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Low coverage 'genome‐skims' are often used to assemble organelle genomes and ribosomal gene sequences for cost‐effective phylogenetic and barcoding studies. Natural history collections hold invaluable biological information, yet poor preservation resulting in degraded DNA often hinders polymerase chain reaction‐based analyses. However, it is possible to generate libraries and sequence the short fragments typical of degraded DNA to generate genome‐skims from museum collections. Here we introduce a snakemake toolkit comprised of three pipelines skim2mito, skim2rrna and gene2phylo, designed to unlock the genomic potential of historical museum specimens using genome skimming. Specifically, skim2mito and skim2rrna perform the batch assembly, annotation and phylogenetic analysis of mitochondrial genomes and nuclear ribosomal genes, respectively, from low‐coverage genome skims. The third pipeline gene2phylo takes a set of gene alignments and performs phylogenetic analysis of individual genes, partitioned analysis of concatenated alignments and a phylogenetic analysis based on gene trees. We benchmark our pipelines with simulated data, followed by testing with a novel genome skimming dataset from both recent and historical solariellid gastropod samples. We show that the toolkit can recover mitochondrial and ribosomal genes from poorly preserved museum specimens of the gastropod family Solariellidae, and the phylogenetic analysis is consistent with our current understanding of taxonomic relationships. The generation of bioinformatic pipelines that facilitate processing large quantities of sequence data from the vast repository of specimens held in natural history museum collections will greatly aid species discovery and exploration of biodiversity over time, ultimately aiding conservation efforts in the face of a changing planet. [ABSTRACT FROM AUTHOR]

Resolving a robust phylogeny of an organismal group is often hindered by the limited availability of samples suitable for genomic or transcriptomic sequencing. Even for lineages of notable importance in evolutionary ecology, our phylogenetic comprehension remains largely unsatisfactory due to the challenges of acquiring samples across the clade. The long‐horned beetle genus Anoplophora Hope exemplifies such a group, globally renowned for two invasive pests—the Asian long‐horned beetle and citrus long‐horned beetle—which have inflicted significant damage to deciduous hardwood forest in North America and Europe. In contrast to the two temperate pests, the remaining 50 species in the genus inhabit subtropical forests of Southeast Asia, where most species are only infrequently encountered. Here, we present the first comprehensive phylogeny of Anoplophora using a PCR‐based target enrichment museomics approach. As a case study of employing PCR‐generated custom probes, we demonstrate the robustness and cost‐effectiveness of this in‐house method in successfully acquiring sequence data from historical specimens. Through extensive sampling of Anoplophora using museum specimens, we reveal a non‐sister relationship between the two temperate species and provide evidence for addressing taxonomic conundrums. Our biogeographical analyses indicate that the adaptation of the two temperate species occurred independently during the late Pliocene and Pleistocene after the establishment of temperate forests in East Asia in the late Miocene. Our findings highlight the importance of comprehensive phylogenetic inference in understanding the patterns and processes of these beetles' adaptation to temperate forests and lay the groundwork for investigating the genetic mechanism underlying life in the cold. [ABSTRACT FROM AUTHOR]

ABSTRACTFormalin preservation of museum specimens has long been considered a barrier to molecular research due to extensive crosslinking and chemical modification. However, recent optimisation of hot alkaline lysis and proteinase K digestion DNA extraction methods have enabled a growing number of studies to overcome these challenges and conduct genome‐wide re‐sequencing and targeted locus‐specific sequencing. The newest, and perhaps most unexpected utility of formalin preservation in archival samples is its ability to preserve in situ DNA‐protein interactions at a molecular level. Retrieving this signal provides information about the relative compaction or accessibility of the genome to the transcriptional machinery required for gene expression. Thus, exposure to formalin essentially corresponds to taking a snapshot of organism‐wide gene expression at the time of death. While DNA methylation and RNA‐Seq analyses of dried tissues have provided glimpses into historical gene regulation, these techniques were previously limited to skeletal or desiccated remains, offering only partial insights. By examining fluid‐preserved specimens, molecular tools can now be applied to a broader range of tissues, enabling more detailed tissue‐specific gene regulation profiling across vertebrates. In this review, we chronicle the historical use of formaldehyde in collections and discuss how targeted chromatin profiling with assays like MNase‐seq and FAIRE‐seq are surmounting fixation challenges and unlocking invaluable insights into historical genomes and gene expression profiles. The deeper integration of molecular genetics with museum collections bridges the gap between past and present and provides a vital tool that could help us predict and mitigate some of the impacts of future environmental change, novel pathogens, or invasive species. [ABSTRACT FROM AUTHOR]

With 334 species, the subtribe Xanthopygina forms a diverse and ecologically dominant component of the Neotropical beetle fauna, ranging from the southern United States south to Argentina. Species can be abundant in a variety of microhabitats and are frequently encountered in tropical forests. Although a number of morphologically distinct genera are now well defined and identifiable, the subtribe still suffers from several poorly defined genera with relatively generalized morphology. The worst of these is the genus Gastrisus Sharp, which has never had a morphological definition per se and has, over time, accumulated many morphologically disparate species. This nebulous concept of Gastrisus has further made it difficult to generically assign and describe new species. Here we assembled a phylogenomic dataset using anchored hybrid enrichment across a broad sample of Xanthopygina, including nearly all described genera, a representation of morphological variation within Gastrisus and a number of undescribed taxa we were unable to assign to a genus. Both maximum likelihood and coalescent analyses converged on a well resolved and stable topology for the subtribe, which will serve as a critical framework for continued taxonomic progress in Xanthopygina. Nine major lineages were identified, most congruent with previous work. The limits of Gastrisus were successfully identified, and the monophyletic core of the genus was recovered as sister to a redefined Nausicotus Sharp, which included Torobus syn. n. Several large species of Gastrisus were resolved as a clade of the Xanthopygus group and are here placed in Drepanagrios gen. n. An additional six new genera were discovered but will be described and treated in detail in future papers. In addition to Gastrisus, Phanolinus Sharp, Xenopygus Bernhauer, Phanolinopsis Scheerpeltz and Ocyolinus Sharp were recovered as paraphyletic, resulting in Elecatopselaphus syn. n. (=Phanolinus), the re‐validation of Leptodiastemus Bernhauer stat. ressur. and the redefinition of Xenopygus, Phanolinopsis and Ocyolinus. We propose Phanolinus scheerpeltzi nom. n. as a replacement name for Phanolinus peruvianus (Scheerpeltz 1972, nec Bernhauer 1917) (previously Elecatopselaphus). [ABSTRACT FROM AUTHOR]

The availability of genetic data from wild populations limits our understanding of primate evolution and conservation, particularly for small nocturnal species such as lorisiforms (galagos, lorises, angwantibos, and pottos). Emerging methods for recovering genomic DNA from historical museum specimens have been rarely used in primate studies. We aimed to optimize extraction and bioinformatics protocols to maximize the recovery of historical DNA to fill important geographic and taxonomic gaps, improve phylogenetic resolution, and inform conservation of Lorisiform primates. First, we compared the performance of two DNA extraction methods by using 238 specimens up to a hundred years old. We then selected 96 samples with the highest DNA yields for shotgun sequencing. To evaluate the impact of phylogenetic divergence in bioinformatic read mapping, we compared coverage depths when using human and three lorisiform reference mitogenomes. Based on whole genomic data, we performed metagenomics and microbial diversity analyses to assess the composition of potentially exogenous content. Lastly, based on the most geographically and taxonomically comprehensive sampling for the West African lorisiforms to date (19/32 currently recognized species), we performed phylogenetic inference using Maximum Likelihood. The results showed that older samples yield lower DNA concentration, with an optimized phenol-chloroform protocol outperforming a commercial kit. However, both extraction methods generated DNA in sufficient amount and quality for phylogenetic inference. Our reference bias comparisons showed that higher phylogenetic proximity between focal species and reference mitogenome increases coverage depth. The metagenomic analysis found human contamination in only one of 96 samples (1%), whereas ten of 96 (11%) samples showed nonnegligible levels of other exogenous contents, among which are certain blood parasites. We inferred low support for the monophyly of Asian and African Lorisids but confirmed the monophyly and previously suggested relationships among Galagid genera. Lastly, we found evidence of cryptic species diversity within the western dwarf galagos (genus Galagoides). Taken together, these results attest to the enormous potential of museomics to advance our understanding of galago evolution, ecology, and conservation, an approach that can be extended to other primate clades. [ABSTRACT FROM AUTHOR]

