1
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Murphy WJ, Harris AJ. Toward telomere-to-telomere cat genomes for precision medicine and conservation biology. Genome Res 2024; 34:655-664. [PMID: 38849156 PMCID: PMC11216403 DOI: 10.1101/gr.278546.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2024]
Abstract
Genomic data from species of the cat family Felidae promise to stimulate veterinary and human medical advances, and clarify the coherence of genome organization. We describe how interspecies hybrids have been instrumental in the genetic analysis of cats, from the first genetic maps to propelling cat genomes toward the T2T standard set by the human genome project. Genotype-to-phenotype mapping in cat models has revealed dozens of health-related genetic variants, the molecular basis for mammalian pigmentation and patterning, and species-specific adaptations. Improved genomic surveillance of natural and captive populations across the cat family tree will increase our understanding of the genetic architecture of traits, population dynamics, and guide a future of genome-enabled biodiversity conservation.
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Affiliation(s)
- William J Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843-4458, USA;
- Department of Biology, Texas A&M University, College Station, Texas 77843-4458, USA
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, Texas 77843-4458, USA
| | - Andrew J Harris
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843-4458, USA
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, Texas 77843-4458, USA
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2
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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: 2] [Impact Index Per Article: 1.0] [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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3
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Orndorf N, Garner AM, Dhinojwala A. Polar bear paw pad surface roughness and its relevance to contact mechanics on snow. J R Soc Interface 2022; 19:20220466. [PMID: 36321372 PMCID: PMC9627446 DOI: 10.1098/rsif.2022.0466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 10/11/2022] [Indexed: 11/04/2023] Open
Abstract
Microscopic papillae on polar bear paw pads are considered adaptations for increased friction on ice/snow, yet this assertion is based on a single study of one species. The lack of comparative data from species that exploit different habitats renders the ecomorphological associations of papillae unclear. Here, we quantify the surface roughness of the paw pads of four species of bear over five orders of magnitude by calculating their surface roughness power spectral density. We find that interspecific variation in papillae base diameter can be explained by paw pad width, but that polar bear paw pads have 1.5 times taller papillae and 1.3 times more true surface area than paw pads of the American black bear and brown bear. Based on friction experiments with three-dimensional printed model surfaces and snow, we conclude that these factors increase the frictional shear stress of the polar bear paw pad on snow by a factor of 1.3-1.5 compared with the other species. Absolute frictional forces, however, are estimated to be similar among species once paw pad area is accounted for, suggesting that taller papillae may compensate for frictional losses resulting from the relatively smaller paw pads of polar bears compared with their close relatives.
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Affiliation(s)
- Nathaniel Orndorf
- School of Polymer Science and Polymer Engineering, The University of Akron, Akron, OH 44325, USA
| | - Austin M. Garner
- Integrated Bioscience Program, Department of Biology, The University of Akron, Akron, OH 44325, USA
| | - Ali Dhinojwala
- School of Polymer Science and Polymer Engineering, The University of Akron, Akron, OH 44325, USA
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4
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Using a Phylogenetic Framework to Assess the Role of Fruit Size in Food Selection by the Andean Night Monkey (Aotus lemurinus). INT J PRIMATOL 2022. [DOI: 10.1007/s10764-021-00274-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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5
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Snow Leopard (Panthera uncia) Genetics: The Knowledge Gaps, Needs, and Implications for Conservation. J Indian Inst Sci 2021. [DOI: 10.1007/s41745-021-00236-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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6
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Marais CA, Crole MR. Gross morphology of the African lion (
Panthera
leo
) heart. ACTA ZOOL-STOCKHOLM 2021. [DOI: 10.1111/azo.12381] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Carmen Alicia Marais
- Department of Anatomy and Physiology Faculty of Veterinary Science University of Pretoria Pretoria South Africa
| | - Martina Rachel Crole
- Department of Anatomy and Physiology Faculty of Veterinary Science University of Pretoria Pretoria South Africa
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7
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Curry CJ, Davis BW, Bertola LD, White PA, Murphy WJ, Derr JN. Spatiotemporal Genetic Diversity of Lions Reveals the Influence of Habitat Fragmentation across Africa. Mol Biol Evol 2021; 38:48-57. [PMID: 32667997 PMCID: PMC8480188 DOI: 10.1093/molbev/msaa174] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Direct comparisons between historical and contemporary populations allow for detecting changes in genetic diversity through time and assessment of the impact of habitat fragmentation. Here, we determined the genetic architecture of both historical and modern lions to document changes in genetic diversity over the last century. We surveyed microsatellite and mitochondrial genome variation from 143 high-quality museum specimens of known provenance, allowing us to directly compare this information with data from several recently published nuclear and mitochondrial studies. Our results provide evidence for male-mediated gene flow and recent isolation of local subpopulations, likely due to habitat fragmentation. Nuclear markers showed a significant decrease in genetic diversity from the historical (HE = 0.833) to the modern (HE = 0.796) populations, whereas mitochondrial genetic diversity was maintained (Hd = 0.98 for both). Although the historical population appears to have been panmictic based on nDNA data, hierarchical structure analysis identified four tiers of genetic structure in modern populations and was able to detect most sampling locations. Mitogenome analyses identified four clusters: Southern, Mixed, Eastern, and Western and were consistent between modern and historically sampled haplotypes. Within the last century, habitat fragmentation caused lion subpopulations to become more geographically isolated as human expansion changed the African landscape. This resulted in an increase in fine-scale nuclear genetic structure and loss of genetic diversity as lion subpopulations became more differentiated, whereas mitochondrial structure and diversity were maintained over time.
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Affiliation(s)
- Caitlin J Curry
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX
| | - Brian W Davis
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX
| | - Laura D Bertola
- Department of Biology, City College of New York, New York, NY
| | - Paula A White
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California Los Angeles, Los Angeles, CA
| | - William J Murphy
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX
| | - James N Derr
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX
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8
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Armstrong EE, Taylor RW, Miller DE, Kaelin CB, Barsh GS, Hadly EA, Petrov D. Long live the king: chromosome-level assembly of the lion (Panthera leo) using linked-read, Hi-C, and long-read data. BMC Biol 2020; 18:3. [PMID: 31915011 PMCID: PMC6950864 DOI: 10.1186/s12915-019-0734-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 12/20/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The lion (Panthera leo) is one of the most popular and iconic feline species on the planet, yet in spite of its popularity, the last century has seen massive declines for lion populations worldwide. Genomic resources for endangered species represent an important way forward for the field of conservation, enabling high-resolution studies of demography, disease, and population dynamics. Here, we present a chromosome-level assembly from a captive African lion from the Exotic Feline Rescue Center (Center Point, IN) as a resource for current and subsequent genetic work of the sole social species of the Panthera clade. RESULTS Our assembly is composed of 10x Genomics Chromium data, Dovetail Hi-C, and Oxford Nanopore long-read data. Synteny is highly conserved between the lion, other Panthera genomes, and the domestic cat. We find variability in the length of runs of homozygosity across lion genomes, indicating contrasting histories of recent and possibly intense inbreeding and bottleneck events. Demographic analyses reveal similar ancient histories across all individuals during the Pleistocene except the Asiatic lion, which shows a more rapid decline in population size. We show a substantial influence on the reference genome choice in the inference of demographic history and heterozygosity. CONCLUSIONS We demonstrate that the choice of reference genome is important when comparing heterozygosity estimates across species and those inferred from different references should not be compared to each other. In addition, estimates of heterozygosity or the amount or length of runs of homozygosity should not be taken as reflective of a species, as these can differ substantially among individuals. This high-quality genome will greatly aid in the continuing research and conservation efforts for the lion, which is rapidly moving towards becoming a species in danger of extinction.
