[{"content":"I am fascinated by the diversity of life.\nWhy is life so abundant and varied? What are the processes that structure life in space and time? I am currently studying the evolution of conspicuous colours in infant primates in the Primate Reproductive Ecology and Evolution Group at New York University. Previously, I studied the evolution of plumage colouration in parrots for my PhD in the Stoddard Lab at Princeton University. Stay tuned for PhD publications!\n","date":"18 May 2026","externalUrl":null,"permalink":"/","section":"","summary":"","title":"","type":"page"},{"content":"I\u0026rsquo;m working on a gallery layout that will help me replace instagram. I have to link to the page where someone made a tutorial on how to create the album layout. I\u0026rsquo;ll use albums to help organise things, but I haven\u0026rsquo;t put captions on any of the photos. I will (soon?).\nAll photos ©️Jarome Ali\n","date":"18 May 2026","externalUrl":null,"permalink":"/photos/","section":"","summary":"","title":"","type":"photos"},{"content":"I grabbed a random assortment of photos from my computer to get the photograph section started. Please enjoy.\n","date":"18 May 2026","externalUrl":null,"permalink":"/photos/album1/","section":"","summary":"A random assortment of photos to get things started. Please enjoy.","title":"First album","type":"gallery"},{"content":"Thank you for reading my writing. Sometimes I will be trying to share the wonder of science. Ssometimes I will present evidence-based arguments from the perspective of a scientist. Other times, it will be personal opinions or poetry. I hope it will be clear (context, citations and such) when each of those modes is being aimed for.\n","date":"17 May 2026","externalUrl":null,"permalink":"/blog/","section":"","summary":"","title":"","type":"blog"},{"content":"\u0026ldquo;Hope\u0026rdquo; is the thing with feathers —\nThat perches in the soul —\nAnd sings the tune without the words —\nAnd never stops — at all —\nAnd sweetest — in the Gale — is heard From “Hope” by Emily Dickinson*\nA flat-bottomed wooden boat navigates its way through shallow wetland channels to witness one of Trinidad and Tobago’s natural spectacles. After a pleasant ride and a few snakes, the boat sits moored in the Caroni Swamp. An expectant group sits chatting when suddenly, “Look! De first one!”. As the tour guide exclaims, the group is overcome by oohs, entranced by the brilliant red shape coming into view. It starts with one, two, a handful. Then, a dramatic scene of colours unfolds as Scarlet Ibises return to roost in massive numbers. Swirling flashes of red descend on the mangroves as the birds soar overhead, circling and swooping before they finally come to rest—intense red decoration on the deep green trees. The Scarlet Ibis (scientific name Eudocimus ruber; ruber means red), one of Trinidad and Tobago’s national birds, has much to teach us.\nScarlet Ibis returning to roost in Caroni Bird Sanctuary. Photo: Jarome Ali Of course, the Scarlet Ibis shares the colour that makes up most of the T\u0026amp;T flag. Red on the flag is said to represent the “vitality of the land and its peoples”1. But how does the Ibis produce its almost dizzying shade of red? There are two main types of colouration in the animal world: pigmentary and structural colouration. Pigmentary colours are produced when a chemical absorbs some colours (or wavelengths) of light and reflects the rest. The feathers of a Scarlet Ibis contain compounds called carotenoids that are very good at absorbing colours other than red. The light reflected back is therefore mostly red, giving these birds their striking appearance. Carotenoid compounds can also be yellow or orange and are widespread across the animal kingdom. The carotenoids pigments that give the Scarlet Ibis its colour are derived from the crustaceans it eats, e.g., fiddler crabs. These carotenoids are processed in the liver, transported through the blood and incorporated into the growing feather. If development goes normally, a young Scarlet Ibis replaces its grey plumage with brilliant red feathers containing carotenoids. Structural colours are produced when very tiny features, or nanostructures, of an object interact with light, causing some wavelengths of light to be cancelled out and amplifying others. In birds, blue feathers are produced by structural colouration. Therefore, if you were to crush a Scarlet Ibis feather into an extremely fine powder, it would remain red because the pigments would still be present. However, if you did the same for a blue feather, the colour might disappear! This is because you would have disrupted the nanostructures within the feather that produce blue colours. You would need extremely powerful equipment to make this happen but in this hypothetical experiment, that’s what would happen!