Emily K. Latch

Maintaining sustainable animal populations is fundamental to zoo and aquarium missions in education, visitor engagement, entertainment, scientific advancement, public health and wellbeing, advocacy, and conservation impact. Yet, sustaining viable populations remains a persistent challenge. Small populations are inherently vulnerable to demographic and genetic challenges which threaten both individual animal welfare and population‐level goals. However, as emerging research advances our understanding of population biology, zoos and aquariums are positioned to transform how we sustain ex situ populations. This commentary highlights pressing questions facing the field today, including how to manage the size and structure of populations, integrate genomic advances and emerging technologies, build on interdisciplinary approaches, and ensure our populations have a conservation impact, as well as how we scale our advances across diverse taxa. We examine both the challenges and opportunities that will shape the future of population management in zoos and aquariums.

Background: The Pacific Northwestern region of North America is inhabited by two distinct subspecies of black-tailed deer, Columbian ( Odocoileus hemionus columbianus ) and Sitka ( O. h. sitkensis ) black-tailed deer, which exhibit a complex evolutionary history shaped by survival in glacial refugia, postglacial expansion, incomplete lineage sorting, and recent introgression. These dynamics make them an ideal system for examining population responses to past climate change. However, limited temporal sampling in previous genetic studies has obscured the timing and mechanisms of postglacial dispersal, and the divergence between the two black-tailed deer subspecies remains unresolved. Results: We analyze genome-scale data from ancient and modern deer spanning the last 13,500 years to reconstruct the evolutionary history of Sitka black-tailed deer in Southeast Alaska. Fossil and genomic evidence supports a primary postglacial expansion from a southern refugium, with asynchronous deglaciation and fluctuating sea levels along the Pacific Northwest Coast influencing northward colonization. Early Southeast Alaska samples (~ 9.2–8.5 cal kyr B.P.) contain mule deer mitochondrial haplotypes, indicating past contact or incomplete lineage sorting, while later individuals (< 6 cal kyr B.P.) carry Sitka black-tailed deer haplotypes, suggesting lineage turnover following mid-Holocene climatic cooling. Conclusions: Our results reject the hypothesis of a distinct northern refugium for Sitka black-tailed deer and instead support postglacial divergence from a shared black-tailed deer refugium south of the Cordilleran Ice Sheet. The asynchronous retreat of ice and dynamic sea-level history fostered repeated dispersal pulses, localized isolation, and secondary contact, shaping the present-day genetic and morphological diversity of O. hemionus .

White‐tailed deer ( Odocoileus virginianus ) are the most abundant and widespread cervid in North America. Genetic data are used as a tool to monitor populations and make management decisions for this game species. However, the development and use of genomic tools that can generate a set of markers suitable for longitudinal genomic data collection, whether for management purposes or to study the demographic and evolutionary processes of widely distributed species, have been challenging. This is mainly due to the cost required to fully implement and interpret the data produced. Here, we generated whole genome resequencing data for 44 free‐ranging deer from three regions in their central and eastern North American range and identified over 89 million single nucleotide polymorphisms (SNPs). We used a subset of these SNPs to develop two nested SNP tools, a high‐density array (702,183 SNPs) and a medium‐density array (72,723 SNPs) to support deer and chronic wasting disease (CWD) management and research. SNPs were selected to ensure an even distribution across scaffolds of the reference genome and include SNPs associated with CWD susceptibility. Using genotyping results for 469 deer from 15 states in the US and Mexico generated by the high‐density array and 1335 deer from 18 states generated by the medium‐density array, we assessed genotyping success across different populations and explored some insights into population structure. These genomic tools offer a standard set of markers that will enable researchers and managers to address important questions related to white‐tailed deer and CWD management. Our SNP arrays also offer the opportunity to examine aspects of white‐tailed deer ecology and evolutionary history that were previously difficult to address.

