Collagen sequence reveals evolutionary history of extinct 'island-shrews' - Nesophontes

With great satisfaction, I announce the publication of our paper on the extinct Greater Antillean endemic: Nesophontes. As you may have read from posts in this blog, the genus Nesophontes is a group of shrew-like mammals for which several species have been identified on the islands of Cuba, Cayman, Hispaniola, and Puerto Rico, but not The Bahamas or Jamaica. Each island had its own exclusive forms. These unique varieties to each island are called endemics. 

Original specimen from which Nesophontes was described: N. edithae (AMNH 14174). 

The genus Nesophontes is grouped within the mammal order Eulipotyphla. This is a group of basal placental mammals that are considered ancestrally associated to the Solenodon of Cuba and Hispaniola. Also, to other North American extinct shrew-like micromammals, but surprisingly not to the African tenrecs despite their physical similarity.  Nesophontes was small, likely venomous, nocturnal, and could tunnel underground. At least eight species are currently recognized: three in Cuba (N. major, N. micrus and N. longirostris); three in Hispaniola (N. paramicrus, N. hypomicrus, and N. zamicrus); one in Puerto Rico (N. edithae) and one in Cayman (N. hemicingulus). However, the identification, naming, and evolutionary history of this diverse group has been somewhat controversial. 

Solenodon paradoxus from Hispaniola. Plate from Allen's (1910) monograph on the species. 

We designed our study to help unravel especially the issue of evolution and species limits. Our paper, formally accepted in the journal Molecular Biology and Evolution this past march, provides the following abstract: 

“Ancient biomolecule analyses are proving increasingly useful in the study of evolutionary patterns, including extinct organisms. Proteomic sequencing techniques complement genomic approaches, having the potential to examine lineages further back in time than achievable using ancient DNA, given the less stringent preservation requirements. In this study, we demonstrate the ability to use collagen sequence analyses via proteomics to provide species delimitation as a foundation for informing evolutionary patterns. We uncover biogeographic information of an enigmatic and recently extinct lineage of Nesophontes across their range on the Caribbean islands. First, evolutionary relationships reconstructed from collagen sequences reaffirm the affinity of Nesophontes and Solenodon as sister taxa within Solenodonota. This relationship helps lay the foundation for testing geographical isolation hypotheses across islands within the Greater Antilles, including movement from Cuba towards Hispaniola. Second, our results are consistent with Cuba having just two species of Nesophontes (N. micrus and N. major) that exhibit intrapopulation morphological variation. Finally, analysis of the recently described species from the Cayman Islands (N. hemicingulus) indicates that it is a closer relative to the Cuban species, N. major rather than N. micrus as previously speculated. Our proteomic sequencing improves our understanding of the origin, evolution, and distribution of this extinct mammal lineage, particularly with respect to approximate timing of speciation. Such knowledge is vital for this biodiversity hotspot, where the magnitude of recent extinctions may obscure true estimates of species richness in the past.”

I take this opportunity to extend my gratitude and thanks to the whole team, for pushing through with persistence for nearly a decade. And to all the friends and colleagues that helped along the way. 

Stay tuned for more details on our findings and these peculiar mammals ahead. 

Recommended Citation

Buckley, Mike; Virginia L. Harvey; Joha Orihuela; Alexis M. Mychajliw; J. Keating; J. N. Almonte Milan; C. Lawless; A. T. Chamberlain; V. M. Egerton; and Phillip L. Manning (2020). Collagen sequence analysis reveals evolutionary history of extinct West Indies Nesophontes ('island-shrews'). Molecular Biology and Evolution: https://doi.org/10.1093/molbev/msaa137

New papers and preprints on antillean vertebrate extinctions now available!

Hi there internet surfers and blog-verse travelers, what a great way to start the new year. There are several new research papers and findings now available on Cuban - generally Antillean  - Late Quaternary land vertebrate extinctions. A lot of exiting and revealing new data, on which I will expand in future blog posts; hopefully, soon.

In the mean time, here I share some links for those interested in our new data and preprints.

Our new paper on Cuba bats is now available on my ResearchGate page here, or on the Novitates Caribaea journal page, here. To see a post on this research, visit here.

