1
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Sun C, Otten F, Hoffman R, Marneweck C, Maimbo H, Petre CA, Joubert D, Riffel T, Becker MS, Fennessy S, Fennessy J, Brown MB. First rangewide density estimate of the endemic and isolated Luangwa giraffe in Zambia. Sci Rep 2025; 15:16435. [PMID: 40355446 PMCID: PMC12069576 DOI: 10.1038/s41598-025-00306-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2025] [Accepted: 04/28/2025] [Indexed: 05/14/2025] Open
Abstract
The Luangwa giraffe (Giraffa tippelskirchi thornicrofti), a subspecies of the Masai giraffe endemic to the Luangwa Valley of northeastern Zambia, inhabits an increasingly human-modified landscape. Accurate and current population estimates are critical to evaluating their status and identifying effective conservation strategies. However, sparse monitoring since the early 1900s has limited inferences about population size, structure, and range. To address this, we conducted the most spatially extensive and systematic survey to date of Luangwa giraffe across its distribution, extending survey effort 120 km south of their officially recognized extent. Using spatial capture recapture modeling, we estimated 651-890 giraffe and an overall density of 0.04-0.05 giraffe/km2. Density decreased to nought beyond 7.5 km from permanent rivers, consistent with preferred forage concentrated in riparian areas. Increasing giraffe density estimates up to a threshold of the Human Footprint Index suggested that limited human presence may have negligible consequences on movement and resource selection. This was likely due to suitable habitat and minimal conflict despite human presence. However, without mitigating land-use planning, rapid land conversion threatens human-giraffe coexistence. An even sex ratio and small proportion of subadults implied a stable population, but sex-biased and temporal dynamics in space use, impacts of predation, and stochastic risks necessitate continued monitoring. This study highlights the value of systematic large-scale monitoring and opportunities for data integration across long-term monitoring programs to evaluate factors driving Luangwa giraffe dynamics and to inform science-based conservation of this unique and isolated population.
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Affiliation(s)
- Catherine Sun
- Zambian Carnivore Programme, Mfuwe, Zambia.
- Montana State University, Bozeman, MT, USA.
| | | | - Rigardt Hoffman
- Giraffe Conservation Foundation, Windhoek, Namibia
- University of Mpumalanga, Mbombela, South Africa
| | - Courtney Marneweck
- Giraffe Conservation Foundation, Windhoek, Namibia
- Applied Behavioural Ecology and Ecosystem Research Unit, University of South Africa, Johannesburg, South Africa
| | - Howard Maimbo
- Zambian Carnivore Programme, Mfuwe, Zambia
- Department of National Parks and Wildlife, Lusaka, Zambia
| | | | | | - Tom Riffel
- Nsanga Conservation, Mfuwe, Zambia
- Caring for Conservation Fund gGmbH, Hirschberg, Germany
| | - Matthew S Becker
- Zambian Carnivore Programme, Mfuwe, Zambia
- Montana State University, Bozeman, MT, USA
| | | | - Julian Fennessy
- Giraffe Conservation Foundation, Windhoek, Namibia
- School of Biology and Environmental Science, University College, Dublin, Ireland
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2
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May SA, Rosenbaum SW, Pearse DE, Kardos M, Primmer CR, Baetscher DS, Waples RS. The Genomics Revolution in Nonmodel Species: Predictions vs. Reality for Salmonids. Mol Ecol 2025:e17758. [PMID: 40249276 DOI: 10.1111/mec.17758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2024] [Revised: 03/12/2025] [Accepted: 03/28/2025] [Indexed: 04/19/2025]
Abstract
The increasing feasibility of whole-genome sequencing has been highly anticipated, promising to transform our understanding of the biology of nonmodel species. Notably, dramatic cost reductions beginning around 2007 with the advent of high-throughput sequencing inspired publications heralding the 'genomics revolution', with predictions about its future impacts. Although such predictions served as useful guideposts, value is added when statements are evaluated with the benefit of hindsight. Here, we review 10 key predictions made early in the genomics revolution, highlighting those realised while identifying challenges limiting others. We focus on predictions concerning applied aspects of genomics and examples involving salmonid species which, due to their socioeconomic and ecological significance, have been frontrunners in applications of genomics in nonmodel species. Predicted outcomes included enhanced analytical power, deeper insights into the genetic basis of phenotype and fitness variation, disease management and breeding program advancements. Although many predictions have materialised, several expectations remain unmet due to technological, analytical and knowledge barriers. Additionally, largely unforeseen advancements, including the identification and management applicability of large-effect loci, close-kin mark-recapture, environmental DNA and gene editing have added under-anticipated value. Finally, emerging innovations in artificial intelligence and bioinformatics offer promising new directions. This retrospective evaluation of the impacts of the genomic revolution offers insights into the future of genomics for nonmodel species.
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Affiliation(s)
- Samuel A May
- National Cold Water Marine Aquaculture Center, Agricultural Research Service, United States Department of Agriculture, Orono, Maine, USA
| | - Samuel W Rosenbaum
- Wildlife Biology Program, Department of Ecosystem and Conservation Sciences, College of Forestry and Conservation, University of Montana, Missoula, Montana, USA
| | - Devon E Pearse
- Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Santa Cruz, California, USA
| | - Marty Kardos
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, USA
| | - Craig R Primmer
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Institute of Biotechnology, Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Diana S Baetscher
- Auke Bay Laboratories, Alaska Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Juneau, Alaska, USA
| | - Robin S Waples
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, USA
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3
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Bercovich U, Rasmussen MS, Li Z, Wiuf C, Albrechtsen A. Measuring linkage disequilibrium and improvement of pruning and clumping in structured populations. Genetics 2025; 229:iyaf009. [PMID: 39907701 DOI: 10.1093/genetics/iyaf009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2024] [Accepted: 12/19/2024] [Indexed: 02/06/2025] Open
Abstract
Standard measures of linkage disequilibrium (LD) are affected by admixture and population structure, such that loci that are not in LD within each ancestral population appear linked when considered jointly across the populations. The influence of population structure on LD can cause problems for downstream analysis methods, in particular those that rely on LD pruning or clumping. To address this issue, we propose a measure of LD that accommodates population structure using the top inferred principal components. We estimate LD from the correlation of genotype residuals and prove that this LD measure remains unaffected by population structure when analyzing multiple populations jointly, even with admixed individuals. Based on this adjusted measure of LD, we can perform LD pruning to remove the correlation between markers for downstream analysis. Traditional LD pruning is more likely to remove markers with high differences in allele frequencies between populations, which biases measures for genetic differentiation and removes markers that are not in LD in the ancestral populations. Using data from moderately differentiated human populations and highly differentiated giraffe populations we show that traditional LD pruning biases FST and principal component analysis (PCA), which can be alleviated with the adjusted LD measure. In addition, we show that the adjusted LD leads to better PCA when pruning and that LD clumping retains more sites with the retained sites having stronger associations.
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Affiliation(s)
- Ulises Bercovich
- Department of Mathematical Sciences, University of Copenhagen, Copenhagen 2100, Denmark
| | - Malthe Sebro Rasmussen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen 2200, Denmark
| | - Zilong Li
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen 2200, Denmark
| | - Carsten Wiuf
- Department of Mathematical Sciences, University of Copenhagen, Copenhagen 2100, Denmark
| | - Anders Albrechtsen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen 2200, Denmark
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4
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Machado RAR, Muller A, Hiltmann A, Bhat AH, Půža V, Malan AP, Castaneda-Alvarez C, San-Blas E, Duncan LW, Shapiro-Ilan D, Karimi J, Lalramliana, Lalramnghaki HC, Baimey H. Genome-wide analyses provide insights into genetic variation, phylo- and co-phylogenetic relationships, and biogeography of the entomopathogenic nematode genus Heterorhabditis. Mol Phylogenet Evol 2025; 204:108284. [PMID: 39778636 DOI: 10.1016/j.ympev.2025.108284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2024] [Revised: 12/19/2024] [Accepted: 01/04/2025] [Indexed: 01/11/2025]
Abstract
Multigene, genus-wide phylogenetic studies have uncovered the limited taxonomic resolution power of commonly used gene markers, particularly of rRNA genes, to discriminate closely related species of the nematode genus Heterorhabditis. In addition, conflicting tree topologies are often obtained using the different gene markers, which limits our understanding of the phylo- and co-phylogenetic relationships and biogeography of the entomopathogenic nematode genus Heterorhabditis. Here we carried out phylogenomic reconstructions using whole nuclear and mitochondrial genomes, and whole ribosomal operon sequences, as well as multiple phylogenetic reconstructions using various single nuclear and mitochondrial genes. Using the inferred phylogenies, we then investigated co-phylogenetic relationships between Heterorhabditis and their Photorhabdus bacterial symbionts and biogeographical patterns. Robust, well-resolved, and highly congruent phylogenetic relationships were reconstructed using both whole nuclear and mitochondrial genomes. Similarly, whole ribosomal operon sequences proved valuable for phylogenomic reconstructions, though they have limited value to discriminate closely related species. In addition, two mitochondrial genes, the cytochrome c oxidase subunit I (cox-1) and the NADH dehydrogenase subunit 4 (nad-4), and two housekeeping genes, the fanconi-associated nuclease 1 (fan-1) and the serine/threonine-protein phosphatase 4 regulatory subunit 1 (ppfr-1), provided the most robust phylogenetic reconstructions compared to other individual genes. According to our findings, whole nuclear and/or mitochondrial genomes are strongly recommended for reconstructing phylogenetic relationships of the genus Heterorhabditis. If whole nuclear and/or mitochondrial genomes are unavailable, a combination of nuclear and mitochondrial genes can be used as an alternative. Under these circumstances, sequences of multiple conspecific isolates in a genus-wide phylogenetic context should be analyzed to avoid artefactual species over-splitting driven by the high intraspecific sequence divergence of mitochondrial genes and to avoid artefactual species lumping driven by the low interspecific sequence divergence of some nuclear genes. On the other hand, we observed that the genera Heterorhabditis and Photorhabdus exhibit diverse biogeographic patterns, ranging from cosmopolitan species to potentially endemic species, and show high phylogenetic congruence, although host switches have also occurred. Our study contributes to a better understanding of the biodiversity and phylo- and co-phylogenetic relationships of an important group of biological control agents and advances our efforts to develop more tools that are compatible with sustainable and eco-friendly agricultural practices.
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Affiliation(s)
- Ricardo A R Machado
- Experimental Biology Research Group, Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland.
| | - Arthur Muller
- Experimental Biology Research Group, Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
| | - Alexandre Hiltmann
- Experimental Biology Research Group, Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
| | - Aashaq Hussain Bhat
- Experimental Biology Research Group, Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland; Department of Biosciences, University Center for Research and Development, Chandigarh University, 140413 Gharuan, India
| | - Vladimír Půža
- Institute of Entomology, Biology Centre of the Czech Academy of Sciences, CAS, 37005 České Budějovice, Czech Republic; Faculty of Agriculture and Technology, University of South Bohemia, 37005 České Budějovice, Czech Republic
| | - Antoinette P Malan
- Department of Conservation Ecology and Entomology, Stellenbosch University, Private Bag X1, 7602 Matieland, South Africa
| | - Carlos Castaneda-Alvarez
- Departamento de Sanidad Vegetal, Facultad de Ciencias Agronómicas, Universidad de Chile, 8820808 Santiago, Chile
| | - Ernesto San-Blas
- Laboratory of Nematology, Institute of Agrifood, Animal and Environmental, Sciences (ICA3), Universidad de O'Higgins, 2820000 O'Higgins, Chile; Centre of System Biology for Crop Protection (BIOSAV-UOH), Universidad de O Higgins, Chile
| | - Larry W Duncan
- University of Florida, IFAS, Citrus Research and Education Center, 33850 Lake Alfred, Florida, USA
| | - David Shapiro-Ilan
- USDA-ARS, SE Fruit and Tree Nut Research Laboratory, 31008 Byron, GA, USA
| | - Javad Karimi
- Department of Plant Protection, School of Agriculture, Ferdowsi University of Mashhad, 9177948978 Mashhad, Iran
| | - Lalramliana
- Department of Zoology, Pachhunga University College, 796001 Aizawl, Mizoram, India
| | - Hrang C Lalramnghaki
- Department of Zoology, Pachhunga University College, 796001 Aizawl, Mizoram, India
| | - Hugues Baimey
- Laboratory of Diagnosis and Integrated Management of Plant Bio-Aggressors. University of Parakou, BP123 Parakou, Borgou, Benin
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5
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Mellor NJ, Webster TH, Byrne H, Williams AS, Edwards T, DeNardo DF, Wilson MA, Kusumi K, Dolby GA. Divergence in Regulatory Regions and Gene Duplications May Underlie Chronobiological Adaptation in Desert Tortoises. Mol Ecol 2025; 34:e17600. [PMID: 39624910 PMCID: PMC11774117 DOI: 10.1111/mec.17600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 11/05/2024] [Accepted: 11/11/2024] [Indexed: 01/07/2025]
Abstract
Many cellular processes and organismal behaviours are time-dependent, and asynchrony of these phenomena can facilitate speciation through reinforcement mechanisms. The Mojave and Sonoran desert tortoises (Gopherus agassizii and G. morafkai respectively) reside in adjoining deserts with distinct seasonal rainfall patterns and they exhibit asynchronous winter brumation and reproductive behaviours. We used whole genome sequencing of 21 individuals from the two tortoise species and an outgroup to understand genes potentially underlying these characteristics. Genes within the most diverged 1% of the genome (FST ≥ 0.63) with putatively functional variation showed extensive divergence in regulatory elements, particularly promoter regions. Such genes related to UV nucleotide excision repair, mitonuclear and homeostasis functions. Genes mediating chronobiological (cell cycle, circadian and circannual) processes were also among the most highly diverged regions (e.g., XPA and ZFHX3). Putative promoter variants had significant enrichment of genes related to regulatory machinery (ARC-Mediator complex), suggesting that transcriptional cascades driven by regulatory divergence may underlie the behavioural differences between these species, leading to asynchrony-based prezygotic isolation. Further investigation revealed extensive expansion of respiratory and intestinal mucins (MUC5B and MUC5AC) within Gopherus, particularly G. morafkai. This expansion could be a xeric-adaptation to water retention and/or contribute to differential Mycoplasma agassizii infection rates between the two species, as mucins help clear inhaled dust and bacterial. Overall, results highlight the diverse array of genetic changes underlying divergence, adaptation and reinforcement during speciation.
