Category Archives: Evolution

Journey into the Heart of Nicaragua: Parque Nacional Saslaya

In northeastern Nicaragua there is a rainforest-clad mountain that has seldom been visited by scientists, or anyone for that matter. It is called Parque Nacional (PN) Saslaya, and it is one of the last places in Central America where the Jaguar is still king, where undisturbed primary rainforest extends along an elevational gradient of over 1000 m, culminating in elfin cloud forest at the mountain’s highest reaches.


Tropical forests once covered Nicaragua like a blanket, but modern satellite imagery reveals a country that was largely denuded of its forest cover in the last century. Not surprisingly, the highest quality forest tracts that remain are found in the North and South Caribbean Autonomous Regions (RACN and RACS, respectively), where infrastructure is underdeveloped (relative to the western half of the country) and about 300,000 indigenous people, descendants of the Pre-Colombian Rama, Mayagna, and Miskitu cultures, still persist in rural communities.


PN Saslaya straddles the border of RACN and Jinotega, and it stands out like the proverbial sore thumb in satellite imagery. Several settlements were created along its boundaries in the years after the Nicaraguan Revolution (1978–79) and subsequent Contra War (1980s), but there are no indigenous people in the park. The people here, and in the nearby town of Siuna, are miners, cattle ranchers, and farmers. A recent wave of monoculture teak and coffee plantations in the area has been rapidly homogenizing the landscape. The only evidence of the extensive humid forests that once grew there, are large epiphytes still clinging to the upper branches of the few (now solitary) old growth trees that were spared the axe on account of their singular beauty or location. The saving grace of PN Saslaya has been its inaccessibility, and for now it remains one of the last strongholds of primeval rainforest in Central America.


In April 2017, we mounted an expedition to PN Saslaya, to collect the first specimens of birds and their associated parasites from the region. Our team included, representing the Academy of Natural Sciences of Drexel University (ANSP), myself and colleague Therese Catanach (right in above pic), a post-doctoral researcher who studies the genomes of bird lice and their hosts; representing the University of Kansas, veteran field ornithologist Mark Robbins (center), collections manager at the University of Kansas (KU) Biodiversity Institute, and KU graduate student Jack Hruska (left), who grew up in Nicaragua and has broad interests in bird systematics, biogeography and behavior. In Nicaragua, we teamed up with ornithologist and tour guide Alexander Acosta Anton, rented a 4×4 pickup truck, and headed off across the country in search of adventure, which we found.


The only scientific surveys of the park’s avifauna to date, are those of Liliana Chavarria Duriaux and Georges Duriaux, intrepid Nicaraguan ornithologists who made nine (!) expeditions into PN Saslaya over the last decade, literally cutting a trail to the cloud forest at 1400m with machetes! They have produced an impressive checklist of over 300 species known to inhabit the park (L. C. and G. Duriaux, pers. comm.), but to date no physical specimens had been collected for genetic and other analyses. We collected data-rich specimens that include frozen tissues for genetic analysis, blood slides (fixed in ethanol) for studying haemosporidians like avian malaria, ectoparasites like lice, ticks and mites (preserved in ethanol), over 400 audio recordings, and numerous census surveys (available on, in addition to the study skins prepared for the museum collections at ANSP and KU. These data will survive for hundreds of years, and enable us to assess the unique value of the biodiversity of PN Saslaya, and in so doing, effectively advocate for its conservation.


Swainson’s Thrush (Catharus ustulatus swainsoni). This species was common around the Río Labú camp from 8–16 April. Several individuals were heard singing, but at much lower volume than during their breeding season in North America.

PN Saslaya is physically and logistically difficult to access, and because there is a history of land-use conflicts (typically involving people illegally removing resources from the park), all visitors are required to have a security escort. It took us several days, and multiple trips to both the Siuna police station and military base (El Batallón Ecológico), to make the necessary arrangements. Our plan was to establish a base camp on the west bank of the Río Labú, about 6 hours hike into the park from the nearest road, where we would work for 10 days (9 nights). In addition to our military escort, we would hire a team of people from the nearby community of Rosa Grande, to porter our equipment to base camp, and arrange for them to return again on the 9th day to assist with our extraction. We stuck to the plan, and it was successful.