\nBonus fact: A related form of light-scattering (Rayleigh scattering) of light by nitrogen and oxygen molecules in the atmosphere is what causes the sky to appear blue.\nDespite its importance to T\u0026amp;T, the Scarlet Ibis was considered locally extinct as a breeding species by the 1970s. The flocks still came to the Caroni Swamp, but no breeding was observed. While it is difficult to say for sure, the causes probably included poaching and changes to the waterflow caused by development. To add insult to injury, the Scarlet Ibis was added to the list of game species in 1981, for unknown reasons. To appreciate the scale of the hunting, the Forestry Division estimated that around 600 birds, many of them Scarlet Ibises, were shot in the Caroni Swamp on just the first day of the 1983 hunting season. Thankfully, the species had its protection restored in 1986. Despite the challenges, Trinbagonians did not stand idly by and watch the species disappear from our wetlands. At the Pointe-a-Pierre Wildfowl Trust, Molly Gaskin, Karilyn Shepherd, and their team worked on a captive breeding program. The first Wildfowl Trust Scarlet Ibis chick was born on July 11, 19912. This breeding and release program has continued. The Caroni Swamp, which had been a forest reserve since 1936, was elevated to a National Park in 1979 and a large portion of the swamp was declared a ‘prohibited area’ in 1987. By 1995, hopeful reports emerged of Scarlet Ibis again breeding in the swamp3. Since then, the species has continued to nest in the swamp, but it always remains under the threat of poaching. A 1990 publication reported that, “the current number of personnel in the park is hopelessly inadequate, and despite patrolling by a well-trained and enthusiastic staff of wildlife biologists and game wardens, poaching continues in the area”4. Sadly, much of that rings true today. Just like the future of T\u0026amp;T, that of the Scarlet Ibis needs continuous protection and we are often doing too little. We will curry anything, including our future.\nThe Scarlet Ibis also teaches us that we cannot just look inward and ignore the outside world. In the 1990s, scientists found elevated rates of mutation in mangroves located near Scarlet Ibis roosts. They were producing leaves that lacked chlorophyll, the pigment that makes plants green. When the scientists investigated, they found that the mangroves and sediment surrounding the roosts had high levels of mercury. Even more striking, the mercury was even in the birds’ feathers, but at levels up to 6 times as much as that in the feathers of other species. How could this be? While the ibises migrate to Venezuela periodically, the other birds do not. Some of the Scarlet Ibis’ feeding areas were likely affected by mercury pollution caused by widespread gold mining in Venezuela. Mercury accumulates in body tissues, so as thousands of birds go back and forth between Trinidad and Venezuela over decades, the moulted feathers at regularly used roosts led to an accumulation of mercury. This mercury was absorbed by the mangroves, resulting in mutations. The lesson here is that, while we can protect our own backyard, we live in an interconnected world. Our well-being is that of our neighbour, and theirs is ours.\nWhen Emily Dickinson compared hope to a bird, a “thing with feathers”, she might have had an Eastern Bluebird, or a Black-capped Chickadee in mind. Beautiful birds, no doubt, but she had never seen the glory of the Scarlet Ibis. I think she would be inspired by its beauty and its hopeful story.\nHow lucky we are.