Specimen-based taxonomic research is essential for understanding diversity and setting management frameworks for threatened mammal faunas, and ancient DNA techniques are increasingly used to extract information from taxonomically relevant historical specimens. The largest survivors of the depleted Caribbean mammal fauna are hutias in the genus Capromys , which is usually interpreted as containing a single species, C. pilorides. Previous studies have demonstrated genetic differentiation of Capromys populations across Cuba, but infrageneric species diversity and nomenclature remain unclear. We conducted ancient DNA analysis of historical Capromys samples using cytochrome b and complete mitogenome data sets, and including the 19th-century holotypes of 2 species now considered synonyms, C. fournieri and C. geayi. Our analyses identify distinct western and central/eastern Capromys clades that diverged 1.75 Mya based upon mitogenome data. These clades are separated by the Havana–Matanzas Channel, which represented a barrier to dispersal throughout the Neogene–Quaternary. Divergence date comparisons with other hutia species provide support for interpreting divergence between Capromys populations as species-level differentiation. Although we were unable to yield amplifiable DNA from the C. fournieri holotype, our analyses confidently assign the C. geayi holotype to the western Capromys clade. We therefore recognize 2 extant Capromys species: C. geayi (western Cuba) and C. pilorides (central/eastern Cuba and Cayman Islands). [ABSTRACT FROM AUTHOR]

A debate in conservation genomics centers on whether to conserve small, fragmented populations independently or blend them through translocations from larger populations. Translocations of red grouse (Lagopus scotica) from Great Britain to supplement the Irish population have been suggested. We incorporate a variety of genetic datasets to address this. We used genome wide data from 23 contemporary and historic red grouse from Great Britain and Ireland. We also investigate microsatellite data, sequence candidate pigmentation genes, and assess phenotypic color variation. Genomic data indicate higher inbreeding in Irish grouse relative to an English population and significant divergence for genomic (FST = 0.095) and microsatellite (FST = 0.03) markers. Contemporary Ne was seven times smaller in the Irish population compared to the English. We identified divergent regions linked to pigmentation, immune response, and food intake. We show phenotypic differences in plumage color and sequence divergence among coding regions in the melanin pathway including MC1R (FST from genomic data of 0.3). The two populations thus appear locally adapted and this divergence between the source and target population when used for conservation translocations can swamp locally adapted alleles and/or introduce maladapted genotypes, leading to outbreeding depression. While it is important to avoid inbreeding by sustaining larger populations, our research emphasizes the need for practitioners to consider population divergence and local adaptation. We advocate against translocations between Ireland and Britain as a conservation strategy in this particular case and underscore the importance of prioritizing local populations where possible. [ABSTRACT FROM AUTHOR]

The rapid diversification of notothenioid fishes in Antarctic waters is a prime example of the process of adaptive radiation. Within around 10 million years, Antarctic notothenioids have diversified into over 100 species with a broad range of lifestyles and ecological adaptations. However, the exact number of species within this radiation has long been unclear. Particularly challenging is the taxonomy of the genus Channichthys, for which between one and nine species have been recognized by different authors. The putative species of this genus are known from a limited number of specimens, of which most were sampled decades ago. Here, we investigated the mitochondrial genomes of museum specimens representing the four species Unicorn Icefish (C. rhinoceratus), Red Icefish (C. rugosus), Sailfish Pike (C. velifer), and Charcoal Icefish (C. panticapaei), complemented by morphological analyses. All analyzed specimens were collected in the 1960s and 1970s and fixed in formaldehyde, and their DNA has been heavily degraded. Applying ancient-DNA protocols for DNA extraction and single-stranded library preparation, we were able to obtain sufficient endogenous DNA to reconstruct the mitochondrial genomes of one specimen per species. These mitochondrial genome sequences were nearly identical for the three specimens assigned to Unicorn Icefish, Red Icefish, and Sailfish Pike, while greater divergence was observed for the Charcoal Icefish specimens. We discuss possible explanations of the contrast between these molecular results and the recognizable morphological variation found among the four species, and recommend that at least the Charcoal Icefish be included in the list of valid notothenioid species. [ABSTRACT FROM AUTHOR]

Abstract Natural history museum collections harbour a record of wild species from the past centuries, providing a unique opportunity to study animals as well as their infectious agents. Thousands of great ape specimens are kept in these collections, and could become an important resource for studying the evolution of DNA viruses. Their genetic material is likely to be preserved in dry museum specimens, as reported previously for monkeypox virus genomes from historical orangutan specimens. Here, we screened 209 great ape museum specimens for 99 different DNA viruses, using hybridization capture coupled with short-read high-throughput sequencing. We determined the presence of multiple viruses within this dataset from historical specimens and obtained several near-complete viral genomes. In particular, we report high-coverage (> 18-fold) hepatitis B virus genomes from one gorilla and two chimpanzee individuals, which are phylogenetically placed within clades infecting the respective host species.

Abstract Objective Environmental DNA (eDNA) methods are crucial for monitoring populations, particularly rare and cryptic species. For confident eDNA application, rigorous assay validation is required including specificity testing with genomic DNA (gDNA). However, this critical step is often difficult to achieve as obtaining fresh tissue samples from at-risk species can be difficult, highly limited, or impossible. Natural history museum collections could serve as a valuable and ethical voucher specimen resource for eDNA assay validation. The present study demonstrates the effectiveness of whole genome amplification (WGA) in providing enough gDNA to assemble high quality mitogenomes from which robust targeted eDNA assays can be designed. Results Using fresh and historical museum tissue samples from six species spanning fish, birds, and mammals, we successfully developed a WGA method with an average yield of 380 to 1,268 ng gDNA per 20 µL reaction. This gDNA was used for whole genome shotgun sequencing and subsequent assembly of high quality mitogenomes using mtGrasp. These mitogenomes were then used to develop six new robust, targeted quantitative real time polymerase chain reaction-based eDNA assays and 200 ng WGA-enriched yielded satisfactory Cq values and near 100% detection frequencies for all assays tested. This approach offers a cost-effective and non-invasive alternative, streamlining eDNA research processes and aiding in conservation efforts.