The hike from Rosa Grande was hot and humid, ~3.5 km of fincas, crop fields, and scrubby secondary growth forest, to the park border at 320 m elevation. Already the topography of the trail ahead was evident: a lot of rapid gains and losses in elevation, as the single-file footpath meandered its way through the ravines cut but the myriad tributaries that fed the Río Labú. As we continued into the park, the forest transitioned into primary humid rainforest. Howler monkeys called out in the distance as we paused at the park boundary, and a Lesser Greenlet (Pachysylvia decurtata) sang from the sub-canopy. Therese and I watched a jaguarundi (Puma yagouaroundi) cross a log about 15 m away, while we paused on the trail for a moment to catch our breath. It clearly knew that we were there, but it did not seem concerned by our presence. So few people venture that far into the park each year, that it is conceivable that it was that individual’s first encounter with a human.



White-whiskered Puffbird (Malacoptila panamensis)

Our team of eight soldiers were on orders to keep us safe, and probably to make sure that we did not get ourselves into any trouble. They took that charge very seriously, sending scouts out ahead of our group, and leaving one behind to ensure that we weren’t flanked. When we finally arrived at the site of our base camp, as the sun was setting and the forest interior already quite dim, we scrambled to get our tents set up before dark. Beginning that night, the soldiers began a 24/7 patrol of the camp, taking turns on the night shift duty. I occasionally left my tent in the middle of the night (~0200) to relieve myself, and couldn’t resist the urge to joke with the patrol, asking him whether he had heard any funny noises. During the day, the soldiers toiled about camp, building thatch-roof huts to cover their hammocks, and trying to get a radio antenna high enough in the tree tops to establish contact with the base. One of the soldiers captured a baby Central American Agouti (Dasyprocta punctata), and kept it for a pet for a couple days until it escaped.


To be continued…

A closer look at the wing of Swainson’s Thrush (Catharus ustulatus swainsoni) in First Basic plumage

Like other migratory Catharus species, juvenile Swainson’s Thrushes (Catharus ustulatus swainsoni) molt into a ‘First Basic’ plumage at the end of their first summer, which they wear for one year before attaining their ‘Adult Basic’ plumage. The partial molt that results in First Basic plumage includes some or all of the median coverts (the little olive feathers above the numbered row), and up to five of the (inner) greater coverts, which are numbered 1–9 in the image. In this case, the bird molted only one greater covert: #1, the fresh olive covert without a buffy tip. The retained juvenile coverts (2–9) are paler and more brown, and numbers 2–6 end with a buffy tip. This is called a molt limit, and it helps us to figure out the age of a bird. For all the juicy details of molt limits in North American passerines, check out Peter Pyle’s Identification Guide to North American Birds, Part 1, 1997.


This bird died in a window collision in Montgomery Co., PA, in late September 2016. After taking the photo, I prepared the specimen for the Ornithology Collection at the Academy of Natural Sciences of Drexel University. Legend: primaries (P1–8); secondaries (S1–9). The 9th and reduced 10th primaries are not visible in the photo.

Genetic sampling of Townsend’s 1835 type specimens of Catharus

In 1834, pioneer naturalists Thomas Nuttall (1786–1859) and John Kirk Townsend (1809–51) ventured westward with the second expedition of Nathaniel Jarvis Wyeth (1802–56), across the Rocky Mountains and eventually to the mouth of the Columbia River. The trip was a huge success, and Townsend discovered numerous bird species that were previously unknown to science. In 1836, Townsend opted to venture farther west to the Sandwich Islands (Hawaii), and so entrusted his bird collection to Nuttall, who returned with it to the Academy of Natural Sciences of Philadelphia. There, the specimens were eagerly awaited by John James Audubon (1785–1851), who was preparing the final plates for The Birds of America:

