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6 recordsLinked to original sources

PubMed2026

Phylogenomics and museomics reveal five distinct species of tiger cats in South America.

The evolutionary history of elusive organisms can be characterized through genomic analyses, which have the power to reveal previously unknown taxa even in groups assumed to be well studied, such as cats. We have analyzed complete genomes of 38 individuals from the Neotropical cat genus Leopardus, including 26 individuals representing multiple evolutionary units of the contentious tiger cat (Leopardus tigrinus) species complex. Eight genomes were generated from museum specimens, which allowed the first genetic assessment of the type locality for L. tigrinus in the Guiana Shield. We found that this complex comprises five distinct species, including a novel cat species, discovered in the Bolivian Yungas and described in this study as L. tilcayo. The Peruvian Yungas unit of this complex also represents a distinct taxonomic entity, which we describe here as a novel subspecies, L. tigrinus antisuyo. Our phylogenomic analyses resolve the evolutionary relationships among the tiger cat geographic units, thus stabilizing their recalcitrant taxonomy and enabling adequate conservation assessment of these threatened felids. We also address other aspects of their evolution, including biogeography, past episodes of interspecies admixture, demographic history of each taxonomic unit, and temporal changes in genetic diversity. Altogether, our results clarify the evolutionary history of a complex radiation of wild cats, reveal novel taxa, and serve as a basis for conservation planning on behalf of these elusive wild cats.

Bolivian Yungas↗

PubMed2025

Temporal Genomics Reveal a Century of Genomic Diversity Shifts Across a Biodiversity Hotspot Avian Assemblage.

Biodiversity has experienced tremendous shifts in community, species, and genetic diversity during the Anthropocene. Understanding temporal diversity shifts is especially critical in biodiversity hotspots, i.e., regions that are exceptionally biodiverse and threatened. Here, we use museomics and temporal genomics approaches to quantify temporal shifts in genomic diversity in an assemblage of eight generalist highland bird species from the Ethiopian Highlands (part of the Eastern Afromontane Biodiversity Hotspot). With genomic data from contemporary and historical samples, we demonstrate an assemblage-wide trend of increased genomic diversity through time, potentially due to improved habitat connectivity within highland regions. Genomic diversity shifts in these generalist species contrast with general trends of genomic diversity declines in specialist or imperiled species. In addition to genetic diversity shifts, we found an assemblage-wide trend of decreased realized mutational load, indicative of overall trends for potentially deleterious variation to be masked or selectively purged. Across this avian assemblage, we also show that shifts in population genomic structure are idiosyncratic, with species-specific trends. These results are in contrast with other charismatic and imperiled African taxa that have largely shown strong increases in population genetic structure over the recent past. This study highlights that not all taxa respond the same to environmental change, and generalists, in some cases, may even respond positively. Future comparative conservation genomics assessments on species groups or assemblages with varied natural history characteristics would help us better understand how diverse taxa respond to anthropogenic landscape changes.

Animals↗

PubMed2026

Short-read genome skimming enables molecular barcoding of old myxomycete collections.

This study evaluates the effectiveness of Illumina-based genome skimming for barcoding myxomycete herbarium collections ranging from 29 to 91 years in age. We successfully retrieved partial sequences of the standard marker gene (nucSSU) in all cases, as well as additional markers (mtSSU, EF1a, and COI) for certain collections. Altogether, 28 genes were recognized in the studied material. In a 33-year-old specimen of Lindbladia tubulina, the assembly reached an N50 of 4.19 kb, enabling the recovery of extended functional loci. The input genomic DNA quantity emerges as the primary determinant of sequencing success. Samples with high DNA yields provide representative amounts of contigs coming confirmedly (matching sequences in the NCBI nucleotide database) or potentially (no-hit fraction) from myxomycetes, regardless of specimen age. In addition to target DNA, we revealed distinct signals of both anthropogenic contamination (human DNA and skin microflora) and natural substrate inhabitants, including oribatid mites and bacteria from dead wood, soil, and grass litter. Thus, even in old collections, metagenomic data still carry information regarding the substrate upon which the myxomycete developed. The results demonstrate that short-read genome skimming may help to integrate historical type material of myxomycetes into contemporary phylogenetic research. This method overcomes the length-dependent limitations of traditional Sanger sequencing, thus providing a roadmap for the future of museomics in myxomycetology.