Natural history museum collections harbour a record of wild species from the past centuries, providing a unique opportunity to study animals as well as their infectious agents. Thousands of great ape specimens are kept in these collections, and could become an important resource for studying the evolution of DNA viruses. Their genetic material is likely to be preserved in dry museum specimens, as reported previously for monkeypox virus genomes from historical orangutan specimens. Here, we screened 209 great ape museum specimens for 99 different DNA viruses, using hybridization capture coupled with short-read high-throughput sequencing. We determined the presence of multiple viruses within this dataset from historical specimens and obtained several near-complete viral genomes. In particular, we report high-coverage (> 18-fold) hepatitis B virus genomes from one gorilla and two chimpanzee individuals, which are phylogenetically placed within clades infecting the respective host species. [ABSTRACT FROM AUTHOR]

Currently, the name Gastrotheca splendens is applied to Bolivian montane forest populations of marsupial frogs that have been associated with G. marsupiata and its allies in the past. Because its comparatively large size evoked taxonomic doubts, we re-examined the holotype of Hyla splendens Schmidt, 1857 and extracted and sequenced archival DNA to clarify its identity. Morphological and molecular data revealed H. splendens as being conspecific with Gastrotheca monticola from northwestern Peru. We place Gastrotheca monticola Barbour & Noble, 1920 as a junior synonym of Hyla splendens Schmidt, 1857, regarding the latter a valid species, Gastrotheca splendens (Schmidt, 1857). We furthermore correct its type locality to 'northwestern Peru'. As a result of these findings and the morphological differences observed among the name-bearing types, the Bolivian taxa Gastrotheca lauzuricae De la Riva, 1992 and G. piperata Duellman & Köhler, 2005 are removed from the synonymy of Hyla splendens. Examination of the external morphology and osteology (inferred from micro-CT images) of the holotypes of G. lauzuricae and G. piperata revealed several differences. However, with the data currently available, we are unable to judge whether these differences represent species-specific diagnostic characters or intraspecific variation. We consider G. lauzuricae a valid species and, applying a principle of parsimony of taxonomic changes, provisionally regard G. piperata as its junior synonym pending future investigations. Furthermore, pending further studies, we tentatively continue to consider Gastrotheca coeruleomaculata (Werner, 1899) a valid species occurring in montane forests of the Departamento La Paz, Bolivia. Finally, Leptodactylus andicola Boettger, 1891 is removed from the synonymy of Gastrotheca marsupiata (Duméril & Bibron, 1841) and regarded a nomen dubium based on the morphological characters mentioned in its original description, which are in disagreement with Gastrotheca and argue for affinities with the genus Yunganastes (Strabomantidae). The results of this study highlight the importance of referring to namebearing type specimens when taxonomically revising complex and species-rich groups of organisms. [ABSTRACT FROM AUTHOR]

With recent advances, nuclear genome data for phylogenomic analyses can now be sequenced from minuscule quantities of DNA 1 and from specimens that are more than a million years old. 2 DNA analysis from hair is a well-established approach 3 widely used in forensic science 4 and wildlife conservation. 5 Hair samples can be effectively decontaminated 6 and can be used to identify the mammalian species from which the hair was shed. 7,8 We aimed to use advances optimized for degraded DNA to systematically identify dietary prey species from hair compacted in the teeth of two Tsavo lions that lived during the 1890s in Kenya (see description of samples in the STAR Methods and Patterson 9 and Kerbis Peterhans and Gnoske 10 for background on the Tsavo "man-eaters"). Analysis of hair DNA identified giraffe, human, oryx, waterbuck, wildebeest, and zebra as prey and also identified hair that originated from lion. DNA preservation allowed for analyses of complete mitogenome profiles of zebra, giraffe, and lion. Giraffe mitogenomes are phylogeographically partitioned, and we found that the lions ate at least two individuals that belong to a subspecies of Masai giraffe (Giraffa tippelskirchi tippelskirchi) typically found in southeast Kenya. The lion mitogenome from a hair sample was identical to the Tsavo lion endogenous mitogenome and most closely matched other East African lions from Kenya and Tanzania. Our approach enables a better understanding of the hunting behaviors, diets, and ecology of historical individuals, populations, and species and holds promise for extinct populations and species. [Display omitted] • Prey hair in the Tsavo lions' tooth cavities contains complete mitogenomes • Cavities contained hair from giraffe, human, oryx, waterbuck, wildebeest, and zebra • A comparison of hair DNA to endogenous lion DNA indicates self- or allogrooming • At least two giraffes from a subspecies typical of Tsavo were eaten de Flamingh et al. use ancient DNA and bioinformatic methodologies to systematically identify dietary prey species from hair compacted in the teeth of two Tsavo "man-eating" lions that lived during the 1890s in Kenya. Analysis of hair DNA identified giraffe, human, oryx, waterbuck, wildebeest, and zebra as prey and also identified hair from lion. [ABSTRACT FROM AUTHOR]

Antarctic krill (Euphausia superba Dana) is a keystone species in the Southern Ocean ecosystem, with ecological and commercial significance. However, its vulnerability to climate change requires an urgent investigation of its adaptive potential to future environmental conditions. Historical museum collections of krill from the early 20th century represent an ideal opportunity to investigate how krill have changed over time due to predation, fishing and climate change. However, there is currently no cost‐effective method for implementing population scale collection genomics for krill given its genome size (48 Gbp). Here, we assessed the utility of two inexpensive methods for population genetics using historical krill samples, specifically low‐coverage shotgun sequencing (i.e. 'genome‐skimming') and exome capture. Two full‐length transcriptomes were generated and used to identify 166 putative gene targets for exome capture bait design. A total of 20 historical krill samples were sequenced using shotgun and exome capture. Mitochondrial and nuclear ribosomal sequences were assembled from both low‐coverage shotgun and off‐target of exome capture data demonstrating that endogenous DNA sequences could be assembled from historical collections. Although, mitochondrial and ribosomal sequences are variable across individuals from different populations, phylogenetic analysis does not identify any population structure. We find exome capture provides approximately 4500‐fold enrichment of sequencing targeted genes, suggesting this approach can generate the sequencing depth required to call identify a significant number of variants. Unlocking historical collections for genomic analyses using exome capture, will provide valuable insights into past and present biodiversity, resilience and adaptability of krill populations to climate change. [ABSTRACT FROM AUTHOR]

Human-induced environmental change and globalization facilitate biological invasions, which can lead to the displacement of native species by non-native ones. 1,2,3,4 Analogously, biodiversity loss may occur within species when habitat modifications facilitate the expansion of a specific population's range, leading to genetic admixture with native local populations. We demonstrate such intraspecific loss in population-level diversity in the Southern Small White (Pieris mannii), an originally sedentary butterfly 5 that recently expanded its range across Central Europe due to urbanization. 6,7,8 Using genome-wide markers from historical museum specimens and contemporary samples, we identify a distinct population initiating this expansion and reveal the genetic homogenization of native local populations by admixture with the expansive one. Our study illustrates how human-made environmental change can simultaneously benefit a species by permitting range expansion and drive cryptic biodiversity loss through the genetic homogenization of conspecific populations. • Range expansion in Pieris mannii butterflies is driven by a distinct population • This population now mixes with formerly isolated local populations • Population mixing causes loss of evolutionary distinctiveness within this species The butterfly Pieris mannii recently expanded its range across Central Europe in response to urbanization. Comparing DNA sequence data from museum and contemporary specimens, Blattner et al. show that this expansion is driven by a distinct lineage and that the mixing of this lineage with local ones results in within-species genetic homogenization. [ABSTRACT FROM AUTHOR]

The family Erinaceidae encompasses 27 extant species in two subfamilies: Erinaceinae, which includes spiny hedgehogs, and Galericinae, which comprises silky‐furred gymnures and moonrats. Although they are commonly recognized by the general public, their phylogenetic history remains incompletely understood, and several species have never been included in any molecular analyses. Additionally, previous research suggested that the species diversity of Erinaceidae might be underestimated. In this study, we sequenced the mitochondrial genomes of 29 individuals representing 18 erinaceid species using 18 freshly collected tissue and 11 historical museum specimens. We also integrated previously published data for a concatenated analysis. We aimed to elucidate the evolutionary relationships within Erinaceidae, estimate divergence times, and uncover potential underestimated species diversity. Our data finely resolved intergeneric and interspecific relationships and presented the first molecular evidence for the phylogenetic position of Mesechinus wangi, Paraechinus micropus, and P. nudiventris. Our results revealed a sister relationship between Neotetracus and Neohylomys gymnures, as well as a sister relationship between Hemiechinus and Mesechinus, supporting previous hypotheses. Additionally, our findings provided a novel phylogenetic position for Paraechinus aethiopicus, placing it in a basal position within the genus. Furthermore, our study uncovered cryptic species diversity within Hylomys suillus as well as in Neotetracus sinensis, Atelerix albiventris, P. aethiopicus, and Hemiechinus auratus, most of which have been previously overlooked. [ABSTRACT FROM AUTHOR]

