Sunday, December 7, 2014

New publications: new eomysticetid Tohoraata, and trace evidence of predation on bone-eating worms in eomysticetid bones

Over the past couple of weeks I've had two papers from my Ph.D. thesis published with my adviser, R. Ewan Fordyce. The first of these, published in mid November in the new journal Papers in Palaeontology, deals with resolving the identity of the fragmentary fossil cetacean "Mauicetus" waitakiensis from the late Oligocene of New Zealand, and another new species.

Tohoraata - dawn whales from the Oligocene of New Zealand

Mauicetus waitakiensis was described in 1956 by former Zoology professor (and Zoology Chair) Brian J. Marples, although collected somewhat earlier by him. Marples was an arachnologist originally, and according to Ewan Fordyce, probably stumbled upon fossils while looking for trap door spiders in North Otago. During the 1940's and 1950's Marples and his sons dug up several cetacean skulls and partial skeletons, also including the dolphin Otekaikea marplesi, recently redescribed and renamed by my labmate/office partner Yoshi Tanaka. Two of these new cetaceans appeared to be baleen whales, and included one specimen with a complete braincase, fragmentary mandible, well-preserved tympanic bullae, scapulae, and some vertebrae; the other included only a fragmentary braincase, tympanic bullae, and neck vertebrae. Both were collected from the Kokoamu Greensand. At the time of writing, only one baleen whale had been named from NZ: Mauicetus parki, an archaic mysticete from the somewhat younger (earliest Miocene) Milburn Limestone, much closer to Otago campus (perhaps only a 45 minute drive out of town). At the time it was reasonable to allocate these new species to Mauicetus: the Mauicetus holotype was fragmentary, seemed to correspond well to what Marples had collected, and the periotic (inner ear bone) had not yet been removed. So, Marples named these two species Mauicetus lophocephalus (for the more complete specimen) and Mauicetus waitakiensis (for the less complete specimen).

Note: this can get somewhat confusing, as Dr. Benham originally named the type species as Lophocephalus parki (which he thought was an archaeocete, until Remington Kellogg corrected him), and upon realizing that Lophocephalus was preoccupied, he named the new genus Mauicetus for it. So Marples, perhaps confusingly, recycled the name for one of his new species of Mauicetus.


The holotype skull and tympanic bulla of "Mauicetus" waitakiensis, figured and described for the first time. From Boessenecker and Fordyce (2014A).

The relationships of Marples' Mauicetus species have remained contentious for nearly 60 years. Unfortunately, Marples never figured more than the first and second vertebrae of Mauicetus waitakiensis, even though it had a partial skull and earbones. To make matters worse, the skull of Mauicetus lophocephalus was chucked in the trash when the Zoology Dept. switched buildings sometime before 1962 - less than six years after being published! The next paleocetologist who came along and had the opportunity to look at this specimen was R.E. Fordyce when he began his Ph.D. in the late 1970's, and the skull of one of the most significant cetacean fossil discoveries in NZ had disappeared without a trace. Fordyce noted in several earlier studies that the remaining material of these two species differed strongly from all previously known baleen whales, and that the material likely represented a baleen-bearing mysticete but more primitive than any described. In 2002, Eomysticetus whitmorei was described by Al Sanders and Larry Barnes from the Oligocene Chandler Bridge Formation of South Carolina - an early toothless baleen whale that had features intermediate between toothed baleen whales and most groups of baleen whales from Neogene rocks, filling a critical gap in cetacean evolution. Eomysticetus had a long, narrow rostrum, a toothless palate, elongate nasal bones, an anteriorly placed blowhole, and an archaeocete-like braincase with archaeocete-like earbones and many archaeocete-like features of the postcrania (note: when I refer to archaeocetes, I'm specifically meaning advanced archaeocetes like basilosaurids). Ewan quickly realized that these specimens of Marples - including many unpublished fossils in our collections - represented similar species, likely referable to the family Eomysticetidae.


The holotype skull, bulla, and periotic of Tohoraata raekohao (OU 22178) from the upper Oligocene Otekaike Limestone, North Otago.

In 1993, Ewan and others collected another fragmentary mysticete from Waipati hill, the type locality of Waipatia maerewhenua (which would be formally named the following year). Other eomysticetid specimens in our collections are far more impressive - but shortly after my arrival here, this struck me as sharing the most in common with Marple's M. waitakiensis. This specimen included a partial skull, mandible, a single vertebra and several ribs, and most critically, well-preserved earbones. A few shared features (synapomorphies) of the tympanic bulla and occipital bone permitted these specimens to be identified, which we interpreted as reflecting a sister-species relationship within a single genus. We named this new genus Tohoraata, which in Maori literally translates as "dawn whale". The new species was named Tohoraata raekohao, which translates as "holes in forehead", referring to a series of peculiar foramina in the frontal bone above the eye socket (orbit); Marples' species was recombined as Tohoraata waitakiensis.


Yours truly posing with the displayed holotype specimen of Tohoraata raekohao. Photo copyright Otago Daily Times.

Discovery of the Tohoraata raekohao holotype not only represents the first record of an eomysticetid from the Oligocene of New Zealand, but also permitted taxonomic revision and identification of "Mauicetus" waitakiensis, resolving a half century of uncertainty over its relationships. This material also preserves the most exquisitely preserved tympanoperiotics of any published stem mysticete - and better yet, there are even better specimens from my thesis studies that have yet to be published (at least one far more spectacular fossil is the focus of another manuscript currently in review, including a revision of "Mauicetus" lophocephalus). Other fossils are more informative with respect to function, and will be featured in future publications.

Aside from publishing ammonium chloride coated photographs, we've constructed 3D models of the holotype periotic and bulla of Tohoraata raekohao, which are downloadable in pdf and obj format here.


A life restoration of Tohoraata raekohao with the skull digitally superimposed - copyright R.W. Boessenecker 2014.

Trace fossil evidence of fish/shark predation upon bone-eating worms

The second new publication also reports aspects of fossil eomysticetids from New Zealand, but is taphonomic in scope rather than taxonomic. Upon arriving down here I was surprised how many of the marine vertebrate fossils have circular pockmarks in them, measuring between 5 and 15 mm in diameter; in some cases, these pockmarks are coalesced and form large areas of bone where the entire surface has been destroyed. Similar pockmarks have been reported from Pliocene and modern whale bones, and in modern specimens, they have been confirmed to be made by the bone eating worm Osedax. Most previous studies of Osedax bioerosion have relied upon CT imaging - which is great, but expensive and impractical for the purposes of most taphonomic studies. Taphonomic studies hoping to mobilize large amounts of data cannot rely upon an expensive slow process such as non-invasive digital imaging, and rather ichnologic features useful for quick identification from a specimen will have more lasting significance for taphonomists. In other words, if you wanted to track the frequency of Osedax bioerosion through time - CT scanning hundreds of bones for a large quantitative study is totally impractical. Not that we had so many bones to work with for this project, we were dealing with a single specimen that had rather revealing traces - but it is a 2 meter long fossil baleen whale skull, and too large to scan at the necessary resolution (hospital CT scanners such as what we would have access to have a failsafe that scales the number of slices to the physical size of the object being scanned, so as to not expose a human patient to too much radiation - if I recall correctly). Also, we do not have the funding to pay for CT scans. So, we relied upon external characteristics in order to identify Osedax traces, which is standard practice anyway with virtually all ichnology (non-invasive digital imaging is generally done only in special cases).


Illustration of the skull (A) of undescribed eomysticetid OU 22044 and various trace fossils found upon it. B: tiny boreholes from Osedax stalks; C, Osedax pockmarks with intersecting tooth scrapes; D, collapsed depressions with tiny boreholes.

