Biology subjects

Springer, M. S.

Publications and source records attributed to Springer, M. S..

10 recordsLinked to original sources

bioRxiv2023

Parallel genetic excisions of the cardiac troponin I N-terminal extension in tachycardic mammals

Mammalian cardiac troponin I (cTnI) contains a highly conserved N-terminal extension harboring protein kinase A targets (Ser23/24) which are phosphorylated during {beta}-adrenergic stimulation to increase cardiomyocyte relaxation rate. Here, we show that the Ser23/24 encoding exon 3 of TNNI3 was pseudoexonized multiple times in shrews and moles to mimic Ser23/24 phosphorylation without adrenergic stimulation, facilitating the evolution of exceptionally high resting heart rates ([~]1000 beats min-1). We further reveal alternative exon 3 splicing in distantly related bat families and that both exon 3- and exon 3+ cTnI isoforms are incorporated into cardiac myofibrils. Finally, exon 3 of human TNNI3 is shown to exhibit a relatively low splice strength score, offering an evolutionarily informed strategy to excise this exon to improve diastolic function during heart failure.

evolutionary biology↗

bioRxiv2022

Genomewide identification of subtelomeric silencing factors in budding yeast

Subtelomeric gene silencing is the negative transcriptional regulation of genes located close to telomeres. This phenomenon occurs in a variety of eukaryotes with salient physiological implications, such as cell adherence, virulence, immune-system escape, and aging. The process has been widely studied in the budding yeast Saccharomyces cerevisiae, where genes involved in this process have been identified mostly on a gene-by-gene basis. Here, we introduce a quantitative approach to study subtelomeric gene silencing, that couples the classical URA3 reporter with GFP monitoring, amenable to high-throughput flow cytometry analysis. This reporter was integrated into several subtelomeric loci in the genome, where it showed a gradual range of silencing effects. By crossing strains with this dual reporter at the COS12 and YFR057W subtelomeric query loci with gene-deletion mutants, we carried out a genome-wide, comprehensive screen for subtelomeric-silencing factors. The approach was replicable and allowed detection of expression changes caused by previously described silencing factors. We also identified new molecular players affecting this process, most of which are related to functions underlying chromatin conformation. This was the case of LGE1, a novel silencing factor herein reported, associated with histone ubiquitination. Our strategy can be readily combined with other reporters and gene perturbation collections, making it a versatile tool to study gene silencing at a genome-wide scale.

genetics↗

bioRxiv2022

Anatomical, ontogenetic, and genomic homologies guide reconstructions of the teeth-to-baleen transition in mysticete whales

The transition in Mysticeti (Cetacea) from capture of individual prey using teeth to bulk filtering batches of small prey using baleen ranks among the most dramatic evolutionary transformations in mammalian history. We review phylogenetic work on the homology of mysticete feeding structures from anatomical, ontogenetic, and genomic perspectives. Six characters with key functional significance for filter-feeding behavior are mapped to cladograms based on 11 morphological datasets to reconstruct evolutionary change across the teeth-to-baleen transition. This comparative summary within a common parsimony framework reveals extensive conflicts among independent systematic efforts but also broad support for the newly named clade Kinetomenta (Aetiocetidae + Chaeomysticeti). Complementary anatomical studies using CTscans and ontogenetic series hint at commonalities between the developmental programs for teeth and baleen, lending further support for a transitional chimaeric feeder scenario that best explains current knowledge on the transition to filter feeding. For some extant mysticetes, the ontogenetic sequence in fetal specimens recapitulates the inferred evolutionary transformation: from teeth, to teeth and baleen, to just baleen. Phylogenetic mapping of inactivating mutations reveals mutational decay of dental genes related to enamel formation before the emergence of crown Mysticeti, while baleen genes that were repurposed or newly derived during the evolutionary elaboration of baleen currently are poorly characterized. Review and meta-analysis of available data suggest that the teeth-to-baleen transition in Mysticeti ranks among the best characterized macroevolutionary shifts due to the diversity of data from the genome, the fossil record, comparative anatomy, and ontogeny that directly bears on this remarkable evolutionary transformation.

evolutionary biology↗

bioRxiv2022

Iterative deletion of gene trees detects extreme biases in distance-based phylogenomic coalescent analyses

