Biology subjects

Riesgo, A.

Publications and source records attributed to Riesgo, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Ocean depth modifies host-microbiome ecology and evolution

A major unsolved question in ecology and evolution is how similar free-living and symbiotic microbial communities are. In marine systems, depth homogenises free-living communities due to stronger dispersal and weaker environmental filtering compared to surface waters. We show that symbiotic communities of marine sponges follow a different pattern, with a subset of sponge species mirroring the increased similarity with depth seen in their free-living counterparts, while others remain highly host-specific both in shallow and deep waters. Moreover, in deep waters, more phylogenetically similar hosts harbor more similar microbiomes, yet host-symbiont cophylogeny nearly vanishes. This reveals two contrasting eco-evolutionary assembly rules: in more constant environments like the deep sea, community assembly is driven by host and environmental filtering with minimal signature of coevolution, whereas in variable environments, like shallow waters, host-symbiont coevolution is strong and key to maintain host-specific microbiomes.

microbiology↗

bioRxiv2026

Pseudocryptic diversity within the Phakellia robusta species complex: description of Phakellia pallida sp. nov. and Phakellia pusilla sp. nov.

The genus Phakellia comprises predominantly fan-shaped deep-sea sponges, but its species diversity and boundaries remain unresolved. Here, we use an integrative approach combining morphological and molecular data to investigate the Phakellia robusta species complex and describe two new species, Phakellia pallida sp. nov. and Phakellia pusilla sp. nov. Overlap in external and spicular morphology makes these taxa challenging to identify. Molecular analyses based on mitochondrial (cox1) and nuclear (28S) markers support the recognition of the three taxa as distinct species, and reveal their close evolutionary relationship. The two new species co-occur in the NE Atlantic Ocean and the Mediterranean Sea, with overlapping depth ranges, although P. pallida sp. nov. is generally found at greater depths. Our results also suggest that several previous records of P. robusta from the Mediterranean and southern parts of the NE Atlantic may instead correspond to either P. pallida sp. nov. or P. pusilla sp. nov., indicating that its distribution requires reassessment. In addition, a group I intron previously reported in the cox1 gene of P. robusta was polymorphically detected at the same insertion site in some, but not all, individuals of P. pusilla sp. nov., but it was absent from P. pallida sp. nov. individuals. Overall, our results reveal pseudocryptic diversity within Phakellia and highlight the value of integrative approaches for resolving species boundaries and reassessing deep-sea sponge diversity and distributions.

zoology↗

bioRxiv2025

Refining a molecular tool kit to capture tropicalization in Mediterranean Marine Protected Areas

Tropicalization, the process by which tropical species expand their ranges poleward due to global ocean warming, is a prominent threat to Mediterranean marine ecosystems, challenging their effective management and conservation. The arrival of non-indigenous fish is exacerbated by the Suez Canal that allows Indo-Pacific species to enter the region from the Red Sea. While some non-indigenous species (NIS) have already changed the composition and function of native Mediterranean communities, many others continue to arrive but often go unnoticed without regular surveys or until they are strongly established. We conducted biodiversity surveys using underwater visual census (UVC), aqueous environmental DNA (eDNA) and sponge-derived eDNA (i.e., eDNA accumulated in sea sponge tissue) at two protected locations in Zakynthos, Greece. Seven NIS were detected by eDNA, but only one (dusky spinefoot, Siganus luridus) was detected with all three methods. The fish assemblages of the two locations could be distinguished based on both UVC and eDNA but not from sponge-derived eDNA data, perhaps given low filtration rates. Of the three methods, aqueous eDNA metabarcoding provided the most comprehensive species list including new NIS detected (with the red-toothed triggerfish, Odonus niger, and the houndfish, Tylosurus crocodilus, being the first and third record in the Mediterranean Sea, respectively). Our findings highlight the potential value of incorporating molecular methods into regular monitoring as early warning tools for detecting NIS in marine protected areas threatened by ocean warming.

ecology↗

bioRxiv2025

Genomic connectivity and adaptation signals of the freshwater sponge Ephydatia muelleri across its distribution

