bcreisler@gmail.com
Joan Ferrer Obiol, Helen F James, R Terry Chesser, Vincent Bretagnolle, Jacob GonzÃlez-SolÃs, Julio Rozas, Marta Riutort & Andreanna J Welch (2021)
Integrating Sequence Capture and Restriction Site-Associated DNA Sequencing to Resolve Recent Radiations of Pelagic Seabirds.
Systematic Biology, syaa101 (advance online publication)
doi: https://doi.org/10.1093/sysbio/syaa101
https://academic.oup.com/sysbio/advance-article/doi/10.1093/sysbio/syaa101/6123758
The diversification of modern birds has been shaped by a number of radiations. Rapid diversification events make reconstructing the evolutionary relationships among taxa challenging due to the convoluted effects of incomplete lineage sorting (ILS) and introgression. Phylogenomic data sets have the potential to detect patterns of phylogenetic incongruence, and to address their causes. However, the footprints of ILS and introgression on sequence data can vary between different phylogenomic markers at different phylogenetic scales depending on factors such as their evolutionary rates or their selection pressures. We show that combining phylogenomic markers that evolve at different rates, such as paired-end double-digest restriction site-associated DNA (PE-ddRAD) and ultraconserved elements (UCEs), allows a comprehensive exploration of the causes of phylogenetic discordance associated with short internodes at different timescales. We used thousands of UCE and PE-ddRAD markers to produce the first well-resolved phylogeny of shearwaters, a group of medium-sized pelagic seabirds that are among the most phylogenetically controversial and endangered bird groups. We found that phylogenomic conflict was mainly derived from high levels of ILS due to rapid speciation events. We also documented a case of introgression, despite the high philopatry of shearwaters to their breeding sites, which typically limits gene flow. We integrated state-of-the-art concatenated and coalescent-based approaches to expand on previous comparisons of UCE and RAD-Seq data sets for phylogenetics, divergence time estimation, and inference of introgression, and we propose a strategy to optimize RAD-Seq data for phylogenetic analyses. Our results highlight the usefulness of combining phylogenomic markers evolving at different rates to understand the causes of phylogenetic discordance at different timescales.Â
Jozef Klembara, Marika MikudÃkovÃ, Stanislav Åtamberg Â& Miroslav Hain (2021)
First record of the stem amniote Discosauriscus (Seymouriamorpha, Discosauriscidae) from the KrkonoÅe Piedmont Basin (the Czech Republic).
Fossil Imprint 76(2): 243â251
DOI: 10.37520/fi.2020.020
http://fi.nm.cz/en/clanek/first-record-of-the-stem-amniote-discosauriscus-seymouriamorpha-discosauriscidae-from-the-krkonose-piedmont-basin-the-czech-republic-2/
The first record of the seymouriamorph stem amniote Discosauriscus from the KrkonoÅe Piedmont Basin (the Czech Republic) is described. The specimen is identified as D. pulcherrimus on the basis of the following features which are absent in D. austriacus: 1) the pointed tip of the ventrolateral process of the postorbital lies anteriorly to the tip of the wedge-shaped dorsomedial process of the jugal; and 2) the rows of small denticles diverge anteromedially and anterolaterally from the midwidth of the ventral surface of the palatal ramus of the pterygoid. This new record increases our knowledge of the occurrence of this seymouriamorph in the Permo-Carboniferous basins of Europe.
Free pdf:
http://fi.nm.cz/wp-content/uploads/2020/12/4_Werneburg.pdf
A new temnospondyl, Korkonterpeton kalnense gen. et sp. nov., is described on the basis of an almost complete specimen from the lover Permian ProseÄnà Formation of the Czech KrkonoÅe Piedmont Basin. The exceptional preservation of the holotype allows a detailed description of the cranial and postcranial characters: Korkonterpeton kalnense gen. et sp. nov. is characterized by the presence of vomerine fangs located anteriorly to the posterior choana, much longer than wide tabulars â as long as the supratemporals, a deeply concave posterior margin of the skull table, extraordinarily elongated exoccipitals, anteriorly widened pterygoids and a parasphenoid cultriform process swollen at its mid-length. In order to clarify the relationship between this new taxon and Intasuchus silvicola Konzhukova, 1956 from the lower Permian (late Kungurian) of the Russian Inta Basin, the latter is also redescribed here: Intasuchus silvicola exhibits a lacrimal entering the septomaxilla, a widened jugal, a posterolaterally widened interpterygoid vacuity, a subtemporal window elongated anteriorly up to the anterior orbital region, an elongated basipterygoid ramus which is as long as the orbit width, a vomer with a parachoanal tooth row, and an ectopterygoid of about the same length as the palatine. The description of Korkonterpeton kalnense gen. et sp. nov. and the revision of Intasuchus silvicola complete our knowledge on the origin and evolution of early stereospondylomorph temnospondyls during the lower Permian.
