• A comparative genomics multitool for scientific discovery and conservation

      Genereux, Diane P.; Serres, Aitor; Armstrong, Joel; Johnson, Jeremy; Marinescu, Voichita D.; Murén, Eva; Juan, David; Bejerano, Gill; Casewell, Nicholas R.; Chemnick, Leona G.; et al. (2020)
      The Zoonomia Project is investigating the genomics of shared and specialized traits in eutherian mammals. Here we provide genome assemblies for 131 species, of which all but 9 are previously uncharacterized, and describe a whole-genome alignment of 240 species of considerable phylogenetic diversity, comprising representatives from more than 80% of mammalian families. We find that regions of reduced genetic diversity are more abundant in species at a high risk of extinction, discern signals of evolutionary selection at high resolution and provide insights from individual reference genomes. By prioritizing phylogenetic diversity and making data available quickly and without restriction, the Zoonomia Project aims to support biological discovery, medical research and the conservation of biodiversity.
    • A high density snp array for the domestic horse and extant Perissodactyla: Utility for association mapping, genetic diversity, and phylogeny studies

      McCue, Molly E.; Bannasch, Danika L.; Petersen, Jessica L.; Gurr, Jessica; Bailey, Ernie; Binns, Matthew M.; Distl, Ottmar; Guérin, Gérard; Hasegawa, Telhisa; Hill, Emmeline W.; et al. (2012)
      An equine SNP genotyping array was developed and evaluated on a panel of samples representing 14 domestic horse breeds and 18 evolutionarily related species. More than 54,000 polymorphic SNPs provided an average inter-SNP spacing of ?43 kb. The mean minor allele frequency across domestic horse breeds was 0.23, and the number of polymorphic SNPs within breeds ranged from 43,287 to 52,085. Genome-wide linkage disequilibrium (LD) in most breeds declined rapidly over the first 50–100 kb and reached background levels within 1–2 Mb. The extent of LD and the level of inbreeding were highest in the Thoroughbred and lowest in the Mongolian and Quarter Horse. Multidimensional scaling (MDS) analyses demonstrated the tight grouping of individuals within most breeds, close proximity of related breeds, and less tight grouping in admixed breeds. The close relationship between the Przewalski's Horse and the domestic horse was demonstrated by pair-wise genetic distance and MDS. Genotyping of other Perissodactyla (zebras, asses, tapirs, and rhinoceros) was variably successful, with call rates and the number of polymorphic loci varying across taxa. Parsimony analysis placed the modern horse as sister taxa to Equus przewalski. The utility of the SNP array in genome-wide association was confirmed by mapping the known recessive chestnut coat color locus (MC1R) and defining a conserved haplotype of -750 kb across all breeds. These results demonstrate the high quality of this SNP genotyping resource, its usefulness in diverse genome analyses of the horse, and potential use in related species.
    • A massively parallel sequencing approach uncovers ancient origins and high genetic variability of endangered Przewalski's horses

      Goto, Hiroki; Ryder, Oliver A.; Fisher, Allison R.; Schultz, Bryant; Kosakovsky Pond, Sergei L.; Nekrutenko, Anton; Makova, Kateryna D. (2011)
      The endangered Przewalski's horse is the closest relative of the domestic horse and is the only true wild horse species surviving today. The question of whether Przewalski's horse is the direct progenitor of domestic horse has been hotly debated. Studies of DNA diversity within Przewalski's horses have been sparse but are urgently needed to ensure their successful reintroduction to the wild. In an attempt to resolve the controversy surrounding the phylogenetic position and genetic diversity of Przewalski's horses, we used massively parallel sequencing technology to decipher the complete mitochondrial and partial nuclear genomes for all four surviving maternal lineages of Przewalski's horses. Unlike single-nucleotide polymorphism (SNP) typing usually affected by ascertainment bias, the present method is expected to be largely unbiased. Three mitochondrial haplotypes were discovered—two similar ones, haplotypes I/II, and one substantially divergent from the other two, haplotype III. Haplotypes I/II versus III did not cluster together on a phylogenetic tree, rejecting the monophyly of Przewalski's horse maternal lineages, and were estimated to split 0.117–0.186 Ma, significantly preceding horse domestication. In the phylogeny based on autosomal sequences, Przewalski's horses formed a monophyletic clade, separate from the Thoroughbred domestic horse lineage. Our results suggest that Przewalski's horses have ancient origins and are not the direct progenitors of domestic horses. The analysis of the vast amount of sequence data presented here suggests that Przewalski's and domestic horse lineages diverged at least 0.117 Ma but since then have retained ancestral genetic polymorphism and/or experienced gene flow.
    • An optimal and near-optimal strategy to selecting individuals for transfer in captive breeding programs