\n* Hilariously, when this article was first published in the Trinidad Newsday, it ran with the byline \"Emily Dickinson\". I never intended a nom de plume, especially not to pretend to the legacy of such a great writer, but here we are. The National Identity Guidelines of The Republic of Trinidad and Tobago\u0026#160;\u0026#x21a9;\u0026#xfe0e;\nhttps://newsday.co.tt/2017/09/17/the-story-of-the-scarlet-ibis/\u0026#160;\u0026#x21a9;\u0026#xfe0e;\nA lot of this info comes from Dave Samayah’s thesis, which you can find here\u0026#160;\u0026#x21a9;\u0026#xfe0e;\nBildstein (1990). Status, Conservation and Management of the Scarlet Ibis Eudocimus ruber in the Caroni Swamp, Trinidad, West Indies. Biological Conservation\u0026#160;\u0026#x21a9;\u0026#xfe0e;\n","date":"17 May 2026","externalUrl":null,"permalink":"/blog/scarlet_ibis/","section":"","summary":"","title":"Lessons from an Ibis","type":"blog"},{"content":"Some birds have a home range, and they stick to it. Others, like the Northern Parula, a charming blue and yellow warbler, do not. Instead, they undertake journeys that span thousands of miles. The Northern Parula, for example, migrates to Central America and the Caribbean in the winter and returns to its breeding grounds in North America in the Spring. These migrations are as complicated as they are long. Many migratory songbirds, which can weigh just a few grams, fly for incredible distances without food or water. Eventually, though, they need to make a pit stop. Despite the work of many scientists, naturalists and hobbyists, we still do not have a comprehensive picture of where these migrating songbirds rest and fuel up. Until now.\nThe Northern Parula is one of many species that undertakes incredible migratory journeys. Photo: Laura Gooch, Flickr Princeton graduate student Fengyi (Freda) Guo has been working with her collaborators to begin mapping out migration “stopover hotspots” – the most popular bird pit stops. The idea is simple – if we can track where birds are landing and taking off from, then it should be easy to know where the stopover hotspots are. Traditionally, this knowledge came from birders, who knew where the best areas were to look for migrating birds. But to map hotspots at a continental scale required innovative use of technology and impressive data crunching.\nIn 1945, the ornithologist David Lack reported that birds showed up on weather radar. This information had been kept a secret during the war but as Lack wrote, “permission has now been obtained to publish the fact that birds can reflect radio waves with sufficient strength to be detected by radar sets.”\nFor the most part, this was an annoyance – birds obscured weather patterns and got in the way of your favourite meteorologist. But to Lack and others, this was a revelation. Weather radar data could be used to track the large numbers of birds that traverse the night sky during migrations. This technology has since been used to keep an eye on migrations and is an invaluable tool for scientists but also provides handy tools like the bird migration forecast, which delights birders nationwide.\nAs anyone who has done a road trip knows, some pit stops are busier than others. Guo and her team wondered how they could use weather radar data to describe migration patterns and understand what makes for a popular stopover for migratory songbirds.\n“One of the puzzles we’ve had is that, while people have been studying this for a long time, and there are lots of conservation efforts, birds are still declining. We suspect that it has something to do with what’s going on during the migration phase, which is the least understood. We think that this might be the missing piece,” \u0026ndash; Fengyi Guo\nThe scientists combined weather radar data for over 60 million hectares spanning 5 years. This required immense computational effort and storage. When Guo requested 30 terabytes of storage (about 60 times the typical laptop), the IT support wrote back, confused. “Thinking that it was a typo, they asked me if I needed 30 gigabytes,” Guo said. To analyse these data, they looked at the radar images just around and after sunset, when birds take off. On a clear night, the radar images are clear but then, all of a sudden, there is a bloom of colour on the radar as millions of birds take off to the night sky.\nAfter analysing these take-off data, the scientists showed that the number of birds was fairly similar across radar sites. This suggests that birds generally migrate across a broad front, rather than through narrow channels. Within these sites, though, some areas consistently supported much higher densities of birds than others. These were the hotspots. Rather than just being randomly distributed, hotspots were more likely to be in deciduous forests, especially those in areas that experienced heavy deforestation. Another concerning finding was that only one third of the hotspots the researchers identified are in protected areas, and most of the protected areas are in large reserves, such as the Great Smoky Mountains National Park. While these protected areas are important, the smaller hotspots and forest fragments are still unprotected, and remain vulnerable to habitat degradation. These findings point out the importance of the remaining forest fragments to the migratory phase of many birds’ lives, when they are especially vulnerable.