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Affiliation(s)
- N. Jade Mellor
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294
| | | | - Hazel Byrne
- Department of Anthropology, University of Utah, Salt Lake City, Utah
| | - Avery S. Williams
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Taylor Edwards
- Arizona Molecular Clinical Core, University of Arizona, Tucson, Arizona 85721
| | - Dale F. DeNardo
- School of Life Sciences, Arizona State University, Tempe, Arizona 85287
| | - Melissa A. Wilson
- School of Life Sciences, Arizona State University, Tempe, Arizona 85287
| | - Kenro Kusumi
- School of Life Sciences, Arizona State University, Tempe, Arizona 85287
| | - Greer A. Dolby
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294
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6
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Kargopoulos N, Marugán-Lobón J, Chinsamy A, Agwanda BR, Brown MB, Fennessy S, Ferguson S, Hoffman R, Lala F, Muneza A, Mwebi O, Otiende M, Petzold A, Winter S, Zabeirou ARM, Fennessy J. Heads up-Four Giraffa species have distinct cranial morphology. PLoS One 2024; 19:e0315043. [PMID: 39700177 DOI: 10.1371/journal.pone.0315043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2024] [Accepted: 11/19/2024] [Indexed: 12/21/2024] Open
Abstract
Giraffe (Giraffa spp.) are among the most unique extant mammals in terms of anatomy, phylogeny, and ecology. However, aspects of their evolution, ontogeny, and taxonomy are unresolved, retaining lingering questions that are pivotal for their conservation. We assembled the largest known dataset of Giraffa skulls (n = 515) to investigate patterns of cranial variability using 3D geometric morphometrics. The results show distinct sexual dimorphism and divergent ontogenetic trajectories of skull shape for the north clade (G. camelopardalis antiquorum, G. c. camelopardalis, G. c. peralta, and G. reticulata) and the south clade (G. giraffa angolensis, G. g. giraffa, G. tippelskirchi tippelskirchi, and G. t. thornicrofti) which was further supported statistically. Discriminant functions found statistically significant cranial shape differences between all four Giraffa species, and in some cases also between subspecies of the same species. Our 3D morphometric analysis shows that the four genetically distinct Giraffa spp. also have distinct cranial morphologies, largely addressable to features of display (ossicones). Our results highlight the importance of focusing future giraffe conservation efforts on each taxon to maintain their unique characteristics and biodiversity in the wild.
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Affiliation(s)
- Nikolaos Kargopoulos
- Department of Biological Science, University of Cape Town, Cape Town, South Africa
- Giraffe Conservation Foundation, Windhoek, Namibia
| | - Jesús Marugán-Lobón
- Department of Biological Science, University of Cape Town, Cape Town, South Africa
- Department of Biology, Unidad de Paleontología, Universidad Autónoma de Madrid, Madrid, Spain
- CIPb-UAM, Center for the Integration in Paleobiology, Universidad Autónoma de Madrid, Madrid, Spain
| | - Anusuya Chinsamy
- Department of Biological Science, University of Cape Town, Cape Town, South Africa
| | | | | | | | | | | | - Fredrick Lala
- Wildlife Research and Training Institute, Naivasha, Kenya
| | | | | | - Moses Otiende
- Wildlife Research and Training Institute, Naivasha, Kenya
| | - Alice Petzold
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Museum für Naturkunde-Leibnitz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Sven Winter
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- Research Institute of Wildlife Ecology, University of Veterinary Medicine, Vienna, Austria
| | - Abdoul Razack Moussa Zabeirou
- Giraffe Conservation Foundation, Windhoek, Namibia
- Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Julian Fennessy
- Giraffe Conservation Foundation, Windhoek, Namibia
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
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7
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Prochotta D, Winter S, Fennessy J, Janke A. Population genomics of the southern giraffe. Mol Phylogenet Evol 2024; 201:108198. [PMID: 39276822 DOI: 10.1016/j.ympev.2024.108198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 07/30/2024] [Accepted: 09/11/2024] [Indexed: 09/17/2024]
Abstract
Studying wildlife taxonomic diversity and identifying distinct populations has traditionally been largely based on morphology and geographic origin. More recently, this method has been supplemented by genetic data from the mitochondrial genome. However, this is limited as only maternally inherited and may not reflect the true nature of a population's genetics. Within the giraffe (Giraffa spp.), subspecies and unique populations were successfully characterized using both mitochondrial and genomic DNA studies, which led to new insights and, in some cases, unexpected results that required further verification. Here, we sequenced the genomes of 85 southern giraffe (G. giraffa) individuals from ten populations across southern Africa for a detailed investigation into the genetic diversity and history of its two subspecies, the Angolan (G. g. angolensis) and the South African (G. g. giraffa) giraffe. While the overall genotypes show low levels of runs of homozygosity compared to other mammals, the degree of heterozygosity is limited despite the large population size of South African giraffe. The nuclear genotype is largely congruent with the mitochondrial genotype. However, we have identified that the distribution of the Angolan giraffe is not as far east as indicated in an earlier mitochondrial DNA study. Botswana's Central Kalahari Game Reserve giraffe are unique, with a clear admixture of Angolan and South African giraffe populations. However, the enigmatic desert-dwelling giraffe of northwest Namibia is locally distinct from other Angolan giraffe yet exhibits intra-subspecies signs of admixture resulting from a recent introduction of individuals from Namibia's Etosha National Park. Whole genome sequencing is an invaluable and nearly indispensable tool for wildlife management to uncover genetic diversity that is undetectable through mitogenomic, geographical, and morphological means.
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Affiliation(s)
- David Prochotta
- Institute for Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Strasse. 9, Frankfurt am Main, Germany; Senckenberg Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Strasse 14-16, Frankfurt am Main, Germany.
| | - Sven Winter
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Strasse 14-16, Frankfurt am Main, Germany; Research Institute of Wildlife Ecology, Vetmeduni Vienna, Vienna, Austria.
| | - Julian Fennessy
- Giraffe Conservation Foundation, PO Box 86099, Eros, Windhoek, Namibia; School of Biology and Environmental Science, University College Dublin, Ireland.
| | - Axel Janke
- Institute for Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Strasse. 9, Frankfurt am Main, Germany; Senckenberg Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Strasse 14-16, Frankfurt am Main, Germany; LOEWE Centre for Translational Biodiversity Genomics, Frankfurt, Germany.
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8
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de Flamingh A, Gnoske TP, Kerbis Peterhans JC, Simeonovski VA, Gitahi N, Mwebi O, Agwanda BR, Catchen JM, Roca AL, Malhi RS. Compacted hair in broken teeth reveals dietary prey of historic lions. Curr Biol 2024; 34:5104-5111.e4. [PMID: 39395415 DOI: 10.1016/j.cub.2024.09.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 07/03/2024] [Accepted: 09/12/2024] [Indexed: 10/14/2024]
Abstract
With recent advances, nuclear genome data for phylogenomic analyses can now be sequenced from minuscule quantities of DNA1 and from specimens that are more than a million years old.2 DNA analysis from hair is a well-established approach3 widely used in forensic science4 and wildlife conservation.5 Hair samples can be effectively decontaminated6 and can be used to identify the mammalian species from which the hair was shed.7,8 We aimed to use advances optimized for degraded DNA to systematically identify dietary prey species from hair compacted in the teeth of two Tsavo lions that lived during the 1890s in Kenya (see description of samples in the STAR Methods and Patterson9 and Kerbis Peterhans and Gnoske10 for background on the Tsavo "man-eaters"). Analysis of hair DNA identified giraffe, human, oryx, waterbuck, wildebeest, and zebra as prey and also identified hair that originated from lion. DNA preservation allowed for analyses of complete mitogenome profiles of zebra, giraffe, and lion. Giraffe mitogenomes are phylogeographically partitioned, and we found that the lions ate at least two individuals that belong to a subspecies of Masai giraffe (Giraffa tippelskirchi tippelskirchi) typically found in southeast Kenya. The lion mitogenome from a hair sample was identical to the Tsavo lion endogenous mitogenome and most closely matched other East African lions from Kenya and Tanzania. Our approach enables a better understanding of the hunting behaviors, diets, and ecology of historical individuals, populations, and species and holds promise for extinct populations and species.
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Affiliation(s)
- Alida de Flamingh
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA.
| | - Thomas P Gnoske
- Field Museum of Natural History, Chicago, IL 60605-2496, USA
| | - Julian C Kerbis Peterhans
- Field Museum of Natural History, Chicago, IL 60605-2496, USA; College of Arts & Sciences, Roosevelt University, Chicago, IL 60605-1394, USA
| | | | - Nduhiu Gitahi
- Department of Public Health, Pharmacology and Toxicology, University of Nairobi, Nairobi, Kenya
| | - Ogeto Mwebi
- Department of Osteology, National Museums of Kenya, Nairobi, Kenya
| | | | - Julian M Catchen
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA; Department of Ecology, Evolution, and Behavior, UIUC, Urbana, IL 61801, USA
| | - Alfred L Roca
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA; Department of Animal Sciences, UIUC, Urbana, IL 61801, USA
| | - Ripan S Malhi
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA; Department of Ecology, Evolution, and Behavior, UIUC, Urbana, IL 61801, USA; Department of Anthropology, UIUC, Urbana, IL 61801, USA.
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9
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Hermosilla-Albala N, Silva FE, Cuadros-Espinoza S, Fontsere C, Valenzuela-Seba A, Pawar H, Gut M, Kelley JL, Ruibal-Puertas S, Alentorn-Moron P, Faella A, Lizano E, Farias I, Hrbek T, Valsecchi J, Gut IG, Rogers J, Farh KKH, Kuderna LFK, Marques-Bonet T, Boubli JP. Whole genomes of Amazonian uakari monkeys reveal complex connectivity and fast differentiation driven by high environmental dynamism. Commun Biol 2024; 7:1283. [PMID: 39379612 PMCID: PMC11461705 DOI: 10.1038/s42003-024-06901-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 09/16/2024] [Indexed: 10/10/2024] Open
Abstract
Despite showing the greatest primate diversity on the planet, genomic studies on Amazonian primates show very little representation in the literature. With 48 geolocalized high coverage whole genomes from wild uakari monkeys, we present the first population-level study on platyrrhines using whole genome data. In a very restricted range of the Amazon rainforest, eight uakari species (Cacajao genus) have been described and categorized into the bald and black uakari groups, based on phenotypic and ecological differences. Despite a slight habitat overlap, we show that posterior to their split 0.92 Mya, bald and black uakaris have remained independent, without gene flow. Nowadays, these two groups present distinct genetic diversity and group-specific variation linked to pathogens. We propose differing hydrology patterns and effectiveness of geographic barriers have modulated the intra-group connectivity and structure of bald and black uakari populations. With this work we have explored the effects of the Amazon rainforest's dynamism on wild primates' genetics and increased the representation of platyrrhine genomes, thus opening the door to future research on the complexity and diversity of primate genomics.
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Grants
- T.M.B gratefully acknowledges the financial support from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 864203), (PID2021-126004NB-100) (MICIIN/FEDER, UE) and from the Secretaria d’Universitats i Recerca and CERCA Programme del Departament d’Economia i Coneixement de la Generalitat de Catalunya (GRC 2021 SGR 00177). J.P.B. gratefully acknowledges the financial support from the Natural Environment Research Council (NERC) (NE/T000341/1). F.E.S. gratefully acknowledges the financial support from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement (801505), the Fonds National de la Recherche Scientifique (F.R.S.-FNRS, Belgium; grant 40017464) Brazilian National Council for Scientific and Technological Development (CNPq) (Processes 303286/2014-8, 303579/2014-5, 200502/2015-8, 302140/2020-4, 300365/2021-7, 301407/2021-5, #301925/2021-6), the International Primatological Society (Conservation grant). The Rufford Foundation (14861-1, 23117-2, 38786-B), the Margot Marsh Biodiversity Foundation (SMA-CCO-G0023, SMA-CCOG0037), the Primate Conservation Inc. (1713 and 1689) and the Gordon and Betty Moore Foundation (Grant 5344) (Mamirauá Institute for Sustainable Development). N.H.-A. gratefully acknowledges the financial support from the Government of Catalonia | Agència de Gestió d'Ajuts Universitaris i de Recerca (Agency for Management of University and Research Grants) (FI_00040).
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Affiliation(s)
- Núria Hermosilla-Albala
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003, Barcelona, Spain.
| | - Felipe Ennes Silva
- Research Unit of Evolutionary Biology and Ecology, Département de Biologie des Organismes, Université libre de Bruxelles (ULB), Brussels, Belgium
- Research Group on Primate Biology and Conservation, Mamirauá Institute for Sustainable Development, Tefé, Amazonas, Brazil
| | - Sebastián Cuadros-Espinoza
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003, Barcelona, Spain
| | - Claudia Fontsere
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003, Barcelona, Spain
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Øster Farimagsgade 5A, 1352, Copenhagen, Denmark
| | - Alejandro Valenzuela-Seba
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003, Barcelona, Spain
| | - Harvinder Pawar
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003, Barcelona, Spain
| | - Marta Gut
- Centro Nacional de Análisis Genómico (CNAG), C/Baldiri Reixac 4, 08028, Barcelona, Spain
| | - Joanna L Kelley
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, 130 McAllister Way, Santa Cruz, CA, 95060, USA
| | - Sandra Ruibal-Puertas
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003, Barcelona, Spain
| | - Pol Alentorn-Moron
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003, Barcelona, Spain
| | - Armida Faella
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003, Barcelona, Spain
| | - Esther Lizano
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003, Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, Cerdanyola del Vallès, 08193, Barcelona, Spain
| | - Izeni Farias
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Amazonas, 69080-900, Brazil
| | - Tomas Hrbek
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Amazonas, 69080-900, Brazil
- Department of Biology, Trinity University, San Antonio, TX, 78212, USA
| | - Joao Valsecchi
- Research Group on Terrestrial Vertebrate Ecology, Mamirauá Institute for Sustainable Development, Tefé, Amazonas, Brazil
- Rede de Pesquisa para Estudos sobre Diversidade, Conservação e Uso da Fauna na Amazônia-RedeFauna, Manaus, Amazonas, Brazil
- Comunidad de Manejo de Fauna Silvestre en la Amazonía y en Latinoamérica-ComFauna, Iquitos, Loreto, Peru
| | - Ivo G Gut
- Centro Nacional de Análisis Genómico (CNAG), C/Baldiri Reixac 4, 08028, Barcelona, Spain
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Kyle Kai-How Farh
- Illumina Artificial Intelligence Laboratory, Illumina Inc., San Diego, CA, 94404, USA
| | - Lukas F K Kuderna
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003, Barcelona, Spain
- Illumina Artificial Intelligence Laboratory, Illumina Inc., San Diego, CA, 94404, USA
| | - Tomas Marques-Bonet
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003, Barcelona, Spain
- Centro Nacional de Análisis Genómico (CNAG), C/Baldiri Reixac 4, 08028, Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, Cerdanyola del Vallès, 08193, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) and Universitat Pompeu Fabra. Pg. Luís Companys 23, 08010, Barcelona, Spain
| | - Jean P Boubli
- School of Science, Engineering & Environment, University of Salford, Salford, M5 4WT, UK
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10
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Koepfli KP. Evolution: Genomes reveal the reticulated history of giraffes. Curr Biol 2024; 34:R533-R536. [PMID: 38834025 DOI: 10.1016/j.cub.2024.04.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
The diversification and taxonomy of modern giraffe lineages have been a riddle for more than 200 years. A new genomic study shows that divergence with gene flow has played a significant role in the history of this zoological icon.
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Affiliation(s)
- Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, George Mason University, 1500 Remount Road, Front Royal, VA 22630, USA.