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Affiliation(s)
| | - Ryan W Taylor
- Department of Biology, Stanford University, Stanford, CA, USA
- End2EndGenomics, LLC, Davis, CA, USA
| | - Danny E Miller
- Department of Pediatrics, Seattle Children's Hospital and The University of Washington, Seattle, WA, USA
| | - Christopher B Kaelin
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Gregory S Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | - Dmitri Petrov
- Department of Biology, Stanford University, Stanford, CA, USA
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9
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Li G, Figueiró HV, Eizirik E, Murphy WJ. Recombination-Aware Phylogenomics Reveals the Structured Genomic Landscape of Hybridizing Cat Species. Mol Biol Evol 2020; 36:2111-2126. [PMID: 31198971 PMCID: PMC6759079 DOI: 10.1093/molbev/msz139] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Current phylogenomic approaches implicitly assume that the predominant phylogenetic signal within a genome reflects the true evolutionary history of organisms, without assessing the confounding effects of postspeciation gene flow that can produce a mosaic of phylogenetic signals that interact with recombinational variation. Here, we tested the validity of this assumption with a phylogenomic analysis of 27 species of the cat family, assessing local effects of recombination rate on species tree inference and divergence time estimation across their genomes. We found that the prevailing phylogenetic signal within the autosomes is not always representative of the most probable speciation history, due to ancient hybridization throughout felid evolution. Instead, phylogenetic signal was concentrated within regions of low recombination, and notably enriched within large X chromosome recombination cold spots that exhibited recurrent patterns of strong genetic differentiation and selective sweeps across mammalian orders. By contrast, regions of high recombination were enriched for signatures of ancient gene flow, and these sequences inflated crown-lineage divergence times by ∼40%. We conclude that existing phylogenomic approaches to infer the Tree of Life may be highly misleading without considering the genomic architecture of phylogenetic signal relative to recombination rate and its interplay with historical hybridization.
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Affiliation(s)
- Gang Li
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX
| | - Henrique V Figueiró
- PUCRS, Escola de Ciências, Laboratory of Genomics and Molecular Biology, Porto Alegre, Brazil.,INCT-EECBio, Brazil
| | - Eduardo Eizirik
- PUCRS, Escola de Ciências, Laboratory of Genomics and Molecular Biology, Porto Alegre, Brazil.,INCT-EECBio, Brazil
| | - William J Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX
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10
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Mittal P, Jaiswal SK, Vijay N, Saxena R, Sharma VK. Comparative analysis of corrected tiger genome provides clues to its neuronal evolution. Sci Rep 2019; 9:18459. [PMID: 31804567 PMCID: PMC6895189 DOI: 10.1038/s41598-019-54838-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 11/14/2019] [Indexed: 01/01/2023] Open
Abstract
The availability of completed and draft genome assemblies of tiger, leopard, and other felids provides an opportunity to gain comparative insights on their unique evolutionary adaptations. However, genome-wide comparative analyses are susceptible to errors in genome sequences and thus require accurate genome assemblies for reliable evolutionary insights. In this study, while analyzing the tiger genome, we found almost one million erroneous substitutions in the coding and non-coding region of the genome affecting 4,472 genes, hence, biasing the current understanding of tiger evolution. Moreover, these errors produced several misleading observations in previous studies. Thus, to gain insights into the tiger evolution, we corrected the erroneous bases in the genome assembly and gene set of tiger using ‘SeqBug’ approach developed in this study. We sequenced the first Bengal tiger genome and transcriptome from India to validate these corrections. A comprehensive evolutionary analysis was performed using 10,920 orthologs from nine mammalian species including the corrected gene sets of tiger and leopard and using five different methods at three hierarchical levels, i.e. felids, Panthera, and tiger. The unique genetic changes in tiger revealed that the genes showing signatures of adaptation in tiger were enriched in development and neuronal functioning. Specifically, the genes belonging to the Notch signalling pathway, which is among the most conserved pathways involved in embryonic and neuronal development, were found to have significantly diverged in tiger in comparison to the other mammals. Our findings suggest the role of adaptive evolution in neuronal functions and development processes, which correlates well with the presence of exceptional traits such as sensory perception, strong neuro-muscular coordination, and hypercarnivorous behaviour in tiger.
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Affiliation(s)
- Parul Mittal
- Metaomics and Systems Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Shubham K Jaiswal
- Metaomics and Systems Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Nagarjun Vijay
- Computational Evolutionary Genomics Lab, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Rituja Saxena
- Metaomics and Systems Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Vineet K Sharma
- Metaomics and Systems Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India.
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11
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Catalano SA, Segura V, Vera Candioti F. PASOS: a method for the phylogenetic analysis of shape ontogenies. Cladistics 2019; 35:671-687. [PMID: 34618936 DOI: 10.1111/cla.12373] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/21/2018] [Indexed: 12/17/2022] Open
Abstract
We present a novel phylogenetic approach to infer ancestral ontogenies of shape characters described as landmark configurations. The method is rooted in previously published theoretical developments to analyse landmark data in a phylogenetic context with parsimony as the optimality criterion, in this case using the minimization of differences in landmark position to define not only ancestral shapes but also the changes in developmental timing between ancestor-descendant shape ontogenies. Evolutionary changes along the tree represent changes in relative developmental timing between ontogenetic trajectories (possible heterochronic events) and changes in shape within each stage. The method requires the user to determine the shape of the specimens between two standard events, for instance birth and onset of sexual maturity. Once the ontogenetic trajectory is discretized into a series of consecutive stages, the method enables the user to identify changes in developmental timing associated with changes in the offset and/or onset of the shape ontogenetic trajectories. The method is implemented in a C language program called SPASOS. The analysis of two empirical examples (anurans and felids) using this novel method yielded results in agreement with previous hypotheses about shape evolution in these groups based on non-phylogenetic analyses.
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Affiliation(s)
- Santiago A Catalano
- Unidad Ejecutora Lillo, Consejo Nacional de Investigaciones Científicas y Técnicas - Fundación Miguel Lillo, Miguel Lillo 251, 4000, S. M. de Tucumán, Argentina.,Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, Miguel Lillo 205, 4000, S. M. de Tucumán, Argentina
| | - Valentina Segura
- Unidad Ejecutora Lillo, Consejo Nacional de Investigaciones Científicas y Técnicas - Fundación Miguel Lillo, Miguel Lillo 251, 4000, S. M. de Tucumán, Argentina
| | - Florencia Vera Candioti
- Unidad Ejecutora Lillo, Consejo Nacional de Investigaciones Científicas y Técnicas - Fundación Miguel Lillo, Miguel Lillo 251, 4000, S. M. de Tucumán, Argentina
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12
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Areewong C, Sangchantip R, Rungphattanachaikul S, Rittipornlertrak A, Fhaikruae I, Wongkalasin W, Nomsiri R, Boontong P, Vongchan P, Sthitmatee N. Production and characterization of polyclonal antibody against Bengal tiger (Panthera tigris tigris) immunoglobulin G. JOURNAL OF APPLIED ANIMAL RESEARCH 2019. [DOI: 10.1080/09712119.2019.1629937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Chanakan Areewong
- Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
- Tiger Kingdom, Chiang Mai, Thailand
| | | | | | | | | | - Waroot Wongkalasin
- Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
| | | | | | - Preeyanat Vongchan
- Faculty of Associated Medical Sciences, Department of Medical Technology, Chiang Mai University, Chiang Mai, Thailand
| | - Nattawooti Sthitmatee
- Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
- Excellence Center in Veterinary Bioscience, Chiang Mai University, Chiang Mai, Thailand
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13
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Benedict BD, Castellanos AA, Light JE. Phylogeographic assessment of the Heermann’s kangaroo rat (Dipodomys heermanni). J Mammal 2018. [DOI: 10.1093/jmammal/gyy166] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- Bridgett D Benedict
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Adrian A Castellanos
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX 77843, USA
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14
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Characterization of major histocompatibility complex class I, and class II DRB loci of captive and wild Indian leopards (Panthera pardus fusca). Genetica 2017; 145:541-558. [DOI: 10.1007/s10709-017-9979-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 08/14/2017] [Indexed: 10/19/2022]
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15
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Guo X, Tang CC, Thomas DC, Couvreur TLP, Saunders RMK. A mega-phylogeny of the Annonaceae: taxonomic placement of five enigmatic genera and support for a new tribe, Phoenicantheae. Sci Rep 2017; 7:7323. [PMID: 28779135 PMCID: PMC5544705 DOI: 10.1038/s41598-017-07252-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 06/26/2017] [Indexed: 11/21/2022] Open
Abstract
The Annonaceae, the largest family in the early-divergent order Magnoliales, comprises 107 genera and c. 2,400 species. Previous molecular phylogenetic studies targeting different taxa have generated large quantities of partially overlapping DNA sequence data for many species, although a large-scale phylogeny based on the maximum number of representatives has never been reconstructed. We use a supermatrix of eight chloroplast markers (rbcL, matK, ndhF, psbA-trnH, trnL-F, atpB-rbcL, trnS-G and ycf1) to reconstruct the most comprehensive tree to date, including 705 species (29%) from 105 genera (98%). This provides novel insights into the relationships of five enigmatic genera (Bocagea, Boutiquea, Cardiopetalum, Duckeanthus and Phoenicanthus). Fifteen main clades are retrieved in subfamilies Annonoideae and Malmeoideae collectively, 14 of which correspond with currently recognised tribes. Phoenicanthus cannot be accommodated in any existing tribe, however: it is retrieved as sister to a clade comprising the tribes Dendrokingstonieae, Monocarpieae and Miliuseae, and we therefore validate a new tribe, Phoenicantheae. Our results provide strong support for many previously recognised groups, but also indicate non-monophyly of several genera (Desmopsis, Friesodielsia, Klarobelia, Oxandra, Piptostigma and Stenanona). The relationships of these non-monophyletic genera-and two other genera (Froesiodendron and Melodorum) not yet sampled-are discussed, with recommendations for future research.