I found quite a few different types of traces on one skull in particular - OU 22044, a nearly complete skull with mandibles representing an unnamed genus and species of eomysticetid (it will hopefully be a type specimen in the future, and is the next chapter I am planning on submitting). For anyone who saw my SVP talk in 2013 at the LA meeting, this is one of the very same specimens. Traces included tiny pin-size holes under 1mm in diameter, which were often found in clusters; other traces included strange structures where the cortex was collapsed like a sinkhole with annular (ring-shaped) fracture systems, and associated with the aforementioned pinholes. The most commonly encountered traces were circular pockmarks (5-15mm in diameter) with irregular surfaces, and which in some regions were laterally coalesced into large eroded fields. Lastly, abundant tooth scrapes - often in parallel sets or cross-cutting - are present. Most are small scrapes, but one large set of three scrapes (B, below) are long and curved, suggestive of a shark. Others (D, below) are totally parallel, resembling traces made by feeding skates (Rajiformes) in feeding experiments (teeth are rasped posteriorly in a straight line to remove soft tissues, forming totally parallel tooth scrapes). The pockmarks are identical to those observed on modern whale bones infested with Osedax. Osedax makes tiny boreholes and excavates a large cavity just under the cortical bone surface, leaving a thin veneer of bone as protection; the roots of the worm - which "digest" bone using bacterial symbionts - inhabit the cavity or gallery, while the stalk and gills protrude from the borehole. This thin veneer of bone is easily damaged, leaving a crater-like pockmark behind. As for the boreholes? Well, OU 22044 preserves those quite well (B, above). We even have direct evidence that the pockmarks are bioeroded galleries with a thin veneer of bone above, with boreholes drilled into it: in D, above, the empty galleries of bone have permitted diagenetic compaction to push the thin rind of cortical bone into the gallery. This is a slam-dunk case for identifying these traces as Osedax borings, and further strengthens the argument that pockmarks - when found - can be attributed to Osedax bioerosion.


More traces from OU 22044. A, bioeroded field of laterally coalesced Osedax pockmarks. B, set of three shark tooth scrapes. C, closeup of Osedax pockmarks with intersecting tooth scrapes. D, parallel set of tooth scrapes, likely from a skate.

This is of course neat, and represents the first record of fossil Osedax traces from the southern hemisphere - but they've been reported before and that novelty is not the selling point of the paper. Instead, the most significant discovery was that these tooth scrapes and pockmarks intersect - the scrapes cross-cut the damaged bioeroded pockmarks attributed to Osedax bioerosion. Osedax tends not to colonize bone surfaces until soft tissue is gone, although it has been observed colonizing soft tissues on sperm whale carcasses. Other tooth scrapes were likely made when soft tissue still remained, being inflicted during the process of scavenging. However, the scrapes that cross-cut the pockmarks are surficial, and only made after the pockmark already existed. If the bone was already colonized by Osedax, then presumably no soft tissue remained for the scavenger to consume. Instead, we attribute these scrapes as reflecting predation (by fish or shark) upon the Osedax worms themselves. Indeed, modern ratfish and tanner crabs have been observed gouging Osedax out of whale bones to consume the fleshy roots entombed within the bone. And now we have evidence for this behavior extending back to the Oligocene. On a broader philosophical level, we are reporting a predatory interaction between two organisms preserved only as traces in the skeletal tissues of a third organism (mind blown).

A couple other points of interest beg noting. 1) The existence of Osedax predators suggests that this process could accelerate the rate of skeletal bioerosion/recycling at the seafloor (if, of course, numerous phases of predation/recolonization happen). 2) We noted abundant pockmarks of similar morphology on fossils of bony fish, sea turtles, dolphins, baleen whales, and sea cows from Oligocene localities on the east coast of the USA as well as Europe, particularly from the Ashley/Chandler Bridge formations of South Carolina. In contrast, we noted no similar pockmarks on Neogene examples from either coast of the USA, including large assemblages from the Purisima, San Diego, San Mateo, and Calvert Formations as well as Sharktooth Hill. Perhaps widespread Osedax bioerosion (or preservation thereof) peaked in the Oligocene? We don't really know, and it's only a suggestion - but one that can be borne out by further (quantitative) study.

For more information, see our department web page (where you can download 3D models of the earbones!) on Tohoraata and these articles:

Stuff.co.nz: Ancient toothless whale skull discovered in Otago
Otago Daily Times: Otago researchers find new whale genus
3 News: 8m serpent like whale fossil found
New Zealand Herald: 20 million-year-old whale fossils found
Radio New Zealand: Researchers identify ancient NZ whale
Zee News: New Zealand researchers identify ancient whale species
Calgary Sun: N.Z. researchers uncover unknown ancient whales
Science World Report: Ancient New Zealand Whales Were the First to be Completely Toothless
Phys.org: Ancient New Zealand ‘Dawn Whale’ identified

These two papers are now out, and the first one on Tohoraata is even freely available online:

Boessenecker, R.W. and R.E. Fordyce. 2014A. A new eomysticetid (Mammalia: Cetacea) from the Late Oligocene of New Zealand and a re-evaluation of 'Mauicetus' waitakiensis. Papers in Palaeontology, Online early DOI:10.1002/spp2.1005

Boessenecker, R.W. and R.E. Fordyce. 2014B. Trace fossil evidence of predation upon bone-eating worms on a baleen whale skeleton from the Oligocene of New Zealand. Lethaia, Online early DOI: 10.1111/let.12108

Saturday, December 6, 2014

Sorry for the hiatus - GSNZ conference and field trip to Waihi/Ohawe beaches, Taranaki

Hey all, as promised, I've only had a minimal amount of time to contribute to blogging this fall, owing to more pressing concerns (such as my thesis, which I have about two months left to complete). It's been one week since I've been back from the Geoscience Society of NZ annual conference, where I presented on my dissertation research on Oligocene eomysticetids from the south island of NZ, specifically on feeding strategy of the earliest toothless mysticetes. I actually won 1st runner up for best student oral presentation, and labmate Yoshi Tanaka received the award for best poster presentation for his poster on Oligocene platanistoid dolphins from the same localities. Otago students did exceedingly well, sweeping 5 out of 6 best presentation awards, all with the exception of top oral presentation. To be fair, Otago students made up almost half of all students attending the conference, but then again we received more than half the awards. All this highlights Otago as one of the best places to study geology in NZ.

Not all of the days were paleontology themed (in fact, only one was) so some plans were made to go out into the field. I have long wanted to visit some fossil sites in South Taranaki, which have recently been getting some attention on places like The Fossil Forum thanks to a series of remarkable discoveries by some private collectors on the North Island. I flew up to Wellington the day before the conference started, rented a car with labmate Josh Corrie, and swung by Waihi Beach.


Fossil invertebrates are abundant in the cliffs, and require little more than a knife or a few casual taps from a rock hammer to be pried loose from the rather soft siltstone. Large scallops, beautifully preserved oysters, and spectacular gastropods are in abundance. Occasional barnacles are present, and bryozoans are rare; I found a single, beautifully preserved bryozoan colony that I handed to Alan Tennyson for Te Papa (National Museum of New Zealand) fossil collections. In concretions, much larger oysters and scallops can be found, but are substantially more difficult to prepare.

Fossil vertebrates include seals (known from isolated braincases, mandibles, humeri, innominates, femora, other postcrania, and partial associated skeletons), dolphins (known from several skulls, mandibles, a single periotic, and vertebrae), rare baleen whales (mostly ribs, although a partial skull and skeleton of a new species of Balaenoptera are in collections at Te Papa), and marine birds including shearwaters, giant petrels, albatrosses, a spheniscid penguin, and a pelagornithid bird (skulls, jaws, partial skeletons). Bony fish and sharks are also known - I saw vertebrae from lamniform sharks including a candidate for Carcharodon carcharias, and toothplates of the elephant fish Callorhynchus (a chimaera) and a single associated set of mandibular/palatoquadrate cartilages with teeth of the angel shark Squatina also exist in private collections. Vertebrates are almost always in small concretions, and are cracked open with large sledgehammers.


The view to the west from Waihi stream.


A large scallop exposed in the Ohawe Siltstone.


Further up the beach, here's the view towards Ohawe Beach off in the distance.


Large gastropods make for a nice prize.


Fordyce student Josh Corrie looks for concretions at Waihi Beach. Right around this spot, a pelagornithid jaw (seen below) was collected less than two months ago.


Some examples of bones in concretions in a private collection from Ohawe/Waihi beach.


A pelagornithid humerus in a concretion, with the Pelagornis sp. I described from the Purisima Formation back in 2011 with N. Adam Smith for comparison.


Spectacular pelagornithid jaw with pseudoteeth from Waihi Beach.


Nearby is Mt. Taranaki, an enormous stratovolcano; we had staggering views of the mountain from New Plymouth. Mt. Taranaki was used as a stand-in for Mt. Fuji in the film "The Last Samurai".


Te Papa paleontology curator Alan Tennyson looking for concretions at Waihi Beach.


