Lyons et al. 2016

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

S. Kathleen Lyons1, Kathryn L. Amatangelo2, Anna K. Behrensmeyer1, Antoine Bercovici1, Jessica L. Blois3, Matt Davis1,4, William A. DiMichele1, Andrew Du5, Jussi T. Eronen6, J. Tyler Faith7, Gary R. Graves8,9, Nathan Jud10,11, Conrad Labandeira1,12,13, Cindy V. Looy14, Brian McGill15, Joshua H. Miller16, David Patterson5, Silvia Pineda-Munoz17, Richard Potts18, Brett Riddle19, Rebecca Terry20, Anikó Tóth1, Werner Ulrich21, Amelia Villaseñor5, Scott Wing1, Heidi Anderson22, John Anderson22,
Donald Waller23 & Nicholas J. Gotelli24

Summarized by Altangerel Tsogtsaikhan

Background:  Exploring the hitten effects and mechanisms of how ecological communities’ assemblage are crucial to making predictions of the effects of climate change. Recent work reported that the co-occurrence of species pairs are getting less and less than how it would be expected by random chance. Chronological details of how this co-occurrence structure by change is still unknown. The current study assesses the changes in plant and animal community organizations over geological time (300 million years) with quantification of 359,896 unique taxon pairs co-occurring in 80 assemblages categorizing the aggregation or segregation.

Questions: how are plant and animal communities organized, and does their structure change through time? 

-Do the patterns of species segregation that characterize modern assemblages also hold in the fossil record, or is the present different?

-If whether the non-random species associations of plant and animal assemblages over the past 300 million years are dominated by segregated or aggregated species pairs? 

-Why are species associations so different in fossil versus modern assemblages?

Methods: Plant datasets arranging from 307 million years ago to present including taxon presence and absence across multiple localities in different time. Also, 80 fossil data (38 mammals and 42 plants) and recent assemblage data from North America and Africa were used. Mammal dataset ranged from 21.4 ma. to present.

Each dataset was compared to a null’ assemblage generated by randomization. 39 modern communities were analyzed and compared.

Detecting of non-random species pairs: using binary presence-absence matrix for each taxon. First, the calculated C score was found.

0.0 (aggregation: maximal co-occurrence of both species)

1.0 (segregation: minimal co-occurrence of both species)

PAIRS calculates C score for each pair of species.

Next, the p-value was estimated for association with each species pair by a randomization test.

Weighted Loess regression. A Loess smoothing line was created with the stat smooth function in the R package ggplot2 version 1.0.0 (ref. 37) using default parameters.

Analysis of climate variability impacts: percentage of aggregated species pairs. Last 65 million years of assemblage dataset was used (European Project for Ice Coring in Antarctica).

Individual Evolution of Terrestrial Ecosystems Program (ETE) data set was used.

Breakpoint analysis: a maximum likelihood approach to estimate the breakpoint time (sharper decline in aggregated species in pairs).

Findings: 87-100% fossil data sets were random taxon pairs. 62 out of 80 assemblages showed significant associations that are stronger than the null model which is different than the modern mainland assemblages (most significant associations in the fossil record are aggregated in positive associations which is consistent with last 300 million years of fossil diverse assemblages include mammals, plant macrofossils, and pollen from all other continents. Around 6000 years ago (beginning of Holocene), there was a significant temporal trend towards a greater proportion of segregated species pairs were found. It is pretty similar to the modern assemblages. 64% of significant pairs were aggregated before the breakpoints which dropped to 37% after the breakpoints. A significant decrease in the percentage of positive associations were found in the Pleistocene-Holocene transition (11.700 years ago) indicating the probable human activity.

Thoughts: this is an important research for assessing macroscale pattern of community structure and their specific associations in different time scale to compare the natural versus human impact. For me it is interesting to see the time 6000. Some religious documents claim that this time as the beginning of the life formation. I wonder it has something to do with the socialized and structured human behavior. Also, I know that the Holocene climate stability is pretty unusual and I wonder if it favored the human activities and intensified the decrease in positive associations of ecological assemblages.

Kirch 1996

Kirch PV. 1996. Late Holocene human-induced modifications to a central Polynesian island ecosystem. Anthropology. 93:5296-5300.

Blog Author: Alex Shupinski

Author: 

Patrick Kirch 

EDUCATION

Ph.D., Yale University, 1975

M. Phil., Yale University, 1973

B.A. (cum laude), University of Pennsylvania, 1971

Punahou Academy (Honolulu), 1968

Prehistory and ethnography of Oceania, ethnoarchaeology and settlement archaeology, prehistoric agricultural systems, cultural ecology and paleoenvironmentalism, ethnobotany and ethnoscience, development of complex societies in Oceania.