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Affiliation(s)
- Xing Guo
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Chin Cheung Tang
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
- School of Science and Technology, The Open University of Hong Kong, Ho Man Tin, Kowloon, Hong Kong, China
| | - Daniel C Thomas
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
- Singapore Botanic Gardens, 1 Cluny Road, Singapore, 259569, Singapore
| | - Thomas L P Couvreur
- Institut de Recherche pour le Développement (IRD), UMR-DIADE, BP 64501, F-34394, Montpellier, cedex 5, France
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16
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Figueiró HV, Li G, Trindade FJ, Assis J, Pais F, Fernandes G, Santos SHD, Hughes GM, Komissarov A, Antunes A, Trinca CS, Rodrigues MR, Linderoth T, Bi K, Silveira L, Azevedo FCC, Kantek D, Ramalho E, Brassaloti RA, Villela PMS, Nunes ALV, Teixeira RHF, Morato RG, Loska D, Saragüeta P, Gabaldón T, Teeling EC, O’Brien SJ, Nielsen R, Coutinho LL, Oliveira G, Murphy WJ, Eizirik E. Genome-wide signatures of complex introgression and adaptive evolution in the big cats. SCIENCE ADVANCES 2017; 3:e1700299. [PMID: 28776029 PMCID: PMC5517113 DOI: 10.1126/sciadv.1700299] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 06/19/2017] [Indexed: 05/05/2023]
Abstract
The great cats of the genus Panthera comprise a recent radiation whose evolutionary history is poorly understood. Their rapid diversification poses challenges to resolving their phylogeny while offering opportunities to investigate the historical dynamics of adaptive divergence. We report the sequence, de novo assembly, and annotation of the jaguar (Panthera onca) genome, a novel genome sequence for the leopard (Panthera pardus), and comparative analyses encompassing all living Panthera species. Demographic reconstructions indicated that all of these species have experienced variable episodes of population decline during the Pleistocene, ultimately leading to small effective sizes in present-day genomes. We observed pervasive genealogical discordance across Panthera genomes, caused by both incomplete lineage sorting and complex patterns of historical interspecific hybridization. We identified multiple signatures of species-specific positive selection, affecting genes involved in craniofacial and limb development, protein metabolism, hypoxia, reproduction, pigmentation, and sensory perception. There was remarkable concordance in pathways enriched in genomic segments implicated in interspecies introgression and in positive selection, suggesting that these processes were connected. We tested this hypothesis by developing exome capture probes targeting ~19,000 Panthera genes and applying them to 30 wild-caught jaguars. We found at least two genes (DOCK3 and COL4A5, both related to optic nerve development) bearing significant signatures of interspecies introgression and within-species positive selection. These findings indicate that post-speciation admixture has contributed genetic material that facilitated the adaptive evolution of big cat lineages.
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Affiliation(s)
- Henrique V. Figueiró
- Laboratório de Biologia Genômica e Molecular, Faculdade de Biociências, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Gang Li
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
| | - Fernanda J. Trindade
- Laboratório de Biologia Genômica e Molecular, Faculdade de Biociências, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Juliana Assis
- Centro de Pesquisa René Rachou, FIOCRUZ/Minas, Belo Horizonte, Minas Gerais, Brazil
| | - Fabiano Pais
- Centro de Pesquisa René Rachou, FIOCRUZ/Minas, Belo Horizonte, Minas Gerais, Brazil
| | - Gabriel Fernandes
- Centro de Pesquisa René Rachou, FIOCRUZ/Minas, Belo Horizonte, Minas Gerais, Brazil
| | - Sarah H. D. Santos
- Laboratório de Biologia Genômica e Molecular, Faculdade de Biociências, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Graham M. Hughes
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Aleksey Komissarov
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, St. Petersburg, Russia
| | - Agostinho Antunes
- Departamento de Biologia, Faculdade de Ciências and CIIMAR/CIMAR, Universidade do Porto, Porto, Portugal
| | - Cristine S. Trinca
- Laboratório de Biologia Genômica e Molecular, Faculdade de Biociências, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Maíra R. Rodrigues
- Laboratório de Biologia Genômica e Molecular, Faculdade de Biociências, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Tyler Linderoth
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720–3140, USA
| | - Ke Bi
- Computational Genomics Resource Laboratory, California Institute for Quantitative Biosciences and Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA 94720, USA
| | | | - Fernando C. C. Azevedo
- Universidade Federal de São João Del Rey, São João Del Rey, Minas Gerais, Brazil
- Instituto Pró-Carnívoros, Atibaia, São Paulo, Brazil
| | - Daniel Kantek
- Laboratório de Biologia Genômica e Molecular, Faculdade de Biociências, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil
- Instituto Chico Mendes de Conservação da Biodiversidade, Brasília, Distrito Federal, Brazil
| | - Emiliano Ramalho
- Instituto Pró-Carnívoros, Atibaia, São Paulo, Brazil
- Instituto de Desenvolvimento Sustentável Mamirauá, Tefé, Amazonas, Brazil
| | - Ricardo A. Brassaloti
- Escola Superior de Agricultura Luiz de Queiroz (ESALQ-USP), Piracicaba, São Paulo, Brazil
| | | | | | - Rodrigo H. F. Teixeira
- Zoológico Municipal de Sorocaba, Sorocaba, São Paulo, Brazil
- Programa de Pós-Graduação em Animais Selvagens, Universidade Estadual Paulista–Botucatu, São Paulo, Brazil
| | - Ronaldo G. Morato
- Instituto Pró-Carnívoros, Atibaia, São Paulo, Brazil
- Instituto Chico Mendes de Conservação da Biodiversidade, Brasília, Distrito Federal, Brazil
| | - Damian Loska
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | | | - Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Emma C. Teeling
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Stephen J. O’Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, St. Petersburg, Russia
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720–3140, USA
| | - Luiz L. Coutinho
- Escola Superior de Agricultura Luiz de Queiroz (ESALQ-USP), Piracicaba, São Paulo, Brazil
| | - Guilherme Oliveira
- Centro de Pesquisa René Rachou, FIOCRUZ/Minas, Belo Horizonte, Minas Gerais, Brazil
- Instituto Tecnológico Vale, Belém, Pará, Brazil
| | - William J. Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
| | - Eduardo Eizirik
- Laboratório de Biologia Genômica e Molecular, Faculdade de Biociências, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil
- Instituto Pró-Carnívoros, Atibaia, São Paulo, Brazil
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17
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Bertola LD, Jongbloed H, van der Gaag KJ, de Knijff P, Yamaguchi N, Hooghiemstra H, Bauer H, Henschel P, White PA, Driscoll CA, Tende T, Ottosson U, Saidu Y, Vrieling K, de Iongh HH. Phylogeographic Patterns in Africa and High Resolution Delineation of Genetic Clades in the Lion (Panthera leo). Sci Rep 2016; 6:30807. [PMID: 27488946 PMCID: PMC4973251 DOI: 10.1038/srep30807] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 07/08/2016] [Indexed: 11/10/2022] Open
Abstract
Comparative phylogeography of African savannah mammals shows a congruent pattern in which populations in West/Central Africa are distinct from populations in East/Southern Africa. However, for the lion, all African populations are currently classified as a single subspecies (Panthera leo leo), while the only remaining population in Asia is considered to be distinct (Panthera leo persica). This distinction is disputed both by morphological and genetic data. In this study we introduce the lion as a model for African phylogeography. Analyses of mtDNA sequences reveal six supported clades and a strongly supported ancestral dichotomy with northern populations (West Africa, Central Africa, North Africa/Asia) on one branch, and southern populations (North East Africa, East/Southern Africa and South West Africa) on the other. We review taxonomies and phylogenies of other large savannah mammals, illustrating that similar clades are found in other species. The described phylogeographic pattern is considered in relation to large scale environmental changes in Africa over the past 300,000 years, attributable to climate. Refugial areas, predicted by climate envelope models, further confirm the observed pattern. We support the revision of current lion taxonomy, as recognition of a northern and a southern subspecies is more parsimonious with the evolutionary history of the lion.
