The genus Sotalia is a natural laboratory for studying one of evolution’s most challenging transitions. The ancient shift from land to water is well documented in the fossil record of whales and dolphins, but much less is known about what happens when aquatic mammals subsequently adapt to sharply different aquatic environments. The Guiana dolphin generally occupies coastal and estuarine habitats, while the tucuxi lives in major South American river systems. Although the animals remain close relatives, their environments impose different pressures. Rivers can be turbid, narrow and seasonally variable, with distinct prey communities, currents and chemical conditions compared with the open coast. Over evolutionary time, such ecological contrasts can reduce encounters between populations, alter natural selection and eventually promote speciation. Because Sotalia’s split is relatively recent in geological terms, the two dolphins preserve a snapshot of divergence before the genetic differences between them become too extensive to reconstruct.

To build that snapshot, Mariana F. Nery and colleagues combined several sequencing technologies and comparative-genomic approaches. The Guiana dolphin reference genome was assembled from PacBio HiFi reads, which are long DNA sequences generated with high accuracy, and organized into chromosomes using Hi-C scaffolding. Hi-C captures the physical proximity of DNA segments inside the nucleus; pieces that frequently contact one another are likely to belong to the same chromosome or nearby chromosomal regions. This strategy produces a chromosome-level assembly rather than a collection of disconnected fragments. The researchers also generated short-read assemblies for Guiana dolphins and an Illumina short-read assembly for the tucuxi, then compared the resulting genomes. Such comparisons can identify conserved synteny—the preservation of gene order across species—as well as inversions, rearrangements and other structural changes that may contribute to reproductive or ecological separation.

The resulting genomic resources extend beyond a simple catalogue of genes. The study examined protein-coding sequences, non-coding RNAs and repetitive DNA, including transposable elements. These mobile or once-mobile sequences can copy or move within genomes, sometimes influencing gene regulation, chromosome structure and the emergence of new genetic variation. The researchers mapped regions enriched in genes and regions enriched in transposable elements across the Guiana dolphin reference genome, finding a heterogeneous architecture in which gene-rich and repeat-rich compartments are interspersed. They also compared mitochondrial genomes, which are inherited separately from the nuclear genome and can provide an additional record of evolutionary relationships. Genome completeness was assessed using conserved single-copy genes and other annotation measures, allowing the assemblies to serve as foundations for future studies rather than merely as preliminary sequences.

Phylogenomic analyses—evolutionary reconstructions based on genome-wide data—place the separation of the two Sotalia species within a period of repeated sea-level change. During the Plio-Pleistocene, advancing and retreating seas reshaped coastal plains, river mouths and connections between aquatic systems. A rise in sea level could expand marine habitat and alter the routes available to coastal dolphins, while later declines could isolate populations in estuaries and river basins. The study’s results are consistent with a scenario in which these shifting landscapes repeatedly changed opportunities for dispersal and gene flow. Gene flow occurs when individuals from different populations reproduce, mixing their DNA; geographic isolation reduces that exchange and allows local adaptations to accumulate. The genomic evidence does not portray speciation as a sudden event. Instead, it supports a gradual process in which environmental change, physical separation and selection worked together while the two dolphin lineages were still evolutionarily young.

The most urgent discovery may be the dolphins’ limited genetic diversity. Genome-wide heterozygosity, a measure of the proportion of DNA sites carrying two different variants, was uniformly low across the assemblies analyzed. Low heterozygosity can indicate that a population has passed through bottlenecks, remained small for long periods or experienced restricted gene flow. The researchers also identified runs of homozygosity, or ROH: long stretches of the genome in which the two chromosome copies are identical or nearly identical. ROHs arise when individuals inherit matching DNA segments from parents who share ancestors, and their extent can reveal recent or historical inbreeding. High homozygosity does not automatically prove that every individual is unhealthy, but it can increase the chance that harmful recessive variants occur in two copies. In a changing environment, reduced variation may also narrow the evolutionary options available to a population.