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11
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Bertola LD, Quinn L, Hanghøj K, Garcia-Erill G, Rasmussen MS, Balboa RF, Meisner J, Bøggild T, Wang X, Lin L, Nursyifa C, Liu X, Li Z, Chege M, Moodley Y, Brüniche-Olsen A, Kuja J, Schubert M, Agaba M, Santander CG, Sinding MHS, Muwanika V, Masembe C, Siegismund HR, Moltke I, Albrechtsen A, Heller R. Giraffe lineages are shaped by major ancient admixture events. Curr Biol 2024; 34:1576-1586.e5. [PMID: 38479386 DOI: 10.1016/j.cub.2024.02.051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 09/29/2023] [Accepted: 02/21/2024] [Indexed: 04/11/2024]
Abstract
Strong genetic structure has prompted discussion regarding giraffe taxonomy,1,2,3 including a suggestion to split the giraffe into four species: Northern (Giraffa c. camelopardalis), Reticulated (G. c. reticulata), Masai (G. c. tippelskirchi), and Southern giraffes (G. c. giraffa).4,5,6 However, their evolutionary history is not yet fully resolved, as previous studies used a simple bifurcating model and did not explore the presence or extent of gene flow between lineages. We therefore inferred a model that incorporates various evolutionary processes to assess the drivers of contemporary giraffe diversity. We analyzed whole-genome sequencing data from 90 wild giraffes from 29 localities across their current distribution. The most basal divergence was dated to 280 kya. Genetic differentiation, FST, among major lineages ranged between 0.28 and 0.62, and we found significant levels of ancient gene flow between them. In particular, several analyses suggested that the Reticulated lineage evolved through admixture, with almost equal contribution from the Northern lineage and an ancestral lineage related to Masai and Southern giraffes. These new results highlight a scenario of strong differentiation despite gene flow, providing further context for the interpretation of giraffe diversity and the process of speciation in general. They also illustrate that conservation measures need to target various lineages and sublineages and that separate management strategies are needed to conserve giraffe diversity effectively. Given local extinctions and recent dramatic declines in many giraffe populations, this improved understanding of giraffe evolutionary history is relevant for conservation interventions, including reintroductions and reinforcements of existing populations.
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Affiliation(s)
- Laura D Bertola
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Liam Quinn
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kristian Hanghøj
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Renzo F Balboa
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jonas Meisner
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Bøggild
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Xi Wang
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Long Lin
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Casia Nursyifa
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Xiaodong Liu
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Zilong Li
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Mumbi Chege
- Institute of Environmental Sciences (CML), Leiden University, Leiden, The Netherlands; Wildlife Research and Training Institute, Naivasha, Kenya
| | - Yoshan Moodley
- Department of Biological Sciences, University of Venda, Private Bag X5050, Thohoyandou 0950, Republic of South Africa
| | | | - Josiah Kuja
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Mikkel Schubert
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Morris Agaba
- School of Life Sciences and Bioengineering, Nelson Mandela African Institution of Science and Technology, Nelson Mandela Road, Arusha, Tanzania
| | - Cindy G Santander
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Vincent Muwanika
- College of Agricultural and Environmental Sciences, Makerere University, P.O. Box 7062, Kampala, Uganda
| | - Charles Masembe
- College of Natural Sciences, Makerere University, P O. Box 7062, Kampala, Uganda
| | - Hans R Siegismund
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Ida Moltke
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | | | - Rasmus Heller
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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12
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Opatova V, Bourguignon K, Bond JE. Species delimitation with limited sampling: An example from rare trapdoor spider genus Cyclocosmia (Mygalomorphae, Halonoproctidae). Mol Ecol Resour 2024; 24:e13894. [PMID: 37971187 DOI: 10.1111/1755-0998.13894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 10/24/2023] [Accepted: 10/31/2023] [Indexed: 11/19/2023]
Abstract
The outcome of species delimitation depends on many factors, including conceptual framework, study design, data availability, methodology employed and subjective decision making. Obtaining sufficient taxon sampling in endangered or rare taxa might be difficult, particularly when non-lethal tissue collection cannot be utilized. The need to avoid overexploitation of the natural populations may thus limit methodological framework available for downstream data analyses and bias the results. We test species boundaries in rare North American trapdoor spider genus Cyclocosmia Ausserer (1871) inhabiting the Southern Coastal Plain biodiversity hotspot with the use of genomic data and two multispecies coalescent model methods. We evaluate the performance of each methodology within a limited sampling framework. To mitigate the risk of species over splitting, common in taxa with highly structured populations, we subsequently implement a species validation step via genealogical diversification index (gdi), which accounts for both genetic isolation and gene flow. We delimited eight geographically restricted lineages within sampled North American Cyclocosmia, suggesting that major river drainages in the region are likely barriers to dispersal. Our results suggest that utilizing BPP in the species discovery step might be a good option for datasets comprising hundreds of loci, but fewer individuals, which may be a common scenario for rare taxa. However, we also show that such results should be validated via gdi, in order to avoid over splitting.
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Affiliation(s)
- Vera Opatova
- Department of Zoology, Faculty of Sciences, Charles University, Prague 2, Czech Republic
| | - Kellie Bourguignon
- Department of Biological Sciences, Auburn University, Auburn, Alabama, USA
| | - Jason E Bond
- Department of Entomology and Nematology, University of California, Davis, California, USA
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13
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Gašparová K, Fennessy J, Moussa Zabeirou AR, Abagana AL, Rabeil T, Brandlová K. Saving the Last West African Giraffe Population: A Review of Its Conservation Status and Management. Animals (Basel) 2024; 14:702. [PMID: 38473087 DOI: 10.3390/ani14050702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/12/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024] Open
Abstract
The West African giraffe (Giraffa camelopardalis peralta) was historically spread across much of the Sudano-Sahelian zone but is now restricted to Niger. Several factors resulted in their dramatic decline during the late 20th century. In 1996, only 49 individuals remained, concentrated in the 'Giraffe Zone'. Conservation activities implemented by the Government of Niger, supported by local communities and NGOs, facilitated their population numbers to increase. This review summarizes past and present conservation activities and evaluates their impact to advise and prioritize future conservation actions for the West African giraffe. The long-term conservation of the West African giraffe is highly dependent on the local communities who live alongside them, as well as supplementary support from local and international partners. Recent conservation initiatives range from community-based monitoring to the fitting of GPS satellite tags to better understand their habitat use, spatial movements to expansion areas, and environmental education to the establishment of the first satellite population of West African giraffe in Gadabedji Biosphere Reserve, the latter serving as a flagship for the future restoration of large mammal populations in West Africa. The integration of modern technologies and methods will hopefully provide better-quality data, improved spatial analyses, and greater understanding of giraffe ecology to inform the long-term management of West African giraffe.
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Affiliation(s)
- Kateřina Gašparová
- Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Prague, Czech Republic
| | - Julian Fennessy
- Giraffe Conservation Foundation, Windhoek 10009, Namibia
- School of Biology and Environmental Science, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Abdoul Razack Moussa Zabeirou
- Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Prague, Czech Republic
- Giraffe Conservation Foundation, Windhoek 10009, Namibia
| | - Ali Laouel Abagana
- Project Sustainable Management of Biodiversity, Ministry of Environment and Sustainable Development, Niamey 920001, Niger
| | - Thomas Rabeil
- Wild Africa Conservation, Kouara Kano, BP32, Niamey 920001, Niger
| | - Karolína Brandlová
- Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Prague, Czech Republic
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14
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Moran PA, Bosse M, Mariën J, Halfwerk W. Genomic footprints of (pre) colonialism: Population declines in urban and forest túngara frogs coincident with historical human activity. Mol Ecol 2024; 33:e17258. [PMID: 38153193 DOI: 10.1111/mec.17258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 11/21/2023] [Accepted: 12/06/2023] [Indexed: 12/29/2023]
Abstract
Urbanisation is rapidly altering ecosystems, leading to profound biodiversity loss. To mitigate these effects, we need a better understanding of how urbanisation impacts dispersal and reproduction. Two contrasting population demographic models have been proposed that predict that urbanisation either promotes (facilitation model) or constrains (fragmentation model) gene flow and genetic diversity. Which of these models prevails likely depends on the strength of selection on specific phenotypic traits that influence dispersal, survival, or reproduction. Here, we a priori examined the genomic impact of urbanisation on the Neotropical túngara frog (Engystomops pustulosus), a species known to adapt its reproductive traits to urban selective pressures. Using whole-genome resequencing for multiple urban and forest populations we examined genomic diversity, population connectivity and demographic history. Contrary to both the fragmentation and facilitation models, urban populations did not exhibit substantial changes in genomic diversity or differentiation compared with forest populations, and genomic variation was best explained by geographic distance rather than environmental factors. Adopting an a posteriori approach, we additionally found both urban and forest populations to have undergone population declines. The timing of these declines appears to coincide with extensive human activity around the Panama Canal during the last few centuries rather than recent urbanisation. Our study highlights the long-lasting legacy of past anthropogenic disturbances in the genome and the importance of considering the historical context in urban evolution studies as anthropogenic effects may be extensive and impact nonurban areas on both recent and older timescales.
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Affiliation(s)
- Peter A Moran
- A-LIFE, Section Ecology & Evolution, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Mirte Bosse
- A-LIFE, Section Ecology & Evolution, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands
| | - Janine Mariën
- A-LIFE, Section Ecology & Evolution, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Wouter Halfwerk
- A-LIFE, Section Ecology & Evolution, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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15
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Balboa RF, Bertola LD, Brüniche-Olsen A, Rasmussen MS, Liu X, Besnard G, Salmona J, Santander CG, He S, Zinner D, Pedrono M, Muwanika V, Masembe C, Schubert M, Kuja J, Quinn L, Garcia-Erill G, Stæger FF, Rakotoarivony R, Henrique M, Lin L, Wang X, Heaton MP, Smith TPL, Hanghøj K, Sinding MHS, Atickem A, Chikhi L, Roos C, Gaubert P, Siegismund HR, Moltke I, Albrechtsen A, Heller R. African bushpigs exhibit porous species boundaries and appeared in Madagascar concurrently with human arrival. Nat Commun 2024; 15:172. [PMID: 38172616 PMCID: PMC10764920 DOI: 10.1038/s41467-023-44105-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 11/30/2023] [Indexed: 01/05/2024] Open
Abstract
Several African mammals exhibit a phylogeographic pattern where closely related taxa are split between West/Central and East/Southern Africa, but their evolutionary relationships and histories remain controversial. Bushpigs (Potamochoerus larvatus) and red river hogs (P. porcus) are recognised as separate species due to morphological distinctions, a perceived lack of interbreeding at contact, and putatively old divergence times, but historically, they were considered conspecific. Moreover, the presence of Malagasy bushpigs as the sole large terrestrial mammal shared with the African mainland raises intriguing questions about its origin and arrival in Madagascar. Analyses of 67 whole genomes revealed a genetic continuum between the two species, with putative signatures of historical gene flow, variable FST values, and a recent divergence time (<500,000 years). Thus, our study challenges key arguments for splitting Potamochoerus into two species and suggests their speciation might be incomplete. Our findings also indicate that Malagasy bushpigs diverged from southern African populations and underwent a limited bottleneck 1000-5000 years ago, concurrent with human arrival in Madagascar. These results shed light on the evolutionary history of an iconic and widespread African mammal and provide insight into the longstanding biogeographic puzzle surrounding the bushpig's presence in Madagascar.
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Affiliation(s)
- Renzo F Balboa
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Laura D Bertola
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Xiaodong Liu
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Guillaume Besnard
- Laboratoire Evolution et Diversité Biologique (EDB), UMR 5174, CNRS, IRD, Université Toulouse Paul Sabatier, 31062, Toulouse, France
| | - Jordi Salmona
- Laboratoire Evolution et Diversité Biologique (EDB), UMR 5174, CNRS, IRD, Université Toulouse Paul Sabatier, 31062, Toulouse, France
| | - Cindy G Santander
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Shixu He
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Dietmar Zinner
- Cognitive Ecology Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077, Göttingen, Germany
- Department of Primate Cognition, Georg-August-Universität Göttingen, 37077, Göttingen, Germany
- Leibniz Science Campus Primate Cognition, 37077, Göttingen, Germany
| | - Miguel Pedrono
- UMR ASTRE, CIRAD, Campus International de Baillarguet, Montpellier, France
| | - Vincent Muwanika
- College of Agricultural and Environmental Sciences, Makerere University, Kampala, Uganda
| | - Charles Masembe
- College of Natural Sciences, Makerere University, Kampala, Uganda
| | - Mikkel Schubert
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Josiah Kuja
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Liam Quinn
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | | | - Long Lin
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Xi Wang
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Kristian Hanghøj
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Anagaw Atickem
- Department of Zoological Sciences, Addis Ababa University, PO Box 1176, Addis Ababa, Ethiopia
| | - Lounès Chikhi
- Laboratoire Evolution et Diversité Biologique (EDB), UMR 5174, CNRS, IRD, Université Toulouse Paul Sabatier, 31062, Toulouse, France
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077, Göttingen, Germany
| | - Philippe Gaubert
- Laboratoire Evolution et Diversité Biologique (EDB), UMR 5174, CNRS, IRD, Université Toulouse Paul Sabatier, 31062, Toulouse, France
- Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR), Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Porto, Portugal
| | - Hans R Siegismund
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Ida Moltke
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | | | - Rasmus Heller
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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16
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Coimbra RTF, Winter S, Muneza A, Fennessy S, Otiende M, Mijele D, Masiaine S, Stacy-Dawes J, Fennessy J, Janke A. Genomic analysis reveals limited hybridization among three giraffe species in Kenya. BMC Biol 2023; 21:215. [PMID: 37833744 PMCID: PMC10576358 DOI: 10.1186/s12915-023-01722-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 10/02/2023] [Indexed: 10/15/2023] Open
Abstract
BACKGROUND In the speciation continuum, the strength of reproductive isolation varies, and species boundaries are blurred by gene flow. Interbreeding among giraffe (Giraffa spp.) in captivity is known, and anecdotal reports of natural hybrids exist. In Kenya, Nubian (G. camelopardalis camelopardalis), reticulated (G. reticulata), and Masai giraffe sensu stricto (G. tippelskirchi tippelskirchi) are parapatric, and thus, the country might be a melting pot for these taxa. We analyzed 128 genomes of wild giraffe, 113 newly sequenced, representing these three taxa. RESULTS We found varying levels of Nubian ancestry in 13 reticulated giraffe sampled across the Laikipia Plateau most likely reflecting historical gene flow between these two lineages. Although comparatively weaker signs of ancestral gene flow and potential mitochondrial introgression from reticulated into Masai giraffe were also detected, estimated admixture levels between these two lineages are minimal. Importantly, contemporary gene flow between East African giraffe lineages was not statistically significant. Effective population sizes have declined since the Late Pleistocene, more severely for Nubian and reticulated giraffe. CONCLUSIONS Despite historically hybridizing, these three giraffe lineages have maintained their overall genomic integrity suggesting effective reproductive isolation, consistent with the previous classification of giraffe into four species.
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Affiliation(s)
- Raphael T F Coimbra
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt, Germany.
- Institute for Ecology, Evolution and Diversity, Goethe University, Frankfurt, Germany.
| | - Sven Winter
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt, Germany
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Vienna, Austria
| | | | | | | | | | | | | | - Julian Fennessy
- Giraffe Conservation Foundation, Windhoek, Namibia
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Axel Janke
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt, Germany.
- Institute for Ecology, Evolution and Diversity, Goethe University, Frankfurt, Germany.
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt, Germany.
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17
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Gu TT, Wu H, Yang F, Gaubert P, Heighton SP, Fu Y, Liu K, Luo SJ, Zhang HR, Hu JY, Yu L. Genomic analysis reveals a cryptic pangolin species. Proc Natl Acad Sci U S A 2023; 120:e2304096120. [PMID: 37748052 PMCID: PMC10556634 DOI: 10.1073/pnas.2304096120] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 07/26/2023] [Indexed: 09/27/2023] Open
Abstract
Eight extant species of pangolins are currently recognized. Recent studies found that two mitochondrial haplotypes identified in confiscations in Hong Kong could not be assigned to any known pangolin species, implying the existence of a species. Here, we report that two additional mitochondrial haplotypes identified in independent confiscations from Yunnan align with the putative species haplotypes supporting the existence of this mysterious species/population. To verify the new species scenario we performed a comprehensive analysis of scale characteristics and 138 whole genomes representing all recognized pangolin species and the cryptic new species, 98 of which were generated here. Our morphometric results clearly attributed this cryptic species to Asian pangolins (Manis sp.) and the genomic data provide robust and compelling evidence that it is a pangolin species distinct from those recognized previously, which separated from the Philippine pangolin and Malayan pangolin over 5 Mya. Our study provides a solid genomic basis for its formal recognition as the ninth pangolin species or the fifth Asian one, supporting a new taxonomic classification of pangolins. The effects of glacial climate changes and recent anthropogenic activities driven by illegal trade are inferred to have caused its population decline with the genomic signatures showing low genetic diversity, a high level of inbreeding, and high genetic load. Our finding greatly expands current knowledge of pangolin diversity and evolution and has vital implications for conservation efforts to prevent the extinction of this enigmatic and endangered species from the wild.
