Best websites to get comprehensive data on museum inventory?

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Best websites to get comprehensive data on museum inventory?

Post by bekateen »

Hi All,

This is a total science-nerd request: when I'm trying to find known collection sites for South American species, I use GBIF.org and Specieslink.net. But it's my understanding that neither of these sites is comprehensive regarding all collection data. What URLs can you recommend that are more comprehensive?

Note: In the examples below, I searched for all Pseudopimelodus. The GBIF site shows collections in mid to lower Peru because the site still classifies Rhyacoglanis pulcher as Pseudopimelodus pulcher. By contrast, the Specieslink page lists these same specimens as Rhyacoglanis pulcher.

Otherwise, neither site records Pseudopimelodus in the upper Huallaga.

Thanks in advance.

Cheers, Eric
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Re: Best websites to get comprehensive data on museum inventory?

Post by Narelle »

VertNet, iDigBio, and FishNet2 (last seems least popular/updated) are widely used databases cataloging specimens in museum collections. The records there should generally include collection site information.

How well populated these databases are depends on individual institutions digitizing their collection records and recording it there. Some collections (like AMNH) just use their own websites rather than adding to these databases, and of course not everyone has digital records of their collections (my undergraduate institution did not).

VertNet and iDigBio are similarly well populated and usually my first stop when searching for specimens. I use them interchangably (I can never remember which has the search format I prefer).

In at least one (I forget) you can do a search, select the fields you care about, and download a csv to have a longer list of useful data, but they're geared towards looking up individual lot records.
You can probably generate some CSVs with locality info to scroll through, but it won't be visual. One of these has a map, but I'm not sure how accurate it is? Specimens are sometimes marked where they don't belong, but I'm not sure if the map sometimes has the location of the museum (perhaps a data entry mistake, entered in the wrong field?) or if there is something else weird about the specimens (ex. many US collected catfish fossils are for some reason listed as members of Bagridae).
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Re: Best websites to get comprehensive data on museum inventory?

Post by Silurus »

You can also try: https://www.amazon-fish.com
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Re: Best websites to get comprehensive data on museum inventory?

Post by characinkid »

I just played around with this and went to the neotropical database here: https://freshwaterfishdata-dev.ird.fr/geography

You can search for a sp and get collection data etc.

Interesting stuff.
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Re: Best websites to get comprehensive data on museum inventory?

Post by bekateen »

Thanks everyone. Here's the list I have now:
characinkid wrote: 16 Aug 2023, 21:49 I just played around with this and went to the neotropical database here: https://freshwaterfishdata-dev.ird.fr/geography

You can search for a sp and get collection data etc.

Interesting stuff.
Not sure I'm using this right. I tried Pseudopimelodus bufonius, and I tried to find just the genus Pseudopimelodus (to include all species and any entries as "Pseudopimelodus sp."). I am able to look up individual species and I can download a CSV fle that looks like the image below, but I don't see the locality info nor do I see the fish mapped on the map that is shown on the screen. Not sure how this helps me unless I'm missing something. Hopefully I am missing things.

What I did find though, on idigbio, is an entry for Pseudopimelodus sp. along the upper Huallaga near Tingo Maria. That is the only documentation I've found so far regarding Pseudopimelodus so high up the Huallaga.

Thanks everyone,
Eric

T
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Re: Best websites to get comprehensive data on museum inventory?

Post by Shane »

Eric,
Be sure to take the locality data with a grain of salt. Much of the data comes from "Fishes of..." books and papers which are often riddled with incorrect identifications. I think the most useful data to collect would be holotype location as you know that record is accurate.
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Re: Best websites to get comprehensive data on museum inventory?

Post by bekateen »

Hi Shane.

Thanks for the warning. I'm thinking you intend it this way: if there's a specimen in a museum with latitude and longitude data, the location is probably right but the name is wrong. That's what you mean, yes?

And yes, the nice thing about some of these websites is that they allow you/ me to select type specimens in searches.

The best outcome here is that the Pseudopimelodus from Tingo Maria is at the CAS in San Francisco, about 90 minutes away from me. I need to plan a visit.

Cheers, Eric
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Re: Best websites to get comprehensive data on museum inventory?

Post by Shane »

Just looking at specimen records is probably more accurate than searching the literature, but yes many students and professionals look at museum collections every year and find new spp or incorrect identifications. Sometimes even among the type material!
I am just saying be cautious if the location information is at odds with the holotype collection data. Chaetostoma milesi was described from, and is restricted to, the Magdalena basin. However, there are dozens of collections of spotted Chaetostoma labeled "C. milesi" from several different drainages in South America.
Hope that makes sense.
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Re: Best websites to get comprehensive data on museum inventory?

Post by bekateen »

Shane wrote: 17 Aug 2023, 14:25 I am just saying be cautious if the location information is at odds with the holotype collection data. Chaetostoma milesi was described from, and is restricted to, the Magdalena basin. However, there are dozens of collections of spotted Chaetostoma labeled "C. milesi" from several different drainages in South America.
Hope that makes sense.
-Shane
Exactly what I meant, yes. In these questionable reports, it's still accurate to say SOMETHING (some kind of fish) was collected at the location specified, but the identity of the fish may be inaccurate.