Otago BSc honors student Alexis Belton helping in the search for concretions. I offered Alexis a lift back to Wellington in exchange for a few bucks for gas and helping us find fossils.


 Alan cracks open a concretion.


Many of the concretions are even in the water still; here's a cluster of several good candidates. None had anything inside them, of course, but this is what to look for. Anything looking silty, spherical, and like a bowling ball (or smaller) without large shells.


We actually ended up breaking one of Alan's two sledge hammers; the haft was a bit old and perhaps somewhat rotten near the head.

Another beautiful gastropod.

Monday, November 3, 2014

The evolutionary history of walruses, part 5: what did tusks evolve for?



 This is the last text-heavy post in the walrus evolution series; one last post remains, which will be up in a few days. I've been busy with job applications and thesis writing, and finalizing and submitting three short manuscripts on various subjects.




Sexual dimorphism in the walrus - male in the background, female in the foreground. Photo from www.marinebio.net.

Tusks in Odobenus rosmarus

Tusks in the modern walrus Odobenus rosmarus occur in both sexes, but are generally larger and longer in males – and like most other pinnipeds, they are polygynous (a single male mates with multiple females) and sexually dimorphic (males are larger than females). The walrus is restricted to the Arctic – and owing to this, tusks were usually assumed to have something to do with ice. For example, walruses tend to use their tusks to assist in hauling out onto ice, leading many to originally propose that tusks evolved for this purpose. Other workers erroneously identified tusks as being used for excavation of mollusks on the seafloor. However, observations by Francis Fay (1982) and Edward Miller (1975) indicate that a use in feeding or haul out behavior is unlikely. Miller (1975) studied aggressive behavior in male walruses, and observed that tusks perform a central role in male interactions. Most interactions consist of tusk threat displays – the aggressor leans his head back so that the tusks are horizontal and pointing toward the target. If the target is somewhat submissive the aggressor will perform a “stabbing” motion. In more aggressive interactions the aggressor strikes the target with the tusks using the same downward stabbing motion, typically striking the hindquarters, back, or neck. These strikes commonly draw blood but Miller (1975) doubted that many cause serious injury (similar to elephant seal combat). Tusks were also frequently used to parry strikes close to the face. Predictably, walruses preferentially threatened smaller males; perhaps more adorably, juvenile males that even lacked tusks performed play fighting that was similarly ritualized. Strikes tended to follow visual threats, and Miller (1975) indicated that ritualized aggressive behavior like this is fundamentally similar to that seen in sea lions, who perform visual displays (prior to striking) by similarly leaning back and opening the mouth to show the canines. Interestingly, the pattern of scarring is completely opposite to the pattern of observed tusk strikes: scarring is mostly present on the anterior neck region, and Miller (1975) attributed this to several reasons: 1) his observations were on land and 2) during the summer. He hypothesized that during the breeding season, more intense “face to face” combat on ice (or more likely, in the water, as some rare anecdotes suggest) is the origin of anterior scarring. So, the relatively violent behavior that Miller (1975) described is not even that which is known to cause the most scarring on walruses – which seems to suggest that walrus breeding behavior might be a bit terrifying and may give the elephant seal a run for its money.


Walrus tusk display and combat. Threat displays frequently prelude tusk strikes. Photo from www.flickr.com

            Many earlier workers (see Fay, 1982: 134-135 and references therein) concluded that walruses dug prey items out of seafloor with their tusks, and this was based primarily on observations of tusk abrasion in dead animals. At least one early study suggested that walruses scraped the seafloor with their tusks in a posterior direction, but later revised to a side-to-side motion as no abrasion exists on the posterior side of the tusks. Some early reports did cast doubt upon these hypotheses, as occasional individuals were identified as lacking tusks but of otherwise healthy appearance. Fay’s (1982) classic study re-examined the abrasion patterns, and concluded that the primary direction of sediment-tusk interaction was from proximal to distal (e.g. base of tusk to tip), which indicates that tusks are passively dragged through the sediment during benthic foraging. Fay (1982) also indicated that tusks are frequently used for locomotion – including hauling out onto sea ice, and even during aquatic sleeping with the tusks hooked over the edge of an ice floe (like a swimmer resting at the edge of a pool). However, he suggested that these were secondary functions and that by far and away the most significant functions were all social in origin. He hypothesized that because all/most pinnipeds are polygynous, the capability for tusk development is probably universal among the group but extreme canine enlargement is probably only possible once a pinniped lineage has made the shift from piscivory (fish eating) to suction feeding. Notably, most toothed whales with tusks (beaked whales, narwhal, Odobenocetops) are all either known or inferred to be suction feeders.




 Abrasion of walrus tusks - figure from Fay (1982). Abrasion is focused on the anterior side of the tusk, indicating passive dragging of the tusks through sediment during foraging rather than active digging.

Temperate and Subtropical tusked walruses

Further eroding ice-related hypotheses for the evolution of tusks in walruses are discoveries of fossil walruses that inhabited drastically warmer waters than the extant Odobenus rosmarus. The earliest known temperate tusked walrus was Alachtherium, which for the past 130 years was known from Belgium, and in the late 1990’s was also reported from the northwestern coast of Africa (Geraads 1997). Subsequently, additional discoveries indicated more occurrences of Alachtherium from Japan and the eastern USA as far south as Florida, and records of the toothless odobenine walrus Valenictus from southern California and even Mexico (Deméré, 1994). Fossils of Valenictus from San Diego and the Imperial Desert indicated to Deméré (1994) that walrus tusks evolved long before walruses became ice-bound in the Arctic, and that tusks are thus “structures with history”.




 Life restoration of Odobenocetops by Smithsonian artist Mary Parrish.

The walrus-faced whale Odobenocetops: implications for tusk use

The 1990 discovery of a bizarre fossil mammal, named in 1993 by Christian de Muizon as Odobenocetops, led to a reinterpretation of tusk function in walruses. Odobenocetops was collected from late-Miocene strata of the Pisco Formation of Peru and initially accidentally misidentified as a walrus; I’ve been told that an early SVP abstract with this mistake can be found. LACM Curator Emeritus takes credit for setting the record straight and asking those involved “why does the skull have premaxillary sac fossae?” These fossae, for the uninitiated, are unique to odontocetes (toothed whales), and Muizon (1993) named it as a new genus and species in a new family, Odobenocetopsidae, which he and others (Muizon et al., 2002) considered to be a sister clade to the Monodontidae – the family that includes the beluga and narwhal (and the fossil belugas, Bohaskaia and Denebola). I won’t go into too much detail irrelevant to the tusks, but Odobenocetops only possesses two teeth: asymmetrical left and right tusks that are posteriorly directed and set into elongate, columnar alveolar processes, and exhibits a deeply concave palate. These features and their similarity with the modern walrus indicated a similar mode of feeding. However, the occurrence of similar tusks in a completely different type of marine mammal that independently evolved benthic suction feeding for mollusks begs the question: did tusks really evolve for social purposes? Muizon et al. (2002) conclude that the orientation of the tusks is a bit too coincidental, and that the alveolar processes likely behaved as “sled runners” to stabilize and properly orient the head of Odobenocetops as it trawled the ocean floor for molluscan prey. They conceded that the asymmetry of the tusks (the left tusk is barely erupted while the right tusk is very long – up to 1.35 meters in Odobenocetops leptodon; Muizon and Domning, 2002) indicates that such a function was not optimized in Odobenocetops, and it likely reflects a social function like the tusk of the narwhal.


Seafloor foraging of a walrus. From this paper by Levermann et al.

Speaking of tusked cetaceans… what the heck is the narwhal tusk for?

