Ordovician origin and subsequent diversification of the brown algae

Developmental pathways underlying sexual differentiation in the U/V sex chromosome system of giant kelp

In many multicellular organisms, sexual development is not determined by XX/XY or ZW/ZZ systems but by U/V sex chromosomes. In U/V systems, sex determination occurs in the haploid phase, with U chromosomes in females and V chromosomes in males. Here, we explore several male, female, and partially sex-reversed male lines of giant kelp to decipher how U/V sex chromosomes and autosomes initiate male versus female development. We identify a key set of genes on the sex chromosomes involved in triggering sexual development and characterize autosomal effector genes underlying sexual differentiation. We show that male, but not female, development involves large-scale transcriptome reorganization with pervasive enrichment in regulatory genes, faster evolutionary rates, and high species-specificity of male-biased genes. Our observations imply that a female-like phenotype is the "ground state", which is complemented by the presence of a U-chromosome but overridden by a dominant male developmental program triggered by the V-chromosome.

Diversification of social complexity following a major evolutionary transition in bees

How social complexity evolved remains a long-standing enigma. In most animal groups, social complexity is typically classified into a few discrete classes. This approach is oversimplified and constrains our inference of social evolution to a narrow trajectory consisting of transitions between classes. Such categorical classifications also limit quantitative studies on the molecular and environmental drivers of social complexity. The recent accumulation of relevant quantitative data has set the stage to overcome these limitations. Here, we propose a data-driven, high-dimensional approach for studying the full diversity of social phenotypes. We curated and analyzed a comprehensive dataset encompassing 17 social traits across 80 species and studied the evolution of social complexity in bees. We found that honey bees, stingless bees, and bumble bees underwent a major evolutionary transition ∼80 mya, inconsistent with the stepwise progression of the social ladder conceptual framework. This major evolutionary transition was followed by a phase of substantial phenotypic diversification of social complexity. Other bee lineages display a continuum of social complexity, ranging from solitary to simple societies, but do not reach the levels of social complexity seen in honey bees, stingless bees, and bumble bees. Bee evolution, therefore, provides a remarkable demonstration of a macroevolutionary process in which a major transition removed biological constraints and opened novel evolutionary opportunities, driving the exploration of the landscape of social phenotypes. Our approach can be extended to incorporate additional data types and readily applied to illuminate the evolution of social complexity in other animal groups.

Multiple pathways to the evolution of positive assortment in aggregative multicellularity

The evolutionary transition to multicellularity requires shifting the primary unit of selection from cells to multicellular collectives. How this occurs in aggregative organisms remains poorly understood. Clonal development provides a direct path to multicellular adaptation through genetic identity between cells, but aggregative organisms face a constraint: selection on collective-level traits cannot drive adaptation without positive genetic assortment. We leveraged experimental evolution of flocculating Saccharomyces cerevisiae to examine the evolution and role of genetic assortment in multicellular adaptation. After 840 generations of selection for rapid settling, 13 of 19 lineages evolved increased positive assortment relative to their ancestor. However, assortment provided no competitive advantage during settling selection, suggesting it arose as an indirect effect of selection on cell-level traits rather than through direct selection on collective-level properties. Genetic reconstruction experiments and protein structure modeling revealed two distinct pathways to assortment: kin recognition mediated by mutations in the FLO1 adhesion gene and generally enhanced cellular adhesion that improved flocculation efficiency independent of partner genotype. The evolution of assortment without immediate adaptive benefit suggests that key innovations enabling multicellular adaptation may arise indirectly through cell-level selection. Our results demonstrate fundamental constraints on aggregative multicellularity and help explain why aggregative lineages have remained simple.

Population genomics reveals strong impacts of genetic drift without purging and guides conservation of bull and giant kelp