      Allen, S.D.; Fathi, Y.; Gross, K.; Mace, Michael E.; (2010)
      As species extinction rates continue to rise, zoos have adopted a more active role in the conservation of endangered species. A central concern is to preserve genetic diversity of zoological populations....
    • Change: Risks and predictability

      Hobohm, Carsten; Vanderplank, Sula E.; Hobohm, Carsten; Cabin, Robert J. (Springer International PublishingCham, Switzerland, 2021)
      ...This study deals with the question of how stochastic effects, changing ecological conditions, the introduction of alien species, and dramatic events in general, can be characterized and quantified. We propose some initial ideas for the establishment of an indicator system for constancy and change through time, with respect to the effect size....
    • Characterization of reproductive gene diversity in the endangered Tasmanian devil

      Brandies, Parice A.; Wright, Belinda R.; Hogg, Carolyn J.; Grueber, Catherine E.; Belov, Katherine (2020)
      ...We characterized single nucleotide polymorphisms (SNPs) at 214 genes involved in reproduction in 37 Tasmanian devils…. We will use this information in future to examine the interplay between reproductive gene variation and reproductive fitness in Tasmanian devil populations.
    • Co-designing behavior change interventions to conserve biodiversity

      Bowie, Matthew J.; Dietrich, Timo; Cassey, Phillip; Veríssimo, Diogo (2020)
      Many threats to biodiversity are the result of human actions, which means that changing human behavior can positively alter the trajectory of our current biodiversity crisis. While there is an increasing number of behavior change interventions being implemented in biodiversity conservation, their design is rarely informed by the people they try to influence, thereby lowering the probability of success. Building successful interventions requires substantial audience research, but this can be challenging for conservation projects with perennially limited time and resources. Here, we critically discuss co-design as a useful and effective approach for gathering audience insights relatively quickly, allowing conservation practitioners to integrate end-user voices when they would otherwise be excluded from intervention design. Specifically, we present a seven-step co-design process, providing an outline and guidance for how to generate more user-centric intervention ideas and transform them into feasible prototype interventions. Further, we show how we applied this seven-step process with coffee consumers in a sustainable conservation context. This study outlines contributions that showcase the value of user-centered design approaches to behavior change interventions for biodiversity conservation.
    • Comparative and demographic analysis of orang-utan genomes

      Locke, Devin P.; Hillier, LaDeana W.; Warren, Wesley C.; Worley, Kim C.; Nazareth, Lynne V.; Muzny, Donna M.; Yang, Shiaw-Pyng; Wang, Zhengyuan; Chinwalla, Asif T.; Minx, Pat; et al. (2011)
      ‘Orang-utan’ is derived from a Malay term meaning ‘man of the forest’ and aptly describes the southeast Asian great apes native to Sumatra and Borneo. The orang-utan species, Pongo abelii (Sumatran) and Pongo pygmaeus (Bornean), are the most phylogenetically distant great apes from humans, thereby providing an informative perspective on hominid evolution. Here we present a Sumatran orang-utan draft genome assembly and short read sequence data from five Sumatran and five Bornean orang-utan genomes. Our analyses reveal that, compared to other primates, the orang-utan genome has many unique features. Structural evolution of the orang-utan genome has proceeded much more slowly than other great apes, evidenced by fewer rearrangements, less segmental duplication, a lower rate of gene family turnover and surprisingly quiescent Alu repeats, which have played a major role in restructuring other primate genomes. We also describe a primate polymorphic neocentromere, found in both Pongo species, emphasizing the gradual evolution of orang-utan genome structure. Orang-utans have extremely low energy usage for a eutherian mammal1, far lower than their hominid relatives. Adding their genome to the repertoire of sequenced primates illuminates new signals of positive selection in several pathways including glycolipid metabolism. From the population perspective, both Pongo species are deeply diverse; however, Sumatran individuals possess greater diversity than their Bornean counterparts, and more species-specific variation. Our estimate of Bornean/Sumatran speciation time, 400,000 years ago, is more recent than most previous studies and underscores the complexity of the orang-utan speciation process. Despite a smaller modern census population size, the Sumatran effective population size (Ne) expanded exponentially relative to the ancestral Ne after the split, while Bornean Ne declined over the same period. Overall, the resources and analyses presented here offer new opportunities in evolutionary genomics, insights into hominid biology, and an extensive database of variation for conservation efforts.
    • Conservation genetics of the black rhinoceros, Diceros bicornis bicornis, in Namibia