This is a bit of a convenient topic to tack on here; I’d like to revisit it in more detail in the future since some interesting papers have come out in recent years on the topic. The narwhal (Monodon monoceros) is also sexually dimorphic, and possesses a pair of tusks, generally only the left tusk erupts from the soft tissue. Rarely males will possess an erupted right tusk. Although formerly considered an incisor, recent CT studies indicate that the tusk is embedded entirely within the maxilla and is therefore the canine tooth; a series of other vestigial postcanine teeth also form (Nweeia et al. 2012) but rarely erupt from the skull or soft tissues (and are therefore detectable only using CT imaging). Sexual tusk dimorphism is a bit more extreme than in the walrus: only 15% of female narwhals ever possess tusks that erupt from the soft tissue, and the tusks are always smaller and shorter than those of males. Significantly, narwhals do not appear to be polygynous. The narwhal tusk is conspicuously “spiraled” (presumably for structural rigidity) and exhibits dentine tubules exposed on the surface of the tooth – which suggests some ability to sense water temperature and salinity (Nweeia et al. 2009). In contrast, in mammals that masticate their food the dentine tubules do not extend to the outer margin of the tooth; indeed, toothaches may be caused by dentine tubules being exposed to the oral environment when a cavity forms. Additionally, a pulp cavity extends along the entire length of the tusks. Field experiments which consisted of exposing a small section of tusk to high salinity solution resulted in rapid head movements and breathing in several different individuals. These observations lead Nweeia et al. (2009) to propose that the narwhal tusk fulfills a sensory function. 


Male and female narwhals underwater. There are surprisingly few underwater photos of narwhals, although this is generally true of most arctic marine mammals and I for one don't blame photographers: it's damned cold! Photo by Paul Nicklen, National Geographic.

However, the above arguments follow for the narwhal: the tusks are indeed dimorphic, and if these functions are not important for females (85% of females lack erupted tusks, making sensory functions useless for nearly half of the species), they probably do not reflect the main purpose of the tusk. The extreme sexual dimorphism strongly indicates a social role, and another recent study (Kelley et al. 2014) has found a strong correlation between narwhal tusk size and testes mass – confirming the sexual/social importance of tusks. More observations of tusk use in the narwhal is necessary, but males have been observed rubbing or slapping tusks together, and broken tips of tusks have been found embedded in other male narwhal heads (and, heads of belugas) – indirect evidence of narwhal combat. Similarly, underwater observations of walrus and narwhal behavior and combat are rare or lacking altogether. 


Adorable bonus photo (by Paul Nicklen, Nationa Geographic/Getty Images).
 
What about other walruses?

Thus far, almost all discussions of tusk evolution in walruses have either been confined to the modern species, or daresay even cetaceans like Odobenocetops. Obviously, the former is a necessary starting point, and the latter merits consideration – but, what about extinct walruses? The only serious consideration of tusk evolution using fossil walruses was Deméré (1994), who (as outlined above) remarked upon tusks in walruses (e.g. Valenictus) from temperate and subtropical latitudes. An important question that hasn’t really been asked before is: who had the first tusks? The answer is remarkably easy and quick: the dusignathine Gomphotaria pugnax, which is 2-3 million years older than the earliest known tusked odobenine fossils. Tusks in Gomphotaria are quite a bit different in morphology than modern Odobenus: the tusks are short and procumbent, lack globular dentine, and a smaller pair of lower tusks are present; similar double-tusks are seen in Dusignathus (particularly D. seftoni). There is some variation even amongst the odobenines: Protodobenus has thickened maxillae and large canine roots, but the emergent canine crowns are barely proportionally larger than that in a sea lion; tusks are absent in Aivukus, and short, curved, and procumbent (forward inclined) tusks are present in Alachtherium/Ontocetus and Valenictus (although somewhat longer but no less precumbent). Morgan Churchill and I discussed a few of these points in our paper on Pelagiarctos (Boessenecker and Churchill, 2013). This pattern tells us several things: 1) “Sled runner” tusk function would have only really been present in the modern walrus, as most earlier forms had somewhat procumbent tusks that would not have been aligned with the seafloor; 2) tusks do not really seem to be correlated with any subset of the marine environment, and association with ice likely reflects a relatively recent (e.g. Pleistocene) adaptation of Odobenus to high latitude environments; and 3) tusks evolved in several directions in the last 8 million years, which if anything signifies sexual selection and recalls horn and antler diversity amongst small clades of sexually dimorphic and selective ungulates.

The moral of the story is this: there is a difference between what a structure evolved for and what its current function(s) is/are; when walrus tusks first evolved, there was no extensive pack ice and walruses inhabited temperate and subtropical latitudes. The walrus tusk continues to serve an important role in social behavior, but has been used for other purposes (locomotion, sleeping) and is thus an exaptation of sorts. This point can be extended to the narwhal: simply because the narwhal tusk can be sensitive to salinity and temperature does not mean that it evolved for that purpose. In both cases the evidence of sexual dental dimorphism is the most significant, and the evidence rather overhwhelmingly supports a social or sexual origin of tusks in both Arctic species.

References

R. W. Boessenecker and M. Churchill. 2013. A Reevaluation of the Morphology, Paleoecology, and Phylogenetic Relationships of the Enigmatic Walrus Pelagiarctos. PLoS One 8(1):e5411.

Deméré, T.A. 1994. Two new species of fossil walruses (Pinnipedia: Odobenidae) from the upper Pliocene San Diego Formation. Proceedings of the San Diego Society of Natural History 29:77-98

Geraads, D. 1997. Carnivores du Pliocene terminal de Ahl al Oughlam (Casablanca, Maroc). Géobios 30(1):127-164

Fay, F.H. 1982. Ecology and biology of the Pacific walrus Odobenus rosmarus divergens Illiger. North American Fauna 74:1-279.

Kelley, T.C., Stewart, R.E.A., Yurkowski, D.J., Ryan, A., and Ferguson, S.H. 2014. Mating ecology of beluga (Delphinapterus leucas) and narwhal (Monodon monoceros) as estimated by reproductive tract metrics. Marine Mammal Science (Online early: DOI: 10.1111/mms.12165

Miller, E.H. 1975. Walrus ethology 1. The social role of tusks and applications of multidimensional scaling. Canadian Journal of Zoology 53: 590-613.

Muizon, C. de. 1993. Walrus-like feeding adaptation in a new cetacean from the Pliocene of Peru. Nature 365-745-748.

Muizon, C. de., and Domning, D.P. 2002. The anatomy of Odobenocetops (Delphinoidea, Mammalia), the walrus-like dolphin from the Pliocene of Peru and its palaeobiological implications. Zoological Journal of the Linnean Society 134: 423-452.

Muizon, C. de., Domning, D.P., and Ketten, D. 2002. Odobenocetops peruvianus, the walrus-convergent delphinoid (Mammalia: Cetacea) from the early Pliocene of Peru. Smithsonian Contributions to Paleobiology 93: 223-261.

Nweeia, M.T., Eichmiller, F.C., Nutarak, C., Eidelman, N., Giuseppetti, A.A., Quinn, J., Mead, J.G., K’issuk, K., Hauschka, P.V., Tyler, E.M., Potter, C., Orr, J.R., Avike, R., Nielsen, P., and Angnatsiak, D. 2009. Considerations of anatomy, morphology, evolution, and function for the narwhal dentition. In Krupnik, I., Lang, M.A., and Miller, S.E. (editors), Smithsonian at the Poles: contributions to International Polar Year science. 223-240.

Nweeia, M.T., Eichmiller, F.C., Hauschka, P.V., Tyler, E., Mead, J.G., Potter, C.W., Angnatsiak, D.P., Richard, P.R., Orr, J.R., and Black, S.R. 2012. Vestigial tooth anatomy and tusk nomenclature for Monodon monoceros. The Anatomical Record 295:1006-1016.

Thursday, October 23, 2014

Paleontology "kickstarter": relationships of Allodesmus



A mount of the partial holotype skeleton of Allodesmus kelloggi, a junior synonym of Allodesmus kernensis (at the Natural History Museum of Los Angeles).

My colleague Reagan Furbish - a master's student under Dr. Annalisa Berta at San Diego State University, has started a kickstarter campaign to fund some of her master's thesis research. Reagan is studying the phylogenetic relationships of the fossil pinniped Allodesmus: controversy exists whether or not it was more closely related to true seals (Phocidae) or to sea lions (Otariidae) and walruses (Otarioidea). She needs to visit several museums including the American Museum of Natural History in New York, the Smithsonian Institution in Washington D.C., and the Natural History Museum of Los Angeles. Reagan asked me to post this here - if any readers happen to have a few spare bucks they can part with, think about sending some in Reagan's direction! I will note that recently, my colleague Rachel Racicot successfully funded some future CT work on the bizarre porpoise Semirostrum using an Experiment.com kickstarter. Go donate!

