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Natural History Collections for future Ecosystems

Last week a bunch of the natural science curators here at the Illinois State Museum presented a poster at a small conference (downloadable PDF here). Normally, a conference poster isn’t a big deal or all that unique, but this may be a first. The theme of this year’s conference was “Taking stock before the connection” and was concerned with establishing accurate and relevant ecological baselines as goals for conservation activities. This isn’t the sort of conference you would normally see studies of zooarchaeological specimens or deer paleopathology, but this year we decided it was time to illustrate the relevance of ISM natural history collections to modern conservation biology.

We aren’t the first to do this. Different disciplines, typically considered the more “historic” sciences like archaeology and paleontology, have been working on these issues for at least a decade. In paleontology this approach is called “Conservation Paleobiology”, in archaeology it’s called “Applied Paleozoology”. Both approaches are very similar to the backwards looking “historical ecology” that goes hand in hand with restoration ecology.  Practitioners of all these disciplines agree that in order to understand the wide range of variability in modern ecosystems, we need an understanding of processes and patterns that go deeper than the historical record. Let’s face it. The picture of historical ecological patterns we get from early Euro-American explorers or early settlers capture a snapshot in time that is not very representative of the larger picture. By the time these early chroniclers were traipsing across the Midwest and Great Plains, pre-contact ecosystems had already been largely altered or even obliterated. Horses were introduced by the Spanish in the late 1500s and by the 17th century had expanded throughout the western US. By the time fur traders first contacted Native groups in the eastern Great Plains, epidemics of European diseases had already decimated their communities. Before the first settlers built rough cabins in what is today central Illinois, years of warfare and genocide had reduced the human footprint to the point that the vegetation in many parts of the Midwest were released from human utilization and in successional stages.  These are just a few examples of large-scale ecological changes brought about by the changes in the human landscape at contact. This begs the question often asked by planners prior to making decisions, what is the ecological baseline that should be the goal for conservation efforts? In many cases, these planners now recognize that there is no single baseline. No single date that we can point to and say, “this is the natural state”. Modern landscapes can be managed to provide basic ecosystem functions, or as one author puts it, “goods and services”. But what were those goods and services in pre-modern ecosystems? Are there metrics that we can use to document BOTH the modern and pre-modern to gauge which management schemes are appropriate? That was what we set out to do with this presentation. We presented five case studies that illustrate possible ways that paleoecological research on natural history collections (i.e., Paleontology, Archaeology, Botany, Zoology) can offer direct advice and specific answers to modern conservation science.

Case Study #1: Niche Characterization of North American Bison (C. Widga, T. Martin, A. Harn)

During the last 10,000 years, bison were a keystone herbivore in grassland ecosystems. They performed vital functions in nutrient cycling, vegetation succession and predator/prey dynamics. Bison were also present east of the Mississippi River in the eastern forests. The earliest record for bison in Illinois is ~8900 BP and sporadic records persist into the historic period (McMillan, 2006). Notable localities include: Anderson and Markman Peat Mines (Whiteside Co., ~3000-8900 BP), Ottawa Silica Co. (LaSalle Co., 4300 BP), and Lonza-Caterpillar (Peoria Co., 2300 BP)(Figure 3). Unfortunately, most historical documents describing bison date to a time period when ecosystems were rapidly changing. For a variety of reasons (e.g., changing human land-use), the historic record of bison is not analogous to the pre-modern baseline. Indeed, historical documents illustrate bison as seasonally mobile large herds, a picture that is completely incongruous with paleoecological patterns. Sub-fossil bison specimens archive valuable paleoecological information on how bison lived in the Midwest.

In habitats dominated by short or mid-grass prairies, the cusps of bison teeth show flat wear by age 5-6 years. This is due to a high silica (i.e., grasses), high grit diet. However, pre-contact bison from the Midwest show a shearing wear pattern in cheek teeth (Figure 2). This pattern is present in herbivores who are browsers or mixed feeders from closed or partially closed habitats (e.g., deer, elk). Stable isotope data also indicate a diet dominated by C3 plants (i.e., shrubs, trees, sedges), despite the prevalence of tallgrass prairie (C4 dominant) in upland habitats (Widga, 2006).

