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Gruiformes and Charadriiformes (2 Viewers)

Congratulations to whoever got the borealis DNA. That is not readily available on the shelf. In 1984 when I saw minutus birders suggested it was an Eskimo, wrongly. So Laurent your tree has minutus basal in the curlews? And there is no whimbrel clade? In your tree is minutus so different that it should be called Mesoscolopax minutus?
Vol 24 (1896) - Catalogue of the Birds in the British Museum - Biodiversity Heritage Library .
We luckily sampled four specimens and a single egg.
 
"We luckily sampled four specimens and a single egg."
My dear Mother used to say you have to crack an egg to get genetic material. Which I always thougt was strange but her two brothers were scientists. Finally Oology collections are cool. I think an article about this part of your research would be welcome in a popular science type journal.
 
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Jason Hill, Erik D. Enbody, Huijuan Bi, Sangeet Lamichhaney, Weipan Lei, Juexin Chen, Chentao Wei, Yang Liu, Doreen Schwochow, Shady Younis, Fredrik Widemo, and Leif Andersson (2023) Low mutation load in a supergene underpinning alternative male mating sStrategies in Ruff (Calidris pugnax). Molecular Biology and Evolution 40: msad224. Low Mutation Load in a Supergene Underpinning Alternative Male Mating Strategies in Ruff (Calidris pugnax)

Abstract
A paradox in evolutionary biology is how supergenes can maintain high fitness despite reduced effective population size, the suppression of recombination, and the expected accumulation of mutational load. The ruff supergene involves 2 rare inversion haplotypes (satellite and faeder). These are recessive lethals but with dominant effects on male mating strategies, plumage, and body size. Sequence divergence to the wild-type (independent) haplotype indicates that the inversion could be as old as 4 million years. Here, we have constructed a highly contiguous genome assembly of the inversion region for both the independent and satellite haplotypes. Based on the new data, we estimate that the recombination event(s) creating the satellite haplotype occurred only about 70,000 yr ago. Contrary to expectations for supergenes, we find no substantial expansion of repeats and only a modest mutation load on the satellite and faeder haplotypes despite high sequence divergence to the non-inverted haplotype (1.46%). The essential centromere protein N (CENPN) gene is disrupted by the inversion and is as well conserved on the inversion haplotypes as on the noninversion haplotype. These results suggest that the inversion may be much younger than previously thought. The low mutation load, despite recessive lethality, may be explained by the introgression of the inversion from a now extinct lineage.

additional commentary:

Casey McGrath (2023) Highlight: Unmasking the supergene beneath the Ruff's mating strategies. Molecular Biology and Evolution 40: msad249.
Highlight: Unmasking the Supergene Beneath the Ruff's Mating Strategies
 
Is there not an error in the distribution of species between the genera Rufirallus and Anurolimnas on BOW ?
 

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Yes, indeed.

castaneiceps is the species that should be in Anurolimnas Sharpe 1893 (it is the type by original designation).
fasciatus is sister to [viridis + schomburgki] in phylogenetic analyses (Kirchman et al 2021, Depino et al 2023), and could either be included in Rufirallus (type Rallus cayennensis Gmelin 1789, a syn. of viridis), or be placed in a monotypic genus (for which no name appear to be available at this point).

(The same error occurs -- expectedly -- in the Clements checklist.)
 
Yes, indeed.

castaneiceps is the species that should be in Anurolimnas Sharpe 1893 (it is the type by original designation).
fasciatus is sister to [viridis + schomburgki] in phylogenetic analyses (Kirchman et al 2021, Depino et al 2023), and could either be included in Rufirallus (type Rallus cayennensis Gmelin 1789, a syn. of viridis), or be placed in a monotypic genus (for which no name appear to be available at this point).

(The same error occurs -- expectedly -- in the Clements checklist.)
Errors happen of course, but this is weird. IOC apparently joined in as well when rearranging Rallidae, putting castaneiceps and viridis in Rufirallus, fasciatus still left in Laterallus though. Is this just a lapse or is there a better reason for this?
 
IOC apparently joined in as well when rearranging Rallidae, putting castaneiceps and viridis in Rufirallus, fasciatus still left in Laterallus though.