Summary coalescent methods offer an alternative to the concatenation (supermatrix) approach for inferring phylogenetic relationships from genome-scale datasets. Given huge datasets, broad congruence between contrasting phylogenomic paradigms is often obtained, but empirical studies commonly show some well supported conflicts between concatenation and coalescence results and also between species trees estimated from alternative coalescent methods. Partitioned support indices can help arbitrate these discrepancies by pinpointing outlier loci that are unjustifiably influential at conflicting nodes. Partitioned coalescence support (PCS) recently was developed for summary coalescent methods, such as ASTRAL and MP-EST, that use the summed fits of individual gene trees to estimate the species tree. However, PCS cannot be implemented when distance-based coalescent methods (e.g., STAR, NJst, ASTRID, STEAC) are applied. Here, this deficiency is addressed by automating computation of partitioned coalescent branch length (PCBL), a novel index that uses iterative removal of individual gene trees to assess the impact of each gene on every clade in a distance-based coalescent tree. Reanalyses of five phylogenomic datasets show that PCBL for STAR and NJst trees helps quantify the overall stability/instability of clades and clarifies disagreements with results from optimality-based coalescent analyses. PCBL scores reveal severe missing taxa, apical nesting, misrooting, and basal dragdown biases. Contrived examples demonstrate the gross overweighting of outlier gene trees that drives these biases. Because of interrelated biases revealed by PCBL scores, caution should be exercised when using STAR and NJst, in particular when many taxa are analyzed, missing data are non-randomly distributed, and widespread gene-tree reconstruction error is suspected. Similar biases in the optimality-based coalescent method MP-EST indicate that congruence among species trees estimated via STAR, NJst, and MP-EST should not be interpreted as independent corroboration for phylogenetic relationships. Such agreements among methods instead might be due to the common defects of all three summary coalescent methods.

evolutionary biology↗

bioRxiv2020

Genomic and anatomical comparisons of skin support independent adaptation to life in water by cetaceans and hippos

The macroevolutionary transition from terra firma to obligatory inhabitance of the marine hydrosphere has occurred twice in the history of Mammalia: Cetacea and Sirenia. In the case of Cetacea (whales, dolphins, porpoises), molecular phylogenies provide unambiguous evidence that fully aquatic cetaceans and semiaquatic hippopotamids (hippos) are each others closest living relatives. Ancestral reconstructions further suggest that some adaptations to the aquatic realm evolved in the common ancestor of Cetancodonta (Cetacea+Hippopotamidae). An alternative hypothesis is that these adaptations evolved independently in cetaceans and hippos. Here, we focus on the integumentary system and evaluate these hypotheses by integrating new histological data for cetaceans and hippos, the first genome-scale data for pygmy hippopotamus, and comprehensive genomic screens and molecular evolutionary analyses for protein-coding genes that have been inactivated in hippos and cetaceans. We identified ten skin-related genes that are inactivated in both cetaceans and hippos, including genes that are related to sebaceous glands, hair follicles, and epidermal differentiation. However, none of these genes exhibit inactivating mutations that are shared by cetaceans and hippos. Mean dates for the inactivation of skin genes in these two clades serve as proxies for phenotypic changes and suggest that hair reduction/loss, the loss of sebaceous glands, and changes to the keratinization program occurred ~16 million years earlier in cetaceans (~46.5 Ma) than in hippos (~30.5 Ma). These results, together with histological differences in the integument and prior analyses of oxygen isotopes from stem hippopotamids ("anthracotheres"), support the hypothesis that aquatic adaptations evolved independently in hippos and cetaceans.