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Affiliation(s)
- L D Bertola
- Leiden University, Institute of Environmental Sciences (CML), PO Box 9518, 2300 RA Leiden, The Netherlands.,Leiden University, Institute of Biology Leiden (IBL), PO Box 9505, 2300 RA Leiden, The Netherlands
| | - H Jongbloed
- Leiden University, Institute of Environmental Sciences (CML), PO Box 9518, 2300 RA Leiden, The Netherlands.,Leiden University, Institute of Biology Leiden (IBL), PO Box 9505, 2300 RA Leiden, The Netherlands
| | - K J van der Gaag
- Forensic Laboratory for DNA Research, Department of Human Genetics, Leiden University Medical Centre, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - P de Knijff
- Forensic Laboratory for DNA Research, Department of Human Genetics, Leiden University Medical Centre, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - N Yamaguchi
- Qatar University, Department of Biological and Environmental Sciences, College of Arts and Sciences, PO Box 2713, Doha, Qatar
| | - H Hooghiemstra
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 904, 1018 XH Amsterdam, The Netherlands
| | - H Bauer
- WildCRU, Recanati-Kaplan Centre, University of Oxford. Tubney House, Abingdon Road, OX13 5QL, UK
| | - P Henschel
- Panthera, 8 West 40th Street, 18th Floor, New York, NY 10018, USA
| | - P A White
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095-1496, USA
| | - C A Driscoll
- Wildlife Institute of India, Dehradun 248001, Uttarakhand, India
| | - T Tende
- A. P. Leventis Ornithological Research Institute, P.O. Box 13404 Jos, Nigeria
| | - U Ottosson
- A. P. Leventis Ornithological Research Institute, P.O. Box 13404 Jos, Nigeria
| | - Y Saidu
- Nigeria National Park Service, PMB 0258 Garki-Abuja, Nigeria
| | - K Vrieling
- Leiden University, Institute of Biology Leiden (IBL), PO Box 9505, 2300 RA Leiden, The Netherlands
| | - H H de Iongh
- Leiden University, Institute of Environmental Sciences (CML), PO Box 9518, 2300 RA Leiden, The Netherlands.,University of Antwerp, Department Biology, Evolutionary Ecology Group, Groenenborgerlaan 171, 2020 Antwerpen, Belgium
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18
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Segura V, Cassini GH, Prevosti FJ. Three-dimensional cranial ontogeny in pantherines ( Panthera leo, P. onca, P. pardus, P. tigris; Carnivora:, Felidae). Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12888] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Valentina Segura
- Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET); San Miguel de Tucumán Argentina
- Unidad Ejecutora Lillo (UEL); Fundación Miguel Lillo-CONICET; San Miguel de Tucumán Argentina
| | - Guillermo H. Cassini
- Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET); San Miguel de Tucumán Argentina
- División Mastozoología; Museo Argentino de Ciencias Naturales “Bernardino Rivadavia (MACN)”; Ciudad Autónoma de Buenos Aires Argentina
- Departamento de Ciencias Básicas; Universidad Nacional de Luján (UNLu); Luján Argentina
| | - Francisco J. Prevosti
- Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET); San Miguel de Tucumán Argentina
- Centro Regional de Investigaciones Científicas y Transferencia Tecnológica de La Rioja (CRILAR); Provincia de La Rioja, UNLaR, SEGEMAR, UNCa, CONICET; Entre Ríos y Mendoza s/n, 5301 - Anillaco La Rioja Argentina
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19
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Wilting A, Patel R, Pfestorf H, Kern C, Sultan K, Ario A, Peñaloza F, Kramer-Schadt S, Radchuk V, Foerster DW, Fickel J. Evolutionary history and conservation significance of the Javan leopard Panthera pardus melas. J Zool (1987) 2016. [DOI: 10.1111/jzo.12348] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- A. Wilting
- Leibniz Institute for Zoo and Wildlife Research; Berlin Germany
| | - R. Patel
- Leibniz Institute for Zoo and Wildlife Research; Berlin Germany
| | - H. Pfestorf
- Leibniz Institute for Zoo and Wildlife Research; Berlin Germany
- Institute for Biochemistry and Biology; Plant Ecology and Nature Conservation; Potsdam University; Potsdam Germany
| | - C. Kern
- Tierpark Berlin; Berlin Germany
| | - K. Sultan
- Taman Safari Indonesia; Bogor West Java Indonesia
| | - A. Ario
- Conservation International Indonesia; Jakarta Selatan Indonesia
| | - F. Peñaloza
- Leibniz Institute for Zoo and Wildlife Research; Berlin Germany
| | | | - V. Radchuk
- Leibniz Institute for Zoo and Wildlife Research; Berlin Germany
| | - D. W. Foerster
- Leibniz Institute for Zoo and Wildlife Research; Berlin Germany
| | - J. Fickel
- Leibniz Institute for Zoo and Wildlife Research; Berlin Germany
- Institute for Biochemistry and Biology; Potsdam University; Potsdam Germany
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20
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Li G, Davis BW, Eizirik E, Murphy WJ. Phylogenomic evidence for ancient hybridization in the genomes of living cats (Felidae). Genome Res 2016; 26:1-11. [PMID: 26518481 PMCID: PMC4691742 DOI: 10.1101/gr.186668.114] [Citation(s) in RCA: 156] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 10/13/2015] [Indexed: 12/27/2022]
Abstract
Inter-species hybridization has been recently recognized as potentially common in wild animals, but the extent to which it shapes modern genomes is still poorly understood. Distinguishing historical hybridization events from other processes leading to phylogenetic discordance among different markers requires a well-resolved species tree that considers all modes of inheritance and overcomes systematic problems due to rapid lineage diversification by sampling large genomic character sets. Here, we assessed genome-wide phylogenetic variation across a diverse mammalian family, Felidae (cats). We combined genotypes from a genome-wide SNP array with additional autosomal, X- and Y-linked variants to sample ∼150 kb of nuclear sequence, in addition to complete mitochondrial genomes generated using light-coverage Illumina sequencing. We present the first robust felid time tree that accounts for unique maternal, paternal, and biparental evolutionary histories. Signatures of phylogenetic discordance were abundant in the genomes of modern cats, in many cases indicating hybridization as the most likely cause. Comparison of big cat whole-genome sequences revealed a substantial reduction of X-linked divergence times across several large recombination cold spots, which were highly enriched for signatures of selection-driven post-divergence hybridization between the ancestors of the snow leopard and lion lineages. These results highlight the mosaic origin of modern felid genomes and the influence of sex chromosomes and sex-biased dispersal in post-speciation gene flow. A complete resolution of the tree of life will require comprehensive genomic sampling of biparental and sex-limited genetic variation to identify and control for phylogenetic conflict caused by ancient admixture and sex-biased differences in genomic transmission.
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Affiliation(s)
- Gang Li
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843, USA
| | - Brian W Davis
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843, USA; Interdisciplinary Program in Genetics, Texas A&M University, College Station, Texas 77843, USA
| | - Eduardo Eizirik
- Faculdade de Biociências, PUCRS, Porto Alegre, RS 90619-900, Brazil
| | - William J Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843, USA; Interdisciplinary Program in Genetics, Texas A&M University, College Station, Texas 77843, USA
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21
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Wilting A, Courtiol A, Christiansen P, Niedballa J, Scharf AK, Orlando L, Balkenhol N, Hofer H, Kramer-Schadt S, Fickel J, Kitchener AC. Planning tiger recovery: Understanding intraspecific variation for effective conservation. SCIENCE ADVANCES 2015; 1:e1400175. [PMID: 26601191 PMCID: PMC4640610 DOI: 10.1126/sciadv.1400175] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 05/05/2015] [Indexed: 05/21/2023]
Abstract
Although significantly more money is spent on the conservation of tigers than on any other threatened species, today only 3200 to 3600 tigers roam the forests of Asia, occupying only 7% of their historical range. Despite the global significance of and interest in tiger conservation, global approaches to plan tiger recovery are partly impeded by the lack of a consensus on the number of tiger subspecies or management units, because a comprehensive analysis of tiger variation is lacking. We analyzed variation among all nine putative tiger subspecies, using extensive data sets of several traits [morphological (craniodental and pelage), ecological, molecular]. Our analyses revealed little variation and large overlaps in each trait among putative subspecies, and molecular data showed extremely low diversity because of a severe Late Pleistocene population decline. Our results support recognition of only two subspecies: the Sunda tiger, Panthera tigris sondaica, and the continental tiger, Panthera tigris tigris, which consists of two (northern and southern) management units. Conservation management programs, such as captive breeding, reintroduction initiatives, or trans-boundary projects, rely on a durable, consistent characterization of subspecies as taxonomic units, defined by robust multiple lines of scientific evidence rather than single traits or ad hoc descriptions of one or few specimens. Our multiple-trait data set supports a fundamental rethinking of the conventional tiger taxonomy paradigm, which will have profound implications for the management of in situ and ex situ tiger populations and boost conservation efforts by facilitating a pragmatic approach to tiger conservation management worldwide.
