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Pogonomyrmex Identification Request


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#41 Offline ClaytonBaby - Posted September 18 2023 - 12:16 AM

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Or where you saying I would need a initial specimen of a known Pogonomyrmex sp. to cross reference with the same caste of the species being described, and submitting any caste for the holotype in the species is acceptable? Ex. I could submit a holotype that is a male of a specific new Pogonomyrmex sp. as long as when describing it, its differences are cross referenced with a known Pogonomyrmex sp.?

One only needs a single specimen to designate a novel species such as M.heureka above. Since there can be diverse morphology between queens and workers (both female we won't discuss males) if let's say one only had a single queen specimen one felt was a novel species candidate. It would be easy to most likely get it down to subfamily then genus. To species level one would need, ideally, confirmed specimens of queens or very throughly written detailed descriptions of queens in that genus to begin comparing and "cross referencing".

The M heureka example is rather extreme since the initial worker found was so unlike any previously described ant from that region that "red flags" were raised. If one had a single worker of a putative Pognomyrmex "X" ant then designating it a novel species would be much more demanding and reviewers and experts in that genus would expect very definitive evidence to accept the claim of "species novum" was worthy. This is what I had to demonstrate when I had found what I was certain was a novel species of Tapinoma from Tennessee and it took time to lay out various forms of evidence: (a) nuclear DNA, (b.) mitochondrial DNA, (c.) unique and distinct morphology, (d) behavior and (e) allochrony and (f) oligogyny colony structure. Thus 7 lines of evidence. Had I found this ant in a rain forest less demanding evidence may have been accepted, but since I found a putative new species in an area where new ants that are not cryptic are rarely or ever found anymore (unless it is a genus level reassessment which these days is almost always based a suit of nuclear genes) and in a genus that has only a limited number of endemic species the bar of "burden of proof"was substantially raised.
and if you don’t mind me asking.. how did you go about acquiring the evidence labeled (a), (B), ©, and (e)???


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#42 Offline PurdueEntomology - Posted September 18 2023 - 12:18 AM

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Generally these days a good suit of nuclear genes (5-10) will do the trick!  For me though I decided that I needed a full-proof-set of evidence that each in it's own weighed heavily to "new species", each may not have been a game changer but it was heavy enough to warrant novel species designation. When I was a kid I wanted to do that too, head down to the Amazon and find something new.  For me though I was doing a separate study that just happened to use 1 mitochondrial gene fragment, but as I worked on the corpus of my ants being used for my study I began to question little things that hinted that something else was going on.  As I begin to bring up the question that "I think this may be a new species" the professors on my committee would each want something stronger and would suggest, do this or that, come back with the results an let's consider.  Each was skeptical: one was an expert on fire ants, one was a renowned evolutionary biologist, one was a world expert on a small family of flies ( had has many new species described), one was a genomics expert and one was just skeptical!  So each would demand thoroughness and wanted to see if there were any "cracks" in my hypothesis i.e., I think this is a novel species. 


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#43 Offline PurdueEntomology - Posted September 18 2023 - 12:25 AM

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As for DNA (evidences a and b.) here is a cut and paste from my current draft of the species description under "Methods and Materials" for the mitochondrial fragment, the nuclear whole genome analysis is much more involved: 

 

 

Mitochondrial DNA:

