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1. Quantifying the Tape of Life: Ancestry-based Metrics Provide Insights and Intuition about Evolutionary Dynamics

   https://doi.org/https://www.mitpressjournals.org/doi/abs/10.1162/isal_a_00020  

   Dolson, Emily; Lalejini, Alexander; Jorgensen, Steven; Ofria, Charles (July 2018, The 2018 Conference on Artificial Life)

   Fine-scale evolutionary dynamics can be challenging to tease out when focused on broad brush strokes of whole populations over long time spans. We propose a suite of diagnostic metrics that operate on lineages and phylogenies in digital evolution experiments with the aim of improving our capacity to quantitatively explore the nuances of evolutionary histories in digital evolution experiments. We present three types of lineage measurements: lineage length, mutation accumulation, and phenotypic volatility. Additionally, we suggest the adoption of four phylogeny measurements from biology: depth of the most-recent common ancestor, phylogenetic richness, phylogenetic divergence, and phylogenetic regularity. We demonstrate the use of each metric on a set of two-dimensional, real-valued optimization problems under a range of mutation rates and selection strengths, confirming our intuitions about what they can tell us about evolutionary dynamics. 

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2. Hereditary Stratigraphy: Genome Annotations to Enable Phylogenetic Inference over Distributed Populations

   https://doi.org/10.1162/isal_a_00550  

   Moreno, Matthew Andres; Dolson, Emily; Ofria, Charles (July 2022, The 2022 Conference on Artificial Life (ALIFE 2022))

   Phylogenies provide direct accounts of the evolutionary trajectories behind evolved artifacts in genetic algorithm and artificial life systems. Phylogenetic analyses can also enable insight into evolutionary and ecological dynamics such as selection pressure and frequency-dependent selection. Traditionally, digital evolution systems have recorded data for phylogenetic analyses through perfect tracking where each birth event is recorded in a centralized data structure. This approach, however, does not easily scale to distributed computing environments where evolutionary individuals may migrate between a large number of disjoint processing elements. To provide for phylogenetic analyses in these environments, we propose an approach to enable phylogenies to be inferred via heritable genetic annotations rather than directly tracked. We introduce a “hereditary stratigraphy” algorithm that enables efficient, accurate phylogenetic reconstruction with tunable, explicit trade-offs between annotation memory footprint and reconstruction accuracy. In particular, we demonstrate an approach that enables estimation of the most recent common ancestor (MRCA) between two individuals with fixed relative accuracy irrespective of lineage depth while only requiring logarithmic annotation space complexity with respect to lineage depth. This approach can estimate, for example, MRCA generation of two genomes within 10% relative error with 95% confidence up to a depth of a trillion generations with genome annotations smaller than a kilobyte. We also simulate inference over known lineages, recovering up to 85.70% of the information contained in the original tree using 64-bit annotations. 

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3. The Cretaceous Diatom Database: A tool for investigating early diatom evolution

   https://doi.org/10.1111/jpy.13499  

   Bryłka, Karolina; Ashworth, Matt P; Alverson, Andrew J; Conley, Daniel J (August 2024, Journal of Phycology)

   The Cretaceous period is the time of the first appearance of the diatoms in the fossil record. These fossils give us direct evidence of the age and early evolution of the diatom lineage. The fossil record, however, is incomplete and therefore often extrapolated through time‐calibrated phylogenies. These two approaches offer different perspectives on the early evolution of diatoms, which is still poorly understood. We compiled the first comprehensive Cretaceous Diatom Database, a tool to investigate the taxonomy, diversity, and occurrence of the earliest known diatom lineages. To further aid the integration and use of the oldest diatom fossils in molecular clock analyses, we present a set of well‐documented Cretaceous fossils that can be placed onto molecular phylogenetic trees of extant and extinct species, making them ideal candidates for the calibration of molecular clocks. The analysis of the fossil record and the Cretaceous Diatom Database revealed Cretaceous diversity is substantially greater than previously thought, yet considerable taxonomic work is still needed. The Cretaceous Diatom Database and the list of Cretaceous fossils for calibrating molecular clocks represent valuable resources for future evolutionary and taxonomic studies of modern and fossil diatoms. 

