Rallidae (2 Viewers)

[Jim LeNomenclatoriste]

What does the figure caption say?

Bayesian time-calibrated phylogeny of Porphyrio using four mitochondrial genes. Node labels denote posterior probability values, while node bars represent the 95% HPD interval for node ages. HPD intervals relating to takahē/moho are coloured. The positions of the takahē (P. hochstetteri) and moho (P. mantelli) are illustrated.

 

[Mysticete]

In that case, while it has been awhile since I have run a Bayesian Phylogenetic analysis, values above .95 are generally considered strongly supported, and I have seen people interpret .9-.95 as representing marginal support.

Anything below these thresholds would be interpreted as having little real support.

I don't know what species goes with Ionornis, but given the supported values that are reported I would lean towards no.

 

[THE_FERN]

Hmm not up with the literature but surprised that some of the Porphyrio divergences are so ancient.

 

[D Halas]

The figure below comes from this article (see also this topic Thread 'Ancient mitogenomes of takahē and moho' Ancient mitogenomes of takahē and moho ). How should the number in front of each node be interpreted? Is there support for recognition of Ionornis Reichenbach, 1853 (or Glaucestes ibid.) ?

https://onlinelibrary.wiley.com/doi/10.1111/mec.17227

Based on a Google search I'm guessing that Ionornis is the clade made up of P. martinica and P. flavirostris (it would be helpful if you told us which species you're referring to, rather than making us guess), in which case, no, there is absolutely no support in this figure for such a clade. Given the support values shown on the figure, there must be nearly as strong support for P. martinica as the sister species to the broader P. porphyrio clade, and also for P. flavirostris as the sister species to the broader P. porphyrio clade. In short, this figure shows strong support for P. alleni as the sister species to all other Porphyrio, and that P. indicus + porphyrio + madagascariensis + hochstetteri + mantelli + poliocephalus + pulverulentus + melanotus form a clade, but it gives absolutely no other information on the placement of P. martinica or P. flavirostris.

 

[Jim LeNomenclatoriste]

Based on a Google search I'm guessing that Ionornis is the clade made up of P. martinica and P. flavirostris (it would be helpful if you told us which species you're referring to, rather than making us guess), in which case, no, there is absolutely no support in this figure for such a clade. Given the support values shown on the figure, there must be nearly as strong support for P. martinica as the sister species to the broader P. porphyrio clade, and also for P. flavirostris as the sister species to the broader P. porphyrio clade. In short, this figure shows strong support for P. alleni as the sister species to all other Porphyrio, and that P. indicus + porphyrio + madagascariensis + hochstetteri + mantelli + poliocephalus + pulverulentus + melanotus form a clade, but it gives absolutely no other information on the placement of P. martinica or P. flavirostris.

In that case, while it has been awhile since I have run a Bayesian Phylogenetic analysis, values above .95 are generally considered strongly supported, and I have seen people interpret .9-.95 as representing marginal support.

Anything below these thresholds would be interpreted as having little real support.

I don't know what species goes with Ionornis, but given the supported values that are reported I would lean towards no.

Ok. Thks. I didn't understand what the "1" at each node meant. We have a "1" in front of Porphyrio alleni, then a "1" at the intersection of the branches which separate on one side Porphyrio martinica and flavirostris, and on the other side the Porphyrio cladev(stricto sensu). And finally a “0.43” in front of the node separating martinica and flavirostris thinking that it indicated the degree of support between the two species.

 

[l_raty]

Ok. Thks. I didn't understand what the "1" at each node meant. We have a "1" in front of Porphyrio alleni, then a "1" at the intersection of the branches which separate on one side Porphyrio martinica and flavirostris, and on the other side the Porphyrio cladev(stricto sensu). And finally a “0.43” in front of the node separating martinica and flavirostris thinking that it indicated the degree of support between the two species.

I'm not clear what the "degree of support between" two species would mean ?

A node does not "separate", it unites. The numbers indicate the degree of support given to the clade that stems from the branch above which they are placed. As Morgan said, a Bayesian posterior probability of 0.43 is pitiful, while a BPP of 1 is very high. The analysis gives strong support (BPP = 1) to a clade equivalent to the broad Porphyrio (= swamp-hens + alleni + martinica + flavirostris), to this clade minus alleni (= swamp-hens + martinica + flavirostris), and to a clade equivalent to the restricted Porphyrio (swamp-hens only). It gives poor support (BPP = .43) to a possible sister-group relationship between martinica (i.e., Ionornis) and flavirostris (i.e., Glaucestes).