A fragment of the mitochondrial cytochrome C oxidase subunit I (COI) was amplified using the primers LEP-F1 (5'-ATTCAACCAATCATAAAGATATTGG-3') and LEP-R1 (5'-TAAACTTCTGGATGTCCAAAAAATCA-3’) targeting a 638-bp fragment (Menke et al., 2010). Conventional PCR using 15 µl of DreamTaq Hot Start Green PCR Master Mix (2X) (Thermo Fisher Scientific, Waltham, MA), 1 µl of primer LEP-F1 (10 µM), 1 µl of primer LEP-R1 (10 µM) and 8 µl nuclease free water with 5µl of extracted DNA for a final volume of 30 µl. PCRs were done in a MyCycler™  thermal cycler (BioRad, Hercules, California) using the following conditions: 95°C for 10 min, 4 cycles of 94°C for 1 min, 45°C for 1.5 min, 72°C for 1.5 min; 34 cycles of 94°C for 1 min, 45°C for 1.5 min, 72°C for 1 min; and a final extension of 72°C for 3 min. The 638-bp products were visualized using a 0.9% agarose gel stained with ethidium bromide ran at 118 volts for 30 min. ExoSAP-IT (Thermo Fisher Scientific, Waltham MA) at 1.5 µl per 5 µl of PCR product was used to remove excess dNTPs and any residual single-stranded primers and DNA. The final products were sent to Eurofins Genomics (Louisville, KY, USA) for bi-directional Sanger sequencing. The resulting files were assembled, trimmed, formatted. and aligned using Sequencher (ver. 5.4.6; Gene Codes Corp., Ann Arbor, Michigan). A total of 64 T. sessile samples were retrieved after using raxmlGUIO (v. 2.0.5) to sort out identical sequences. The mitochondrial COI sequences of the outgroups Liometopum microcephalum (Panzer, 1798) and Tapinoma opacum (Wheeler and Mann, 1914) and Tapinoma melanocephalum were obtained using GenBank under the accession numbers DQ353340, KT8446245 and KX054889 respectively. Alignments of these three outgroups were made with the 64 T. sessile resulting in 638 bp sequences using AliView (v.1.26. Larson 2014).  


Edited by PurdueEntomology, September 18 2023 - 12:26 AM.

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#44 Offline ClaytonBaby - Posted September 18 2023 - 12:31 AM

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Generally these days a good suit of nuclear genes (5-10) will do the trick! For me though I decided that I needed a full-proof-set of evidence that each in it's own weighed heavily to "new species", each may not have been a game changer but it was heavy enough to warrant novel species designation. When I was a kid I wanted to do that too, head down to the Amazon and find something new. For me though I was doing a separate study that just happened to use 1 mitochondrial gene fragment, but as I worked on the corpus of my ants being used for my study I began to question little things that hinted that something else was going on. As I begin to bring up the question that "I think this may be a new species" the professors on my committee would each want something stronger and would suggest, do this or that, come back with the results an let's consider. Each was skeptical: one was an expert on fire ants, one was a renowned evolutionary biologist, one was a world expert on a small family of flies ( had has many new species described), one was a genomics expert and one was just skeptical! So each would demand thoroughness and wanted to see if there were any "cracks" in my hypothesis i.e., I think this is a novel species.

What are the odds! That’s awesome how things work out LOL. So all this was done in a lab setting? Would something like examining the DNA sequence of a ant from the comfort of home be possible?


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#45 Offline ClaytonBaby - Posted September 18 2023 - 12:36 AM

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As for DNA (evidences a and b.) here is a cut and paste from my current draft of the species description under "Methods and Materials" for the mitochondrial fragment, the nuclear whole genome analysis is much more involved:


Mitochondrial DNA:
A fragment of the mitochondrial cytochrome C oxidase subunit I (COI) was amplified using the primers LEP-F1 (5'-ATTCAACCAATCATAAAGATATTGG-3') and LEP-R1 (5'-TAAACTTCTGGATGTCCAAAAAATCA-3’) targeting a 638-bp fragment (Menke et al., 2010). Conventional PCR using 15 µl of DreamTaq Hot Start Green PCR Master Mix (2X) (Thermo Fisher Scientific, Waltham, MA), 1 µl of primer LEP-F1 (10 µM), 1 µl of primer LEP-R1 (10 µM) and 8 µl nuclease free water with 5µl of extracted DNA for a final volume of 30 µl. PCRs were done in a MyCycler thermal cycler (BioRad, Hercules, California) using the following conditions: 95°C for 10 min, 4 cycles of 94°C for 1 min, 45°C for 1.5 min, 72°C for 1.5 min; 34 cycles of 94°C for 1 min, 45°C for 1.5 min, 72°C for 1 min; and a final extension of 72°C for 3 min. The 638-bp products were visualized using a 0.9% agarose gel stained with ethidium bromide ran at 118 volts for 30 min. ExoSAP-IT (Thermo Fisher Scientific, Waltham MA) at 1.5 µl per 5 µl of PCR product was used to remove excess dNTPs and any residual single-stranded primers and DNA. The final products were sent to Eurofins Genomics (Louisville, KY, USA) for bi-directional Sanger sequencing. The resulting files were assembled, trimmed, formatted. and aligned using Sequencher (ver. 5.4.6; Gene Codes Corp., Ann Arbor, Michigan). A total of 64 T. sessile samples were retrieved after using raxmlGUIO (v. 2.0.5) to sort out identical sequences. The mitochondrial COI sequences of the outgroups Liometopum microcephalum (Panzer, 1798) and Tapinoma opacum (Wheeler and Mann, 1914) and Tapinoma melanocephalum were obtained using GenBank under the accession numbers DQ353340, KT8446245 and KX054889 respectively. Alignments of these three outgroups were made with the 64 T. sessile resulting in 638 bp sequences using AliView (v.1.26. Larson 2014).