Here's the link: https://experiment.com/projects/written-in-bone-was-the-fossil-allodesmus-a-seal-or-sea-lion

Sunday, October 19, 2014

Beautiful new Oligocene dolphin in the prep lab

 A couple of months ago the Haugh's quarry triage project started - we had dozens of unopened plaster jackets from Haugh's Quarry in South Canterbury. About a dozen medium to large size jackets were prepped out, including this one, which was found to have a beautifully preserved odontocete skull, mandible, and partial postcranial skeleton from the upper Oligocene Otekaike Limestone.


Here's a view of the skull and mandible; the gray pieces at the upper right are parts of a large echinoid.


And a mandible with numerous in situ teeth - with the exception of a handful of specimens, most fossil odontocetes in the Otekaike Limestone have teeth that are mostly disarticulated.


And the skull has quite a nice dentition as well! Unfortunately, the tip of the rostrum is missing.


Here it is with a little more preparation. The teeth are quite a bit narrower and more needle-like than other Otekaike Limestone odontocetes.


Here's some nice postcrania...


And more teeth; a single tooth resembles Microcetus hectori (a taxon currently being redescribed by Yoshi Tanaka). There are some tusk-like teeth that were found loose - almost all of the Oligocene odontocetes from NZ appear to have had procumbent tusk-like anterior teeth. Provisionally the skull is similar to odontocetes that have been identified previously as "dalpiazinids". It should be a beauty when preparation is done!

Friday, October 10, 2014

How should we report the age of fossils? Pitfalls and implications for paleontologists.


A few years ago during a talk I was watching at a conference (the details are better left unstated), I realized that there is quite a variety - both in terms of methodology (or lack thereof) and quality of format - of ways to report the geologic age of fossils. Ever since I have wanted to write up a post since the topic has been nagging at the back of my mind. Paleontologists often frustrate geologists for poor understanding of certain major geological principles - something I never really understood when I was an undergraduate student; at Montana State U., we had a pretty strong background in geology. Further to the point, my undergraduate Dave Varricchio is a specialist in taphonomy, and hammered into our poor little heads the importance of geology in our field - which was subsequently galvanized by a master's thesis in the subject, my adviser for which was (gasp!) a sedimentologist (Jim Schmitt). After attending various conferences, however, statements about geology and taphonomy in various talks have left me slack-jawed, and I unfortunately understand why paleontologists get ribbed about it.

I'll start by saying this:  we study fossils because they give us unique insight into the history of life on earth, and we risk missing the true impact of paleontological data if we are careless about it. Now that that's out of the way, here's some of the topics I'm going to touch on: 1) basics of geologic age, 2) sources of age data, 3) recently proposed best practices for reporting ages for molecular clock data, 4) dates from the paleontologic and stratigraphic literature, 5) pitfalls of the paleobiology database, and 6) some suggestions for how to present age data for paleontologists. I'll try to keep this informative and useful instead of a rant, but there will be specific points where I just won't be able to help myself. 

As a quick note: while I am perhaps conversant in stratigraphy and geology, I am by no means an expert (I spend far more time looking at bones!), so anybody who knows better than I do - if you have anything to add to this, whether it be corrections, hate mail, tweaks to suggestions or even additional suggestions - your input can help improve this.


Basics of Geologic Age

I think that since this blog attracts readers with a wide variety of experience, some very basic geology is worth retreading what some have probably/hopefully read elsewhere. The geologic time scale was first assembled during the early 19th century in western Europe primarily based upon biostratigraphy. Pioneering geologists like William Smith used index fossils to identify zones that he identified as being the same age, and in 1815, Smith published the first large geologic map - looking at the beautifully exposed bands of strata in England, it's no wonder it formed the basis for the early understanding of geologic time and stratigraphy.

Charles Lyell introduced the terms Paleozoic, Mesozoic, and Cenozoic, to replace the Primary, Secondary, and Tertiary "periods" (as they were known then; Tertiary is the only one that lingers on). Lyell also introduced epoch divisions for the Cenozoic, and coined the epochs Pliocene, Miocene, and Eocene - at first, these formed the only divisions of the Cenozoic. Eocene roughly translates to "new dawn", referring to the dawn of the "new" Cenozoic invertebrate fauna; Miocene translates to "less new" and Pliocene as "more new", and the latter roughly means "continuation of the recent", referring to the relatively "young" aspect of the invertebrate fauna. These epochs were originally defined by Lyell based upon what percentage of invertebrates were extant: only 3.5% of Eocene mollusks and 17% of Miocene mollusks were extant; on the other hand, the "older Pliocene" was defined upon a mollusk fauna composed of 30-50% extant taxa. Lastly, the "newer Pliocene" was based upon mollusk faunas that were 90-95% extant. Subsequently, additional epochs were added, and over the next century, piecemeal advances in biostratigraphy clarified the stratigraphic distribution of many invertebrates and a geologic time scale was cobbled together across Europe.
What is obviously missing thus far is the sense of time; dating of radioisotopes was not discovered until the early 20th century and not perfected until the nuclear age. Until radiometric dating was employed, geologists worked effectively in a vaccum of numerical age data - all work was done in an understanding of relative time; Lyell would never learn that the Eocene was far longer than the Pliocene, for example, or that the Miocene-Pliocene boundary was only about 5 million years ago - but the Cenozoic in total had a 65 million year duration.


The geologic time scale updated for 2014. [From http://www.stratigraphy.org]
 
This abstract idea of time - otherwise referred to as Geochronology - regardless of absolute dates, has always been separated from chronostratigraphy. Chronostratigraphy can be viewed as the rock record itself with all of its imperfections. This dichotomy may sound a bit strange for the uninitiated, and indeed, it seems strange to many paleontologists (this is actually not a jest). Chronostratigraphic units are in a sense material units, while Geochronologic units are immaterial and refer only to periods of time. For example, the Paleogene period in geochronology is a period of time from about 65 to 25 mya, while in chronostratigraphy the Paleogene system comprises all rocks deposited during that time period. This dichotomy serves to highlight epistemological differences between the two frameworks (e.g. they are defined based upon different sets of criteria). Why the difference? Further to the point: the rock record, as reflected by the deposition of sediment, is like a barcode through time: surprisingly little time is represented by packages of sediment, and the majority is locked up instead in erosional surfaces (e.g. unconformities). Because one framework is purely based upon rocks (Chronostratigraphy) and the other is purely time (Geochronology), we need to be careful about using terms like upper versus late: upper denotes a position within the stratigraphic column, whereas late refers to time. This is why if you write something like "the late Miocene Santa Margarita Sandstone" geologists will either yell at you or make fun of you. This would be better written as "the upper Miocene Santa Margarita Sandstone" as we're discussing a rock unit; however, it would be acceptable to say "the Santa Margarita Sandstone is of late Miocene age". I'll admit that I've been slack about this before and this slipped through in at least one article, and I've gotten considerably more careful about it after being chewed out. A bunch of super-helpful writing tips for some of these confusing issues is given by Owen (2009).


Chronostratigraphy (left) versus Geochronology (right). From Owen (2009).

One last point: capitalization of time period modifiers. Some periods and epochs are formally subdivided, others are not; if a period of time has been formally subdivided, then it should be capitalized. For example, the Late Cretaceous is a formally subdivided period of time; the middle Miocene is not. Some confusion exists about the Pliocene and Pleistocene; some stratigraphers such as John Van Couvering have designated various international stages (e.g. Zanclean, Piacenzian) and their boundaries as defining partitions within the Pliocene and thus formally subdivided the Pliocene, and only some partitions of the Pleistocene have been formally subdivided. Further complicating matters is that according to the Geologic Time Scale 2012 the Pliocene and some of the Pleistocene subdivisions are formally designated (and thus can be capitalized), but the International Committee for Stratigraphy (www.ics.org) do not recognize these as being formally subdivided (except for the Upper and Middle Pleistocene). So it's admittedly a huge headache, but the moral of the story of this: paleontologists frequently screw this up too, but then again so to geologists: there is disagreement within stratigraphy about these things, so as long as you cite a particular framework (e.g. GTS 2012 or ICS.org, or others) and follow that consistently, you'll be fine. This is perhaps not totally relevant to some of the specific points I'll be making, but is good ground to cover as relevant background, as these issues are often a source of confusion.

Sources of Age Data in Geology and Paleontology

With that out of the way, what sources of age data do we have at our disposal? My list is far from comprehensive, but these are the major methods used.