1.Freshwater sponges fulfill critical ecological functions, including maintaining water quality, regulating nutrient dynamics, offering habitats for diverse taxa, and serving as a vital food source for various species. However, their patterns of dispersal and genetic connectivity remain inadequately understood, posing significant challenges to effective conservation assessments. We examined genetic connectivity and genetic adaptation to local environmental conditions in Ephydatia muelleri across its geographic range using ddRADseq-derived SNPs from 106 individuals collected from 11 localities spanning North America, Europe, and Asia. Analysis of 3,182 neutral SNPs revealed low connectivity and strong genetic structure among regions within two main genetic clusters of North America and Eurasia, while 115 SNPs identified to be under selection showed considerable evidence for differentiated, polygenic adaptation to light and temperature conditions across sampled locations, as well as selection on gene regulatory processes. These findings align with the "monopolization hypothesis", suggesting that historical climatic and geological conditions of the Last Glacial Maximum, including habitat expansion, contraction, and natural barriers, have contributed more to the current genetic structure of E. muelleri populations than contemporary gene flow, which is restricted by monopolistic habitat colonization by this species. Our results provide novel support for ecological theory on dispersal in aquatic invertebrates, as well as insights into the plasticity of E. muelleri in the face of varying environmental conditions that are fundamentally important for freshwater ecosystem conservation.

evolutionary biology↗

bioRxiv2025

ERGA-BGE genome of Stigmatoteuthis arcturi Robson, 1948: the jewelled squid

The Stigmatoteuthis arcturi reference genome offers a valuable resource for understanding the evolutionary patterns of oceanic squids, who perform important ecological roles as both predators and prey in mesopelagic and deep-sea environments, while their genomes remain understudied. The entirety of the genome sequence was assembled into 46 contiguous chromosomal pseudomolecules. This chromosome-level assembly encompasses 3.25 Gb, composed of 1,268 contigs and 497 scaffolds, with contig and scaffold N50 values of 11.0 Mb and 74.6 Mb, respectively.

genomics↗

bioRxiv2025

ERGA-BGE genome of the Spanish Moon Moth Graellsia isabellae Graells, 1849: a nocturnal lepidopteran protected by the Habitats Directive

The reference genome of the Spanish Moon Moth, Graellsia isabellae, will be of great importance for evolutionary and conservation genomics. Firstly, this reference genome, alongside phylogenomic analyses, may finally resolve the longstanding debate regarding the scientific name of this iconic species--whether it should be Graellsia isabellae (Graells, 1849) or Actias isabellae (Graells, 1849). Secondly, the reference genome will be instrumental in the genetic monitoring of this protected species, enabling advanced methods to calculate contemporary population genomics estimates. The genome was assembled into 31 contiguous chromosomal pseudomolecules (Z chromosome included). The mitochondrial genome has also been assembled and is 15,247 bp in length. This chromosome-level assembly encompasses 0.56 Gb, composed of 38 contigs and 32 scaffolds, with contig and scaffold N50 values of 18.9 Mb and 20.4 Mb, respectively.

genomics↗

bioRxiv2024

Spatial and seasonal biodiversity variation in a large Mediterranean lagoon using environmental DNA metabarcoding through sponge tissue collection

Ecosystem monitoring is a fundamental tool to avert biodiversity loss, gathering valuable information that can be used to develop conservation policies, evaluating management outcomes, and guiding science-based decision-making. The Mar Menor costal lagoon (South-East of Spain) has experienced episodes of eutrophication due to intensive agriculture and other human activities, causing mass mortalities of marine fauna. In this scenario, biodiversity monitoring is crucial to evaluate the status of fauna and flora and take appropriate measures. Here, our main objective was to assess faunal composition and its spatial and temporal structure associated with the pillars used to support the built recreational well-being facilities along the Mar Menor. We capitalised on the many sea sponges that settle on these structures by collecting tissue samples for subsequent extraction of filtered environmental DNA (i.e. natural sampler DNA, nsDNA) in northern and southern areas of the lagoon, both in spring and summer. We metabarcoded all samples at the cytochrome oxidase subunit I gene (COI), and reliably identified 76 taxa belonging to nine different phyla, with annelids, poriferans, molluscs and cnidarians being the richest groups. We detected emblematic species of threatened status, such as pipefishes (genus Syngnathus) and the piddock clam, Pholas dactylus, and others known to become invasive, such as the ascidians Styela canopus and Botrylloides niger, the barnacle Amphibalanus amphitrite, and the polychaetes Branchiomma bairdi and Branchiomma boholense. The use of common and widely distributed sponges as natural eDNA samplers allowed us to characterise both spatial and temporal diversity, further emphasizing the importance of this low-cost approach to monitoring biological communities in shallow coastal ecosystems.

