Andrew Du

Holocene shifts in the assembly of plant and animal communities implicate human impacts.

Understanding how ecological communities are organized and how they change through time is critical to predicting the effects of climate change. Recent work documenting the co-occurrence structure of modern communities found that most significant species pairs co-occur less frequently than would be expected by chance. However, little is known about how co-occurrence structure changes through time. Here we evaluate changes in plant and animal community organization over geological time by quantifying the co-occurrence structure of 359,896 unique taxon pairs in 80 assemblages spanning the past 300 million years. Co-occurrences of most taxon pairs were statistically random, but a significant fraction were spatially aggregated or segregated. Aggregated pairs dominated from the Carboniferous period (307 million years ago) to the early Holocene epoch (11,700 years before present), when there was a pronounced shift to more segregated pairs, a trend that continues in modern assemblages. The shift began during the Holocene and coincided with increasing human population size and the spread of agriculture in North America. Before the shift, an average of 64% of significant pairs were aggregated; after the shift, the average dropped to 37%. The organization of modern and late Holocene plant and animal assemblages differs fundamentally from that of assemblages over the past 300 million years that predate the large-scale impacts of humans. Our results suggest that the rules governing the assembly of communities have recently been changed by human activity.Understanding how ecological communities are organized and how they change through time is critical to predicting the effects of climate change. Recent work documenting the co-occurrence structure of modern communities found that most significant species pairs co-occur less frequently than would be expected by chance. However, little is known about how co-occurrence structure changes through time. Here we evaluate changes in plant and animal community organization over geological time by quantifying the co-occurrence structure of 359,896 unique taxon pairs in 80 assemblages spanning the past 300 million years. Co-occurrences of most taxon pairs were statistically random, but a significant fraction were spatially aggregated or segregated. Aggregated pairs dominated from the Carboniferous period (307 million years ago) to the early Holocene epoch (11,700 years before present), when there was a pronounced shift to more segregated pairs, a trend that continues in modern assemblages. The shift began during the Holocene and coincided with increasing human population size and the spread of agriculture in North America. Before the shift, an average of 64% of significant pairs were aggregated; after the shift, the average dropped to 37%. The organization of modern and late Holocene plant and animal assemblages differs fundamentally from that of assemblages over the past 300 million years that predate the large-scale impacts of humans. Our results suggest that the rules governing the assembly of communities have recently been changed by human activity.

Ecological fidelity of functional traits based on species presence- absence in a modern mammalian bone assemblage (Amboseli, Kenya)

Abstract Comparisons between modern death assemblages and their source communities have demonstrated fidelity to species diversity across a variety of environments and taxonomic groups. However, differential species preservation and collection (including body-size bias) in both modern and fossil death assemblages may still skew the representation of other important ecological characteristics. Here, we move beyond live-dead taxonomic fidelity and focus on the recovery of functional ecology (how species interact with their ecosystem) at the community level for a diverse non-volant mammal community (87 species; Amboseli, Kenya). We use published literature to characterize species, using four functional traits and their associated categorical attributes (i) dietary mode (11 attributes; e.g., browser, grazer), (ii) preferred feeding habitat (16 attributes; e.g., grassland, woodland), (iii) preferred sheltering habitat (17 attributes; e.g., grassland, underground cavity), and (iv) activity time (7 attributes; e.g., diurnal, nocturnal, nocturnally dominated crepuscular). For each functional ecological trait we compare the death assemblages recovered richness and abundance structure of constituent functional attributes with those of the source community, using Jaccard similarity, Spearmans rho, and the Probability of Interspecific Encounter (evenness). We use Monte Carlo simulations to evaluate whether these empirical comparisons are significantly different from expectations calculated from randomized sampling of species from the source community. Results indicate that although the Amboseli death assemblage is significantly overrepresented by large-bodied species relative to the Amboseli source community, it captures many functional dimensions of the ecosystem within expectations of a randomized collection of species. Additional resampling simulations and logistic regressions further illustrate that the size bias inherent to the Amboseli death assemblage is not a major driver of deviations between the functional ecological properties of the death assemblage and its source community. Finally, the Amboseli death assemblage also enhances our understanding of the mammal community by adding nine species and two functional attributes previously unknown from the ecosystem.

Pleistocene footprints show intensive use of lake margin habitats by Homo erectus groups

Reconstructing hominin paleoecology is critical for understanding our ancestors’ diets, social organizations and interactions with other animals. Most paleoecological models lack fine-scale resolution due to fossil hominin scarcity and the time-averaged accumulation of faunal assemblages. Here we present data from 481 fossil tracks from northwestern Kenya, including 97 hominin footprints attributed to Homo erectus. These tracks are found in multiple sedimentary layers spanning approximately 20 thousand years. Taphonomic experiments show that each of these trackways represents minutes to no more than a few days in the lives of the individuals moving across these paleolandscapes. The geology and associated vertebrate fauna place these tracks in a deltaic setting, near a lakeshore bordered by open grasslands. Hominin footprints are disproportionately abundant in this lake margin environment, relative to hominin skeletal fossil frequency in the same deposits. Accounting for preservation bias, this abundance of hominin footprints indicates repeated use of lakeshore habitats by Homo erectus. Clusters of very large prints moving in the same direction further suggest these hominins traversed this lakeshore in multi-male groups. Such reliance on near water environments, and possibly aquatic-linked foods, may have influenced hominin foraging behavior and migratory routes across and out of Africa.

