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opencc-zeroDec 2016View details →

Data from: Continental divide: predicting climate-mediated fragmentation and biodiversity loss in the boreal forest

Climate change threatens natural landscapes through shifting distribution and abundance of species and attendant change in the structure and function of ecosystems. However, it remains unclear how climate-mediated variation in species' environmental niche space may lead to large-scale fragmentation of species distributions, altered meta-population dynamics and gene flow, and disrupted ecosystem integrity. Such change may be especially relevant when species distributions are restricted either spatially or to a narrow environmental niche, or when environments are rapidly changing. Here, we use range-wide environmental niche models to posit that climate-mediated range fragmentation aggravates the direct effects of climate change on species in the boreal forest of North America. We show that climate change will directly alter environmental niche suitability for boreal-obligate species of trees, birds and mammals (n=12), with most species ranges becoming smaller and shifting northward through time. Importantly, species distributions will become increasingly fragmented, as characterized by smaller mean size and greater isolation of environmentally-suitable landscape patches. This loss is especially pronounced along the Ontario-Québec border, where the boreal forest is narrowest and roughly 78% of suitable niche space could disappear by 2080. Despite the diversity of taxa surveyed, patterns of range fragmentation are remarkably consistent, with our models predicting that spruce grouse (Dendragapus canadensis), boreal chickadee (Poecile hudsonicus), moose (Alces americanus) and caribou (Rangifer tarandus) could have entirely disjunct east-west population segments in North America. These findings reveal potentially dire consequences of climate change on population continuity and species diversity in the boreal forest, highlighting the need to better understand: 1) extent and primary drivers of anticipated climate-mediated range loss and fragmentation; 2) diversity of species to be affected by such change; 3) potential for rapid adaptation in the most strongly-affected areas; and 4) potential for invasion by replacement species.

opencc-zeroJun 2019View details →

Data from: Overlooked biodiversity loss in tropical smallholder agriculture

Smallholder agriculture is the main driver of deforestation in the western Amazon, where terrestrial biodiversity reaches its global maximum. Understanding the biodiversity value of the resulting mosaics of cultivations and secondary forest is therefore crucial for conservation planning. However, Amazonian communities are organized across multiple forest‐types that support distinct species assemblages, and little is known about smallholder impacts across the range of forest habitats that are essential for sustaining biodiversity. We address this issue with a large‐scale field inventory of birds and trees in primary forest and smallholder agriculture in northern Peru, spanning three key forest‐types that structure Amazonian biodiversity. For birds, smallholder agriculture supported species richness comparable to primary forest within each forest‐type, but biotic homogenization across forest‐types resulted in substantial losses of biodiversity overall. These overall losses are invisible to studies that focus solely on upland (terra firme) forest. For trees, biodiversity losses in upland forests dominated the signal across all habitats combined, and homogenization across habitats did not exacerbate biodiversity loss. Proximity to forest strongly predicted the persistence of forest‐associated bird and tree species in the smallholder mosaic, and because intact forest is ubiquitous in our study area, our results probably represent a best‐case scenario for biodiversity in Amazonian agriculture. Land‐use planning both inside and outside of protected areas should recognize that tropical smallholder agriculture has pervasive biodiversity impacts that are not apparent in typical single‐habitat studies. The full range of forest‐types must be surveyed to accurately assess biodiversity losses, and primary forests must be protected to prevent landscape‐scale biodiversity loss.

opencc-by-4.0Aug 2024View details →

Variation in species' dispersal capacities amplifies effects of habitat loss and fragmentation on biodiversity loss

Simulation data and model belonging to the manuscript 'Variation in species’ dispersal capacities amplifies effects of habitat loss and fragmentation on biodiversity loss', by Monique de Jager and Edwin Pos. The folder 'Generated data' holds the generated simulation data. The folder 'Model' contains the 2-dimensional, semi-spatial, near-neutral, individual-based model. A description of the model can be found in the file 'README.md'.

opencc-zeroOct 2021View details →

Biodiversity-productivity relationships in a natural grassland community vary under diversity loss scenarios