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Affiliation(s)
- Tong-Tong Gu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming650500, China
| | - Hong Wu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming650500, China
| | - Feng Yang
- Kadoorie Farm and Botanic Garden, Tai Po, Hong Kong Special Administrative Region999077, China
| | - Philippe Gaubert
- Laboratoire Evolution et Diversité Biologique, Université Toulouse III–Paul Sabatier, 31062Toulouse Cedex 9, France
- Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Porto4450-208, Portugal
| | - Sean P. Heighton
- Laboratoire Evolution et Diversité Biologique, Université Toulouse III–Paul Sabatier, 31062Toulouse Cedex 9, France
| | - Yeyizhou Fu
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing100871, China
| | - Ke Liu
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing100871, China
| | - Shu-Jin Luo
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing100871, China
| | - Hua-Rong Zhang
- Kadoorie Farm and Botanic Garden, Tai Po, Hong Kong Special Administrative Region999077, China
| | - Jing-Yang Hu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming650500, China
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming650500, China
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18
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Jabin G, Joshi BD, Wang MS, Mukherjee T, Dolker S, Wang S, Chandra K, Chinnadurai V, Sharma LK, Thakur M. Mid-Pleistocene Transitions Forced Himalayan ibex to Evolve Independently after Split into an Allopatric Refugium. BIOLOGY 2023; 12:1097. [PMID: 37626983 PMCID: PMC10451794 DOI: 10.3390/biology12081097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 08/27/2023]
Abstract
Pleistocene glaciations had profound impact on the spatial distribution and genetic makeup of species in temperate ecosystems. While the glacial period trapped several species into glacial refugia and caused abrupt decline in large populations, the interglacial period facilitated population growth and range expansion leading to allopatric speciation. Here, we analyzed 40 genomes of four species of ibex and found that Himalayan ibex in the Pamir Mountains evolved independently after splitting from its main range about 0.1 mya following the Pleistocene species pump concept. Demographic trajectories showed Himalayan ibex experienced two historic bottlenecks, one each c. 0.8-0.5 mya and c. 50-30 kya, with an intermediate large population expansion c. 0.2-0.16 mya coinciding with Mid-Pleistocene Transitions. We substantiate with multi-dimensional evidence that Himalayan ibex is an evolutionary distinct phylogenetic species of Siberian ibex which need to be prioritized as Capra himalayensis for taxonomic revision and conservation planning at a regional and global scale.
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Affiliation(s)
- Gul Jabin
- Zoological Survey of India, Kolkata 700053, India
- Department of Zoology, University of Calcutta, Kolkata 700019, India
| | | | - Ming-Shan Wang
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | | | - Stanzin Dolker
- Zoological Survey of India, Kolkata 700053, India
- Department of Zoology, University of Calcutta, Kolkata 700019, India
| | - Sheng Wang
- Kunming Institute of Zoology, Kunming 650223, China
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19
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Ferguson S, Kaitho T, Lekolool I, Muneza A, Michelmore J, McFeeters L, Wells E, Ahl K, Hoffman R, Brown M, Fennessy S, Fennessy J. Congenital and Neoplastic Cranial Deformities in Wild Giraffe (Giraffa spp.). J Wildl Dis 2023; 59:472-478. [PMID: 37269548 DOI: 10.7589/jwd-d-22-00102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 02/07/2023] [Indexed: 06/05/2023]
Abstract
Congenital deformities and neoplasia are poorly documented in wildlife, owing to the difficulty of detection in wild populations. Congenital deformities may lead to premature mortality, thus reducing the chances of thorough documentation. Importantly, neoplasia diagnoses depend on either sampling suspicious lesions from living individuals or access to fresh, undisturbed carcasses, which can prove challenging. We describe five cases of suspected congenital cranial deformities (midfacial cleft, wry nose, and brachygnathia inferior) and two possible cases of cranial neoplasia (orbital bone mass and a soft tissue mass) opportunistically observed in wild giraffe (Giraffa spp.) across their range in Africa. Although cases are largely limited to subjective description because physical examination is often not possible, it is critical to document such observations to help identify and track potential health concerns in wild giraffe populations.
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Affiliation(s)
- Sara Ferguson
- Giraffe Conservation Foundation, PO Box 86099 Eros, Windhoek, Namibia
| | - Titus Kaitho
- Kenya Wildlife Service, Veterinary Services Department, PO Box 40241-0100 Nairobi, Kenya
| | - Isaac Lekolool
- Kenya Wildlife Service, Veterinary Services Department, PO Box 40241-0100 Nairobi, Kenya
| | - Arthur Muneza
- Giraffe Conservation Foundation, PO Box 86099 Eros, Windhoek, Namibia
| | - Jordan Michelmore
- Giraffe Conservation Foundation, PO Box 86099 Eros, Windhoek, Namibia
| | - Lachlan McFeeters
- Giraffe Conservation Foundation, PO Box 86099 Eros, Windhoek, Namibia
| | - Emma Wells
- Giraffe Conservation Foundation, PO Box 86099 Eros, Windhoek, Namibia
| | - Katherine Ahl
- Giraffe Conservation Foundation, PO Box 86099 Eros, Windhoek, Namibia
| | - Rigardt Hoffman
- Giraffe Conservation Foundation, PO Box 86099 Eros, Windhoek, Namibia
| | - Michael Brown
- Giraffe Conservation Foundation, PO Box 86099 Eros, Windhoek, Namibia
- Smithsonian National Zoo and Conservation Biology Institute, Conservation Ecology Center, 1500 Remount Rd., Front Royal, Virginia 22630, USA
| | | | - Julian Fennessy
- Giraffe Conservation Foundation, PO Box 86099 Eros, Windhoek, Namibia
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20
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Brown MB, Fennessy JT, Crego RD, Fleming CH, Alves J, Brandlová K, Fennessy S, Ferguson S, Hauptfleisch M, Hejcmanova P, Hoffman R, Leimgruber P, Masiaine S, McQualter K, Mueller T, Muller B, Muneza A, O'Connor D, Olivier AJ, Rabeil T, Seager S, Stacy-Dawes J, van Schalkwyk L, Stabach J. Ranging behaviours across ecological and anthropogenic disturbance gradients: a pan-African perspective of giraffe ( Giraffa spp .) space use. Proc Biol Sci 2023; 290:20230912. [PMID: 37357852 PMCID: PMC10291724 DOI: 10.1098/rspb.2023.0912] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 05/26/2023] [Indexed: 06/27/2023] Open
Abstract
Animal movement behaviours are shaped by diverse factors, including resource availability and human impacts on the landscape. We generated home range estimates and daily movement rate estimates for 149 giraffe (Giraffa spp.) from all four species across Africa to evaluate the effects of environmental productivity and anthropogenic disturbance on space use. Using the continuous time movement modelling framework and a novel application of mixed effects meta-regression, we summarized overall giraffe space use and tested for the effects of resource availability and human impact on 95% autocorrelated kernel density estimate (AKDE) size and daily movement. The mean 95% AKDE was 359.9 km2 and the mean daily movement was 14.2 km, both with marginally significant differences across species. We found significant negative effects of resource availability, and significant positive effects of resource heterogeneity and protected area overlap on 95% AKDE size. There were significant negative effects of overall anthropogenic disturbance and positive effects of the heterogeneity of anthropogenic disturbance on daily movements and 95% AKDE size. Our results provide unique insights into the interactive effects of resource availability and anthropogenic development on the movements of a large-bodied browser and highlight the potential impacts of rapidly changing landscapes on animal space-use patterns.
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Affiliation(s)
- Michael Butler Brown
- Giraffe Conservation Foundation, PO Box 86099, Eros, Windhoek, Namibia
- Smithsonian National Zoo and Conservation Biology Institute, Conservation Ecology Center, 1500 Remount Rd, Front Royal, VA 22630, USA
| | | | - Ramiro D. Crego
- Smithsonian National Zoo and Conservation Biology Institute, Conservation Ecology Center, 1500 Remount Rd, Front Royal, VA 22630, USA
| | - Christen H. Fleming
- Smithsonian National Zoo and Conservation Biology Institute, Conservation Ecology Center, 1500 Remount Rd, Front Royal, VA 22630, USA
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Joel Alves
- Wildscapes Veterinary & Conservation Services, Hoedspruit, South Africa
| | - Karolina Brandlová
- Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamycka 129, 16500 Prague, Czechia
| | | | - Sara Ferguson
- Giraffe Conservation Foundation, PO Box 86099, Eros, Windhoek, Namibia
| | - Morgan Hauptfleisch
- Biodiversity Research Centre, Namibia University of Science and Technology, 8 Johann Albrecht Street, Windhoek, Namibia
| | - Pavla Hejcmanova
- Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamycka 129, 16500 Prague, Czechia
| | - Rigardt Hoffman
- Giraffe Conservation Foundation, PO Box 86099, Eros, Windhoek, Namibia
| | - Peter Leimgruber
- Smithsonian National Zoo and Conservation Biology Institute, Conservation Ecology Center, 1500 Remount Rd, Front Royal, VA 22630, USA
| | - Symon Masiaine
- Conservation Science & Wildlife Health, San Diego Zoo Wildlife Alliance, San Diego, CA, USA
| | - Kylie McQualter
- Centre for Ecosystem Studies, School of Biological Earth and Environmental Sciences, University of New South Wales, Kensington, NSW, 2052, Australia
| | - Thomas Mueller
- Senckenberg Biodiversity and Climate Research Centre and Department of Biological Science, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Ben Muller
- Wildscapes Veterinary & Conservation Services, Hoedspruit, South Africa
| | - Arthur Muneza
- Giraffe Conservation Foundation, PO Box 86099, Eros, Windhoek, Namibia
| | - David O'Connor
- Smithsonian National Zoo and Conservation Biology Institute, Conservation Ecology Center, 1500 Remount Rd, Front Royal, VA 22630, USA
- Senckenberg Biodiversity and Climate Research Centre and Department of Biological Science, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Adriaan Jacobus Olivier
- Department of Conservation Ecology and Entomology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | | | | | - Jenna Stacy-Dawes
- Conservation Science & Wildlife Health, San Diego Zoo Wildlife Alliance, San Diego, CA, USA
| | - Louis van Schalkwyk
- Office of the State Veterinarian, Department of Agriculture, Land Reform and Rural Development, Kruger National Park, Skukuza, South Africa
- Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa
| | - Jared Stabach
- Smithsonian National Zoo and Conservation Biology Institute, Conservation Ecology Center, 1500 Remount Rd, Front Royal, VA 22630, USA
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21
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Sørensen EF, Harris RA, Zhang L, Raveendran M, Kuderna LFK, Walker JA, Storer JM, Kuhlwilm M, Fontsere C, Seshadri L, Bergey CM, Burrell AS, Bergman J, Phillips-Conroy JE, Shiferaw F, Chiou KL, Chuma IS, Keyyu JD, Fischer J, Gingras MC, Salvi S, Doddapaneni H, Schierup MH, Batzer MA, Jolly CJ, Knauf S, Zinner D, Farh KKH, Marques-Bonet T, Munch K, Roos C, Rogers J. Genome-wide coancestry reveals details of ancient and recent male-driven reticulation in baboons. Science 2023; 380:eabn8153. [PMID: 37262153 DOI: 10.1126/science.abn8153] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 09/27/2022] [Indexed: 06/03/2023]
Abstract
Baboons (genus Papio) are a morphologically and behaviorally diverse clade of catarrhine monkeys that have experienced hybridization between phenotypically and genetically distinct phylogenetic species. We used high-coverage whole-genome sequences from 225 wild baboons representing 19 geographic localities to investigate population genomics and interspecies gene flow. Our analyses provide an expanded picture of evolutionary reticulation among species and reveal patterns of population structure within and among species, including differential admixture among conspecific populations. We describe the first example of a baboon population with a genetic composition that is derived from three distinct lineages. The results reveal processes, both ancient and recent, that produced the observed mismatch between phylogenetic relationships based on matrilineal, patrilineal, and biparental inheritance. We also identified several candidate genes that may contribute to species-specific phenotypes.
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Affiliation(s)
- Erik F Sørensen
- Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark
| | - R Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Liye Zhang
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lukas F K Kuderna
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Artificial Intelligence Lab, Illumina Inc., San Diego, CA 92122, USA
| | - Jerilyn A Walker
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | | | - Martin Kuhlwilm
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, 1030 Vienna, Austria
| | - Claudia Fontsere
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Lakshmi Seshadri
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
| | - Christina M Bergey
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Andrew S Burrell
- Department of Anthropology, New York University, New York, NY 10003, USA
| | - Juraj Bergman
- Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark
- Section for Ecoinformatics and Biodiversity, Department of Biology, Aarhus University, 8000 Aarhus C, Denmark
| | - Jane E Phillips-Conroy
- Department of Neuroscience, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
- Department of Anthropology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | | | - Kenneth L Chiou
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85281, USA
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | | | | | - Julia Fischer
- Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
- Department of Primate Cognition, Georg-August-Universität Göttingen, 37077 Göttingen, Germany
- Leibniz ScienceCampus Primate Cognition, 37077 Göttingen, Germany
| | - Marie-Claude Gingras
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sejal Salvi
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Harshavardhan Doddapaneni
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mikkel H Schierup
- Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark
| | - Mark A Batzer
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Clifford J Jolly
- Department of Anthropology, New York University, New York, NY 10003, USA
| | - Sascha Knauf
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald-Insel Riems, Germany
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
- Department of Primate Cognition, Georg-August-Universität Göttingen, 37077 Göttingen, Germany
- Leibniz ScienceCampus Primate Cognition, 37077 Göttingen, Germany
| | - Kyle K-H Farh
- Artificial Intelligence Lab, Illumina Inc., San Diego, CA 92122, USA
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluis Companys, 23, 08010 Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Baldiri i Reixac 4, 08028 Barcelona, Spain
- Institut Catala de Paleontologia Miquel Crusafont, Universitat Autonoma de Barcelona, Edifici ICTA-ICP, cl Columnes s/n, 08193 Cerdanyola del Valles, Barcelona, Spain
| | - Kasper Munch
- Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark
| | - Christian Roos
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
- Gene Bank of Primates, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
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22
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Lohay GG, Lee DE, Wu‐Cavener L, Pearce DL, Hou X, Bond ML, Cavener DR. Genetic evidence of population subdivision among Masai giraffes separated by the Gregory Rift Valley in Tanzania. Ecol Evol 2023; 13:e10160. [PMID: 37313272 PMCID: PMC10259769 DOI: 10.1002/ece3.10160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 05/17/2023] [Accepted: 05/22/2023] [Indexed: 06/15/2023] Open
Abstract
The Masai giraffe has experienced a population decline from 70,000 to 35,000 in the past three decades and was declared an endangered subspecies by the IUCN in 2019. The remaining number of Masai giraffe are geographically separated by the steep cliffs of the Gregory Rift escarpments (GRE) in Tanzania and Kenya dividing them into two populations, one west and one east of the GRE. The cliffs of the GRE are formidable barriers to east-west dispersal and gene flow and the few remaining natural corridors through the GRE are occupied by human settlements. To assess the impact of the GRE on Masai giraffe gene flow, we examined whole genome sequences of nuclear and mitochondrial DNA (mtDNA) variation in populations located east (Tarangire ecosystem) and west (Serengeti ecosystem) of the GRE in northern Tanzania. Evidence from mtDNA variation, which measures female-mediated gene flow, suggests that females have not migrated across the GRE between populations in the Serengeti and Tarangire ecosystems in the past ~289,000 years. The analysis of nuclear DNA variation compared to mtDNA DNA variation suggests that male-mediated gene flow across the GRE has occurred more recently but stopped a few thousand years ago. Our findings show that Masai giraffes are split into two populations and fulfill the criteria for designation as distinct evolutionary significant units (ESUs), which we denote as western Masai giraffe and eastern Masai giraffe. While establishing giraffe dispersal corridors across the GRE is impractical, conservation efforts should be focused on maintaining connectivity among populations within each of these two populations. The importance of these efforts is heightened by our finding that the inbreeding coefficients are high in some of these Masai giraffe populations, which could result in inbreeding depression in the small and fragmented populations.