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4. Recent lineage diversification in a venomous snake through dispersal across the Amazon River

   GIBBS, HL. (January 2018, Biological Journal of the Linnean Society)

   Identifying the evolutionary and ecological mechanisms that drive lineage diversification in the species-rich tropics is of broad interest to evolutionary biologists. Here, we use phylogeographic and demographic analyses of genomic scale RADseq data to assess the impact of a large geographic feature, the Amazon River, on lineage formation in a venomous pitviper, Bothrops atrox. We compared genetic differentiation in samples from four sites near Santarem, Brazil that spanned the Amazon and represented major habitat types. A species delimitation analysis identified each population as a distinct evolutionary lineage while a species tree analysis with populations as taxa revealed a phylogenetic tree consistent with dispersal across the Amazon from north to south. Phylogenetic analyses of mtDNA variation confirmed this pattern and suggest that all lineages originated during the mid- to late-Pleistocene. Historical demographic analyses support a population model of lineage formation through isolation between lineages with low ongoing migration between large populations and reject a model of differentiation through isolation by distance alone. Our results provide a rare example of a phylogeographic pattern demonstrating dispersal over evolutionary time scales across a large tropical river and suggest a role for the Amazon River as a driver of in-situ divergence by both impeding (but not preventing) gene flow and through parapatric differentiation along an ecological gradient. 

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5. Phylogenomics, Lineage Diversification Rates, and the Evolution of Diadromy in Clupeiformes (Anchovies, Herrings, Sardines, and Relatives)

   https://doi.org/10.1093/sysbio/syae022  

   Egan, Joshua_P; Simons, Andrew_M; Alavi-Yeganeh, Mohammad_Sadegh; Hammer, Michael_P; Tongnunui, Prasert; Arcila, Dahiana; Betancur-R, Ricardo; Bloom, Devin_D; Albert, ed., James (May 2024, Systematic Biology)

   Abstract Migration independently evolved numerous times in animals, with a myriad of ecological and evolutionary implications. In fishes, perhaps the most extreme form of migration is diadromy, the migration between marine and freshwater environments. Key and long-standing questions are: how many times has diadromy evolved in fishes, how frequently do diadromous clades give rise to non-diadromous species, and does diadromy influence lineage diversification rates? Many diadromous fishes have large geographic ranges with constituent populations that use isolated freshwater habitats. This may limit gene flow between some populations, increasing the likelihood of speciation in diadromous lineages relative to nondiadromous lineages. Alternatively, diadromy may reduce lineage diversification rates if migration is associated with enhanced dispersal capacity that facilitates gene flow within and between populations. Clupeiformes (herrings, sardines, shads, and anchovies) is a model clade for testing hypotheses about the evolution of diadromy because it includes an exceptionally high proportion of diadromous species and several independent evolutionary origins of diadromy. However, relationships among major clupeiform lineages remain unresolved, and existing phylogenies sparsely sampled diadromous species, limiting the resolution of phylogenetically informed statistical analyses. We assembled a phylogenomic dataset and used multi-species coalescent and concatenation-based approaches to generate the most comprehensive, highly resolved clupeiform phylogeny to date, clarifying associations among several major clades and identifying recalcitrant relationships needing further examination. We determined that variation in rates of sequence evolution (heterotachy) and base-composition (nonstationarity) had little impact on our results. Using this phylogeny, we characterized evolutionary patterns of diadromy and tested for differences in lineage diversification rates between diadromous, marine, and freshwater lineages. We identified 13 transitions to diadromy, all during the Cenozoic Era (10 origins of anadromy, 2 origins of catadromy, and 1 origin of amphidromy), and 7 losses of diadromy. Two diadromous lineages rapidly generated nondiadromous species, demonstrating that diadromy is not an evolutionary dead end. We discovered considerably faster transition rates out of diadromy than to diadromy. The largest lineage diversification rate increase in Clupeiformes was associated with a transition to diadromy, but we uncovered little statistical support for categorically faster lineage diversification rates in diadromous versus nondiadromous fishes. We propose that diadromy may increase the potential for accelerated lineage diversification, particularly in species that migrate long distances. However, this potential may only be realized in certain biogeographic contexts, such as when diadromy allows access to ecosystems in which there is limited competition from incumbent species. 

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