ecology↗

bioRxiv2024

The archaeal class Nitrososphaeria is a key player of the reproductive microbiome in sponges during gametogenesis

Sponge-associated microbes play fundamental roles in regulating their hosts physiology, yet their contribution to sexual reproduction has been largely overlooked. Most studies have concentrated on the proportion of the microbiome transmitted from parents to offspring, providing little evidence of the putative microbial functions during gametogenesis in sponges. Here, we use 16S rRNA gene analysis to assess whether the microbial composition of five gonochoristic sponge species differs between reproductive and non-reproductive individuals and correlate these changes with their gametogenic stages. In sponges with mature oocytes, reproductive status did not influence either beta or alpha microbial diversity. Interestingly, in two of the studied species, Geodia macandrewii and Petrosia ficiformis, which presented oocytes at the previtellogenic stage, significant microbial composition changes were detected between reproductive and non-reproductive individuals. These disparities were primarily driven by differentially abundant taxa affiliated with the Nitrososphaeria archaeal class in both species. We speculate that the previtellogenic stages are more energetically demanding, leading to microbial changes due to the phagocytosis of microbes to meet nutritional demands during this period. Supporting our hypothesis, we observed significant transcriptomic differences in G. macandrewii, mainly associated with the immune system, indicating potential changes in the sponges recognition system. Overall, we provide the first insights into the possible roles of sponge microbiomes during reproductive periods, potentially uncovering critical interactions that support reproductive success.

microbiology↗

bioRxiv2024

Independent origins of spicules reconcile the evolutionary history of sponges

Sponges (Porifera) play a critical role in global biogeochemical processes. However, their evolutionary timeline remains unclear hampering our understanding of Neoproterozoic paleoecology. Molecular data suggest a Tonian or Cryogenian origin, while the oldest confirmed sponge fossils, represented by siliceous spicules, date to the Ediacaran. To understand this 150-million-year discrepancy, we compiled a new phylogenomic dataset, revised fossil evidence, derived a new dated sponge phylogeny, and tested whether ancestral sponges were aspiculated or not. We infer the last common sponge ancestor to have been early Ediacaran in age and aspiculated. Siliceous spicules evolved independently at least four times, and calcareous spicules at least two times in crown sponges. We performed a diversification rate analysis showing that siliceous spicules did not drive species radiations. Our study reconciles molecular and fossil evidence, indicating that while sponges emerged in the early Ediacaran, they are largely absent from the Neoproterozoic fossil record because they had not yet evolved spicules. TeaserSponges emerged in the Precambrian, were soft-bodied and did not produce mineralized spicules, which emerged multiple times independently.

evolutionary biology↗

bioRxiv2024

Towards the identification of the molecular toolkit involved in scale worm bioluminescence (Polinoidae, Annelida)

