Historical specimens and the limits of subspecies phylogenomics in the New World quails (Odontophoridae)

As phylogenomics focuses on comprehensive taxon sampling at the species and population/subspecies levels, incorporating genomic data from historical specimens has become increasingly common. While historical samples can fill critical gaps in our understanding of the evolutionary history of diverse groups, they also introduce additional sources of phylogenomic uncertainty, making it difficult to discern novel evolutionary relationships from artifacts caused by sample quality issues. These problems highlight the need for improved strategies to disentangle artifactual patterns from true biological signal as historical specimens become more prevalent in phylogenomic datasets. Here, we tested the limits of historical specimen-driven phylogenomics to resolve subspecies-level relationships within a highly polytypic family, the New World quails (Odontophoridae), using thousands of ultraconserved elements (UCEs). We found that relationships at and above the species-level were well-resolved and highly supported across all analyses, with the exception of discordant relationships within the two most polytypic genera which included many historical specimens. We examined the causes of discordance and found that inferring phylogenies from subsets of taxa resolved the disagreements, suggesting that analyzing subclades can help remove artifactual causes of discordance in datasets that include historical samples. At the subspecies-level, we found well-resolved geographic structure within the two most polytypic genera, including the most polytypic species in this family, Northern Bobwhites (Colinus virginianus), demonstrating that variable sites within UCEs are capable of resolving phylogenetic structure below the species level. Our results highlight the importance of complete taxonomic sampling for resolving relationships among polytypic species, often through the inclusion of historical specimens, and we propose an integrative strategy for understanding and addressing the uncertainty that historical samples sometimes introduce to phylogenetic analyses.

Arthropod prey vary among orders in their nutrient and exoskeleton content

Insectivores gain macronutrients and elements from consuming arthropod prey, but must also deal with indigestible components (i.e., exoskeleton) of prey. For example, avian chicks (e.g. northern bobwhites; Colinus virginianus) have limited gut space, and ingesting prey with relatively higher proportions of indigestible components may impact assimilation efficiency, growth, and survival. The ability of insectivores to choose higher quality prey would depend on prey taxa varying consistently in nutritional content. We tested if there were consistent differences among taxonomic orders of arthropod prey in their macronutrient (protein and lipid), elemental (C and N), and exoskeleton content. We used northern bobwhite chicks as our focal insectivore and focused on their potential prey as a case study. We also tested the influence of indigestible exoskeleton on the measurement of macronutrient content and the ability of elemental content to predict macronutrients. We found large and consistent variation in macronutrient and elemental content within and between arthropod orders. Some orders had consistently high protein content and low exoskeleton content (i.e., Araneae) and are likely higher quality prey for insectivores. Abundant orders common in the diets of insectivores, like Hymenoptera and Coleoptera, had high exoskeleton content and low protein content. We also found support for the ability of elements to predict macronutrients, and found that metabolizable (i.e. exoskeleton removed) elemental content better predicted macronutrient content. A better understanding of arthropod nutrient content is critical for elucidating the role of spatial and temporal variation in prey communities in shaping the growth and survival of insectivores.

Efficacy of acclimating and releasing captive-reared and wild-translocated Northern bobwhites

Northern bobwhite populations are dwindling across their range. Accordingly, in areas with bobwhite habitat restoration and no nearby populations, effective population restoration techniques are needed. Here, we evaluated three bobwhite restoration release strategies: (1) release of captive-reared bobwhites on sites with and without resident populations, (2) translocation of wild-trapped bobwhites from a region of high population density to a region with no population, and (3) release of captive-reared and wild-translocated bobwhites acclimated on site prior to release in year 2. Wild-translocated birds survived longer than captive-reared birds. Mean survival for captive-reared bobwhites was 2.42 weeks, and 4.27 weeks in year 1, and 1.91 and 1.40 weeks in year 2, for study sites without resident and with resident birds present, respectively. Mean survival for wild-translocated birds was 8.50 weeks in year 1, and 11.54 weeks in year 2. Wild-translocated birds dispersed shorter distances than captive-reared birds. Both captive-reared and wild-translocated bobwhites only nested on study sites with conspecifics. Captive-reared birds had 0 nesting attempts on the site with no resident bobwhites, and ⩾8 nests on the site with resident bobwhites. Wild-translocated females nested six times and were subsequently observed with juveniles. On-site acclimation did not increase post-release survival for northern bobwhites. Acclimation increased site fidelity but reduced survival for captive-reared birds and had no impact on survival for wild-translocated bobwhites. Population restoration by release of captive-reared or wild-translocated birds is not irrelevant, but further investigation is needed into the relationship between captive-reared birds and predators, and methods to increase survival and reproduction of released birds.

Assessment of the helminth fauna in northern bobwhites (Colinus virginianus) occurring within South Texas

Populations of northern bobwhites (Colinus virginianus; hereafter bobwhite) have been declining across their geographic range in North America, prompting consideration of the role parasites may play. We conducted this study to learn about the helminth fauna in South Texas, a region that supports a sustainable bobwhite population. Helminths were examined from 356 bobwhites collected during the 2014–2015 (n = 124) and 2015–2016 (n = 232) hunting seasons, when increasing trends in precipitation were observed in comparison with the previous two years. Ten helminth species were found, consisting of 14,127 individuals. Of these, all are heteroxenous parasites and three are pathogenic (Dispharynx nasuta, Tetrameres pattersoni and Oxyspirura petrowi). Aulonocephalus pennula numerically dominated the component community (81% prevalence, 99% of the total helminths found), whereas each of the remaining species occurred rarely (≤9% prevalence) and contributed few individuals (≤0.4%) to the helminth community. Prevalence and abundance of A. pennula were not influenced by host age, sex or body mass, but abundance was higher during the 2014–2015 than the 2015–2016 hunting season. Our findings indicate that the helminth community in bobwhites from South Texas can vary during long-term, highly variable precipitation conditions and these communities are more similar to those found in the Rolling Plains of Texas than those found in the eastern part of the bobwhite's geographic range in the US.