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Affiliation(s)
- George G. Lohay
- Biology DepartmentPenn State UniversityUniversity ParkPennsylvaniaUSA
- Research Innovation for the Serengeti Ecosystem, Grumeti FundMaraTanzania
| | - Derek E. Lee
- Biology DepartmentPenn State UniversityUniversity ParkPennsylvaniaUSA
- Wild Nature InstituteConcordNew HampshireUSA
| | - Lan Wu‐Cavener
- Biology DepartmentPenn State UniversityUniversity ParkPennsylvaniaUSA
| | - David L. Pearce
- Department of Ecosystem Science and ManagementPenn State UniversityUniversity ParkPennsylvaniaUSA
| | - Xiaoyi Hou
- Biology DepartmentPenn State UniversityUniversity ParkPennsylvaniaUSA
| | - Monica L. Bond
- Biology DepartmentPenn State UniversityUniversity ParkPennsylvaniaUSA
- Wild Nature InstituteConcordNew HampshireUSA
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurichSwitzerland
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23
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Sørensen EF, Harris RA, Zhang L, Raveendran M, Kuderna LFK, Walker JA, Storer JM, Kuhlwilm M, Fontsere C, Seshadri L, Bergey CM, Burrell AS, Bergmann J, Phillips-Conroy JE, Shiferaw F, Chiou KL, Chuma IS, Keyyu JD, Fischer J, Gingras MC, Salvi S, Doddapaneni H, Schierup MH, Batzer MA, Jolly CJ, Knauf S, Zinner D, Farh KKH, Marques-Bonet T, Munch K, Roos C, Rogers J. Genome-wide coancestry reveals details of ancient and recent male-driven reticulation in baboons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.02.539112. [PMID: 37205419 PMCID: PMC10187195 DOI: 10.1101/2023.05.02.539112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Baboons (genus Papio ) are a morphologically and behaviorally diverse clade of catarrhine monkeys that have experienced hybridization between phenotypically and genetically distinct phylogenetic species. We used high coverage whole genome sequences from 225 wild baboons representing 19 geographic localities to investigate population genomics and inter-species gene flow. Our analyses provide an expanded picture of evolutionary reticulation among species and reveal novel patterns of population structure within and among species, including differential admixture among conspecific populations. We describe the first example of a baboon population with a genetic composition that is derived from three distinct lineages. The results reveal processes, both ancient and recent, that produced the observed mismatch between phylogenetic relationships based on matrilineal, patrilineal, and biparental inheritance. We also identified several candidate genes that may contribute to species-specific phenotypes. One-Sentence Summary Genomic data for 225 baboons reveal novel sites of inter-species gene flow and local effects due to differences in admixture.
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24
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Li C, Xiao H, Zhang X, Lin H, Elmer KR, Zhao J. Deep genome-wide divergences among species in White Cloud Mountain minnow Tanichthys albonubes (Cypriniformes: Tanichthyidae) complex: Conservation and species management implications. Mol Phylogenet Evol 2023; 182:107734. [PMID: 36804428 DOI: 10.1016/j.ympev.2023.107734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 02/09/2023] [Accepted: 02/13/2023] [Indexed: 02/17/2023]
Abstract
Identifying cryptic species is important for the assessments of biodiversity. Further, untangling mechanisms underlying the origins of cryptic species can facilitate our understanding of evolutionary processes. Advancements in genomic approaches for non-model systems have offered unprecedented opportunities to investigate these areas. The White Cloud Mountain minnow (Tanichthys albonubes) is a popular freshwater pet fish worldwide but its wild populations in China are critically endangered. Recent research based on a few molecular markers suggested that this species in fact comprised seven cryptic species, of which six were previously unknown. Here, we tested six of these cryptic species and quantified genomic interspecific divergences between species in the T. albonubes complex by analyzing genome-wide restriction site-associated DNA sequencing (RADseq) data generated from 189 individuals sampled from seven populations (including an outgroup congeneric species, T. micagemmae). We found that six cryptic species previously suggested were well supported by RADseq data. The genetic diversity of each species in the T. albonubes complex was low compared with T. micagemmae and the contemporary effective population sizes (Ne) of each cryptic species were small. Phylogenetic analysis showed seven clades with high support values confirmed with Neighbor-Net trees. The pairwise divergences between species in T. albonubes complex were deep and the highly differentiated loci were evenly distributed across the genome. We proposed that the divergence level of T. albonubes complex is at a late stage of cryptic speciation and lacking gene flow. Our findings provide new insights into cryptic speciation and have important implications for conservation and species management of T. albonubes complex.
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Affiliation(s)
- Chao Li
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally Friendly Aquaculture, School of Life Sciences, South China Normal University, Guangzhou, China; Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Han Xiao
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
| | - Xiuxia Zhang
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally Friendly Aquaculture, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Hungdu Lin
- The Affiliated School of National Tainan First Senior High School, Tainan, Taiwan
| | - Kathryn R Elmer
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Jun Zhao
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally Friendly Aquaculture, School of Life Sciences, South China Normal University, Guangzhou, China.
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25
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Schöneberg Y, Winter S, Arribas O, Riccardo Di Nicola M, Master M, Benjamin Owens J, Rovatsos M, Wüster W, Janke A, Fritz U. Genomics reveals broad hybridization in deeply divergent Palearctic grass and water snakes (Natrix spp.). Mol Phylogenet Evol 2023; 184:107787. [PMID: 37080398 DOI: 10.1016/j.ympev.2023.107787] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 04/03/2023] [Accepted: 04/13/2023] [Indexed: 04/22/2023]
Abstract
Understanding speciation is one of the cornerstones of biological diversity research. Currently, speciation is often understood as a continuous process of divergence that continues until genetic or other incompatibilities minimize or prevent interbreeding. The Palearctic snake genus Natrix is an ideal group to study speciation, as it comprises taxa representing distinct stages of the speciation process, ranging from widely interbreeding parapatric taxa through parapatric species with very limited gene flow in narrow hybrid zones to widely sympatric species. To understand the evolution of reproductive isolation through time, we have sequenced the genomes of all five species within this genus and two additional subspecies. We used both long-read and short-read methods to sequence and de-novo-assemble two high-quality genomes (Natrix h. helvetica, Natrix n. natrix) to their 1.7 Gb length with a contig N50 of 4.6 Mbp and 1.5 Mbp, respectively, and used these as references to assemble the remaining short-read-based genomes. Our phylogenomic analyses yielded a well-supported dated phylogeny and evidence for a surprisingly complex history of interspecific gene flow, including between widely sympatric species. Furthermore, evidence for gene flow was also found for currently allopatric species pairs. Genetic exchange among these well-defined, distinct, and several million-year-old reptile species emphasizes that speciation and maintenance of species distinctness can occur despite continued genetic exchange.
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Affiliation(s)
- Yannis Schöneberg
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; Institute for Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Straße 9, 60325 Frankfurt am Main, Germany
| | - Sven Winter
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Savoyenstraße 1, 1160 Vienna, Austria
| | - Oscar Arribas
- IES Castilla, Junta de Castilla, Castilla y León, 42003 Soria, Spain
| | | | - Maya Master
- Molecular Ecology and Evolution at Bangor (MEEB), School of Natural Sciences, Bangor University, Environment Centre Wales, Bangor LL57 2UW, Wales, UK
| | - John Benjamin Owens
- Molecular Ecology and Evolution at Bangor (MEEB), School of Natural Sciences, Bangor University, Environment Centre Wales, Bangor LL57 2UW, Wales, UK
| | - Michail Rovatsos
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, 12844 Praha 2, Czech Republic
| | - Wolfgang Wüster
- Molecular Ecology and Evolution at Bangor (MEEB), School of Natural Sciences, Bangor University, Environment Centre Wales, Bangor LL57 2UW, Wales, UK
| | - Axel Janke
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; Institute for Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Straße 9, 60325 Frankfurt am Main, Germany; LOEWE-Centre for Translational Biodiversity Genomics (TBG), Senckenberg Nature Research Society, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Uwe Fritz
- Senckenberg Dresden, Museum of Zoology, A. B. Meyer Building, 01109 Dresden, Germany.
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Wolf M, Zapf K, Gupta DK, Hiller M, Árnason Ú, Janke A. The genome of the pygmy right whale illuminates the evolution of rorquals. BMC Biol 2023; 21:79. [PMID: 37041515 PMCID: PMC10091562 DOI: 10.1186/s12915-023-01579-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 03/27/2023] [Indexed: 04/13/2023] Open
Abstract
BACKGROUND Baleen whales are a clade of gigantic and highly specialized marine mammals. Their genomes have been used to investigate their complex evolutionary history and to decipher the molecular mechanisms that allowed them to reach these dimensions. However, many unanswered questions remain, especially about the early radiation of rorquals and how cancer resistance interplays with their huge number of cells. The pygmy right whale is the smallest and most elusive among the baleen whales. It reaches only a fraction of the body length compared to its relatives and it is the only living member of an otherwise extinct family. This placement makes the pygmy right whale genome an interesting target to update the complex phylogenetic past of baleen whales, because it splits up an otherwise long branch that leads to the radiation of rorquals. Apart from that, genomic data of this species might help to investigate cancer resistance in large whales, since these mechanisms are not as important for the pygmy right whale as in other giant rorquals and right whales. RESULTS Here, we present a first de novo genome of the species and test its potential in phylogenomics and cancer research. To do so, we constructed a multi-species coalescent tree from fragments of a whole-genome alignment and quantified the amount of introgression in the early evolution of rorquals. Furthermore, a genome-wide comparison of selection rates between large and small-bodied baleen whales revealed a small set of conserved candidate genes with potential connections to cancer resistance. CONCLUSIONS Our results suggest that the evolution of rorquals is best described as a hard polytomy with a rapid radiation and high levels of introgression. The lack of shared positive selected genes between different large-bodied whale species supports a previously proposed convergent evolution of gigantism and hence cancer resistance in baleen whales.
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Affiliation(s)
- Magnus Wolf
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Strasse 14-16, Frankfurt Am Main, Germany
- Institute for Ecology, Evolution and Diversity, Goethe University, Max-Von-Laue-Strasse. 9, Frankfurt Am Main, Germany
| | - Konstantin Zapf
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Strasse 14-16, Frankfurt Am Main, Germany
- Institute for Ecology, Evolution and Diversity, Goethe University, Max-Von-Laue-Strasse. 9, Frankfurt Am Main, Germany
| | - Deepak Kumar Gupta
- LOEWE-Centre for Translational Biodiversity Genomics (TBG), Senckenberg Nature Research Society, Georg-Voigt-Straße 14-16, Frankfurt Am Main, Germany
| | - Michael Hiller
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Strasse 14-16, Frankfurt Am Main, Germany
- LOEWE-Centre for Translational Biodiversity Genomics (TBG), Senckenberg Nature Research Society, Georg-Voigt-Straße 14-16, Frankfurt Am Main, Germany
- Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Max-Von-Laue-Str. 9, Frankfurt Am Main, Germany
| | - Úlfur Árnason
- Department of Clinical Sciences Lund, Lund University, Lund, Sweden
- Department of Neurosurgery, Skane University Hospital in Lund, Lund, Sweden
| | - Axel Janke
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Strasse 14-16, Frankfurt Am Main, Germany
- Institute for Ecology, Evolution and Diversity, Goethe University, Max-Von-Laue-Strasse. 9, Frankfurt Am Main, Germany
- LOEWE-Centre for Translational Biodiversity Genomics (TBG), Senckenberg Nature Research Society, Georg-Voigt-Straße 14-16, Frankfurt Am Main, Germany
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27
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Historical demography and climatic niches of the Natal multimammate mouse (Mastomys natalensis) in the Zambezian region. Mamm Biol 2023. [DOI: 10.1007/s42991-023-00346-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
AbstractThe Natal multimammate mouse (Mastomys natalensis) is the most widespread rodent species in sub-Saharan Africa, often studied as an agricultural pest and reservoir of viruses. Its mitochondrial (Mt) phylogeny revealed six major lineages parapatrically distributed across open habitats of sub-Saharan Africa. In this study we used 1949 sequences of the mitochondrial cytochrome b gene to elaborate on distribution and evolutionary history of three Mt lineages inhabiting the open habitats of the Zambezian region (corresponding roughly to the African savannas south of the Equator). We describe in more detail contact zones between the lineages—their location and extent of co-occurrence within localities—and infer past population trends. The estimates are interpreted in the light of climatic niche models. The lineages underwent reduction in effective population size during the last glacial, but they spread widely after that: two of them after the last glacial maximum and the last one in mid-Holocene. The centers of expansion, i.e., possible long-term savanna refugia, were estimated to lie close to the Eastern Arc Mountains and lakes of the Great African Rift, geomorphological structures likely to have had long-term influence on geographical distribution of the lineages. Environmental niche modeling shows climate could also affect the broad scale distribution of the lineages but is unlikely to explain the narrow width of the contact zones. The intraspecific Mt differentiation of M. natalensis echoes phylogeographic patterns observed in multiple co-distributed mammal species, which suggests the mammal communities in the region are shaped by the same long-term processes.
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Bernstein-Kurtycz LM, Dunham NT, Evenhuis J, Brown MB, Muneza AB, Fennessy J, Dennis PM, Lukas KE. Evaluating the effects of giraffe skin disease and wire snare wounds on the gaits of free-ranging Nubian giraffe. Sci Rep 2023; 13:1959. [PMID: 36737637 PMCID: PMC9898309 DOI: 10.1038/s41598-023-28677-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 01/23/2023] [Indexed: 02/05/2023] Open
Abstract
Giraffe skin disease (GSD), a condition that results in superficial lesions in certain giraffe (Giraffa spp.) populations, has emerged as a potential conservation threat. Preliminary findings suggested that individuals with GSD lesions move with greater difficulty which may in turn reduce their foraging efficiency or make them more vulnerable to predation. A current known threat to some giraffe populations is their mortality associated with entrapment in wire snares, and the morbidity and potential locomotor deficiencies associated with wounds acquired from snares. The goal of our study was to quantify the locomotor kinematics of free-ranging Nubian giraffe (G. camelopardalis camelopardalis) in Murchison Falls National Park (MFNP), Uganda, and compare spatiotemporal limb and neck angle kinematics of healthy giraffe to those of giraffe with GSD lesions, snare wounds, and both GSD lesions and snare wounds. The presence of GSD lesions did not significantly affect spatiotemporal limb kinematic parameters. This finding is potentially because lesions were located primarily on the necks of Nubian giraffe in MFNP. The kinematic parameters of individuals with snare wounds differed from those of healthy individuals, resulting in significantly shorter stride lengths, reduced speed, lower limb phase values, and increased gait asymmetry. Neck angle kinematic parameters did not differ among giraffe categories, which suggests that GSD neck lesions do not impair normal neck movements and range of motion during walking. Overall, MFNP giraffe locomotor patterns are largely conservative between healthy individuals and those with GSD, while individuals with snare wounds showed more discernible kinematic adjustments consistent with unilateral limb injuries. Additional studies are recommended to assess spatiotemporal limb kinematics of giraffe at sites where lesions are found predominantly on the limbs to better assess the potential significance of GSD on their locomotion.