Man your living the dream!!! I’ve been thoroughly motivated through this convo, THANK YOU!!


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#46 Offline PurdueEntomology - Posted September 18 2023 - 12:37 AM

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Generally these days a good suit of nuclear genes (5-10) will do the trick! For me though I decided that I needed a full-proof-set of evidence that each in it's own weighed heavily to "new species", each may not have been a game changer but it was heavy enough to warrant novel species designation. When I was a kid I wanted to do that too, head down to the Amazon and find something new. For me though I was doing a separate study that just happened to use 1 mitochondrial gene fragment, but as I worked on the corpus of my ants being used for my study I began to question little things that hinted that something else was going on. As I begin to bring up the question that "I think this may be a new species" the professors on my committee would each want something stronger and would suggest, do this or that, come back with the results an let's consider. Each was skeptical: one was an expert on fire ants, one was a renowned evolutionary biologist, one was a world expert on a small family of flies ( had has many new species described), one was a genomics expert and one was just skeptical! So each would demand thoroughness and wanted to see if there were any "cracks" in my hypothesis i.e., I think this is a novel species.

What are the odds! That’s awesome how things work out LOL. So all this was done in a lab setting? Would something like examining the DNA sequence of a ant from the comfort of home be possible?


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Unless one had the requisite equipment, not likely.  Right now the portable sequencers are being developed but what I am able to tell only limited number of samples can be done etc.  I would say within the next decade this portable sequencing technology will be more ubiquitous. 


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#47 Offline PurdueEntomology - Posted September 18 2023 - 12:40 AM

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Here is a product, just remember this is new technology so expect rapid development:

 

https://us.vwr.com/s...t/36202184/null


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#48 Offline ClaytonBaby - Posted September 18 2023 - 12:44 AM

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Here is a product, just remember this is new technology so expect rapid development:

https://us.vwr.com/s...t/36202184/null

Oh darn I'm gonna need a better job to mess with these! LOL


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#49 Offline 100lols - Posted September 18 2023 - 7:51 AM

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Thanks for sharing all this awesome information. :D

With DNA sequencing technology becoming more involved in taxonomy, I could definitely see new novelty species popping up due to hidden diversity.

Will DNA evidence lead to more comprehensive, universal, and accurate taxonomic studies?
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#50 Offline ClaytonBaby - Posted September 18 2023 - 10:41 AM

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Thanks for sharing all this awesome information. :D

With DNA sequencing technology becoming more involved in taxonomy, I could definitely see new novelty species popping up due to hidden diversity.

Will DNA evidence lead to more comprehensive, universal, and accurate taxonomic studies?

Along with Micro CT scans it’s gonna get wild!


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#51 Offline PurdueEntomology - Posted September 18 2023 - 5:19 PM

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https://www.academia...card=view-paper

 

A bit academic but an important discussion


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#52 Offline ClaytonBaby - Posted September 18 2023 - 5:33 PM

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https://www.academia...card=view-paper

A bit academic but an important discussion

Gonna check it out and meet back here with some opinions and questions!!! Thank you for sharing!