BackgroundBioluminescence, or the ability of a living organism to produce light, has evolved independently in numerous taxa inhabiting a panoply of ecosystems, although it is more frequent among marine animals. Scale worms are a group of marine polynoid annelids characterized by having dorsal scales, known as elytra, capable of emitting bioluminescent light by a mostly unknown molecular mechanism that may involve a photoprotein called polynoidin. Here, we used RNA-seq data to characterize the expression of genes potentially involved in light production in the polynoid species Harmothoe imbricata (Linnaeus, 1767) and Harmothoe areolata (Grube, 1860) across tissues of the specimens. We also compared the transcriptomes of the selected species with other bioluminescent and non-bioluminescent polynoids, to identify shared orthologous genes potentially involved in light production. In addition, we investigated the disposition of the photocytes on the elytra using confocal microscopy and histological analyses. ResultsOur results showed a total of 16 candidate genes, 15 orthologous genes and 12 enriched GO terms potentially involved in bioluminescence, including genes related with oxidative stress, cytoskeleton, nervous system, stress response, wounding response, eye constituents and metabolic pathways. We also confirmed the presence of photocytes in both species, which appeared distributed around the elytrophore. ConclusionsAmong the genes found potentially implicated in bioluminescence we suggest that the oxidoreductase protein, peroxidasin, could be a polynoidin candidate since it appears overexpressed in the elytra of both species and it is located in the endoplasmic reticulum, where this photoprotein has been described to be found.

evolutionary biology↗

bioRxiv2023

Unveiling the Hidden Viromes Across the Animal Tree of Life: Insights from a Taxonomic Classification Pipeline Applied to Invertebrates of 31 Metazoan Phyla

Invertebrates constitute the majority of animal species on Earth, including most disease-causing agents or vectors, with more diverse viromes when compared to vertebrates. Recent advancements in high-throughput sequencing have significantly expanded our understanding of invertebrate viruses, yet this knowledge remains biased toward a few well-studied animal lineages. In this study, we analyze invertebrate DNA and RNA viromes for 31 phyla using 417 publicly available RNA-Seq datasets from diverse environments in the marine-terrestrial and marine-freshwater gradients. This study aims to (i) estimate virome compositions at the family level for the first time across the Animal Tree of Life, including the first exploration of the virome in several phyla, (ii) quantify the diversity of invertebrate viromes and characterize the structure of invertebrate-virus interaction networks, and (iii) investigate host phylum and habitat influence on virome differences. Results showed that a set of few viral families of eukaryotes, comprising Retroviridae, Flaviviridae and several families of giant DNA viruses, were ubiquitous and highly abundant. Nevertheless, some differences emerged between phyla, revealing for instance a less diverse virome in Ctenophora compared to the other animal phyla. Compositional analysis of the viromes showed that the host phylum explained over five times more variance in composition than its habitat. Moreover, significant similarities were observed between the viromes of some phylogenetically related phyla, which could highlight the influence of co-evolution in shaping invertebrate viromes. ImportanceThis study significantly enhances our understanding of the global animal virome by characterizing the viromes of previously unexamined invertebrate lineages from a large number of animal phyla. It showcases the great diversity of viromes within each phylum and investigates the role of habitat shaping animal viral communities. Furthermore, our research identifies dominant virus families in invertebrates and distinguishes phyla with analogous viromes. This study sets the road towards a deeper understanding of the virome across the Animal Tree of Life.

ecology↗

bioRxiv2023

Trapped DNA fragments in marine sponge specimens unveil north Atlantic deep-sea fish diversity

Sponges pump water to filter feed and for diffusive oxygen uptake. In doing so, trace DNA fragments from a multitude of organisms living around them are trapped in their tissues. Here we show that the environmental DNA retrieved from archived marine sponge specimens can reconstruct the fish communities at the place of sampling and discriminate North Atlantic assemblages according to biogeographic region (from Western Greenland to Svalbard), depth habitat (80-1600m), and even the level of protection in place. Given the cost associated with ocean biodiversity surveys, we argue that targeted and opportunistic sponge samples - as well as the specimens already stored in museums and other research collections - represent an invaluable trove of biodiversity information that can significantly extend the reach of ocean monitoring.

ecology↗

bioRxiv2022

The compact genome of the sponge Oopsacas minuta (Hexactinellida) is lacking key metazoan core genes