Xanthium is a genus of annual herbaceous plants that stands out within Asteraceae for being wind‐pollinated, diclinous monoecious, and bearing solitary pistillate flowers in peculiar spiny structures (burs). Xanthium sect. Acanthoxanthium is native to South America and characterized by the presence of trifurcate spines at the base of the leaves. Past taxonomic treatments of the section have been contradictory, some recognising up to six species, others reducing all to a single polymorphic species. Altogether, 42 samples of X. sect. Acanthoxanthium were analysed, the vast majority taken from herbarium specimens between 20 and 160 years old. We sampled multiple specimens of X. spinosum from throughout its broad range as well as those taxa with narrower distributions, covering the whole range of morphological variation in the section. When possible, we included types and original material. We used Hyb‐Seq techniques to obtain information from about 1000 single‐copy nuclear genes and complete plastomes. Phylogenomic data were submitted to coalescent‐based species delimitation approaches (SPEEDEMON). Additionally, we performed geometric morphometric analysis of leaf outlines. The results strongly support the identification of four lineages in the section favouring the acceptance of four of the hitherto described species, i.e., X. ambrosioides, X. argenteum, X. catharticum, and X. spinosum. These results were to some extent corroborated by morphometric analyses. While X. ambrosioides was well distinct from X. spinosum based on leaf morphology, such difference was not observed between X. spinosum and X. catharticum. However, X. catharticum differs from X. spinosum in its ecological requirements, being a species rather adapted to high‐mountain environments of the Neotropics. Intriguingly, X. argenteum – a taxon described from a single herbarium collection – was also inferred as a species. [ABSTRACT FROM AUTHOR]

The Irrawaddy dolphin (Orcaella brevirostris) is an endangered cetacean that ranges throughout much of Southeast Asia and lives in coastal, estuarine, and riverine habitats including three river systems: Ayeyarwady, Mekong, and Mahakam. Many populations face risks from human interference, but overall rangewide diversity and connectivity is not well‐understood. Here we sequenced 77 complete mitogenomes from across the range of the Irrawaddy dolphin including all obligate riverine populations; eighteen of these were sequenced from historical museum specimens. Phylogenetic analysis showed haplotypes from each riverine population formed separate clades nested within the wider species implying each river system was separately invaded only once. All Irrawaddy dolphin mitogenomes were dated to a last common ancestor ~764 kya. Most lineages appeared after inundation cycles of the Sunda Shelf were initiated ~400 kya. Despite the lack of monophyly among many haplotypes from the same population, no population shared any haplotypes. Rangewide nucleotide diversity was average compared to other odontocetes, but riverine populations were especially low. Differentiation was significant among all populations analyzed with the most divergence occurring between isolated riverine populations. These analyses add more evidence for the necessity of conservation efforts directed towards riverine and other isolated populations of the Irrawaddy dolphin. [ABSTRACT FROM AUTHOR]

Objective: Environmental DNA (eDNA) methods are crucial for monitoring populations, particularly rare and cryptic species. For confident eDNA application, rigorous assay validation is required including specificity testing with genomic DNA (gDNA). However, this critical step is often difficult to achieve as obtaining fresh tissue samples from at-risk species can be difficult, highly limited, or impossible. Natural history museum collections could serve as a valuable and ethical voucher specimen resource for eDNA assay validation. The present study demonstrates the effectiveness of whole genome amplification (WGA) in providing enough gDNA to assemble high quality mitogenomes from which robust targeted eDNA assays can be designed. Results: Using fresh and historical museum tissue samples from six species spanning fish, birds, and mammals, we successfully developed a WGA method with an average yield of 380 to 1,268 ng gDNA per 20 µL reaction. This gDNA was used for whole genome shotgun sequencing and subsequent assembly of high quality mitogenomes using mtGrasp. These mitogenomes were then used to develop six new robust, targeted quantitative real time polymerase chain reaction-based eDNA assays and 200 ng WGA-enriched yielded satisfactory Cq values and near 100% detection frequencies for all assays tested. This approach offers a cost-effective and non-invasive alternative, streamlining eDNA research processes and aiding in conservation efforts. [ABSTRACT FROM AUTHOR]

Natural history museums house the largest biodiversity collections in the world and represent an enormous repository of genetic information. Much of this information, however, has remained inaccessible until recently. Emerging technologies, such as techniques for isolation of historical DNA (hDNA) and target enrichment sequencing of ultraconserved elements (UCEs) that can utilize degraded DNA as input material, have the potential to unlock museum collections for genomics research. Here, we demonstrate that hDNA extracted from dried Pocillopora coral specimens, collected up to 90 yrs ago, can be used as input for UCE target enrichment sequencing. The resulting sequence data can be used in phylogenetic studies to resolve questions about taxonomic species identities, biogeographic distributions, and evolutionary histories. Our results provide a blueprint for research groups seeking to take advantage of untapped genetic information stored in natural history museum collections. [ABSTRACT FROM AUTHOR]

Sengis (Macroscelidea) are members of the Afroinsectivora, a group of mammals belonging to the supercohort Afrotheria. Sengis' low population densities and their distribution, which includes politically unstable regions with ongoing armed conflicts, hinder contemporary sampling of comprehensive datasets. We overcome this obstacle for the species Petrodromus tetradactylus , one of the most widely distributed sengi species, by utilizing 44 historical museum samples from multiple natural history museums. These historical samples were combined with newly generated or published data of 11 modern samples, thus creating a dataset of 55 P. tetradactylus individuals covering most of the species' distribution. Phylogenetic reconstruction with 11 nuclear loci in conjunction with mostly complete mitochondrial genomes reveals multiple deeply divergent and formerly unknown lineages within this monotypic genus, highlighting the need for a taxonomic revision. Furthermore, we can show that the assumed allopatric distribution of P. tetradactylus in Central Africa most likely represents a sampling artifact. Biogeographic character mapping indicates that the African forest system and its dynamics through climate fluctuations shaped the evolutionary and biogeographic history of this taxon. We show that lineages within Petrodromus that were able to adapt to dryer woodland ecosystems are much more widely distributed than lineages restricted to moist forest systems. The evolution and radiation of the four-toed sengi (P. tetradactylus) mirrors the patterns of its distant relative, the giant sengis (Rhynchocyon) in both ecotype variation and overall distribution, implying a significant influence of climate and landscape features in shaping diversification. [ABSTRACT FROM AUTHOR]

The gray wolf (Canis lupus) population on the Iberian Peninsula was the largest in western and central Europe during most of the 20th century, with its size apparently never under a few hundred individuals. After partial legal protection in the 1970s in Spain, the northwest Iberian population increased to about 300 to 350 packs and then stabilized. In contrast to many current European wolf populations, which have been connected through gene flow, the Iberian wolf population has been isolated for decades. Here, we measured changes in genomic diversity and inbreeding through the last decades in a geographic context. We find that the level of genomic diversity in Iberian wolves is low compared with other Eurasian wolf populations. Despite population expansion in the last 50 years, some modern wolves had very high inbreeding, especially in the recently recolonized and historical edge areas. These individuals contrast with others with low inbreeding within the same population. The high variance in inbreeding despite population expansion seems associated with small-scale fragmentation of the range that is revealed by the genetic similarity between modern and historical samples from close localities despite being separated by decades, remaining differentiated from other individuals that are just over 100 km away, a small distance for a species with great dispersal capacity inhabiting a continuous range. This illustrates that, despite its demographically stable condition, the population would probably benefit from favoring connectivity within the population as well as genetic exchange with other European wolf populations to avoid excessive fragmentation and local inbreeding depression. [ABSTRACT FROM AUTHOR]