evolutionary biology↗

bioRxiv2020

ILS-Aware Analyses of Retroelement Insertions in the Anomaly Zone

A potential shortcoming of concatenation methods for species tree estimation is their failure to account for incomplete lineage sorting. Coalescent methods address this problem but make various assumptions that, if violated, can result in worse performance than concatenation. Given the challenges of analyzing DNA sequences with both concatenation and coalescent methods, retroelement insertions (RIs) have emerged as powerful phylogenomic markers for species tree estimation. Here, we show that two recently proposed quartet-based methods, SDPquartets and ASTRAL BP, are statistically consistent estimators of the unrooted species tree topology under the coalescent when RIs follow a neutral infinite-sites model of mutation and the expected number of new RIs per generation is constant across the species tree. The accuracy of these (and other) methods for inferring species trees from RIs has yet to be assessed on simulated data sets, where the true species tree topology is known. Therefore, we evaluated eight methods given RIs simulated from four model species trees, all of which have short branches and at least three of which are in the anomaly zone. In our simulation study, ASTRAL BP and SDPquartets always recovered the correct species tree topology when given a sufficiently large number of RIs, as predicted. A distance-based method (ASTRID BP) and Dollo parsimony also performed well in recovering the species tree topology. In contrast, unordered, polymorphism, and Camin-Sokal parsimony typically fail to recover the correct species tree topology in anomaly zone situations with more than four ingroup taxa. Of the methods studied, only ASTRAL BP automatically estimates internal branch lengths (in coalescent units) and support values (i.e. local posterior probabilities). We examined the accuracy of branch length estimation, finding that estimated lengths were accurate for short branches but upwardly biased otherwise. This led us to derive the maximum likelihood (branch length) estimate for when RIs are given as input instead of binary gene trees; this corrected formula produced accurate estimates of branch lengths in our simulation study, provided that a sufficiently large number of RIs were given as input. Lastly, we evaluated the impact of data quantity on species tree estimation by repeating the above experiments with input sizes varying from 100 to 100 000 parsimony-informative RIs. We found that, when given just 1 000 parsimony-informative RIs as input, ASTRAL BP successfully reconstructed major clades (i.e clades separated by branches > 0.3 CUs) with high support and identified rapid radiations (i.e. shorter connected branches), although not their precise branching order. The local posterior probability was effective for controlling false positive branches in these scenarios.

evolutionary biology↗

bioRxiv2019

Six new reference-quality bat genomes illuminate the molecular basis and evolution of bat adaptations

Bats account for ~20% of all extant mammal species and are considered exceptional given their extraordinary adaptations, including biosonar, true flight, extreme longevity, and unparalleled immune systems. To understand these adaptations, we generated reference-quality genomes of six species representing the key divergent lineages. We assembled these genomes with a novel pipeline incorporating state-of-the-art long-read and long-range sequencing and assembly techniques. The genomes were annotated using a maximal evidence approach, de novo predictions, protein/mRNA alignments, Iso-seq long read and RNA-seq short read transcripts, and gene projections from our new TOGA pipeline, retrieving virtually all (>99%) mammalian BUSCO genes. Phylogenetic analyses of 12,931 protein coding-genes and 10,857 conserved non-coding elements identified across 48 mammalian genomes helped to resolve bats closest extant relatives within Laurasiatheria, supporting a basal position for bats within Scrotifera. Genome-wide screens along the bat ancestral branch revealed (a) selection on hearing-involved genes (e.g LRP2, SERPINB6, TJP2), which suggest that laryngeal echolocation is a shared ancestral trait of bats; (b) selection (e.g INAVA, CXCL13, NPSR1) and loss of immunity related proteins (e.g. LRRC70, IL36G), including pro-inflammatory NF-kB signalling; and (c) expansion of the APOBEC family, associated with restricting viral infection, transposon activity and interferon signalling. We also identified unique integrated viruses, indicating that bats have a history of tolerating viral pathogens, lethal to other mammal species. Non-coding RNA analyses identified variant and novel microRNAs, revealing regulatory relationships that may contribute to phenotypic diversity in bats. Together, our reference-quality genomes, high-quality annotations, genome-wide screens and in-vitro tests revealed previously unknown genomic adaptations in bats that may explain their extraordinary traits.

genomics↗

bioRxiv2019

Retroposon Insertions within a Multispecies Coalescent Framework Suggest that Ratite Phylogeny is not in the ‘Anomaly Zone’

