• Bonobo personality traits are heritable and associated with vasopressin receptor gene 1a variation

      Staes, Nicky; Weiss, Alexander; Helsen, Philippe; Korody, Marisa L.; Eens, Marcel; Stevens, Jeroen M. G. (2016)
      Despite being closely related, bonobos and chimpanzees show remarkable behavioral differences, the proximate origins of which remain unknown. This study examined the link between behavioral variation and variation in the vasopressin 1a receptor gene (Avpr1a) in bonobos. Chimpanzees are polymorphic for a ~360bp deletion (DupB), which includes a microsatellite (RS3) in the 5′ promoter region of Avpr1a. In chimpanzees, the DupB deletion has been linked to lower sociability, lower social sensitivity, and higher anxiety. Chimpanzees and bonobos differ on these traits, leading some to believe that the absence of the DupB deletion in bonobos may be partly responsible for these differences, and to the prediction that similar associations between Avpr1a genotypes and personality traits should be present in bonobos. We identified bonobo personality dimensions using behavioral measures (SociabilityB, BoldnessB, OpennessB, ActivityB) and trait ratings (AssertivenessR, ConscientiousnessR, OpennessR, AgreeablenessR, AttentivenessR, ExtraversionR). In the present study we found that all 10 dimensions have nonzero heritabilities, indicating there is a genetic basis to personality, and that bonobos homozygous for shorter RS3 alleles were lower in AttentivenessR and higher in OpennessB. These results suggest that variations in Avpr1a genotypes explain both within and between species differences in personality traits of bonobos and chimpanzees.
    • Center for Plant Conservation's Best Practice Guidelines for the reintroduction of rare plants

      Maschinski, Joyce; Albrecht, Matthew A. (2017)
      Recent estimates indicate that one-fifth of botanical species worldwide are considered at risk of becoming extinct in the wild. One available strategy for conserving many rare plant species is reintroduction, which holds much promise especially when carefully planned by following guidelines and when monitored long-term. We review the Center for Plant Conservation Best Reintroduction Practice Guidelines and highlight important components for planning plant reintroductions. Before attempting reintroductions practitioners should justify them, should consider alternative conservation strategies, understand threats, and ensure that these threats are absent from any recipient site. Planning a reintroduction requires considering legal and logistic parameters as well as target species and recipient site attributes. Carefully selecting the genetic composition of founders, founder population size, and recipient site will influence establishment and population growth. Whenever possible practitioners should conduct reintroductions as experiments and publish results. To document whether populations are sustainable will require long-term monitoring for decades, therefore planning an appropriate monitoring technique for the taxon must consider current and future needs. Botanical gardens can play a leading role in developing the science and practice of plant reintroduction.
    • Characterization of Prdm9 in equids and sterility in mules

      Steiner, Cynthia C.; Ryder, Oliver A. (2013)
      Prdm9 (Meisetz) is the first speciation gene discovered in vertebrates conferring reproductive isolation. This locus encodes a meiosis-specific histone H3 methyltransferase that specifies meiotic recombination hotspots during gametogenesis. Allelic differences in Prdm9, characterized for a variable number of zinc finger (ZF) domains, have been associated with hybrid sterility in male house mice via spermatogenic failure at the pachytene stage. The mule, a classic example of hybrid sterility in mammals also exhibits a similar spermatogenesis breakdown, making Prdm9 an interesting candidate to evaluate in equine hybrids. In this study, we characterized the Prdm9 gene in all species of equids by analyzing sequence variation of the ZF domains and estimating positive selection. We also evaluated the role of Prdm9 in hybrid sterility by assessing allelic differences of ZF domains in equine hybrids. We found remarkable variation in the sequence and number of ZF domains among equid species, ranging from five domains in the Tibetan kiang and Asiatic wild ass, to 14 in the Grevy’s zebra. Positive selection was detected in all species at amino acid sites known to be associated with DNA-binding specificity of ZF domains in mice and humans. Equine hybrids, in particular a quartet pedigree composed of a fertile mule showed a mosaic of sequences and number of ZF domains suggesting that Prdm9 variation does not seem by itself to contribute to equine hybrid sterility.
    • Conservation genetics of Roatán Spiny-tailed Iguanas, Ctenosaura oedirhina.