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Affiliation(s)
- L M Bernstein-Kurtycz
- Division of Conservation and Science, Cleveland Metroparks Zoo, 4200 Wildlife Way, Cleveland, OH, 44109, USA.,Department of Biology, Case Western Reserve University, Cleveland, OH, USA.,Little Rock Zoo, Little Rock, AR, USA
| | - N T Dunham
- Division of Conservation and Science, Cleveland Metroparks Zoo, 4200 Wildlife Way, Cleveland, OH, 44109, USA. .,Department of Biology, Case Western Reserve University, Cleveland, OH, USA.
| | - J Evenhuis
- Department of Biology, Case Western Reserve University, Cleveland, OH, USA.,College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - M B Brown
- Giraffe Conservation Foundation, P.O. Box 86099, Eros, Namibia.,Smithsonian National Zoo and Conservation Biology Institute, Front Royal, VA, 22630, USA.,Department of Biological Sciences Program in Ecology, Evolution, Ecosystems, and Society, Dartmouth College, Hanover, NH, USA
| | - A B Muneza
- Giraffe Conservation Foundation, P.O. Box 86099, Eros, Namibia
| | - J Fennessy
- Giraffe Conservation Foundation, P.O. Box 86099, Eros, Namibia
| | - P M Dennis
- Division of Conservation and Science, Cleveland Metroparks Zoo, 4200 Wildlife Way, Cleveland, OH, 44109, USA.,Department of Biology, Case Western Reserve University, Cleveland, OH, USA.,Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH, USA
| | - K E Lukas
- Division of Conservation and Science, Cleveland Metroparks Zoo, 4200 Wildlife Way, Cleveland, OH, 44109, USA.,Department of Biology, Case Western Reserve University, Cleveland, OH, USA
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29
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Lopes GP, Rohe F, Bertuol F, Polo E, Lima IJ, Valsecchi J, Santos TCM, Nash SD, da Silva MNF, Boubli JP, Farias IP, Hrbek T. Taxonomic review of Saguinus mystax (Spix, 1823) (Primates, Callitrichidae), and description of a new species. PeerJ 2023; 11:e14526. [PMID: 36647446 PMCID: PMC9840391 DOI: 10.7717/peerj.14526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 11/15/2022] [Indexed: 01/13/2023] Open
Abstract
Although the Amazon has the greatest diversity of primates, there are still taxonomic uncertainties for many taxa, such as the species of the Saguinus mystax group. The most geographically broadly distributed and phenotypically diverse species in this group is S. mystax, and its phenotypic diversity has been recognized as three subspecies-S. mystax mystax, S. mystax pileatus and S. mystax pluto-with non-overlapping geographic distributions. In this sense, we carried out an extensive field survey in their distribution areas and used a framework of taxonomic hypothesis testing of genomic data combined with an integrative taxonomic decision-making framework to carry out a taxonomic revision of S. mystax. Our tests supported the existence of three lineages/species. The first species corresponds to Saguinus mystax mystax from the left bank of the Juruá River, which was raised to the species level, and we also discovered and described animals from the Juruá-Tefé interfluve previously attributed to S. mystax mystax as a new species. The subspecies S. m. pileatus and S. m. pluto are recognized as a single species, under a new nomenclatural combination. However, given their phenotypic distinction and allopatric distribution, they potentially are a manifestation of an early stage of speciation, and therefore we maintain their subspecific designations.
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Affiliation(s)
- Gerson Paulino Lopes
- Programa em Pós-Graduação em Zoologia, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil
- Grupo de Pesquisa em Ecologia e Conservação de Primatas, Instituto de Desenvolvimento Sustentável Mamirauá, Tefé, Amazonas, Brazil
- Laboratório de Evolução e Genética Animal/Departamento de Genética/Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil
- Grupo de Pesquisa em Ecologia de Vertebrados Terrestres, Instituto de Desenvolvimento Sustentável Mamirauá, Tefé, Amazonas, Brazil
| | - Fábio Rohe
- Laboratório de Evolução e Genética Animal/Departamento de Genética/Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil
- Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
| | - Fabrício Bertuol
- Laboratório de Evolução e Genética Animal/Departamento de Genética/Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil
| | - Erico Polo
- Laboratório de Evolução e Genética Animal/Departamento de Genética/Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil
| | - Ivan Junqueira Lima
- Grupo de Pesquisa em Ecologia de Vertebrados Terrestres, Instituto de Desenvolvimento Sustentável Mamirauá, Tefé, Amazonas, Brazil
- Programa de Pós-Graduação em Ecologia Aplicada, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil
| | - João Valsecchi
- Grupo de Pesquisa em Ecologia e Conservação de Primatas, Instituto de Desenvolvimento Sustentável Mamirauá, Tefé, Amazonas, Brazil
- Grupo de Pesquisa em Ecologia de Vertebrados Terrestres, Instituto de Desenvolvimento Sustentável Mamirauá, Tefé, Amazonas, Brazil
- Rede de Pesquisa em Diversidade, Conservação e Uso da Fauna da Amazônia, Manaus, Amazonas, Brazil
- Comunidad de Manejo de Fauna Silvestre en América Latina, Iquitos, Peru
| | - Tamily Carvalho Melo Santos
- Grupo de Pesquisa em Ecologia de Vertebrados Terrestres, Instituto de Desenvolvimento Sustentável Mamirauá, Tefé, Amazonas, Brazil
| | - Stephen D. Nash
- Department of Anatomical Sciences/Health Sciences Center, Stony Brook University, New York, United States of America
| | | | - Jean P. Boubli
- Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
- School of Science, Engineering and the Environment, University of Salford, Salford, United Kingdom
| | - Izeni Pires Farias
- Programa em Pós-Graduação em Zoologia, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil
- Laboratório de Evolução e Genética Animal/Departamento de Genética/Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil
| | - Tomas Hrbek
- Programa em Pós-Graduação em Zoologia, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil
- Laboratório de Evolução e Genética Animal/Departamento de Genética/Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil
- Department of Biology, Trinity University, San Antonio, Texas, United States
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30
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Armstrong EE, Campana MG, Solari KA, Morgan SR, Ryder OA, Naude VN, Samelius G, Sharma K, Hadly EA, Petrov DA. Genome report: chromosome-level draft assemblies of the snow leopard, African leopard, and tiger (Panthera uncia, Panthera pardus pardus, and Panthera tigris). G3 (BETHESDA, MD.) 2022; 12:jkac277. [PMID: 36250809 PMCID: PMC9713438 DOI: 10.1093/g3journal/jkac277] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 09/14/2022] [Indexed: 04/07/2024]
Abstract
The big cats (genus Panthera) represent some of the most popular and charismatic species on the planet. Although some reference genomes are available for this clade, few are at the chromosome level, inhibiting high-resolution genomic studies. We assembled genomes from 3 members of the genus, the tiger (Panthera tigris), the snow leopard (Panthera uncia), and the African leopard (Panthera pardus pardus), at chromosome or near-chromosome level. We used a combination of short- and long-read technologies, as well as proximity ligation data from Hi-C technology, to achieve high continuity and contiguity for each individual. We hope that these genomes will aid in further evolutionary and conservation research of this iconic group of mammals.
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Affiliation(s)
- Ellie E Armstrong
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Department of Biology, Washington State University, Pullman, WA 99164, USA
| | - Michael G Campana
- Center for Conservation Genomics, Smithsonian’s National Zoological Park and Conservation Biology Institute, Washington, DC 20008, USA
| | | | - Simon R Morgan
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Wildlife ACT Fund Trust, Cape Town 8001, South Africa
| | - Oliver A Ryder
- San Diego Zoo Wildlife Alliance, Beckman Center for Conservation Research, San Diego, CA 92027, USA
| | - Vincent N Naude
- Department of Conservation Ecology and Entomology, University of Stellenbosch, Stellenbosch, 7602, South Africa
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg 2000, South Africa
| | | | - Koustubh Sharma
- Snow Leopard Trust, Seattle, WA 98103, USA
- Nature Conservation Foundation, Mysore 570 017, India
| | | | - Dmitri A Petrov
- Department of Biology, Stanford University, Stanford, CA 94305, USA
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31
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Kasozi H, Linden DW, Roloff GJ, Montgomery RA. Evaluating the prevalence and spatial distribution of giraffes injured by non‐target poaching. J Zool (1987) 2022. [DOI: 10.1111/jzo.13033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- H. Kasozi
- Department of Zoology, Entomology and Fisheries Sciences Makerere University Kampala Uganda
| | - D. W. Linden
- NOAA National Marine Fisheries Service Gloucester MA USA
| | - G. J. Roloff
- Department of Fisheries and Wildlife Michigan State University East Lansing MI USA
| | - R. A. Montgomery
- Wildlife Conservation Research Unit, Department of Zoology University of Oxford Tubney Oxon UK
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32
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Using spot pattern recognition to examine population biology, evolutionary ecology, sociality, and movements of giraffes: a 70-year retrospective. Mamm Biol 2022. [DOI: 10.1007/s42991-022-00261-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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33
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Broekman MJE, Hilbers JP, Huijbregts MAJ, Mueller T, Ali AH, Andrén H, Altmann J, Aronsson M, Attias N, Bartlam‐Brooks HLA, van Beest FM, Belant JL, Beyer DE, Bidner L, Blaum N, Boone RB, Boyce MS, Brown MB, Cagnacci F, Černe R, Chamaillé‐Jammes S, Dejid N, Dekker J, L. J. Desbiez A, Díaz‐Muñoz SL, Fennessy J, Fichtel C, Fischer C, Fisher JT, Fischhoff I, Ford AT, Fryxell JM, Gehr B, Goheen JR, Hauptfleisch M, Hewison AJM, Hering R, Heurich M, Isbell LA, Janssen R, Jeltsch F, Kaczensky P, Kappeler PM, Krofel M, LaPoint S, Latham ADM, Linnell JDC, Markham AC, Mattisson J, Medici EP, de Miranda Mourão G, Van Moorter B, Morato RG, Morellet N, Mysterud A, Mwiu S, Odden J, Olson KA, Ornicāns A, Pagon N, Panzacchi M, Persson J, Petroelje T, Rolandsen CM, Roshier D, Rubenstein DI, Saïd S, Salemgareyev AR, Sawyer H, Schmidt NM, Selva N, Sergiel A, Stabach J, Stacy‐Dawes J, Stewart FEC, Stiegler J, Strand O, Sundaresan S, Svoboda NJ, Ullmann W, Voigt U, Wall J, Wikelski M, Wilmers CC, Zięba F, Zwijacz‐Kozica T, Schipper AM, Tucker MA. Evaluating expert-based habitat suitability information of terrestrial mammals with GPS-tracking data. GLOBAL ECOLOGY AND BIOGEOGRAPHY : A JOURNAL OF MACROECOLOGY 2022; 31:1526-1541. [PMID: 36247232 PMCID: PMC9544534 DOI: 10.1111/geb.13523] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 04/14/2022] [Accepted: 04/19/2022] [Indexed: 06/16/2023]
Abstract
Aim Macroecological studies that require habitat suitability data for many species often derive this information from expert opinion. However, expert-based information is inherently subjective and thus prone to errors. The increasing availability of GPS tracking data offers opportunities to evaluate and supplement expert-based information with detailed empirical evidence. Here, we compared expert-based habitat suitability information from the International Union for Conservation of Nature (IUCN) with habitat suitability information derived from GPS-tracking data of 1,498 individuals from 49 mammal species. Location Worldwide. Time period 1998-2021. Major taxa studied Forty-nine terrestrial mammal species. Methods Using GPS data, we estimated two measures of habitat suitability for each individual animal: proportional habitat use (proportion of GPS locations within a habitat type), and selection ratio (habitat use relative to its availability). For each individual we then evaluated whether the GPS-based habitat suitability measures were in agreement with the IUCN data. To that end, we calculated the probability that the ranking of empirical habitat suitability measures was in agreement with IUCN's classification into suitable, marginal and unsuitable habitat types. Results IUCN habitat suitability data were in accordance with the GPS data (> 95% probability of agreement) for 33 out of 49 species based on proportional habitat use estimates and for 25 out of 49 species based on selection ratios. In addition, 37 and 34 species had a > 50% probability of agreement based on proportional habitat use and selection ratios, respectively. Main conclusions We show how GPS-tracking data can be used to evaluate IUCN habitat suitability data. Our findings indicate that for the majority of species included in this study, it is appropriate to use IUCN habitat suitability data in macroecological studies. Furthermore, we show that GPS-tracking data can be used to identify and prioritize species and habitat types for re-evaluation of IUCN habitat suitability data.