      Van Coeverden de Groot, Peter J.; Putnam, Andrea S.; Erb, Peter; Scott, Candace; Melnick, Don; O’Ryan, Colleen; Boag, Peter T. (2011)
      Poaching and habitat destruction across sub-Saharan Africa brought the black rhinoceros (Diceros bicornis) close to extinction. Over the past few decades, however, one of four subspecies, D. b. bicornis, has experienced a significant population increase as a consequence of its protection within Etosha National Park (ENP), Namibia. We report here on the level and spatial distribution of black rhinoceros genetic diversity within ENP….
    • Environmental violence and the socio-environmental (de)evolution of a landscape in the San Quintín Valley.

      Narchi, Nemer E.; Vanderplank, Sula E.; Medina-Rodríguez, Jesús; Alfaro-Mercado, Enrique (2020)
      The social and environmental effects of industrial agriculture in the San Quintín Valley of Baja California are closely related. An environmental history of the...
    • Funding should come to those who wait

      Swaisgood, Ronald R.; Terborgh, John W.; Blumstein, Daniel T.; (2010)
      ... If long-term research is to flourish, we must build a reward system for studies characterized by deferred gratification. A sea change in these values must precede attempts to address funding....
    • Genetic structure of Rhinoceros Rock Iguanas, Cyclura cornuta, in the Dominican Republic, with insights into the impact of captive facilities and the taxonomic status of Cyclura on Mona Island

      Pasachnik, Stesha A.; Colosimo, Giuliano; Carreras-De León, Rosanna; Gerber, Glenn P. (2020)
      …To better understand the population structure of this species, we used a combination of mtDNA and nuclear markers to elucidate the genetic variation of wild populations across 13 sampling regions in the Dominican Republic (DR), as well as neighboring Mona Island, home to a Cyclura population of uncertain taxonomic status…. Our results suggest that the captive facilities may pose a threat to wild populations and increased regulation of these facilities is needed….
    • Genetic variability in three native Iranian chicken populations of the Khorasan province based on microsatellite markers

      Mohammadabadi, M.R.; Nikbakhti, M.; Mirzaee, H.R.; Shandi, A.; Saghi, D.A.; Romanov, Michael N.; Moiseyeva, I.G.; (2010)
      This paper represents the results of a study on the genetic diversity in three native chicken populations (Barred, Brown and Black) of Khorasan, a province in northeastern Iran, by using four microsatellite markers (MCW0005, MCW0016, MCW0018 and MCW0034). Average number of alleles was found to be 5.25 per locus across all populations....
    • Hope springs eternal: biodiversity conservation requires that we see the glass as half full

      Swaisgood, Ronald R.; Sheppard, James (2011)
      ...we prescribed a commonsense balance of realism based on good science with a rejuvenated sense of purpose and aspiration. This is hope with its sleeves rolled up—not as an emotional buffer against cold hard facts but as a stoic, clear-eyed, and utilitarian alternative to apathy, inaction, and despair....
    • Induced pluripotent stem cells from highly endangered species

      Ben-Nun, Inbar Friedrich; Montague, Susanne C; Houck, Marlys L.; Tran, Ha T; Garitaonandia, Ibon; Leonardo, Trevor R; Wang, Yu-Chieh; Charter, Suellen J.; Laurent, Louise C; Ryder, Oliver A.; et al. (2011)
      For some highly endangered species there are too few reproductively capable animals to maintain adequate genetic diversity, and extraordinary measures are necessary to prevent extinction. We report generation of induced pluripotent stem cells (iPSCs) from two endangered species: a primate, the drill, Mandrillus leucophaeus and the nearly extinct northern white rhinoceros, Ceratotherium simum cottoni. iPSCs may eventually facilitate reintroduction of genetic material into breeding populations.
    • Land use change and the future of biodiversity