We examined DNA sequences of 328 individuals of three lineages (species or species complexes) of Amazonian antwrens to evaluate their degree of geographical and historical concordance. All lineages (Myrmotherula longipennis, M. menetriesii, and the Isleria guttata-hauxwelli species complex) consist of small insectivorous birds that occupy understory or midstory of terra firme forest and are widely distributed across the Amazon Basin. Individuals of each of the three lineages grouped into genetic clades mainly separated by the Amazon and some major tributaries, although members of different clades of both M. menetriesii and I. hauxwelli were documented in the Madeira-Tapajós interfluvium. Branching patterns differed among taxa, but all taxa were highly differentiated across the lower or upper Amazon. Despite the morphological, ecological, and phylogenetic similarities among lineages, and despite the fact that nearly all taxa are bounded by rivers, the effect of the other major rivers as biogeographic barriers was highly variable. The Marañón, Ucayali, Madeira, Tapajós, Xingu, Napo, Negro, and Branco all separated main clades in one or two lineages but not in the others. Levels of genetic differentiation along the Teles Pires were substantially higher than those across the Tapajós in M. menetriesii and I. hauxwelli, consistent with a proposed historical change of river course for the Tapajós. Genetic units in this study were comparable for the most part to taxonomic units delineated by analyses of vocal and morphological variation, and identical, with one exception, to units defined solely by vocal variation in a companion paper (Isler et al. 2025). These results, in conjunction with those of Isler et al. (2025), provide additional instances of the variability of responses to the historical dynamism of Amazonia, in this case in closely related and ecologically similar species; highlight the consistency of genetic differentiation with vocal differentiation in additional species of Neotropical suboscine birds; support the importance of Amazonian rivers in creating conditions that result in the differentiation of independent evolutionary lineages; and demonstrate that species richness in two of the lineages studied (M. longipennis and M. menetriesii) was previously underestimated.

Chronic Wasting Disease (CWD) research has experienced significant growth, spanning diverse disciplines such as genetics, immunology, modelling, and behaviour. To gain a broad understanding of the changes in CWD research focusing cervids, we analysed temporal trends in study location, species, genus investigated, infection types, and population type since the discovery of CWD in 1980s. Our findings indicate that Colorado, USA, published the highest number of articles, followed by Wisconsin, and publication numbers correlated with reported CWD cases in states/provinces. Odocoileus emerged as the most studied genus. Wild populations are studied more commonly than captive populations. Keyword analysis of transmission types shows the discovery of novel transmission modes in the recent past. We also used a novel approach to categorize studies into five themes: field-based, lab-based, math/analytics/modelling-based, management-based, and human dimensions. Overall, most studies captured had a lab-based component. The interdisciplinary or transdisciplinary nature of major disciplines and evolving trends in keywords, particularly the increased reliance on genetics/genomics, accentuate the beginning of using genomics to under and tackle CWD at a fundamental scale. Encapsulated in our analysis, these dynamic changes offer valuable insights for navigating CWD through scientifically informed proactive management decisions in conjunction with existing surveillance efforts not only for the commonly studied species but also for potentially susceptible species.

Studies of evolution and biodiversity require solid understanding of species systematics revealed by molecular phylogeny using multilocus genomic data. Multilocus analyses, nevertheless, remain difficult in non-model taxa due to limited access to samples and molecular resources. To help overcome this limitation, ultra-conserved elements (UCEs) have been developed to generate large nuclear datasets and build more robust species phylogenies. Recently, MitoFinder pipeline was developed to further extract mitochondrial genes from the off-target sequences in UCE libraries to allow mito-nuclear comparison and increase the mitochondrial genomic database. Here we applied MitoFinder to published UCE datasets of serotine bats (genus Eptesicus) and focused on E. (Histiotus) whose evolutionary history is poorly understood. Our results showed extensive mito-nuclear discordances in the divergence of major clades in Eptesicus and within E. (Histiotus), indicating potential incomplete lineage sorting and historical mitochondrial introgression within and across subgenera. Moreover, we collected several new samples of E. (Histiotus), including the first molecular data of the recently described E. (H) diaphanopterus, and combined available published sequences to generate the most taxa-complete mitochondrial phylogeny of E. (Histiotus) bats. Results supported the early divergence of E. (H.) magellanicus and the species status of E. (H.) diaphanopterus. In addition, we found strong evidence of cryptic diversity, with potentially new taxa in Peru, Uruguay, and Brazil, which needs to be evaluated in future studies using complementary data. Our study enriched the sequence database of serotine bats and shed light on the hidden diversity and complex evolutionary history of E. (Histiotus).

This chapter addresses the origin, classification, and distribution of the deer family (Cervidae), which arose out of the Miocene from a group of early hoofed animals in Eurasia. The large tusk-like canines of these primitive deer gradually gave way to the development of antlers that were replaced annually. Later, well-developed cervids entered North America through Beringia, across what is now Alaska 7–5 million years before present (YBP). The earliest deer in North America are represented by 3 forms that appear nearly simultaneously in the fossil record about 5 million YBP. One of those forms was the genus Odocoileus, which includes 2 species of medium-sized deer whose distribution is centered on North America: black-tailed and mule deer and white-tailed deer. Mule deer have been divided into as many as 11 subspecies, but this chapter explains, based on phylogeny reflected by concordant phenotypic and genetic characteristics, that they are more appropriately called ecotypes. Given the totality of all the evidence, the chapter demonstrates support for 5 subspecies of black-tailed and mule deer: Sitka black-tailed deer, Columbian black-tailed deer, Cedros Island mule deer, Tiburón Island mule deer, and mule deer on the mainland.