The measurement of taxonomic evenness in zooarchaeology

Zooarchaeologists frequently measure taxonomic evenness to document subsistence change and to understand the response of faunal communities to paleoenvironmental change. Although the measurement of evenness is commonplace, there are numerous challenges involved. Evenness indices are sensitive to changing richness, and by extension sample size, and various indices respond differently to changing taxonomic abundances (i.e., changing evenness). To refine protocol for comparing assemblages of varied sampling effort and identify indices that may be more useful for zooarchaeological applications, we examine the quantitative behavior of the widely used Shannon evenness and Simpson indices and two others more commonly used by ecologists. These indices are examined in relation to varied richness, sample size, and taxonomic abundances. We show that although zooarchaeologists are concerned with identifying and correcting for the effects of sample size on evenness, it may be appropriate to instead focus on how richness modulates evenness. Based on our analyses, we recommend the Simpson index for most zooarchaeological applications, except when comparing evenness across assemblages that are very even.

Pattern and process in hominin brain size evolution are scale-dependent

A large brain is a defining feature of modern humans, yet there is no consensus regarding the patterns, rates and processes involved in hominin brain size evolution. We use a reliable proxy for brain size in fossils, endocranial volume (ECV), to better understand how brain size evolved at both clade- and lineage-level scales. For the hominin clade overall, the dominant signal is consistent with a gradual increase in brain size. This gradual trend appears to have been generated primarily by processes operating within hypothesized lineages—64% or 88% depending on whether one uses a more or less speciose taxonomy, respectively. These processes were supplemented by the appearance in the fossil record of larger-brained Homo species and the subsequent disappearance of smaller-brained Australopithecus and Paranthropus taxa. When the estimated rate of within-lineage ECV increase is compared to an exponential model that operationalizes generation-scale evolutionary processes, it suggests that the observed data were the result of episodes of directional selection interspersed with periods of stasis and/or drift; all of this occurs on too fine a timescale to be resolved by the current human fossil record, thus producing apparent gradual trends within lineages. Our findings provide a quantitative basis for developing and testing scale-explicit hypotheses about the factors that led brain size to increase during hominin evolution.

Homo erectus paleoecology and behavior based on 1.5 million year old footprints from northwestern Kenya

Leprosy is one of the few specific infectious diseases that can be studied in bioarchaeology due to its characteristic debilitating and disfiguring skeletal changes. Leprosy has been, and continues to be, one of the most socially stigmatising diseases in history, over-riding all other aspects of social identity for the sufferers and frequently resulting in social exclusion. This study examines the stable isotopic evidence of mobility patterns of children, adolescents, and young adult individuals with the lepromatous form of leprosy in Medieval England (10 th –12 th centuries AD) to assess whether the individuals buried with the disease were non-locals, possibly from further afield. Enamel samples from 19 individuals from the St. Mary Magdalen Leprosy Hospital, Winchester (UK) were selected for strontium ( 87 Sr/ 86 6U DQG R[\JHQ į 18 O) stable isotope analysis based on age at death (<30 years), the presence of bone changes associated with lepromatous leprosy, and the underlying geology of their burial locations. The results from these data indicate that the St. Mary Magdalen Leprosy Hospital received an almost equal mixture of local and non-local individuals from further afield, including early pilgrims. At present, the St. Mary Magdalen Leprosy Hospital is the earliest dedicated leprosaria found within Britain and mobility studies such as these can help elucidate and test some of the broader historical notions and identities associated with the movements of those infected with the disease in Medieval England.

How foreign is the past? Reply

Since Humboldt and Darwin, ecologists have puzzled over what determines community assembly and structure and how community structure may change with time. Human activity is one potential driver. Impacts of modern human societies on the environment and its biota are massive, with many forms of pollution, loss and fragmentation of habitats, and extensive introductions of exotic species changing many ecological and biogeographical patterns. Prehistoric societies might be expected to have had a much lower impact on their environment. However, Lyons and colleagues1 propose that plant and mammal assemblages are so fragile that the limited settlements, agriculture, and associated activities 6000 years ago in North America were sufficient to fundamentally change community-assembly rules. They base this conclusion on temporal patterns in the proportion of aggregated taxon-pairs in species presence-absence data-sets from the past 300 million years. We demonstrate that their conclusions result from the use of inappropriate modern data-sets and from biases when detecting segregated taxon-pairs in different sized data-sets. Lyons et al. analysed co-occurrence patterns between taxon pairs in 71 fossil (age 307 Myr – 100 yr) and 9 recent (<100 yr) presence-absence assemblages using an empirical Bayes approach2 that classifies each taxon-pair as random, aggregated, or segregated. Lyons et al. supplemented their analyses by including 39 modern ‘mainland’ data-sets, and 59 ‘island’ data-sets in some analyses. 2

The effects of craniodental sampling on ecological variables in modern and fossil mammal landscape assemblages

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