1) Radiometric dates. More often than not these are ash/tuff beds that have been dated using Ar/Ar or K/Ar from feldspars, although occasionally we get interbedded basalts that are even easier to date. Additionally, albeit less common, are radiometric dates from glauconite (that's right, ordinary greensand lends itself towards radiometric dates, randomly). These are generally quite good, and can be recalculated using updated decay constants. There are other types of dating methods under this category, such as U-Pb series dating.


A cute infographic showing the basics of radiometric dating (in this case, the isotope is Carbon-14). [Borrowed from www.glogster.com]

2) Fission track dates. Elements undergoing radioactive decay like Uranium-238 leave little damaged tracks in the crystal lattice of minerals like zircon each time the uranium undergoes spontaneous fission. Because the decay rate of U-238 is known, the number of fission tracks can reliably tell us how long ago the zircon cooled from a magma. This is best used as a dating method when fresh zircons are sampled from an ash bed and were formed during that eruption.


Fission tracks in a zircon. [Ironically, this is borrowed from a creationist website: www.detectingdesign.com]

3) Ash correlation. Not all ash beds are datable - indeed, many ash beds lack phenocrysts large enough to sample by radiometric means or execute a fission track count. However, because every volcano has punched through a slightly different suite of rocks, every eruption has a distinct chemical fingerprint which can be used to tie non-dated ash beds to dated basalts or proximal ashes (e.g. an ash bed may have larger phenocrysts within it close to the volcanic vent). Ash fingerprinting - otherwise known as tephrochronology - is immensely important in Cenozoic marine and terrestrial rocks in the western U.S., as volcanism was fairly active during the Cenozoic.


A tephrochronologic correlation web for the late Neogene of Northern California. 
From Powell et al. (2007).

4) Magnetostratigraphy. Little iron rich grains in sediment align themselves with the earth's magnetic field - just like iron filaments on a sheet of paper adjacent to a bar magnet as illustrated in literally every science textbook ever made. Every so often the earth's magnetic poles switch, and when that happens the grains will point in the opposite direction - so a geologist (specifically a magnetostratigrapher) can take hundreds of oriented samples from a section of rock and identify which sections have normal or reversed polarity - this data can then be organized into a vertical "barcode" which can be calibrated using microfossils (see below). This vertical barcode can of course be matched to stripes on the Atlantic seafloor parallel to the mid-Atlantic Spreading Ridge; as new oceanic crust cools at the ridge, iron-rich grains also align with the magnetic field, resulting in magnetic stripes along the entire seafloor. These stripes go back to the mid-Mesozoic (as much of the pre-Cretaceous Atlantic oceanic crust has been subducted). In concert with biostratigraphy, a robust paleomagnetic framework exists and can be applied to virtually any strata on earth (generally Cretaceous or younger), provided that some biostratigraphically useful fossil content is preserved in the strata in question. A bonus is that because mid Atlantic seafloor spreading is more or less continuous (and rates of change in spreading are well-known), paleomagnetism can be a good way to tell if a significant hiatus in deposition exists; indeed, paleomagnetic work identified that a single bonebed in the Purisima Formation (=Bonebed 6 of my thesis/PLOS One article) recorded a 1 million year gap in deposition.

 
Paleomagnetism of the mid Atlantic spreading ridge and within a sediment core: matching the vertical barcode to the horizontal barcode is essentially the main principle of magnetostratigraphy. [Images borrowed from http://www.geo.arizona.edu and http://www.fromquarkstoquasars.com]
 
5) Biostratigraphy. This is the oldest method for age determination and is a form of relative dating. Whereas during the 19th and early 20th century fossils told us how old the rocks were in a sense relative to other strata, we now have a whole host of absolute dates determined from the other four methods which have allowed assignment of well-constrained dates to biostratigraphic boundaries. Biostratigraphic zones (aka biozones) are historically defined based upon a number of zones, including A) taxon range zones (e.g. range of a single species), B) concurrent range zones (overlap range of two species), C) assemblage zones (overlap range of several species), D) interval zones (defined based on the bracketing of two bioevents, such as the extinction of two separate species at different times), and E) acme zones (defined based on abundance of a particular species; very susceptible to taphonomic processes). Taxa useful for biostratigraphy include microfossils such as diatoms (siliceous algae), benthic and planktic foraminifera (calcareous protists), calcareous nannoplankton (aka coccolithophores), radiolarians (also siliceous, but protists), dinoflagellates, conodonts (Paleozoic and Triassic only; actually a phosphatic element of early vertebrates); useful macroinvertebrate groups include bivalves, gastropods, and particularly ammonites for the Mesozoic - echinoderms have also been used in places. In terrestrial settings mammals are frequently used (e.g. North American Land Mammal Ages) as well as pollen. Useful fossils (index fossils) need to be widespread, easy to identify (and preserved well enough to be easily identifiable), and have a rate of morphological change that permits reasonable biostratigraphic subdivision. In other words, a hypothetical brachiopod that has changed little since the Triassic, only lives in deep sea environments, and is usually too poorly preserved to identify would be a pretty shitty choice for an index fossil. On the other hand, foraminifera tend to live everywhere in the marine realm and are widespread and evolve somewhat rapidly, and are therefore one of the most useful groups.




 Examples of biozone types and definitions from the North American Stratigraphic Code.

So what sort of age data do these provide? The first three generally all provide classical "dates" in the sense that it is presented as a midpoint with error bars: 25 ± 0.2 Ma, for example. The third sort is an ash correlation, so while the date is not intrinsic to the section of rock in question, it is chemically unique to an ash or lava bed somewhere else that has been dated, and thus the date can be applied to the correlative ash bed in our section. The last two are a bit of a mixed bag. Many boundaries of magnetozones are well-dated, so if we have the Gauss-Matuyama chronozone boundary preserved in our section, we can slap a date of 2.58 Ma to that magnetic reversal in our section. Many biozone boundaries - particularly for marine microfossils - have known absolute dates established based upon other methods. If a zone boundary is reflected in our section, we can use that; however, if a fossil in question just has "Boringmicrofossil taxon subzone B" attached to it, then the range of that subzone must be used - let's say the zone is 45.5-48.7 Ma in age, for example. What if our fossil is just above or below a well-dated biozone boundary, but is not bracketed by another date or biozone boundary? In that case, we're stuck with a range as well - whatever biozone our fossil belongs to, from whichever side of the zone boundary it came from. To be totally honest, most absolute ages for biozone boundaries are derived from methods reporting error bars, but are rarely reported as such and thus for biozone boundary ages it's not necessary to report a "±" range as few biostratigaphers bother. Lastly, what if our fossil occurrence has a biozone determination that lacks absolutely dated zone boundaries? Well, for the time being we're out of luck until a nice geologist fixes it for us.



An example of a robust set of dates for a vertebrate fossil: a fossil of the bony toothed bird Pelagornis from the Purisima Formation in California dated to ~2.5-3.35 Ma, from Boessenecker and Smith (2011). The fossil occurred in a stratum bracketed by two ash beds, and remains the youngest well-dated pelagornithid from the Pacific Basin.

Ideally, we would have radiometric dates that bracket a fossil occurrence nicely - for example, a fossil of Pelagornis that N. Adam Smith and I reported in 2011 was bracketed by a 2.5 ± 0.2 Ma ash below and a 3.35 ± 0.05 Ma ash above; using the midpoints of each results in an age of 2.5-3.35 Ma for the fossil. Alternatively, we could be slightly more conservative and utilize the endpoints (e.g. 2.3-3.34 Ma in this example). Rarely does this happen, and often we need to cobble together dates from various sources and dating methods in order to get the most tightly constrained age determination possible. For example, our fossil may be 10 meters below a dated ash, but 50 meters above the next dated ash - and a foraminiferal zone boundary may be 10 meters below our fossil. In which case, it's totally fine to use that zone boundary and the upper ash. Or, perhaps microfossils associated with the fossil itself have a substantially younger maximum age than the lower ash bed; in that case, it's fine to use the endpoint of that zone as a maximum age control, and the overlying ash date for the minimum age. We have to use whatever age control we can get our hands on - and age determinations for fossils are best regarded as ranges. Rarely do we ever get a date right from a fossil - radiocarbon dating in the Pleistocene is a notable exception (or, a fossil preserved directly in an ash bed, or a greensand unit with a K/Ar date) - and in these cases, a midpoint with a "±" is appropriate. If, for the purposes of graphical portrayal of geologic age, a range is needed (or for methodical purposes), the range of error could perhaps be used (e.g. 67 ± 0.5 Ma would be come 67.5-66.5 Ma). In general, one could use the minimum and maximum endpoints no matter what: the message here is that consistency is important, even if our age data have different sources. Lastly, it is necessary to point out that the most up-to-date papers on the geology and stratigraphy of a particular locality should be read and cited.