“Dr Townsend’s collection was at Philadelphia; my anxiety to examine his specimens was extreme…Having obtained access to the collection I turned over and over the new and rare species but he [Townsend] was absent at Fort Vancouver on the shores of the Columbia River, Thomas Nuttall had not yet come from Boston and loud murmurs were uttered by the soidisant friends of science, who objected to my seeing, much less portraying and describing, these valuable relics of birds, many of which had not yet been introduced into our fauna.” Audubon (1838:xi)


Paralectotype of Catharus guttatus nanus, collected by Townsend and described by Audubon (1839)

Among the specimens in the collection were two thrushes new to science, that we now know as Catharus ustulatus Nuttall (i.e., Swainson’s Thrush) and Catharus guttatus nanus Audubon (now considered a subspecies of Hermit Thrush). The prepared specimens are still in the Academy collection. See my previous post about the discovery and description of the C. ustulatus type.

Today, I harvested a tiny sample of skin from the C. ustulatus holotype, and a paralectotype of C. g. nanus—both collected by Townsend during the Wyeth expedition. The samples will be prepared and submitted for DNA sequencing—genetic data that will be included in my dissertation work on the systematics, evolution, and taxonomy of the genus Catharus. These two type specimens, which were examined 180 years ago by Townsend, Nuttall, and Audubon, will now be used again to clarify the ancestry and taxonomy of these species. I hope that, if they were alive today, Townsend and the rest would approve!


Collecting skin tissue for DNA sequencing from the holotype of Catharus ustulatus (ANSP #23644)—collected by Townsend and described by Nuttall (1840). Courtesy of the Academy of Natural Sciences of Drexel University. Photo: Steve Miller.



FIELD NOTES: An unusual observation at a hybrid Manakin lek in Panama


The indigenous village of Changuinola Arriba, as seen in 2005. Photo credit: Cory Neidig.

I was digging through some old field notes yesterday, and came across an interesting entry from a research expedition to western Panama in 2005. The crew was led by the inimitable Adam Stein, followed by Kyle Elliott, Cory Neidig, and myself. The expedition was intended to gather data for Adam’s dissertation research, on the evolutionary dynamics of a unique avian hybrid zone, where Manacus candei meets and interbreeds with Manacus vitellinus), in the remote Changuinola river valley of northwestern Panama (see publication credits at the end of this post). Our study site was located in the environs of the indigenous Guaymi village of Changuinola Arriba, ten hours upriver in a motorized dugout canoe.

We located leks (i.e., courtship display sites) by sound, using machetes to build and maintain temporary access trails through the dense secondary growth along the riverbank. We trapped each of our target birds in mist-nets, color-banded the males and took various measurements; blood and semen samples were obtained and frozen in a portable liquid-nitrogen tank, photospectrometer readings were taken from the plumage of each male, and morphological measurements were taken with calipers. We studied aggressive interactions by presenting taxodermied mounts (both yellow & white) and non-manakin control mounts to a sample of males at both sites, and then recording their reactions.

I spent many days working alone, or paired with another member of the team. Our study sample was largely split between two riverside lekking sites, separated by a considerable distance of river, and we had only one canoe. Many days, due to limited transportation, I made my way back to camp via muddy jungle slope or swift jungle river, gear slung overhead in a waterproof dry-bag – often a two or three hour process.


White-collared Manakin (left) and hybrid Manakin (candei X vitellinus, right). Photo credit: Kyle Elliott.

Typically, each male manakin maintains its own court for display. Although courts can be placed in proximity to one another (resulting in a congregation of courts – a lek), most courts are occupied by a single territorial male who is not tolerant of other males within its immediate vicinity. However, on March 30, 2005, I had an interesting observation of two males (one yellow, one white) that were displaying together on the same court. I counted the number of cheers that each bird made during a 20-min (yellow) mount presentation, and then continued to observe them for 2 hours afterwards. Here is a transcript of my field notes:


A behavioral observation at a manakin court, which can be seen in the distance. Photo credit: Cory Neidig.