Kelp forests are declining in many parts of the northeast Pacific.1,2,3,4 In small populations, genetic drift can reduce adaptive variation and increase fixation of recessive deleterious alleles,5,6,7 but natural selection may purge harmful variants.8,9,10 To understand evolutionary dynamics and inform restoration strategies, we investigated genetic structure and the outcomes of genetic drift and purging by sequencing the genomes of 429 bull kelp (Nereocystis luetkeana) and 211 giant kelp (Macrocystis sp.) from the coastlines of British Columbia and Washington. We identified 6 to 7 geographically and genetically distinct clusters in each species. Low effective population size was associated with low genetic diversity and high inbreeding coefficients (including increased selfing rates), with extreme variation in these genetic health indices among bull kelp populations but more moderate variation in giant kelp. We found no evidence that natural selection is purging putative recessive deleterious alleles in either species. Instead, genetic drift has fixed many such alleles in small populations of bull kelp, leading us to predict (1) reduced within-population inbreeding depression in small populations, which may be associated with an observed shift toward increased selfing rate, and (2) hybrid vigor in crosses between small populations. Our genomic findings imply several strategies for optimal sourcing and crossing of populations for restoration and aquaculture, but these require experimental validation. Overall, our work reveals strong genetic structure and suggests that conservation strategies should consider the multiple health risks faced by small populations whose evolutionary dynamics are dominated by genetic drift.

Evolution: Structure and surprises in the diversification of golden algae

A new study reports the most complete phylogeny of the Ochrophyta, providing understanding of how and why they have repeatedly evolved different cellular phenotypes from a single ancestry.

Evolutionary genomics of the emergence of brown algae as key components of coastal ecosystems

Brown seaweeds are keystone species of coastal ecosystems, often forming extensive underwater forests, and are under considerable threat from climate change. In this study, analysis of multiple genomes has provided insights across the entire evolutionary history of this lineage, from initial emergence, through later diversification of the brown algal orders, down to microevolutionary events at the genus level. Emergence of the brown algal lineage was associated with a marked gain of new orthologous gene families, enhanced protein domain rearrangement, increased horizontal gene transfer events, and the acquisition of novel signaling molecules and key metabolic pathways, the latter notably related to biosynthesis of the alginate-based extracellular matrix, and halogen and phlorotannin biosynthesis. We show that brown algal genome diversification is tightly linked to phenotypic divergence, including changes in life cycle strategy and zoid flagellar structure. The study also showed that integration of large viral genomes has had a significant impact on brown algal genome content throughout the emergence of the lineage.

A transcriptomic hourglass in brown algae

Complex multicellularity has emerged independently across a few eukaryotic lineages and is often associated with the rise of elaborate, tightly coordinated developmental processes1,2. How multicellularity and development are interconnected in evolution is a major question in biology. The hourglass model of embryonic evolution depicts how developmental processes are conserved during evolution, and predicts morphological and molecular divergence in early and late embryogenesis, bridged by a conserved mid-embryonic (phylotypic) period linked to the formation of the basic body plan3,4. Initially found in animal embryos5-8, molecular hourglass patterns have recently been proposed for land plants and fungi9,10. However, whether the hourglass pattern is an intrinsic feature of all complex multicellular eukaryotes remains unknown. Here we tested the presence of a molecular hourglass in the brown algae, a eukaryotic lineage that has evolved multicellularity independently from animals, fungi and plants1,11,12. By exploring transcriptome evolution patterns of brown algae with distinct morphological complexities, we uncovered an hourglass pattern during embryogenesis in morphologically complex species. Filamentous algae without canonical embryogenesis display transcriptome conservation in multicellular stages of the life cycle, whereas unicellular stages are more rapidly evolving. Our findings suggest that transcriptome conservation in brown algae is associated with cell differentiation stages, but is not necessarily linked to embryogenesis. Together with previous work in animals, plants and fungi, we provide further evidence for the generality of a developmental hourglass pattern across complex multicellular eukaryotes.

Insights into the molecular bases of multicellular development from brown algae

The transition from simple to complex multicellularity represents a major evolutionary step that occurred in only a few eukaryotic lineages. Comparative analyses of these lineages provide insights into the molecular and cellular mechanisms driving this transition, but limited understanding of the biology of some complex multicellular lineages, such as brown algae, has hampered progress. This Review explores how recent advances in genetic and genomic technologies now allow detailed investigations into the molecular bases of brown algae development. We highlight how forward genetic techniques have identified mutants that enhance our understanding of pattern formation and sexual differentiation in these organisms. Additionally, the existence and nature of morphogens in brown algae and the potential influence of the microbiome in key developmental processes are examined. Outstanding questions, such as the identity of master regulators, the definition and characterization of cell types, and the molecular bases of developmental plasticity are discussed, with insights into how recent technical advances could provide answers. Overall, this Review highlights how brown algae are emerging as alternative model organisms, contributing to our understanding of the evolution of multicellular life and the diversity of body plans.