The signal was particularly concerning in coastal populations, where demographic genomic analyses indicated both low present-day diversity and low historical diversity. That pattern suggests the problem is not solely a recent consequence of modern human activity; some populations may have been small or isolated for extended periods. Yet ancient vulnerability can amplify current pressures. Coastal Guiana dolphins face industrial development, pollution, fishing activity, vessel traffic and habitat degradation, while tucuxi populations are exposed to the rapidly changing conditions of river ecosystems. Freshwater dolphins are especially sensitive to barriers and disruptions because dams, altered flows and declining water quality can fragment the connected habitats on which they depend. The new genomes provide a baseline against which conservation scientists can measure future changes, identify populations with distinctive genetic variants and evaluate whether management actions preserve connectivity rather than allowing further loss of diversity.

The researchers also searched for molecular signs of natural selection. Using branch-site models, which test whether particular branches of an evolutionary tree show accelerated changes in protein-coding genes, they identified genes inferred to have experienced positive selection in the two species and in their shared ancestral lineage. The statistical framework compares models that permit a subset of sites to evolve faster than expected under neutral or purifying selection with models that constrain the ratio of nonsynonymous to synonymous substitutions. Nonsynonymous changes alter amino acids in proteins, whereas synonymous changes do not; an excess of the former can suggest adaptive evolution. The study cautions that very large estimates of the selection parameter can be numerical artifacts when synonymous substitutions are absent or nearly absent, a realistic issue for closely related species. The researchers therefore relied on likelihood-ratio tests and false-discovery-rate correction rather than treating an apparently infinite estimate as literal evidence of extraordinary adaptation.

By linking evolutionary history with conservation genomics, the study turns Sotalia into a powerful model for understanding how ecological speciation begins—and how it can leave species vulnerable. The Guiana dolphin and tucuxi genomes make it possible to investigate whether differences in sensory systems, metabolism, immunity, reproduction or other biological functions helped dolphins exploit coastal and river habitats. They can also support non-invasive monitoring through DNA recovered from environmental samples, although applying such methods will require additional validation. For conservationists, the immediate value lies in distinguishing populations, tracking genetic connectivity and detecting whether isolated groups are losing variation. The genome sequences cannot by themselves rescue dolphins from polluted waters, entanglement or disrupted rivers, but they reveal the biological costs of isolation with unprecedented clarity. In a genus shaped by ancient changes in sea level, the next evolutionary challenge may be whether modern landscapes leave these dolphins enough room—and enough genetic diversity—to adapt.

The work was carried out by the Telomere-to-Telomere, or T2T, Consortium using HG002, a human genome sample obtained from a living donor and widely used as a reference material by sequencing and diagnostic laboratories. The researchers assembled each chromosome from one telomere, the protective structure at one end, to the other, producing two separate chromosome sets that represent the maternal and paternal genomes. This is technically more difficult than assembling a single genome because the two copies are highly similar but not identical. Computational systems must determine which DNA fragments belong to which parental chromosome while preserving every small difference between them.

The new sequence adds more than 900 million DNA letters that were absent from previous benchmarks and reveals roughly 15% more of the genome than the earlier reference standard. These newly accessible regions include parts of both sex chromosomes, highly repetitive stretches, and sequences containing genes and regulatory elements that may influence disease risk. Such regions have often been excluded from clinical sequencing because standard technologies struggled to read them accurately or because researchers could not determine their correct position within the genome. By resolving these difficult segments, the T2T approach could expose genetic variants that have remained invisible in routine testing.

The advance builds on the consortium’s landmark 2022 completion of the first truly complete human genome sequence. That project filled in approximately the final 8% of a single reference genome, including many repetitive regions and the previously incomplete Y chromosome. The new effort goes further by applying improved sequencing platforms, assembly algorithms and validation methods to a diploid genome. Long-read sequencing technologies were central to the work because they generate DNA fragments thousands or even millions of letters long, allowing researchers to span repetitive sequences that would be broken into ambiguous pieces by older short-read methods.

Accurately assigning genes to each chromosome copy was another essential part of the project. Scientists at Johns Hopkins led by computational biologist Steven Salzberg analyzed the two chromosome sets to identify and annotate their genes, while Michael Schatz’s laboratory contributed to extensive validation of the assembly. Independent checks were used to test whether the reconstructed sequence contained errors, missing segments or incorrectly joined fragments. The result is intended not only as a biological reference but also as a measurement standard for companies developing DNA sequencing instruments, analysis software and clinical diagnostics.