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Affiliation(s)
- Maarten J. E. Broekman
- Department of Environmental ScienceInstitute for Wetland and Water Research, Faculty of Science, Radboud UniversityNijmegenThe Netherlands
| | - Jelle P. Hilbers
- Department of Environmental ScienceInstitute for Wetland and Water Research, Faculty of Science, Radboud UniversityNijmegenThe Netherlands
| | - Mark A. J. Huijbregts
- Department of Environmental ScienceInstitute for Wetland and Water Research, Faculty of Science, Radboud UniversityNijmegenThe Netherlands
| | - Thomas Mueller
- Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für NaturforschungFrankfurt (Main)Germany
- Department of Biological SciencesGoethe UniversityFrankfurt (Main)Germany
| | | | - Henrik Andrén
- Grimsö Wildlife Research Station, Department of EcologySwedish University of Agricultural SciencesRiddarhyttanSweden
| | - Jeanne Altmann
- Department of Ecology and Evolutionary BiologyPrinceton UniversityPrincetonNew JerseyUSA
| | - Malin Aronsson
- Grimsö Wildlife Research Station, Department of EcologySwedish University of Agricultural SciencesRiddarhyttanSweden
- Department of ZoologyStockholm UniversityStockholmSweden
| | - Nina Attias
- Ecology and Conservation Graduate ProgramFederal University of Mato Grosso do SulCampo GrandeMato Grosso do SulBrazil
- Instituto de Conservação de Animais Silvestres (ICAS)Campo GrandeMato Grosso do SulBrazil
| | | | | | - Jerrold L. Belant
- Global Wildlife Conservation CenterState University of New York College of Environmental Science and ForestrySyracuseNew YorkUSA
| | - Dean E. Beyer
- Department of Fisheries and WildlifeMichigan State UniversityEast LansingMichiganUSA
| | - Laura Bidner
- Department of AnthropologyUniversity of CaliforniaDavisCaliforniaUSA
| | - Niels Blaum
- Plant Ecology and Nature ConservationUniversity of PotsdamPotsdamGermany
| | - Randall B. Boone
- Department of Ecosystem Science and SustainabilityColorado State UniversityFort CollinsColoradoUSA
| | - Mark S. Boyce
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
| | - Michael B. Brown
- Giraffe Conservation FoundationErosNamibia
- Conservation Ecology CenterSmithsonian National Zoo and Conservation Biology InstituteFront RoyalVirginiaUSA
| | - Francesca Cagnacci
- Department of Biodiversity and Molecular EcologyResearch and Innovation Centre, Fondazione Edmund MachTrentoItaly
| | - Rok Černe
- Slovenia Forest ServiceLjubljanaSlovenia
| | - Simon Chamaillé‐Jammes
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3MontpellierFrance
| | - Nandintsetseg Dejid
- Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für NaturforschungFrankfurt (Main)Germany
| | | | - Arnaud L. J. Desbiez
- Instituto de Conservação de Animais Silvestres (ICAS)Campo GrandeMato Grosso do SulBrazil
- IPÊ (Instituto de Pesquisas Ecológicas; Institute for Ecological Research)São PauloBrazil
- Royal Zoological Society of Scotland (RZSS)EdinburghUK
| | - Samuel L. Díaz‐Muñoz
- Department of Microbiology and Molecular GeneticsUniversity of CaliforniaDavisCaliforniaUSA
| | | | - Claudia Fichtel
- German Primate Center, Behavioral Ecology and Sociobiology UnitGöttingenGermany
| | - Christina Fischer
- Faunistics and Wildlife Conservation, Department of Agriculture, Ecotrophology, and Landscape DevelopmentAnhalt University of Applied SciencesBernburgGermany
| | - Jason T. Fisher
- School of Environmental StudiesUniversity of VictoriaVictoriaBritish ColumbiaCanada
| | | | - Adam T. Ford
- Department of Biology, Faculty of ScienceUniversity of British ColumbiaKelownaBritish ColumbiaCanada
| | - John M. Fryxell
- Department of Integrative BiologyUniversity of GuelphGuelphOntarioCanada
| | - Benedikt Gehr
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurichSwitzerland
| | - Jacob R. Goheen
- Department of Zoology and PhysiologyUniversity of WyomingLaramieWyomingUSA
| | - Morgan Hauptfleisch
- Department of Agriculture And Natural Resources Sciences, Biodiversity Research CentreNamibia University of Science and TechnologyWindhoekNamibia
| | - A. J. Mark Hewison
- Université de Toulouse, INRAE, CEFSCastanet‐TolosanFrance
- LTSER ZA Pyrénées GaronneAuzeville‐TolosaneFrance
| | - Robert Hering
- Plant Ecology and Nature ConservationUniversity of PotsdamPotsdamGermany
| | - Marco Heurich
- Department of Conservation and ResearchBavarian Forest National ParkGrafenauGermany
- Chair of Wildlife Ecology and ManagementAlbert Ludwigs University of FreiburgFreiburgGermany
- Department of Forestry and Wildlife ManagementInland Norway University of Applied SciencesKoppangNorway
| | - Lynne A. Isbell
- Department of AnthropologyUniversity of CaliforniaDavisCaliforniaUSA
- Animal Behavior Graduate GroupUniversity of CaliforniaDavisCaliforniaUSA
| | | | - Florian Jeltsch
- Plant Ecology and Nature ConservationUniversity of PotsdamPotsdamGermany
| | - Petra Kaczensky
- Department of Forestry and Wildlife ManagementInland Norway University of Applied SciencesKoppangNorway
- Norwegian Institute for Nature ResearchTrondheimNorway
- Research Institute of Wildlife EcologyUniversity of Veterinary Medicine ViennaViennaAustria
| | - Peter M. Kappeler
- German Primate Center, Behavioral Ecology and Sociobiology UnitGöttingenGermany
| | - Miha Krofel
- Department of Forestry and Renewable Forest Resources, Biotechnical FacultyUniversity of LjubljanaLjubljanaSlovenia
| | - Scott LaPoint
- Black Rock ForestCornwallNew YorkUSA
- Lamont‐Doherty Earth ObservatoryColumbia UniversityPalisadesNew YorkUSA
| | - A. David M. Latham
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
- Wildlife Ecology and ManagementManaaki Whenua – Landcare ResearchLincolnNew Zealand
| | - John D. C. Linnell
- Department of Forestry and Wildlife ManagementInland Norway University of Applied SciencesKoppangNorway
- Norwegian Institute for Nature ResearchTrondheimNorway
| | | | | | - Emilia Patricia Medici
- IPÊ (Instituto de Pesquisas Ecológicas; Institute for Ecological Research)São PauloBrazil
- International Union for Conservation of Nature (IUCN) Species Survival Commission (SSC) Tapir Specialist Group (TSG)Campo GrandeMato Grosso do SulBrazil
| | | | | | - Ronaldo G. Morato
- National Research Center for Carnivores ConservationChico Mendes Institute for the Conservation of BiodiversityAtibaiaBrazil
| | - Nicolas Morellet
- Université de Toulouse, INRAE, CEFSCastanet‐TolosanFrance
- LTSER ZA Pyrénées GaronneAuzeville‐TolosaneFrance
| | - Atle Mysterud
- Centre for Ecological and Evolutionary Synthesis, Department of BiosciencesUniversity of OsloOsloNorway
| | - Stephen Mwiu
- Wildlife Research and Training InstituteNaivashaKenya
| | - John Odden
- Norwegian Institute for Nature ResearchOsloNorway
| | - Kirk A. Olson
- Wildlife Conservation Society, Mongolia ProgramUlaanbaatarMongolia
| | - Aivars Ornicāns
- Latvian State Forest Research Institute “Silava”SalaspilsLatvia
| | | | | | - Jens Persson
- Grimsö Wildlife Research Station, Department of EcologySwedish University of Agricultural SciencesRiddarhyttanSweden
| | - Tyler Petroelje
- Global Wildlife Conservation CenterState University of New York College of Environmental Science and ForestrySyracuseNew YorkUSA
| | | | - David Roshier
- Australian Wildlife ConservancySubiacoWestern AustraliaAustralia
| | - Daniel I. Rubenstein
- Department of Ecology and Evolutionary BiologyPrinceton UniversityPrincetonNew JerseyUSA
| | - Sonia Saïd
- Direction de la Recherche et de l'Appui ScientifiqueOffice Français de la BiodiversitéBirieuxFrance
| | - Albert R. Salemgareyev
- Association for the Conservation of Biodiversity of Kazakhstan (ACBK)Nur‐SultanKazakhstan
| | - Hall Sawyer
- Western Ecosystems Technology Inc.LaramieWyomingUSA
| | - Niels Martin Schmidt
- Department of BioscienceAarhus UniversityRoskildeDenmark
- Arctic Research CentreAarhus UniversityAarhusDenmark
| | - Nuria Selva
- Institute of Nature Conservation Polish Academy of SciencesKrakowPoland
| | - Agnieszka Sergiel
- Institute of Nature Conservation Polish Academy of SciencesKrakowPoland
| | - Jared Stabach
- Conservation Ecology CenterSmithsonian National Zoo and Conservation Biology InstituteFront RoyalVirginiaUSA
| | - Jenna Stacy‐Dawes
- Conservation Science and Wildlife HealthSan Diego Zoo Wildlife AllianceEscondidoCaliforniaUSA
| | - Frances E. C. Stewart
- School of Environmental StudiesUniversity of VictoriaVictoriaBritish ColumbiaCanada
- Department of BiologyWilfrid Laurier UniversityWaterlooOntarioCanada
| | - Jonas Stiegler
- Plant Ecology and Nature ConservationUniversity of PotsdamPotsdamGermany
| | - Olav Strand
- Norwegian Institute for Nature ResearchTrondheimNorway
| | | | - Nathan J. Svoboda
- Carnivore Ecology Laboratory, Forest and Wildlife Research CenterMississippi State UniversityMississippi StateMississippiUSA
- Alaska Department of Fish and GameKodiakAlaskaUSA
| | - Wiebke Ullmann
- Plant Ecology and Nature ConservationUniversity of PotsdamPotsdamGermany
| | - Ulrich Voigt
- Institute for Terrestrial and Aquatic Wildlife ResearchUniversity of Veterinary Medicine Hannover FoundationHannoverGermany
| | | | - Martin Wikelski
- Department of MigrationMax Planck Institute of Animal BehaviorRadolfzellGermany
- Centre for the Advanced Study of Collective BehaviourUniversity of KonstanzConstanceGermany
| | - Christopher C. Wilmers
- Center for Integrated Spatial Research, Environmental Studies DepartmentUniversity of CaliforniaSanta CruzCaliforniaUSA
| | | | | | - Aafke M. Schipper
- Department of Environmental ScienceInstitute for Wetland and Water Research, Faculty of Science, Radboud UniversityNijmegenThe Netherlands
- PBL Netherlands Environmental Assessment AgencyThe HagueThe Netherlands
| | - Marlee A. Tucker
- Department of Environmental ScienceInstitute for Wetland and Water Research, Faculty of Science, Radboud UniversityNijmegenThe Netherlands
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Winter S, Coimbra RTF, Helsen P, Janke A. A chromosome-scale genome assembly of the okapi (Okapia johnstoni). J Hered 2022; 113:568-576. [PMID: 35788365 PMCID: PMC9584810 DOI: 10.1093/jhered/esac033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 06/30/2022] [Indexed: 12/05/2022] Open
Abstract
The okapi (Okapia johnstoni), or forest giraffe, is the only species in its genus and the only extant sister group of the giraffe within the family Giraffidae. The species is one of the remaining large vertebrates surrounded by mystery because of its elusive behavior as well as the armed conflicts in the region where it occurs, making it difficult to study. Deforestation puts the okapi under constant anthropogenic pressure, and it is currently listed as “Endangered” on the IUCN Red List. Here, we present the first annotated de novo okapi genome assembly based on PacBio continuous long reads, polished with short reads, and anchored into chromosome-scale scaffolds using Hi-C proximity ligation sequencing. The final assembly (TBG_Okapi_asm_v1) has a length of 2.39 Gbp, of which 98% are represented by 28 scaffolds > 3.9 Mbp. The contig N50 of 61 Mbp and scaffold N50 of 102 Mbp, together with a BUSCO score of 94.7%, and 23 412 annotated genes, underline the high quality of the assembly. This chromosome-scale genome assembly is a valuable resource for future conservation of the species and comparative genomic studies among the giraffids and other ruminants.
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Affiliation(s)
- Sven Winter
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage, Frankfurt am Main, Germany.,Research Institute of Wildlife Ecology, Vetmeduni Vienna, Savoyenstraße, Vienna, Austria
| | - Raphael T F Coimbra
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage, Frankfurt am Main, Germany.,Institute for Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Straße, Frankfurt am Main, Germany
| | - Philippe Helsen
- Centre for Research and Conservation, Royal Zoological Society of Antwerp, Koningin Astridplein, Antwerp, Belgium
| | - Axel Janke
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage, Frankfurt am Main, Germany.,LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage, Frankfurt am Main, Germany.,Institute for Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Straße, Frankfurt am Main, Germany
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35
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Kim D, Taylor AT, Near TJ. Phylogenomics and species delimitation of the economically important Black Basses (Micropterus). Sci Rep 2022; 12:9113. [PMID: 35668124 PMCID: PMC9170712 DOI: 10.1038/s41598-022-11743-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 04/28/2022] [Indexed: 01/25/2023] Open
Abstract
Informed management and conservation efforts are vital to sustainable recreational fishing and biodiversity conservation. Because the taxonomic rank of species is important in conservation and management strategies, success of these efforts depends on accurate species delimitation. The Black Basses (Micropterus) are an iconic lineage of freshwater fishes that include some of the world’s most popular species for recreational fishing and world's most invasive species. Despite their popularity, previous studies to delimit species and lineages in Micropterus suffer from insufficient geographic coverage and uninformative molecular markers. Our phylogenomic analyses of ddRAD data result in the delimitation of 19 species of Micropterus, which includes 14 described species, the undescribed but well-known Altamaha, Bartram’s, and Choctaw basses, and two additional undescribed species currently classified as Smallmouth Bass (M. dolomieu). We provide a revised delimitation of species in the Largemouth Bass complex that necessitates a change in scientific nomenclature: Micropterus salmoides is retained for the Florida Bass and Micropterus nigricans is elevated from synonymy for the Largemouth Bass. The new understanding of diversity, distribution, and systematics of Black Basses will serve as important basis for the management and conservation of this charismatic and economically important clade of fishes.
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Affiliation(s)
- Daemin Kim
- Department of Ecology and Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, CT, 06511, USA.
| | - Andrew T Taylor
- Department of Biology, University of Central Oklahoma, Edmond, OK, 73034, USA.,Department of Biology, University of North Georgia, Dahlonega, GA, 30597, USA
| | - Thomas J Near
- Department of Ecology and Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, CT, 06511, USA.,Peabody Museum, Yale University, New Haven, CT, 06511, USA
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36
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Cryopreservation of Giraffe Epidydimal Spermatozoa Using Different Extenders and Cryoprotectants. Animals (Basel) 2022; 12:ani12070857. [PMID: 35405846 PMCID: PMC8997136 DOI: 10.3390/ani12070857] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/23/2022] [Accepted: 03/25/2022] [Indexed: 01/04/2023] Open
Abstract
Simple Summary Giraffe numbers have been plummeting over the last 30 years by 30–40%. As such, efforts to manage in situ and ex situ populations are increasing. Assisted reproduction techniques such as sperm cryopreservation can help preserve the genetic diversity of giraffe subspecies or enhance genetic exchange between populations. However, to date, the post-thaw motility of recovered sperm has been variable. In this study, spermatozoa were collected from the epididymides of seven giraffes to investigate whether an alternative cryoprotectant could improve sperm motility following conventional cryopreservation. For this, we compared the motility and viability of sperm prior to and after freezing in three different extenders: a commercial equine extender (BotuCrio®; Nidacon, Moedal, Schweden), a commercial bovine extender (Steridyl, Minitube, Tiefenbach, Germany), and an in-house “made” bovine egg yolk extender (TEY). Each was further supplemented with either glycerol or a mix of glycerol and methylformamide cryoprotectants. The results show that spermatozoa frozen with a mix of two cryoprotectants had significantly higher post-thaw motility compared to glycerol alone. Specifically, spermatozoa frozen in TEY and a mix of cryoprotectants achieved post-thaw sperm motility of 57 ± 3%. These results might serve as a blueprint for an improved protocol for giraffe sperm cryopreservation. Abstract Giraffe numbers have plummeted over the last 30 years by 30–40%. Thus, their conservation status has been raised from least concern to vulnerable. Efforts to manage in situ and ex situ populations are increasing. Assisted reproduction techniques (ART) such as sperm cryopreservation could help preserve the genetic diversity of giraffe subspecies and, when used for artificial inseminations, enhance genetic exchange between isolated populations. However, to date, the post-thaw motility of recovered sperm has been low and inconsistent. In this study, epididymal sperm collected from the testes of giraffes (n = 7) was frozen in three different extenders, namely, BotuCrio, Steridyl, and test egg yolk (TEY), each supplemented with one of two different cryoprotectants (5% glycerol or a mix of 1% glycerol and 4% methylformamide) and frozen over liquid nitrogen vapor. Across all three extenders, sperm showed significantly better post-thaw results when frozen with a mix of glycerol and methylformamide compared with glycerol alone. Sperm frozen with TEY and a mix of glycerol and methylformamide achieved superior post-thaw total and progressive sperm motility of 57 ± 3% and 45 ± 3%, respectively. These results show the benefit of using alternative cryoprotectants for freezing giraffe spermatozoa and could aid in the application of ARTs for giraffe subspecies or the closely related endangered Okapi.
