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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. Ecological selectivity and the evolution of mammalian substrate preference across the K–Pg boundary

   https://doi.org/10.1002/ece3.8114  

   Hughes, Jonathan J. ; Berv, Jacob S. ; Chester, Stephen G. B. ; Sargis, Eric J. ; Field, Daniel J. ( October 2021 , Ecology and Evolution)

   The Cretaceous–Paleogene (K–Pg) mass extinction 66 million years ago was characterized by a worldwide ecological catastrophe and rapid species turnover. Large‐scale devastation of forested environments resulting from the Chicxulub asteroid impact likely influenced the evolutionary trajectories of multiple clades in terrestrial environments, and it has been hypothesized to have biased survivorship in favour of nonarboreal lineages across the K–Pg boundary. Here, we evaluate patterns of substrate preferences across the K–Pg boundary among crown group mammals, a group that underwent rapid diversification following the mass extinction. Using Bayesian, likelihood, and parsimony reconstructions, we identify patterns of mammalian ecological selectivity that are broadly similar to those previously hypothesized for birds. Models based on extant taxa indicate predominant K–Pg survivorship among semi‐ or nonarboreal taxa, followed by numerous independent transitions to arboreality in the early Cenozoic. However, contrary to the predominant signal, some or all members of total‐clade Euarchonta (Primates + Dermoptera + Scandentia) appear to have maintained arboreal habits across the K–Pg boundary, suggesting ecological flexibility during an interval of global habitat instability. We further observe a pronounced shift in character state transitions away from plesiomorphic arboreality associated with the K–Pg transition. Our findings are consistent with the hypothesis that predominantly nonarboreal taxa preferentially survived the end‐Cretaceous mass extinction, and emphasize the pivotal influence of the K‐Pg transition in shaping the early evolutionary trajectories of extant terrestrial vertebrates.

    

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3. 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)

   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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4. 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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5. Multiple historical processes obscure phylogenetic relationships in a taxonomically difficult group (Lobariaceae, Ascomycota)

   https://doi.org/10.1038/s41598-019-45455-x  

   Widhelm, Todd J. ; Grewe, Felix ; Huang, Jen-Pan ; Mercado-Díaz, Joel A. ; Goffinet, Bernard ; Lücking, Robert ; Moncada, Bibiana ; Mason-Gamer, Roberta ; Lumbsch, H. Thorsten ( June 2019 , Scientific Reports)

   In the age of next-generation sequencing, the number of loci available for phylogenetic analyses has increased by orders of magnitude. But despite this dramatic increase in the amount of data, some phylogenomic studies have revealed rampant gene-tree discordance that can be caused by many historical processes, such as rapid diversification, gene duplication, or reticulate evolution. We used a target enrichment approach to sample 400 single-copy nuclear genes and estimate the phylogenetic relationships of 13 genera in the lichen-forming family Lobariaceae to address the effect of data type (nucleotides and amino acids) and phylogenetic reconstruction method (concatenation and species tree approaches). Furthermore, we examined datasets for evidence of historical processes, such as rapid diversification and reticulate evolution. We found incongruence associated with sequence data types (nucleotide vs. amino acid sequences) and with different methods of phylogenetic reconstruction (species tree vs. concatenation). The resulting phylogenetic trees provided evidence for rapid and reticulate evolution based on extremely short branches in the backbone of the phylogenies. The observed rapid and reticulate diversifications may explain conflicts among gene trees and the challenges to resolving evolutionary relationships. Based on divergence times, the diversification at the backbone occurred near the Cretaceous-Paleogene (K-Pg) boundary (65 Mya) which is consistent with other rapid diversifications in the tree of life. Although some phylogenetic relationships within the Lobariaceae family remain with low support, even with our powerful phylogenomic dataset of up to 376 genes, our use of target-capturing data allowed for the novel exploration of the mechanisms underlying phylogenetic and systematic incongruence.

    

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