Although large bison assemblages of 100+ animals are present during the early Holocene in the Great Plains, the smaller sizes of the eastern Plains assemblages are consistent with small-scale, temporary social groups that have been documented in modern conservation herds. The maximum herd size for midwestern bison assemblages is ~20 (Simonsen Site, NW Iowa). Other midwestern assemblages in MN, WI, and IL are smaller than this maximum. Females contributed less to overall herd populations in the archaeological assemblages than in modern herds, suggesting that managed sex ratios in the latter are uncommon in prehistoric bison groups (Figure 4). Although there may be economic and safety reasons for maintaining high numbers of females, these sex ratios should not be considered characteristic of natural variability in pre-contact bison herds. Furthermore, many modern herds maintain large juvenile populations (<4 years old), often approaching or exceeding half of the overall herd size. None of the archaeological assemblages contain more than a handful of juveniles.

Bison in the Midwest were ecologically distinct from their counterparts on the Great Plains. The pre-modern bison niche in Illinois can be characterized as small, local herds browsing shrubs and woody vegetation along river valleys.

Case Study #2: Baseline Expectations for the Distribution of Illinois Carnivores (M. Mahoney, E. Grimm)


Mountain lion (Puma concolor), gray wolf (Canis lupus), and American black bear (Ursus americanus) suffered sizeable reductions in distribution over the past 250 years when they were eradicated from much of eastern North America (Whitaker and Hamilton, 1998). All three species were extirpated from Illinois by 1870 (Hoffmeister, 1989). Today, large carnivore populations in many regions are healthy and increasing in size due to a combination of factors including species-specific protections at the state and federal level, protection of habitat, and regulation of hunting.

Two of these three apex predators are occasional migrants into Illinois (Figs. 1 and 2) and the third is likely to appear soon. It is a matter of time before they establish populations in Illinois as they expand from other parts of their ranges. What was the former distribution of these species in Illinois? What habitats are available today? Can we use past distributions to either predict where they might become established or to restore appropriate habitat types?

Historical records provide limited information on the distribution of large carnivores in Illinois as encountered by explorers, trappers, and early settlers and mostly serve to document the last known localities of large carnivores before their extirpation from Illinois in the mid-1800s (Hoffmeister, 1989, Fig. 2). These records have other known weaknesses. For example, mountain lion and bobcat (Lynx rufus) were not reliably distinguished until the early 1800s and wolves and coyotes were often conflated even after wolves were extirpated (Hoffmeister, 1989).

The Neotoma Paleoecology Database is an online resource for fossil and archeological site and sample information. It is a freely searchable compilation of datasets from numerous researchers and institutions. The primary components are fossil mammal (FAUNMAP) and North American pollen (NAPD) including data from sites spanning the last 5 million years. The Neotoma data (Fig. 3) expand our knowledge of the range of apex carnivores in Illinois both geographically and over time.

Bear is reported from over 40 Late Holocene localities (0-3500 BP). Wolf records (N=30) extend further south in Illinois than historical records indicate and some sites date to over 6000 BP. There are fewer mountain lion records (N=12), but they are widespread and occur up to 4000 BP. One intriguing result is the substantial overlap in site occurrences between gray wolf and black bear. Mountain lion co-occurs with bear at a few sites, and not at all with wolf. These data provide information on species’ occurrence over a deeper time span than is possible from historical records. This gives insight into the presence of animals on the landscape prior to and during past ecological changes, both natural and human mediated.

Case Study #3: Resilience of Deer to Traumatic Limb Injuries (T. Martin, D. Lawler)

Investigations of large archaeological faunal assemblages often reveal unique incidences of animal pathology. Although interesting as curiosities, pathological specimens can disclose insights on past animal populations and the human groups that were exploiting these animals. Four specimens from the Fort St. Joseph (20BE23) and Fort Ouiatenon(12T9) sites illustrate incidences of trauma suffered by white-tailed deer (Odocoileus virginianus) at eighteenth-century trading posts that were inhabited by French settlers and their Native American wives and trading partners. Gross examination and application of x-ray radiography and micro-computed tomography shows a pattern of severely broken front legs on individual deer that survived their initial injuries long enough to permit bone healing and remodeling before the deer ultimately became the victims of Native American or French hunters. Specifically, environmental sheltering from predation, food and water availability in immediate surroundings, and fractured bone ends in reasonable apposition could accomplish functional healing through the downward pull of gravity, heavy limb weight, and limited movement. Individual diagnoses can reveal details about the traumatic injury, malnutrition, and/or infections, and the resiliency of the animal in surviving injuries that initially might be considered to be fatal.