Researchers say the development could change the logic of medical genomics. Current clinical analyses generally search for variants that differ from a standard reference genome. This strategy can perform well when a patient’s DNA resembles the reference, but it becomes less reliable in genomic regions where the reference is incomplete or structurally different. A complete genome assembled for each patient would instead provide an individualized baseline. Genetic analysis could then examine substitutions, insertions, deletions, duplications and larger rearrangements across the entire sequence without automatically discarding regions that do not align well with the traditional reference.

The immediate medical benefit could be improved diagnosis for children and adults with rare genetic disorders. Genome sequencing is already used in such cases, but more than half of patients may still leave testing without a clear molecular explanation. Missing or misread regions can conceal the mutation responsible for disease, particularly when it lies in a repetitive sequence or involves a complex structural change. A complete diploid assembly could help clinicians identify these causes more accurately, potentially ending years of uncertainty for families and guiding treatment, monitoring and reproductive decisions.

The same approach may eventually strengthen predictions for common diseases. Variants in the BRCA1 and BRCA2 genes are already used to estimate breast cancer risk, but researchers believe that many additional risk-associated changes remain undiscovered in difficult-to-sequence portions of the genome. More complete reference data could improve studies of cancer, cardiovascular disease, immune disorders and neuropsychiatric conditions. When combined with genomes from large and diverse populations, these sequences could also support artificial intelligence models trained to recognize disease-related patterns while reducing the bias created by relying on a single, historically limited reference genome.

The consortium estimates that a complete and highly accurate human genome can now be generated for about $5,000, compared with the roughly $5 billion, in current dollars, spent on the Human Genome Project, which concluded in 2003. Although routine whole-genome sequencing still raises questions about privacy, data storage, consent and the interpretation of uncertain findings, the technical barrier is rapidly falling. The researchers envision a future in which a person’s complete genome is sequenced early in life, securely linked to medical records and revisited as scientific knowledge improves. The study is part of a broader package of work in Cell and Cell Genomics that also presents complete or near-complete genomes for macaques, marmosets, zebra finches, rats, voles, horses, donkeys and giraffes, extending the same genomic precision to research on evolution, biodiversity, agriculture and animal health.

Subject of Research: Complete diploid human genome sequencing and personalized genomics

Article Title: Complete, high-quality diploid human genome reconstructed from telomere to telomere

Web References:
https://engineering.jhu.edu/faculty/adam-phillippy/
https://hub.jhu.edu/2022/03/31/johns-hopkins-scientists-first-complete-sequence-human-genome/
https://www.bme.jhu.edu/people/faculty/steven-l-salzberg/
https://engineering.jhu.edu/faculty/michael-schatz/

References:
Cell, DOI: 10.1016/j.cell.2026.06.016

Keywords

Human genome sequencing, diploid genome, Telomere-to-Telomere Consortium, personalized genomics, genetic disease diagnosis, long-read sequencing, genomic medicine, structural variants, precision medicine, genome assembly

The Sichuan taimen, a charismatic fish species endemic to the Yangtze River basin, has seen its populations reduce drastically due to a myriad of factors, including habitat loss, overfishing, and pollution. With the new genomic data at hand, the researchers aim to elucidate the genetic factors contributing to its vulnerability. The study emphasizes the urgency of addressing the challenges facing aquatic ecosystems and the rich diversity of species they harbor. This comprehensive genomic work also serves as a vital tool for conservationists and ecologists aiming to restore and stabilize populations of the Sichuan taimen.

The research team, led by Zhang and featuring co-authors Xiong and Jian, undertook a meticulous approach to construct a high-quality reference genome. They employed cutting-edge sequencing technologies paired with advanced bioinformatics tools to assemble the genome with unprecedented accuracy and resolution. Such a detailed genome assembly offers insights into the evolutionary history of this species and serves as a benchmark for comparing the genetic diversity within and between populations of the Sichuan taimen.