Three of our preprints posted on BioRxiv are available there, and they are citable as:

J. Orihuela, Lázaro W. Viñola, Osvaldo Jiménez Vázquez, Alexis Mychajliw, Odlanyer Hernández de Lara, Logel Lorenzo, J. Angel Soto-Centeno "Assessing the role of humans in Greater Antillean land vertebrate extinctions: new insights from Cuba" bioRxiv 2020.01.27.922237;doi: https://doi.org/10.1101/2020.01.27.922237

J. Orihuela, Leonel Pérez Orozco, Jorge L. Álvarez Licourt, Ricardo A. Viera Muñoz, Candido Santana Barani "Late Holocene land vertebrate fauna from Cueva de los Nesofontes, Western Cuba: stratigraphy, last appearance dates, diversity and paleoecology"
bioRxiv 2020.01.17.909663; doi: https://doi.org/10.1101/2020.01.17.909663

J. Orihuela, Yasmani Ceballos Izquierdo, Roger W. Portell "First report of the Eocene bivalve Schedocardia (Mollusca, Cardiidae) from Cuba" bioRxiv 2020.02.03.932756; doi: https://doi.org/10.1101/2020.02.03.932756

Extinct Cuban ground sloth Megalocnus rodens. Specimen mounted with remains discovered by Carlos de la Torre
This skeleton is part of the collection at the Cuban National Museum.

Describing the impossible: a sauropod fossil from Cuba

A joint effort of Cuban-Argentinian paleontologists have recently published a detailed description of a dinosaur fossil found in the rocks of Cuba. With it, the researchers concluded that the fragmentary remain could have belonged to a rare dinosaur group that inhabited the surrounding landmasses of the proto-Caribbean Sea, preserving it in rocks that are now part of the Cuban terrain.

The interesting fossil was discovered at the start of the 20th century, in Jurassic-age rocks of the Jagua Formation, which crop out near Viñales, western Cuba. The fossil, however, did not gain certain attention until it was described and figured in a small note published by the Cuban geologist Alfredo de la Torre y Callejas, in 1949. In it, de la Torre credits the discovery to America Ana Cuervo, a professor of Geology and Paleontology at the University of Havana, and who had published several articles on Cuban fossil reptiles. Apparently, professor Cuervo donated the specimen to the University’s museum, where it was later available to de la Torre.



Metacarpal position for the somphospondylan sauropod from Cuba.
With insert of original specimen found by Prof. America A. Cuervo.
Courtesy of Yasmani Ceballos.

Unfortunately, the fossil has been lost since, and its whereabouts are still a mystery. All that remains of the enigmatic fossil are de la Torre’s vague descriptions and the small photograph published in 1949 (see figure below). Classifying it, based on such scanty data, has no doubt been challenging for the research team, but also very rewarding for Cuban paleontology. Comprising a  rare and noteworthy record indeed.

The research team, composed of Yasmani Ceballos Izquierdo – an upcoming Cuban paleontologist – and Dr. Manuel Iturralde-Vinent – the Cuban geologist-paleontologist extraordinaire, were led by the Argentinian dinosaur specialist Dr. Sebastián Apesteguía. Together, they recently published the interesting findings of their study in the prestigious journal Historical Biology.

Based on detailed comparisons, they have been able to identify the lost fossil bone as pertaining to the hand bone – a metacarpal – representing an old lineage of the Somphospondylii or a basal titanosaurid. These dinosaurs belonged to a group of giant herbivore sauropods that inhabited the coastal lands of Laurasia and Gondwanaland.

Alliance between Cuban and Argentinian paleontologists has spanned over a hundred years, starting with the Argentinian paleontologist Florentino Ameghino, who collaborated with Cuban researchers through the late 19th century. During the 1990s, Dr. Manuel Iturralde worked with Dr. Zulma Gasparini in the identification of rare reptilian fossils found in Jurassic-age rocks from Cuba. The most recent collaboration with Dr. Sebastián Apesteguía, like in the past, has no doubt bore fruitful results.



Metacarpal from somphospondylan sauropod from Cuba.
Original specimen found by Prof. America A. Cuervo.
Courtesy of Yasmani Ceballos.

 

Not only is this the first and only dinosaur yet reported from Cuba, but the fossil is also of biogeographical importance. It brings evidence of the extinct animals that inhabited the area that was to become the Caribbean Sea and some of its islands, like Cuba, several millions of years before the end-Cretaceous mass extinction that wiped out the dinosaurs.

Idealized scene of the western Tethys - early Caribbean seaway, and fauna
known from fossil remains found in Cuba.
Artwork by Roilan. Courtesy of Yasmani Ceballos.

After the supercontinent Pangea broke up, around 200-180 million years ago, it divided into several landmasses. Some to the northern hemisphere, others to the southern hemisphere. Laurasia is the landmass that existed when the North American continent was interconnected to its Eurasian counterpart, several hundred million years ago. The surrounding landmasses had a narrow seaway in which this fossil was probably washed into. The rocks of the bottom of that seaway have long since moved and incorporated to form parts of the main island of Cuba. This fossil, among other biological remains known from similar rocks formations, support the presence of emerged land nearby the proto-Caribbean seaway – known as the western Tethys.



The Earth during the Jurassic period (~200 -145 million years ago). Red circle shows area of proto Caribbean
Artwork and geologic interpretation by Christopher Scotese.