The flagging says W but a yellow bird is hanging out. There is a white [bird] that is always with him. I watched them for 2+ hours. The 2 birds fly back and forth between 2 courts, always together. They even display together on one court. They both came in and cheered at the mount. Yellow seems to own Court B but shares it with White. White will follow Yellow into Court B; they hang out there and chirp together; and then White flies back to his court, and Yellow follows. Yellow then leads the way back to Court B, and White follows. Neither seemed too concerned with mount. The cheers they made seemed more directed at each other. They flew back and forth between both courts (always together) at least 20 times during 30 minute [mount] presentation. When they are in White’s court, they both cheer. Occasionally, they both left the area together, but always flying together. Eventually, Yellow would show up at Court B again, and White would arrive 2 seconds later. Literally no attention was paid to the mount by either bird. They cheered the same amount while they were in the other court as when they were in Court B.

Yellow spent slightly more time in Court B than White, although it was never more than 1 minute before White arrived. White was never in Court B alone. This is nuts. They even followed each other from perch to perch, and sitting next to each other on one perch. It was like a game of tag.



The research that we conducted in Panama was supported by J.A.C. Uy’s lab at Syracuse University, Smithsonian Tropical Research Institute, and a large number of people including A. Pineda Jr., R. Santos, A. Santos, H. Santos, F. Abrego, M. Leone, O. Orsomena, C. De Leo´n, U. Gonzalez, D. Santos and the community of Changuinola Arriba.


Concannon, M. R., Stein, A. C., and J. A. C. Uy. 2012. Kin selection may contribute to lek evolution and trait introgression across an avian hybrid zone. Molecular Ecology 21: 1477–1486.

Stein, A. C., and J. A. C. Uy. 2006. Unidirectional introgression of a sexually selected trait across an avian hybrid zone: a role for female choice? Evolution 60: 1476–1485.

Stein, A. C. 2009. Plumage evolution in bearded manakins (Manacus spps.). Ph.D. Dissertation, Syracuse University.

Uy, J. A. C., and A. C. Stein. 2007. Variable visual habitats may influence the spread of colorful plumage across an avian hybrid zone.Journal of Evolutionary Biology 20: 1847–1858.

Scientific musings on the future of the Polar Bear (Ursus maritimus) in an era of climate change


FIG. 1: From Hailer et al. (2013): “Schematic scenario for mtDNA inheritance in bears. Speciation occurred in the middle Pleistocene, but hybridization during the late Pleistocene led to mtDNA similarity between extant polar bears and brown bears”

Polar bears (Ursus maritimus) share a close ancestry with the brown bear (U. arctos), and are currently distributed as a metapopulation, viz., an assemblage of smaller populations with limited gene flow between them. These disjunct populations are found within an Arctic land matrix dominated by sea-ice and island habitats (Kurten 1964, Ferguson et al. 1998). Genomic analysis has revealed that polar bears represent a surprisingly ancient lineage, with divergence estimates for the common ancestor of polar and brown bears likely occurring 934,000338,000 years ago (Hailer et al. 2012); occasional hybridization between the two lineages is evident in introgressed mitochondrial DNA (mtDNA) sequences, suggesting that male brown bears occasionally mixed with isolated polar bear populations during warm interglacial periods when sea-ice receded (FIG. 1, Cahill et al. 2013). Scientific evidence suggests that the circumpolar distribution of the modern polar bear is the result of a rapid range expansion that followed a population bottleneck, perhaps induced, as Lindqvist et al. (2010) suggest, by variability in habitat and climate during the Eemian interglacial (~130,000–114,000 years before present).

If the early divergence estimates of Hailer et al. (2012) are accurate, the ancient polar bear lineage that squeezed through the Eemian bottleneck necessarily survived multiple prior bottlenecks as well (during previous interglacial periods, FIG. 2). The modern polar bear has also thus far survived the Holocene interglacial (10,000 years ago until present day), during which time the extent of sea-ice has fluctuated with an amplitude that far exceeds the current trend of sea-ice loss documented in the late 20th and early 21st centuries (McKay et al. 2008). The polar bear has persisted during these periods because a few subpopulations in ice-covered refugia made it through.

FIG. 2: Temperature data for the Pleistocene to present day, as determined from benthic stable isotopes (Lisiecki & Raymo 2005), and speciation events in bears. From Hailer et al. (2012): “a” denotes the origination of the polar bear lineage and “b” the diversification of extant brown bear lineages. Shaded gray bars are 95% credibility intervals; black lines denote median estimates."