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Affiliation(s)
- Andreas Wilting
- Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Straße 17, 10315 Berlin, Germany
| | - Alexandre Courtiol
- Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Straße 17, 10315 Berlin, Germany
| | | | - Jürgen Niedballa
- Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Straße 17, 10315 Berlin, Germany
| | - Anne K. Scharf
- Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Straße 17, 10315 Berlin, Germany
| | - Ludovic Orlando
- Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark
| | - Niko Balkenhol
- Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Straße 17, 10315 Berlin, Germany
| | - Heribert Hofer
- Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Straße 17, 10315 Berlin, Germany
| | - Stephanie Kramer-Schadt
- Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Straße 17, 10315 Berlin, Germany
| | - Jörns Fickel
- Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Straße 17, 10315 Berlin, Germany
- Institute for Biochemistry and Biology, Potsdam University, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Andrew C. Kitchener
- Department of Natural Sciences, National Museums Scotland, Edinburgh EH1 1JF, UK
- Institute of Geography, School of Geosciences, University of Edinburgh, Edinburgh EH8 9XP, UK
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22
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Brekke TD, Good JM. Parent-of-origin growth effects and the evolution of hybrid inviability in dwarf hamsters. Evolution 2014; 68:3134-48. [PMID: 25130206 PMCID: PMC4437546 DOI: 10.1111/evo.12500] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 07/11/2014] [Indexed: 12/24/2022]
Abstract
Mammalian hybrids often show abnormal growth, indicating that developmental inviability may play an important role in mammalian speciation. Yet, it is unclear if this recurrent phenotype reflects a common genetic basis. Here, we describe extreme parent-of-origin-dependent growth in hybrids from crosses between two species of dwarf hamsters, Phodopus campbelli and Phodopus sungorus. One cross type resulted in massive placental and embryonic overgrowth, severe developmental defects, and maternal death. Embryos from the reciprocal cross were viable and normal sized, but adult hybrid males were relatively small. These effects are strikingly similar to patterns from several other mammalian hybrids. Using comparative sequence data from dwarf hamsters and several other hybridizing mammals, we argue that extreme hybrid growth can contribute to reproductive isolation during the early stages of species divergence. Next, we tested if abnormal growth in hybrid hamsters was associated with disrupted genomic imprinting. We found no association between imprinting status at several candidate genes and hybrid growth, though two interacting genes involved in embryonic growth did show reduced expression in overgrown hybrids. Collectively, our study indicates that growth-related hybrid inviability may play an important role in mammalian speciation but that the genetic underpinnings of these phenotypes remain unresolved.
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Affiliation(s)
- Thomas D. Brekke
- Division of Biological Sciences, The University of Montana, Missoula Montana, 59812
| | - Jeffrey M. Good
- Division of Biological Sciences, The University of Montana, Missoula Montana, 59812
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23
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Barnett R, Yamaguchi N, Shapiro B, Ho SYW, Barnes I, Sabin R, Werdelin L, Cuisin J, Larson G. Revealing the maternal demographic history of Panthera leo using ancient DNA and a spatially explicit genealogical analysis. BMC Evol Biol 2014; 14:70. [PMID: 24690312 PMCID: PMC3997813 DOI: 10.1186/1471-2148-14-70] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 03/13/2014] [Indexed: 11/15/2022] Open
Abstract
Background Understanding the demographic history of a population is critical to conservation and to our broader understanding of evolutionary processes. For many tropical large mammals, however, this aim is confounded by the absence of fossil material and by the misleading signal obtained from genetic data of recently fragmented and isolated populations. This is particularly true for the lion which as a consequence of millennia of human persecution, has large gaps in its natural distribution and several recently extinct populations. Results We sequenced mitochondrial DNA from museum-preserved individuals, including the extinct Barbary lion (Panthera leo leo) and Iranian lion (P. l. persica), as well as lions from West and Central Africa. We added these to a broader sample of lion sequences, resulting in a data set spanning the historical range of lions. Our Bayesian phylogeographical analyses provide evidence for highly supported, reciprocally monophyletic lion clades. Using a molecular clock, we estimated that recent lion lineages began to diverge in the Late Pleistocene. Expanding equatorial rainforest probably separated lions in South and East Africa from other populations. West African lions then expanded into Central Africa during periods of rainforest contraction. Lastly, we found evidence of two separate incursions into Asia from North Africa, first into India and later into the Middle East. Conclusions We have identified deep, well-supported splits within the mitochondrial phylogeny of African lions, arguing for recognition of some regional populations as worthy of independent conservation. More morphological and nuclear DNA data are now needed to test these subdivisions.
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Affiliation(s)
- Ross Barnett
- Durham Evolution and Ancient DNA, Department of Archaeology, Durham University, Durham DH1 3LE, UK.
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24
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Tseng ZJ, Wang X, Slater GJ, Takeuchi GT, Li Q, Liu J, Xie G. Himalayan fossils of the oldest known pantherine establish ancient origin of big cats. Proc Biol Sci 2014; 281:20132686. [PMID: 24225466 PMCID: PMC3843846 DOI: 10.1098/rspb.2013.2686] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 10/18/2013] [Indexed: 11/12/2022] Open
Abstract
Pantherine felids ('big cats') include the largest living cats, apex predators in their respective ecosystems. They are also the earliest diverging living cat lineage, and thus are important for understanding the evolution of all subsequent felid groups. Although the oldest pantherine fossils occur in Africa, molecular phylogenies point to Asia as their region of origin. This paradox cannot be reconciled using current knowledge, mainly because early big cat fossils are exceedingly rare and fragmentary. Here, we report the discovery of a fossil pantherine from the Tibetan Himalaya, with an age of Late Miocene-Early Pliocene, replacing African records as the oldest pantherine. A 'total evidence' phylogenetic analysis of pantherines indicates that the new cat is closely related to the snow leopard and exhibits intermediate characteristics on the evolutionary line to the largest cats. Historical biogeographic models provide robust support for the Asian origin of pantherines. The combined analyses indicate that 75% of the divergence events in the pantherine lineage extended back to the Miocene, up to 7 Myr earlier than previously estimated. The deeper evolutionary origin of big cats revealed by the new fossils and analyses indicate a close association between Tibetan Plateau uplift and diversification of the earliest living cats.