Acknowledgments

I extend my thanks to and appreciation for Yasmani Ceballos, who shared revealing information to prepare this post.

Recommended citation:

Apesteguía, S., Ceballos Izquierdo, Y., and Iturralde-Vinent, M. (2019). New taxonomic assignment for a dinosaur sauropod bone from Cuba. Historical Biology, https://doi.org/10.1080/08912963.2019.1661406

When did the turkey vulture arrive in Cuba?

All the American vultures belong to the Cathartidae, a neotropical endemic and diverse bird family of carrion scavengers. Currently, the family is integrated by four buzzard-like vultures and three condors including the turkey vulture (Cathartes aura), the black vulture (Coragyps atratus), up to the California condor (Gymnogyps californianus) and the Andean condor (Vulture gryphus).

 

Of these New World vultures, the genus Cathartes is the most diverse with three species, C. burrovianus, C. melanbrothus, and C. aura. Of these, the turkey vulture Cathartes aura, along with the black vulture Coragyps atratus, are the most widespread, inhabiting nearly all the American continent and parts of the West Indies, including the island of Cuba. Turkey vultures abound on the island and is easily observable today. But when did it reach Cuba? When did it become part of its fauna? Was it before or after the arrival of Europeans?

Cathartidae fossils are known in the New World, confidently, since at least late Miocene, and more so during the Pliocene-Pleistocene epoch, meaning during the last 6 million years. Interestingly, fossil Cathartidae have been reported from the late Oligocene (~23 million years) of Mongolia (Emslie, 1988). With such a long fossil record, one would think that the presence of the turkey vulture in Cuba spans to the Pleistocene. At least, that was what was originally thought by Cuban paleontologists.

The source of uncertainty is because turkey vultures seem to have a poor fossil record in Cuba. Several remains found in cave deposits near the capital city of La Habana, in Cueva Lamas and Cueva del Túnel, were at first interpreted as Late Pleistocene in age (see Arredondo, 1984). These specimens were later revised by the Cuban paleornithologist extraordinaire, William Suárez, who concluded that these were modern specimens and not fossil material (mixing of bone remains in caves is a common phenomenon, and one must be extra careful in discerning what is a fossil, or subfossil, and what is modern).

Based on the research of the Cuban zooarchaeologist Osvaldo Jiménez, turkey vulture remains have been identified in early 17th-century colonial contexts of La Habana Vieja (Old Havana), which agree with documentation of the time. Jiménez argues that the species was already considered common in Jamaica by 1680, where it adopted the name of John Crow. It was from this island that the species spread into Cuba, Hispaniola, and Bahamas, becoming established by the late 18th century. It was further introduced in Puerto Rico during the 19th century for sanitary reasons (Jiménez and Arrazcaeta, 2008).

Two important accounts document the presence and widespread of the turkey vulture in Cuba during the colonial period. One is a mention made by the governor of the eastern department of Cuba, Juan Garcia de Navia Castrillón, in June of 1617. The other is a watercolor sketch made by soldier Henry Fletcher in august 1762, during the Siege of Havana by the British (see figure below). This illustration brings an interesting note that reads “head of a turkey buzzard or carrion crow, a fowl common in the West Indies. The body resembles very much a large brown turkey”.  Both accounts support the apparent widespread of this species on the islands by then.

"head of a turkey buzzard or carrion crow, a fowl common in the West Indies.
The body resembles very much a large brown turkey"
By Henry Fletcher (august 1762).
Digital scan of the John Carter Brown Library, Rhode Island.

More recently, however, during our excavations of Cueva de los Nesofontes at Palenque Hill (source of several posts in this blog, available here and here), we encountered several unequivocal Cathartes aura subfossil remains in beds dated to less than a couple thousand years before the present (Orihuela, 2019). These fossils seem to reinstate that the turkey vulture was present in Cuba before European arrival for at least several thousands of years.

Cathartes aura from a cave deposit at Cueva de los Nesofontes, Cuba
 

This makes sense biogeographically, due to the proximity of the Greater Antilles and the continental mainland. In fact, many of the turkey vulture groups that migrate between parts of the continents, do so by flying over the same span of Caribbean ocean (Moore, 2000). Moreover, fossils of the species have also been found in Bahamian sinkhole deposits (Ficus Pit, in San Salvador, see Olson et al., 1990). Olson and colleagues reached the conclusion, as we do here, that turkey vultures likely arrived in the Greater Antilles due to natural expansion, especially after the extinction of many of the islands large and diverse raptors probably during the Holocene.



Cited Literature

Arredondo, O. (1980). Sinopsis de las aves halladas en depósitos fosilíferos Pleisto-Holocenicos de Cuba. Reporte de Investigación del Instituto de Zoología, 17: 1-35.

