Morando, M. | Search bioRxiv

bioRxiv2026

Cryptic diversification proceeds despite historical and contemporary hybridization in Patagonian ants

Understanding how independently evolving lineages arise despite ongoing gene flow remains a central question in evolutionary biology. Although genomic studies increasingly suggest that hybridization can accompany diversification, empirical evidence from ecologically dominant insect groups remains limited. Here, we present the first population-scale phylogenomic analysis of Patagonian ants, sampling Dorymyrmex across approximately 450,000 km2. Using genome-wide SNPs, coalescent phylogenetics, phylogenetic networks, demographic modelling, species delimitation, and genome scans, we reconstruct the evolutionary history of this widespread genus. We discovered extensive cryptic diversity with strong genomic differentiation and detected both recent and historical hybridization, demonstrating that substantial genomic divergence accumulated despite recurrent gene flow events. Genome scans further identify candidate loci associated with adaptation to Patagonias contrasting environments, suggesting that ecological divergence contributed to lineage diversification. Our results show that cryptic diversification can proceed despite recurrent gene flow, supporting hybridization as an integral component of the diversification process. More broadly, this study illustrates how genome-scale data can reveal hidden biodiversity and the evolutionary processes shaping it in ecologically important but genomically understudied taxa.

evolutionary biology↗

bioRxiv2024

Global biogeography of N2-fixing microbes: nifH amplicon database and analytics workflow

Marine nitrogen (N) fixation is a globally significant biogeochemical process carried out by a specialized group of prokaryotes (diazotrophs), yet our understanding of their ecology is constantly evolving. Although marine dinitrogen (N2)-fixation is often ascribed to cyanobacterial diazotrophs, indirect evidence suggests that non-cyanobacterial diazotrophs (NCDs) might also be important. One widely used approach for understanding diazotroph diversity and biogeography is polymerase chain reaction (PCR)-amplification of a portion of the nifH gene, which encodes a structural component of the N2-fixing enzyme complex, nitrogenase. An array of bioinformatic tools exists to process nifH amplicon data, however, the lack of standardized practices has hindered cross-study comparisons. This has led to a missed opportunity to more thoroughly assess diazotroph biogeography, diversity, and their potential contributions to the marine N cycle. To address these knowledge gaps a bioinformatic workflow was designed that standardizes the processing of nifH amplicon datasets originating from high-throughput sequencing (HTS). Multiple datasets are efficiently and consistently processed with a specialized DADA2 pipeline to identify amplicon sequence variants (ASVs). A series of customizable post-pipeline stages then detect and discard spurious nifH sequences and annotate the subsequent quality-filtered nifH ASVs using multiple reference databases and classification approaches. This newly developed workflow was used to reprocess nearly all publicly available nifH amplicon HTS datasets from marine studies, and to generate a comprehensive nifH ASV database containing 7909 ASVs aggregated from 21 studies that represent the diazotrophic populations in the global ocean. For each sample, the database includes physical and chemical metadata obtained from the Simons Collaborative Marine Atlas Project (CMAP). Here we demonstrate the utility of this database for revealing global biogeographical patterns of prominent diazotroph groups and highlight the influence of sea surface temperature. The workflow and nifH ASV database provide a robust framework for studying marine N2 fixation and diazotrophic diversity captured by nifH amplicon HTS. Future datasets that target understudied ocean regions can be added easily, and users can tune parameters and studies included for their specific focus. The workflow and database are available, respectively, in GitHub (https://github.com/jdmagasin/nifH-ASV-workflow) and Figshare (https://doi.org/10.6084/m9.figshare.23795943.v1).

bioinformatics↗

bioRxiv2021

Alphaproteobacteria facilitate Trichodesmium community trimethylamine utilization