That being said :

• Poor support given to a clade in an analysis does not amount to evidence running against the existence of this clade. The node uniting martinica and flavirostris was strongly supported in Garcia-R & Trewick 2015, using a broader genetic data set than in Verry et al 2023 (the same 4 mitochondrial genes, plus two nuclear genes) -- there is nothing in the 2023 tree that can be interpreted as invalidating the 2015 results.
• I'd generally be cautious with purely Bayesian analyses, as they sometimes give high support to nodes that get poor support in ML analyses. I would hesitate to interpret a node with a BPP of 1 but a ML bootstrap support below, say, 70 as very strongly supported.

As an aside : Gray made Glaucestes an invalid synonym of Ionornis at subgeneric rank in 1871 : pt.3 (1871) - Hand-list of genera and species of birds - Biodiversity Heritage Library. Unless there is something earlier, this is a first reviser act and makes Ionornis senior.

 

[Jim LeNomenclatoriste]

I'm not clear what the "degree of support between" two species would mean ?

I didn't know how to explain that 😅

A node does not "separate", it unites. The numbers indicate the degree of support given to the clade that stems from the branch above which they are placed. As Morgan said, a Bayesian posterior probability of 0.43 is pitiful, while a BPP of 1 is very high. The analysis gives strong support (BPP = 1) to a clade equivalent to the broad Porphyrio (= swamp-hens + alleni + martinica + flavirostris), to this clade minus alleni (= swamp-hens + martinica + flavirostris), and to a clade equivalent to the restricted Porphyrio (swamp-hens only). It gives poor support (BPP = .43) to a possible sister-group relationship between martinica (i.e., Ionornis) and flavirostris (i.e., Glaucestes).

That being said :

• Poor support given to a clade in an analysis does not amount to evidence running against the existence of this clade. The node uniting martinica and flavirostris was strongly supported in Garcia-R & Trewick 2015, using a broader genetic data set (the same 4 mitochondrial genes, plus two nuclear genes) than in Verry et al 2023 -- there is nothing in the 2023 tree that can be interpreted as invalidating the 2015 results.
• I'd generally be cautious with purely Bayesian analyses, as they sometimes give high support to nodes that get poor support in ML analyses. I would hesitate to interpret a node with a BPP of 1 but a ML bootstrap support below, say, 70 as very strongly supported.

I understood a little even if in the majority of cases, it will remain gibberish to me.

 

[albertonykus]

Chavez, D.E., T. Hains, S. Espinoza, R.K. Wayne, and J. Chaves (2024)
Whole-genome analysis reveals the diversification of Galapagos rail (Aves: Rallidae) and confirms the success of goat eradication programs
Journal of Heredity (advance online publication)
doi: 10.1093/jhered/esae017

Similar to other insular birds around the world, the Galapagos rail (Laterallus spilonota Gould, 1841) exhibits reduced flight capacity following its colonization of the archipelago ~1.2 mya. Despite their short evolutionary history, rails have colonized seven different islands spanning the entire width of the archipelago. Galapagos rails were once common on islands with sufficiently high altitudes to support shrubs in humid habitats. After humans introduced goats, this habitat was severely reduced due to overgrazing. Habitat loss devastated some rail populations, with less than 50 individuals surviving, rendering the genetic diversity of Galapagos rail a pressing conservation concern. Additionally, one enigma is the reappearance of rails on the island of Pinta after they were considered extirpated. Our approach was to investigate the evolutionary history and geographic distribution of Galapagos rails as well as examine the genome-wide effects of historical population bottlenecks using 39 whole genomes across different island populations. We recovered an early divergence of rail ancestors leading to the isolated populations on Pinta and a second clade comprising the rest of the islands, historically forming a single landmass. Subsequently, the separation of the landmass ~900 kya may have led to the isolation of the Isabela population with more panmictic populations found on Santa Cruz and Santiago islands. We found that rails genomes contain long runs of homozygosity (>2Mb) that could be related to the introduction of goats. Finally, our findings show that the modern eradication of goats was critical to avoiding episodes of inbreeding in most populations.