Emslie, S. D. (1988). The fossil history and phylogenetic relationships of condors (Ciconiiformes: Vulturidae) in the New World. Journal of Vertebrate Paleontology, 8(2):212-228.

Fletcher, Henry (1757–1765) Seven Year’s War journal of the 35th regiment on foot (unedited 1409 manuscript). John Carter Brown Library, Rhode Island.

Jiménez Vázquez, O. and Arrazcaeta, R. 2008. Las aves en la arqueología histórica de La
Habana Vieja. Boletín del Gabinete de Arqueología, 7:17–29.
Moore, R. (2000). A fallout of turkey vultures over Florida Bay with notes on water crossing behavior. Florida Field Naturalist, 28(3): 118-121.

Olson, S. L., G. K. Pregill, and W. B. Hilgartner (1990). Studies on fossil and extant vertebrates from San Salvador (Watling’s) Island, Bahamas. Smithsonian Institution Press, Washington.

Orihuela, J. (2019). An annotated list of Late Quaternary extinct birds of Cuba. Ornitología
Neotropical, 30: 57–67.

 

 

First Sirenian brain endocast from the Miocene of Cuba

With great pleasure, I announce the recent publication of our paper on the first sirenian endocranial casts yet known from the Caribbean. Our paper, coauthored by the paleontologists Lázaro W. Viñola and Ted Macrini, was published on the specialized Journal of Vertebrate Paleontology this month (link here and here).



Fossilized brain mold of a Dugongid specimen from Matanzas, Cuba

A resume of the major findings can be read in the abstract:

We report and describe the first sirenian endocranial casts from the West Indies based on three specimens collected from two quarries of the late Oligocene-early Miocene Colón Formation, in the Province of Matanzas, western Cuba. We assign them to Dugongidae incertae sedis, based on a phylogenetic analysis of fossil and extant sirenians. Thus, these new specimens provide a unique opportunity to describe the endocranial neuroanatomy of a long-extinct sirenian. The endocasts suggest a dugongid with limited vision and olfactory, based on the diminished olfactory and optic nerves. Additionally, we provide a geologic reinterpretation of the Colón Formation and its paleoecological setting. Altogether, these data provide further insight into the diversity and evolution of sirenians, especially Caribbean dugongs.

For the interested reader, sirenians are marine mammals which include the manatees of the Atlantic Ocean and the dugongs of the Indo-Pacific Ocean. These aquatic mammals were originally called sirenians because seem by sailors from afar, they looked similar to humans or the famed sirens of mythological lore (example from Homer’s The Odyssey). These extraordinary mammals were also documented by Columbus’s and its chroniclers after 1492 (see our post on the matter here).



Main differences between manatees (Trichechydae) and dugongs (Dugongidae).
From Enciclopedia Britanica.

One of the first fossil sirenians discovered in Cuba was found by a local researcher named Eustaquio Calera, from Matanzas. He discovered few remains in the limestones of the town of Cabezas, on the road to Union de Reyes, in central Matanzas Province, Cuba. The significance of these fossils, however, remained undetected until the archaeologist Manuel Rivero found them while studying Calera’s collection. Rivero pressed the matter to Luis S. Varona, the main mastozoologist in Cuba at the time, who published his accounts in 1972.



Anatomy of one of the dugongid brain molds from Matanzas (Cuba) described
in our paper.

This discovery is significant for several reasons:

The first being, that this is thus far, the first brain mold (endocast) reported from any sirenian in the Caribbean fossil record. Second, it suggests the presence of at least two unknown species yet undescribed from the region. Although the Caribbean basin is known to have been a hotspot of sirenian speciation and evolution since the Eocene (~40 million years ago), these additional species support a higher level of diversity during the last 20 million years or during the Miocene. Last, but not least, these kind of fossils are very rare, and represent a unique phenomenon of fossilization. For an endocast or mold to form, the organism must be covered, almost immediately after death, in sediment. That sediment must be fine enough to invade all the nicks and crannies, including the brain cavity. After that, that parcel of mud must become stone o lithified enough to preserve the specimen it encapsulates.

In nature, these events are extremely rare or very low probability. Making this finding a unique and one of a kind opportunity to study the brain anatomy of long-gone organisms that we can study today only through their fossil matter.

We take this opportunity to thank all those that were involved in our project. The discoverers of the fossils in the quarries and the museum curator that allowed us to study their collections. Many thanks are due to our friends and family who supported us with guidance and critical commentaries that no doubt made our work better. Many thanks to all.

Reference:

Orihuela, J., L. W. Vinola Lopez, and T. Macrini (2019). First cranial endocasts of early Miocene sirenians (Dugongidae) from the West Indies. Journal of Vertebrate Paleontology 39: DOI:10.1080/02724634.2019.1584565