The Seychelles magpie‐robin's (SMR) five island populations exhibit some of the lowest recorded levels of genetic diversity among endangered birds, and high levels of inbreeding. These populations collapsed during the 20th century, and the species was listed as Critically Endangered in the IUCN Red List in 1994. An assisted translocation‐for‐recovery program initiated in the 1990s increased the number of mature individuals, resulting in its downlisting to Endangered in 2005. Here, we explore the temporal genomic erosion of the SMR based on a dataset of 201 re‐sequenced whole genomes that span the past ~150 years. Our sample set includes individuals that predate the bottleneck by up to 100 years, as well as individuals from contemporary populations established during the species recovery program. Despite the SMR's recent demographic recovery, our data reveal a marked increase in both the genetic load and realized load in the extant populations when compared to the historical samples. Conservation management may have reduced the intensity of selection by increasing juvenile survival and relaxing intraspecific competition between individuals, resulting in the accumulation of loss‐of‐function mutations (i.e. severely deleterious variants) in the rapidly recovering population. In addition, we found a 3‐fold decrease in genetic diversity between temporal samples. While the low genetic diversity in modern populations may limit the species' adaptability to future environmental changes, future conservation efforts (including IUCN assessments) may also need to assess the threats posed by their high genetic load. Our computer simulations highlight the value of translocations for genetic rescue and show how this could halt genomic erosion in threatened species such as the SMR. [ABSTRACT FROM AUTHOR]

The Hoopoe Starling Fregilupus varius is an extinct species of the Sturnidae that was endemic to Réunion Island in the Indian Ocean. The species rapidly disappeared in the middle of the 19th century, primarily because of overexploitation by humans. We generated an approximately 11× coverage genome to reconstruct the demographic history of the Hoopoe Starling and compared these results with the demographic histories of other starlings and myna species. Our analyses confirmed the close affinities of the Hoopoe Starling with the genera Sturnia, Leucopsar and Sturnornis, and revealed that it went through a strong population bottleneck during its evolutionary history, but that its effective population size was not particularly low when compared with other extinct or critically endangered species of birds. [ABSTRACT FROM AUTHOR]

Island species are particularly vulnerable to various anthropogenic impacts. Because several island endemics are rare and not accessible, obtaining genetic information and reconstructing their biogeographical and evolutionary history becomes increasingly difficult. In the present study, we investigated the endangered freshwater gastropod Paludomus ajanensis (family Paludomidae) endemic to the Seychelles (Mahé and Silhouette) in the western Indian Ocean. By analysing historical DNA of this species, we were able to place this species in the family Paludomidae and to uncover its Asian affinity. The patchy distribution plus the documented recent population decline suggests this species should be considered 'Critically Endangered'. [ABSTRACT FROM AUTHOR]

Numerous genomic methods developed over the past two decades have enabled the discovery and extraction of orthologous loci to help resolve phylogenetic relationships across various taxa and scales. Genome skimming (or low‐coverage genome sequencing) is a promising method to not only extract high‐copy loci but also 100s to 1000s of phylogenetically informative nuclear loci (e.g., ultraconserved elements [UCEs] and exons) from contemporary and museum samples. The subphylum Anthozoa, including important ecosystem engineers (e.g., stony corals, black corals, anemones, and octocorals) in the marine environment, is in critical need of phylogenetic resolution and thus might benefit from a genome‐skimming approach. We conducted genome skimming on 242 anthozoan corals collected from 1886 to 2022. Using existing target‐capture baitsets, we bioinformatically obtained UCEs and exons from the genome‐skimming data and incorporated them with data from previously published target‐capture studies. The mean number of UCE and exon loci extracted from the genome skimming data was 1837 ± 662 SD for octocorals and 1379 ± 476 SD loci for hexacorals. Phylogenetic relationships were well resolved within each class. A mean of 1422 ± 720 loci was obtained from the historical specimens, with 1253 loci recovered from the oldest specimen collected in 1886. We also obtained partial to whole mitogenomes and nuclear rRNA genes from >95% of samples. Bioinformatically pulling UCEs, exons, mitochondrial genomes, and nuclear rRNA genes from genome skimming data is a viable and low‐cost option for phylogenetic studies. This approach can be used to review and support taxonomic revisions and reconstruct evolutionary histories, including historical museum and type specimens. [ABSTRACT FROM AUTHOR]

The Ornate Moth, Utetheisa ornatrix, has served as a model species in chemical ecology studies for decades. Like in the widely publicized stories of the Monarch and other milkweed butterflies, the Ornate Moth and its relatives are tropical insects colonizing whole continents assisted by their chemical defenses. With the recent advances in genomic techniques and evo-devo research, it is becoming a model for studies in other areas, from wing pattern development to phylogeography, from toxicology to epigenetics. We used a genomic approach to learn about Utetheisa's evolution, detoxification, dispersal abilities, and wing pattern diversity. We present an evolutionary genomic analysis of the worldwide genus Utetheisa, then focusing on U. ornatrix. Our reference genome of U. ornatrix reveals gene duplications in the regions possibly associated with detoxification abilities, which allows them to feed on toxic food plants. Finally, comparative genomic analysis of over 100 U. ornatrix specimens from the museum with apparent differences in wing patterns suggest the potential roles of cortex and lim3 genes in wing pattern formation of Lepidoptera and the utility of museum-preserved collection specimens for wing pattern research. [ABSTRACT FROM AUTHOR]

Malaria is a disease of global significance. Ongoing changes to the earth's climate, antimalarial resistance, insecticide resistance, and socioeconomic decline test the resilience of malaria prevention programs. Museum insect specimens present an untapped resource for studying vector-borne pathogens, spurring the question: Do historical mosquito collections contain Plasmodium DNA, and, if so, can museum specimens be used to reconstruct the historical epidemiology of malaria? In this Perspective, we explore molecular techniques practical to pathogen prospecting, which, more broadly, we define as the science of screening entomological museum specimens for human, animal, or plant pathogens. Historical DNA and pathogen prospecting provide a means of describing the coevolution of human, vector, and parasite, informing the development of insecticides, diagnostics, therapeutics, and vaccines. [ABSTRACT FROM AUTHOR]

The Andes mountains of western South America are a globally important biodiversity hotspot, yet there is a paucity of resolved phylogenies for plant clades from this region. Filling an important gap in our understanding of the World's richest flora, we present the first phylogeny of Freziera (Pentaphylacaceae), an Andean-centered, cloud forest radiation. Our dataset was obtained via hybrid-enriched target sequence capture of Angiosperms353 universal loci for 50 of the ca. 75 spp. obtained almost entirely from herbarium specimens. We identify high phylogenomic complexity in Freziera , including the presence of data artifacts. Via by-eye observation of gene trees, detailed examination of warnings from recently improved assembly pipelines, and gene tree filtering, we identified that artifactual orthologs (i.e. the presence of only one copy of a multicopy gene due to differential assembly) were an important source of gene tree heterogeneity that had a negative impact on phylogenetic inference and support. These artifactual orthologs may be common in plant phylogenomic datasets, where multiple instances of genome duplication are common. After accounting for artifactual orthologs as source of gene tree error, we identified a significant, but nonspecific signal of introgression using Patterson's D and f4 statistics. Despite phylogenomic complexity, we were able to resolve Freziera into 9 well-supported subclades whose evolution has been shaped by multiple evolutionary processes, including incomplete lineage sorting, historical gene flow, and gene duplication. Our results highlight the complexities of plant phylogenomics, which are heightened in Andean radiations, and show the impact of filtering data processing artifacts and standard filtering approaches on phylogenetic inference. [ABSTRACT FROM AUTHOR]

