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Myers EA, Rautsaw RM, Borja M, Jones J, Grünwald CI, Holding ML, Grazziotin F, Parkinson CL. Phylogenomic discordance is driven by wide-spread introgression and incomplete lineage sorting during rapid species diversification within rattlesnakes (Viperidae: Crotalus and Sistrurus). Syst Biol 2024:syae018. [PMID: 38695290 DOI: 10.1093/sysbio/syae018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Indexed: 08/11/2024] Open
Abstract
Phylogenomics allows us to uncover the historical signal of evolutionary processes through time and estimate phylogenetic networks accounting for these signals. Insight from genome-wide data further allows us to pinpoint the contributions to phylogenetic signal from hybridization, introgression, and ancestral polymorphism across the genome. Here we focus on how these processes have contributed to phylogenetic discordance among rattlesnakes (genera Crotalus and Sistrurus), a group for which there are numerous conflicting phylogenetic hypotheses based on a diverse array of molecular datasets and analytical methods. We address the instability of the rattlesnake phylogeny using genomic data generated from transcriptomes sampled from nearly all known species. These genomic data, analyzed with coalescent and network-based approaches, reveal numerous instances of rapid speciation where individual gene trees conflict with the species tree. Moreover, the evolutionary history of rattlesnakes is dominated by incomplete speciation and frequent hybridization, both of which have likely influenced past interpretations of phylogeny. We present a new framework in which the evolutionary relationships of this group can only be understood in light of genome-wide data and network-based analytical methods. Our data suggest that network radiations, like seen within the rattlesnakes, can only be understood in a phylogenomic context, necessitating similar approaches in our attempts to understand evolutionary history in other rapidly radiating species.
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Affiliation(s)
- Edward A Myers
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
- Department of Herpetology, California Academy of Sciences, San Francisco, CA 94118, USA
| | - Rhett M Rautsaw
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
| | - Miguel Borja
- Facultad de Ciencias Biológicas, Universdad Juárez del Estado de Durango, Av. Universidad s/n. Fracc. Filadelfia, Gómez Palacio, Durango., Mex
| | - Jason Jones
- Herp.mx A.C. C.P. 28989, Villa de Álvarez, Colima, Mexico
| | - Christoph I Grünwald
- Herp.mx A.C. C.P. 28989, Villa de Álvarez, Colima, Mexico
- Biodiversa A.C., Avenida de la Ribera #203, C.P. 45900, Chapala, Jalisco, Mexico
| | - Matthew L Holding
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Felipe Grazziotin
- Laboratório Especial de Coleções Zoológicas, Instituto Butantan, Avenida Vital Brasil, São Paulo, 05503-900, Brazil
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Venom comparisons of endemic and micro-endemic speckled rattlesnakes Crotalus mitchellii, C. polisi and C. thalassoporus from Baja California Peninsula. Toxicon 2023; 224:107030. [PMID: 36649760 DOI: 10.1016/j.toxicon.2023.107030] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 01/05/2023] [Accepted: 01/12/2023] [Indexed: 01/15/2023]
Abstract
A high diversity of rattlesnake species can be found in the Baja California peninsula and the island of the Gulf of California, nevertheless, their venom has been poorly evaluated. The aim of this work was to present the first characterization of endemic Crotalus mitchellii, micro endemic C. polisi and C. thalassoporus venoms. All samples provoke human plasma coagulation showing doses in the rank of 2.3-41.0 μg and also produce rapid hydrolysis of the alpha chain of bovine fibrinogen while the beta chain is attacked at larger incubation periods by C. polisi and especially by C. thalassoporus. Phospholipase activity ranging from 23.2 to 173.8 U/mg. The venoms of C. thalassoporus and C. polisi show very high hemorrhagic activity (from 0.03 to 0.31 μg). A total of 130 toxin-related proteins were identified and classified into ten families. Crotalus mitchellii venom was characterized by high abundance of crotoxin-like and other phospholipase proteins (34.5%) and serine proteinases (29.8%). Crotalus polisi showed a similar proportion of metalloproteinases (34%) and serine proteinases (22.8%) components with important contribution of C-type lectins (14.3%) and CRiSP (14.0%) proteins. Venom of C. thalassoporus is dominated by metalloproteases that amount to more than 66% of total toxin proteins. These results provide a foundation for comprehending the biological, ecological and evolutionary significance of venom composition of speckled rattlesnake from the Baja California peninsula.