FIG. 2: Temperature data for the Pleistocene to present day, as determined from benthic stable isotopes (Lisiecki & Raymo 2005), and speciation events in bears. From Hailer et al. (2012): “a” denotes the origination of the polar bear lineage and “b” the diversification of extant brown bear lineages. Shaded gray bars are 95% credibility intervals; black lines denote median estimates.”

Although the polar bear may be unlikely to persist through a period of no sea-ice (i.e., not even refugia), the metapopulation is likely to exhibit long-term resiliency to climate change as long as some sea-ice remains. Indeed, it has previously demonstrated this resiliency in more extreme conditions (FIG. 2). It is the metapopulation structure and genetic variability (yes, even those introgressed brown bear genes) that have allowed the species to persist through periods of extreme environmental change. Theoretically, genetic bottlenecks should also have made the species more adapted to climate fluctuations, as those surviving subpopulations carry well-adapted genes and behaviors that improve resiliency to future change. Of course, the metapopulation itself may become extinct if the environmental pressure is sufficiently great, just as so many species in the vast history of the Earth have perished.

To be sure, human-exacerbated climate change poses a threat to polar bear populations, and may end up extirpating some populations. But considering what they have previously been through, it seems that it would take a serious blow to destroy the entire metapopulation and render the species extinct. After taking a look at the last 2 million years of temperature changes (FIG. 2), it seems hard to imagine that the current interglacial is here to stay; might the current warming trend just be the “calm before the storm”, a brief period of rapid warming before the next glacial period begins? To me, this scenario seems more likely than one of perpetual warming.

Is our current fossil fuel binge enough to stop the unfathomable momentum of the Pleistocene glaciation cycle?  If yes, the future of the polar bear might truly be uncertain. If no, I bet it will make it through just fine until the next glaciation….and judging by the duration of the most recent interglacials, we’ve still got a few thousand years until the next ice age begins. Unless of course, humanity keeps priming the pump.


This graph shows the newest Ice Core data for Atmospheric CO2 from air bubbles in the ice. I tried to connect it to the glacial cycles by marking 230 ppm as a transition level and colored “glacial periods” blue and interglacial periods yellow. There’s a clear 80,000-110,000 period of repeating glacier even if they vary in quality. Human deforestation and burning of fossil fuel has raised atmospheric CO2 to over 380 ppm in the last century, well above pre-industrialized levels, and “off the scale” of this graph top. Figure and caption by Tom Ruen, re-published from Wikipedia.
Source data: (Combined)
Law Dome: 1006 A.D.-1978 A.D
Vostok ice core: 417,160 – 2,342 years BP
Dome C ice core: 650,000 – 415,000 BP-(or 648th millennium BC to 413th millennium BC)

Literature Cited

Cahill, J. A., et al. 2013. Genomic evidence for island population conversion resolves conflicting theories of polar bear evolution. PLOS Genetics 9:3, 1–8. doi:10.1371/journal.pgen.1003345.

Ferguson, S. H., M. K. Taylor, E. W. Born, and F. Messier. 1998. Fractals, sea-ice landscape and spatial patterns of polar bears. Journal of Biogeography 25:1081–1092.

Hailer, F., et al. 2013. Nuclear genome sequences reveal that polar bears are an old and distinct lineage. Science 336, 344–347.

Kurten, B. 1964. The evolution of the polar bear, Ursus maritimus. Phipps. Acta Zool. Fennica, 108, 1-30.

Lindqvist et al. 2010. Complete mitochondrial genome of a Pleistocene jawbone unveils the origin of polar bear. PNAS 107:5053–5057.

Lisiecki, L. E. and M. E. Raymo. 2005. A Pliocene–Pleistocene stack of 57 globally distributed benthic δ18O records. Paleoceanography 20, PA1003.

McKay, J. L., A. de Vernal, C. Hillaire-Marcel, C. Not, L Polyak, and D. Darby. 2008. Holocene fluctuations in Arctic sea-ice cover: Dinocyst-based reconstructions for the eastern Chukchi Sea. Canadian Journal of Earth Science 45:1377–1397.