Scientific names permit humans and search engines to access knowledge about the biodiversity that surrounds us, and names linked to DNA sequences are playing an ever-greater role in search-and-match identification procedures. Here, we analyze how users and curators of the National Center for Biotechnology Information (NCBI) are flagging and curating sequences derived from nomenclatural type material, which is the only way to improve the quality of DNA-based identification in the long run. For prokaryotes, 18,281 genome assemblies from type strains have been curated by NCBI staff and improve the quality of prokaryote naming. For Fungi, type-derived sequences representing over 21,000 species are now essential for fungus naming and identification. For the remaining eukaryotes, however, the numbers of sequences identifiable as type-derived are minuscule, representing only 739 species of arthropods, 1542 vertebrates, and 125 embryophytes. An increase in the production and curation of such sequences will come from (i) sequencing of types or topotypic specimens in museum collections, (ii) the March 2023 rule changes at the International Nucleotide Sequence Database Collaboration requiring more metadata for specimens, and (iii) efforts by data submitters to facilitate curation, including informing NCBI curators about a specimen's type status. We illustrate different type-data submission journeys and provide best-practice examples from a range of organisms. Expanding the number of type-derived sequences in DNA databases, especially of eukaryotes, is crucial for capturing, documenting, and protecting biodiversity. [ABSTRACT FROM AUTHOR]

ABSTRACT Peru holds a high mammalian diversity in its Amazonian region, with 326 species. However, our knowledge about the actual diversity is still considered incomplete, and the molecular information for those species in genetic databases is even less comprehensive. To assess the availability of genetic information for Peruvian Amazonian mammals relative to known diversity, we surveyed the Amazonian mammals with at least one molecular marker in the most widely used repositories for nucleotide sequences, GenBank and BOLD Systems. Our survey focused on widely used molecular markers in evolutionary biology-cytochrome b [cyt-b], cytochrome oxidase I [COI], 12S ribosomal RNA [12S], and the mitogenome [mit]-derived from Peruvian Amazon mammals. Additionally, to gain insights into the current mammalian sampling effort in Peruvian Amazonia, we generated a map of unique sampling localities and a heat map, utilizing 41951 records, which identified six major information gaps. This comprehensive analysis found 1597 genetic sequences corresponding to 180 mammalian species (55.2% of Peruvian Amazonian species): COI (38 species), cyt-b (167 species), 12S (56 species), and mitogenome (16 species). Taxonomically, Rodentia (53 species, four markers), Chiroptera (63 species, three markers), and Didelphimorphia (27 species, four markers) represented most molecular data, with a concentration of molecular markers in the orders Chiroptera (703) and Rodentia (499). Geographically, the Loreto department has the largest genetic information (530 records, 99 species). These results confirm a worrying underrepresentation of Peruvian Amazonian diversity in molecular databases. Consequently, we advocate for the use of scientific collections as an alternative source to systematically generate genetic information for the Amazonian mammal diversity in Peru to compensate for the current underrepresentation.

Intentionally preserved biological material in natural history collections represents a vast repository of biodiversity. Advances in laboratory and sequencing technologies have made these specimens increasingly accessible for genomic analyses, offering a window into the genetic past of species and often permitting access to information that can no longer be sampled in the wild. Due to their age, preparation and storage conditions, DNA retrieved from museum and herbarium specimens is often poor in yield, heavily fragmented and biochemically modified. This not only poses methodological challenges in recovering nucleotide sequences, but also makes such investigations susceptible to environmental and laboratory contamination. In this paper, we review the practical challenges associated with making the recovery of DNA sequence data from museum collections more routine. We first review key operational principles and issues to address, to guide the decision-making process and dialogue between researchers and curators about when and how to sample museum specimens for genomic analyses. We then outline the range of steps that can be taken to reduce the likelihood of contamination including laboratory set-ups, workflows and working practices. We finish by presenting a series of case studies, each focusing on protocol practicalities for the application of different mainstream methodologies to museum specimens including: (i) shotgun sequencing of insect mitogenomes, (ii) whole genome sequencing of insects, (iii) genome skimming to recover plant plastid genomes from herbarium specimens, (iv) target capture of multi-locus nuclear sequences from herbarium specimens, (v) RAD-sequencing of bird specimens and (vi) shotgun sequencing of ancient bovid bone samples.

The Afghan pika Ochotona rufescens (Gray, 1842) is widely distributed across the mountains of Afghanistan, Iran, Pakistan, and southwestern Turkmenistan, most often at elevations between 2,000 and 3,000 m. Here we present, for the first time, the complete mitochondrial genomes of two specimens of the nominotypical subspecies Ochotona rufescens rufescens, de novo assembled from Illumina short reads of fragmented probe-enriched DNA. The lengths of the circular mitogenomes are 16,408 bp and 16,407 bp, respectively. Both mitogenomes contain 13 protein-coding genes (PCGs), two ribosomal RNAs (16S rRNA and 12S rRNA), 22 transfer RNA genes, and a control region. The gene NAD6 and the tRNA (Gln), tRNA (Ala), tRNA (Asn), tRNA (Cys), tRNA (Tyr), tRNA (Ser), tRNA (Glu), and tRNA (Pro) are encoded on the light strand while the rest are encoded on the heavy strand. The overall nucleotide composition was ∼30% for A, 25% for T, 15% for G, and 29% for C. The mitogenome data are available in the GenBank under the accession numbers ON859136 and ON859137.

The bushbuck (Tragelaphus scriptus) is an antelope widely distributed throughout sub-Saharan Africa that varies greatly in body size, horn length and coat patterning. Recent taxonomic work has suggested reclassification as two or more species. Molecular studies have shown a deep mitochondrial divergence between north-western (scriptus) and south-eastern (sylvaticus) bushbuck populations, and morphological assessments, based largely on coat patterning, have divided the bushbuck into as many as eight species and 32 subspecies. Molecular and morphological approaches have, to date, not been brought together in a single integrative study. Using 43 museum cranial specimens, we sequenced complete mitochondrial genomes and used three-dimensional geometric morphometrics to compare genetic and phenotypic divergence between the two main subclades of the T. scriptus species complex. We found a significant but weak relationship between phenotypic and genetic distances. Mean body size differed between males of each subclade, but morphological differences attributable to sexual dimorphism within subclades were greater than differences between subclades. Despite a mitochondrial divergence of nearly 3 Myr, cranial morphological differences between subclades were minor and could be accounted for largely by minor size differences between males (size–shape allometry). These results support the recognition of a single bushbuck species, as indicated by nuclear genetic data. [ABSTRACT FROM AUTHOR]

Peru holds a high mammalian diversity in its Amazonian region, with 326 species. However, our knowledge about the actual diversity is still considered incomplete, and the molecular information for those species in genetic databases is even less comprehensive. To assess the availability of genetic information for Peruvian Amazonian mammals relative to known diversity, we surveyed the Amazonian mammals with at least one molecular marker in the most widely used repositories for nucleotide sequences, GenBank and BOLD Systems. Our survey focused on widely used molecular markers in evolutionary biology--cytochrome b [cyt-b], cytochrome oxidase I [COI], 12S ribosomal RNA [12S], and the mitogenome [mit]--derived from Peruvian Amazon mammals. Additionally, to gain insights into the current mammalian sampling effort in Peruvian Amazonia, we generated a map of unique sampling localities and a heat map, utilizing 41951 records, which identified six major information gaps. This comprehensive analysis found 1597 genetic sequences corresponding to 180 mammalian species (55.2% of Peruvian Amazonian species): COI (38 species), cyt-b (167 species), 12S (56 species), and mitogenome (16 species). Taxonomically, Rodentia (53 species, four markers), Chiroptera (63 species, three markers), and Didelphimorphia (27 species, four markers) represented most molecular data, with a concentration of molecular markers in the orders Chiroptera (703) and Rodentia (499). Geographically, the Loreto department has the largest genetic information (530 records, 99 species). These results confirm a worrying underrepresentation of Peruvian Amazonian diversity in molecular databases. Consequently, we advocate for the use of scientific collections as an alternative source to systematically generate genetic information for the Amazonian mammal diversity in Peru to compensate for the current underrepresentation. [ABSTRACT FROM AUTHOR]

