Complexity of avian evolution revealed by family-level genomes

Nature, Год журнала: 2024, Номер 629(8013), С. 851 - 860

Опубликована: Апрель 1, 2024

Abstract Despite tremendous efforts in the past decades, relationships among main avian lineages remain heavily debated without a clear resolution. Discrepancies have been attributed to diversity of species sampled, phylogenetic method and choice genomic regions 1–3 . Here we address these issues by analysing genomes 363 bird 4 (218 taxonomic families, 92% total). Using intergenic coalescent methods, present well-supported tree but also marked degree discordance. The confirms that Neoaves experienced rapid radiation at or near Cretaceous–Palaeogene boundary. Sufficient loci rather than extensive taxon sampling were more effective resolving difficult nodes. Remaining recalcitrant nodes involve are challenge model due either extreme DNA composition, variable substitution rates, incomplete lineage sorting complex evolutionary events such as ancient hybridization. Assessment effects different partitions showed high heterogeneity across genome. We discovered sharp increases population size, rates relative brain size following extinction event, supporting hypothesis emerging ecological opportunities catalysed diversification modern birds. resulting estimate offers fresh insights into birds provides taxon-rich backbone for future comparative studies.

Язык: Английский

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Incomplete lineage sorting and phenotypic evolution in marsupials

Cell, Год журнала: 2022, Номер 185(10), С. 1646 - 1660.e18

Опубликована: Апрель 20, 2022

Incomplete lineage sorting (ILS) makes ancestral genetic polymorphisms persist during rapid speciation events, inducing incongruences between gene trees and species trees. ILS has complicated phylogenetic inference in many lineages, including hominids. However, we lack empirical evidence that leads to incongruent phenotypic variation. Here, performed phylogenomic analyses show the South American monito del monte is sister of all Australian marsupials, although over 31% its genome closer Diprotodontia than other groups due ancient radiation. Pervasive conflicting signals across whole are consistent with some morphological variation among extant marsupials. We detected hundreds genes experienced stochastic fixation ILS, encoding same amino acids non-sister species. Using functional experiments, confirm how may have directly contributed hemiplasy traits were established marsupial ca. 60 mya.

Язык: Английский

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Phylogenomic resolution of lampreys reveals the recent evolution of an ancient vertebrate lineage

Proceedings of the Royal Society B Biological Sciences, Год журнала: 2025, Номер 292(2038)

Опубликована: Янв. 1, 2025

Jawless vertebrates once dominated Palaeozoic waters, but just two lineages have persisted to the present day: lampreys and hagfishes. Living are a relatively small clade, with over 50 species described, knowledge of their evolutionary relationships has always been based on either few mitochondrial genes or number taxa. Biogeographers noted disjunct antitropical distribution living lamprey families. Here, we comprehensive phylogenomic analysis fossil lampreys, sampling 36 data 46 in total genetic data. We new divergence time estimates nuclear diversification dynamics. Our indicates central role for extreme global warming during Late Cretaceous Cenomanian–Turonian Boundary Event as likely cause notable increase lineage Northern Hemisphere Miocene corresponding period cooling.

Язык: Английский

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Conceptual and empirical advances in Neotropical biodiversity research

PeerJ, Год журнала: 2018, Номер 6, С. e5644 - e5644

Опубликована: Окт. 4, 2018

The unparalleled biodiversity found in the American tropics (the Neotropics) has attracted attention of naturalists for centuries. Despite major advances recent years our understanding origin and diversification many Neotropical taxa biotic regions, questions remain to be answered. Additional biological geological data are still needed, as well methodological that capable bridging these research fields. In this review, aimed primarily at advanced students early-career scientists, we introduce concept "trans-disciplinary biogeography," which refers integration from multiple areas biology (e.g., community ecology, phylogeography, systematics, historical biogeography) Earth physical sciences geology, climatology, palaeontology), a means reconstruct giant puzzle evolution space time. We caution against extrapolating results derived study one or few convey general scenarios landscape formation. urge more coordination ideas among disciplines, transcending their traditional boundaries, basis advancing tomorrow's ground-breaking research. Our review highlights great opportunities studying biota understand life.

Язык: Английский

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Recombination-Aware Phylogenomics Reveals the Structured Genomic Landscape of Hybridizing Cat Species

Molecular Biology and Evolution, Год журнала: 2019, Номер 36(10), С. 2111 - 2126

Опубликована: Июнь 10, 2019

Current phylogenomic approaches implicitly assume that the predominant phylogenetic signal within a genome reflects true evolutionary history of organisms, without assessing confounding effects postspeciation gene flow can produce mosaic signals interact with recombinational variation. Here, we tested validity this assumption analysis 27 species cat family, local recombination rate on tree inference and divergence time estimation across their genomes. We found prevailing autosomes is not always representative most probable speciation history, due to ancient hybridization throughout felid evolution. Instead, was concentrated regions low recombination, notably enriched large X chromosome cold spots exhibited recurrent patterns strong genetic differentiation selective sweeps mammalian orders. By contrast, high were for signatures flow, these sequences inflated crown-lineage times by ∼40%. conclude existing infer Tree Life may be highly misleading considering genomic architecture relative its interplay historical hybridization.