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Affiliation(s)
- Z. Jack Tseng
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
- Department of Vertebrate Paleontology, Natural History Museum of Los Angeles County, 900 Exposition Boulevard, Los Angeles, CA 90007, USA
- Division of Paleontology, American Museum of Natural History, New York, NY 10024, USA
| | - Xiaoming Wang
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
- Department of Vertebrate Paleontology, Natural History Museum of Los Angeles County, 900 Exposition Boulevard, Los Angeles, CA 90007, USA
- Division of Paleontology, American Museum of Natural History, New York, NY 10024, USA
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, People's Republic of China
| | - Graham J. Slater
- Department of Paleobiology and Division of Mammals, National Museum of Natural History, The Smithsonian Institution (NHB, MRC 121), PO Box 37012, Washington, DC 20013-7012, USA
| | - Gary T. Takeuchi
- Department of Vertebrate Paleontology, Natural History Museum of Los Angeles County, 900 Exposition Boulevard, Los Angeles, CA 90007, USA
- The George C. Page Museum, 5801 Wilshire Boulevard, Los Angeles, CA 90036, USA
| | - Qiang Li
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, People's Republic of China
| | - Juan Liu
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, People's Republic of China
- Department of Biological Sciences, University of Alberta, Edmonton, CanadaT6G 2E9
| | - Guangpu Xie
- Gansu Provincial Museum, Lanzhou 730050, People's Republic of China
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25
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The Structure of the Mammalian Predator Guild in the Santa Cruz Formation (Late Early Miocene). J MAMM EVOL 2013. [DOI: 10.1007/s10914-013-9243-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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26
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Bagatharia SB, Joshi MN, Pandya RV, Pandit AS, Patel RP, Desai SM, Sharma A, Panchal O, Jasmani FP, Saxena AK. Complete mitogenome of Asiatic lion resolves phylogenetic status within Panthera. BMC Genomics 2013; 14:572. [PMID: 23968279 PMCID: PMC3765570 DOI: 10.1186/1471-2164-14-572] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Accepted: 08/12/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The origin, evolution and speciation of the lion, has been subject of interest, debate and study. The present surviving lions of the genus Panthera comprise of eight sub-species inclusive of Asiatic lion Panthera leo persica of India's Gir forest. Except for the Asiatic lion, the other seven subspecies are found in different parts of Africa. There have been different opinions regarding the phylogenetic status of Panthera leo, as well as classifying lions of different geographic regions into subspecies and races. In the present study, mitogenome sequence of P. leo persica deduced, using Ion Torrent PGM to assess phylogeny and evolution which may play an increasingly important role in conservation biology. RESULTS The mtDNA sequence of P. leo persica is 17,057 bp in length with 40.8% GC content. Annotation of mitogenome revealed total 37 genes, including 13 protein coding, 2 rRNA and 22 tRNA. Phylogenetic analysis based on whole mitogenome, suggests Panthera pardus as a neighbouring species to P. leo with species divergence at ~2.96 mya. CONCLUSION This work presents first report on complete mitogenome of Panthera leo persica. It sheds light on the phylogenetic and evolutionary status within and across Felidae members. The result compared and evaluated with earlier reports of Felidae shows alteration of phylogenetic status and species evolution. This study may provide information on genetic diversity and population stability.
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Affiliation(s)
- Snehal B Bagatharia
- Gujarat State Biotechnology Mission, Department of Science and Technology, Government of Gujarat, Block-11, 9th Floor, Udyog Bhavan, Sector 11, Gandhinagar 382 017, Gujarat, India
| | - Madhvi N Joshi
- Gujarat State Biotechnology Mission, Department of Science and Technology, Government of Gujarat, Block-11, 9th Floor, Udyog Bhavan, Sector 11, Gandhinagar 382 017, Gujarat, India
| | - Rohan V Pandya
- Gujarat State Biotechnology Mission, Department of Science and Technology, Government of Gujarat, Block-11, 9th Floor, Udyog Bhavan, Sector 11, Gandhinagar 382 017, Gujarat, India
| | - Aanal S Pandit
- Gujarat State Biotechnology Mission, Department of Science and Technology, Government of Gujarat, Block-11, 9th Floor, Udyog Bhavan, Sector 11, Gandhinagar 382 017, Gujarat, India
| | - Riddhi P Patel
- Gujarat State Biotechnology Mission, Department of Science and Technology, Government of Gujarat, Block-11, 9th Floor, Udyog Bhavan, Sector 11, Gandhinagar 382 017, Gujarat, India
| | - Shivangi M Desai
- Gujarat State Biotechnology Mission, Department of Science and Technology, Government of Gujarat, Block-11, 9th Floor, Udyog Bhavan, Sector 11, Gandhinagar 382 017, Gujarat, India
| | - Anu Sharma
- Gujarat State Biotechnology Mission, Department of Science and Technology, Government of Gujarat, Block-11, 9th Floor, Udyog Bhavan, Sector 11, Gandhinagar 382 017, Gujarat, India
| | - Omkar Panchal
- Gujarat State Biotechnology Mission, Department of Science and Technology, Government of Gujarat, Block-11, 9th Floor, Udyog Bhavan, Sector 11, Gandhinagar 382 017, Gujarat, India
| | - Falguni P Jasmani
- Gujarat State Biotechnology Mission, Department of Science and Technology, Government of Gujarat, Block-11, 9th Floor, Udyog Bhavan, Sector 11, Gandhinagar 382 017, Gujarat, India
| | - Akshay K Saxena
- Gujarat State Biotechnology Mission, Department of Science and Technology, Government of Gujarat, Block-11, 9th Floor, Udyog Bhavan, Sector 11, Gandhinagar 382 017, Gujarat, India
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27
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Abstract
Panthera pardus (leopard; Linnaeus, 1758) is the smallest of the 4 large felids in the genus Panthera. A solitary and adaptable species, P. pardus is the widest ranging of all wild felids, inhabiting rain forests, mountains, semiarid environments, and suburban areas throughout sub-Saharan Africa, the Middle East, and South Asia to the Russian Far East. Despite this distribution, P. pardus is listed as “Near Threatened” by the International Union for Conservation of Nature and Natural Resources and several Asian subspecies are listed as endangered. P. pardus primarily feeds on small to medium-sized ungulates, but has a varied diet including fish, reptiles, birds, and small mammals.
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Affiliation(s)
- Andrew B. Stein
- Department of Natural Resources Conservation, University of Massachusetts, Amherst, MA 01003, USA;
| | - Virginia Hayssen
- Department of Biology, Smith College, Northampton, MA 01063, USA;
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28
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Wang JF, Zhang YP, Yu L. [Summary of phylogeny in family Felidae of Carnivora]. YI CHUAN = HEREDITAS 2012. [PMID: 23208134 DOI: 10.3724/sp.j.1005.2012.01365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Felidae (cats) is one of the strict carnivorous groups in the order Carnivora, many of which are most familiar and spectacular to us. They are the top predators in the world. Thirty-six of 37 living cat species are considered as either "endangered" or "threatened". The relationships among species of the family Felidae, which evolved recently and rapidly, are difficult to resolve, and have been the subject of debate. Construction of a reliable Felidae phylogeny will be of evolutionarily significance and conservation value. In this paper, we summarized phylogeny of Felidae, including cytological, morphological and molecular evidence, and pointed out the existing phylogenetic problems. This review is expected to guide future researches of Felidae phylogeny, and to lay a theoretic foundation for the protection of this animal group.
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Affiliation(s)
- Jin-Feng Wang
- Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming, China.
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29
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Molecular phylogeny of extant equids and effects of ancestral polymorphism in resolving species-level phylogenies. Mol Phylogenet Evol 2012; 65:573-81. [DOI: 10.1016/j.ympev.2012.07.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Revised: 05/18/2012] [Accepted: 07/14/2012] [Indexed: 11/19/2022]
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30
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Dávalos LM, Cirranello AL, Geisler JH, Simmons NB. Understanding phylogenetic incongruence: lessons from phyllostomid bats. Biol Rev Camb Philos Soc 2012; 87:991-1024. [PMID: 22891620 PMCID: PMC3573643 DOI: 10.1111/j.1469-185x.2012.00240.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Revised: 07/04/2012] [Accepted: 07/18/2012] [Indexed: 12/25/2022]
Abstract
All characters and trait systems in an organism share a common evolutionary history that can be estimated using phylogenetic methods. However, differential rates of change and the evolutionary mechanisms driving those rates result in pervasive phylogenetic conflict. These drivers need to be uncovered because mismatches between evolutionary processes and phylogenetic models can lead to high confidence in incorrect hypotheses. Incongruence between phylogenies derived from morphological versus molecular analyses, and between trees based on different subsets of molecular sequences has become pervasive as datasets have expanded rapidly in both characters and species. For more than a decade, evolutionary relationships among members of the New World bat family Phyllostomidae inferred from morphological and molecular data have been in conflict. Here, we develop and apply methods to minimize systematic biases, uncover the biological mechanisms underlying phylogenetic conflict, and outline data requirements for future phylogenomic and morphological data collection. We introduce new morphological data for phyllostomids and outgroups and expand previous molecular analyses to eliminate methodological sources of phylogenetic conflict such as taxonomic sampling, sparse character sampling, or use of different algorithms to estimate the phylogeny. We also evaluate the impact of biological sources of conflict: saturation in morphological changes and molecular substitutions, and other processes that result in incongruent trees, including convergent morphological and molecular evolution. Methodological sources of incongruence play some role in generating phylogenetic conflict, and are relatively easy to eliminate by matching taxa, collecting more characters, and applying the same algorithms to optimize phylogeny. The evolutionary patterns uncovered are consistent with multiple biological sources of conflict, including saturation in morphological and molecular changes, adaptive morphological convergence among nectar-feeding lineages, and incongruent gene trees. Applying methods to account for nucleotide sequence saturation reduces, but does not completely eliminate, phylogenetic conflict. We ruled out paralogy, lateral gene transfer, and poor taxon sampling and outgroup choices among the processes leading to incongruent gene trees in phyllostomid bats. Uncovering and countering the possible effects of introgression and lineage sorting of ancestral polymorphism on gene trees will require great leaps in genomic and allelic sequencing in this species-rich mammalian family. We also found evidence for adaptive molecular evolution leading to convergence in mitochondrial proteins among nectar-feeding lineages. In conclusion, the biological processes that generate phylogenetic conflict are ubiquitous, and overcoming incongruence requires better models and more data than have been collected even in well-studied organisms such as phyllostomid bats.