This is an older change. The rearrangement was made in IOC Version 10.2 (July 25, 2020) -- see Taxonomic Updates – IOC World Bird List -- before Kirchman et al 2021 and Depino et al 2023, at a time when no data were available yet for several of the involved species.
And it's not a nomenclatural impossibility -- they did not use a generic name (Anurolimnas) for a species (fasciatus) while putting its type (castaneiceps) in another genus (Rufirallus).
 
Bukowski, B., Campagna, L., Rodríguez-Cajarville, M. J., Cabanne, G. S., Tubaro, P. L., and Lijtmaer, D. A. (2024) The role of glaciations in the evolutionary history of a widely distributed Neotropical open habitat bird [Vanellus chilensis]. Journal of Biogeography 51: 199–214. https://doi.org/10.1111/jbi.14738

Abstract
Aim
The Neotropics constitute the most biodiverse region of the world, yet its patterns of diversification and speciation differ among Neotropical areas and are not equally well understood. Particularly, avian evolutionary processes are understudied in the open habitats of temperate South America, where the role of glacial cycles is not clear. We analysed the evolutionary history of a Neotropical widespread bird species as a case study to evaluate its continental-scale patterns and processes of diversification, with a focus on Patagonia.

Location
Open habitats of the Neotropics.

Taxon
Vanellus chilensis (Aves, Charadriiformes).

Methods
We obtained reduced representation genomic and mitochondrial data from the four subspecies of V. chilensis to perform a phylogenetic/phylogeographical analysis and study the evolutionary history of the species. We complemented these analyses with the study of vocalizations, a reproductive signal in birds.

Results
The initial diversification event within V. chilensis, approximately 600,000 years ago, split a Patagonian lineage from one containing individuals from the rest of the Neotropics. We found considerable gene flow between these two lineages and a contact zone in northern Patagonia, and showed that genomic admixture extends to northwestern Argentina. Shallower divergence was detected between the two non-Patagonian subspecies, which are separated by the Amazon River. Vocalizations were significantly different between the two main lineages and were intermediate in their temporal and frequency characteristics in the contact zone.

Main Conclusions
Patagonian populations of V. chilensis are clearly differentiated from those of the rest of the Neotropics, possibly as a consequence of Pleistocene glaciations. A secondary contact zone in northern Patagonia with extensive gene flow among lineages appears to be the consequence of post-glacial, northward expansion of the Patagonian populations. Future analyses focused on the dynamics of the contact zone will allow us to establish whether the species continues to diverge or is homogenizing.
 
Praveen J. and Giorgio Aimassi (2024) Re-restricting the type locality of Burhinus [= Oedicnemus] indicus Salvadori, 1866 [Indian Thick-knee]. Bulletin of the British Ornithologists' Club 144: 74-75.
Re-restricting the type locality of Burhinus [= Oedicnemus] indicus Salvadori, 1866

Abstract
The type locality of Indian Thick-knee Burhinus indicus is currently restricted to the surroundings of Mussoorie, Uttarakhand, India. We provide evidence for revising this to the environs of Sardhana, Uttar Pradesh, which is c.150 km south-southwest of Mussoorie.
 
Seasonal migration and the evolution of an inverse latitudinal diversity gradient in shorebirds
https://doi.org/10.1111/geb.13817

Interesting! Haven’t read what they base their phylogeny on, but a couple of notes from looking at the tree in the supplementary document:

  • Pluvialis plovers sister to ibisbill, stilts, avocets and oystercatchers
  • Yet another study revealing how young the above clade minus Pluvialis is. Time to unify in one family! Morphologically they’re more similar than, say, Scolopacidae or Glareolidae!

Also, what’s with the new trend with phylogeny “wheels”? Pretty, yes, but completely unreadable!
 
Haven’t read what they base their phylogeny

They used a supermatrix of genetic sequences downloaded from GenBank, i.e., largely the same data as in earlier studies.
(I'd have loved to see a complete list of the sequences they actually used, but they did not provide one. Their data set was certainly not problem-free -- just look at the position of Charadrius peronii.)
 

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