An ulvophycean marine green alga produces large parthenogenetic isogametes as predicted by the gamete dynamics model for the evolution of anisogamy

In eukaryotes, gamete size difference between the two sexes (anisogamy) evolved from gametes of equal size in both mating types (isogamy). The gamete dynamics (GD) model for anisogamy evolution combines gamete limitation and competition and predicts that if gametes of both mating types can develop parthenogenetically (i.e. without fusing with the opposite mating type), large isogamy can evolve under gamete-limited conditions. Ulvophycean marine green algae that have been claimed to exhibit various gametic systems from isogamy to anisogamy are important models for testing such theories. However, in most previous papers, whether a species is isogamous or anisogamous has not been examined statistically. Caution is necessary regarding claims of slight anisogamy because of gamete size variation. We reveal (i) that the gametic system of Struvea okamurae is large isogamy using a generalized linear mixed model, which accounted for the variation of gamete size among individual gametophytes, and (ii) that gametes of this alga can actually develop parthenogenetically, contrary to a previous report. Its habitat environments and protracted duration of gamete release suggest that this alga might experience gamete-limited conditions. Struvea okamurae seems to produce large parthenogenetic isogametes following GD model predictions, as an adaptation to deep waters.

Phylogenomic analyses of ochrophytes (stramenopiles) with an emphasis on neglected lineages

Ochrophyta is a photosynthetic lineage that crowns the phylogenetic tree of stramenopiles, one of the major eukaryotic supergroups. Due to their ecological impact as a major primary producer, ochrophytes are relatively well-studied compared to the rest of the stramenopiles, yet their evolutionary relationships remain poorly understood. This is in part due to a number of missing lineages in large-scale multigene analyses, and an apparently rapid radiation leading to many short internodes between ochrophyte subgroups in the tree. These short internodes are also found across deep-branching lineages of stramenopiles with limited phylogenetic signal, leaving many relationships controversial overall. We have addressed this issue with other deep-branching stramenopiles recently, and now examine whether contentious relationships within the ochrophytes may be resolved with the help of filling in missing lineages in an updated phylogenomic dataset of ochrophytes, along with exploring various gene filtering criteria to identify the most phylogenetically informative genes. We generated ten new transcriptomes from various culture collections and a single-cell isolation from an environmental sample, added these to an existing phylogenomic dataset, and examined the effects of selecting genes with high phylogenetic signal or low phylogenetic noise. For some previously contentious relationships, we find a variety of analyses and gene filtering criteria consistently unite previously unstable groupings with strong statistical support. For example, we recovered a robust grouping of Eustigmatophyceae with Raphidophyceae-Phaeophyceae-Xanthophyceae while Olisthodiscophyceae formed a sister-lineage to Pinguiophyceae. Selecting genes with high phylogenetic signal or data quality recovered more stable topologies. Overall, we find that adding under-represented groups across different lineages is still crucial in resolving phylogenetic relationships, and discrete gene properties affect lineages of stramenopiles differently. This is something which may be explored to further our understanding of the molecular evolution of stramenopiles.

Repeated co-option of HMG-box genes for sex determination in brown algae and animals

In many eukaryotes, genetic sex determination is not governed by XX/XY or ZW/ZZ systems but by a specialized region on the poorly studied U (female) or V (male) sex chromosomes. Previous studies have hinted at the existence of a dominant male-sex factor on the V chromosome in brown algae, a group of multicellular eukaryotes distantly related to animals and plants. The nature of this factor has remained elusive. Here, we demonstrate that an HMG-box gene acts as the male-determining factor in brown algae, mirroring the role HMG-box genes play in sex determination in animals. Over a billion-year evolutionary timeline, these lineages have independently co-opted the HMG box for male determination, representing a paradigm for evolution's ability to recurrently use the same genetic "toolkit" to accomplish similar tasks.

Algal evolution: A touch of brown in a Paleozoic sea of greens and reds

Previous molecular clock studies indicated a Mesozoic origin for the brown algae (Phaeophyceae). New research based on phylogenetic evidence challenges this notion and provides novel insights into the origin and diversification of brown algae, which includes multiple transitions within the group from isogamy to oogamy (and back again!).