BackgroundBilaterian animals today represent 99% of animal biodiversity. Elucidating how bilaterian hallmarks emerged is a central question of animal evo-devo and evolutionary genomics. Studies of non-bilaterian genomes have suggested that the ancestral animal already possessed a diversified developmental toolkit, including some pathways required for bilaterian body plans. Comparing genomes within the early branching metazoan Porifera phylum is key to identify which changes and innovations contributed to the successful transition towards bilaterians. ResultsHere, we report the first whole genome comprehensive analysis of a glass sponge, Oopsacas minuta, a member of the Hexactinellida. Studying this class of sponge is evolutionary relevant because it differs from the three other Porifera classes in terms of development, tissue organization, ecology and physiology. Although O. minuta does not exhibit drastic body simplifications, its genome is among the smallest animal genomes sequenced so far, surprisingly lacking several metazoan core genes (including Wnt and several key transcription factors). Our study also provided the complete genome of the symbiotic organism dominating the associated microbial community: a new Thaumarchaeota species. ConclusionsThe genome of the glass sponge O. minuta differs from all other available sponge genomes by its compactness and smaller number of predicted proteins. The unexpected losses of numerous genes considered as ancestral and pivotal for metazoan morphogenetic processes most likely reflect the peculiar syncytial organization in this group. Our work further documents the importance of convergence during animal evolution, with multiple emergences of sponge skeleton, electrical signaling and multiciliated cells.

evolutionary biology↗

bioRxiv2022

Optimised DNA isolation from marine sponges for natural sampler DNA (nsDNA) metabarcoding

Marine sponges have recently been recognised as natural samplers of environmental DNA (eDNA) due to their effective water filtration and their ubiquitous, sessile and regenerative nature. However, laboratory workflows for metabarcoding of sponge tissue have not been optimised to ensure that these natural samplers achieve their full potential for community survey. We used a phased approach to investigate the influence of DNA isolation procedures on the biodiversity information recovered from sponges. In Phase 1, we compared three treatments of residual ethanol preservative in sponge tissue alongside five DNA extraction protocols. The results of Phase 1 informed which ethanol treatment and DNA extraction protocol should be used in Phase 2, where we assessed the effect of starting tissue mass on extraction success and whether homogenisation of sponge tissue is required. Phase 1 results indicated that ethanol preservative may contain unique and/or additional biodiversity information to that present in sponge tissue, but blotting tissue dry generally recovered more taxa and generated more sequence reads from the wild sponge species. Tissue extraction protocols performed best in terms of DNA concentration, taxon richness and proportional read counts, but the non-commercial tissue protocol was selected for Phase 2 due to cost-efficiency and greater recovery of target taxa. In Phase 2 overall, we found that homogenisation may not be required for sponge tissue and more starting material does not necessarily improve taxon detection. These results combined provide an optimised DNA isolation procedure for sponges to enhance marine biodiversity assessment using natural sampler DNA metabarcoding.

molecular biology↗

bioRxiv2022

Environmental DNA persistence and fish detection in captive sponges

Large and hyper-diverse marine ecosystems pose significant challenges to biodiversity monitoring. While environmental DNA (eDNA) promises to meet many of these challenges, recent studies suggested that sponges, as natural samplers of eDNA, could further streamline the workflow for detecting marine vertebrates. However, beyond pilot studies demonstrating the ability of sponges to capture eDNA, little is known about the journey of eDNA particles in the sponge tissues, and the effectiveness of the latter compared to water samples. Here, we present the results of a controlled aquarium experiment to examine the persistence and detectability of eDNA from three encrusting sponge species and how these compare with established water filtration techniques. Our results indicate that sponges and water samples have highly similar detectability for fish of different sizes and abundances, but different sponge species exhibit considerable variance in performance. Interestingly, one sponge appeared to mirror the eDNA degradation profile of water samples, while another sponge retained eDNA throughout the experiment. A third sponge yielded virtually no DNA sequences at all. Overall, our study suggests that some sponges will be suitable as natural samplers, while others will introduce significant problems for laboratory processing. We suggest that an initial optimization phase will be required in any future studies aiming to employ sponges for biodiversity assessment. With time, factoring in technical and natural accessibility, it is expected that specific sponge taxa may become the chosen natural samplers in certain habitats and regions.

ecology↗

bioRxiv2021

Insights into early stages of the establishment of host:algal endosymbioses: Genetic responses to live versus heat-killed algae and bacterial prey in a sponge host

