system where multiple females and males deposit young in a common nest, or organisms with external fertilisation that breed in aggregations).

We hope to publish the accompaning scientific paper very soon!

Last year field technician Rafael Martig (with some help of PhD student Magali Frauendorf and others) launched the citizen science website www.scholekstersophetdak.nl about roof nesting oystercatchers. This website provides information about the birds, explains their behaviour and provides tips about what you can do when one of these birds is nesting on your roof and help their young survive the urban jungle. The website also allows people from the public to enter data on the location of nests as well as various other information about the type of roof and the fate of the nest. In the first year over 1000 nests were reported, which was many more than expected. First results of analysis suggested that there are likely twice to thrice as many urban oystercatchers than previously estimated.

This year is the second breeding season of the website, and with many people in lockdown for months already due to the COVID-19 pandemic the question is how this will turn out for the contribution by citzien scientists this year. People will be more at home, so will they have more time to see the birds and report them on the website? On the other hand, many reports of roof nesting oystercatchers actually come from people at work in their offices (as many flat roofs, which the birds need for nesting are in industrial/commercial areas). Will we get more or less reports this COVID year? So far , after a slow start, numbers are fairly similar as last year, with over700 nest reported at the end of May, but of course breeding season is far from over, so still time to place your bets!

Our Centre of Avian Population studies (CAPS) has available a small grant (max. 5000€) to help postdocs write a grant application on any topic related to the ecology and conservation of birds. The project should combine at least two institutes involved in the Centre (our lab qualifies as one) and should tackle a topic on a transnational (e.g. European-wide) scale and ideally integrate different sources of, movement, banding, demographic and/or population time series data. See this document for more information, deadline 1 April 2020

In the week of 2-7 February together with Stephanie Jenouvrier (Woods Hole Oceanic Institute, USA), Sandra Hamel (Laval Univ. Canada) and Bernt-Erik Saether (NTNU, Norway) I organized a workshop at he Lorentz centre at Leiden University. During the workshop a team of 25 international researchers from across the world worked on a comparative analyses on 15 of some of the most long-term individual-based studies on birds and mammals. Basically we want to know what the role is of both observed and unobserved individual heterogeneity in reproduction and survvial is for variation in life-history and population dynamics. A week of lots of discussion, developing our JAGS models and number crunching was lots of fun and let to many new plans for the future. For more info see this link.

The new year started with postdoc Dr. Andrew Allen joining our team at the Netherlands Institute of Ecology for two years. Andy is working on the meta-population modelling of the cumulative human impacts on bird populations. Actually, he was already working on this project for the past years based at Radboud University (lab of Dr. Eelke Jongejans), but will now move to the NIOO giving more opportunity to integrate his work with the PhD students working on this project. Welcome Andy!

Over the christmas period we heared that our application was awarded by the academy (3V fund of KNAW)! A short project blurp: In many animals boys and girls look quite alike. Especially in birds the genitals are not located on the outside, and there may be little differences in appearance that allow us to distinguish between the sexes. In fact, in bird studies scientists generally rely on taking a tissue sample and perform DNA analysis in the lab to reveal the sex of an individual. We are working on a quicker, cheaper and non-invasive method to separate the boys from the girls using machine learning. We train a machine learning algorithm to use subtle differences in appearance in photos of birds (colour, shape) in combination with additional biometric measures (wing, leg and bill length, body mass) to classify birds from photos into either sex. We train this algorithm with photos of birds of which we have determined the sex in the lab. Subsequently we test how well this algorithm is able to predict the sex in a new dataset of photographed birds. Our aim is to explore how reliable ‘sex machine learning’ is and whether it can be used on a large variety of species using and develop a freely available software tool. This project is in collaboration with Track32, Dr. Bruno Ens (Sovon) and Dr. Henk van der Jeugd (Dutch Centre for Avian Demography).

Can animals adapt to climate change? The answer, based on close analysis of 10,000 studies, is a simple one. They may be able to adapt, but not fast enough.

The question is a serious one. Earth is home to many millions of species that have evolved – and adapted or gone extinct – with successive dramatic shifts in climate over the last 500 million years. The rapid heating of the planet in a climate emergency driven by profligate fossil fuel use threatens a measurable shift in climate conditions and is in any case coincident with what looks like the beginning of a mass extinction that could match any recorded in the rocks of the Permian, or other extinctions linked with global climate change. The difference is that climate is now changing at a rate far faster than any previous episode. So can those animals that cannot migrate to cooler climates adjust locally to changing conditions?

In a paper in Nature Communications led by Dr. Viktoriia Radchuk (IZW Berlin), that was coverd by over 200 news-outlets around the world, we examined whether animals could change either their physiology, size or behaviour to accommodate a rise in temperature accompanied by a change in the timing of the seasons. The message is that even if populations can change with their environmental conditions, they may not be able to do so at the speed necessary to time their life-cycle events to coincide with ever-earlier spring flowering, or nesting to match the explosion of insect populations that provide food for offspring.

Many international news outlets, including National Geographic, the Gaurdian, NewsWeek and Der Spiegel, have covered our paper showing that across the existing scientific literature the overall pattern emerges that most species have insufficient adaptive response to climate change. Insufficient adaptive responses are likely to have negative consequences for population numbers of these species, and in the ongoing project sTraitChange we aim to look more into detail into the population consequences of climatic change driving change in traits, such as the timing of reproduction. For a complete list of news coverage click here and for the paper here. Congrats to our collaborator and lead author Viktoriia Radchuk!

Former PhD student Liam Bailey – now a postdoc at IZW Berlin- is interviewed by the Journal Of Animal Ecology about his PhD research on extreme climatic events. This half hour in depth interview touches upon topics such as climate change, developing R software, fieldwork stories and much more. The interview coincided with the publication of the study led by Liam on’ Habitat selection can reduce effects of extreme climatic events in a long‐lived shorebird.’ This study uses our 35-year study population of Schiermonnikoog to show that shorebirds do not start nesting higher during their life after more frequent flooding of their nesting sites, but that young birds are more likely to settle in higher areas. This slow inter-generational response however appears insufficient for the population to keep up with the rapid sea level rise and climate change.

FIeld technician Rafael Martig was on Vroege Vogels TV talking about roof nesting oystercatchers in the city. Click here for the website, scroll down for the video (duration 5:37 minutes)

Always wondered why sometimes our summer nights are ablaze with silent sparks, while other years we might barely see a flash in the exact same spot? In a project led by Tracy Evans (Illinois, USA) we showed how fluctuations in firefly abundance across the USA depend on climate fluctuations, for more info see the news item What’s behind a fabulous firefly season? and our paper.

Following his publciation of an article on the migratory connectivity of shorebirds in the journal Auk, Andrew Allen blogs about the increasingly crucial role of citizen science in our research, and ecology more general. Below is a figure that Andrew used to illustrate how over a ten year period numbers over resightings of colour-banded oystercatchers have increased five-fold, now reaching 5000 per month in summer. For a full read cick here.

Vroege vogels TV made an entire episode on the nature and research at the Vlieland barrier islands, which is also the island where Henk-Jan studies the impact of disturbance on shorebirds. Vlieland is particularly interesting from a disturbance perspective, as there is a NATO shooting range on the island, where miltary aircraft and helicopters regularly perfrom maneuvering, shooting and bombing excercises. The item wit Henk-Jan starts at 36:50 minutes, the shooting range and excercises are shown at 23:20 minutes.