In the surface waters of the warm oligotrophic ocean, filaments and aggregated colonies of the nitrogen (N)-fixing cyanobacterium Trichodesmium create microscale nutrient-rich oases. These hotspots fuel primary productivity and harbor a diverse consortium of heterotrophs. Interactions with associated microbiota can affect the physiology of Trichodesmium, often in ways that have been predicted to support its growth. Recently, it was found that trimethylamine (TMA), a globally-abundant organic N compound, inhibits N2 fixation in cultures of Trichodesmium without impairing growth rate, suggesting that Trichodesmium receives nitrogen from TMA. In this study, 15N-TMA DNA stable isotope probing (SIP) of a Trichodesmium enrichment was employed to further investigate TMA metabolism and determine if TMA-N is incorporated directly or secondarily via cross-feeding facilitated by microbial associates. Herein we identify two members of the marine Roseobacter clade (MRC) of Alphaproteobacteria as the likely metabolizers of TMA and provide genomic evidence that they converted TMA into a more readily available form of N, e.g., NH4+, which was subsequently used by Trichodesmium and the rest of the community. The results implicate microbiome-mediated carbon (C) and N transformations in modulating N2 fixation, and thus highlight the involvement of host-associated heterotrophs in global biogeochemical cycling.

microbiology↗

bioRxiv2020

Metagenomics and quantitative stable isotope probing offer insights into metabolism of polycyclic aromatic hydrocarbons degraders in chronically polluted seawater

Bacterial biodegradation is a significant contributor to remineralization of polycyclic aromatic hydrocarbons (PAHs): toxic and recalcitrant components of crude oil as well as byproducts of partial combustion chronically introduced into seawater via atmospheric deposition. The Deepwater Horizon oil spill demonstrated the speed at which a seed PAH-degrading community maintained by low chronic inputs can respond to acute pollution. We investigated the diversity and functional potential of a similar seed community in the Port of Los Angeles, a chronically polluted site, using stable isotope probing with naphthalene, deep-sequenced metagenomes and carbon incorporation rate measurements at the port and in two sites further into the San Pedro Channel. We demonstrate the ability of a local seed community of degraders at the Port of LA to incorporate carbon from naphthalene, leading to a quick shift in the microbial community composition to be dominated by these normally rare taxa. We were able to directly show that assembled genomes belonged to naphthalene degraders by matching their 16S-rRNA gene with experimental stable isotope probing data. Surprisingly, we did not find a full PAH degradation pathway in those genomes and even when combining genes from the entire microbial community. We analyze metabolic pathways identified in 29 genomes whose abundance increased in the presence of naphthalene to generate metagenomic-based recommendations for future optimization of PAHs bioremediation. ImportanceOil spills in the marine environment have a devastating effect on marine life and biogeochemical cycles. Oil-degrading bacteria occur naturally in the ocean, especially where they are supported by chronic inputs of oil, and have a significant role in degradation of oil spills. The most recalcitrant and toxic component of oil is polycyclic aromatic hydrocarbons. Therefore, the bacteria who can break those molecules down are of particular importance. We identified such bacteria at the port of Los Angeles, one of the busiest ports worldwide, and characterized their metabolic capabilities. Based on those analyses we proposed chemical targets to stimulate the activity of these bacteria in case of an oil spill in the port of LA.

microbiology↗

bioRxiv2020

An integrative multi-approach workflow resolves species limits in the southernmost members of the Liolaemus kingii group (Squamata: Liolaemini)

Recent conceptual and methodological advances have enabled an increasing number of studies to address the problem of species delimitation in a comprehensive manner. This is of particular interest in cases of species whose divergence times are recent, where the conclusions obtained from a single source of evidence can lead to the incorrect delimitation of entities or assignment of individuals to species. The southernmost species of the Liolaemus kingii group (namely L. baguali, L. escarchadosi, L. sarmientoi, L. tari and the candidate species L. sp. A) show widely overlapping distributions as well as recent mitochondrial divergences, thus phylogenetic relationships and species boundaries are ambiguous. Here we use a comprehensive approach to assess species limits and corroborate their status as independent lineages through the use of four sources of molecular and morphological information (mitochondrial cytochrome-b, nuclear sequences collected by ddRADseq, and linear, meristic and landmark-based morphometrics). We found concordance among the different datasets, but signs of admixture were detected between some of the species. Our results indicate that the L. kingii group can serve as a model system in studies of diversification accompanied by hybridization in nature. We emphasize the importance of using multiple lines of evidence in order to solve evolutionary stories, and minimizing potential erroneous results that may arise when relying on a single source of information.

evolutionary biology↗

bioRxiv2019

Is the replication crisis a problem for biologists? A geometric morphometric approach.