One of the standout findings of the study is the extraordinary proportion of tandem repeats within the genome of Hucho bleekeri. These repetitive sequences play significant roles in various genomic processes, including gene regulation and evolution. The researchers discovered that these tandem repeats might be linked to the species’ adaptive traits and responses to environmental pressures. Understanding how these repeats function could illuminate the underlying mechanisms driving the Sichuan taimen’s genetic resilience or susceptibility to population declines.

In addition to these genetic insights, the study provides a sobering overview of the persistent population shrinkage experienced by the Sichuan taimen. The analysis revealed significant declines in genetic diversity, which can have detrimental effects on population viability and long-term survival. The loss of genetic diversity can result in reduced adaptability to changing environmental conditions, making the species more susceptible to extinction. This underscores the importance of genomic studies in informing conservation efforts, helping to identify genetic bottlenecks, and formulating strategies to mitigate these risks.

Moreover, the research highlights how genomic tools can be applied to monitor and manage aquatic biodiversity effectively. By integrating genomic data with ecological assessments, scientists can develop comprehensive conservation plans tailored to the specific needs of the Sichuan taimen and other similarly threatened species. The collaboration across disciplines—spanning genomics, ecology, and conservation biology—serves as an exemplary model for addressing the complex challenges faced by biodiversity in the age of anthropogenic pressures.

As the study reaches a wider audience through publication, the researchers hope to bring more attention to the plight of the Sichuan taimen. They advocate for coordinated conservation efforts involving policymakers, local communities, and environmental organizations. The integration of scientific research with community-driven conservation initiatives is crucial for the long-term protection of not just the Sichuan taimen, but the broader ecosystems they inhabit.

Another essential aspect raised by this study is the role of environmental management in preserving genetic diversity. The researchers call for a holistic approach that combines habitat restoration, pollution control, and sustainable fishing practices. Such strategies are vital for improving the prospects for the Sichuan taimen and ensuring the survival of its genetic lineage. The findings from the genomic analysis could inform policymakers about the critical actions needed to halt the decline of this iconic species and promote healthier ecosystems.

The intricate relationship between the Sichuan taimen and its habitat emphasizes the broader implications of this research. Freshwater environments are among the most diverse yet also the most threatened ecosystems on the planet. The literature consistently highlights the need for urgent and coordinated global efforts to conserve freshwater biodiversity, reinforcing the significance of studies like the one conducted by Zhang et al. As researchers continue to uncover the links between genetics and population health, there is hope for more effective conservation planning.

This remarkable study is a significant milestone in fish genomics and conservation science. The chromosome-level assembly of the Sichuan taimen’s genome is not just another scientific achievement; it serves as a clarion call for the urgent need to protect this and other at-risk species. The specificity of genetic findings offers conservationists a unique opportunity to influence policies and practices aimed at sustaining the populations of the Sichuan taimen.

In conclusion, the collaborative research presented in this study is a vital contribution to the understanding of Hucho bleekeri’s biology and conservation. The genomic insights gained from this research will serve as a foundation for future studies aimed at unraveling the complexities of its population dynamics and ecology. The scientists involved are hopeful that their work will inspire further research on related species facing similar threats and will promote awareness of the need for urgency in conservation efforts.

The study sets a precedent in the field of genomic research on endangered species and showcases the capability of modern science to confront biodiversity crises. It exemplifies the power of genomic tools in informing conservation decisions and enhancing our understanding of the intricate relationships within ecosystems. As we move closer to a future where science and conservation go hand in hand, the case of the Sichuan taimen remains a poignant reminder of the importance of preserving our planet’s rich biological heritage.

Subject of Research: Sichuan taimen genome assembly and population dynamics

Article Title: Chromosome-level genome assembly for Sichuan taimen (Hucho bleekeri) reveals the extraordinary tandem repeat proportions and its persistent population shrinkage.

Article References:

Zhang, X., Xiong, D., Jian, S. et al. Chromosome-level genome assembly for Sichuan taimen (Hucho bleekeri) reveals the extraordinary tandem repeat proportions and its persistent population shrinkage.
BMC Genomics 26, 839 (2025). https://doi.org/10.1186/s12864-025-12057-z

Image Credits: AI Generated

DOI: 10.1186/s12864-025-12057-z

Keywords: genome assembly, Sichuan taimen, biodiversity conservation, tandem repeats, population dynamics