      Hobohm, Carsten; Beierkuhnlein, Carl; Börtitz, Christine; Ralph Clark, V.; El Balti, Nadja; Fichtner, Andreas; Franklin, Scott; Gaens, Thomas; Härdtle, Werner; Hansen, Andreas Skriver; et al. (Springer International PublishingCham, Switzerland, 2021)
      This synthesis report is a meta-analysis of perspectives for biodiversity and ecosystems, with a strong focus on human impacts on the environment, and a work order to enable and manage the protection, survival and evolution of all species on Earth. The goal is to protect nature without any further species loss (Zero Extinction)....
    • On the phylogeny of Mustelidae subfamilies: analysis of seventeen nuclear non-coding loci and mitochondrial complete genomes

      Yu, Li; Peng, Dan; Liu, Jiang; Luan, Pengtao; Liang, Lu; Lee, Hang; Lee, Muyeong; Ryder, Oliver A.; Zhang, Yaping (2011)
      Background Mustelidae, as the largest and most-diverse family of order Carnivora, comprises eight subfamilies. Phylogenetic relationships among these Mustelidae subfamilies remain argumentative subjects in recent years. One of the main reasons is that the mustelids represent a typical example of rapid evolutionary radiation and recent speciation event. Prior investigation has been concentrated on the application of different mitochondrial (mt) sequence and nuclear protein-coding data, herein we employ 17 nuclear non-coding loci (>15 kb), in conjunction with mt complete genome data (>16 kb), to clarify these enigmatic problems. Results The combined nuclear intron and mt genome analyses both robustly support that Taxidiinae diverged first, followed by Melinae. Lutrinae and Mustelinae are grouped together in all analyses with strong supports. The position of Helictidinae, however, is enigmatic because the mt genome analysis places it to the clade uniting Lutrinae and Mustelinae, whereas the nuclear intron analysis favores a novel view supporting a closer relationship of Helictidinae to Martinae. This finding emphasizes a need to add more data and include more taxa to resolve this problem. In addition, the molecular dating provides insights into the time scale of the origin and diversification of the Mustelidae subfamilies. Finally, the phylogenetic performances and limits of nuclear introns and mt genes are discussed in the context of Mustelidae phylogeny. Conclusion Our study not only brings new perspectives on the previously obscured phylogenetic relationships among Mustelidae subfamilies, but also provides another example demonstrating the effectiveness of nuclear non-coding loci for reconstructing evolutionary histories in a group that has undergone rapid bursts of speciation.
    • Peatlands of the Madre de Dios River of Peru: Distribution, geomorphology, and habitat diversity

      Householder, J. Ethan; Janovec, John P.; Tobler, Mathias W.; Page, Susan; Lähteenoja, Outi (2012)
      We present results of research concerning the distribution, depth, volume, geomorphology, and habitat diversity of peatlands in the southern Peruvian Amazon. We identified 295 peatlands covering 294 km2 and ranging in size from 10 to 3,500 ha….
    • Reducing the extinction risk of populations threatened by infectious diseases

      Glassock, Gael L.; Grueber, Catherine E.; Belov, Katherine; Hogg, Carolyn J. (2021)
      Extinction risk is increasing for a range of species due to a variety of threats, including disease. Emerging infectious diseases can cause severe declines in wild animal populations, increasing population fragmentation and reducing gene flow. Small, isolated, host populations may lose adaptive potential and become more susceptible to extinction due to other threats. Management of the genetic consequences of disease-induced population decline is often necessary. Whilst disease threats need to be addressed, they can be difficult to mitigate. Actions implemented to conserve the Tasmanian devil (Sarcophilus harrisii), which has suffered decline to the deadly devil facial tumour disease (DFTD), exemplify how genetic management can be used to reduce extinction risk in populations threatened by disease. Supplementation is an emerging conservation technique that may benefit populations threatened by disease by enabling gene flow and conserving their adaptive potential through genetic restoration. Other candidate species may benefit from genetic management via supplementation but concerns regarding outbreeding depression may prevent widespread incorporation of this technique into wildlife disease management. However, existing knowledge can be used to identify populations that would benefit from supplementation where risk of outbreeding depression is low. For populations threatened by disease and, in situations where disease eradication is not an option, wildlife managers should consider genetic management to buffer the host species against inbreeding and loss of genetic diversity.