      Pasachnik, Stesha A.; Hudman, S.; Iverson, John B.; Grant, Tandora D.; Knapp, Charles R.; Pasachnik, Stesha A. (2016)
      Roatán Spiny-tailed Iguanas, Ctenosaura oedirhina, are assessed as Endangered by the IUCN Red List of Threatened Species and listed in Appendix II of the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). Occurring in less than 1% of the available habitat on Roatán, due primarily to hunting... pressure, this species faces severe fragmentation.
    • Evolutionary genomics and conservation of the endangered Przewalski’s horse

      Der Sarkissian, Clio; Ermini, Luca; Schubert, Mikkel Heide; Yang, Melinda A.; Librado, Pablo; Fumagalli, Matteo; Jónsson, Hákon; Bar-Gal, Gila Kahila; Albrechtsen, Anders; Vieira, Filipe G.; et al. (2015)
      Przewalski’s horses (PHs, Equus ferus ssp. przewalskii) were discovered in the Asian steppes in the 1870s and represent the last remaining true wild horses. PHs became extinct in the wild in the 1960s but survived in captivity, thanks to major conservation efforts....
    • Exploring the limits of saving a subspecies: The ethics and social dynamics of restoring northern white rhinos (Ceratotherium simum cottoni)

      Ryder, Oliver A.; Friese, Carrie; Greely, Henry T.; Sandler, Ronald; Saragusty, Joseph; Durrant, Barbara S.; Redford, Kent H. (2020)
      The northern white rhino (Ceratotherium simum cottoni) is functionally extinct with only two females left alive. However, cryopreserved material from a number of individuals represents the potential to produce additional individuals using advanced reproductive and genetic rescue technologies and perhaps eventually a population to return to their native range. If this could and were done, how should it be done responsibly and thoughtfully. What issues and questions of a technical, bioethical, and societal nature will it raise that need to be anticipated and addressed? Such issues are explored in this article by an interdisciplinary team assembled to provide context to the northern white rhino project of the San Diego Zoo Global.
    • Genetic variation of complete mitochondrial genome sequences of the Sumatran rhinoceros (Dicerorhinus sumatrensis)

      Steiner, Cynthia C.; Houck, Marlys L.; Ryder, Oliver A. (2018)
      The Sumatran rhinoceros (Dicerorhinus sumatrensis) is the smallest and one of the most endangered rhinoceros species, with less than 100 individuals estimated to live in the wild. It was originally divided into three subspecies but only two have survived, D. sumatrensis sumatrensis (Sumatran subspecies), and D. s. harrissoni (Bornean)....
    • Highly polymorphic colour vision in a New World monkey with red facial skin, the bald uakari Cacajao calvus

      Corso, Josmael; Bowler, Mark; Heymann, Eckhard W.; Roos, Christian; Mundy, Nicholas I. (2016)
      Colour vision is highly variable in New World monkeys (NWMs). Evidence for the adaptive basis of colour vision in this group has largely centred on environmental features such as foraging benefits for differently coloured foods or predator detection, whereas selection on colour vision for sociosexual communication is an alternative hypothesis that has received little attention. The colour vision of uakaris (Cacajao) is of particular interest because these monkeys have the most dramatic red facial skin of any primate, as well as a unique fission/fusion social system and a specialist diet of seeds. Here, we investigate colour vision in a wild population of the bald uakari, C. calvus, by genotyping the X-linked opsin locus. We document the presence of a polymorphic colour vision system with an unprecedented number of functional alleles (six), including a novel allele with a predicted maximum spectral sensitivity of 555 nm. This supports the presence of strong balancing selection on different alleles at this locus. We consider different hypotheses to explain this selection. One possibility is that trichromacy functions in sexual selection, enabling females to choose high-quality males on the basis of red facial coloration. In support of this, there is some evidence that health affects facial coloration in uakaris, as well as a high prevalence of blood-borne parasitism in wild uakari populations. Alternatively, the low proportion of heterozygous female trichromats in the population may indicate selection on different dichromatic phenotypes, which might be related to cryptic food coloration. We have uncovered unexpected diversity in the last major lineage of NWMs to be assayed for colour vision, which will provide an interesting system to dissect adaptation of polymorphic trichromacy.
    • Large numbers of vertebrates began rapid population decline in the late 19th century

      Li, Haipeng; Xiang-Yu, Jinggong; Dai, Guangyi; Gu, Zhili; Ming, Chen; Yang, Zongfeng; Ryder, Oliver A.; Li, Wen-Hsiung; Fu, Yun-Xin; Zhang, Ya-Ping (2016)
      ...Here we analyzed the genetic diversity data of nuclear and mitochondrial loci of 2,764 vertebrate species and found that the mean genetic diversity is lower in threatened species than in related nonthreatened species. Our coalescence-based modeling suggests that in many threatened species the RPD began ∼123 y ago (a 95% confidence interval of 20–260 y)....
    • Linking Behavioral Diversity with Genetic and Ecological Variation in the Nigeria-Cameroon Chimpanzee (Pan troglodytes ellioti)

      Abwe, Ekwoge E. (Drexel UniversityPhiladelphia, PA, 2018)
      The chimpanzees of Cameroon present a unique opportunity to investigate how ecological variation contributes to promoting intraspecific divergences in the endemic mammals of the region.... This thesis explores environmental and ecological differences between rainforest and ecotone habitats at a fine geographic scale, and compares and contrasts chimpanzee socioecology patterns between these habitats.
    • Lost iguanas: Trouble in paradise

