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@article{Safi2013a,
abstract = {Background Conservation of phylogenetic diversity allows maximising evolutionary information preserved within fauna and flora. The “EDGE of Existence” programme is the first institutional conservation initiative that prioritises species based on phylogenetic information. Species are ranked in two ways: one according to their evolutionary distinctiveness (ED) and second, by including IUCN extinction status, their evolutionary distinctiveness and global endangerment (EDGE). Here, we describe the global patterns in the spatial distribution of priority ED and EDGE species, in order to identify conservation areas for mammalian and amphibian communities. In addition, we investigate whether environmental conditions can predict the observed spatial pattern in ED and EDGE globally. Methods and Principal Findings Priority zones with high concentrations of ED and EDGE scores were defined using two different methods. The overlap between mammal and amphibian zones was very small, reflecting the different phylo-biogeographic histories. Mammal ED zones were predominantly found on the African continent and the neotropical forests, whereas in amphibians, ED zones were concentrated in North America. Mammal EDGE zones were mainly in South-East Asia, southern Africa and Madagascar; for amphibians they were in central and south America. The spatial pattern of ED and EDGE was poorly described by a suite of environmental variables. Conclusions Mapping the spatial distribution of ED and EDGE provides an important step towards identifying priority areas for the conservation of mammalian and amphibian phylogenetic diversity in the EDGE of existence programme.},
author = {Safi, Kamran and Armour-marshall, Katrina and Baillie, Jonathan E M and Isaac, Nick J B},
doi = {10.1371/journal.pone.0063582},
file = {:Users/Ty/Documents/Mendeley Desktop/Safi et al.{\_}2013{\_}Global Patterns of Evolutionary Distinct and Globally Endangered Amphibians and Mammals.PDF:PDF},
journal = {PLoS ONE},
number = {5},
pages = {e63582 -- e63582},
title = {{Global Patterns of Evolutionary Distinct and Globally Endangered Amphibians and Mammals}},
url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0063582},
volume = {8},
year = {2013}
}
@article{Bowles2011,
abstract = {Did foragers become farmers because cultivation of crops was simply a better way to make a living? If so, what is arguably the greatest ever revolution in human livelihoods is readily explained. To answer the question, I estimate the caloric returns per hour of labor devoted to foraging wild species and cultivating the cereals exploited by the first farmers, using data on foragers and land-abundant hand-tool farmers in the ethnographic and historical record, as well as archaeological evidence. A convincing answer must account not only for the work of foraging and cultivation but also for storage, processing, and other indirect labor, and for the costs associated with the delayed nature of agricultural production and the greater exposure to risk of those whose livelihoods depended on a few cultivars rather than a larger number of wild species. Notwithstanding the considerable uncertainty to which these estimates inevitably are subject, the evidence is inconsistent with the hypothesis that the productivity of the first farmers exceeded that of early Holocene foragers. Social and demographic aspects of farming, rather than its productivity, may have been essential to its emergence and spread. Prominent among these aspects may have been the contribution of farming to population growth and to military prowess, both promoting the spread of farming as a livelihood.},
author = {Bowles, Samuel},
doi = {10.1073/pnas.1010733108},
file = {:Users/Ty/Documents/Mendeley Desktop/Bowles{\_}2011{\_}Cultivation of cereals by the first farmers was not more productive than foraging.pdf:pdf},
isbn = {0027-8424},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
number = {12},
pages = {4760--4765},
pmid = {21383181},
title = {{Cultivation of cereals by the first farmers was not more productive than foraging}},
url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3064343/{\%}5Cnhttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC3064343/pdf/pnas.201010733.pdf},
volume = {108},
year = {2011}
}
@incollection{Nunn2006,
abstract = {Anthropologists and archaeologists increasingly use phylogenetic methods to test hypotheses involving cross-cultural traits, but the appropriateness of applying tree-based methods to analyze cultural traits is unclear. The authors developed a spatially explicit computer simulation model to investigate trait evolution in relation to phylogeny and geography and used the simulation to assess the sensitivity of two comparative methods (independent contrasts and partial Mantel tests) to different degrees of horizontal transmission. Simulation results show that (a) the method of independent contrasts is sensitive to even small amounts of horizontal transmission in cultural data sets, (b) Mantel tests fail to cleanly discriminate between datasets characterized by different levels of horizontal and vertical trait transmission, and (c) partial Mantel tests do not produce markedly improved statistical performance when testing for associations among traits (as compared to independent contrasts). The results highlight the need for empirical estimates of horizontal transmission and extinction rates in cross-cultural datasets.},
author = {Nunn, Charles L and Mulder, Monique Borgerhoff and Langley, Sasha},
booktitle = {Cross-Cultural Research},
doi = {10.1177/1069397105283401},
file = {:Users/Ty/Documents/Mendeley Desktop/Nunn, Mulder, Langley{\_}2006{\_}Comparative Methods for Studying Cultural Trait Evolution A Simulation Study.pdf:pdf},
isbn = {1069397105},
issn = {1069-3971},
number = {2},
pages = {177--209},
title = {{Comparative Methods for Studying Cultural Trait Evolution: A Simulation Study}},
volume = {40},
year = {2006}
}
@article{Platt1964,
abstract = {Certain systematic methods of scientific thinking may produce much more rapid progress than others.},
archivePrefix = {arXiv},
arxivId = {arXiv:1011.1669v3},
author = {Platt, John R.},
doi = {10.1126/science.146.3642.347},
eprint = {arXiv:1011.1669v3},
file = {:Users/Ty/Documents/Mendeley Desktop/Platt{\_}1964{\_}Strong inference.pdf:pdf},
isbn = {2819641016},
issn = {0036-8075},
journal = {Science},
number = {3642},
pages = {347--353},
pmid = {17739513},
title = {{Strong inference}},
volume = {146},
year = {1964}
}
@article{Lemmen2012,
abstract = {Farming and herding were introduced to Europe from the Near East and Anatolia; there are, however, considerable arguments about the mechanisms of this transition. Were it the people who moved and either outplaced or admixed with the indigenous hunter-gatherer groups? Or was it material and information that moved-the Neolithic Package-consisting of domesticated plants and animals and the knowledge of their use? The latter process is commonly referred to as cultural diffusion and the former as demic diffusion. Despite continuous and partly combined efforts by archaeologists, anthropologists, linguists, palaeontologists and geneticists, a final resolution of the debate has not yet been reached. In the present contribution we interpret results from the Global Land Use and technological Evolution Simulator (GLUES). This mathematical model simulates regional sociocultural development embedded in the geoenvironmental context during the Holocene. We demonstrate that the model is able to realistically hindcast the expansion speed and the inhomogeneous space-time evolution of the transition to agropastoralism in western Eurasia. In contrast to models that do not resolve endogenous sociocultural dynamics, our model describes and explains how and why the Neolithic advanced in stages. We uncouple the mechanisms of migration and information exchange and also of migration and the spread of agropastoralism. We find that (1) an indigenous form of agropastoralism could well have arisen in certain Mediterranean landscapes but not in northern and central Europe, where it depended on imported technology and material; (2) both demic diffusion by migration and cultural diffusion by trade may explain the western European transition equally well; (3) migrating farmers apparently contribute less than local adopters to the establishment of agropastoralism. Our study thus underlines the importance of adoption of introduced technologies and economies by resident foragers. {\textcopyright} 2011 Elsevier Ltd.},
archivePrefix = {arXiv},
arxivId = {1104.1905},
author = {Lemmen, Carsten and Khan, Aurangzeb},
doi = {10.1029/2012GM001217},
eprint = {1104.1905},
file = {:Users/Ty/Documents/Mendeley Desktop/Lemmen, Khan{\_}2012{\_}A simulation of the Neolithic transition in the Indus Valley.pdf:pdf},
isbn = {0305-4403},
issn = {03054403},
journal = {Geophysical Monograph Series},
number = {12},
pages = {107--114},
publisher = {Elsevier Ltd},
title = {{A simulation of the Neolithic transition in the Indus Valley}},
url = {http://dx.doi.org/10.1016/j.jas.2011.08.008},
volume = {198},
year = {2012}
}
@article{Perez-Losada2011,
abstract = {The transition from hunter-gathering to agriculture (Neolithic) spread gradually across Europe from the Southeast. A reduction in cultural diversity of crop farming practices has been previously observed by comparing pre-LBK Neolithic sites in Greece and the Balkans (dated about 8500 yr BP) to LBK Neolithic sites in Central Europe (dated about 7000 yr BP). The decrease in crop diversity is statistically significant even when considering only the species less likely to have been subject to smaller productivity due to climatic factors (reductions in growing season, temperature, daylight, etc.). This reduction in cultural diversity has not been explained previously. In this paper we show that spatial drift, which occurred on the front of the advancing wave of pioneer settlements, can explain the observed loss of diversity during the LBK range expansion. Our results suggest that spatial dimensions can have a relevant effect also in other case studies in which cultural drift is important. ?? 2011 Elsevier Ltd.},
author = {P{\'{e}}rez-Losada, Joaquim and Fort, Joaquim},
doi = {10.1016/j.jas.2011.01.004},
file = {:Users/Ty/Documents/Mendeley Desktop/P{\'{e}}rez-Losada, Fort{\_}2011{\_}Spatial dimensions increase the effect of cultural drift.pdf:pdf},
isbn = {03054403},
issn = {03054403},
journal = {Journal of Archaeological Science},
keywords = {Cultural drift,Demic diffusion,Neolithic,Spatial dimensions,Waves of advance},
number = {6},
pages = {1294--1299},
publisher = {Elsevier Ltd},
title = {{Spatial dimensions increase the effect of cultural drift}},
url = {http://dx.doi.org/10.1016/j.jas.2011.01.004},
volume = {38},
year = {2011}
}
@article{Banks2013,
abstract = {The Neolithic Revolution, which witnessed the transformation of hunter-gatherer groups into farming communities, is traditionally viewed as the event that allowed human groups to create systems of production that, in the long run, led to present-day societies. Despite the large corpus of research focused on the mechanisms and outcomes of the Neolithic transition, relatively little effort has been devoted to evaluating whether particular production-oriented adaptations could be integrated into a broad range of ecological conditions, and if specific cultural traditions differed ecologically. In order to investigate whether the differences between the adaptations and geographic distributions of three major Early Neolithic archaeological cultures are related to the exploitation of different suites of environmental conditions, we apply genetic algorithm and maximum entropy ecological niche modeling techniques to reconstruct and compare the ecological niches within which three principal Neolithic cultures (Impressed Ware, Cardial Ware, and Linearbandkeramik) spread across Europe between ca. 8000 and 7000 cal yr BP. Results show that these cultures occupied mutually exclusive suites of environmental conditions and, thus, were adapted to distinct and essentially non-overlapping ecological niches. We argue that the historical processes behind the Neolithization of Europe were influenced by environmental factors predisposing occupation of regions most suited to specific cultural adaptations. ?? 2013 Elsevier Ltd.},