In the case of the Tingo Maria report, my question is this: since that specimen was not keyed to species level (it's reported simply as Pseudopimelodus), is it in fact really Pseudopimelodus? Or is it Rhyacoglanis? If it turns out to be Rhyacoglanis, then I'm back to where I started (in terms of trying to figure out what my fish are), since I find no other reports of medium-large Pseudopimelodids of any kind in this region. But if it is indeed a Pseudopimelodus, then at least I have a documented report of the genus this far up the Huallaga, in the region where my fish are reportedly caught (if the exporter is right). And if it is Pseudopimelodus, is it Pseudopimelodus bufonius, which is the only species that is close to mine in color pattern?

On a different thought, I'm told my fish were collected in the Huallaga highlands in a place where Rhyacoglanis should be found. If the habitat is similar, would ecological factors support the evolution of a larger fish like Pseudopimelodus bufonius in a habitat like that? Cooler temperatures, more violent water currents and shallower water don't seem so conducive large predators, as compared to living in a main channel of a bigger, slower river. I hold out hope that if there is a form of Pseudopimelodus (maybe undescribed) native to a Rhyacoglanis habitat, maybe natural selection pressures would lead to a reduction in body size, just as is seen in Rhyacoglanis. But then, I also realize that juveniles of such large species might take refuge in more harsh habitats, so really, I can't predict anything as to why my fish might be there.

Wishful thinking can be gratifying but it is rarely fulfilling.

Cheers, Eric
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Re: Best websites to get comprehensive data on museum inventory?

Post by Shane »

Have you read

Ancient genetic divergence in bumblebee catfish of the genus Pseudopimelodus (Pseudopimelodidae: Siluriformes) from northwestern South America

Until a lot more work like this is done I am not sure it's worth trying to apply the current scientific names. They were only looking at Colombia and showed that numerous, genetically distinct spp were "lumped." I can't begin to imagine how many genetically distinct sp currently fall under P. bufonius!

What does keep showing up in these DNA studies (there was a recent paper on Chaetostoma as well) is that most smaller fishes appear to be restricted to their confined drainage. Based on my years of collecting this always held true. Cross from one drainage to another and you get different fishes. You don't get fishes that magically crossed mountains that are 10s of millions of years old.

So much more work to be done.

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Re: Best websites to get comprehensive data on museum inventory?

Post by bekateen »

Shane wrote: 17 Aug 2023, 22:07 Have you read

Ancient genetic divergence in bumblebee catfish of the genus Pseudopimelodus (Pseudopimelodidae: Siluriformes) from northwestern South America
Yes. It's saved on my computer and a must-read reference on this subject, along with the 2021 Silva paper on similar subject, Chuctaya et al's 2023 Rediscovery of Rhyacoglanis pulcher and the 2017 Shibatta paper describing Rhyacoglanis as a genus.
Shane wrote: 17 Aug 2023, 22:07Until a lot more work like this is done I am not sure it's worth trying to apply the current scientific names. They were only looking at Colombia and showed that numerous, genetically distinct spp were "lumped." I can't begin to imagine how many genetically distinct sp currently fall under P. bufonius!

What does keep showing up in these DNA studies (there was a recent paper on Chaetostoma as well) is that most smaller fishes appear to be restricted to their confined drainage. Based on my years of collecting this always held true. Cross from one drainage to another and you get different fishes. You don't get fishes that magically crossed mountains that are 10s of millions of years old.

So much more work to be done.

-Shane
Exactly. That's why I created the entry here in the CLOGs and if you look on the occurrence map, it's all over the continent. I've endeavored to include all photograph-based Rhyacoglanis data (either Rhyacoglanis sp., NOT near type locality, and all reported reports. I put them in one entry (just as I've done for ) so that for now nobody mistakes them as the respective species sensu stricto, and so that later on, if ever any of these gets described as n.s. or identified to an existing species, then these photos can be shifted accordingly in the CLOGs.

I don't have weighted illusions either way that the upper Huallaga specimens in museums, or the fish I now possess (which alas, I wish I could know with more certainty their catch location) might be a new species or a range-expansion for true , but given how far-flung it is from the type locality of P. bufonius, and considering that the Rhyacoglanis from the same region are not the same as true Rhyacoglanis pulcher, I think the odds are good that the Pseudopimelodus are new. Now, whether they are a dwarf Pseudopimelodus or just juveniles waiting to grow out remains to be seen.

Cheers, Eric
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Re: Best websites to get comprehensive data on museum inventory?

Post by Kirin »

I just noticed GBIF and Inaturalist were lacking a lot so I think it varies and honestly it seems in general you have to go direct. Several times I've tried locating specimens particularly and just ended up going to the museum catalog if they have one.
Then for geographic data I do think there is more to it as there are locations I cannot find a reference to and in discussion with others it's likely areas changing names with politics. Modern era we are more precise with coordinates where we can.
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