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Affiliation(s)
- Liliana M Dávalos
- Department of Ecology and Evolution, and Consortium for Inter-Disciplinary Environmental Research, State University of New York at Stony BrookStony Brook, NY 11794, USA
| | - Andrea L Cirranello
- Division of Vertebrate Zoology (Mammalogy), American Museum of Natural HistoryNew York, NY 10024, USA
- Department of Anatomical Sciences, State University of New York at Stony BrookStony Brook, NY 11794, USA
| | - Jonathan H Geisler
- Department of Anatomy, New York College of Osteopathic MedicineOld Westbury, NY 11568, USA
| | - Nancy B Simmons
- Division of Vertebrate Zoology (Mammalogy), American Museum of Natural HistoryNew York, NY 10024, USA
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31
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Hinchliff CE, Roalson EH. Using supermatrices for phylogenetic inquiry: an example using the sedges. Syst Biol 2012; 62:205-19. [PMID: 23103590 DOI: 10.1093/sysbio/sys088] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
In this article, we use supermatrix data-mining methods to reconstruct a large, highly inclusive phylogeny of Cyperaceae from nucleotide data available on GenBank. We explore the properties of these trees and their utility for phylogenetic inference, and show that even the highly incomplete alignments characteristic of supermatrix approaches may yield very good estimates of phylogeny. We present a novel pipeline for filtering sparse alignments to improve their phylogenetic utility by maximizing the partial decisiveness of the matrices themselves through a technique we call "phylogenetic scaffolding," and we present a new method of scoring tip instability (i.e. "rogue taxa") based on the I statistic implemented in the software Mesquite. The modified statistic, which we call I(S), is somewhat more straightforward to interpret than similar statistics, and our implementation of it may be applied to large sets of large trees. The largest sedge trees presented here contain more than 1500 tips (about one quarter of all sedge species) and are based on multigene alignments with more than 20 000 sites and more than 90% missing data. These trees match well with previously supported phylogenetic hypotheses, but have lower overall support values and less resolution than more heavily filtered trees. Our best-resolved trees are characterized by stronger support values than any previously published sedge phylogenies, and show some relationships that are incongruous with previous studies. Overall, we show that supermatrix methods offer powerful means of pursuing phylogenetic study and these tools have high potential value for many systematic biologists.
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Affiliation(s)
- Cody E Hinchliff
- School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA.
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32
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Diogo R, Pastor F, De Paz F, Potau JM, Bello-Hellegouarch G, Ferrero EM, Fisher RE. The head and neck muscles of the serval and tiger: homologies, evolution, and proposal of a mammalian and a veterinary muscle ontology. Anat Rec (Hoboken) 2012; 295:2157-78. [PMID: 22961868 DOI: 10.1002/ar.22589] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Revised: 08/09/2012] [Accepted: 08/09/2012] [Indexed: 11/10/2022]
Abstract
Here we describe the head and neck muscles of members of the two extant felid subfamilies (Leptailurus serval: Felinae; Panthera tigris: Pantherinae) and compare these muscles with those of other felids, other carnivorans (e.g., domestic dogs), other eutherian mammals (e.g., rats, tree-shrews and modern humans), and noneutherian mammals including monotremes. Another major goal of the article is to discuss and help clarify nomenclatural discrepancies found in the Nomina Anatomica Veterinaria and in veterinary atlases and textbooks that use cats and dogs as models to understand the anatomy of domestic mammals and to stress differences with modern humans. We propose a unifying nomenclature that is expanded to all the head and neck muscles and to all mammalian taxa in order to help build veterinary and mammalian muscle ontologies. Our observations and comparisons and the specific use of this nomenclature point out that felids such as tigers and servals and other carnivorans such as dogs have more facial muscle structures related to the mobility of both the auricular and orbital regions than numerous other mammals, including modern humans, which might be the result of an ancient adaptation related to the remarkable predatory capacities of carnivorans. Interestingly, the skeletal differences, mainly concerning the hyoid apparatus, pharynx, and larynx, that are likely associated with the different types of vocalizations seen in the Felinae (mainly purring) and Pantherinae (mainly roaring) are not accompanied by clear differences in the musculature connected to these structures in the feline L. serval and the pantherine P. tigris.
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Affiliation(s)
- Rui Diogo
- Department of Anatomy, Howard University College of Medicine, Washington, DC, USA.
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33
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Michelet L, Dauga C. Molecular evidence of host influences on the evolution and spread of human tapeworms. Biol Rev Camb Philos Soc 2012; 87:731-41. [PMID: 22321512 DOI: 10.1111/j.1469-185x.2012.00217.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The taeniasis/cysticercosis complex is included in the list of neglected zoonotic diseases by the World Health Organization due to its significant impact on public health in tropical areas. Cysticercosis is still endemic in many regions of Asia, Africa and Latin America. Long absent in Europe and in other developed countries, cysticercosis has recently re-emerged in the United States and Canada, due to immigration, travel and local transmission. This has encouraged the use of molecular data to understand better the influence of animal and human hosts on the emergence and spread of Taenia species. The increasing number of mitochondrial sequences now available from human tapeworms and recent advances in computational tools has enabled reconstruction of the biogeography and evolutionary history of these organisms. New molecular data have provided insights into the biogeography of T. solium, T. asiatica and T. saginata. A Bayesian statistical framework using variable evolutionary rates from lineage to lineage has allowed an improved timescale analysis of human tapeworms. The dates of divergence obtained were compared to the timing of evolutionary events in the history of their hosts, based on the hypothesis that Taenia spp. and their hosts share a common history. Herein, we review changes in the definitive and secondary hosts and human interactions that underlie the differentiation and evolution of tapeworms. Species diversification of Taenia seems to be closely linked with the evolution of intermediate hosts in response to climatic events during the Pleistocene. Different genotypes of T. solium emerged when European and Asian wild boar Sus spp. populations diverged. Taenia saginata emerged when wild cattle Bos primigenius evolved and when zebu Bos indicus and taurine Bos taurus ancestors separated. Humans through migrations and later with the development of farming and animal husbandry may have had a significant impact on the spread and diversification of tapeworms. Migrations of Homo erectus from Africa to Asia and later of Homo sapiens facilitated the diversification and dispersal of T. solium and T. saginata populations. The development of animal husbandry, making Sus scrofa and Bos taurus preferential intermediate hosts, led to the worldwide distribution of parasites. New molecular data combined with an innovative dating method allow us to explain the ways in which ancient human migrations promoted the emergence and spread of taeniasis and cysticercosis around the world. Another intriguing phenomenon explained better by our approach is the influence of human settlement on the spread of these parasites in recently inhabited areas. The diverse nature of T. solium currently observed in Madagascar may correspond to multiple imports of the parasite during Austronesian migrations, while in Mexico a recent influence of humans during the colonial period is more likely. Human activities, especially food preparation and husbandry methods, remain responsible for the transmission and persistence of these parasites.
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Affiliation(s)
- Lorraine Michelet
- EA3174 NETEC Neuroépidémiologie Tropicale et Comparée, Faculté de Médécine, 2 rue du Docteur Marcland, 87025 Limoges, France.