author = {Banks, William E and Antunes, Nicolas and Rigaud, Solange and Francesco d'Errico},
doi = {10.1016/j.jas.2013.02.013},
file = {:Users/Ty/Documents/Mendeley Desktop/Banks, Antunes, Rigaud{\_}2013{\_}Ecological constraints on the fi rst prehistoric farmers in Europe.pdf:pdf},
isbn = {0305-4403},
issn = {03054403},
journal = {Journal of Archaeological Science},
keywords = {Cardial Ware culture,Eco-cultural niche modeling,European Early Neolithic,Impressed Ware culture,Linearbandkeramik},
number = {6},
pages = {2746--2753},
publisher = {Elsevier Ltd},
title = {{Ecological constraints on the first prehistoric farmers in Europe}},
url = {http://dx.doi.org/10.1016/j.jas.2013.02.013},
volume = {40},
year = {2013}
}
@article{Davison2009,
abstract = {We present a mathematical model, based on the compilation and statistical processing of radiocarbon dates, of the transition from the Mesolithic to the Neolithic, from about 7000 to 4000 BC in Europe. With the arrival of the Neolithic, hunting and food gathering gave way to agriculture and stock breeding in many parts of Europe; pottery-making spread into even broader areas. Archaeological evidence, radiocarbon dates and genetic markers are consistent with the spread of farming from a source in the Near East. However, farming was less important in the East; the Eastern and Western Neolithic have distinct signatures. We use a population dynamics model to suggest that this distinction can be attributed to the presence of two waves of advance, one from the Near East, and another through Eastern Europe. Thus, we provide a quantitative framework in which a unified interpretation of the Western and Eastern Neolithic can be developed. ?? 2008 Elsevier Ltd and INQUA.},
archivePrefix = {arXiv},
arxivId = {q-bio/0607049},
author = {Davison, K and Dolukhanov, P M and Sarson, G R and Shukurov, A and Zaitseva, G I},
doi = {10.1016/j.quaint.2008.04.013},
eprint = {0607049},
file = {:Users/Ty/Documents/Mendeley Desktop/Davison et al.{\_}2009{\_}Multiple sources of the European Neolithic Mathematical modelling constrained by radiocarbon dates.pdf:pdf},
isbn = {1040-6182},
issn = {10406182},
journal = {Quaternary International},
number = {1-2},
pages = {10--18},
primaryClass = {q-bio},
publisher = {Elsevier Ltd and INQUA},
title = {{Multiple sources of the European Neolithic: Mathematical modelling constrained by radiocarbon dates}},
url = {http://dx.doi.org/10.1016/j.quaint.2008.04.013},
volume = {203},
year = {2009}
}
@article{Bathurst2010,
abstract = {Diatoms recovered from archaeological features on a Viking Age farmstead excavation in the Mosfell Valley in southwestern Iceland are utilized as microscopic indicators of turf-based structures. Eroded turf can be difficult to distinguish macroscopically from naturally occurring sediments because turf foundations erode and melt into the landscape over time, leaving minimal evidence of site use. Turf was a principle building component in Iceland until the early 20th century. Turf strips and blocks were harvested from lowlands where organically rich peat and abundant water contributed to the development of bog plants with thick root mats that produced premium turf. Diatoms embedded in turf reflect the ecological conditions of the peat-bog at the time of deposition. Turf was cut from the bog and transported to higher elevations where drainage was more conducive to house construction. Siliceous diatom frustules are resistant to decay and preserve well archaeologically. The presence of diatoms in archaeological sediments is considered a marker of sediment provenience and an indication of human site use and anthropogenic modification of natural substrates. This paper demonstrates how diatom analysis can determine the presence and delimitation of archaeological features otherwise difficult to distinguish with the naked eye. {\textcopyright} 2010 Elsevier Ltd.},
author = {Bathurst, Rhonda R and Zori, Davide and Byock, Jesse},
doi = {10.1016/j.jas.2010.07.002},
file = {:Users/Ty/Documents/Mendeley Desktop/Bathurst, Zori, Byock{\_}2010{\_}Diatoms as bioindicators of site use Locating turf structures from the Viking Age.pdf:pdf},
isbn = {0305-4403},
issn = {03054403},
journal = {Journal of Archaeological Science},
number = {11},
pages = {2920--2928},
publisher = {Elsevier Ltd},
title = {{Diatoms as bioindicators of site use: Locating turf structures from the Viking Age}},
url = {http://dx.doi.org/10.1016/j.jas.2010.07.002},
volume = {37},
year = {2010}
}
@article{Diamond2009,
abstract = {The largest movements and replacements of human populations since the end of the Ice Ages resulted from the geographically uneven rise of food production around the word. The first farming societies thereby gained great advantages over hunter-gatherer societies. But most of those resulting shifts of populations and languages are complex, controversial, or both. We discuss the main complications and specific examples involving 15 language families. Further progress will depend on interdisciplinary research that combines archaeology, crop and livestock studies, physical anthropology, genetics, and linguistics.},
author = {Diamond, Jared and Bellwood, Peter},
doi = {10.1126/science.1078208},
file = {:Users/Ty/Documents/Mendeley Desktop/Diamond{\_}2009{\_}Farmers and Their Languages The first expansion.pdf:pdf},
isbn = {00368075},
issn = {1095-9203},
journal = {Science},
number = {2003},
pages = {597},
pmid = {12714734},
title = {{Farmers and their languages: the first expansions}},
url = {http://go.galegroup.com/ps/i.do?id=GALE{\%}7CA101941643{\&}v=2.1{\&}u=merc33727{\&}it=r{\&}p=AIM{\&}sw=w{\&}asid=952ae068b75394db4eca505c6f07f4d9},
volume = {597},
year = {2003}
}
@article{Isern2012,
abstract = {The expansion of the Neolithic transition in Europe took place gradually from the Near East across the whole continent. At Northern Europe, observations show a slowdown in the speed of the Neolithic front in comparison to other regions of the continent. It has been suggested that the presence of high population densities of hunter-gatherers at the North could have been the main cause for this slowdown. This proposal has recently been described by a mathematical model that takes into account: (i) the resistance opposed by the Mesolithic populations to the advance of Neolithic populations in their territory, and (ii) a limitation on the population growth dynamics due to the competition for space and resources. But these two effects are not equally responsible for the slowdown of the spread. Indeed, here we show that the limitation on the population growth dynamics seems to have been the main cause of the delay of the expansion of farming in Northern Europe. ?? 2012 Elsevier Ltd.},
author = {Isern, Neus and Fort, Joaquim},
doi = {10.1016/j.jas.2012.06.027},
file = {:Users/Ty/Documents/Mendeley Desktop/Isern, Fort{\_}2012{\_}Modelling the effect of Mesolithic populations on the slowdown of the Neolithic transition.pdf:pdf},
isbn = {0305-4403},
issn = {03054403},
journal = {Journal of Archaeological Science},
keywords = {87.23.Cc,89.20.-a,89.65.Ef,Neolithic transition,Neolithic-Mesolithic interaction,Northern Europe,Reaction-diffusion equations,Slowdown of Neolithic expansion},
number = {12},
pages = {3671--3676},
publisher = {Elsevier},
title = {{Modelling the effect of Mesolithic populations on the slowdown of the Neolithic transition}},
url = {http://dx.doi.org/10.1016/j.jas.2012.06.027},
volume = {39},
year = {2012}
}
@article{Colless1982,
author = {Colless, Donald H.},
file = {:Users/Ty/Documents/Mendeley Desktop/Colless{\_}1982{\_}Review of phylogenetics the theory and practice of phylogenetic systematics.pdf:pdf},
journal = {Systematic Zoology},
number = {1},
pages = {100--104},
title = {{Review of phylogenetics: the theory and practice of phylogenetic systematics.}},
url = {http://www.jstor.org/stable/2413420},
volume = {31},
year = {1982}
}
@article{Tucker2016,
abstract = {The use of phylogenies in ecology is increasingly common and has broadened our understanding of biological diversity. Ecological sub-disciplines, particularly conservation, community ecology and macroecology, all recognize the value of evolutionary relationships but the resulting development of phylogenetic approaches has led to a proliferation of phylogenetic diversity metrics. The use of many metrics across the sub-disciplines hampers potential meta-analyses, syntheses, and generalizations of existing results. Further, there is no guide for selecting the appropriate metric for a given question, and different metrics are frequently used to address similar questions. To improve the choice, application, and interpretation of phylo-diversity metrics, we organize existing metrics by expanding on a unifying framework for phylogenetic information. Generally, questions about phylogenetic relationships within or between assemblages tend to ask three types of question: how much; how different; or how regular? We show that these questions reflect three dimensions of a phylogenetic tree: richness, divergence, and regularity. We classify 70 existing phylo-diversity metrics based on their mathematical form within these three dimensions and identify 'anchor' representatives: for $\alpha$-diversity metrics these are PD (Faith's phylogenetic diversity), MPD (mean pairwise distance), and VPD (variation of pairwise distances). By analysing mathematical formulae and using simulations, we use this framework to identify metrics that mix dimensions, and we provide a guide to choosing and using the most appropriate metrics. We show that metric choice requires connecting the research question with the correct dimension of the framework and that there are logical approaches to selecting and interpreting metrics. The guide outlined herein will help researchers navigate the current jungle of indices.},
archivePrefix = {arXiv},
arxivId = {1303.1374},
author = {Tucker, Caroline M. and Cadotte, Marc W. and Carvalho, Silvia B. and Davies, T. Jonathan and Ferrier, Simon and Fritz, Susanne A. and Grenyer, Rich and Helmus, Matthew R. and Jin, Lanna S. and Mooers, Arne O. and Pavoine, Sandrine and Purschke, Oliver and Redding, David W. and Rosauer, Dan F. and Winter, Marten and Mazel, Florent},
doi = {10.1111/brv.12252},
eprint = {1303.1374},
file = {:Users/Ty/Documents/Mendeley Desktop/Tucker et al.{\_}2016{\_}A guide to phylogenetic metrics for conservation, community ecology and macroecology.pdf:pdf},
isbn = {1461-0248},
issn = {1469185X},
journal = {Biological Reviews},
keywords = {Biodiversity hotspots,Biogeography,Community assembly,Conservation,Diversity metrics,Evolutionary history,Phylogenetic diversity,Prioritization,Range size},
pmid = {26785932},
title = {{A guide to phylogenetic metrics for conservation, community ecology and macroecology}},
url = {http://onlinelibrary.wiley.com/store/10.1111/brv.12252/asset/brv12252.pdf?v=1{\&}t=iylt97ky{\&}s=f27fdf594739c9c832a764a810559f01ac5144a3},
year = {2016}
}
@misc{Tresset2011,
abstract = {The Neolithisation of Europe has seen the transformation of hunting-gathering societies into farming communities. At least partly exogenous in its origins, this process led to major transformations in many aspects of life-styles, such as social structures, land use or diet. It involved the arrival of new human populations and gave way to the importation, intentional or unwanted of many non-European animal and plant species. It also provoked important changes in interactions between humans and natural environments. In many respects, it set the foundations of long-term European peasantry developments and prefigured later agropastoral colonizations. As such, it must be seen as a major turning point in the history of European populations. {\textcopyright} 2010 Acad{\'{e}}mie des sciences.},
