• Using genome-wide measures of coancestry to maintain diversity and fitness in endangered and domestic pig populations

      Bosse, Mirte; Megens, Hendrik-Jan; Madsen, Ole; Crooijmans, Richard P. M. A.; Ryder, Oliver A.; Austerlitz, Frédéric; Groenen, Martien A. M.; Cara, M. Angeles R. de (2015)
      Conservation and breeding programs aim at maintaining the most diversity, thereby avoiding deleterious effects of inbreeding while maintaining enough variation from which traits of interest can be selected. Theoretically, the most diversity is maintained using optimal contributions based on many markers to calculate coancestries, but this can decrease fitness by maintaining linked deleterious variants. The heterogeneous patterns of coancestry displayed in pigs make them an excellent model to test these predictions. We propose methods to measure coancestry and fitness from resequencing data and use them in population management. We analyzed the resequencing data of Sus cebifrons, a highly endangered porcine species from the Philippines, and genotype data from the Pietrain domestic breed. By analyzing the demographic history of Sus cebifrons, we inferred two past bottlenecks that resulted in some inbreeding load. In Pietrain, we analyzed signatures of selection possibly associated with commercial traits. We also simulated the management of each population to assess the performance of different optimal contribution methods to maintain diversity, fitness, and selection signatures. Maximum genetic diversity was maintained using marker-by-marker coancestry, and least using genealogical coancestry. Using a measure of coancestry based on shared segments of the genome achieved the best results in terms of diversity and fitness. However, this segment-based management eliminated signatures of selection. We demonstrate that maintaining both diversity and fitness depends on the genomic distribution of deleterious variants, which is shaped by demographic and selection histories. Our findings show the importance of genomic and next-generation sequencing information in the optimal design of breeding or conservation programs.
    • Using spatially-explicit population models to evaluate habitat restoration plans for the San Diego cactus wren (Campylorhynchus brunneicapillus sandiegensis)

      Conlisk, Erin; Motheral, Sara; Chung, Rosa; Wisinski, Colleen L.; Endress, Bryan A. (2014)
      A long-standing debate within conservation is how best to allocate limited management resources: should reserve area be increased, should anthropogenic disturbances be mitigated, or should connectivity be increased? We explore these issues for the San Diego cactus wren, a California Species of Special Concern…. Our modeling approach provides insight into the relative benefit of several realistic restoration scenarios, providing an important tool for species conservation and habitat restoration on complex landscapes.
    • Using the gut microbiota as a novel tool for examining colobine primate GI health

      Amato, Katherine R.; Metcalf, Jessica L.; Song, Se Jin; Hale, Vanessa L.; Clayton, Jonathan; Ackermann, Gail; Humphrey, Greg; Niu, Kefeng; Cui, Duoying; Zhao, Hongxia; et al. (2016)
      Primates of the Colobinae subfamily are highly folivorous. They possess a sacculated foregut and are believed to rely on a specialized gut microbiota to extract sufficient energy from their hard-to-digest diet. Although many colobines are endangered and would benefit from captive breeding programs, maintaining healthy captive populations of colobines can be difficult since they commonly suffer from morbidity and mortality due to gastrointestinal (GI) distress of unknown cause. While there is speculation that this GI distress may be associated with a dysbiosis of the gut microbiota, no study has directly examined the role of the gut microbiota in colobine GI health. In this study, we used high-throughput sequencing to examine the gut microbiota of three genera of colobines housed at the San Diego Zoo: doucs (Pygathrix) (N=7), colobus monkeys (Colobus) (N=4), and langurs (Trachypithecus) (N=5). Our data indicated that GI-healthy doucs, langurs, and colobus monkeys possess a distinct gut microbiota. In addition, GI-unhealthy doucs exhibited a different gut microbiota compared to GI-healthy individuals, including reduced relative abundances of anti-inflammatory Akkermansia. Finally, by comparing samples from wild and captive Asian colobines, we found that captive colobines generally exhibited higher relative abundances of potential pathogens such as Desulfovibrio and Methanobrevibacter compared to wild colobines, implying an increased risk of gut microbial dysbiosis. Together, these results suggest an association between the gut microbiota and GI illness of unknown cause in doucs. Further studies are necessary to corroborate these findings and determine cause-and-effect relationships. Additionally, we found minimal variation in the diversity and composition of the gut microbiota along the colobine GI tract, suggesting that fecal samples may be sufficient for describing the colobine gut microbiota. If these findings can be validated in wild individuals, it will facilitate the rapid expansion of colobine gut microbiome research.
    • Using the movement patterns of reintroduced animals to improve reintroduction success