A quick note that doesn't fit elsewhere nicely: most strata are diachronous. That means that the age of the rock unit changes laterally. This makes sense because a given rock unit is generally a mappable unit of similar lithology, generally produced by a single depositional environments; depositional environments tend to move around through time (think of beaches during periods of sea level rise or fall). What this means is that geologic/stratigraphic data from the same locality (or close nearby) is preferable as it will decrease the chance of using dates that are too old or too young, owing to diachroneity.


Time transgressive strata, using beach deposited sand as an example here. [From www.geol.umd.edu]
 
Otherwise, it is important to note that this is all empirical: species and their geologic age are not abstract units existing in some intangible ether - the range of a species, or genus, is defined based upon the youngest and oldest occurring specimens identifiable to the taxon in question. This is all based on specimens - physical objects somebody dug out of a hole somewhere that are reasonably assigned to a given taxon, and are sitting in some museum collection someplace (which we can go and visit!). All fossil specimens sitting in a museum drawer were once part of the rock record - which technically makes paleontologists earth scientists. Sometimes specimens are misidentified, which may throw a wrench or two into the machine. The point is this: geochronology, chronostratigraphy, and biostratigraphy are dynamic and based upon real data, and refinements in methodology and framework "anatomy" (e.g. zone boundaries) as well as new dates are constantly being published. More on this below.

Best practices for molecular clock calibrations

Up to this point the discussion has been mostly academic with little application outside paleontology or geology. However, many enterprising biologists have over the past two decades used certain fossils as calibration points for molecular clocks; these clocks, if properly calibrated using paleontological evidence, can provide powerful estimates for the dating of certain nodes on a phylogeny. The problem with all this is that some paleontologists have been notably sloppy in publishing age data for fossils; most biologists are complete novices when it comes to geology, and lack the background to discern whether age data sounds "bullshitty" or not. I won't cite a specific example so as to avoid offending anyone, but here's an example of a bad geologic age determination for an important fossil with specifics modified or omitted: "XXX part of the XXX Formation, middle XXXocene, correlative with the XXX North American Land Mammal age, ca XX-XX Ma (citations of paleontologic papers that didn't actually provide primary age information for the locality)". First off: whenever we see "circa", it means it's an estimate; estimates are fine, so long as they're understood to be such (which means it must be obvious from the text). Secondly, in this case no actual land mammals were found in that unit; the author(s) wished to indicate that the formation in question was thought to be broadly correlative with the XXX NALMA, but not actually based upon any information. The problems with this are twofold: at the time of writing, the author(s) of the paper in question had access to up-to-date papers on the stratigraphy of the unit which actually constrained the time fairly well - and this was either unknown, or simply ignored out of laziness. The second problem is that fairly irrelevant papers were cited. What might a biologist see when reading this, however? If I were a biologist I'd say "look, so and so said this fossil was about 35-37 million years old, I can't really argue with him, so let's go with that." The author in particular regularly publishes papers that do not cite geological papers published after 1990. It sounds silly, but unfortunately this is the state of affairs.

Because of issues like this and other lapses in quality on behalf of certain molecular clock papers - Jim Parham and a huge lot of other authors (2012) published a fantastic paper advocating a set of "best practices" for identifying extinct taxa for molecular clock calibration points. Various studies have failed to identify individual fossil specimens, anatomical criteria (e.g. synapomorphies) for explaining why such fossils were identified as relevant for calibration, the formations they come from, or detailed age and locality information. Without this information, it is not necessarily possible to track down the rationale behind the use of certain criteria - indeed, certain molecular calibration points have even been based upon unpublished fossil specimens (that other researchers are not allowed to see) where the rationale for selection boils down to"one of our coauthors is a paleontologist and this is their opinion". Well, that doesn't sound very repeatable. So, Parham et al. (2012) outlined 5 recommended steps to ensure that a "readily auditable chain of evidence" could be established for each fossil selected as a calibration point. These steps designed by Parham et al. (2012) include:

1) Museum numbers of specimen(s) that demonstrate all the relevant characters and provenance data should be listed. Referrals of additional specimens to the focal taxon should be justified.

2) An apomorphy-based diagnosis of the specimen(s) or an explicit, up-to-date, phylogenetic analysis that includes the specimen(s) should be referenced.

3) Explicit statements on the reconciliation of morphological and molecular data should be given.

4) The locality and stratigraphic level (to the best of current knowledge) from which the calibrating fossil(s) was/were collected should be specified.



5) Reference to a published radiosotopic age and/or numeric timescale and details of numeric age selection should be given.

In retrospect, none of these sound very demanding and are altogether reasonable - points 4 and 5 are italicized because they apply specifically to this topic. In general these "best practices" emphasize repeatability. Last year I published a paper on the baleen whale Herpetocetus from the Pleistocene and included a phylogeny with the stratigraphic ranges of various mysticetes. In order to firmly establish the duration of different mysticete lineages, I spent some time reading the most recent literature and compiled some notes; these notes turned into a supplementary appendix for the paper that included a short (~1 paragraph) justification for each species shown in the cladogram (Boessenecker 2013B: appendix). Altogether this entailed an extra few days of work - well worth it for getting a publication that will hopefully be useful, or at least blatantly transparent.

Dates from the paleontologic and stratigraphic literature

Should we use/read/cite up-to-date stratigraphic literature? It feels asinine to even ask the question. If you answer 'no', you're lazy. Many paleontologists are satisfied with papers published as long ago as the 1960's for stratigraphic information about particular fossil occurrences. Well, one of the great things about paleontology is that we're a small field and because we're a historical science, many early papers will always be relevant, unlike fields such as physics and medicine where some studies may be totally irrelevant and outdated within a decade (or less) of being published. Lets say we wanted to cite the age of some fossil that Cope or Marsh described - we surely wouldn't rely upon a Victorian account of local geology and take Ed or Charles's statement on the matter at face value. Victorian era publications are, effectively by default, outdated in terms of stratigraphic knowledge. Why is that? Could it be, perhaps, that geologists are still poking around hillsides, badlands, coastal cliffs, and roadcuts, collecting ever more data? Last I checked, geology is still a pretty dynamic field (with far more researchers than paleontology, for starters) and hundreds of journals crank out new publications every week. If it makes sense to double check for up-to-date stratigraphy for Victorian-era discoveries, than it follows to do the same for fossils published in the 1960's, 1970's, 1980's, and 1990's. Hell, you should make sure to double check up to date stratigraphy even for something you published a year ago (this week I found out that one of my published age determinations is off by about 0.4 Ma, thanks to an overlooked piece of data). It's not like we don't have magical internet machines and google to find this sort of stuff - it's not that hard to find, thanks to the power of the internet. Parham et al. (2012) eloquently point out that "Any numeric age is merely the best current estimate and can be refined through time." I'll give a series of "what if?" questions and some answers, since there are numerous issues to tackle:

What if a paleo article doesn't cite any geology articles, but gives an estimate of the age?

           Shame on them. Use google, georef, or web of science to search for the formation name. Using what papers you can, try to find stratigraphic data for that locality.

What if I can only find stratigraphic data for a different locality?

            Sometimes this can't be avoided. If it really can't be avoided, make sure to state that available evidence is from a separate locality.

What if I can't find any information about that formation at that locality?

            Stratigraphic terminology has changed a lot, with formations being promoted to Group status or demoted to members, or completely renamed in some cases. For example, the Drakes Bay Formation at Point Reyes in Northern California is now known to actually be three different formations already known from other localities (Santa Margarita Sandstone, Santa Cruz Mudstone, and Purisima Formation). Again, use google; see if papers on regional geology make any reference to nomenclatural changes.

What if the guy who described this fossil said it was Pliocene, but other papers indicate the fossil is Miocene?

            Just like lithostratigraphy, chronostratigraphic stages and boundaries have been modified and refined through time. In many papers published pre-1980, the Pliocene included much of what is now late Miocene. Read the available literature, and use whatever is most careful and up-to-date. Also, use google (again).