author = {Tresset, Anne and Vigne, Jean Denis},
booktitle = {Comptes Rendus - Biologies},
doi = {10.1016/j.crvi.2010.12.010},
file = {:Users/Ty/Documents/Mendeley Desktop/Tresset, Vigne{\_}2011{\_}Last hunter-gatherers and first farmers of Europe.pdf:pdf},
isbn = {1768-3238},
issn = {16310691},
keywords = {Cultigens,Diet change,Domesticates,Europe,Farming techniques,Neolithic,Population adaptations},
number = {3},
pages = {182--189},
pmid = {21377612},
publisher = {Academie des sciences},
title = {{Last hunter-gatherers and first farmers of Europe}},
url = {http://dx.doi.org/10.1016/j.crvi.2010.12.010},
volume = {334},
year = {2011}
}
@article{Faith1992,
author = {Faith, Daniel P},
file = {:Users/Ty/Documents/Mendeley Desktop/Faith{\_}1992{\_}Conservation evaluation and phylogenetic diversity.pdf:pdf},
journal = {Biological Conservation},
pages = {1--10},
title = {{Conservation evaluation and phylogenetic diversity}},
url = {http://www.sciencedirect.com/science/article/pii/0006320792912013},
volume = {61},
year = {1992}
}
@article{Nielsen,
author = {Nielsen, Rasmus and Akey, Joshua M and Jakobsson, Mattias and Pritchard, Jonathan K and Tishkoff, Sarah and Willerslev, Eske},
doi = {10.1038/nature21347},
file = {:Users/Ty/Documents/Mendeley Desktop/Nielsen et al.{\_}2017{\_}Tracing the peopling of the world through genomics.pdf:pdf},
issn = {0028-0836},
journal = {Nature},
pages = {302--310},
pmid = {28102248},
title = {{Tracing the peopling of the world through genomics}},
volume = {541},
year = {2017}
}
@article{Cabral2016,
abstract = {Macroecology and biogeography are concerned with understanding biodiversity patterns across space and time. In the past, the two disciplines have addressed this question mainly with correlative approaches, despite frequent calls for more mechanistic explanations. Recent advances in computational power, theoretical understanding, and statistical tools are, however, currently facilitating the development of more system-oriented, mechanistic models. We review these models, identify different model types and theoretical frameworks, compare their processes and properties, and summarize emergent findings. We show that ecological (physiology, demographics, dispersal, biotic interactions) and evolutionary processes, as well as environmental and human-induced drivers, are increasingly modelled mechanistically; and that new insights into biodiversity dynamics emerge from these models. Yet, substantial challenges still lie ahead for this young research field. Among these, we identify scaling, calibration, validation, and balancing complexity as pressing issues. Moreover, particular process combinations are still understudied, and so far models tend to be developed for specific applications. Future work should aim at developing more flexible and modular models that not only allow different ecological theories to be expressed and contrasted, but which are also built for tight integration with all macroecological data sources. Moving the field towards such a ‘systems macroecology' will test and improve our understanding of the causal pathways through which eco-evolutionary processes create diversity patterns across spatial and temporal scales.},
author = {Cabral, Juliano Sarmento and Valente, Luis and Hartig, Florian},
doi = {10.1111/ecog.02480},
file = {:Users/Ty/Documents/Mendeley Desktop/Cabral, Valente, Hartig{\_}2016{\_}Mechanistic simulation models in macroecology and biogeography state-of-art and prospects.pdf:pdf},
isbn = {6503251521},
issn = {09067590},
journal = {Ecography},
keywords = {Diversity patterns,process-based models,systems ecology},
number = {November},
pages = {1--14},
pmid = {26044706},
title = {{Mechanistic simulation models in macroecology and biogeography: state-of-art and prospects}},
url = {http://doi.wiley.com/10.1111/ecog.02480},
year = {2016}
}
@article{Silva2014,
abstract = {We introduce a methodology for reconstructing geographical effects on dispersal and diffusion patterns, using georeferenced archaeological radiocarbon databases. Fast Marching methods for modelling front propagation enable geographical scenarios to be explored regarding barriers, corridors, and favoured and unfavoured habitat types. The use of genetic algorithms as optimal search tools also enables the derivation of new geographical scenarios, and is especially useful in high-dimensional parameter spaces that cannot be characterized exhaustively due to computer runtime constraints. Model selection is guided by goodness-of-fit statistics for observed and predicted radiocarbon dates.We also introduce an important additional model output, namely, modelled phylogenies of the dispersing population or diffusing cultural entity, based on branching networks of shortest or 'least cost' paths. These 'dispersal trees' can be used as an additional tool to evaluate dispersal scenarios, based on their degree of congruence with phylogenies of the dispersing population reconstructed independently from other kinds of information.We illustrate our approach with a case study, the spread of the Neolithic transition in Europe, using a database from the literature (Pinhasi, Fort and Amerman 2005). Our methods find support for a geographical model in which dispersal is limited by an altitudinal cut-off and in which there is a climate-related latitudinal gradient in rate of spread. This model leads to a deceleration in front propagation rate with geodesic distance, which is also consistent with models of the propagation of the Neolithic transition under space competition with pre-existing populations of hunter-gatherers. Our genetic algorithms meanwhile searched the parameter space and found support for an alternative model involving fast spread along the northern Mediterranean coast and the Danube/Rhine riverine corridor. Both these models outperformed the geography-free Great Circle distance model, and both also outperformed another, almost geography-free, model that constrains dispersal to land to and near-offshore coastal waters. The adjusted coefficient of determination for modelled and observed radiocarbon dates for first arrival supports the GA-derived model; the shortest path network analysis, however, gives greater support to the model with altitudinal cut-off and latitudinal gradient in dispersal rate, since it produces branching 'dispersal trees' that are more congruent with these archaeological sites' clade memberships (as defined by archaeological material culture).},
author = {Silva, Fabio and Steele, James},
doi = {10.1016/j.jas.2014.04.021},
file = {:Users/Ty/Documents/Mendeley Desktop/Silva, Steele{\_}2014{\_}New methods for reconstructing geographical effects on dispersal rates and routes from large-scale radiocarbon databa.pdf:pdf},
isbn = {0305-4403},
issn = {10959238},
journal = {Journal of Archaeological Science},
keywords = {Cultural Phylogenetics,Fast Marching methods,Front propagation,Human dispersal,Neolithic transition,Phylogeography,Radiocarbon},
pages = {609--620},
publisher = {Elsevier Ltd},
title = {{New methods for reconstructing geographical effects on dispersal rates and routes from large-scale radiocarbon databases}},
url = {http://dx.doi.org/10.1016/j.jas.2014.04.021},
volume = {52},
year = {2014}
}
@incollection{Vellend2011,
address = {Oxford, UK},
author = {Vellend, Mark and Cornwell, William K and Magnuson-ford, Karen and Mooers, Arne {\O}},
booktitle = {Biological diversity: frontiers in measurement and assessment},
file = {:Users/Ty/Documents/Mendeley Desktop/Vellend et al.{\_}2011{\_}Measuring phylogenetic biodiversity.pdf:pdf},
pages = {194--207},
publisher = {Oxford University Press},
title = {{Measuring phylogenetic biodiversity}},
url = {http://phylodiversity.net/wcornwell/Vellend{\_}etal{\_}2011{\_}bookchap.pdf},
year = {2011}
}
@article{Bocquet-Appel2012,
abstract = {If the overall expansion of the farming system was determined by the Neolithic Demographic Transition (NDT), i.e. by demographic pressure, what determined the rate of expansion? What is the link between the rate of expansion, the farming system and demographic density? In a first approach, the issue of the different rates of expansion of the farming system on the map is addressed in terms of 21 geo-ecological, climatic and cultural factors and forager populations, via an ordinary least square regression technique (OLS). In a second approach, the variability of the rate of expansion is analyzed in terms of specific patterns identified for the ceramic culture areas, via a cluster analysis. The expansion rate is negatively correlated with the intensification of the agricultural system, as well as with demographic density. Expansion is slow in ecosystems with an intensive farming system with relatively high demographic density, and vice-versa. ?? 2011 Elsevier Ltd.},
author = {Bocquet-Appel, Jean Pierre and Naji, Stephan and {Vander Linden}, Marc and Kozlowski, Janusz},
doi = {10.1016/j.jas.2011.10.010},
file = {:Users/Ty/Documents/Mendeley Desktop/Bocquet-Appel et al.{\_}2012{\_}Understanding the rates of expansion of the farming system in Europe.pdf:pdf},
isbn = {0305-4403},
issn = {03054403},
journal = {Journal of Archaeological Science},
keywords = {European,Neolithic demographic transition,Neolithic farming system,Rate of expansion},
number = {2},
pages = {531--546},
publisher = {Elsevier Ltd},
title = {{Understanding the rates of expansion of the farming system in Europe}},
url = {http://dx.doi.org/10.1016/j.jas.2011.10.010},
volume = {39},
year = {2012}
}
@article{Izsak2000,
abstract = {The practice of environmental planning and protection frequently necessitates the quantification of ecological diversity. Traditional ‘ecological diversity indices' are based on the abundances of species present. However, such indices are insensitive to taxonomic or similar differences. With equal species abundances they measure the species richness (species number) only. Conversely, so-called ‘biodiversity indices' are based on species differences, but are insensitive to the abundance conditions. The quadratic entropy index is the only ecological diversity index, the value of which reflects both the differences ‘and' abundances of the species. When a species list is given without abundance data, then, using the quadratic entropy index and postulating equal abundances, one gets the only biodiversity index derived from a traditional ecological index of diversity. Its extensive form is identical with the sum of differences or distances between the species present. This index trivially satisfies set monotonicity, an important property for biodiversity indices.},
author = {Izsak, Janos and Papp, Laszio},
journal = {Ecological Modelling},
number = {1-3},
pages = {151--156},
title = {{A link between ecological diversity indices and measure of biodiversity}},
url = {http://www.sciencedirect.com/science/article/pii/S0304380000002039},
volume = {130},
year = {2000}
}
@article{Guerrero2011,
abstract = {The study of Near Eastern Neolithic villages provides a unique means of tracing subsistence strategy, population growth, health, and emerging social inequality associated with agricultural origins. However, disentangling these patterns requires a detailed comprehension of the chronological placement of individual households in the site. In this paper, we present a test to determine the reliability and applicability of the fluoride dating method (a relative dating method) on human dentition of 40 samples from 28 Pre-Pottery Neolithic B (or PPNB) burials from the site of Tell Halula, in Syria. This method, applied here for the first time on a Neolithic Near East case study, is an alternative when other dating methods, like radiocarbon dates, do not provide the required temporal resolution to address particular research problems. Nonetheless, the results obtained in the fluoride analysis show how both the age at death of individuals, and the integrity of the burial plug enormously affect the amount of fluoride absorbed by teeth, so that only a small subset of the full dataset was suitable for fluoride dating. Although the distribution of fluoride values of dentine from the small sample of burials from suitable contexts matches the expected chronology, and corroborates the hypothesis that the occupation at Halula extends from the Middle to the Late PPNB, our analysis illustrates the need for a better understanding of the different sources of error in fluoride dating to improve the method itself, and to obtain more reliable fluoride chronologies. ?? 2011 Elsevier Ltd.},