Talbot, S.L. & Shields, G.F. 1996. Phylogeography of brown bears (Ursus arctos) of Alaska and paraphyly within the Ursidae. Mol Phylogenetics Evol. 5, 477-494.

On death as the mother of beauty, and frog embryos.

Embryo_Deformities“Objects which in themselves we view with pain, we delight to contemplate when reproduced with minute fidelity: such as the forms of the most ignoble animals and of dead bodies. The cause of this again is, that to learn gives the liveliest pleasure, not only to philosophers but to men in general…” — Aristotle, in Poetics (335 B.C.E.)

In a large egg mass of the Wood Frog (Rana sylvatica),  I observed several deformed embryos, each grotesque, beautiful, and captivating to the eye. Most of the frog spawn contained tiny spherical blastulas, each rapidly dividing according to its unique set of genetic instructions, but the deformed individuals took on many disturbing shapes. Perhaps the bane of their development was a single genetic mutation, an error that occurred during recombination that resulted in a gene that did not function the way it should. One tiny glitch in development, and before long the cumulative effects of the change are manifest in a striking departure from the typical Bauplan of the species.

In many cases, the result of such a gene mutation will be something akin to these deformed embryos, an utterly failed organism that will not survive to adulthood, much less transfer its genes to the next generation. In other cases, the mutation will not preclude adult development, but will nevertheless have some strange detrimental effect on the animal (e.g., infertility or deformed limbs); this animal will be out-competed by its neighbors, and the mutation will not persist very long in the population, even if it survives a generation or two.

But every once in a while, on the most fortuitous of occasions, such a mutation will actually cause a change that improves the fitness of the mutant. Perhaps it causes the frog’s webbing to extend all the way to the end of its toe rather than to the first knuckle. Such a slight adjustment might allow it to be a faster swimmer, thus facilitating its survival and reproduction.

It is a wonderful thought:   That which is most abhorrent in Nature provides the raw material for Its evolutionary transformation, and thus Its beauty.


It’s pretty amazing that you and I started our lives as blastulas. In the early days following our conception, we were little more than a ball of cells, rapidly dividing according to the instructions in our genetic code (found in the nucleus of every one of those cells). As a consequence of our shared evolutionary history, all vertebrates begin their lives this way; our genetic code is comprised of thousands of nucleotide sequences, each containing a set of instructions, “build this protein, build that protein, etc.”, and the cells keep replicating and replicating. Eventually, just like building a massive spaceship or castle out of legos, a structure that has simple beginnings gets more and more complex, and the differences that we observe between species start to manifest themselves in development according to each species’ unique DNA blueprints.

Here are some photos that I took of embryogenesis in the Wood Frog (Rana sylvatica). In the first picture you see the blastula, a little ball of cells that is growing and growing as the cells continuously divide.  Eventually, the blastula starts to fold inward (i.e., gastrulation) and we start to see the bilaterally symmetrical body plan take shape. The white stuff at the bottom of the second picture is the part that will eventually turn into the frog’s anus. The embryo keeps growing and begins to elongate. In the third picture in the sequence (center left), we see the head begin to differentiate. The frog’s brain is now beginning to form (upper right of the embryo in the center left pic), and the central nervous system and other vital organs are all developing as per the instructions found in the genetic code. The very same process happened to you and I in the earliest days of our lives.

I went away for a few days, and when I returned the tiny embryo had developed into a healthy tadpole (bottom picture).  Eventually, as per the instructions in its genetic code, the animal grew legs and transitioned into a terrestrial lifeform as an adult Wood Frog (center right). Next year, this frog (if it survives) will find a mate and start the reproductive cycle all over again, just like its ancestors have done for millions of years. We have been doing the same thing, and if you trace our family trees back far enough, they eventually converge. That’s right, this frog and I share a common ancestor. It is one of the most beautiful and profound truths of nature, and for me, a source of deep meaning. The proof is right there in our shared genetic code, and in the highly conserved early stages of embryonic development.