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oharac / bd_chi

Repository for code and generated data for "At-risk marine biodiversity faces extensive, expanding, and intensifying human impacts": O’Hara, C. C., Frazier, M., & Halpern, B. S. (2021), Science, 372(6537), 84–87. https://doi.org/10.1126/science.abe6731
http://ohi-science.nceas.ucsb.edu/visualizing_human_impacts/
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Intro to biodiversity/cumulative human impacts project #1

Open oharac opened 5 years ago

oharac commented 5 years ago

Some quick notes from our meeting last week:

Wilderness biodiversity

Overlay recent wilderness paper with map of biodiversity to examine status (etc) of biodiversity within wilderness areas. What % of species in wilderness areas are threatened? Is biodiversity status within wilderness areas different from non-wilderness?

These can be broken out by taxonomic groups, and perhaps types of habitat or ecoregion.

First steps - get a hold of wilderness maps.

Spatial comparison of BD status to CHI

Similar to Selig et al 2014 - define "bins" of cumulative impact (high/low) as well as trend (increasing/decreasing/stable); compare these to metrics of biodiversity magnitude (species richness, range-rarity-weighted species richness, maybe normalized range-rarity-weighted species richness, as in Selig paper) as well as biodiversity status (mean status, % threatened, trend, etc).

These can be broken out by classes of stressors, as well as taxonomic groups.

With multiple dimensions of comparison (BD magnitude, status, CHI stressors, trends) it becomes important to identify which overlaps indicate what kinds of prioritization.

Species-specific comparison of status to CHI

For each species in the dataset, identify how its spatial distribution overlaps with cumulative impact maps. Consider like a density plot of presence in various levels of CHI (low-medium-high) on one axis and density plot of presence vs. CHI trend in another, described by distribution parameters (i.e. mean and variance probably)

These can be aggregated up to taxonomic group level to get a sense of the taxon's general exposure to stressors. How to aggregate - area weighted? all species equally weighted? inverse area weighted?

Perhaps regional aggregation might be interesting as well.

Melsteroni commented 5 years ago

Additional notes on approaches to BD/CHI

Wilderness biodiversity

Another interesting project is to determine proportion of species (all species and threatened species only) that would be protected if the wilderness areas are protected. The issue is that using "wilderness" as a primary (or significant) criteria for protection might not result in protecting much of anything.

So, this approach to designating protected areas might not have a great return.

bshalpern commented 5 years ago

FYI Kendall Jones is leading a paper that is looking at the % of ocean needed to adequately protect marine species, within wilderness, KBAs, MPAs, and gap areas.  The paper is also overlapping threat layers (from our 2015 paper). Let's discuss where this leaves us.

On 2/5/2019 8:54 AM, Melsteroni wrote:

Additional notes on approaches to BD/CHI

  Wilderness biodiversity

Another interesting project is to determine proportion of species (all species and threatened species only) that would be protected if the wilderness areas are protected. The issue is that using "wilderness" as a primary (or significant) criteria for protection might not result in protecting much of anything.

So, this approach to designating protected areas might not have a great return.

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--

Benjamin S. Halpern Director, Nat'l. Center for Ecol. Anal. & Synth. (NCEAS) University of California 735 State St., Suite 300, Santa Barbara, CA 93101 (ph) 805.893.7527 (web) http://www.nceas.ucsb.edu

Professor, Bren School of Environmental Science and Management UCSB, Santa Barbara, CA 93106

Senior Fellow, UN Envir. Prog.- World Conserv. Monitor. Cent. (UNEP-WCMC)

Melsteroni commented 5 years ago

Goal: Convert our brainstorming ideas into more specific questions/issues we would like to address

Part 1 of 3

Wilderness areas

Question: Is the protection of "wilderness" areas a good management decision?

Approach:

  1. Do wilderness areas coincide with high diversity/endemism areas?
  2. How many species would this protect? How many vulnerable species? How does this compare to other regions?

Overview: This seems like it would be relatively easy to do from an analytical and writing perspective (the framing of the paper could follow the Selig paper).

But, based on Ben's comment, it sounds like this might be taken care of?

Melsteroni commented 5 years ago

Goal: Convert our brainstorming ideas into more specific questions/issues we would like to address

Part 2 of 3

BD and CHI

I am still trying to figure out our larger goal here....HELP!

I generally get that we are looking at how the following variables coincide: CHI, CHI-Trend, species vulnerability, diversity, endemism. The endpoint isn't clear to me, but here are some possibilities:

  1. Exploring the true threat to species due to high/increasing CHI. If a large majority of global biodiversity hotspots (and endemism and vulnerable species hotspots) are located in high/increasing CHI areas this suggests we are more screwed than looking at a CHI map would suggest.
  2. Identify priority conservation areas using high/low CHI/CHI-Trend and species vulnerability/diversity/endemism data. This is basically the Selig paper, but now incorporating CHI trend and species vulnerability.
  3. Explore potential causal relationships between CHI and/or changes in CHI with species vulnerability and/or changes in vulnerability.