author = {Guerrero, E and Schurr, M and Kuijt, I and Anfruns, J and Molist, M},
doi = {10.1016/j.jas.2011.02.013},
file = {:Users/Ty/Documents/Mendeley Desktop/Guerrero et al.{\_}2011{\_}Timing the Neolithic transition the application of fl uoride dating at Tell Halula , Syria.pdf:pdf},
isbn = {0305-4403},
issn = {03054403},
journal = {Journal of Archaeological Science},
keywords = {Fluoride,Human dentition,Near East,Neolithic,Relative dating method},
number = {7},
pages = {1496--1501},
publisher = {Elsevier Ltd},
title = {{Timing the Neolithic transition: The application of fluoride dating at Tell Halula, Syria}},
url = {http://dx.doi.org/10.1016/j.jas.2011.02.013},
volume = {38},
year = {2011}
}
@article{Rosauer2009,
abstract = {We present a new, broadly applicable measure of the spatial restriction of phylogenetic diversity, termed phylogenetic endemism (PE). PE combines the widely used phylogenetic diversity and weighted endemism measures to identify areas where substantial components of phylogenetic diversity are restricted. Such areas are likely to be of considerable importance for conservation. PE has a number of desirable properties not combined in previous approaches. It assesses endemism consistently, independent of taxonomic status or level, and independent of previously defined political or biological regions. The results can be directly compared between areas because they are based on equivalent spatial units. PE builds on previous phylogenetic analyses of endemism, but provides a more general solution for mapping endemism of lineages. We illustrate the broad applicability of PE using examples of Australian organisms having contrasting life histories: pea-flowered shrubs of the genus Daviesia (Fabaceae) and the Australian species of the Australo-Papuan tree frog radiation within the family Hylidae.},
author = {Rosauer, Dan F and Laffan, Shawn W and Crisp, Michael D and Donnellan, Stephen C},
doi = {10.1111/j.1365-294X.2009.04311.x},
file = {:Users/Ty/Documents/Mendeley Desktop/Rosauer et al.{\_}2009{\_}Phylogenetic endemism a new approach for identifying geographical concentrations of evolutionary history.pdf:pdf},
journal = {Molecular Ecology},
keywords = {daviesia,endemism,hylidae,phylogenetic diversity,phylogenetic endemism},
pages = {4061--4072},
title = {{Phylogenetic endemism : a new approach for identifying geographical concentrations of evolutionary history}},
url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-294X.2009.04311.x/full},
volume = {18},
year = {2009}
}
@article{Davison2006,
abstract = {The causes and implications of the regional variations in the spread of the incipient agriculture in Europe remain poorly understood. We use population dynamics models to study the dispersal of the Neolithic in Europe from a localised area in the Near East, solving the two-dimensional reaction-diffusion equation on a spherical surface. We focus on the role of major river paths and coastlines in the advance of farming, to model the rapid advances of the Linear Pottery (LBK) and the Impressed Ware traditions along the Danube-Rhine corridor and the Mediterranean coastline, respectively. We argue that the random walk of individuals, which results in diffusion of the population, can be anisotropic in those areas and hence lead to an effective advection. The standard reaction-diffusion equation is thus supplemented with an advection term, confined to the proximity of major rivers and coastlines. The model allows for the spatial variation in both the human mobility (diffusivity) and the carrying capacity, reflecting the local altitude and latitude. This approach can easily be generalised to include other environmental factors, such as the bioproductivity of landscapes. Our model successfully accounts for the regional variations in the spread of the Neolithic, consistent with the radiocarbon data, and reproduces a time delay in the spread of farming to the Eastern Europe, Britain and Scandinavia. {\textcopyright} 2005 Elsevier Ltd. All rights reserved.},
author = {Davison, Kate and Dolukhanov, Pavel and Sarson, Graeme R and Shukurov, Anvar},
doi = {10.1016/j.jas.2005.09.017},
file = {:Users/Ty/Documents/Mendeley Desktop/Davison et al.{\_}2006{\_}The role of waterways in the spread of the Neolithic.pdf:pdf},
isbn = {0305-4403},
issn = {03054403},
journal = {Journal of Archaeological Science},
keywords = {Environmental effects,Europe,Expansion rate,Neolithic,Population dynamics},
number = {5},
pages = {641--652},
title = {{The role of waterways in the spread of the Neolithic}},
volume = {33},
year = {2006}
}
@article{Clarke2001,
abstract = {A further biodiversity index is proposed, based on taxonomic (or phylogenetic) related- ness of species, namely the ‘variation in taxonomic distinctness' (VarTD, $\Lambda$+) between every pair of species recorded in a study. It complements the previously defined ‘average taxonomic distinctness' (AvTD, ∆+), which is the mean path length through the taxonomic tree connecting every pair of spe- cies in the list. VarTD is simply the variance of these pairwise path lengths and reflects the uneven- ness of the taxonomic tree. For example, a species list in which there are several different orders rep- resented only by a single species, but also some genera which are very species-rich, would give a high $\Lambda$+ by comparison with a list (of equivalent ∆+) in which all species tended to be from different families but the same order. VarTD is shown to have the same desirable sampling properties as AvTD, primarily a lack of dependence of its mean value on the sample size (except for unrealistically small samples). Such unbiasedness is of crucial importance in making valid biodiversity comparisons between studies at different locations or times, with differing or uncontrolled degrees of sampling effort. This feature is emphatically not shared by indices related to species richness and also not by properties of the phylogeny adapted from proposals in other, conservation contexts, such as ‘average phylogenetic diversity' (AvPD, $\Phi$+). As with AvTD, the VarTD statistic for any local study can be tested for ‘departure from expectation', based on a master taxonomy for that region, by constructing a simulation distribution from random subsets of the master list. The idea can be extended to sum- marising the joint distribution of AvTD and VarTD, so that values from real data sets are compared with a fitted simulation ‘envelope' in a 2 d (∆+, $\Lambda$+) plot. The methodology is applied to 14 species lists of free-living marine nematodes, and related to a master list for UK waters. The combination of AvTD and VarTD picks out, in different ways, some degraded locations (low ∆+, low to normal $\Lambda$+) and the pristine island fauna of the Scillies (normal ∆+, high $\Lambda$+). The 2 indices are also demonstrated to be measuring effectively independent features of the taxonomic tree, at least for this faunal group (al- though it is shown theoretically that this will not always be the case). The combination of ∆+ and $\Lambda$+ is therefore seen to provide a statistically robust summary of taxonomic (or phylogenetic) relatedness patterns within an assemblage, which has the potential to be applied to a wide range of historical data in the form of simple species lists.},
author = {Clarke, KR and Warwick, RM},
file = {:Users/Ty/Documents/Mendeley Desktop/Clarke, Warwick{\_}2001{\_}A further biodiversity index applicable to species lists variation in taxonomic distinctness.pdf:pdf},
journal = {Marine Ecology Progress Series},
keywords = {biodiversity,british marine nematodes,of the publisher,permitted without written consent,phylogenetic diversity,resale or republication not,sampling properties,simulation,taxonomic distinctness},
pages = {265--278},
title = {{A further biodiversity index applicable to species lists: variation in taxonomic distinctness}},
url = {http://researchrepository.murdoch.edu.au/id/eprint/23107/},
volume = {216},
year = {2001}
}
@article{Barker2002,
abstract = {The value of biodiversity lies in its option value for the future, the greater the complement of contemporary biodi- versity conserved today, the greater the possibilities for future biodiversity because of the diverse genetic resource needed to ensure continued evolution in a changing and uncertain world. From this perspective, biodiversity option value can be equated with richness in the different features expressed by species. An individual species of greater value is one contributing more novel features to a given subset. The feature diversity of species and communities is difficult to estimate directly, but can be predicted by the phylogenetic relationships among the species. The ‘Phy- logenetic Diversity' measure (PD) (Faith, 1992a) estimates the relative feature diversity of any nominated set of species by the sum of the lengths of all those branches spanned by the set. These branch lengths reflect patristic or path-length distances. This study first reviews and expands on some of the properties of PD, and develops simple modifications of the measure (DnPD and enPD) to enable capture of both the phylogenetic relatedness of species and their abundances in each sample. Then the application of PD, DnPD and enPD to a wide range of conservation and resource management issues is demonstrated using avian case studies. Supertree construction procedures (matrix representation using parsimony analysis; average consensus) were used to combine the extensive DNA–DNA hybridization tree of Sibley {\&} Ahlquist (1990) with numerous, recently published phylogenetic recon- structions to derive a phylogenetic tree for the global avian fauna. Using this supertree as a systematic framework, the utility of PD was demonstrated in four case studies: (i) state of the environment reporting, with changes in avian faunas resulting from extinctions quantified as indicators of the state of biodiversity at Global, New Zealand and Waikato region scales, and changes in available habitat quantified as indicators of pressures on biodiversity in the Waikato region; (ii) setting priorities for threatened species management, with PD as a measure of option value integrated with information on survivorship expectations to develop a ranking among threatened New Zealand forest bird species; (iii) monitoring biotic response to management, with data from 5-minute counts used to analyse changes in forest bird communities under three management regimes in New Zealand; and (iv) selection of indica- tor species, with PD used to objectively identify subsets of species in the Global, New Zealand and Waikato avian faunas that comprise a high proportion of the option value in those faunas.},
author = {Barker, Gary M},
file = {:Users/Ty/Documents/Mendeley Desktop/Barker{\_}2002{\_}Phylogenetic diversity a quantitative framework for measurement of priority and achievement in biodiversity conservation.pdf:pdf},
journal = {Biological Journal of the Linnean Society},
pages = {165--194},
title = {{Phylogenetic diversity : a quantitative framework for measurement of priority and achievement in biodiversity conservation}},
url = {http://www.jstor.org/stable/3070944?seq=1{\#}page{\_}scan{\_}tab{\_}contents},