Amoebozoa↗

PubMed2026

Museum genomics links MC1R alleles to adaptive winter coat color polymorphism in the long-tailed weasel.

Understanding the architecture of biological adaptations is a major endeavor of evolutionary biology. Using Natural History collections, we study the genetic basis and evolution of white/brown winter coat color variation in the long-tailed weasel (Neogale frenata), a crucial phenological adaptation for camouflage in habitats with seasonal snow. We produced whole-genome sequencing data for museum specimens, along two winter color morph transition areas in North America, at the West and East coasts. Genome-wide association scans identified a single genomic region linked to color variation polymorphism with approximately 300 kb and 200 kb in the West and East regions, respectively, which included the pigmentation gene MC1R. We identified three MC1R alleles, two of which with deletions of nine or eight amino acids, alternatively associated with the winter brown morphs in the West and East, respectively. These deletions affect the second transmembrane domain, and in one case also the first extracellular loop, which in silico analyses predicted to impact the protein's function. Our findings show alternative intraspecific evolutionary solutions for environmental adaptation in long-tailed weasels, building on the evidence that major genes of the melanin production pathway are hotspots for recurrent and independent evolution of winter camouflage adaptation. This adaptive variation may be crucial to anchor adaptive responses facing future environmental change.

Receptor, Melanocortin, Type 1↗

PubMed2025

Uncovering new lineages in the Sunda pangolin (Manis javanica) with museum mitogenomics.

Accurately identifying evolutionarily significant units (ESUs) is crucial for conservation planning, especially for species like pangolins threatened by overhunting and habitat loss. ESUs help categorize different pangolin populations, aiding in understanding their genetic diversity and distribution, which is vital for targeted conservation efforts. This research generated mitochondrial genomes from historical museum specimens of Sunda pangolins (Manis javanica) from underrepresented locations, uncovering a new evolutionary lineage from the Mentawai Islands that diverged from Indochina and west Sundaland populations around 760 000 years ago. This population thereby represents a divergent ESU with a small distribution, important for conservation planning. The novel sequences provide resources for forensic labs tracing the origin of confiscated scales and shed light into the potential distribution of the 'mysterious pangolin'. Additionally, this research confirmed the presence of the two major M. javanica lineages in Java and extended the known distribution of the eastern clade to Bali and East Kalimantan. Our findings potentially suggest a recent bottleneck and postglacial expansion of pangolins across Indochina and west Sundaland. Further investigation with genomic and morphological evidence, contact area sampling and type sequencing will be required to evaluate the taxonomic status of different M. javanica lineages and M. culionensis.

Genomics↗

PubMed2026

Phylogenomics of Manticorini tiger beetles supports ancient Gondwanan vicariance and recent American amphitropical disjunction.

Disjunct distributions have long fascinated biologists, particularly those found in the Southern Hemisphere. Gondwanan vicariance has been invoked to explain these patterns, with relatively limited studies having phylogenetically tested this hypothesis. Another intriguing pattern of disjunction involving South America is the American amphitropical distribution, where Western Hemisphere taxa have close relatives either north or south of the tropics. While better known in plants, this pattern is rarely proposed for animals and only phylogenetically tested in a handful of studies on hymenopteran insects. The Manticorini is a tribe of large-bodied, flightless tiger beetles whose members possess a complex distribution pattern attributable to both Gondwanan vicariance and American amphitropical disjunction. Using genomic-scale data we perform phylogenetic analyses to produce a time-calibrated evolutionary history of the Manticorini. With the resultant time tree we perform ancestral range reconstruction in order to recover the historical biogeography of this group. Our results show deep divergence between most manticorine genera, contrasted with young crown ages indicative of recent diversification. Our analyses support Gondwanan vicariance and amphitropical disjunction resulting from recent dispersal as part of the historical biogeography of the tribe. These findings highlight the role of both vicariance and dispersal in shaping diversification and complex modern distributions.

Animals↗