Understanding the biodiversity-productivity relationship and underlying mechanisms in natural ecosystems under realistic diversity loss scenarios remains a major challenge for ecologists despite its importance for predicting impacts of rapid loss of biodiversity worldwide. Here we report the results of a plant functional group (PFG) removal experiment conducted on the Mongolian Plateau, the largest remaining natural grassland in the world. Our results demonstrated that the biodiversity-productivity relationship varied among positive linear, neutral, and unimodal forms under different PFG loss patterns. Moreover, the form of this relationship with the same PFG loss pattern sometimes changed through time. The abundance of the remaining PFG(s) before removal and their compensation following the loss of other PFGs were two major mechanisms affecting the biodiversity-productivity relationship under diversity loss scenarios. The abundance effect promoted positive responses of productivity to biodiversity, but the compensation effect caused several biodiversity-productivity relationships, hinging on its direction (positive or negative) and strength. As indicated by the values of the compensation index, negative, zero and partial compensations contributed to the positive relationships, while full compensation resulted in a neutral relationship. Over-compensation at intermediate PFG richness levels created a unimodal curve in our system, but it could also lead to a negative linear relationship. Synthesis. Our experiment provides a vivid picture of how the form of the biodiversity-productivity relationship varies among different diversity loss patterns in a natural ecosystem. We argue that compensation by the remaining species, which is not revealed by synthesized biodiversity experiments, plays a critical role in shaping the form of this relationship when diversity is lost from existing systems. The direction and strength of compensation are highly dependent on extirpation scenarios. Thus, impacts of biodiversity loss on natural ecosystems are likely more complex than predicted by the canonical positive saturating curve obtained from the synthesized biodiversity experiments. We suggest that models forecasting the consequences of biodiversity declines on natural ecosystems should take into account diversity loss patterns and the ensuing compensation.

Fig. 3 in Amphibian fungal panzootic causes catastrophic and ongoing loss of biodiversity

Fig. 3. Timing of chytridiomycosis-associated amphibian declines. (A) Declines by year. Bars indicate the number of declines in a given year, stacked by decline severity. For species for which the exact year of decline is uncertain, the figure shows the middle year of the interval of uncertainty, as stated by experts or inferred from available data. (B) Cumulative declines. Curves indicate the cumulative number of declines in each decline-severity category over time. In (A) and (B), the arrows mark the discovery of chytridiomycosis in 1998.

Fig. 2 in Amphibian fungal panzootic causes catastrophic and ongoing loss of biodiversity

Fig. 2. Taxonomic distribution of chytridiomycosis-associated amphibian declines. Each bar represents one species, and color denotes the severity of its decline. Concentric circles indicate, from inner to outer, order (Caudata or Anura), family, and genus. Full names are given only for families and genera that include>5 and>2 species, respectively; details for all taxa are in table S4. Within each taxonomic level, sublevels are ordered alphabetically. Protruding bars indicate species for which there is evidence of recovery. [Photo credits (left to right): Telmatobius bolivianus, I.D.l.R.; Atelopus zeteki, B.G.; and Craugastor crassidigitus, B.G.]

Fig. 4 in Amphibian fungal panzootic causes catastrophic and ongoing loss of biodiversity

Fig. 4. Severity of chytridiomycosis-associated amphibian declines in relation to the geographic and elevational ranges of species. (A) Declines in relation to geographic range. Each dot indicates a species, located randomly along the perimeter of a circle with radius equal to the log10 of the species's geographic range in kilometers squared. (B) Declines in relation to elevational range. Horizontal bars, boxes, and vertical bars indicate, respectively, mean, first and second quartiles, and 95% quantiles of elevation ranges within each category of decline severity.

Fig. 1 in Amphibian fungal panzootic causes catastrophic and ongoing loss of biodiversity

Fig. 1. Global distribution of chytridiomycosis-associated amphibian species declines. Bar plots indicate the number (N) of declined species, grouped by continental area and classified by decline severity. Brazilian species are plotted separately from all other South American species (South America W); Mesoamerica includes Central America, Mexico, and the Caribbean Islands; and Oceania includes Australia and New Zealand. No declines have been reported in Asia. n, total number of declines by region. [Photo credits (clockwise from top left): Anaxyrus boreas, C. Brown, U.S. Geological Survey; Atelopus varius, B.G.; Salamandra salamandra, D. Descouens, Wikimedia Commons; Telmatobius sanborni, I.D.l.R; Cycloramphus boraceiensis, L.F.T.; Cardioglossa melanogaster, M.H.; and Pseudophryne corroboree, C. Doughty]