Abstract

7,000 years of geomorphological and palynological data during the Holocene for Pacific Island (Cook Island) tracking resource exploitation.

2500-1800 were the most significant years from changes and coincided with the arrival of Polynesian people colonizing the island. These human-induced effects included major forest clearance, increased erosion of volcanic hillsides and alluvial deposition in valley bottoms, significant increases in charcoal influx, extinctions of endemic terrestrial species, and the introduction of exotic species.

Introduction

Humans have influenced the land for a long time, it is not a modern phenomenon. 

Perfect ecosystem to study because it is separated from the mainland and has a steady-state equilibra.

Austronesians were a horticultural economy, used marine exploitation, transferred livestock, used fire to clear habitats, used stone, shell, bone, fiber.

Managaia Island, 16-18 million years old along the volcanic chain.  Deep stratigraphic record and strong archeological evidence makes the island very useful.

-Includes 5 vegetative zones on the island, few animal species, possibly colonized by 2.5 kyr.

Methods

25 cores used for stratigraphic records.  

-archeological evidence was obtained from bones (birds, fish, invertebrates), wood charcoal, plant parts and rock shelters. 14C allowed for radiometric dating, 23 bone samples, 40 charcoal samples. 89 samples total

increases in sio2 and A1203, along with free iron, and a decrease in P205. These trends correlate with the pollen evidence indicating removal of climax forest vegetationfrom the central volcanic cone, erosion of the thin organic soil horizon, and exposure of the deeply weathered laterite. Organic content of cores drops in top levels

-increase in erosion and clay deposition

-1.6 kyr signals the removal of indigenous forest vegetation, increase in fernland. Decrease in diversity.  Wood charcoal shows the conversion from native forests to anthropogenic vegetation.

-decrease in bird diversity, introduced invasive species like the Pacific rat, crops

-marine and aquatic changes over 1,000 years: freshwater eels were exploited, decrease in gastropod shell size

Discussion 

Before the arrival of humans the island had high levels of biodiversity, a forested landscape with insignificant amounts of natural fires and only slight erosion. Major environmental changes occurring during the early-to-mid Holocene were lake formation and peat deposition over Pleistocene land surfaces in the valley bottoms, resulting from rapid sea level rise. Polynesian arrival precipitated the following interrelated changes

-burning, erosion, population reduction, introduction of invasive and domestic animals, introduction of anthropogenic vegetation

Humans were fully capable of dramatically altering the environment even before industrialism.

Thoughts 

I really enjoyed this paper because I appreciate tying in all these environmental aspects to drive home the extent of human impact so early on.  I was shocked by the rate of change in such a short period of time even after reading many other papers similar to this.  We used the evidence of this paper to argue in a debate about recognizing the Anthropocene against the idea that by 1945 we have not made enough of a stratigraphic impact to be recognized as a new epoch.

Dornelas et al. 2014

Assemblage Time Series Reveal Biodiversity Change but Not Systematic Loss

Dornelas et al. 2014. Science 344: 296-299

Blog by Willow Guy

Authors

Maria Dornelas

            Reader at U. St. Andrews, UK.

My research focuses on quantifying biodiversity and understanding the processes that shape it. I often work on tropical systems and specifically coral reefs, but I also work with tropical freshwater fish, mangrove crabs and plants for example, as I am more question-driven that organism-driven. I like to combine ecological theory, synthesis of existing data, and fieldwork in my research, and most of the research questions I’m interested in fall under the disciplines of community ecology, macroecology and biogeography. I tend to work on intermediate spatio-temporal scales (that is communities and networks of communities over time-scales of years to tens of years).

Nicholas J. Gotelli

            Professor at U. Vermont

My research addresses basic questions about the organization of animal and plant communities. What are the forces that determine the species composition and abundance of natural assemblages? How do competition and predation affect local community structure? What are the biotic and abiotic factors that control population growth and the risk of extinction?

Brian McGill

            Professor at U. Maine

I seek to understand the patterns and processes controlling the distribution and abundance of organisms at medium to large scales to lead to more predictive theories of how distribution and abundance will change under anthropogenic global change (especially climate change and landcover change).

Intro

There are increasing numbers of threatened species across the globe, but most of this data comes from local analyses.

Goal: to quantify and assess global patterns of temporal change in species diversity

Background

α diversity- diversity at a site

β diversity- diversity overlap between sites

Temporal β diversity- here is a measure of diversity overlap between the same site at different times. Treating site 1 at time A as different than site 1 at time B.