Replicability of findings is the key factor of scientific reliability. However, literature on this topic is scarce and apparently taboo for large scientific areas. Some authors named the failure to reproduce scientific findings replication crisis. Geometric morphometrics, a vastly used technique, is especially silent on replication crisis concern. Nevertheless, some works pointed out that sharing morphogeometric information is not a trivial fact, but need to be careful and meticulous. Here, we investigated the replicability of geometric morphometrics protocols on complex shapes and measurement error extension in three different types of taxa, as well as the potentiality of these protocols to discriminate among closely related species. We found a wide range of replication error that contributed from 19.5% to 60% of the total variation. Although, measurement error decreased with the complexity of the quantified shape, it often maintained high values. All protocols were able to discriminate between species, but more morphogeometric information does not imply better performance. We present evidence of replication crisis in life sciences and highlight the need to explore in deep different sources of variation that could lead to low replicability findings. Lastly, we enunciate some recommendations in order to improve the replicability and reliability of scientific findings.

scientific communication and education↗

bioRxiv2019

Metagenomics and stable isotope probing offer insights into metabolism of polycyclic aromatic hydrocarbons degraders in chronically polluted seawater

Bacterial biodegradation is a significant contributor to remineralization of polycyclic aromatic hydrocarbons (PAHs): toxic and recalcitrant components of crude oil as well as byproducts of partial combustion chronically introduced into seawater via atmospheric deposition. The Deepwater Horizon oil spill demonstrated the speed at which a seed PAH-degrading community maintained by low chronic inputs can respond to an acute pollution. We investigated the diversity and functional potential of a similar seed community in the Port of Los Angeles, a chronically polluted site, using stable isotope probing with naphthalene, deep-sequenced metagenomes and carbon incorporation rate measurements at the port and in two sites further into the San Pedro Channel. We show a switch in the composition of the PAH degrading community from diverse early-responding generalists to late-blooming specialized degraders. This switch demonstrates the ability of the local seed community of degraders at the Port of LA to incorporate carbon from PAHs independently of a labile-hydrocarbon degrading succession. We were able to directly show that assembled genomes belonged to naphthalene degraders by matching their 16S-rRNA gene with experimental stable isotope probing data. Surprisingly, we did not find a full PAH degradation pathway in any of those genomes and even when combining genes from the entire microbial community. We use metabolic pathways identified in those genomes to generate metagenomic-based recommendations for future optimization of PAHs bioremediation.

microbiology↗

bioRxiv2019

How important is it to consider lineage diversification heterogeneity in macroevolutionary studies: lessons from the lizard family Liolaemidae

Macroevolutionary studies commonly apply multiple models to test state-dependent diversification. These models track the association between states of interest along a phylogeny, but they do not consider whether independent shifts in character states are associated with shifts in diversification rates. This potentially problematic issue has received little theoretical attention, while macroevolutionary studies implementing such models in increasing larger scale studies continue growing. A recent macroevolutionary study has found that Andean orogeny has acted as a species pump driving diversification of the family Liolaemidae, a highly species-rich lizard family native to temperate southern South America. This study approaches a distribution-dependent hypothesis using the Geographic State Speciation and Extinction model (GeoSSE). However, more recent analyses have shown that there is a clear heterogeneous diversification pattern in the Liolaemidae, which likely biased the GeoSSE analysis. Specifically, we show here that there are two shifts to accelered speciation rates involving species groups that were classified as "Andean" in their distributions. We demonstrate that this GeoSSE result is meaningless when heterogeneous diversification rates are included. We use the lizard family Liolaemidae to demonstrate potential risks of ignoring clade-specific differences in diversification rates in macroevolutionary studies.

evolutionary biology↗