The freshwater sponge Ephydatia muelleri and its Chlorella-like green algal partner is an emerging model for studying animal:algal endosymbiosis. The sponge host is a highly tractable laboratory organism, and the symbiotic algae are easily cultured. We took advantage of these traits to experimentally interrogate fundamental questions about cellular mechanisms that govern the establishment of durable intracellular partnerships between hosts and symbionts in facultative symbioses. We modified a classical experimental approach to discern the phagocytotic mechanisms that might be co-opted to permit persistent infections, and identified genes differentially expressed in E. muelleri sponges early in the establishment of endosymbiosis. We exposed algal-free E. muelleri to live native algal symbionts, native heat-killed algae, and bacteria, and then performed RNASeq so we could compare patterns of gene expression in each treatment. We contrasted differential gene expression patterns between potential food items (bacteria and heat-killed algae) and the live native Chlorella-like symbiont. We found a relatively small but interesting suite of genes that are uniquely and differentially expressed in the host exposed to live algal symbionts, and a larger number of genes uniquely triggered by host exposure to heat-killed algae. One of the host genes, an ABC transporter that is downregulated in response to live algal symbionts, was further evaluated for its possible role in establishment of the algal symbiosis. We discuss the gene expression profiles associated with host responses to living algal cells in the context of conditions necessary for long-term residency within host cells by phototrophic symbionts as well as the genetic responses to sponge phagocytosis and immune driven pathways.

evolutionary biology↗

bioRxiv2020

The genomic basis of animal origins: a chromosomal perspective from the sponge Ephydatia muelleri

The genomes of non-bilaterian metazoans are key to understanding the molecular basis of early animal evolution. However, a full comprehension of how animal-specific traits such as nervous systems arose is hindered by the scarcity and fragmented nature of genomes from key taxa, such as Porifera. Ephydatia muelleri is a freshwater sponge found across the northern hemisphere. Here we present its 326 Mb genome, assembled to high contiguity (N50: 9.88 Mb) with 23 chromosomes on 24 scaffolds. Our analyses reveal a metazoan-typical genome architecture, with highly shared synteny across Metazoa, and suggest that adaptation to the extreme temperatures and conditions found in freshwater often involves gene duplication. The pancontinental distribution and ready laboratory culture of E. muelleri make this a highly practical model system, which with RNAseq, DNA methylation and bacterial amplicon data spanning its development and range allows exploration of genomic changes both within sponges and in early animal evolution.

evolutionary biology↗

bioRxiv2018

Freshwater Adaptation at the Molecular Scale in the Unique Sponges of Lake Baikal

Freshwater sponges (Spongillida) are a unique lineage of demosponges that secondarily colonized lakes and rivers and are now found ubiquitously in these ecosystems. They developed specific adaptations to freshwater systems, including the ability to survive extreme thermal ranges, long-lasting dessication, anoxia, and resistance to a variety of pollutants. While spongillids have colonized all freshwater systems, the family Lubomirskiidae is endemic to Lake Baikal, and plays a range of key roles in this ecosystem. Our work compares the genomic content and microbiome of individuals of three species of the Lubomirskiidae, providing hypotheses for how molecular evolution has allowed them to adapt to their unique environments. We have sequenced deep (>92% of the metazoan Benchmarking Universal Single-Copy Orthologs (BUSCO) set) transcriptomes from three species of Lubomirskiidae and a draft genome resource for Lubomirskia baikalensis. We note Baikal sponges contain unicellular algal and bacterial symbionts, as well as the dinoflagellate Gyrodinium. We investigated molecular evolution, gene duplication and novelty in freshwater sponges compared to marine lineages. Sixty one orthogroups have consilient evidence of positive selection. Transporters (e.g. zinc transporter-2), transcription factors (aristaless-related homeobox) and structural proteins (for example actin-3), alongside other genes, are under strong evolutionary pressure in freshwater, with duplication driving novelty across the Spongillida, but especially in the Lubomirskiidae. This addition to knowledge of freshwater sponge genetics provides a range of tools for understanding the molecular biology and, in the future, the ecology (for example, colonization and migration patterns) of these key species.

zoology↗