Conservation and management professionals often work across jurisdictional boundaries to identify broad ecological patterns. These collaborations help to protect populations whose distributions span political borders. One common limitation to multijurisdictional collaboration is consistency in data recording and reporting. This limitation can impact genetic research, which relies on data about specific markers in an organism's genome. Incomplete overlap of markers between separate studies can prevent direct comparisons of results. Standardized marker panels can reduce the impact of this issue and provide a common starting place for new research. Genotyping‐in‐thousands (GTSeq) is one approach used to create standardized marker panels for nonmodel organisms. Here, we describe the development, optimization, and early assessments of a new GTSeq panel for use with walleye (Sander vitreus) from the Great Lakes region of North America. High genome‐coverage sequencing conducted using RAD capture provided genotypes for thousands of single nucleotide polymorphisms (SNPs). From these markers, SNP and microhaplotype markers were chosen, which were informative for genetic stock identification (GSI) and kinship analysis. The final GTSeq panel contained 500 markers, including 197 microhaplotypes and 303 SNPs. Leave‐one‐out GSI simulations indicated that GSI accuracy should be greater than 80% in most jurisdictions. The false‐positive rates of parent‐offspring and full‐sibling kinship identification were found to be low. Finally, genotypes could be consistently scored among separate sequencing runs >94% of the time. Results indicate that the GTSeq panel that we developed should perform well for multijurisdictional walleye research throughout the Great Lakes region.

Conservation and management professionals often works across jurisdictional boundaries to identify broad ecological patterns. These collaborations help to protect populations whose distributions span political borders. One common limitation to multijurisdictional collaboration is consistency in data recording and reporting. This limitation can impact genetic research which relies on data about specific markers in an organism’s genome. Incomplete overlap of markers between separate studies can prevent direct comparisons. Standardized marker panels can reduce the impact this issue and provide a common starting place for new research. Genotyping-in-thousands (GTSeq) is one approach used to create standardized marker panels for non-model organisms. Here we describe the development, optimization, and early assessments of a new GTSeq panel for use with walleye ( Sander vitreus ) from the Great Lakes region of North America. High genome-coverage sequencing conducted using RAD-capture provided genotypes for thousands of single nucleotide polymorphisms (SNPs). From these markers, SNP and microhaplotype makers were chosen that were informative for genetic stock identification (GSI) and kinship analysis. The final GTSeq panel contained 500 markers, including 197 microhaplotypes and 303 SNPs. Leave-one-out GSI simulations indicated that GSI accuracy should be greater than 80% in most jurisdictions. The false-positive rates of parent-offspring and full-sibling kinship identification was found to be low. Finally, genotypes could be consistently scored among separate sequencing runs >94% of the time. Results indicate that the GTSeq panel we developed should perform well for multijurisdictional research throughout the Great Lakes region.

Context: Meaningful intraspecific taxonomy allows for robust classification of within-species diversity and effective conservation and management. Subspecies definitions broadly agree that subspecies are groups of populations that exhibit some degree of geographic separation, phenotypic distinctiveness, and unique evolutionary potential. The most powerful assessments of within-species taxonomy are those that employ multiple lines of evidence, including phenotypic, ecological, geographic and genetic, to delineate evolutionarily definable units. Aims: Here we describe how genetic data can be integrated into intraspecific taxonomy. Methods: We use our experiences incorporating genetic data to assess taxonomy within black-tailed and mule deer (Odocoileus hemionus), a widespread and highly mobile species with significant phenotypic variation and a complex evolutionary history. Key results: High-resolution sampling of individuals across the landscape and loci across the genome yielded accurate estimates of genetic variation in black-tailed and mule deer and better insight into the evolutionary processes that generate and maintain diversity. Conclusions: Integrating genetic data has informed meaningful intraspecific taxonomy within O. hemionus, showing support for the following five subspecies: two black-tailed deer subspecies (Columbian O. h. columbianus and Sitka O. h. sitkensis) and three mule deer subspecies (mainland O. h. hemionus and the two island subspecies, O. h. cerrosensis on Cedros Island and O. h. sheldoni on Tiburón Island). Implications: Our integrative approach provides a framework for incorporating genetic data in intraspecific taxonomy in other deer species.