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34
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Simmons MP. Radical instability and spurious branch support by likelihood when applied to matrices with non-random distributions of missing data. Mol Phylogenet Evol 2011; 62:472-84. [PMID: 22067131 DOI: 10.1016/j.ympev.2011.10.017] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Revised: 10/10/2011] [Accepted: 10/23/2011] [Indexed: 10/16/2022]
Abstract
Non-random distributions of missing data are a general problem for likelihood-based statistical analyses, including those in a phylogenetic context. Extensive non-randomly distributed missing data are particularly problematic in supermatrix analyses that include many terminals and/or loci. It has been widely reported that missing data can lead to loss of resolution, but only very rarely create misleading or otherwise unsupported results in a parsimony context. Yet this does not hold for all parametric-based analyses because of their assumption of homogeneity across characters and lineages, which can lead to both long-branch attraction and long-branch repulsion. Contrived examples were used to demonstrate that non-random distributions of missing data, even without rate heterogeneity among characters and a well fitting model, can provide misleading likelihood-based topologies and branch-support values that are radically unstable based on slight modifications to character sampling. The same can occur despite complete absence of parsimony-informative characters. Otherwise unsupported resolution and high branch support for these clades were found to occur frequently in 22 empirical examples derived from a published supermatrix. Partitioning characters based on the distribution of missing data helped to decrease, but did not eliminate, these artifacts. These artifacts were exacerbated by low quality tree searches, particularly when holding only a single optimal tree that must be fully resolved.
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Affiliation(s)
- Mark P Simmons
- Department of Biology, Colorado State University, Fort Collins, CO 80523-1878, USA.
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35
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Wei L, Wu X, Zhu L, Jiang Z. Mitogenomic analysis of the genus Panthera. SCIENCE CHINA-LIFE SCIENCES 2011; 54:917-30. [PMID: 22038004 DOI: 10.1007/s11427-011-4219-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2011] [Accepted: 06/10/2011] [Indexed: 11/25/2022]
Abstract
The complete sequences of the mitochondrial DNA genomes of Panthera tigris, Panthera pardus, and Panthera uncia were determined using the polymerase chain reaction method. The lengths of the complete mitochondrial DNA sequences of the three species were 16990, 16964, and 16773 bp, respectively. Each of the three mitochondrial DNA genomes included 13 protein-coding genes, 22 tRNA, two rRNA, one O(L)R, and one control region. The structures of the genomes were highly similar to those of Felis catus, Acinonyx jubatus, and Neofelis nebulosa. The phylogenies of the genus Panthera were inferred from two combined mitochondrial sequence data sets and the complete mitochondrial genome sequences, by MP (maximum parsimony), ML (maximum likelihood), and Bayesian analysis. The results showed that Panthera was composed of Panthera leo, P. uncia, P. pardus, Panthera onca, P. tigris, and N. nebulosa, which was included as the most basal member. The phylogeny within Panthera genus was N. nebulosa (P. tigris (P. onca (P. pardus, (P. leo, P. uncia)))). The divergence times for Panthera genus were estimated based on the ML branch lengths and four well-established calibration points. The results showed that at about 11.3 MYA, the Panthera genus separated from other felid species and then evolved into the several species of the genus. In detail, N. nebulosa was estimated to be founded about 8.66 MYA, P. tigris about 6.55 MYA, P. uncia about 4.63 MYA, and P. pardus about 4.35 MYA. All these estimated times were older than those estimated from the fossil records. The divergence event, evolutionary process, speciation, and distribution pattern of P. uncia, a species endemic to the central Asia with core habitats on the Qinghai-Tibetan Plateau and surrounding highlands, mostly correlated with the geological tectonic events and intensive climate shifts that happened at 8, 3.6, 2.5, and 1.7 MYA on the plateau during the late Cenozoic period.
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Affiliation(s)
- Lei Wei
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
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36
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Mazák JH, Christiansen P, Kitchener AC. Oldest known pantherine skull and evolution of the tiger. PLoS One 2011; 6:e25483. [PMID: 22016768 PMCID: PMC3189913 DOI: 10.1371/journal.pone.0025483] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Accepted: 09/05/2011] [Indexed: 11/18/2022] Open
Abstract
The tiger is one of the most iconic extant animals, and its origin and evolution have been intensely debated. Fossils attributable to extant pantherine species-lineages are less than 2 MYA and the earliest tiger fossils are from the Calabrian, Lower Pleistocene. Molecular studies predict a much younger age for the divergence of modern tiger subspecies at <100 KYA, although their cranial morphology is readily distinguishable, indicating that early Pleistocene tigers would likely have differed markedly anatomically from extant tigers. Such inferences are hampered by the fact that well-known fossil tiger material is middle to late Pleistocene in age. Here we describe a new species of pantherine cat from Longdan, Gansu Province, China, Panthera zdanskyi sp. nov. With an estimated age of 2.55-2.16 MYA it represents the oldest complete skull of a pantherine cat hitherto found. Although smaller, it appears morphologically to be surprisingly similar to modern tigers considering its age. Morphological, morphometric, and cladistic analyses are congruent in confirming its very close affinity to the tiger, and it may be regarded as the most primitive species of the tiger lineage, demonstrating the first unequivocal presence of a modern pantherine species-lineage in the basal stage of the Pleistocene (Gelasian; traditionally considered to be Late Pliocene). This find supports a north-central Chinese origin of the tiger lineage, and demonstrates that various parts of the cranium, mandible, and dentition evolved at different rates. An increase in size and a reduction in the relative size of parts of the dentition appear to have been prominent features of tiger evolution, whereas the distinctive cranial morphology of modern tigers was established very early in their evolutionary history. The evolutionary trend of increasing size in the tiger lineage is likely coupled to the evolution of its primary prey species.
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Affiliation(s)
- Ji H Mazák
- Shanghai Science and Technology Museum, Shanghai, People's Republic of China.
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37
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Abstract
The utility of molecular genetic approaches in conservation of endangered taxa is now commonly recognized. Over the past decade, conservation genetic analyses based on mitochondrial DNA sequencing and microsatellite genotyping have provided powerful tools to resolve taxonomy uncertainty of tiger subspecies, to define conservation units, to reconstruct phylogeography and demographic history, to examine the genetic ancestry of extinct subspecies, to assess population genetic status non-invasively, and to verify genetic background of captive tigers worldwide. The genetic status of tiger subspecies and populations and implications for developing strategies for the survival of this charismatic species both in situ and ex situ are discussed.
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Affiliation(s)
- Shu-Jin Luo
- School of Life Sciences, Peking University, Beijing, ChinaLaboratory of Genomic Diversity, National Cancer Institute, Frederick, MD, USA
| | - Warren E Johnson
- School of Life Sciences, Peking University, Beijing, ChinaLaboratory of Genomic Diversity, National Cancer Institute, Frederick, MD, USA
| | - Stephen J O'Brien
- School of Life Sciences, Peking University, Beijing, ChinaLaboratory of Genomic Diversity, National Cancer Institute, Frederick, MD, USA
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38
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Li G, Janecka JE, Murphy WJ. Accelerated evolution of CES7, a gene encoding a novel major urinary protein in the cat family. Mol Biol Evol 2010; 28:911-20. [PMID: 20966115 DOI: 10.1093/molbev/msq281] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Cauxin is a novel urinary protein recently identified in the domestic cat that regulates the excretion of felinine, a pheromone precursor involved in sociochemical communication and territorial marking of domestic and wild felids. Understanding the evolutionary history of cauxin may therefore illuminate molecular adaptations involved in the evolution of pheromone-based communication, recognition, and mate selection in wild animals. We sequenced the gene encoding cauxin, CES7, in 22 species representing all major felid lineages, and multiple outgroups and showed that it has undergone rapid evolutionary change preceding and during the diversification of the cat family. A comparison between feline cauxin and orthologous carboxylesterases from other mammalian lineages revealed evidence of strong positive Darwinian selection within and between several cat lineages, enriched at functionally important sites of the protein. The higher rate of radical amino acid replacements in small felids, coupled with the lack of felinine and extremely low levels of cauxin in the urine of the great cats (Panthera), correlates with functional divergence of this gene in Panthera, and its putative loss in the snow leopard. Expression studies found evidence for several alternatively spliced transcripts in testis and brain, suggesting additional roles in male reproductive fitness and behavior. Our work presents the first report of strong positive natural selection acting on a major urinary protein of nonrodent mammals, providing evidence for parallel selection pressure on the regulation of pheromones in different mammalian lineages, despite the use of different metabolic pathways. Our results imply that natural selection may drive rapid changes in the regulation of pheromones in urine among the different cat species, which in turn may influence social behavior, such as territorial marking and conspecific recognition, therefore serving as an important mechanism for the radiation of this group of mammals.
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Affiliation(s)
- Gang Li
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, TX, USA
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