volume = {76},
year = {2002}
}
@article{Helmus2010,
author = {Helmus, Matthew R and Keller, Wendel (Bill) and Paterson, Michael J and Yan, Norman D and Cannon, Charles H and Rusak, James A},
doi = {10.1111/j.1461-0248.2009.01411.x},
file = {:Users/Ty/Documents/Mendeley Desktop/Helmus et al.{\_}2010{\_}Communities contain closely related species during ecosystem disturbance.pdf:pdf},
journal = {Ecology letters},
keywords = {biodiversity,disturbance ecology,environmental filtering,extinction prediction,ph,phylogenetic,phylogenetic community structure,phylogenetic comparative methods,signal,whole-lake experiment,zooplankton},
pages = {162--174},
title = {{Communities contain closely related species during ecosystem disturbance}},
url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1461-0248.2009.01411.x/full},
volume = {13},
year = {2010}
}
@article{Rao1982,
abstract = {Three general methods for obtaining measures of diversity within a population and dissimilarity between populations are discussed. One is based on an intrinsic notion of dissimilarity between individuals and others make use of the concepts of entropy and discrimination. The use of a diversity measure in apportionment of diversity between and within populations is discussed.},
author = {Rao, Radhakrishna C},
file = {:Users/Ty/Documents/Mendeley Desktop/Rao{\_}1982{\_}Diversity and Dissimilarity coefficients a unified approach.pdf:pdf},
journal = {Theoretical population biology},
pages = {24--43},
title = {{Diversity and Dissimilarity coefficients: a unified approach}},
url = {http://www.sciencedirect.com/science/article/pii/0040580982900041},
volume = {21},
year = {1982}
}
@article{Webb2002,
abstract = {As better phylogenetic hypotheses become available for many groups of organisms, studies in community ecology can be informed by knowledge of the evolutionary relationships among coexisting species. We note three primary approaches to integrating phylogenetic information into studies of community organization: 1. examining the phylogenetic structure of community assemblages, 2. exploring the phylogenetic basis of community niche structure, and 3. adding a community context to studies of trait evolution and biogeography. We recognize a common pattern of phylogenetic conservatism in ecological character and highlight the challenges of using phylogenies of partial lineages. We also review phylogenetic approaches to three emergent properties of communities: species diversity, relative abundance distributions, and range sizes. Methodological advances in phylogenetic supertree construction, character reconstruction, null models for community assembly and character evolution, and metrics of community phylogenetic structure underlie the recent progress in these areas. We highlight the potential for community ecologists to benefit from phylogenetic knowledge and suggest several avenues for future research.},
author = {Webb, Campbell O and Ackerly, David D and Mcpeek, Mark A and Donoghue, Michael J},
doi = {10.1146/annurev.ecolsys.33.010802.150448},
file = {:Users/Ty/Documents/Mendeley Desktop/Webb et al.{\_}2002{\_}Phylogenies and Community Ecology.pdf:pdf},
journal = {Annual Review of Ecology and Systematics},
keywords = {biogeography,can be informed by,community assembly and organization,for many groups,knowledge of the evo-,niche differentiation,of organisms,phylogenetic conservatism,phylogenetic hypotheses become available,s abstract as better,species diversity,studies in community ecology},
pages = {475--505},
title = {{Phylogenies and Community Ecology}},
url = {http://annualreviews.org/doi/abs/10.1146/annurev.ecolsys.33.010802.150448},
volume = {33},
year = {2002}
}
@article{Kembel2010,
abstract = {Picante is a software package that provides a comprehensive set of tools for analyzing the phylogenetic and trait diversity of ecological communities. The package calculates phylogenetic diversity metrics, performs trait comparative analyses, manipulates phenotypic and phylogenetic data, and performs tests for phylogenetic signal in trait distributions, community structure and species interactions. Availability: Picante is a package for the R statistical language and environment written in R and C, released under a GPL v2 open-source license, and freely available on the web (http://picante.r-forge.r-project.org) and from CRAN (http://cran.r-project.org).},
author = {Kembel, Steven W and Cowan, Peter D and Helmus, Matthew R and Cornwell, William K and Morlon, Helene and Ackerly, David D and Blomberg, Simon P and Webb, Campbell O},
doi = {10.1093/bioinformatics/btq166},
file = {:Users/Ty/Documents/Mendeley Desktop/Kembel et al.{\_}2010{\_}Picante R tools for integrating phylogenies and ecology.pdf:pdf},
journal = {Bioinformatics},
number = {11},
pages = {1463--1464},
title = {{Picante : R tools for integrating phylogenies and ecology}},
url = {https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btq166},
volume = {26},
year = {2010}
}
@article{Webb2008,
abstract = {Motivation: The increasing availability of phylogenetic and trait data for communities of co-occurring species has created a need for software that integrates ecological and evolutionary analyses. Capabilities: Phylocom calculates numerous metrics of phyloge- netic community structure and trait similarity within communities. Hypothesis testing is implemented using several null models. Within the same framework, it measures phylogenetic signal and correlated evolution for species traits. A range of utility functions allow community and phylogenetic data manipulation, tree and trait generation, and integration into scientific workflows. Availability: Open source at: http://phylodiversity.net/phylocom/},
author = {Webb, Campbell O and Ackerly, David D and Kembel, Steven W},
doi = {10.1093/bioinformatics/btn358},
file = {:Users/Ty/Documents/Mendeley Desktop/Webb, Ackerly, Kembel{\_}2008{\_}Phylocom software for the analysis of phylogenetic community structure and trait evolution.pdf:pdf},
journal = {Bioinformatics},
number = {18},
pages = {2098--2100},
title = {{Phylocom: software for the analysis of phylogenetic community structure and trait evolution}},
url = {http://phylodiversity.net/cwebb/pubs/webb2008{\_}phylocom.pdf},
volume = {24},
year = {2008}
}
@misc{Yunfei2009,
abstract = {Recently, rice fields dated between 5000 and 2500 BC were found at the Tianluoshan sit in east China. The early rice fields dated between 5000 and 4500 BC are the oldest rice fields known. The discovery has provided data of recovering reclamation, cultivation, and the ecological system of rice fields in the Neolithic age. People opened up marshes of dense reeds with fire and wooden or bone spades, in order to create rice fields. In the rice fields, there was not only rice, but a lot of weeds as well. The excavations proved that little or even no weeding or irrigation was adopted. However, tilling soil by wooden and bone tools was evidenced. The average yields are estimated to have been about 830 kg for the early period and 950 kg per hectare for the later period. The cultivation system was low-level. Although the Tianluoshan people cultivated rice, they still obtained a great deal of food by gathering and hunting. ?? 2009 Elsevier Ltd. All rights reserved.},
author = {Yunfei, Zheng and Guoping, Sun and Ling, Qin and Chunhai, Li and Xiaohong, Wu and Xugao, Chen},
booktitle = {Journal of Archaeological Science},
doi = {10.1016/j.jas.2009.09.026},
file = {:Users/Ty/Documents/Mendeley Desktop/Yunfei et al.{\_}2009{\_}Rice fields and modes of rice cultivation between 5000 and 2500 BC in east China.pdf:pdf},
isbn = {0305-4403},
issn = {03054403},
keywords = {Archaeobotany,Hemudu Culture,Macro-remains,Origin of agriculture,Paddy fields,Phytoliths,Pollen,Tianluoshan},
number = {12},
pages = {2609--2616},
publisher = {Elsevier Ltd},
title = {{Rice fields and modes of rice cultivation between 5000 and 2500 BC in east China}},
url = {http://dx.doi.org/10.1016/j.jas.2009.09.026},
volume = {36},
year = {2009}
}
@article{Shennan2007,
abstract = {Summed probability distributions of radiocarbon dates are used to make inferences about the history of population fluctuations from the Mesolithic to the late Neolithic for three countries in central and northern Europe: Germany, Poland and Denmark. Two different methods of summing the dates produce very similar overall patterns. The validity of the aggregate patterns is supported by a number of regional studies based on other lines of evidence. The dramatic rise in population associated with the arrival of farming in these areas that is visible in the date distributions is not surprising. Much more unexpected are the fluctuations during the course of the Neolithic, and especially the indications of a drop in population at the end of the LBK early Neolithic that lasted for nearly a millennium. Possible reasons for the pattern are discussed. {\textcopyright} 2006 Elsevier Ltd. All rights reserved.},
author = {Shennan, Stephen and Edinborough, Kevan},
doi = {10.1016/j.jas.2006.10.031},
file = {:Users/Ty/Documents/Mendeley Desktop/Shennan, Edinborough{\_}2007{\_}Prehistoric population history from the Late Glacial to the Late Neolithic in Central and Northern Europe.pdf:pdf},
isbn = {0305-4403},
issn = {03054403},
journal = {Journal of Archaeological Science},
keywords = {Mesolithic,Neolithic,Population history,Radiocarbon dates},
number = {8},
pages = {1339--1345},
title = {{Prehistoric population history: from the Late Glacial to the Late Neolithic in Central and Northern Europe}},
volume = {34},
year = {2007}
}
@article{Chaput2015,
abstract = {As the Cordilleran and Laurentide Ice Sheets retreated,North America was colonized by human populations; however, the spatial patterns of subsequent population growth are unclear. Temporal frequency distributions of aggregated radiocarbon (14C) dates are used as a proxyof populationsizeand canbeusedtotrack this expansion. The Canadian Archaeological Radiocarbon Database contains more than 35,000 14Cdates and isusedinthisstudy tomap the spatiotem- poral demographic changes of Holocene populations in North Amer- ica at a continental scale for the past 13,000 y. We use the kernel method, which converts the spatial distribution of 14C dates into estimates of population density at 500-y intervals. The resultingmaps reveal temporally distinct, dynamic patterns associated with paleo- demographic trends that correspond well to genetic, archaeological, and ethnohistoric evidence of human occupation. These results have implications for hypothesizing and testing migration routes into and across North America aswell as the relative influence of North Amer- ican populations on the evolution of the North American ecosystem.},
author = {Chaput, Michelle A and Kriesche, Bj{\"{o}}rn and Betts, Matthew and Martindale, Andrew and Kulik, Rafal and Schmidt, Volker and Gajewski, Konrad},
doi = {10.1073/pnas.1505657112},
file = {:Users/Ty/Documents/Mendeley Desktop/Chaput et al.{\_}2015{\_}Spatiotemporal distribution of Holocene populations in North America.pdf:pdf},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences},
keywords = {Canadian Archaeological Radiocarbon Database,Holocene,North America,paleodemography,paleoecology},
number = {39},
pages = {12127--12132},
pmid = {26351683},
title = {{Spatiotemporal distribution of Holocene populations in North America}},
volume = {112},
year = {2015}
}
@article{Clarke1998,
