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1. Phylogenetic Signal of Indels and the Neoavian Radiation

   https://doi.org/10.3390/d11070108  

   Houde, Peter; Braun, Edward L.; Narula, Nitish; Minjares, Uriel; Mirarab, Siavash (July 2019, Diversity)

   The early radiation of Neoaves has been hypothesized to be an intractable “hard polytomy”. We explore the fundamental properties of insertion/deletion alleles (indels), an under-utilized form of genomic data with the potential to help solve this. We scored >5 million indels from >7000 pan-genomic intronic and ultraconserved element (UCE) loci in 48 representatives of all neoavian orders. We found that intronic and UCE indels exhibited less homoplasy than nucleotide (nt) data. Gene trees estimated using indel data were less resolved than those estimated using nt data. Nevertheless, Accurate Species TRee Algorithm (ASTRAL) species trees estimated using indels were generally similar to nt-based ASTRAL trees, albeit with lower support. However, the power of indel gene trees became clear when we combined them with nt gene trees, including a striking result for UCEs. The individual UCE indel and nt ASTRAL trees were incongruent with each other and with the intron ASTRAL trees; however, the combined indel+nt ASTRAL tree was much more congruent with the intronic trees. Finally, combining indel and nt data for both introns and UCEs provided sufficient power to reduce the scope of the polytomy that was previously proposed for several supraordinal lineages of Neoaves. 

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2. Gene tree quality affects empirical coalescent branch length estimation

   https://doi.org/10.1111/zsc.12512  

   Forthman, Michael; Braun, Edward L.; Kimball, Rebecca T. (September 2021, Zoologica Scripta)

   Abstract Assessing effects of gene tree error in coalescent analyses have widely ignored coalescent branch lengths (CBLs) despite their potential utility in estimating ancestral population demographics and detecting species tree anomaly zones. However, the ability of coalescent methods to obtain accurate estimates remains largely unexplored. Errors in gene trees should lead to underestimates of the true CBL, and for a given set of comparisons, longer CBLs should be more accurate. Here, we furthered our empirical understanding of how error in gene tree quality (i.e., locus informativeness and gene tree resolution) affect CBLs using four datasets comprised of ultraconserved elements (UCE) or exons for clades that exhibit wide ranges of branch lengths. For each dataset, we compared the impact of locus informativeness (assessed using number of parsimony‐informative sites) and gene tree resolution on CBL estimates. Our results, in general, showed that CBLs were drastically shorter when estimates included low informative loci. Gene tree resolution also had an impact on UCE datasets, with polytomous gene trees producing longer branches than randomly resolved gene trees. However, resolution did not appear to affect CBL estimates from the more informative exon datasets. Thus, as expected, gene tree quality affects CBL estimates, though this can generally be minimized by using moderate filtering to select more informative loci and/or by allowing polytomies in gene trees. These approaches, as well as additional contributions to improve CBL estimation, should lead to CBLs that are useful for addressing evolutionary and biological questions. 

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3. Shifts in trophic architecture and ecospace stability determining survivorship and extinction at the end-Cretaceous

   Chiarenza, Alfio Alessandro; García-Girón, Jorge; Alahuhta, Janne; DeMar, D. G.; Jani, Heino; Mannion, P. D.; Williamson, T. E.; Wilson Mantilla, G. P.; Brusatte, S. L. (November 2022, Journal of Vertebrate Paleontology)

   An explanation for why some species, such as non-avian dinosaurs, became extinct, whereas others, including mammals, survived the Cretaceous/Paleogene (K/Pg) mass extinction, 66 million years ago (Ma) is still debated. What were the mechanisms behind community restructuring and the emergence of new ecological opportunities after the K/Pg event, selectively driving extinction and survivorship patterns? Using Markov networks, ecological niche partitioning and Earth System models, we reconstructed disruptions in continental food web dynamics, simulating long-term trajectories in ecospace occupancy through the latest Cretaceous (83.6–66.0 Ma) and early Paleogene (66.0–61.6 Ma). This method uses partial correlation networks to represent how different trophic groups interact in a food web and builds on empirical spatial co-variations to explore dependencies between trophic groups. Our analyses are based on a spatiotemporally and taxonomically standardized dataset, comprising more than 1,600 fossil occurrences representing more than 470 genera of fish, salamanders, frogs, albanerpetontids, lizards, snakes, champsosaurs, turtles, crocodylians, dinosaurs (including birds), and mammals across the best sampled region for this interval, the Western Interior of North America. We explicitly tested whether: 1) shifts in food web architecture underwent major restructuring before and after the K/Pg transition, including whether some trophic guilds were more prone to these shifts than others; and 2) any of these changes were associated with fluctuations in the realized niche space, helping to explain survivorship and extinction patterns at the boundary. We find a shift in latest Cretaceous dinosaur faunas, as medium-sized species counterbalanced a loss of large herbivores, but that dinosaur niches were otherwise resilient and static until the K/Pg boundary. Smaller terrestrial vertebrates, including mammals, followed a consistent trajectory of increasing trophic impact and relaxation of ecological niche limits that began in the Cretaceous and continued after the extinction. Patterns of mammalian ecological radiation and niche restructuring indicate that these taxa did not simply proliferate after the extinction; rather, their earlier ecological diversification might have helped them survive the K/Pg event, whereas the static niche of dinosaurs might have contributed to their demise. 