Some non-dino paper not yet mentioned, some with free pdfs;
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Free pdf:
Joan Ferrer Obiol, Helen F James, R Terry Chesser, Vincent Bretagnolle, Jacob GonzÃlez-SolÃs, Julio Rozas, Marta Riutort & Andreanna J Welch (2021)
Integrating Sequence Capture and Restriction Site-Associated DNA Sequencing to Resolve Recent Radiations of Pelagic Seabirds.
Systematic Biology, syaa101 (advance online publication)
doi: https://doi.org/10.1093/sysbio/syaa101
https://academic.oup.com/sysbio/advance-article/doi/10.1093/sysbio/syaa101/6123758
The diversification of modern birds has been shaped by a number of radiations. Rapid diversification events make reconstructing the evolutionary relationships among taxa challenging due to the convoluted effects of incomplete lineage sorting (ILS) and introgression. Phylogenomic data sets have the potential to detect patterns of phylogenetic incongruence, and to address their causes. However, the footprints of ILS and introgression on sequence data can vary between different phylogenomic markers at different phylogenetic scales depending on factors such as their evolutionary rates or their selection pressures. We show that combining phylogenomic markers that evolve at different rates, such as paired-end double-digest restriction site-associated DNA (PE-ddRAD) and ultraconserved elements (UCEs), allows a comprehensive exploration of the causes of phylogenetic discordance associated with short internodes at different timescales. We used thousands of UCE and PE-ddRAD markers to produce the first well-resolved phylogeny of shearwaters, a group of medium-sized pelagic seabirds that are among the most phylogenetically controversial and endangered bird groups. We found that phylogenomic conflict was mainly derived from high levels of ILS due to rapid speciation events. We also documented a case of introgression, despite the high philopatry of shearwaters to their breeding sites, which typically limits gene flow. We integrated state-of-the-art concatenated and coalescent-based approaches to expand on previous comparisons of UCE and RAD-Seq data sets for phylogenetics, divergence time estimation, and inference of introgression, and we propose a strategy to optimize RAD-Seq data for phylogenetic analyses. Our results highlight the usefulness of combining phylogenomic markers evolving at different rates to understand the causes of phylogenetic discordance at different timescales.Â
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Jozef Klembara, Marika MikudÃkovÃ, Stanislav Åtamberg Â& Miroslav Hain (2021)
First record of the stem amniote Discosauriscus (Seymouriamorpha, Discosauriscidae) from the KrkonoÅe Piedmont Basin (the Czech Republic).
Fossil Imprint 76(2): 243â251
DOI: 10.37520/fi.2020.020
http://fi.nm.cz/en/clanek/first-record-of-the-stem-amniote-discosauriscus-seymouriamorpha-discosauriscidae-from-the-krkonose-piedmont-basin-the-czech-republic-2/
Free pdf:
The first record of the seymouriamorph stem amniote Discosauriscus from the KrkonoÅe Piedmont Basin (the Czech Republic) is described. The specimen is identified as D. pulcherrimus on the basis of the following features which are absent in D. austriacus: 1) the pointed tip of the ventrolateral process of the postorbital lies anteriorly to the tip of the wedge-shaped dorsomedial process of the jugal; and 2) the rows of small denticles diverge anteromedially and anterolaterally from the midwidth of the ventral surface of the palatal ramus of the pterygoid. This new record increases our knowledge of the occurrence of this seymouriamorph in the Permo-Carboniferous basins of Europe.
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Korkonterpeton kalnense gen. et sp. nov.ÂÂ
Ralf Werneburg, Stanislav Åtamberg & Jean-SÃbastien Steyer (2020)
A new stereospondylomorph, Korkonterpeton kalnense gen. et sp. nov., from lower Permian of the Czech KrkonoÅe Piedmont Basin and a redescription of Intasuchus silvicola from the lower Permian of Russia (Temnospondyli, Amphibia).
Fossil Imprint 76(2):217-242
DOI: 10.37520/fi.2020.019
http://fi.nm.cz/en/clanek/a-new-stereospondylomorph-korkonterpeton-kalnense-gen-et-sp-nov-from-lower-permian-of-the-czech-krkonose-piedmont-basin-and-a-redescription-of-intasuchus-silvicola-from-the-lower-permian-of-russi-2/
A new stereospondylomorph, Korkonterpeton kalnense gen. et sp. nov., from lower Permian of the Czech KrkonoÅe Piedmont Basin and a redescription of Intasuchus silvicola from the lower Permian of Russia (Temnospondyli, Amphibia).