As the only direct records of the history of evolution, it is critical to determine the geological source of biota-bearing fossils. Through the application of synchrotron-radiation micro-computed tomography (SR-µ-CT), Fourier-transformed infrared-spectroscopy (FT-IR), visual evaluation of ultraviolet fluorescence (UV-VS), radiocarbon dating (14C quantification), and historical sleuthing, we were able to identify and sort 161 (83 Baltic amber, 71 Copal and 7 Kauri gum pieces) individually numbered and largely mislabeled pieces of East African Defaunation resin (~145 years old) and copal (~390 years old), as well as Baltic amber (~35 million years old) from the Phyletisches Museum collection. Based on this collection, we define two new species: ‡Amphientomum knorrei Weingardt, Bock & Boudinot, sp. nov. (Psocodea: Amphientomidae, copal) and †Baltistena nigrispinata Batelka, Tröger & Bock, sp. nov. (Coleoptera: Mordellidae, Baltic amber). For selected taxa, we provide systematic reviews of the fossil record, including: Amphientomidae, for which we provide a key to all species of Amphientomum, extant and extinct, and recognize the junior synonymy of Am. ectostriolatum Li, 2002 (an unjustified emendation) under Am. ectostriolate Li, 1999 (syn. nov.); the fossil ant genus †Yantaromyrmex and the clades Dorylinae, Plagiolepidini, Camponotus, Crematogaster, and Pheidole (Formicidae); the Nevrorthidae (Neuroptera); and Doliopygus (Coleoptera: Curculionidae: Platypodinae). We synonymize Palaeoseopsis Enderlein, 1925 with Amphientomum Pictet, 1854, syn. nov. and transfer one species from Amphientomum, forming Lithoseopsis indentatum (Turner, 1975), comb. nov. To prevent the uncritical usage of unidentifiable fossils attributed to Camponotus for macroevolutionary analysis, we transfer 29 species to the form genus †Camponotites Steinbach, 1967, which we consider to be most useful as incertae sedis in the Formicinae. We treat †Ctt. ullrichi (Bachmayer, 1960), comb. nov. as unidentifiable hence invalid stat. nov. We also transfer †Ca. mengei Mayr, 1868 and its junior synonym †Ca. igneus Mayr, 1868 to a new genus, †Eocamponotus Boudinot, gen. nov. , which is incertae sedis in the Camponotini. Concluding our revision of Camponotus fossils, we transfer †Ca. palaeopterus (Zhang, 1989) to Liometopum (Dolichoderinae), resulting in †L. palaeopterum comb. nov. and the junior synonymy of †Shanwangella Zhang, 1989, syn. nov. under Liometopum Mayr, 1861. Because the type specimens of the genera †Palaeosminthurus Pierce & Gibron, 1962, stat. rev. and †Pseudocamponotus Carpenter, 1930 are unidentifiable due to poor preservation, we consider these taxa unidentifiable hence invalid stat. nov. To avoid unsupported use of the available fossils names attributed to Crematogaster for divergence dating calibration points, we transfer three species to a new collective taxon that is incertae sedis in Myrmicinae, †Incertogaster Boudinot, gen. nov. , forming †In. aurora (LaPolla & Greenwalt, 2015), †In. praecursor (Emery, 1891), comb. nov. , and †In. primitiva (Radchenko & Dlussky, 2019), comb. nov. Finally, we transfer †Ph. cordata (Holl, 1829) back to Pheidole, and designate a neotype from our copal collection based on all available evidence. All new species plus the neotype of ‡Ph. cordata are depicted with 3D cybertypes from our µ-CT scan data. We introduce the convention of a double dagger symbol (‡) to indicate fossils in copal or Defaunation resin, as these may yet be extant. To further contextualize our results, we provide a discussion of amber history and classification, as well as the Kleinkuhren locality, to which multiple specimens were attributed. We conclude with conspecti on key biological problems and increasing potential of µ-CT for phylogenetic paleontology. [ABSTRACT FROM AUTHOR]

Genetic and genomic data are increasingly used to aid conservation management of endangered species by providing insights into evolutionary histories, factors associated with extinction risks, and potential for future adaptation. For the 'Alalā, or Hawaiian crow (Corvus hawaiiensis), genetic concerns include negative correlations between inbreeding and hatching success. However, it is unclear if low genetic diversity and inbreeding depression are consequences of a historical population bottleneck, or if 'Alalā had historically low genetic diversity that predated human influence, perhaps as a result of earlier declines or founding events. In this study, we applied a hybridization-based sequence capture to generate a genome-wide single nucleotide polymorphism (SNP) dataset for comparing historical specimens collected in the 1890s, when 'Alalā were more numerous, to samples taken between 1973 and 1998, when 'Alalā population densities were near the lowest documented levels in the wild, prior to all individuals being collected for captive rearing. We found low genome-wide diversity in both sample groups, however, the modern sample group (1973 to 1998 cohort) exhibited relatively fewer polymorphic alleles, a lower proportion of polymorphic loci, and lower observed heterozygosity, consistent with a population decline and potential bottleneck effects. These results combined with a current low population size highlight the importance of continued efforts by conservation managers to mitigate inbreeding and maintain founder representation to preserve what genetic diversity remains. [ABSTRACT FROM AUTHOR]

The genus Podaxis was first described from India by Linnaeus in 1771, but several revisions of the genus have left the taxonomy unclear. Forty-four Podaxis species names and nine intraspecific varieties are currently accepted, but most fungarium specimens are labelled Podaxis pistillaris. Recent molecular analyses based on barcoding genes suggest that the genus comprises several species, but their status is largely unresolved. Here we obtained basidiospores and photographs from 166 fungarium specimens from around the world and generated a phylogeny based on rDNA internal transcribed spacer ITS1, 5.8S and ITS2 (ITS), and a phylogenomic analysis of 3 839 BUSCO genes from low-coverage genomes for a subset of the specimens. Combining phylogenetics, phylogenomics, morphology, ecology, and geographical distribution, spanning 250 years of collections, we propose that the genus includes at least 16 unambiguous species. Based on 10 type specimens (holotype, paratype, and syntype), four recorded species were confirmed, P. carcinomalis, P. deflersii, P. emerici, and P. farlowii. Comparing phylogenetic analysis with described species, including morphology, ecology, and distribution, we resurrected P. termitophilus and designated neotypes, epitypes, or lectotypes for five previously described species, P. aegyptiacus, P. africana, P. beringamensis, P. calyptratus, and P. perraldieri. Lastly, based on phylogenies and morphology of type material, we synonymized three reported species, P. algericus, P. arabicus, and P. rugospora with P. pistillaris, and described five new species that we named P. desolatus, P. inyoensis, P. mareebaensis, P. namaquensis, and P. namibensis. [ABSTRACT FROM AUTHOR]

Low-coverage whole-genome sequencing (also known as "genome skimming") is becoming an increasingly affordable approach to large-scale phylogenetic analyses. While already routinely used to recover organellar genomes, genome skimming is rather rarely utilized for recovering single-copy nuclear markers. One reason might be that only few tools exist to work with this data type within a phylogenomic context, especially to deal with fragmented genome assemblies. We here present a new software tool called Patchwork for mining phylogenetic markers from highly fragmented short-read assemblies as well as directly from sequence reads. Patchwork is an alignment-based tool that utilizes the sequence aligner DIAMOND and is written in the programming language Julia. Homologous regions are obtained via a sequence similarity search, followed by a "hit stitching" phase, in which adjacent or overlapping regions are merged into a single unit. The novel sliding window algorithm trims away any noncoding regions from the resulting sequence. We demonstrate the utility of Patchwork by recovering near-universal single-copy orthologs within a benchmarking study, and we additionally assess the performance of Patchwork in comparison with other programs. We find that Patchwork allows for accurate retrieval of (putatively) single-copy genes from genome skimming data sets at different sequencing depths with high computational speed, outperforming existing software targeting similar tasks. Patchwork is released under the GNU General Public License version 3. Installation instructions, additional documentation, and the source code itself are all available via GitHub at https://github.com/fethalen/Patchwork. [ABSTRACT FROM AUTHOR]