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37
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Han S, Dadone L, Ferguson S, Bapodra-Villaverde P, Dennis PM, Aruho R, Sadar MJ, Fennessy J, Driciru M, Muneza AB, Brown MB, Johnston M, Lahmers K. Giraffe skin disease: Clinicopathologic characterization of cutaneous filariasis in the critically endangered Nubian giraffe ( Giraffa camelopardalis camelopardalis). Vet Pathol 2022; 59:467-475. [DOI: 10.1177/03009858221082606] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Giraffe skin disease (GSD) is an emerging disease of free-ranging giraffe recognized in the last 25 years in several species, including the critically endangered Nubian giraffe ( Giraffa camelopardalis camelopardalis) of Uganda. Identifying the cause of GSD and understanding its impact on health were deemed paramount to supporting these vulnerable populations. Sixty-four giraffes were immobilized in Murchison Falls National Park, Uganda, from 2017 to 2019, and GSD lesions were opportunistically biopsied. Fifty-five giraffes (86%) had GSD lesions on the neck, axilla, chest, and cranial trunk. Lesions were categorized into early, intermediary, and dormant stages based on gross and histological characteristics. Early lesions were smaller, crusted nodules with eosinophilic and pyogranulomatous dermatitis and furunculosis. Intermediary lesions were thick plaques of proliferative and fissured hyperkeratosis and acanthosis with dense dermal granulation tissue and severe eosinophilic and granulomatous dermatitis. Lesions appeared to resolve to dormancy, with dormant lesions consisting of hairless plaques of hyperkeratosis with dermal scarring and residual inflammation. The periphery of early and intermediary lesions included follicular granulomas containing adult filarid nematodes, with myriad encysted microfilariae in the superficial dermis. Stage L3 larvae were common in early and intermediary lesions, and dormant lesions had remnant encysted microfilariae with no adult or stage L3 larvae. Nematodes were morphologically and genetically novel with close identity to Stephanofilaria spp. and Brugia malayi, which cause infectious filariasis. Identification of potential insect vectors, long-term monitoring of GSD lesions, and evaluating response to therapy is ongoing in the efforts to help conserve the Nubian giraffe.
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Affiliation(s)
- Sushan Han
- Colorado State University, Fort Collins, CO
| | | | | | | | | | | | | | | | | | | | - Michael B. Brown
- Giraffe Conservation Foundation, Windhoek, Namibia
- Smithsonian’s National Zoo & Conservation Biology Institute, Front Royal, VA
- Dartmouth College, Hanover, NH
| | | | - Kevin Lahmers
- Virginia Tech Animal Laboratory Services, Blacksburg, VA
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Conservation Genomics of Two Threatened Subspecies of Northern Giraffe: The West African and the Kordofan Giraffe. Genes (Basel) 2022; 13:genes13020221. [PMID: 35205265 PMCID: PMC8872558 DOI: 10.3390/genes13020221] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/22/2022] [Accepted: 01/23/2022] [Indexed: 11/17/2022] Open
Abstract
Three of the four species of giraffe are threatened, particularly the northern giraffe (Giraffa camelopardalis), which collectively have the smallest known wild population estimates. Among the three subspecies of the northern giraffe, the West African giraffe (Giraffa camelopardalis peralta) had declined to 49 individuals by 1996 and only recovered due to conservation efforts undertaken in the past 25 years, while the Kordofan giraffe (Giraffa camelopardalis antiquorum) remains at <2300 individuals distributed in small, isolated populations over a large geographical range in Central Africa. These combined factors could lead to genetically depauperated populations. We analyzed 119 mitochondrial sequences and 26 whole genomes of northern giraffe individuals to investigate their population structure and assess the recent demographic history and current genomic diversity of West African and Kordofan giraffe. Phylogenetic and population structure analyses separate the three subspecies of northern giraffe and suggest genetic differentiation between populations from eastern and western areas of the Kordofan giraffe’s range. Both West African and Kordofan giraffe show a gradual decline in effective population size over the last 10 ka and have moderate genome-wide heterozygosity compared to other giraffe species. Recent inbreeding levels are higher in the West African giraffe and in Kordofan giraffe from Garamba National Park, Democratic Republic of Congo. Although numbers for both West African and some populations of Kordofan giraffe have increased in recent years, the threat of habitat loss, climate change impacts, and illegal hunting persists. Thus, future conservation actions should consider close genetic monitoring of populations to detect and, where practical, counteract negative trends that might develop.
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Santos D, Ribeiro GC. Areas of endemism in the Afrotropical region based on the geographical distribution of Tipulomorpha (Insecta: Diptera). AUSTRAL ECOL 2021. [DOI: 10.1111/aec.13137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Daubian Santos
- Centro de Ciências Naturais e Humanas Universidade Federal do ABC Rua Santa Adélia, 166, Bairro Bangu Santo André SP 09210‐170 Brazil
| | - Guilherme Cunha Ribeiro
- Centro de Ciências Naturais e Humanas Universidade Federal do ABC Rua Santa Adélia, 166, Bairro Bangu Santo André SP 09210‐170 Brazil
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40
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Dadone L, Foxworth S, Aruho R, Schilz A, Joyet A, Barrett M, Morkel P, Crooks G, Fennessy J, Johnston MS. Foot shape and radiographs of free-ranging Nubian giraffe in Uganda. PLoS One 2021; 16:e0252929. [PMID: 34914724 PMCID: PMC8675736 DOI: 10.1371/journal.pone.0252929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 10/10/2021] [Indexed: 11/30/2022] Open
Abstract
Foot health in zoo giraffe has been a topic of recent research, although little is known about the foot health of free-ranging giraffe. This study describes the foot shape and radiographic pathological changes in 27 young adult Nubian giraffe (Giraffa camelopardalis camelopardalis) from a translocation in Uganda (August 2017). Giraffe feet were observed to have a concave sole, the hoof wall was longest by the toe tip, and the weight-bearing surface of the foot was primarily along the periphery of the foot including hoof wall, parts of the heel, and the edge of the sole. Radiographs showed that pedal osteitis and sesamoid bone cysts were relatively uncommon (3/24 giraffe with osteitis, 1/24 giraffe with sesamoid cysts), and that no giraffe in the study had P3 joint osteoarthritis, P3 rotation, or P3 fractures. Radiographs consistently demonstrated a positive palmar/plantar angle with the sole of the hoof thicker at the heel than by the toe tip, with the non weight-bearing palmar/plantar angle measuring 1.6°- 4.3°. This is the first systematic review of foot shape and radiographs in free-ranging giraffe and demonstrates a low prevalence of foot pathologies. This study suggests qualitative differences in foot shape, foot health, radiographic anatomy, and foot pathologies when comparing free-ranging and zoo giraffe. Further research is needed to identify why these differences occur and whether husbandry modifications could help improve zoo giraffe foot health and prevent associated lameness.
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Affiliation(s)
- Liza Dadone
- Veterinary Department, Cheyenne Mountain Zoo, Colorado Springs, Colorado, United States of America
| | - Steve Foxworth
- Zoo Hoofstock Trim Program, Equine Lameness Prevention Organization, Berthoud, Colorado, United States of America
| | - Robert Aruho
- Department of Veterinary Medicine, Uganda Wildlife Authority, Kampala, Uganda
| | - Amy Schilz
- Animal Department, Cheyenne Mountain Zoo, Colorado Springs, Colorado, United States of America
| | - Andrea Joyet
- Zoo Hoofstock Trim Program, Equine Lameness Prevention Organization, Berthoud, Colorado, United States of America
| | - Myra Barrett
- Department of Environmental Health and Radiological Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Peter Morkel
- Wildlife Veterinary Consultant, Karasburg, Namibia
| | - Garrett Crooks
- Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | | | - Matthew S. Johnston
- Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America
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41
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Petersen M, Winter S, Coimbra R, J de Jong M, Kapitonov VV, Nilsson MA. Population analysis of retrotransposons in giraffe genomes supports RTE decline and widespread LINE1 activity in Giraffidae. Mob DNA 2021; 12:27. [PMID: 34836553 PMCID: PMC8620236 DOI: 10.1186/s13100-021-00254-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 10/25/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND The majority of structural variation in genomes is caused by insertions of transposable elements (TEs). In mammalian genomes, the main TE fraction is made up of autonomous and non-autonomous non-LTR retrotransposons commonly known as LINEs and SINEs (Long and Short Interspersed Nuclear Elements). Here we present one of the first population-level analysis of TE insertions in a non-model organism, the giraffe. Giraffes are ruminant artiodactyls, one of the few mammalian groups with genomes that are colonized by putatively active LINEs of two different clades of non-LTR retrotransposons, namely the LINE1 and RTE/BovB LINEs as well as their associated SINEs. We analyzed TE insertions of both types, and their associated SINEs in three giraffe genome assemblies, as well as across a population level sampling of 48 individuals covering all extant giraffe species. RESULTS The comparative genome screen identified 139,525 recent LINE1 and RTE insertions in the sampled giraffe population. The analysis revealed a drastically reduced RTE activity in giraffes, whereas LINE1 is still actively propagating in the genomes of extant (sub)-species. In concert with the extremely low activity of the giraffe RTE, we also found that RTE-dependent SINEs, namely Bov-tA and Bov-A2, have been virtually immobile in the last 2 million years. Despite the high current activity of the giraffe LINE1, we did not find evidence for the presence of currently active LINE1-dependent SINEs. TE insertion heterozygosity rates differ among the different (sub)-species, likely due to divergent population histories. CONCLUSIONS The horizontally transferred RTE/BovB and its derived SINEs appear to be close to inactivation and subsequent extinction in the genomes of extant giraffe species. This is the first time that the decline of a TE family has been meticulously analyzed from a population genetics perspective. Our study shows how detailed information about past and present TE activity can be obtained by analyzing large-scale population-level genomic data sets.
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Affiliation(s)
- Malte Petersen
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108, Freiburg, Germany
| | - Sven Winter
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Raphael Coimbra
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
- Institute for Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Straße 13, 60438, Frankfurt am Main, Germany
| | - Menno J de Jong
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Vladimir V Kapitonov
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Maria A Nilsson
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325, Frankfurt am Main, Germany.
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt am Main, Germany.
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Abstract
Natural populations currently face a wide variety of threats including climate change, habitat loss, over-harvesting, invasive species and disease. The most recent report by the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES) found that ecosystems have declined by approximately 50% relative to historical pristine conditions, and that approximately 25% of species are now threatened by extinction. This human-caused biodiversity crisis calls for using all available scientific tools to understand and reverse the increasing rate of extinction. While extinction is inherently a demographic process, being driven by changes in the population growth rate, the field of genetics plays an important role in the conservation of biodiversity. 'Conservation genetics' is a diverse field that applies genetic principles and methods to characterize and advance the preservation of biodiversity. Here, I first provide a short history of the development of the field and then list examples of the most important ways that genetics contributes to conservation.
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Affiliation(s)
- Marty Kardos
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA 98112, USA.
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43
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Galla SJ, Brown L, Couch-Lewis Ngāi Tahu Te Hapū O Ngāti Wheke Ngāti Waewae Y, Cubrinovska I, Eason D, Gooley RM, Hamilton JA, Heath JA, Hauser SS, Latch EK, Matocq MD, Richardson A, Wold JR, Hogg CJ, Santure AW, Steeves TE. The relevance of pedigrees in the conservation genomics era. Mol Ecol 2021; 31:41-54. [PMID: 34553796 PMCID: PMC9298073 DOI: 10.1111/mec.16192] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 09/12/2021] [Accepted: 09/17/2021] [Indexed: 01/21/2023]
Abstract
Over the past 50 years conservation genetics has developed a substantive toolbox to inform species management. One of the most long‐standing tools available to manage genetics—the pedigree—has been widely used to characterize diversity and maximize evolutionary potential in threatened populations. Now, with the ability to use high throughput sequencing to estimate relatedness, inbreeding, and genome‐wide functional diversity, some have asked whether it is warranted for conservation biologists to continue collecting and collating pedigrees for species management. In this perspective, we argue that pedigrees remain a relevant tool, and when combined with genomic data, create an invaluable resource for conservation genomic management. Genomic data can address pedigree pitfalls (e.g., founder relatedness, missing data, uncertainty), and in return robust pedigrees allow for more nuanced research design, including well‐informed sampling strategies and quantitative analyses (e.g., heritability, linkage) to better inform genomic inquiry. We further contend that building and maintaining pedigrees provides an opportunity to strengthen trusted relationships among conservation researchers, practitioners, Indigenous Peoples, and Local Communities.
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Affiliation(s)
- Stephanie J Galla
- Department of Biological Sciences, Boise State University, Boise, Idaho, USA.,School of Biological Sciences, University of Canterbury, Christchurch, Canterbury, New Zealand
| | - Liz Brown
- New Zealand Department of Conservation, Twizel, Canterbury, New Zealand
| | | | - Ilina Cubrinovska
- School of Biological Sciences, University of Canterbury, Christchurch, Canterbury, New Zealand
| | - Daryl Eason
- New Zealand Department of Conservation, Invercargill, Southland, New Zealand
| | - Rebecca M Gooley
- Smithsonian-Mason School of Conservation, Front Royal, Maryland, USA.,Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia, USA
| | - Jill A Hamilton
- Department of Biological Sciences, North Dakota State University, Fargo, North Dakota, USA
| | - Julie A Heath
- Department of Biological Sciences, Boise State University, Boise, Idaho, USA
| | - Samantha S Hauser
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Emily K Latch
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Marjorie D Matocq
- Department of Natural Resources and Environmental Science, Program in Ecology, Evolution and Conservation Biology, University of Nevada Reno, Reno, Nevada, USA
| | - Anne Richardson
- The Isaac Conservation and Wildlife Trust, Christchurch, Canterbury, New Zealand
| | - Jana R Wold
- School of Biological Sciences, University of Canterbury, Christchurch, Canterbury, New Zealand
| | - Carolyn J Hogg
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Anna W Santure
- School of Biological Sciences, University of Auckland, Auckland, Auckland, New Zealand
| | - Tammy E Steeves
- School of Biological Sciences, University of Canterbury, Christchurch, Canterbury, New Zealand
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44
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Abstract
Ecotourism can fuel an important source of financial income for African countries and can therefore help biodiversity policies in the continent. Translocations can be a powerful tool to spread economic benefits among countries and communities; yet, to be positive for biodiversity conservation, they require a basic knowledge of conservation units through appropriate taxonomic research. This is not always the case, as taxonomy was considered an outdated discipline for almost a century, and some plurality in taxonomic approaches is incorrectly considered as a disadvantage for conservation work. As an example, diversity of the genus Giraffa and its recent taxonomic history illustrate the importance of such knowledge for a sound conservation policy that includes translocations. We argue that a fine-grained conservation perspective that prioritizes all remaining populations along the Nile Basin is needed. Translocations are important tools for giraffe diversity conservation, but more discussion is needed, especially for moving new giraffes to regions where the autochthonous taxa/populations are no longer existent. As the current discussion about the giraffe taxonomy is too focused on the number of giraffe species, we argue that the plurality of taxonomic and conservation approaches might be beneficial, i.e., for defining the number of units requiring separate management using a (majority) consensus across different concepts (e.g., MU—management unit, ESU—evolutionary significant unit, and ECU—elemental conservation unit). The taxonomically sensitive translocation policy/strategy would be important for the preservation of current diversity, while also supporting the ecological restoration of some regions within rewilding. A summary table of the main translocation operations of African mammals that have underlying problems is included. Therefore, we call for increased attention toward the taxonomy of African mammals not only as the basis for sound conservation but also as a further opportunity to enlarge the geographic scope of ecotourism in Africa.
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