Fossil Imprint 76(2):217-242
DOI: 10.37520/fi.2020.019
http://fi.nm.cz/en/clanek/a-new-stereospondylomorph-korkonterpeton-kalnense-gen-et-sp-nov-from-lower-permian-of-the-czech-krkonose-piedmont-basin-and-a-redescription-of-intasuchus-silvicola-from-the-lower-permian-of-russi-2/
Free pdf:
http://fi.nm.cz/wp-content/uploads/2020/12/4_Werneburg.pdf
A new temnospondyl, Korkonterpeton kalnense gen. et sp. nov., is described on the basis of an almost complete specimen from the lover Permian ProseÄnà Formation of the Czech KrkonoÅe Piedmont Basin. The exceptional preservation of the holotype allows a detailed description of the cranial and postcranial characters: Korkonterpeton kalnense gen. et sp. nov. is characterized by the presence of vomerine fangs located anteriorly to the posterior choana, much longer than wide tabulars â as long as the supratemporals, a deeply concave posterior margin of the skull table, extraordinarily elongated exoccipitals, anteriorly widened pterygoids and a parasphenoid cultriform process swollen at its mid-length. In order to clarify the relationship between this new taxon and Intasuchus silvicola Konzhukova, 1956 from the lower Permian (late Kungurian) of the Russian Inta Basin, the latter is also redescribed here: Intasuchus silvicola exhibits a lacrimal entering the septomaxilla, a widened jugal, a posterolaterally widened interpterygoid vacuity, a subtemporal window elongated anteriorly up to the anterior orbital region, an elongated basipterygoid ramus which is as long as the orbit width, a vomer with a parachoanal tooth row, and an ectopterygoid of about the same length as the palatine. The description of Korkonterpeton kalnense gen. et sp. nov. and the revision of Intasuchus silvicola complete our knowledge on the origin and evolution of early stereospondylomorph temnospondyls during the lower Permian.
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Also, recent coelacanth papers:
F.J. Meunier, C. Cupello, M. Herbin, G. ClÃment & P.M. Brito (2021)
The lungs of extinct and extant coelacanths: a morphological and histological review.
Cybium 45(1) : 021-030
doi: https://doi.org/10.26028/cybium/2021-451-002
http://sfi-cybium.fr/fr/lungs-extinct-and-extant-coelacanths-morphological-and-histological-review
The lungs of extinct and extant coelacanths: a morphological and histological review.
Cybium 45(1) : 021-030
doi: https://doi.org/10.26028/cybium/2021-451-002
http://sfi-cybium.fr/fr/lungs-extinct-and-extant-coelacanths-morphological-and-histological-review
This review deals with recent studies on the lungs of fossil and extant coelacanths with classical techniques (dissections, photonic histology) and modern techniques (SEM, X-ray tomography). This recent knowledge allows to attest the homology between: i) the large bony plates of the calcified organ of extinct coelacanths and the small plates that surround the lung of the extant coelacanth Latimeria; ii) the (supposed functional) lung covered with bony plates of extinct coelacanths and the vestigial (non-functional) lung of the extant coelacanth Latimeria. These results point to the fatty organ of Latimeria as probably a mesenteric specialization, questioning its previous attribution to its pulmonary origin.
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Free pdf:
Isaac Yellan, Ally W. H. Yang & Timothy R. Hughes (2021)
Diverse Eukaryotic CGG Binding Proteins Produced by Independent Domestications of hAT Transposons.
Molecular Biology and Evolution, msab007
doi: https://doi.org/10.1093/molbev/msab007
https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msab007/6129264
The human transcription factor (TF) CGGBP1 ("CGG Binding Protein") is conserved only in amniotes, and is believed to derive from the zf-BED and Hermes transposase DNA-binding domains (DBDs) of a hAT DNA transposon. Here, we show that sequence-specific DNA binding proteins with this bipartite domain structure have resulted from dozens of independent hAT domestications in different eukaryotic lineages. CGGBPs display a wide range of sequence specificity, usually including preferences for CGG or CGC trinucleotides, while some bind AT-rich motifs. The CGGBPs are almost entirely non-syntenic, and their protein sequences, DNA binding motifs, and patterns of presence or absence in genomes are uncharacteristic of ancestry via speciation. At least eight CGGBPs in the coelacanth Latimeria chalumnae bind distinct motifs, and the _expression_ of the corresponding genes varies considerably across tissues, suggesting tissue-restricted function.
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News:
So-called 'living fossil' fish actually evolved dozens of new genes, University of Toronto researchers find
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