      Berger-Tal, Oded; Saltz, David (2014)
      Despite their importance to conservation, reintroductions are still a risky endeavor and tend to fail, highlighting the need for more efficient post-release monitoring techniques…. We demonstrate our conceptual approach using data from two ungulate species reintroduced in Israel: the Persian fallow deer Dama mesopotamica and the Arabian oryx Oryx leucoryx
    • Using tri-axial accelerometers to identify wild polar bear behaviors

      Pagano, Anthony M.; Rode, K. D.; Cutting, A; Owen, Megan A.; Jensen, S; Ware, J. V.; Robbins, Ct; Durner, Gm; Atwood, Todd C.; Obbard, M. E.; et al. (2017)
      Tri-axial accelerometers have been used to remotely identify the behaviors of a wide range of taxa. Assigning behaviors to accelerometer data often involves the use of captive animals or surrogate species, as their accelerometer signatures are generally assumed to be similar to those of their wild counterparts. However, this has rarely been tested. Validated accelerometer data are needed for polar bears Ursus maritimus to understand how habitat conditions may influence behavior and energy demands. We used accelerometer and water conductivity data to remotely distinguish 10 polar bear behaviors. We calibrated accelerometer and conductivity data collected from collars with behaviors observed from video-recorded captive polar bears and brown bears U. arctos, and with video from camera collars deployed on free-ranging polar bears on sea ice and on land. We used random forest models to predict behaviors and found strong ability to discriminate the most common wild polar bear behaviors using a combination of accelerometer and conductivity sensor data from captive or wild polar bears. In contrast, models using data from captive brown bears failed to reliably distinguish most active behaviors in wild polar bears. Our ability to discriminate behavior was greatest when species- and habitat-specific data from wild individuals were used to train models. Data from captive individuals may be suitable for calibrating accelerometers, but may provide reduced ability to discriminate some behaviors. The accelerometer calibrations developed here provide a method to quantify polar bear behaviors to evaluate the impacts of declines in Arctic sea ice.
    • Utilizing first occurrence, nursing behavior, and growth data to enhance animal management: An example with African elephants (Loxodonta africana)

      Miller, Lance J.; Andrews, Jeff (2013)
      One of the many goals of zoological institutions is to actively breed endangered species to enhance conservation efforts. Unfortunately, many of these species are not reproducing at high enough levels to sustain populations within zoos. Low reproductive success and high infant mortality are two areas of concern for some of these species. Collecting behavioral data on developmental milestones following successful births can create a database of information to aide animal management to help make more informed decisions during subsequent births. The current study provides valuable information for African elephant calf developmental norms and demonstrates how data on first occurrences, nursing behavior and growth patterns can aide animal management. Data were collected on eleven African elephants (Loxodonta africana) at the San Diego Zoo Safari Park in Escondido, CA of which ten have survived. Results show that on average African elephant calves were standing within 40 minutes, attempted to nurse within an hour and a half, and successfully nursed within six hrs. There were no significant differences in nursing rates, growth patterns, or first occurrence behaviors between males and females during the first 75 days of life and elephants gained on average 0.59 kg/day over that same period of time. Results also show a significant change in nursing behavior on day 22 for the elephant calf that died. This information is intended to serve as a resource for elephant managers with newborn African elephants and to serve as a model to develop similar type databases for other species in need within zoological institutions.
    • Utilizing first occurrence, nursing behavior, and growth data to enhance animal management: An example with African elephants (Loxodonta africana)

      Miller, Lance J.; Andrews, J. (2013)
      One of the many goals of zoological institutions is to actively breed endangered species to enhance conservation efforts. Unfortunately, many of these species are not reproducing at high enough levels to sustain populations within zoos. Low reproductive success and high infant mortality are two areas of concern for some of these species. Collecting behavioral data on developmental milestones following successful births can create a database of information to aide animal management to help make more informed decisions during subsequent births. The current study provides valuable information for African elephant calf developmental norms and demonstrates how data on first occurrences, nursing behavior and growth patterns can aide animal management. Data were collected on eleven African elephants (Loxodonta africana) at the San Diego Zoo Safari Park in Escondido, CA of which ten have survived. Results show that on average African elephant calves were standing within 40 minutes, attempted to nurse within an hour and a half, and successfully nursed within six hrs. There were no significant differences in nursing rates, growth patterns, or first occurrence behaviors between males and females during the first 75 days of life and elephants gained on average 0.59 kg/day over that same period of time. Results also show a significant change in nursing behavior on day 22 for the elephant calf that died. This information is intended to serve as a resource for elephant managers with newborn African elephants and to serve as a model to develop similar type databases for other species in need within zoological institutions.
    • Validation of mercury tip-switch and accelerometer activity sensors for identifying resting and active behavior in bears