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4. Intense Changes in the Main Source of Organic Carbon to the Gulf Coastal Plain Following the Cretaceous‐Paleogene Boundary

   https://doi.org/10.1029/2024PA004887  

   Sosa‐Montes_de_Oca, C; Witts, J D; Lowery, C M; Kearns, L E; Garb, M P; Naujokaityte, J; Myers, C E; Landman, N H; Pancost, R D (August 2024, Paleoceanography and Paleoclimatology)

   Abstract To explore both environmental change and the response of non‐fossilizing phytoplankton across the Cretaceous‐Paleogene (K‐Pg) boundary mass extinction event, we determined changes in organic matter (OM) sources using a range of apolar (n‐alkanes, acyclic isoprenoids, steranes, and hopanes) and polar (BIT index) biomarkers. We analyzed two K‐Pg proximal sections, located in the Mississippi Embayment, Gulf Coastal Plain (USA), covering ∼300 kyrs prior to and ∼3 myrs after the K‐Pg event. The OM abundance and composition changed dramatically across the boundary. The post‐impact ejecta layer and burrowed unit are characterized by an increase in the mass accumulation rate (MAR) of plant and soil biomarkers, including high‐molecular‐weightn‐alkanes and C₂₉steranes as well as the BIT index, related to an erosive period which transported terrestrial OM to the ocean in the aftermath of the impact event. At the same time, MARs of putative aquatic biomarkers decrease (low‐molecular‐weightn‐alkanes, C₂₇steranes and pristane and phytane), which suggests a collapse of the marine phytoplankton community. The increase of terrestrial OM to the ocean, during the first 280 kyrs after the Chicxulub impact event, is a combination of reworked kerogen, soil and some plant material. Crucially, within the latter part of this erosion period, only ∼160 kyrs after the K‐Pg do biomarkers return to distributions similar to those in the upper Cretaceous, although not to pre‐impact MARs. Thus, our results suggest a long‐term interval for the full sedimentary and ecological recovery of the non‐fossilizing phytoplankton community after this event. 

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5. New insights on the evolutionary relationships between the major lineages of Amoebozoa

   https://doi.org/10.1038/s41598-022-15372-7  

   Tekle, Yonas I.; Wang, Fang; Wood, Fiona C.; Anderson, O. Roger; Smirnov, Alexey (July 2022, Scientific Reports)

   Abstract The supergroup Amoebozoa unites a wide diversity of amoeboid organisms and encompasses enigmatic lineages that have been recalcitrant to modern phylogenetics. Deep divergences, taxonomic placement of some key taxa and character evolution in the group largely remain poorly elucidated or controversial. We surveyed available Amoebozoa genomes and transcriptomes to mine conserved putative single copy genes, which were used to enrich gene sampling and generate the largest supermatrix in the group to date; encompassing 824 genes, including gene sequences not previously analyzed. We recovered a well-resolved and supported tree of Amoebozoa, revealing novel deep level relationships and resolving placement of enigmatic lineages congruent with morphological data. In our analysis the deepest branching group is Tubulinea. A recent proposed major clade Tevosa, uniting Evosea and Tubulinea, is not supported. Based on the new phylogenetic tree, paleoecological and paleontological data as well as data on the biology of presently living amoebozoans, we hypothesize that the evolution of Amoebozoa probably was driven by adaptive responses to a changing environment, where successful survival and predation resulted from a capacity to disrupt and graze on microbial mats-a dominant ecosystem of the mid-Proterozoic period of the Earth history. 

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