      Pasachnik, Stesha A.; Carreras De Leon, R. (2014)
      Hispaniola is second only to Cuba in size and biodiversity among West Indian islands, and is unique in being the only island with two native species of Rock Iguanas, the Rhinoceros Iguana (Cyclura cornuta; Fig. 1) and Ricord’s Iguana (C. ricordii). The island’s geologic history is likely responsible. Hispaniola was formed during the middle Miocene when North and South paleoislands joined (Graham 2003). A logical hypothesis suggests that each paleoisland held one species, and when the two islands joined, the ranges of both species shifted, eventually resulting in the distributions seen today. Cyclura ricordii is restricted to the southwestern Dominican Republic (DR) and just across the southern border into Haiti, whereas C. cornuta has a larger distribution throughout much of the arid lowlands across the entire island.
    • Low MHC variation in the polar bear: Implications in the face of Arctic warming?

      Weber, D.S.; Van Coeverden de Groot, P.J.; Schrenzel, Mark D.; Perez, D.A.; Thomas, S. (2013)
      Animals in the Arctic have low pathogen diversity but with rapid climate warming, this is expected to change. One insidious consequence of climate change is exposure of Arctic species to new pathogens derived from more southern species expanding their range northward. To assess potential vulnerability of polar bears to disease exposure, we examined genetic variation in major histocompatibility complex (MHC) loci (part of immune system) in Canadian polar bears and found low genetic diversity, consistent with long?standing exposure to low pathogen/parasite loads....
    • Oxytocin and vasopressin receptor gene variation as a proximate base for inter- and intraspecific behavioral differences in bonobos and chimpanzees

      Staes, Nicky; Stevens, Jeroen M. G.; Helsen, Philippe; Hillyer, Mia; Korody, Marisa L.; Eens, Marcel (2014)
      Recent literature has revealed the importance of variation in neuropeptide receptor gene sequences in the regulation of behavioral phenotypic variation. Here we focus on polymorphisms in the oxytocin receptor gene (OXTR) and vasopressin receptor gene 1a (Avpr1a) in chimpanzees and bonobos. In humans, a single nucleotide polymorphism (SNP) in the third intron of OXTR (rs53576 SNP (A/G)) is linked with social behavior, with the risk allele (A) carriers showing reduced levels of empathy and prosociality. Bonobos and chimpanzees differ in these same traits, therefore we hypothesized that these differences might be reflected in variation at the rs53576 position. We sequenced a 320 bp region surrounding rs53576 but found no indications of this SNP in the genus Pan. However, we identified previously unreported SNP variation in the chimpanzee OXTR sequence that differs from both humans and bonobos. Humans and bonobos have previously been shown to have a more similar 5' promoter region of Avpr1a when compared to chimpanzees, who are polymorphic for the deletion of ~360 bp in this region (+/- DupB) which includes a microsatellite (RS3). RS3 has been linked with variation in levels of social bonding, potentially explaining part of the interspecies behavioral differences found in bonobos, chimpanzees and humans. To date, results for bonobos have been based on small sample sizes. Our results confirmed that there is no DupB deletion in bonobos with a sample size comprising approximately 90% of the captive founder population, whereas in chimpanzees the deletion of DupB had the highest frequency. Because of the higher frequency of DupB alleles in our bonobo population, we suggest that the presence of this microsatellite may partly reflect documented differences in levels of sociability found in bonobos and chimpanzees.
    • Species concepts for conservation – Reply to Russello and Amato

      Frankham, Richard; Lacy, Robert C.; Ballou, Jonathan D.; Dudash, Michele R.; Eldridge, Mark D.B.; Fenster, Charles B.; Mendelson, Joseph R.; Porton, Ingrid J.; Ralls, Katherine; Ryder, Oliver A. (2014)
      There are two critical steps required in assessing the taxonomic identity of populations (especially fragmented ones) for conservation purposes. The first is to define the criteria for distinguishing species and the second is to implement the delineation....
    • The Genome 10K Project: A Way Forward

      Koepfli, Klaus-Peter; Benedict, Paten; The Genome 10K Community of Scientists; Antunes, Agostinho; Belov, Kathy; Bustamante, Carlos; Castoe, Todd A.; Clawson, Hiram; Crawford, Andrew J.; Diekhans, Mark; et al. (2015)
      The Genome 10K Project was established in 2009 by a consortium of biologists and genome scientists determined to facilitate the sequencing and analysis of the complete genomes of 10,000 vertebrate species. Since then the number of selected and initiated species has risen from ∼26 to 277 sequenced or ongoing with funding, an approximately tenfold increase in five years....