abstract = {In multivariate analyses of the e ects of both natural and anthropogenic environmental variability on community composition, many species are interchange- able in the way that they characterise the samples, giving rise to the concept of structural redundancy in com- munity composition. Here, we develop a method of quantifying the extent of this redundancy by extracting a series of subsets of species, the multivariate response pattern of each of which closely matches that for the whole community. Structural redundancy is then re- ̄ected in the number of such subsets, which we term ``response units'', that can be extracted without re- placement. We have applied this technique to the e ects of the Amoco-Cadiz oil-spill on marine macrobenthos in the Bay of Morlaix, France, and to the natural inter- annual variability of macrobenthos at two stations o the coast of Northumberland, England. Structural redundancy is shown to be remarkably high, with the number and sizes of subsets being comparable in all three examples. Taxonomic/functional groupings of species within the di ering response units change in abundance in the same way over time. The response units are shown to possess a wide taxonomic spread and, using two di erent types of randomisation test, dem- onstrated to have a taxonomically and functionally co- herent structure. The level of structural redundancy may therefore be an indirect measure of the resilience or compensation potential within an assemblage.},
author = {Clarke, KR and Warwick, RM},
file = {:Users/Ty/Documents/Mendeley Desktop/Clarke, Warwick{\_}1998{\_}Quantifying structural redundancy in ecological communities.pdf:pdf},
journal = {Oecologia},
keywords = {macrobenthos {\'{a}},multivariate analysis {\'{a}} marine,oil pollution {\'{a}} compensation,potential {\'{a}}},
pages = {278--289},
title = {{Quantifying structural redundancy in ecological communities}},
url = {http://link.springer.com/article/10.1007/s004420050379},
volume = {113},
year = {1998}
}
@article{Dehling2014,
abstract = {Tropical mountains are hotspots of biodiversity, but the factors that generate this high diversity remain poorly understood. To identify possible mechanisms that influence avian species assemblages in the tropical Andes, we studied the functional and phylogenetic diversity and the structure of species assemblages of an avian feeding guild. We analysed how functional and phylogenetic diversity, structure and composition of frugivorous bird assemblages changed along a 3300 m elevational transect from the lowlands to the tree line with a novel combination of functional and phylogenetic approaches, and used null models to infer possible drivers of the observed patterns. Species richness, functional richness and phylogenetic diversity decreased almost monotonically with increasing elevation, but assemblage structure and composition changed abruptly in the Andean foothills at around 1200 m. In the lowland assemblages, species were functionally and phylogenetically less similar than expected from null models, whereas species in the highland assemblages were functionally and phylogenetically more similar than expected by chance, suggesting an abrupt reduction in the number of functionally and phylogenetically distinct species in the transition from lowlands to the highlands. Nevertheless, the functional and phylogenetic evenness of the assemblages, i.e. the regularity of the spacing of species in functional trait space and phylogeny, remained constant along the gradient, which suggests that the mechanisms that influence the co-occurrence of species within the assemblages are similar in lowlands and highlands. The observed differences between lowland and highland assemblages imply sharp distributional limits for frugivorous bird species in the Andean foothills, probably caused by environmental factors other than climate, e.g. changes in habitat types or topography, or independent species radiations in lowlands and highlands. These strong distributional limits may hinder uphill range shifts of frugivorous bird species, and the plant species they disperse, in the tropical Andes as a response to climate change.},
author = {Dehling, D Matthias and Fritz, Susanne A and T{\"{o}}pfer, Till and P{\"{a}}ckert, Martin and Estler, Patrizia and B{\"{o}}hning-gaese, Katrin and Schleuning, Matthias},
doi = {10.1111/ecog.00623},
file = {:Users/Ty/Documents/Mendeley Desktop/Dehling et al.{\_}2014{\_}Functional and phylogenetic diversity and assemblage structure of frugivorous birds along an elevational gradient in.pdf:pdf},
journal = {Ecography},
pages = {1047--1055},
title = {{Functional and phylogenetic diversity and assemblage structure of frugivorous birds along an elevational gradient in the tropical Andes IBS special issue}},
url = {http://onlinelibrary.wiley.com/doi/10.1111/ecog.00623/full},
volume = {37},
year = {2014}
}
@phdthesis{Redding2003,
author = {Redding, David W.},
school = {University of East Anglia, Norwich},
title = {{Incorporating genetic distinctness and reserve occupancy into a conservation priorisation approach}},
type = {Master's thesis},
year = {2003}
}
@article{Villeger2008,
abstract = {Functional diversity is increasingly identified as an importa nt driver ofecosystem functioning. Various indices have been proposed to measure the functionaldiversity of a community, but there is still no consensus on which are most suitable. Indeed,none of the existing indices meets all the criteria required for general use. The main criteria arethat they must be designed to deal with several traits, take into account abundances, andmeasure all the facets of functional diversity. Here we propose three indices to quantify eachfacet of functional diversity for a community with species distributed in a multidimensionalfunctional space: functional richness (volume of the functional space occupied by thecommunity), functional evenness (regularity of the distribution of abundance in this volume),and functional divergence (divergence in the distribution of abundance in this volume).Functional richness is estimated using the existing convex hull volume index. The newfunctional evenness index is based on the minimum spanning tree which links all the species inthe multidimensional functional space. Then this new index quantifies the regularity withwhich species abundances are distributed along the spanning tree. Functional divergence ismeasured using a novel index which quantifies how species diverge in their distances (weightedby their abundance) from the center of gravity in the functional space. We show that none ofthe indices meets all the criteria required for a functional diversity index, but instead we showthat the set of three complementary indices meets these criteria. Through simulations ofartificial data sets, we demonstrate that functional divergence and functional evenness areindependent of species richness and that the three functional diversity indices are independentof each other. Overall, our study suggests that decomposition of functional diversity into itsthree primary components provides a meaningful framework for its quantification and for theclassification of existing functional diversity indices. This decomposition has the potential toshed light on the role of biodiversity on ecosystem functioning and on the influence of bioticand abiotic filters on the structure of species communities. Finally, we propose a generalframework for applying these three functional diversity indices.},
author = {Villeger, Sebastien and Mason, Norman WH and Mouillot, David},
file = {:Users/Ty/Documents/Mendeley Desktop/Villeger, Mason, Mouillot{\_}2008{\_}New multidimensional functional diversity indices for a multifaceted framework in functional ecology.pdf:pdf},
journal = {Ecology},
keywords = {competitive filtering,environmental filtering,functional divergence,functional evenness,functional niche,functional richness,functional traits,null model},
number = {8},
pages = {2290--2301},
title = {{New multidimensional functional diversity indices for a multifaceted framework in functional ecology}},
url = {http://onlinelibrary.wiley.com/doi/10.1890/07-1206.1/full},
volume = {89},
year = {2008}
}
@article{Hardy2007,
abstract = {1 Analysing the phylogenetic structure of natural communities may illuminate theprocesses governing the assembly and coexistence of species in ecological communities. 2 Unifying previous works, we present a statistical framework to quantify thephylogenetic structure of communities in terms of average divergence time betweenpairs of individuals or species, sampled from different sites. This framework allows anadditive partitioning of the phylogenetic signal into alpha (within-site) and beta(among-site) components, and is closely linked to Simpson diversity. It unifies thetreatment of intraspecific (genetic) and interspecific diversity, leading to the definitionof differentiation coefficients among community samples (e.g. I ST , P ST ) analogous toclassical population genetics coefficients expressing differentiation among populations(e.g. F ST , N ST ). 3 Two coefficients which express community differentiation among sites from speciesidentity ( I ST ) or species phylogeny ( P ST ) require abundance data (number of individualsper species per site), and estimators that are unbiased with respect to sample size aregiven. Another coefficient ( $\Pi$ ST ) expresses the gain of the mean phylogenetic distancebetween species found in different sites compared with species found within sites, andrequires only incidence data (presence/absence of each species in each site). 4 We present tests based on phylogenetic tree randomizations to detect communityphylogenetic clustering ( P ST {\textgreater} I ST or $\Pi$ ST {\textgreater} 0) or phylogenetic overdispersion ( P ST {\textless} I ST or $\Pi$ ST {\textless} 0). In addition, we propose a novel approach to detect phylogenetic clusteringor overdispersion in different clades or at different evolutionary time depths usingpartial randomizations. 5 I ST , P ST or $\Pi$ ST can also be used as distances between community samples andregressed on ecological or geographical distances, allowing us to investigate the factorsresponsible for the phylogenetic signal and the critical scales at which it appears. 6 We illustrate the approach on forest tree communities in Equatorial Guinea,where a phylogenetic clustering signal was probably due to phylogenetically conservedadaptations to the elevation gradient and was mostly contributed to by ancient cladesubdivisions. 7 The approach presented should find applications for comparing quantitativelyphylogenetic patterns of different communities, of similar communities in different regionsor continents, or of populations (within species) vs. communities (among species).},
author = {Hardy, Olivier J and Senterre, Bruno},
doi = {10.1111/j.1365-2745.2007.01222.x},
file = {:Users/Ty/Documents/Mendeley Desktop/Hardy, Senterre{\_}2007{\_}Characterizing the phylogenetic structure of communities by an additive partitioning of phylogenetic diversity.pdf:pdf},
journal = {Journal of Ecology},
pages = {493--506},
title = {{Characterizing the phylogenetic structure of communities by an additive partitioning of phylogenetic diversity}},
url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2745.2007.01222.x/full},
volume = {95},
year = {2007}
}
@article{Pavoine2005,
abstract = {Rao has developed quadratic entropy to measure diversity in a set of entities divided up among a fixed set of categories. This index depends on a chosen matrix of dissimilarities among categories and a frequency distribution of these categories. With certain choices of dissimilarities, this index could be maximized over all frequency distributions by eliminating several categories. This unexpected result is radically opposite to those obtained with usual diversity indices. We demonstrate that the elimination of categories to maximize the quadratic entropy depends on mathematical properties of the chosen dissimilarities. In particular, when quadratic entropy is applied to ultrametric dissimilarities, all categories are retained in order to reach its maximal value. Three examples, varying from simple one-dimensional to ultrametric dissimilarity matrices, are provided. We conclude that, as far as diversity measurement is concerned, quadratic entropy is most relevant when applied to ultrametric dissimilarities},
author = {Pavoine, S {\~{A}} and Ollier, S and Pontier, D},
doi = {10.1016/j.tpb.2005.01.004},