Case Study #4: Pre-Modern Fisheries and Aquatic Ecosystems (B. Styles, T. Martin, M. Wiant)

Although wetland ecologists draw on a variety of modern and historical resources to achieve conservation goals, many system-altering events occurred prior to documentation. The Illinois River and its flood plain were dramatically transformed between 1870 and 1930 by the construction of locks and dams, levees, and the Sanitary and Ship Canal. Drawing on a long-term Illinois River valley archaeological research program, zooarchaeologists have acquired a deep-time perspective on changes to terrestrial and aquatic ecosystems.

A total of 59 fish species have been recorded from four Illinois valley archaeological sites. However, only 12 species, Buffalo, Redhorse sucker, Black and Brown bullheads, Channel catfish, Bass, Sunfish, Bowfin, Gar, Freshwater drum, Northern Pike, and Pike spp., were found in every assemblage. Analysis of proportional data based on the Minimum Number of Individuals indicates that a few species dominate the combined assemblage (Figure 1). These include: Black bullhead, Indeterminate catfish, Bowfin, and Gar, each of which accounts for more than 20% of the total number of individuals. All of these species are common in Illinois River floodplain backwater lakes. However, it is difficult to discern whether this particular distribution represents food preference, the exploitation of particular habitats with specific technology, or some combination thereof.

Case Study #5: Freshwater Mussel Fauna in the Illinois River Basin, Compositional Variation and Change (R. Warren)

Malacologists have compiled invaluable lists of freshwater mussel species native to the Illinois River Basin based on museum collections and historical records. However, lists alone tell us little about the compositions and habitat associations of mussel communities before they were transformed by dam construction and other human impacts during the 19th and 20th centuries. This study uses archaeological shell collections to explore compositional variation among native mussel communities in the Illinois Basin, and to develop a proxy baseline for looking at the magnitude of compositional change in modern mussel faunas. The archaeological material includes 49 shell samples from 30 archaeological sites (Figure 1). The samples represent prehistoric and historic Native American mussel collections that were deposited in village or mortuary contexts. They range in age from 200-9500 BP, although most date to the late Holocene (<2000 BP). Fifty species occur in the total sample of 29,407 identified specimens.

In the archaeological samples, species diversity increases downstream in the Illinois Basin. Species composition is highly variable in the basin as a whole. In most samples the leading dominant species is either the threeridge (Amblema plicata) or the spike (Elliptio dilatata), but five other species predominate in at least one sample. A multivariate ordination of abundance data using detrended correspondence analysis (DCA) orders samples and species along two principal axes of variation (Figure 2). Correlations of sample DCA coordinates with independent environmental variables, mussel habitat scores, and proportions of modified shell indicate that compositional variation reflects (1) down-valley geographical differences among mussel communities, (2) local access to an array of aquatic habitats (large river, creeks, and backwater lakes and sloughs), and (3) cultural selection, in a few cases, of certain species as raw material for creating shell artifacts (Figure 3).

Analysis of mussel samples likely gathered from the Illinois River mainstem shows evidence of community variability and habitat associations that are missing in modern mussel faunas. Samples dominated by the spike (E. dilatata) and mucket (Actinonaias ligamentina) are indicative of a shallow large river with coarse substrate, whereas samples dominated by the threeridge (A. plicata) are indicative of a deeper large river with fine substrate. Shoal habitats are indicated not just in the upper Illinois River, which was historically infamous for its dangerous rapids, but also in the central and lower sections of the valley where reaches of deeper water also occurred. A 1960s mussel survey of the river showed a significant decline in species diversity during the 20th century, when about half of the species were extirpated. Baseline data from the archaeological model indicate there was also a narrowing of mussel community variability and a constriction of habitat associations. These changes may be related to historical human impacts on the stream including pollution, sedimentation, and dam construction.

Suggested Reading

Dietl, G. P., & Flessa, K. W. (2011). Conservation paleobiology: putting the dead to work. Trends in Ecology & Evolution26(1), 30-37.

Hoffmeister, D. F. (1989). Mammals of Illinois. Urbana: University of Illinois Press.

Jackson, S. T., & Hobbs, R. J. (2009). Ecological restoration in the light of ecological history. Science325(5940), 567.

McMillan, R. B. (2006). Perspectives on the biogeography and archaeology of bison in Illinois. In: Records of Early Bison in Illinois, R. B. McMillan, editor, pp. 67-147. Illinois State Museum Scientific Papers 31. Springfield.