What if the paper that reported the fossil reported some sort of new data associated with the fossil?

            Perfect! A best-case scenario as this means the separation between the fossil and geologic data is minimized. In this case, please cite whatever data they report. If biostratigraphic data is involved, double check that that zone is still in use. Also, in the case of diatom biochronology in the North Pacific, the names of different zones have changed; they used to have roman numerals (I, II, III etc.) but in the 1980's were switched to taxon-range and concurrent-range zones using the names of the various diatom species.

What if the aforementioned example is sort of old?

            Then you should double check the biostratigraphic literature to see if refinements have been made to the boundary dates and zone definitions. If an absolute date is involved, it may be prudent to recalculate the age using updated constants. Personally I don't feel qualified to do this myself, but for my personal research purposes most of the absolute dates I've cited are less than a decade old or have already been recalculated by others. Refinements in radiometric dating methods mean that old dates ought to be updated.

What if age data is available only at the level of the formation?

            It happens unfortunately - sometimes a given unit is not well studied and lacks internal age determinations, and perhaps the formation corresponds to a single biozone or magnetic chronozone, or has a date from the top and base. Well, there's not much else you can do other than accept formation-level data; sometimes it's not a big deal as many units are thin and record a short period of time - but you're a bit hosed if it's a long-duration unit like the Monterey Formation.

What if the locality is virtually unstudied, but the author said it was a certain epoch?

            This is sort of an almost worse case scenario, but for some poorly studied localities, perhaps "Pliocene" (or better yet a stage, like "Maastrichtian") is all you're going to get; in that case, you can use the known age boundaries for the epoch (or other period of time). Often the original author doesn't have a hope in hell of knowing exactly how old it is, but this is still defensible as we're leaving a "citation trail".

What if I got these neat dates off of the Paleobiology Database?

            Much of the other concerns listed above apply to dates from the PBDB. Read the following section.

What if I’m putting together an analysis that requires “binning” of age data for different taxa into interval time bins? I’ve already binned it so I might as well use the binned age data for reporting the actual age (e.g. in a figure showing lineage ranges or a time-calibrated phylogeny showing lineage duration).

For heaven’s sakes don’t do that either! Binning is great for paleobiologic analyses of diversity data, but why bother with converting the real age data into something less accurate? Let’s say, for example, that you have an unusually long time bin, based on a long stage: a lineage that ends at the beginning of the time bin and another lineage that begins at the end of the time bin, but do not actually overlap in time would be assigned the same time bin. Based upon the modified data, this would artificially make it appear that the two taxa lived at the same time. Although technically defensible as it can be applied consistently, we should be reporting the actual geochronologic age of particular fossils.

Should I publish citations of which stratigraphic articles I looked at, so that the reader can tell the difference between the citation for the fossil occurrence and the geologic age if they come from different papers?

An emphatic YES! This should always be done so as not to leave the reader guessing (guessing ≠
science). Here are two examples of how you can organize such data.


This is just a tiny part of an enormous table I put together for my 2013 Geodiversitas paper. Geochronologic ages are frequently derived from non paleontological sources. From Boessenecker (2013A).


In this case the table includes hard dates for fossil occurrences where the paleontologists provided reasonable dates, and one exception where several sources are cited thanks to refinements in stratigraphy. From Churchill et al. (2014).


To wrap up this section, I'll include another quote from Parham et al. (2012) that explains the point behind all this: "Anatomically trained fossil systematists may not be able to retrieve [geologic age] data any more easily than molecular systematists, but by listing the specimen numbers, rock units, and ages in a standardized way, others may check the claim, thus facilitating the refinement of numeric dates over time."

Pitfalls of the PaleoBiology Database

The PBDB is an excellent reservoir of data, and is used frequently for analyses of diversity and paleobiogeography. For the uninitiated, the PBDB is a database recording various types of data directly from the paleontological literature, foremost of which are geochronologic age and the taxonomic identification of fossil occurrences. The problem with dates provided by the PBDB is that the quality is only as high as the investment by the data enterer: most fossil occurrences just use the date from the original article the data is taken from. In some rare cases primary stratigraphic literature is cited; rarer yet are cases where unpublished stratigraphic data are supplied.

Because the PBDB is just an aggregator of data – data primarily from the paleontological (rather than stratigraphic) literature – it suffers from many of the same problems I’ve already discussed earlier. In addition to possessing these limitations, it also suffers from having outdated age determinations – including the shift in recognition of the Miocene-Pliocene boundary from ~12 Ma to 5.33 Ma, and also recording dates from old paleontological articles that cited stratigraphic works that are long out of date. Because of the lack of double-checking the stratigraphic literature, most of the age data on the PBDB should be assumed to be as accurate to the time at which the article was published. Another issue is binning: unless pinpointed dates are given in a paleontological article, if a stage or epoch was given – hard numbers for the boundaries are given. This is not necessarily a problem because I advocate that above (e.g. so and so said the fossil is “Pliocene”, so the fossil is assigned an age of 5.33-1.81 Ma). However, it’s important to evaluate the manner in which age was determined for each occurrence. I strongly recommend that age data from the PBDB be double checked using the stratigraphic literature. Much of the PBDB is “reasonably” accurate, but reidentifications in the literature are not always recorded accurately – which will affect age ranges. I don’t expect PBDB data enterers to bother with the stratigraphic literature as it would multiply the amount of work involved tenfold – but if someone is serious about getting accurate ages for fossils, the PBDB is an excellent tool and a great bibliography, but should not be accepted at face value.

Suggested Methodology

1) Familiarize yourself with the stratigraphic literature for a given fossil occurrence. Old paleontological publications are almost guaranteed to require citations of more recent stratigraphic studies (and many do a piss-poor job of even citing current geological work at the time of publication!).

2) Double check that subsequent paleontological papers have not reidentified the fossil in question. Is it really a fossil of the walrus Pontolis, or is it an Imagotaria?

3) If the age of a fossil occurrence was given using biostratigraphic zones, they are probably out of date! Find the most up to date zone boundary ages available in the literature. Similarly, old radiometric dates can (and should) be recalculated (although often these dates can be found recalculated in more recent geological literature).

4) Justify the geochronologic age range that is being reported. Now that you’ve read the stratigraphic literature, cite it! Other researchers need to know how you arrived at your age determination – as Parham et al. (2012) stated, a readily auditable chain of evidence” is the goal. At the bare minimum, at least include a table showing a citation for the fossil occurrence (primary paleontologic literature) and a citation for the geochronologic age from the best source possible (occasionally within paleontologic literature, but most often from the stratigraphic literature). The distinction between the two is very important! If age data are important to your study, then an appendix with a short description of the occurrences and age - filled with both of the aforementioned citation types – is a good idea.

5) Always vet fossil occurrences on the PBDB in a similar manner as you would for published occurrences.

References

Boessenecker, R.W. and N.A. Smith. 2011. Latest Pacific basin record of a bony-toothed bird (Aves, Pelagornithidae) from the Pliocene Purisima Formation of California, U.S.A. Journal of Vertebrate Paleontology 31(3):652-657.


Boessenecker, R.W. 2013. A new marine vertebrate assemblage from the Late Neogene Purisima Formation in Central California, Part II: Pinnipeds and Cetaceans. Geodiversitas 35:4:815-940.

Boessenecker, R.W. 2013. Pleistocene survival of an archaic dwarf baleen whale (Mysticeti: Cetotheriidae). Naturwissenschaften 100:4:365-371.


Churchill, M.M., Boessenecker, R.W., and Clementz, M. 2014. Colonization of the Southern Hemisphere by fur seals and sea lions (Carnivora: Otariidae), revealed by combined evidence phylogenetic and Bayesian biogeographic analysis. Zoological Journal of the Linnean Society 172:200-225.

Owen, D.E. 2009. How to use stratigraphic terminology in papers, illustrations, and talks. Stratigraphy 6:106-116.

Parham, J.F., and many other authors. 2012. Best practices for justifying fossil calibrations. Systematic Biology 61:346-359.

Powell, C. L., II, J. A. Barron, A. M. Sarna-Wojcicki, J. C. Clark, F. A. Perry, E. E. Brabb, and R. J. Fleck. 2007. Age, stratigraphy, and correlation of the late Neogene Purisima Formation, central California coast ranges. U.S. Geological Survey Professional Paper 1740:1–32.