file = {:Users/Ty/Documents/Mendeley Desktop/Pavoine, Ollier, Pontier{\_}2005{\_}Measuring diversity from dissimilarities with Rao's quadratic entropy Are any dissimilarities suitable.pdf:pdf},
journal = {Theoretical population biology},
keywords = {dissimilarity,diversity,quadratic entropy,smallest enclosing hypersphere,ultrametric},
number = {4},
pages = {231--239},
title = {{Measuring diversity from dissimilarities with Rao's quadratic entropy: Are any dissimilarities suitable?}},
url = {http://www.sciencedirect.com/science/article/pii/S0040580905000183},
volume = {67},
year = {2005}
}
@article{Dolukhanov2005,
abstract = {We analyze statistically representative samples of radiocarbon dates from key Early Neolithic sites in Central Europe belonging to the Linear Pottery Ceramic Culture (LBK), and of pottery-bearing cultures on East European Plain (Yelshanian, Rakushechnyi Yar, Buh-Dniestrian, Serteya and boreal East European Plain). The dates from the LBK sites form a statistically homogeneous set with the probability distribution similar to a single-date Gaussian curve. This implies that the duration of the spread of the LBK is shorter than the available temporal resolution of the radiocarbon dating; therefore, the rate of spread must be larger than 4 km/yr, in agreement with earlier estimates. The East European sites exhibit a broad probability distribution of dates. We identify in these data a spatio-temporal sequence from south-east to north-west, which implies the rate of spread of the initial pottery-making of the order of 1.6 km/yr, comparable to the average rate of spread of the Neolithic in Western and Central Europe. We argue that this spatio-temporal sequence is consistent with an idea that the tradition of the initial pottery-making on East European Plain developed under an early impulse from the Eastern Steppe. {\textcopyright} Published by Elsevier Ltd.},
author = {Dolukhanov, Pavel and Shukurov, Anvar and Gronenborn, Detlef and Sokoloff, Dmitry and Timofeev, Vladimir and Zaitseva, Ganna},
doi = {10.1016/j.jas.2005.03.021},
file = {:Users/Ty/Documents/Mendeley Desktop/Dolukhanov et al.{\_}2005{\_}The chronology of Neolithic dispersal in Central and Eastern Europe.pdf:pdf},
isbn = {0305-4403},
issn = {03054403},
journal = {Journal of Archaeological Science},
keywords = {Eastern Europe,LBK,Neolithic,Propagation rate,Radiocarbon,Statistical analysis},
number = {10},
pages = {1441--1458},
title = {{The chronology of Neolithic dispersal in Central and Eastern Europe}},
volume = {32},
year = {2005}
}
@article{Goodale2010,
abstract = {In Southwest Asia, sickle blades first appear early in the sequence of the transition to agriculture. In the past, detailed qualitative research on silica bearing blade stone tools focus on the characterization of use-wear traces such as polish types and accrual rates. In this paper we approach the study of sickle blades slightly different, choosing to examine tool life-history by developing a method to quantitatively estimate harvesting intensity. The method centers on an experiment of cutting cereal stalks and measuring stone blade edge thickness under a scanning electron microscope as a proxy for cutting time. We end with regressing the experimental results to provide an estimation of how intensively archaeological sickle blades recovered from the site of Dhra', Jordan were used for harvesting. The results, while preliminary, enable an initial interpretation of sickle blades as important tools with long use-life histories during the early Neolithic in the Southern Levant. {\textcopyright} 2009 Elsevier Ltd.},
author = {Goodale, Nathan and Otis, Heather and Andrefsky, William and Kuijt, Ian and Finlayson, Bill and Bart, Ken},
doi = {10.1016/j.jas.2009.12.017},
file = {:Users/Ty/Documents/Mendeley Desktop/Goodale et al.{\_}2010{\_}Sickle blade life-history and the transition to agriculture An early Neolithic case study from Southwest Asia.pdf:pdf},
isbn = {0305-4403},
issn = {03054403},
journal = {Journal of Archaeological Science},
keywords = {Curation,Lithics,Neolithic,Scanning electron microscope analysis,Sickle blades,Southwest Asia,Use-wear},
number = {6},
pages = {1192--1201},
publisher = {Elsevier Ltd},
title = {{Sickle blade life-history and the transition to agriculture: An early Neolithic case study from Southwest Asia}},
url = {http://dx.doi.org/10.1016/j.jas.2009.12.017},
volume = {37},
year = {2010}
}
@article{Arranz-Otaegui2016,
abstract = {Recent studies have broadened our knowledge regarding the origins of agriculture in southwest Asia by highlighting the multiregional and protracted nature of plant domestication. However, there have been few archaeobotanical data to examine whether the early adoption of wild cereal cultivation and the subsequent appearance of domesti-cated-type cereals occurred in parallel across southwest Asia, or if chronological differences existed between regions. The evaluation of the available archaeobotanical evidence indicates that during Pre-Pottery Neolithic A (PPNA) cultivation of wild cereal species was common in regions such as the southern-central Levant and the Upper Euphrates area, but the plant-based subsistence in the eastern Fertile Crescent (southeast Turkey, Iran, and Iraq) focused on the exploitation of plants such as legumes, goatgrass, fruits, and nuts. Around 10.7–10.2 ka Cal BP (early Pre-Pottery Neolithic B), the pre-dominant exploitation of cereals continued in the southern-central Levant and is correlated with the appearance of significant propor-tions (∼30{\%}) of domesticated-type cereal chaff in the archaeobotan-ical record. In the eastern Fertile Crescent exploitation of legumes, fruits, nuts, and grasses continued, and in the Euphrates legumes predominated. In these two regions domesticated-type cereal chaff ({\textgreater}10{\%}) is not identified until the middle and late Pre-Pottery Neolithic B (10.2–8.3 ka Cal BP). We propose that the cultivation of wild and domesticated cereals developed at different times across southwest Asia and was conditioned by the regionally diverse plant-based sub-sistence strategies adopted by Pre-Pottery Neolithic groups. plant domestication | agriculture | southwest Asia | Pre-Pottery Neolithic | archaeobotany P lant domestication is defined as an evolutionary process that resulted from the systematic cultivation of morphologically wild plants and eventually led to the appearance of agriculture (1, 2). In southwest Asia, the archaeobotanical evidence indicates that during the Epipaleolithic (c. 23–11.6 ka Cal BP), the plant-based sub-sistence focused primarily on the collection of wild plant species, including several species that are the ancestors of modern-day do-mesticated cereals and legumes (3–6). Around 11.},
author = {Arranz-Otaegui, Amaia and Colledge, Sue and Zapata, Lydia and Teira-Mayolini, Luis Cesar and Ib{\'{a}}{\~{n}}ez, Juan Jos{\'{e}}},
doi = {10.1073/pnas.1612797113},
file = {:Users/Ty/Documents/Mendeley Desktop/Arranz-Otaegui et al.{\_}2016{\_}Regional diversity on the timing for the initial appearance of cereal cultivation and domestication in southw.pdf:pdf},
isbn = {1612797113},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences},
number = {49},
pages = {201612797},
pmid = {27930348},
title = {{Regional diversity on the timing for the initial appearance of cereal cultivation and domestication in southwest Asia}},
url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1612797113},
volume = {113},
year = {2016}
}
@article{BorgerhoffMulder2006,
abstract = {Cultural traits are distributed across human societies in a patterned way. Study of the mechanisms whereby cultural traits persist and change over time is key to understanding human cultural diversity. For more than a century, a central question has engaged anthropologists interested in the study of cultural trait variation: What is the source of cultural variation? More precisely, are cultural traits transmitted primarily from ancestral to descendant populations (vertical transmission) or between contemporary, typically neighboring populations (horizontal transmission), or do they emerge as independent innovations? While debates among unilineal evolutionists and diffusionists have long since faded, there is still much uncertainty about how traits are transmitted at this macroevolutionary level, as well as about the implications of these transmission patterns for testing hypotheses regarding the adaptive function of particular cultural traits across human populations.},
author = {{Borgerhoff Mulder}, Monique and Nunn, Charles L and Towner, Mary C},
doi = {10.1002/evan.20088},
file = {:Users/Ty/Documents/Mendeley Desktop/Borgerhoff Mulder, Nunn, Towner{\_}2006{\_}Cultural macroevolution and the transmission of traits.pdf:pdf},
isbn = {1060-1538},
issn = {10601538},
journal = {Evolutionary Anthropology},
number = {2},
pages = {52--64},
pmid = {8705},
title = {{Cultural macroevolution and the transmission of traits}},
volume = {15},
year = {2006}
}
@article{Cabanes2010,
abstract = {Esquilleu cave site has provided a moderately well preserved archaeological cave deposit from the Late Pleistocene in the Cantabrian area. Phytolith quantification, identification and determination of the refractive index have been carried out, together with FTIR analyses, from sediment samples collected in the profile. The comparison of the data obtained with the previous micromorphological results allows us to make inferences about the site formation processes and the Neanderthals use of the cave. Phytolith results show the presence of grass leaves nearby the hearth suggesting the repetitive existence of a bedding zone on the same area. Neanderthal behavioral patterns should be revised on the light of high resolution analyses, since diagenetic processes can obscure the existence of differentiated activity areas in the site. ?? 2010 Elsevier Ltd.},
author = {Cabanes, Dan and Mallol, Carolina and Exp{\'{o}}sito, Isabel and Baena, Javier},
doi = {10.1016/j.jas.2010.07.010},
file = {:Users/Ty/Documents/Mendeley Desktop/Cabanes et al.{\_}2010{\_}Phytolith evidence for hearths and beds in the late Mousterian occupations of Esquilleu cave (Cantabria, Spain).pdf:pdf},
isbn = {0305-4403},
issn = {03054403},
journal = {Journal of Archaeological Science},
keywords = {Bedding,FTIR,Hearths,Phytoliths,Site formation processes},
number = {11},
pages = {2947--2957},
publisher = {Elsevier Ltd},
title = {{Phytolith evidence for hearths and beds in the late Mousterian occupations of Esquilleu cave (Cantabria, Spain)}},
url = {http://dx.doi.org/10.1016/j.jas.2010.07.010},
volume = {37},
year = {2010}
}
@article{Pybus2000,
abstract = {Phylogenies reconstructed from gene sequences can be used to investigate the tempo and mode of species diversification. Here we develop and use new statistical methods to infer past patterns of speciation and extinction from molecular phylogenies. Specifically, we test the null hypothesis that per-lineage speciation and extinction rates have remained constant through time. Rejection of this hypothesis may provide evidence for evolutionary events such as adaptive radiations or key adaptations. In contrast to previous approaches, our methods are robust to incomplete taxon sampling and are conservative with respect to extinction. Using simulation we investigate, first, the adverse effects of failing to take incomplete sampling into account and, second, the power and reliability of our tests. When applied to published phylogenies our tests suggest that, in some cases, speciation rates have decreased through time.},
author = {Pybus, Oliver G and Harvey, Paul H},
doi = {10.1098/rspb.2000.1278},
file = {:Users/Ty/Documents/Mendeley Desktop/Pybus, Harvey{\_}2000{\_}Testing macro-evolutionary models using incomplete molecular phylogenies.pdf:pdf},
isbn = {0962-8452 (Print)},
issn = {0962-8452},
journal = {Proceedings of the Royal Society B},
keywords = {be asked once the,but note,dendroica,extinction,former has been,paper we concentrate on,phylogeny,primates,sorex,speciation,that it can only,the latter question},