The blue antelope or bluebuck (Hippotragus leucophaeus) is an extinct species of antelope that lived in South Africa until ca. 1799–1800. Disappearing only 34 years after it was described, it was the first large African mammal species to have become extinct in recent times. Therefore, current scientific knowledge of the blue antelope is limited to museum specimens. However, these are extremely rare and further complicated by uncertainties surrounding their taxonomic status due to morphological similarity with the closely related extant roan antelope (Hippotragus equinus) and sable antelope (Hippotragus niger). A previous study found that only four (out of ten) genetically analysed historical museum specimens could be confirmed as Hippotragus leucophaeus. Here, we analyse a further five potential blue antelope specimens, two of which had been morphologically identified as blue antelope (one from the Natural History Museum (NHM) in London and one from National Museums Scotland in Edinburgh), plus an additional three specimens identified here as candidate blue antelope specimens (from the NHM). We find that only one of the five specimens can be genetically validated as Hippotragus leucophaeus, whereas the other four specimens were identified as H. equinus. Furthermore, using hybridisation capture, we generated two complete mitochondrial genomes for blue antelope specimens that were formerly known only from partial mitochondrial genomes. The diversity analyses including all newly generated genomes further confirm that the mitochondrial nucleotide diversity across this species was low. [ABSTRACT FROM AUTHOR]

Wolbachia is one of the most common bacterial endosymbionts, which is frequently found in numerous arthropods and nematode taxa. Wolbachia infections can have a strong influence on the evolutionary dynamics of their hosts since these bacteria are reproductive manipulators that affect the fitness and life history of their host species for their own benefit. Host–symbiont interactions with Wolbachia are perhaps best studied in the model organism Drosophila melanogaster , which is naturally infected with at least 5 different variants among which w Mel and w MelCS are the most frequent ones. Comparisons of infection types between natural flies and long-term lab stocks have previously indicated that w MelCS represents the ancestral type, which was only very recently replaced by the nowadays dominant w Mel in most natural populations. In this study, we took advantage of recently sequenced museum specimens of D. melanogaster that have been collected 90 to 200 yr ago in Northern Europe to test this hypothesis. Our comparison to contemporary Wolbachia samples provides compelling support for the replacement hypothesis. Our analyses show that sequencing data from historic museum specimens and their bycatch are an emerging and unprecedented resource to address fundamental questions about evolutionary dynamics in host–symbiont interactions. However, we also identified contamination with DNA from crickets that resulted in co-contamination with cricket-specific Wolbachia in several samples. These results underpin the need for rigorous quality assessments of museomic data sets to account for contamination as a source of error that may strongly influence biological interpretations if it remains undetected. [ABSTRACT FROM AUTHOR]

Abstract Psalidodon jequitinhonhae was originally proposed as a variety of Tetragonopterus rutilus, based on the analysis of 14 specimens from the Jequitinhonha River, Brazil. In 1910 it was relocated in Astyanax, as A. fasciatus jequitinhonhae in Tetragonopterinae and in 2020 in Psalidodon, as Stethaprioninae member. However, in none of these revisions, P. jequitinhonhae was morphologically redescribed. A short sequence of the Cytochrome c oxidase subunit I (COI) gene obtained from one of the syntypes is compared to sequences obtained from new samples, allowing the recognition of the species and its morphological redescription based on new specimens. Both morphological and molecular data converged and corroborated P. jequitinhonhae as a valid species, occurring in the Jequitinhonha and Pardo river basins in Brazil. The syntype that provided the analyzed COI sequence is referred to as the lectotype by present designation.

We describe here a new species of oecophorid moth from specimens found in West London and Western Australia. This taxon is part of the Tachystola hemisema (Meyrick, 1885) DNA barcode complex, which consists of at least five different clusters, each with a distinct Barcode Index Number (BIN) on the Barcode Database of Life (BoLD). Illumina sequencing and bioinformatic processing techniques were applied to the lectotype of T. hemisema (collected in 1884) and the designated holotype of the new taxon (collected in 1886) and all 13 mitochondrial protein coding genes were recovered. Recent specimens from West London were DNA barcoded and compared to the BoLD clusters. The morphology of these specimens was compared to the extent possible (both historical specimens lack abdomens). The pairwise distance between typical T. hemisema and the new taxon measures 3.65% for CoI-5P, while there are some amino acid differences in CoI-3P and eight other genes. We also identify morphological differences for the new taxon. The generic placement of the new taxon and T. hemisema with respect to Tachystola acroxantha (Meyrick, 1885) is also considered. [ABSTRACT FROM AUTHOR]

Conservation and restoration planning of extremely rare species relies on an understanding of the genetic diversity and population dynamics within a species to overcome potential inbreeding depression. Nānū or Nāʻū (Gardenia remyi H. Mann.) is an endemic tree native to the Hawaiian Islands and is one of more than 200 endangered plant species in Hawaiʻi with less than 50 individuals remaining in the wild. Efforts to understand the genetic diversity and connectivity between wild populations are foundational to conservation management plans, however little is known of the population structure of the species. In this study we utilize double digest restriction‐site associated sequencing (ddRADSeq) on both historical herbarium specimens and samples from living ex situ collections to: (1) Test the hypothesis that we can capture genetic diversity in herbarium material of G. remyi using ddRADSeq, and (2) test the hypothesis that there are genetically distinct populations or subpopulation units among different Hawaiian islands. Usable sequencing data from thirty‐seven samples of herbarium specimens collected between 1952 and 2017 and twenty wild sourced living collection samples were obtained representing all four islands where G. remyi is known to occur. Phylogenetic and population structure analysis revealed a monophyletic ingroup and a clear division between G. remyi samples of the northern island of Kauaʻi and those from the more southeastern younger islands of Molokaʻi, Maui and Hawaiʻi islands. The Kauaʻi samples were further split into a subpopulation from Southern Kauaʻi and the subpopulations from Northern Kauaʻi. Some admixed samples were detected. Our results are consistent with subpopulations of G. remyi, which needs to be considered in future conservation planning and breeding efforts to minimize inbreeding depression. [ABSTRACT FROM AUTHOR]

Intentionally preserved biological material in natural history collections represents a vast repository of biodiversity. Advances in laboratory and sequencing technologies have made these specimens increasingly accessible for genomic analyses, offering a window into the genetic past of species and often permitting access to information that can no longer be sampled in the wild. Due to their age, preparation and storage conditions, DNA retrieved from museum and herbarium specimens is often poor in yield, heavily fragmented and biochemically modified. This not only poses methodological challenges in recovering nucleotide sequences, but also makes such investigations susceptible to environmental and laboratory contamination. In this paper, we review the practical challenges associated with making the recovery of DNA sequence data from museum collections more routine. We first review key operational principles and issues to address, to guide the decision-making process and dialogue between researchers and curators about when and how to sample museum specimens for genomic analyses. We then outline the range of steps that can be taken to reduce the likelihood of contamination including laboratory set-ups, workflows and working practices. We finish by presenting a series of case studies, each focusing on protocol practicalities for the application of different mainstream methodologies to museum specimens including: (i) shotgun sequencing of insect mitogenomes, (ii) whole genome sequencing of insects, (iii) genome skimming to recover plant plastid genomes from herbarium specimens, (iv) target capture of multi-locus nuclear sequences from herbarium specimens, (v) RAD-sequencing of bird specimens and (vi) shotgun sequencing of ancient bovid bone samples. [ABSTRACT FROM AUTHOR]

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