Whitaker, J. O., & Hamilton, W. J. (1998). Mammals of the eastern United States. Cornell University Press.

Widga, C. (2006). Niche variability in late Holocene bison: a perspective from Big Bone Lick, KY. Journal of archaeological science33(9), 1237-1255.

Wolverton, S., & Lyman, R. L. (Eds.). (2012). Conservation biology and applied zooarchaeology. University of Arizona Press.

Fossils in the round: 3D scanning and printing

Dunlap Canis dirus

This 3D model was rendered from a CT scan. The original specimen was recovered by W.D. Frankforter in 1959 near Dunlap, IA and is in the collection of the Sanford Museum and Planetarium, Cherokee, IA.

Note: It is January 2014 and this blog has been sitting stagnant for quite awhile. Over the next few months, I have a number of posts planned. Most are about the paleontology/paleoecology of Ice Age mammals, but I’m planning a few that will focus on methods and documentation–especially for the amateur community. So stay tuned!

A few weeks ago, this article appeared in the Springfield Journal Register. I thought it was a very good article–evidently my head even made it “above the fold” on the front page (which I’m told is a good thing). I’m always surprised at the “big deal” factor of 3D. Yes, some of it may be because the technology is coming down in price, and the free and open source (FOSS) software resources are out there–and very good. But part of me hopes that it is something bigger, a profound change in the way we think about museum objects and who has access to them.

For my part, thinking in 3D is simply an extension of what we’ve always done. Bone morphology (size and shape) is the bread and butter of most paleontologists. We are always trying to tease out the reasons why a bone is this species rather than that species, and 99% of the time, the answer hinges on its shape. The new 3D technologies are making this easier. So we’ve been scanning specimens from our collections–almost constantly–for the last few months. Everything from Dire Wolves, to Tully Monsters, Mastodon feet to trilobites. At this stage, we’re still in the “let’s see how this works” phase, but soon, perhaps very soon, we’re hoping to put many of these 3D models on the web. We’re in good company here. The Smithsonian released a number of 3D scans that can be found here, including a very nice woolly mammoth (it is 3D printer ready!). We’re almost there.

But why would a person want to 3D print a mastodon foot? How might scanned museum specimens be useful to, well, everybody else? Museums have been in the replicating business for a long time. We mold and cast our most significant specimens so they can be shared with researchers and other museums. However, this “analog” way to replicate fossils was sometimes imprecise, and definitely required quite a bit of skilled time and labor. For a number of years, we made mastodons and ground sloths to order. They weren’t cheap, and they were never a money-making proposition. But they provided a valuable service to museums that were not as rich in collections as we are.

Fast forward to the 21st century. Awhile back we reported a very interesting saber-toothed cat find in southeastern Minnesota Cave (see a great blog post on it here). The Minnesota Karst Conservancy, who owns the cave (and therefore the fossils) preferred that the fossils stay in the state. So after our analysis is complete, they will be returned to the Science Museum of Minnesota where an exhibit awaits. Because we spent a lot of time analyzing these materials, I wanted to retain casts here at the Illinois State Museum. In the future, when researchers visit to look at other similar specimens, they can at least capture basic measurements on fossils from this locality. When it came time to discussing making casts of the major bones, it soon became clear that a traditional mold/cast would sacrifice detail and be very labor intensive. Being the sort of person who likes to avoid hard work for the sake of work, I started dreaming up alternatives. Ultimately, we scanned most of the major bones in a CT scanner at a local hospital. The resulting images could be rendered as a 3D model and printed on a 3D printer at MAD Systems in CA (here).

Left: 3D print of Homotherium skull from Tyson Spring Cave, MN. Right, original.

Left: 3D print of Homotherium skull from Tyson Spring Cave, MN. Right, original.

But that’s not the only reason to 3D print things. A physical object can be manipulated and examined in ways that photos cannot. Our current scanning efforts have focused on the most significant fossils in our collections, including: some of North America’s earliest dogs (Koster Site, Greene Co., IL) and the continent’s largest Mastodont (from Boney Spring, MO). It is our job to see that the public benefit and learn from our collections. That they don’t sit on a shelf, forgotten. The more people that can enjoy these objects for themselves, the better!

Where are we going with this technology? We’re not entirely sure yet. Certainly, we will integrate this into ongoing efforts to digitize our collections. We will work 3D models into our outreach and education activities. Will there be more? Undoubtedly. Stay tuned to our FB page and the Think3D website for new developments!

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