\n“People know that fragmentation is not good for breeding birds. Even though birds do not do well breeding there, birds need to use these fragments during migration,” Guo said, expressing her hope that this research promotes “full annual cycle conservation”. That is, while bird populations might be protected in their breeding and wintering grounds, the chain of protection is only as strong as its weakest link. The migratory part of the annual cycle might be particularly at risk but, as this research points out, directed conservation of stopover hotspots has incredible potential for supporting and protecting migratory species.\nGuo, Fengyi, Jeffrey J. Buler, Jaclyn A. Smolinsky, and David S. Wilcove. “Autumn Stopover Hotspots and Multiscale Habitat Associations of Migratory Landbirds in the Eastern United States.” Proceedings of the National Academy of Sciences 120, no. 3 (January 17, 2023): e2203511120. https://doi.org/10.1073/pnas.2203511120\nGuo, Fengyi, Jeffrey J. Buler, Jaclyn A. Smolinsky, and David S. Wilcove. “Seasonal patterns and protection status of stopover hotspots for migratory landbirds in the eastern United States.” Current Biology. https://doi.org/10.1016/j.cub.2023.11.033\n","date":"19 October 2025","externalUrl":null,"permalink":"/blog/migration_stopovers/","section":"","summary":"","title":"It’s the journey, not just the destination. How scientists used weather radar to map the pit stops migratory songbirds take.","type":"blog"},{"content":" Research # Primate Natal Coat Colouration # The explanation for animal colours can sometimes seem obvious\u0026ndash;conspicuous male colours are thought to be for attracting mates and drab colours function for camouflage. However, there are some cases that present a mystery. Some infant animals are brightly coloured, the exact opposite of what one would expect for an animal at the most vulnerable time in its life. At New York University, I study the evolution of conspicuous colouration in primates, as part of the NYU Primatology Reproduction and Evolution Group with Prof. James Higham. Sensory Ecology \u0026amp; Parrot Colour Evolution # No facet of biodiversity is more striking than the resplendent variety of animal colouration. Thus, understanding the mechanisms and functions underlying this variety is pivotal to understanding biodiversity itself. For my PhD in the Stoddard Lab at Princeton University, I studied the ecology and evolution of plumage colouration in parrots, arguably the most social, vocal, intelligent and colourful birds. Functional Diversity # As a master\u0026rsquo;s student at Imperical College London (Silwood Park, supervised by Dr Joe Tobias and co-supervised by Dr Ben Blonder), I studied the properties of the avian hypervolume, which exists within a functional space whose axes are defined by traits or principal components of traits. In these spaces, each point represents the data for a single species. In the case of the avian hypervolume, I showed that threatened species are more functionally unique (have more unique combinations of traits) than non-threatened species. This means that impending extinctions will cause more loss of functional diversity (variety of traits) than if extinction were to occur randomly. This work might also help identify species of conservation importance. Invasion Ecology \u0026amp; Social Behaviour # Guppies have an extraordinary capacity to invade new environments. Native to Trinidad and north-east South America, guppies have now spread to every continent except Antarctica. I worked with Dr Amy Deacon at the University of the West Indies to study how social behaviour (shoaling) might be affected by the presence of other species, and if familiarity with that species changes this relationship. I also carried out experiments that examined whether guppies are good mosquito control agents. I use guppies as a model system for behavioural experiments, looking at shoaling behaviour and the transmission of information between species. Speciation \u0026amp; Morphometrics # For my undergraduate dissertation, I worked with Dr Julia Day and Dr Antonia Ford to test whether there were morphological differences among populations of a suckermouth catfish (Chiloglanis anoterus). Using geometric morphometrics, we