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To address the challenges of sampling endangered or extinct species in the field, many studies have turned to historically underutilized sources of genetic material: natural history museums. Despite the fact that DNA from specimens collected decades or even hundreds of years ago is often fragmented and degraded, research has shown that historical DNA can still be used effectively to infer phylogenetic relationships and intra-specific patterns of population genetic structure. This synthesis aims to provide students and conservation practitioners with a solid understanding of the methodological strategies needed to apply genetic tools to natural history museum specimens. Specifically, we offer clear definitions and essential considerations for designing a conservation genomics project that includes both modern and historical samples. We recommend that instructors use this synthesis to introduce the foundational knowledge required for two companion exercises: “The Application of Conservation Museomics Approaches to the Protection of the Iberian Lynx (Lynx pardinus)” and “Designing a Conservation Genetics Project Incorporating DNA from Museum Specimens.” 

This exercise is intended to provide students with a real-world example of how museum specimens can provide additional context to challenges and considerations in the broader field of applied conservation genomics. After a brief introduction to the study system—the conservation status of Iberian lynx (Lynx pardinus)—students will be asked to review an open-access, peer-reviewed publication that features samples from varied museum, archaeological, and paleontological contexts. Through reading the guide and discussion questions, students will reflect upon study design, concepts, and challenges presented at the intersection between the fields of conservation genomics and museum-based studies. The exercise ends with students breaking down the research into the main components (e.g., research question, independent and dependent variables, hypotheses, predictions) to set a structure for critically reading other scientific studies or designing their own research question. 

This exercise is intended to provide students with a real-world example of how museum specimens can provide additional context to challenges and considerations in the broader field of applied conservation genomics. After a brief introduction to the study system—the conservation status of Iberian lynx (Lynx pardinus)—students will be asked to review an open-access, peer-reviewed publication that features samples from varied museum, archaeological, and paleontological contexts. Through reading the guide and discussion questions, students will reflect upon study design, concepts, and challenges presented at the intersection between the fields of conservation genomics and museum-based studies. The exercise ends with students breaking down the research into the main components (e.g., research question, independent and dependent variables, hypotheses, predictions) to set a structure for critically reading other scientific studies or designing their own research question. 

An accurate representation of species diversity is critical in primatology; most of the questions in evolutionary biology, ecology, and conservation hinge on species as a fundamental unit of analysis. Galagos are among the least-known primates. Because of their cryptic morphology, broad distribution, and sampling challenges arising from elusive habits and political instability, substantial knowledge gaps about their taxonomy, evolutionary history, and biogeography remain. Despite these limitations, recent research that integrated field surveys, acoustic, morphological, and genetic analyses helped us to better understand the taxonomic diversity of this primate group. In this paper, we (1) review the current status of galagid taxonomy; (2) synthesize our current understanding of their phylogenetics, origins, and biogeography; and (3) explore current and future approaches to elucidate galagid cryptic species diversity. The onset of galago systematics dates back to the early 19th century, with taxonomic descriptions following natural history expeditions and comparative anatomy studies. Although morphology has historically dominated systematic research on galagos, the coupling of acoustic analyses with genetic data has revolutionized the field. Taxonomic rearrangements include the discovery of new species in the wild (e.g., Galagoides kumbirensis) and the description of a new genus (Paragalago). Technological advances have allowed the collection of acoustic data in remote areas, and molecular techniques have the potential to help researchers fill important geographic gaps. Improving the resolution of galago species diversity also has implications for the conservation of wild populations, as a better understanding of species boundaries and ranges can aid in the implementation of conservation strategies. 

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. 

Macroevolutionary biologists have classically rejected the notion that higher-level patterns of divergence arise through microevolutionary processes acting within populations. For morphology, this consensus partly derives from the inability of quantitative genetics models to correctly predict the behaviour of evolutionary processes at the scale of millions of years. Developmental studies (evo-devo) have been proposed to reconcile micro- and macroevolution. However, there has been little progress in establishing a formal framework to apply evo-devo models of phenotypic diversification. Here we reframe this issue by asking whether using evo-devo models to quantify biological variation can improve the explanatory power of comparative models, thus helping us bridge the gap between micro- and macroevolution. We test this prediction by evaluating the evolution of primate lower molars in a comprehensive dataset densely sampled across living and extinct taxa. Our results suggest that biologically informed morphospaces alongside quantitative genetics models allow a seamless transition between the micro- and macroscales, whereas biologically uninformed spaces do not. We show that the adaptive landscape for primate teeth is corridor like, with changes in morphology within the corridor being nearly neutral. Overall, our framework provides a basis for integrating evo-devo into the modern synthesis, allowing an operational way to evaluate the ultimate causes of macroevolution. 

Abstract Assessing the true lineage diversity in elusive nocturnal organisms is particularly challenging due to their subtle phenotypic variation in diagnostic traits. The cryptic small-eared greater galago (Otolemur garnettii) offers a great opportunity to test if currently recognized subspecies, suggested by discontinuities in coat colour pattern and geographic barriers, represent distinct evolutionary lineages. To answer this question, we conducted the first population-level phylogeographic study of the species, sampling wild specimens from across almost its entire latitudinal range, including the Zanzibar Archipelago. We applied five species-delimitation algorithms to investigate the genetic diversity and distribution pattern of mitochondrial DNA across the geographic range of three out of four subspecies. Our results suggest that far-northern populations of O. g. lasiotis potentially represent an independently evolving lineage, but populations assigned to O. g. garnettii from Zanzibar Island and of O. g panganiensis from mainland Tanzania do not constitute two independent lineages. A dated phylogeny suggests that this northern clade diverged from all remaining samples approximately 4 Mya. Such old divergence age is in line with the split between many galagid species. This northern lineage could potentially represent an incipient species; however, there is not yet enough evidence to support a new taxonomic status for this unique mitochondrial group. 

Abstract In recent years, multiple technological and methodological advances have increased our ability to estimate phylogenies, leading to more accurate dating of the primate tree of life. Here we provide an overview of the limitations and potentials of some of these advancements and discuss how dated phylogenies provide the crucial temporal scale required to understand primate evolution. First, we review new methods, such as thetotal‐evidence datingapproach, that promise a better integration between the fossil record and molecular data. We then explore how the ever‐increasing availability of genomic‐level data for more primate species can impact our ability to accurately estimate timetrees. Finally, we discuss more recent applications of mutation rates to date divergence times. We highlight example studies that have applied these approaches to estimate divergence dates within primates. Our goal is to provide a critical overview of these new developments and explore the promises and challenges of their application in evolutionary anthropology.