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#53 Offline PurdueEntomology - Posted September 19 2023 - 2:54 AM

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I found the unified species concept of de Queiroz (see link below for original paper) the most reasonable and the need to acquire secondary properties (morphology, allochrony, genomics, colony structure, nest construction, etc) to establish support that a lineage (population) is distinct from another.  It is a concept that theoretically does away with taxonomic hierarchies family/genus/species which are inherited from Linnaeus and the early taxonomists, but since they are ingrained and have a deep tradition will not be discarded.  For me de Queiroz's approach is to amass different "secondary property" evidences and see if they give strong support for a whole lineage being distinct enough from other lineages to be called "species".   It is reminiscent of how  I see the colony of ants as the "ant" while each worker/queen(s) is just a part of the "ant" since ultimately it is the colony as the "ant" that must survive not necessarily each individual ant, even the queen at times, for many "ant" colonies survive without a queen.  Thus the species Tapinoma sessile is the collective lineage of colonies from founding queens to mega super colonies coving 40 acres such as at Purdue, each ant is important but is not T. sessile, it is the unique lineage that is.  Yeah, it is perhaps a bit to think about but we have come a long way from where Medieval peoples thought salamanders came from fire!

 

https://researcharch...6_n18_SuppI.pdf


Edited by PurdueEntomology, September 19 2023 - 3:08 AM.

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#54 Online ANTdrew - Posted September 19 2023 - 11:18 AM

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This is the longest ID thread in the history of FC.
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"The ants are a people not strong, yet they prepare their meat in the summer." Prov. 30:25
Keep ordinary ants in extraordinary ways.

#55 Offline PurdueEntomology - Posted September 19 2023 - 1:56 PM

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This is the longest ID thread in the history of FC.

haha!!!


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#56 Offline ClaytonBaby - Posted September 19 2023 - 4:17 PM

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This is the longest ID thread in the history of FC.

Full of juicy info! LOL


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#57 Offline ClaytonBaby - Posted September 19 2023 - 4:26 PM

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I found the unified species concept of de Queiroz (see link below for original paper) the most reasonable and the need to acquire secondary properties (morphology, allochrony, genomics, colony structure, nest construction, etc) to establish support that a lineage (population) is distinct from another. It is a concept that theoretically does away with taxonomic hierarchies family/genus/species which are inherited from Linnaeus and the early taxonomists, but since they are ingrained and have a deep tradition will not be discarded. For me de Queiroz's approach is to amass different "secondary property" evidences and see if they give strong support for a whole lineage being distinct enough from other lineages to be called "species". It is reminiscent of how I see the colony of ants as the "ant" while each worker/queen(s) is just a part of the "ant" since ultimately it is the colony as the "ant" that must survive not necessarily each individual ant, even the queen at times, for many "ant" colonies survive without a queen. Thus the species Tapinoma sessile is the collective lineage of colonies from founding queens to mega super colonies coving 40 acres such as at Purdue, each ant is important but is not T. sessile, it is the unique lineage that is. Yeah, it is perhaps a bit to think about but we have come a long way from where Medieval peoples thought salamanders came from fire!

https://researcharch...6_n18_SuppI.pdf

Super hyped that you ended up responding to this ID request man! I hope you don’t mind me messaging you to pick your brain a bit more when my time comes to try and name/describe one myself!!


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#58 Offline PurdueEntomology - Posted September 21 2023 - 4:04 AM

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Dr. Bernhard Seifert of the Senckenberg Museum of Natural History in Görlitz, Germany.  He is unquestionably, to my opinion, the leading ant expert in Europe and in his expertise ranks with Dr. Philip Ward of UC Davies.  Dr. Seifert is the author of "The Ants of Central and North Europe", he is a founder of Myrmecological News and you can search him there for published works.    I consulted with him on the idea of oligogyny when I first began to describe the colony structure of the novel Tapinoma I discovered in Tennessee, he was was the expert who introduced me to this unique form of polygyny. 

 

https://blog.myrmeco...d-north-europe/

 

Dr. Seifert has indicated a shift of pragmatic systematics in the past 20 years as has been demonstrated from published academic works, either on species descriptions, reassignments of whole genera or on theoretical discussion on conceptual framing of the idea of a species.  The following link is an important work of his:

 

 

https://www.academia...work_card=title


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