Язык: Английский

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Neoproterozoic origin and multiple transitions to macroscopic growth in green seaweeds

Proceedings of the National Academy of Sciences, Год журнала: 2020, Номер 117(5), С. 2551 - 2559

Опубликована: Янв. 7, 2020

The Neoproterozoic Era records the transition from a largely bacterial to predominantly eukaryotic phototrophic world, creating foundation for complex benthic ecosystems that have sustained Metazoa Ediacaran Period onward. This study focuses on evolutionary origins of green seaweeds, which play an important ecological role in benthos modern sunlit oceans and likely played crucial part evolution early animals by structuring habitats providing novel niches. By applying phylogenomic approach, we resolve deep relationships core Chlorophyta (Ulvophyceae or freshwater terrestrial Chlorophyceae Trebouxiophyceae) unveil rapid radiation principal lineages Ulvophyceae late Era. Our time-calibrated tree points origin diversification seaweeds Tonian Cryogenian periods, interval marked two global glaciations with strong consequent changes amount available marine habitat. We hypothesize unicellular simple multicellular ancestors survived these extreme climate events isolated refugia, diversified environments became increasingly as ice retreated. An increased supply nutrients biotic interactions, such grazing pressure, triggered independent macroscopic growth via different strategies, including true multicellularity, multiple types giant-celled forms.

Язык: Английский

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Whole-Genome Analyses Resolve the Phylogeny of Flightless Birds (Palaeognathae) in the Presence of an Empirical Anomaly Zone

Systematic Biology, Год журнала: 2019, Номер 68(6), С. 937 - 955

Опубликована: Апрель 11, 2019

Palaeognathae represent one of the two basal lineages in modern birds, and comprise volant (flighted) tinamous flightless ratites. Resolving palaeognath phylogenetic relationships has historically proved difficult, short internal branches separating major previous molecular phylogenies suggest that extensive incomplete lineage sorting (ILS) might have accompanied a rapid ancient divergence. Here, we investigate using genome-wide data sets three types noncoding nuclear markers, together totaling 20,850 loci over 41 million base pairs aligned sequence data. We recover fully resolved topology placing rheas as sister to kiwi emu + cassowary is congruent across marker for species tree methods (MP-EST ASTRAL-II). This corroborated by patterns insertions 4274 CR1 retroelements identified from multispecies whole-genome screening, robustly supported phylogenomic subsampling analyses, with MP-EST demonstrating particularly consistent performance replicates compared ASTRAL. In contrast, analyses concatenated supermatrices all other nonostrich palaeognaths, an alternative lacks retroelement support shows inconsistent behavior under approaches. While statistically supporting topology, conflicting also occur imply high amounts ILS successive branches, observed gene heterogeneity. Coalescent simulations tests indicate majority topological incongruence among trees coalescent variation rather than arising estimation error alone, estimated branch lengths internodes inferred fall within theoretical range encompassing anomaly zone. Distributions empirical confirm most common each type differs tree, signifying existence zone palaeognaths.

Язык: Английский

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Phylogenetic Trees and Networks Can Serve as Powerful and Complementary Approaches for Analysis of Genomic Data

Systematic Biology, Год журнала: 2019, Номер 69(3), С. 593 - 601

Опубликована: Авг. 16, 2019

Abstract Genomic data have had a profound impact on nearly every biological discipline. In systematics and phylogenetics, the thousands of loci that are now being sequenced can be analyzed under multispecies coalescent model (MSC) to explicitly account for gene tree discordance due incomplete lineage sorting (ILS). However, MSC assumes no flow post divergence, calling additional methods accommodate this limitation. Explicit phylogenetic network emerged, which simultaneously ILS by representing evolutionary history as directed acyclic graph. point view, we highlight some strengths limitations networks argue tree-based inference should not blindly abandoned in favor simply because they represent more parameter rich models. Attention given selection reticulation complexity, most robust conclusions regarding likely obtained when combining tree- network-based inference.

Язык: Английский

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New Approaches for Inferring Phylogenies in the Presence of Paralogs

Trends in Genetics, Год журнала: 2020, Номер 37(2), С. 174 - 187

Опубликована: Сен. 10, 2020

Язык: Английский

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Defining Coalescent Genes: Theory Meets Practice in Organelle Phylogenomics

Systematic Biology, Год журнала: 2021, Номер 71(2), С. 476 - 489

Опубликована: Июнь 28, 2021

The species tree paradigm that dominates current molecular systematic practice infers trees from collections of sequences under assumptions the multispecies coalescent (MSC), is, there is free recombination between and no (or very low) within them. These genes (c-genes) are thus defined in an historical rather than sense can theory be as large entire genome or small a single nucleotide. A debate about how to define c-genes centers on contention nuclear gene used many analyses undergo too much recombination, such their introns comprise multiple c-genes, violating key assumption MSC. Recently similar argument has been made for plastid (e.g., chloroplast) mitochondrial genomes, which last 30 more years have considered represent c-gene purposes phylogeny reconstruction because they nonrecombining sense. Consequently, it suggested these genomes should analyzed using methods treat genes-over 70 protein-coding case most (plastomes)-as independent estimates phylogeny, contrast usual concatenation, appropriate generating trees. However, although certainly occurs plastome, recognized since 1970's, unlikely phylogenetically relevant. This historically effective only occur when plastomes with incongruent histories brought together same plastid. plastids sort rapidly into different cell lineages rarely fuse. Thus, biology, plastome canonical average multi-intron mammalian gene. continue treated estimate underlying genome. implications this long-held insight systematics studies phylogenomic era explored. [c-gene; gene; concatalescence; organelle genome; plastome; recombination; tree.].

Язык: Английский

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