      Ware, Jasmine V.; Rode, Karyn D.; Pagano, Anthony M.; Bromaghin, Jeffrey F.; Robbins, Charles T.; Erlenbach, Joy; Jensen, Shannon; Cutting, Amy; Nicassio-Hiskey, Nicole; Hash, Amy; et al. (2015)
      In this study, we examined the performance of a mercury tip-switch and a tri-axial accelerometer housed in collars to determine whether sensor data can be accurately classified as resting and active behaviors and whether data are comparable for the 2 sensor types. Five captive bears (3 polar [Ursus maritimus] and 2 brown [U. arctos horribilis]) were fitted with a collar specially designed to internally house the sensors. The bears’ behaviors were recorded, classified, and then compared with sensor readings…
    • Variation in reproductive success across captive populations: Methodological differences, potential biases and opportunities

      Griffith, Simon C.; Crino, Ondi L.; Andrew, Samuel C.; Nomano, Fumiaki Y.; Adkins-Regan, Elizabeth; Alonso-Alvarez, Carlos; Bailey, Ida E.; Bittner, Stephanie S.; Bolton, Peri E.; Boner, Winnie; et al. (2017)
      ...The zebra finch remains an excellent captive animal system and our aim is to sharpen the insight that future studies of this species can provide, both to our understanding of this species and also with respect to the reproduction of captive animals more widely. We hope to improve systematic reporting methods and that further investigation of the issues we raise will lead both to advances in our fundamental understanding of avian reproduction as well as to improvements in future welfare and experimental efficiency….
    • Viable cell culture banking for biodiversity characterization and conservation

      Ryder, Oliver A.; Onuma, Manabu (2018)
      Because living cells can be saved for indefinite periods, unprecedented opportunities for characterizing, cataloging, and conserving biological diversity have emerged as advanced cellular and genetic technologies portend new options for preventing species extinction. Crucial to realizing the potential impacts of stem cells and assisted reproductive technologies on biodiversity conservation is the cryobanking of viable cell cultures from diverse species, especially those identified as vulnerable to extinction in the near future. The advent of in vitro cell culture and cryobanking is reviewed here in the context of biodiversity collections of viable cell cultures that represent the progress and limitations of current efforts. The prospects for incorporating collections of frozen viable cell cultures into efforts to characterize the genetic changes that have produced the diversity of species on Earth and contribute to new initiatives in conservation argue strongly for a global network of facilities for establishing and cryobanking collections of viable cells.
    • Vocal behaviour predicts mating success in giant pandas

      Charlton, Benjamin D.; Martin-Wintle, Meghan S.; Owen, Megan A.; Zhang, Hemin; Swaisgood, Ronald R. (2018)
      Surprisingly little is known about how mammal vocal signals are used to achieve behavioural synchrony in the lead up to copulation. The ability to signal short-term fluctuations in arousal levels and behavioural intention is likely to be particularly important for synchronizing mating behaviour in asocial species, which must overcome their natural avoidance and aggressive tendencies to mate. Here, we examined vocal behaviour during breeding encounters in captive giant pandas (Ailuropoda melanoleuca) to gain a greater understanding of how close-range vocal signalling mediates reproduction in this asocial, and conservation-dependent species. Our results revealed that the occurrence of different giant panda vocalizations and acoustic variation within these calls is predictive of successful encounters leading to copulation, as opposed to unsuccessful encounters that do not. In addition, key differences were detected between vocalizations produced during and just prior to copulation. These findings illustrate that vocal exchanges are crucial for achieving behavioural synchrony and signalling intention to mate in giant pandas, and could also provide a valuable tool for breeding programmes, helping conservation managers to assess the likelihood of breeding introductions leading to copulation or potentially injurious failure.
    • Vocal repertoire and signal characteristics of 'Alalā, the Hawaiian Crow (Corvus hawaiiensis)

      Tanimoto, Ann M.; Hart, Patrick J.; Pack, Adam A.; Switzer, Richard A. (2017)
      The critically endangered Hawaiian Crow or ′Alalā (Corvus hawaiiensis) is currently extinct in the wild and the remaining 115 individuals are being captively managed on Hawai′i and Maui Islands by the Zoological Society of San Diego. Here we provide the first comprehensive analysis of the vocal repertoire of this species....
    • West Indian iguana Cyclura spp reintroduction and recovery programmes: Zoo support and involvement

      Grant, Tandora D.; Hudson, R. D. (2015)
      Many West Indian rock iguanas Cyclura spp comprise small restricted island populations that are threatened by habitat conversion and degradation, free-ranging domestic animals and invasive species. In the 1980s, concerted conservation efforts were initiated for Caribbean iguanas, using a combination of captive-breeding programmes and head-starting of wild-collected hatchlings for reintroduction, and habitat protection….
    • What evidence exists on the effectiveness of different types of olfactory lures as attractants for invasive mammalian predators? A systematic map protocol