Summary coalescence methods were developed to address the negative impacts of incomplete lineage sorting on species tree estimation with concatenation. Coalescence methods are statistically consistent if certain requirements are met including no intralocus recombination, neutral evolution, and no gene tree reconstruction error. However, the assumption of no intralocus recombination may not hold for many DNA sequence data sets, and neutral evolution is not the rule for genetic markers that are commonly employed in phylogenomic coalescence analyses. Most importantly, the assumption of no gene tree reconstruction error is routinely violated, especially for rapid radiations that are deep in the Tree of Life. With the sequencing of complete genomes and novel pipelines, phylogenetic analysis of retroposon insertions has emerged as a valuable alternative to sequence-based phylogenetic analysis. Retroposon insertions avoid or reduce several problems that beset analysis of sequence data with summary coalescence methods: 1) intralocus recombination is avoided because retroposon insertions are singular evolutionary events, 2) neutral evolution is approximated in many cases, and 3) gene tree reconstruction errors are rare because retroposons have low rates of homoplasy. However, the analysis of retroposons within a multispecies coalescent framework has not been realized. Here, we propose a simple workaround in which a retroposon insertion matrix is first transformed into a series of incompletely resolved gene trees. Next, the program ASTRAL is used to estimate a species tree in the statistically consistent framework of the multispecies coalescent. The inferred species tree includes support scores at all nodes and internal branch lengths in coalescent units. As a test case, we analyzed a retroposon dataset for palaeognath birds (ratites and tinamous) with ASTRAL and compared the resulting species tree to an MP-EST species tree for the same clade derived from thousands of sequence-based gene trees. The MP-EST species tree suggests an empirical case of the anomaly zone with three very short internal branches at the base of Palaeognathae, and as predicted for anomaly zone conditions, the MP-EST species tree differs from the most common gene tree. Although identical in topology to the MP-EST tree, the ASTRAL species tree based on retroposons shows branch lengths that are much longer and incompatible with anomaly zone conditions. Simulation of gene trees from the retroposon-based species tree reveals that the most common gene tree matches the species tree. We contend that the wide discrepancies in branch lengths between sequence-based and retroposon-based species trees are explained by the greater accuracy of retroposon gene trees (bipartitions) relative to sequence-based gene trees. Coalescence analysis of retroposon data provides a promising alternative to the status quo by reducing gene tree reconstruction error that can have large impacts on both branch length estimates and evolutionary interpretations.

evolutionary biology↗

bioRxiv2019

Genes lost during the transition from land to water in cetaceans highlight genomic changes involved in aquatic adaptations

The transition from land to water in whales and dolphins (cetaceans) was accompanied by remarkable anatomical, physiological and behavioral adaptations. To better understand the genomic changes that occurred during this transition, we systematically screened for protein-coding genes that were inactivated in the ancestral cetacean lineage. We discovered genes whose loss is likely beneficial for cetaceans by reducing the risk of thrombus formation during diving (F12, KLKB1), improving the fidelity of oxidative DNA damage repair (POLM), and protecting from oxidative stress-induced lung inflammation (MAP3K19). Additional gene losses may reflect other diving-related adaptations, such as enhanced vasoconstriction during the diving response (mediated by SLC6A18) and altered pulmonary surfactant composition (SEC14L3), while loss of SLC4A9 relates to a reduced need for saliva in aquatic environments. Finally, the complete loss of melatonin synthesis and receptor genes (AANAT, ASMT, MTNR1A/B) may have been a precondition for the evolution of unihemispheric sleep. Our findings suggest that some genes lost in the ancestral cetacean lineage may have been involved in adapting to a fully-aquatic lifestyle.

evolutionary biology↗

bioRxiv2018

Partitioned coalescence support reveals biases in species-tree methods and detects gene trees that determine phylogenomic conflicts

Genomic datasets sometimes support unconventional or conflicting phylogenetic relationships when different tree-building methods are applied. Coherent interpretations of such results are enabled by partitioning support for controversial relationships among the constituent genes of a phylogenomic dataset. For the supermatrix (= concatenation) approach, several simple methods that measure the distribution of support and conflict among loci were introduced over 15 years ago. More recently, partitioned coalescence support (PCS) was developed for phylogenetic coalescence methods that account for incomplete lineage sorting and use the summed fits of gene trees to estimate the species tree. Here, we automate computation of PCS to permit application of this index to genome-scale matrices that include hundreds of loci. Reanalyses of four phylogenomic datasets for amniotes, land plants, skinks, and angiosperms demonstrate how PCS scores can be used to: 1) compare conflicting results favored by alternative coalescence methods, 2) identify outlier gene trees that have a disproportionate influence on the resolution of contentious relationships, 3) assess the effects of missing data in species-trees analysis, and 4) clarify biases in commonly-implemented coalescence methods and support indices. We show that key phylogenomic conclusions from these analyses often hinge on just a few gene trees and that results can be driven by specific biases of a particular coalescence method and/or the extreme weight placed on gene trees with high taxon sampling. Attributing exceptionally high weight to some gene trees and very low weight to other gene trees counters the basic logic of phylogenomic coalescence analysis; even clades in species trees with high support according to commonly used indices (likelihood-ratio test, bootstrap, Bayesian local posterior probability) can be unstable to the removal of only one or two gene trees with high PCS. Computer simulations cannot adequately describe all of the contingencies and complexities of empirical genetic data. PCS scores complement simulation work by providing specific insights into a particular dataset given the assumptions of the phylogenetic coalescence method that is applied. In combination with standard measures of nodal support, PCS provides a more complete understanding of the overall genomic evidence for contested evolutionary relationships in species trees.

evolutionary biology↗