Overview: Cut 3 because it is fraught with statistical assumptions and challenges.

I think framing the paper from the 1st option seems the most interesting. And, we could say that our approach also helps identify priority conservation areas (2). I also think breaking the impacts into the 4 main groups (fishing, land-based, ocean-based, climate change) for the analyses would be useful because protected areas are unlikely to do much for mitigating climate change impacts.

One cool way to visualize the results might be:

image Each point is a raster cell (so there would be wwwwaaaaayyyyyyy more points in the actual figure and it would be much messier...but there are cool ways to convey this). A pattern like this would suggest that the CHI maps are actually more scary than they appear because high diversity areas are under relatively more threat.

Melsteroni commented 5 years ago

Goal: Convert our brainstorming ideas into more specific questions/issues we would like to address

Part 3 of 3

Species risk due to CHI

Question: Which species are most at threat due to high CHI and increasing CHI?

Methods: Overlay each species on a CHI/CHI trend category map and determine the proportion of their range falling into 9 categories: image (this species has elevated risk)

Then summarize this information across all species and taxa groups and vulnerability groups. This would tell us:

  1. Overall, are species at higher overall risk than we would predict by chance alone given their distribution relative to the global distribution of high, fast increasing CHI.
  2. Which taxonomic groups appear at most/least at risk based on this criteria (and consider integrating with IUCN status)?
  3. What is the risk status of IUCN threatened species?
  4. This may present an alternative approach to identifying conservation priority areas. For example, there might be areas with a high proportion of at risk species (based on a large proportion of their range falling in high risk areas and/or IUCN threatened status) but also having relatively low CHI/slow increasing CHI.
Melsteroni commented 5 years ago

Conclusions (for now)

I think we should pick one of the projects to focus our efforts....clarify our question/objectives...and then figure out the next steps!

oharac commented 5 years ago

thanks so much for the helpful thinking and I love the visualization idea, @Melsteroni !

In related news, I just looked at my code for the BD risk paper, thinking I had to update some of the analysis to address the reviewer comments about resolution and such, but nope - looks like I nailed it the first time. So a good portion of the "major revisions" becomes "explaining the methods a little bit better."

Melsteroni commented 5 years ago

Well, that must have been very satisfying! Yay for "major revisions" transforming into "minor revisions"!

On Thu, Feb 7, 2019 at 4:37 PM oharac notifications@github.com wrote:

thanks so much for the helpful thinking and I love the visualization idea, @Melsteroni https://github.com/Melsteroni !

In related news, I just looked at my code for the BD risk paper, thinking I had to update some of the analysis to address the reviewer comments about resolution and such, but nope - looks like I nailed it the first time. So a good portion of the "major revisions" becomes "explaining the methods a little bit better."

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/oharac/bd_chi/issues/1#issuecomment-461636476, or mute the thread https://github.com/notifications/unsubscribe-auth/AFbBDfs7QvxiCjjCG9YY-Ubrr6jMPe2oks5vLLihgaJpZM4aa77N .

bshalpern commented 5 years ago

replying to all 3 parts.

Kendall's paper is looking at all biodiversity (23K species) without regard to threatened status but with one part of the analysis focused on threats to species (from our previous CHI layers). So a focus on threatened status is novel no matter what the question.

Wilderness question framed only on diversity or endemism is not novel, so I would skip this.

Adapting the vulnerability weights to species and tracking species risk to CHI trends would both be novel and interesting. The former will likely be done under the new OceanKind project but not available until later this year. The latter could be the focus of this immediate paper. Updating the Selig paper (and/or the Kendall Jones paper) to account for biodiversity hotspots and CHI trends could be interesting, but not a huge leap forward on the science.

In short, I think I like @melstroni idea #3 of 3, which builds on the species risk + CHI trend idea from idea #2 of 3.

On 2/5/19 2:06 PM, Melsteroni wrote:

  Conclusions (for now)

I think we should pick one of the projects to focus our efforts....clarify our question/objectives...and then figure out the next steps!

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/oharac/bd_chi/issues/1#issuecomment-460822811, or mute the thread https://github.com/notifications/unsubscribe-auth/AG7Ke6x3jZ88kd5Md9rVmV_483iXo5feks5vKgBpgaJpZM4aa77N.

--

Benjamin S. Halpern Director, Nat'l. Center for Ecol. Anal. & Synth. (NCEAS) University of California 735 State St., Suite 300, Santa Barbara, CA 93101 (ph) 805.893.7527 (web) http://www.nceas.ucsb.edu

Professor, Bren School of Environmental Science and Management UCSB, Santa Barbara, CA 93106

Senior Fellow, UN Envir. Prog.- World Conserv. Monitor. Cent. (UNEP-WCMC)