number = {1459},
pages = {2267--2272},
pmid = {11413642},
title = {{Testing macro-evolutionary models using incomplete molecular phylogenies.}},
url = {http://rspb.royalsocietypublishing.org/content/267/1459/2267.short},
volume = {267},
year = {2000}
}
@article{Berger2009,
abstract = {A major environmental and societal event struck the Mediterranean basin during the 9th millennium cal BP. A sudden and major climatic crisis occurred in the Northern Hemisphere around 8200 cal BP leading to hyper arid conditions along a tropical zone between 15° and 40° North (Near and Middle East), cooler and wetter conditions in western and central Europe, and marked climatic irregularity in the northern Mediterranean basin. At the same time, frequent cultural gaps are observed in cave infillings from Greece to the Spanish peninsula between 8500 and 8000 cal BP, making the vision of the European Mesolithic-Neolithic transition more complex. Furthermore, a stratigraphic and socio-economic rupture associated with a spatial redistribution of sites characterizes the PPNB-NC/Yarmoukian transition in the Near East. The impact of these climatic and environmental changes in the first centuries of the neolithisation of Mediterranean Europe is discussed, using the socio-cultural, economic, stratigraphic and chronological evidence for the first farmers and last hunter-gatherers. This evidence is compared to recent paleoclimatic and geo-archaeological data obtained from prehistoric contexts, in order to measure the hydro-morphological impact on activities in valleys and karstic rockshelters. {\textcopyright} 2008 Elsevier Ltd and INQUA.},
author = {Berger, Jean Fran{\c{c}}ois and Guilaine, Jean},
doi = {10.1016/j.quaint.2008.05.013},
file = {:Users/Ty/Documents/Mendeley Desktop/Berger, Guilaine{\_}2009{\_}The 8200 cal BP abrupt environmental change and the Neolithic transition A Mediterranean perspective.pdf:pdf},
isbn = {1040-6182},
issn = {10406182},
journal = {Quaternary International},
number = {1-2},
pages = {31--49},
title = {{The 8200 cal BP abrupt environmental change and the Neolithic transition: A Mediterranean perspective}},
volume = {200},
year = {2009}
}
@article{Morueta-holme2016,
abstract = {Community assembly rules have been extensively studied, but its association with regional environmental variation, while land use history remains largely unexplored. Land use history might be especially important in Mediterranean forests, considering their historical deforestation and recent afforestation. Using forest inventories and historical (1956) and recent (2000) land cover maps, we explored the following hypotheses: 1) woody species assembly is driven by environmental factors, but also by historical landscape attributes; 2) recent forests exhibit lower woody species richness than pre-existing due to the existence of colonization credits; 3) these credits are modulated by species' life-forms and dispersal mechanisms. We examined the association of forest historical type (pre-existing versus recent) with total species richness and that of diverse life-forms and dispersal groups, also considering the effects of current environment and past landscape factors. When accounting for these effects, no significant differences in woody species richness were found between forest historical types except for vertebrate-dispersed species. Species richness of this group was affected by the interaction of forest historical type with distance to coast and rainfall: vertebrate-dispersed species richness increased with rainfall and distance to the coast in recent forests, while it was higher in dryer sites in pre-existing forests. In addition, forest historical types showed differences in woody species composition associated to diverse environmental and past landscape factors. In view of these results we can conclude that: 1) community assembly in terms of species richness is fast enough to exhaust most colonization credit in recent Mediterranean forests except for vertebrate-dispersed species; 2) for these species, colonization credit is affected by the interplay of forest history and a set of proxies of niche and landscape constraints of species dispersal and establishment; 3) woody species assemblage is mostly shaped by the species' ecological niches in these forests.},
author = {Morueta-Holme, Naia and Blonder, Benjamin and Sandel, Brody and McGill, Brian J. and Peet, Robert K and Ott, Jeffrey E and Violle, Cyrille and Enquist, Brian J and J??rgensen, Peter M. and Svenning, Jens Christian},
doi = {10.1111/ecog.01892},
file = {:Users/Ty/Documents/Mendeley Desktop/Morueta-holme et al.{\_}2016{\_}A network approach for inferring species associations from co-occurrence data.pdf:pdf},
isbn = {6503251521},
issn = {16000587},
journal = {Ecography},
number = {12},
pages = {1139--1150},
title = {{A network approach for inferring species associations from co-occurrence data}},
volume = {39},
year = {2016}
}
@article{Quinn2010,
abstract = {Data from time-lapse single-beam and multi-beam bathymetric surveys are used to assess the rate and scale of morphological change at shipwreck sites caused by anthropogenic forcing. The technique is illustrated by characterizing changes in wreck site morphology over two sites located on the east coast of Ireland - the Drogheda Boat site on the River Boyne and the Arklow Bank site in the Irish Sea. Results indicate that repeated bathymetric surveys accurately and rapidly capture morphological change, with time-lapse accretion-erosion models indicating possible erosion rates of up to 0.04. m per day and accretion rates of 0.36. m per day at dynamic riverine and marine sites in response to external triggers. These data are valuable in understanding site formation processes at fully submerged archaeological sites and in the derivation of high-resolution site formation models. ?? 2010 Elsevier Ltd.},
author = {Quinn, Rory and Boland, Donal},
doi = {10.1016/j.jas.2010.07.005},
file = {:Users/Ty/Documents/Mendeley Desktop/Quinn, Boland{\_}2010{\_}The role of time-lapse bathymetric surveys in assessing morphological change at shipwreck sites.pdf:pdf},
issn = {03054403},
journal = {Journal of Archaeological Science},
keywords = {Accretion-erosion,Bathymetry,Shipwreck,Site formation,Time-lapse},
number = {11},
pages = {2938--2946},
publisher = {Elsevier Ltd},
title = {{The role of time-lapse bathymetric surveys in assessing morphological change at shipwreck sites}},
url = {http://dx.doi.org/10.1016/j.jas.2010.07.005},
volume = {37},
year = {2010}
}
@article{Cadotte2010,
author = {Cadotte, Marc W. and Davies, T. Jonathan and Regetz, James and Kembel, Steven W and Cleland, Elsa and Oakley, Todd H.},
doi = {10.1111/j.1461-0248.2009.01405.x},
file = {:Users/Ty/Documents/Mendeley Desktop/Cadotte et al.{\_}2010{\_}Phylogenetic diversity metrics for ecological communities integrating species richness, abundance and evolutionary.pdf:pdf},
journal = {Ecology letters},
keywords = {abundance distribution,biodiversity,cadotte,ecophylogenetic diversity,evenness,evolutionary,history,jasper ridge biological preserve,jonathan,marc w,null models,shannon index,t},
pages = {96--105},
title = {{Phylogenetic diversity metrics for ecological communities : integrating species richness, abundance and evolutionary history}},
url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1461-0248.2009.01405.x/abstract},
volume = {13},
year = {2010}
}
@article{Isaac2007,
abstract = {Conservation priority setting based on phylogenetic diversity has frequently been proposed but rarely implemented. Here, we define a simple index that measures the contribution made by different species to phylogenetic diversity and show how the index might contribute towards species-based conservation priorities. We describe procedures to control for missing species, incomplete phylogenetic resolution and uncertainty in node ages that make it possible to apply the method in poorly known clades. We also show that the index is independent of clade size in phylogenies of more than 100 species, indicating that scores from unrelated taxonomic groups are likely to be comparable. Similar scores are returned under two different species concepts, suggesting that the index is robust to taxonomic changes. The approach is applied to a near-complete species-level phylogeny of the Mammalia to generate a global priority list incorporating both phylogenetic diversity and extinction risk. The 100 highest-ranking species represent a high proportion of total mammalian diversity and include many species not usually recognised as conservation priorities. Many species that are both evolutionarily distinct and globally endangered (EDGE species) do not benefit from existing conservation projects or protected areas. The results suggest that global conservation priorities may have to be reassessed in order to prevent a disproportionately large amount of mammalian evolutionary history becoming extinct in the near future.},
author = {Isaac, Nick J B and Turvey, Samuel T and Collen, Ben and Waterman, Carly and Baillie, Jonathan E M},
doi = {10.1371/journal.pone.0000296},
file = {:Users/Ty/Documents/Mendeley Desktop/Isaac et al.{\_}2007{\_}Mammals on the EDGE Conservation Priorities Based on Threat and Phylogeny.PDF:PDF},
journal = {PLoS ONE},
number = {3},
pages = {e296},
title = {{Mammals on the EDGE : Conservation Priorities Based on Threat and Phylogeny}},
url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0000296},
volume = {2},
year = {2007}
}
@article{Larson2014a,
abstract = {It is difficult to overstate the cultural and biological impacts that the domestication of plants and animals has had on our species. Fundamental questions regarding where, when, and how many times domestication took place have been of primary interest within a wide range of academic disciplines. Within the last two decades, the advent of new archaeological and genetic techniques has revolutionized our understanding of the pattern and process of domestication and agricultural origins that led to our modern way of life. In the spring of 2011, 25 scholars with a central interest in domestication representing the fields of genetics, archaeobotany, zooarchaeology, geoarchaeology, and archaeology met at the National Evolutionary Synthesis Center to discuss recent domestication research progress and identify challenges for the future. In this introduction to the resulting Special Feature, we present the state of the art in the field by discussing what is known about the spatial and temporal patterns of domestication, and controversies surrounding the speed, intentionality, and evolutionary aspects of the domestication process. We then highlight three key challenges for future research. We conclude by arguing that although recent progress has been impressive, the next decade will yield even more substantial insights not only into how domestication took place, but also when and where it did, and where and why it did not.},
author = {Larson, Greger and Piperno, Dolores R and Allaby, Robin G and Purugganan, Michael D and Andersson, Leif and Arroyo-Kalin, Manuel and Barton, Loukas and {Climer Vigueira}, Cynthia and Denham, Tim and Dobney, Keith and Doust, Andrew N and Gepts, Paul and Gilbert, M Thomas P and Gremillion, Kristen J and Lucas, Leilani and Lukens, Lewis and Marshall, Fiona B and Olsen, Kenneth M and Pires, J Chris and Richerson, Peter J and {Rubio de Casas}, Rafael and Sanjur, Oris I and Thomas, Mark G and Fuller, Dorian Q},
doi = {10.1073/pnas.1323964111},
file = {:Users/Ty/Documents/Mendeley Desktop/Larson et al.{\_}2014{\_}Current perspectives and the future of domestication studies(2).pdf:pdf},
isbn = {0027-8424},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences},
number = {17},
pages = {6139--6146},
pmid = {24757054},
title = {{Current perspectives and the future of domestication studies}},
url = {http://www.pnas.org/content/111/17/6139.abstract},
volume = {111},
year = {2014}
}