found that significant morphological differences existed only among male tail morphologies for different populations. Combined with genetic data, this is an exciting example of sexual selection in the process of generating new species. Publications # 2025\nPrice-Waldman, R. M., Ali, J. R., Shultz, A. J., Hogan, B. G., \u0026amp; Stoddard, M. C. (2025). Hidden white and black feather layers enhance plumage coloration in tanagers and other songbirds. Science Advances Morrison, E.S., … , Ali, J. R., … \u0026amp; Shultz, A.J. (2025) Geographical variation in signals and responses: individual identity signals linked with capacity for individual face learning across Polistes fuscatus wasp populations. PloS one 2024\nWeise, C., Ali, J. R., Ortiz, C.C., Tibbetts, E.A. (2024) Geographical variation in signals and responses: individual identity signals linked with capacity for individual face learning across Polistes fuscatus wasp populations. Animal Behaviour 2023\nAli, J. R., Blonder, B, Pigot, A. L. \u0026amp; Tobias, J. A. (2023) Bird extinctions threaten to cause disproportionate reductions of functional diversity and uniqueness. Functional Ecology 2022\nTobias, J. A., … , Ali, J. R., … \u0026amp; Schleuning, M. (2022). AVONET: morphological, ecological and geographical data for all birds. Ecology Letters, 25(3), 581-597. 2018\nAli, J. R., Deacon, A. E., Mahabir, K., Ramnarine, I. W., \u0026amp; Magurran, A. E. (2018). Heterospecific shoaling in an invasive poeciliid: shared history does not affect shoal cohesion. Animal Behaviour, 138, 1-8. 2015\nMorris, J., Ford, A. G. P., Ali, J. R., Peart, C. R., Bills R., \u0026amp; Day, J. J. (2015) High levels of genetic structure and striking phenotypic variability in a sexually dimorphic suckermouth catfish from the African Highveld. Biological Journal of the Linnean Society. Scicomm # Some of this probably belongs in the blog section, or the other way around. Reorganisation is in progress.\nArticle: Sea squirts and the origin of the vertebrate brain # My second article for Princeton Insights! This time I delve into what studying the nervous system of sea squirts can tell us about how complex brains originated. Photo: Biodiversity Heritage Library.\nRead more here.\nPodcast episode: nonspectral colours # I co-hosted a podcast for the first time! This was a follow-up to an article I wrote about hummingbird vision. I spoke with Dr Cassie Stoddard (my PhD advisor) about the experiments she did to determine if hummingbirds can see colours that are not in the rainbow\u0026ndash;nonspectral colours!\nListen to find out more.\nArticle: Prince, perception and purple # My first article for Princeton Insights! I explore how behavioural experiments are teaching us what colours hummingbirds can and can\u0026rsquo;t see. Image by Becky Matsubara on Flickr.\nRead more here.\nOutreach # (still building out this section)\nEmbankment Coalition # I am lucky to assist with public outreach via sensory walks which I lead along the Jersey City Embankment. The goal is to help members of my community engage with a space that is being developed as a green haven for the city, while talking about sensory ecology science! For example, what are the visual properties of a tree versus a brick wall? And, unironically, how does that make you feel? Image via the Embankment Coalition. Find out more here. Princeton EEB Scholars # The Princeton EEB Scholars Program serves students historically excluded from EEB, and aims to demystify the graduate school application process, as well as prepare these students for grad school interviews. I was lucky to be coordinator for two years. Image by Ken Lund. Letters to a Pre-scientist # Letters to a pre-scientist connects Stem professionals with students. This is a super rewarding pen pal experience! It was really exciting to learn about my pen pal’s passions and dreams, and do my best to help grow his love for science! ","externalUrl":null,"permalink":"/science/","section":"","summary":"","title":"","type":"article"},{"content":"","externalUrl":null,"permalink":"/authors/","section":"Authors","summary":"","title":"Authors","type":"authors"},{"content":"","externalUrl":null,"permalink":"/categories/","section":"Categories","summary":"","title":"Categories","type":"categories"},{"content":"","externalUrl":null,"permalink":"/series/","section":"Series","summary":"","title":"Series","type":"series"},{"content":"","externalUrl":null,"permalink":"/tags/","section":"Tags","summary":"","title":"Tags","type":"tags"}]