      Price, Catherine J.; Banks, Peter B.; Greggor, Alison L. (2019)
      Alien mammalian predators are a major cause of species extinction and decline globally. Baits and lures, usually human-food based (for example meat, nuts or oils), are widely deployed in trapping programs to attract target species, but their effectiveness compared to other types of olfactory lures, for example social odours or prey odours, has never been systematically examined. Depending on the context, there can be high proportions of non-target captures, for example when targeting feral cats using cage traps, or low capture success, for example, when targeting introduced rats on tropical islands. Here we use a systematic process to map evidence on the effectiveness of different categories of olfactory attractants for invasive mammalian predators within different ecological contexts. We aim to look for where evidence clusters and knowledge gaps occur, for example, across different lure types or across different habitat-types, and highlight opportunities for future research into behaviourally-relevant olfactory lures.
    • Where to now? An uncertain future for Jamaica's largest endemic vertebrate

      Veen, Rick van; Wilson, Byron S.; Grant, Tandora D.; Hudson, Richard (2014)
    • Which parasites should we be most concerned about in wildlife translocations?

      Rideout, Bruce; Sainsbury, Anthony W.; Hudson, Peter J. (2017)
    • White-footed sportive lemur (Lepilemur leucopus). The IUCN Red List of Threatened Species.

      Eppley, Timothy M.; Ferguson, B; Louis, E.E.; Rakotondranary, S.J.; Ganzhorn, J. (2020)
      The extent of occurrence (EOO) of this species covers 2,315 km2. This geographic range is severely fragmented and undergoing continuing decline in area, extent and quality of habitat. The number of mature individuals is also suspected to be in decline. Based on these premises, the species is listed as Endangered
    • White-fronted lemur (Eulemur albifrons). The IUCN Red List of Threatened Species 2020

      Borgerson, C.; Eppley, Timothy M.; Donati, G; Colquhoun, I.C; Irwin, M; Johnson, S; Louis, E.E.; Patel, E.; Ralainasolo, F.B; Ravaloharimanitra, M.; et al. (2020)
      Listed as Vulnerable, Eulemur albifrons is suspected to have undergone a population decline greater than or equal to 30% over a period of 24 years (three generations), due primarily to unsustainable hunting pressure and continuing decline in area, extent and quality of habitat. These causes have not ceased, and will, to a large extent, not be easily reversible
    • Whole genome sequencing and re-sequencing of the sable antelope (Hippotragus niger): A resource for monitoring diversity in ex situ and in situ populations

      Koepfli, Klaus-Peter; Tamazian, Gaik; Wildt, David; Dobrynin, Pavel; Kim, Changhoon; Frandsen, Paul B.; Godinho, Raquel; Yurchenko, Andrey A.; Komissarov, Aleksey; Krasheninnikova, Ksenia; et al. (2019)
      Genome-wide assessment of genetic diversity has the potential to increase the ability to understand admixture, inbreeding, kinship and erosion of genetic diversity affecting both captive (ex situ) and wild (in situ) populations of threatened species. The sable antelope (Hippotragus niger), native to the savannah woodlands of sub-Saharan Africa, is a species that is being managed ex situ in both public (zoo) and private (ranch) collections in the United States. Our objective was to develop whole genome sequence resources that will serve as a foundation for characterizing the genetic status of ex situ populations of sable antelope relative to populations in the wild. Here we report the draft genome assembly of a male sable antelope, a member of the subfamily Hippotraginae (Bovidae, Cetartiodactyla, Mammalia). The 2.926 Gb draft genome consists of 136,532 contigs with an N50 of 45.5 Kbp and 16,931 scaffolds with an N50 of 4.59 Mbp. De novo annotation identified 21,276 protein-coding genes and repetitive sequences encompassing 46.97% of the genome. The discovery of single nucleotide variants (SNVs) was assisted by the re-sequencing of seven additional captive and wild individuals, representing two different subspecies, leading to the identification of 1,987,710 bi-allelic SNVs. Assembly of the mitochondrial genomes revealed that each individual was defined by a unique haplotype and these data were used to infer the mitochondrial gene tree relative to other hippotragine species. The sable antelope genome constitutes a valuable resource for assessing genome-wide diversity and evolutionary potential, thereby facilitating long-term conservation of this charismatic species.
    • Whole-genome analyses resolve early branches in the tree of life of modern birds

      Jarvis, Erich D.; Mirarab, Siavash; Aberer, Andre J.; Li, Bo; Houde, Peter; Li, Cai; Ho, Simon Y. W.; Faircloth, Brant C.; Nabholz, Benoit; Howard, Jason T.; et al. (2014)
      To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships.....