Fig. 1 in Amphibian fungal panzootic causes catastrophic and ongoing loss of biodiversity

Fig. 1 in Amphibian fungal panzootic causes catastrophic and ongoing loss of biodiversity

Fig. 2 in Amphibian fungal panzootic causes catastrophic and ongoing loss of biodiversity

Fig. 4 in Amphibian fungal panzootic causes catastrophic and ongoing loss of biodiversity

opencc-zeroJun 2021View details →

Data and R code from: Fire-induced loss of the world's most biodiverse forests in Latin America

Fire plays a dominant role in deforestation, particularly in the tropics, but the relative extent of transformations and influence of fire frequency on eventual forest loss remain unclear. Here we analyze the frequency of fire and its influence on post-fire forest trajectories between 2001-2018. We account for ~1.1% of Latin American forests burnt in 2002-2003 (8,465,850 ha). Although 40.1% of forests (3,393,250 ha) burned only once, by 2018~48% of the evergreen forests converted to other, primarily grass-dominated uses. While greater fire frequency yielded more transformation, our results reveal the staggering impact of even a single fire. Increasing fire frequency imposes greater risks of irreversible forest loss, transforming forests into ecosystems increasingly vulnerable to disturbance and degradation. Reversing this trend is indispensable to both mitigate and adapt to climate change globally. As climate change transforms fire regimes across the region, key actions are needed to conserve Latin American forests.

opencc-zeroSep 2021View details →

Data from: The sensitivity of Neotoma to climate change and biodiversity loss over the late Quaternary

The late Quaternary was a time of considerable environmental change in North America. Not only was climate highly variable, but a megafaunal extinction at the terminal Pleistocene led to considerable loss of biodiversity. These combined perturbations likely had cascading effects across communities and ecosystems. Here, we focus on a detailed fossil record on the Edwards Plateau in Texas and the response of Neotoma, a genus of herbivorous rodents, to these environmental and ecological perturbations. We characterized changes in Neotoma body mass and diet across the past 20,000 years; body mass was estimated using measurements of fossil teeth and diet quantified using stable isotope analysis of carbon and nitrogen isotope from fossil bone collagen. We found that prior to ~7,000 cal yr BP, maximum mass was positively and significantly correlated to precipitation and negatively correlated to temperature. Independently, body mass was significantly and negatively correlated to communtiy composition becoming more similar to modern over time. Moreover, while Neotoma diet in the Pleistocene was primarily sourced from C3 resources, it became progressively more reliant on C4 (and potentially CAM) plants through the Holocene. The combination of decreasing population body mass and higher C4/CAM consumption was associated with a regional transition from a mesic forest to a xeric savanna grassland. Our results suggest that Neotoma during the terminal Pleistocene were responding to climatic factors through changes in body size, while changes in local resource availability during the Holocene likely led to changes in the relative abundance of different Neotoma species in the community.

opencc-by-4.0Jan 2023View details →

African biodiversity loss overview - data and scripts

Data and scripts used in an overview of African biodiversity loss (link to come). Mainly map data, but also R scripts, and instructions on how to draw the maps. The instructions are somewhat over-detailed, and will likely not be relevant for very many years, but could be useful for anyone just getting started in mapping biodiversity loss data.

opencc-by-4.0Sep 2023View details →

Neutral model data from "Fragmentation mitigates biodiversity loss immediately after habitat destruction"

Raw community data from the manuscript "Fragmentation mitigates biodiversity loss immediately after habitat destruction." The folder contains text files of raw community data from the neutral model. Filenames contain the parameter values used in the simulation of that community. In the text files, each number is a different species and its position in the vector indicates its x, y coordinate in the 2D map. See <a href="https://github.com/cmsmith91/fragmentation/blob/main/python_code/neutral_mod-amarel15june2021.py">code</a> in the manuscript github repository.

publicDec 2018View details →

Data from: Primary rainforest amount at the landscape scale mitigates bird biodiversity loss and biotic homogenization

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publicOct 2015View details →

Data from: Genetic diversity loss in a biodiversity hotspot: ancient DNA quantifies genetic decline and former connectivity in a critically endangered marsupial.

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publicJul 2017View details →

Data from: The impacts of oil palm on recent deforestation and biodiversity loss

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