Methods

100 time series (1 time series= collections of data made at one site in different years= a time progression of community change)

Measure α diversity at each time slice and find the slopes of the lines for each community

Measure temporal β diversity with similarity indices 

Results/Discussion

α diversity- there are variations within sites, but no global pattern of change in α diversity

This means that sites around the globe generally have the same number of species in them across time even though they vary locally

-there is no significant difference between marine and terrestrial species

-When sorted by taxonomic group, plants have a slightly positive slope indicating they have, on average, more species in a site today

-When sorted by climatic zone, temperate sites have a positive trend. Tropical sites were nonsignificant and global trends were significantly negative.

This means that temperate sites have more species in them today even though globally there are fewer species.

temporal β diversity- communities exhibit a long-term negative trend in similarity

This means that a community sampled in 1850 has significantly different species in it than the same community sampled today.

Although turnover is expected, this rate of turnover is much more pronounced than expected.

            -Globally, β diversity measures are increasing regardless of sorting

This means that the same species are now found in more sites around the globe =homogenization!

Conclusions

Local and regional assemblages are not losing numbers of species, but numbers of different species. This happens through substitution of species at a site. Communities are becoming more homogenous. 

            “Assemblages are undergoing biodiversity change, but not systematic biodiversity loss”

Thoughts

I thought this was a really neat way to look at this- treating a community at different times like a completely separate community was an interesting way to examine β diversity. I like that homogenization was kind of a surprise result. I got looking at the trends and puzzling over why, then they hit me with the homogenization hypothesis. Wow! I do think they could have improved their climatic analysis, though. Looking at their map, most series fall in the temperatre-tropical and few fall as just tropical and I think that could have influenced how they viewed some of their trends, but not the results as a whole.

Gonzalez et al. 2016

Estimating local biodiversity change: a critique of papers claiming no net loss of local diversity

Authors: Andrew Gonzalez, Bradley J. Cardinale, Ginger R. H. Allington, Jarrett Byrnes, K. Arthur Endsley, Daniel G. Brown, David U. Hooper, Forest Isbell, Mary I. O’Connor, and Michel Loreau. 2016. Ecology97(8): 1949 – 1960.

Blog author: Maria Goller

First author bio: Andrew Gonzalez

Professor at McGill University

His lab focuses on causes and consequences of changes in biodiversity. They translate their research into conservation policy and are particularly interested in retaining ecological connectivity in cities.

Twitter handle is @bio_diverse

Second author bio: Bradley Cardinale

Professor at University of Michigan

Director of the Cooperative Institute for Great Lakes Research, CIGLR

He uses modeling, meta-analyses, and observational research to look at how human behavior impacts biodiversity.

Overview

Earth is losing many species incredibly quickly.

Biodiversity is decreasing but it is unclear what local trends are.

            Locally, species richness varies with human impact.

            Locally, humans can increase diversity (introducing new species, etc...).

This paper is a direct critique of Velland et al. (2013) and Dornelas et al. (2014), who argued that local biodiversity is remaining the same (species turnover may occur, but total richness is constant). 

These authors wanted to know whether the findings of these two papers are representative of global trends in biodiversity. 

They quantified three potential areas of bias in the two meta-analyses.

1) Quantified spatial bias

Created maps of human impact across globe using various impact databases

Randomly sampled same number of locations as used in each paper's dataset, did this 1,000 times, then looked at spatial bias of their studies.

Caveat: human impact maps weren't created to show impact on biodiversity specifically

Spatial bias of both studies

            V. et al. study focused on US and EU => underrepresentation of tropics, boreal forest, tundra, desert

                        Overrepresentation of forests now recovering from logging

            D. et al. study focused on only one of the oceans (North Atlantic), but did include the most heavily impacted areas based on their maps

RESULTS: studies limited in scope to specific areas, ignoring areas of major changes in human impact, and also focused on recovering habitats

2) Quantified temporal bias

Analyses based on short time scales do not accurately reflect changes to diversity

Used the datasets and did a linear regression looking at the effect of study duration on biodiversity decrease => excluding long studies underestimates diversity loss

They argue this is because "extinction debt" may be "repaid" only after many years (local extinctions take time)

3) Quantified post-disturbance bias

Studies often include species richness measures AFTER the ecosystem has begun to recover, so overall it seems that fewer species were lost

When they removed post-disturbance categories, significant negative effect on richness

Take-away: 

Richness is decreasing locally

Scientists should be careful about applying their findings on different scales