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3
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Weaver S, McGaugh SE, Kono TJY, Macip-Rios R, Gluesenkamp AG. Assessing genomic and ecological differentiation among subspecies of the Rough-footed Mud Turtle, Kinosternon hirtipes. J Hered 2022; 113:538-551. [PMID: 35922036 DOI: 10.1093/jhered/esac036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 08/02/2022] [Indexed: 11/13/2022] Open
Abstract
Combining genetic and ecological measures of differentiation can provide compelling evidence for ecological and genetic divergence among lineages. The Rough-footed Mud Turtle, Kinosternon hirtipes, is distributed from the Trans-Pecos region of Texas to the highlands of Central Mexico and contains six described subspecies, five of which are extant. We use ddRAD sequencing and species distribution models to assess levels of ecological and genetic differentiation among these subspecies. We also predict changes in climatically suitable habitat under different climate change scenarios and assess levels of genetic diversity and inbreeding within each lineage. Our results show that there is strong genetic and ecological differentiation among multiple lineages within K. hirtipes, and that this differentiation appears to be the result of vicariance associated with the Trans-Mexican Volcanic Belt. We propose changes to subspecies designations to more accurately reflect the evolutionary relationships among populations and assess threats to each subspecies.
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Affiliation(s)
- Sam Weaver
- Ecology, Evolution, and Behavior, University of Minnesota, 140 Gortner Lab, Saint Paul, MN 55108, USA
| | - Suzanne E McGaugh
- Ecology, Evolution, and Behavior, University of Minnesota, 140 Gortner Lab, Saint Paul, MN 55108, USA
| | - Thomas J Y Kono
- Ecology, Evolution, and Behavior, University of Minnesota, 140 Gortner Lab, Saint Paul, MN 55108, USA
| | - Rodrigo Macip-Rios
- Escuela Nacional de Estudios Superiores, Unidad Morelia, Universidad Nacional Autónoma de México, Antigua Carretera a Pátzcuaro No.8701, Col. Ex Hacienda de San José de la Huerta, CP 58190 Morelia, Michoacán, México.,Laboratorio Nacional de Síntesis Ecológica, Unidad Morelia, Universidad Nacional Autónoma de México, Antigua Carretera a Pátzcuaro No.8701, Col. Ex Hacienda de San José de la Huerta, CP 58190 Morelia, Michoacán, México
| | - Andrew G Gluesenkamp
- Center for Conservation and Research, San Antonio Zoo, 3903 N. St. Mary's Street, San Antonio, Texas 78212 USA
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4
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VenomMaps: Updated species distribution maps and models for New World pitvipers (Viperidae: Crotalinae). Sci Data 2022; 9:232. [PMID: 35614080 PMCID: PMC9132920 DOI: 10.1038/s41597-022-01323-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 04/19/2022] [Indexed: 11/19/2022] Open
Abstract
Beyond providing critical information to biologists, species distributions are useful for naturalists, curious citizens, and applied disciplines including conservation planning and medical intervention. Venomous snakes are one group that highlight the importance of having accurate information given their cosmopolitan distribution and medical significance. Envenomation by snakebite is considered a neglected tropical disease by the World Health Organization and venomous snake distributions are used to assess vulnerability to snakebite based on species occurrence and antivenom/healthcare accessibility. However, recent studies highlighted the need for updated fine-scale distributions of venomous snakes. Pitvipers (Viperidae: Crotalinae) are responsible for >98% of snakebites in the New World. Therefore, to begin to address the need for updated fine-scale distributions, we created VenomMaps, a database and web application containing updated distribution maps and species distribution models for all species of New World pitvipers. With these distributions, biologists can better understand the biogeography and conservation status of this group, researchers can better assess vulnerability to snakebite, and medical professionals can easily discern species found in their area. Measurement(s) | Species Distributions | Technology Type(s) | Geographic Information System • Species Distribution Model (MaxEnt/kuenm) | Factor Type(s) | Occurrence Records • Environmental Data | Sample Characteristic - Organism | Crotalinae | Sample Characteristic - Location | North America • South America |
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5
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OUP accepted manuscript. Biol J Linn Soc Lond 2022. [DOI: 10.1093/biolinnean/blab174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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6
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Myers EA. Genome-wide data reveal extensive gene flow during the diversification of the western rattlesnakes (Viperidae: Crotalinae: Crotalus). Mol Phylogenet Evol 2021; 165:107313. [PMID: 34537323 DOI: 10.1016/j.ympev.2021.107313] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 08/28/2021] [Accepted: 09/14/2021] [Indexed: 11/15/2022]
Abstract
Hybridization and introgression are important, but often overlooked processes when inferring phylogenies. When these processes are not accounted for and a strictly diverging phylogenetic model is applied to groups with a history of hybridization, phylogenetic inference and parameter estimation can be inaccurate. Recent developments in phylogenetic network approaches coupled with the increasing availability of genomic data allow inferences of reticulate evolutionary histories across the tree of life. The western rattlesnake species group (C. viridis species complex, C. mitchellii species complex, C. scutulutas, and C. tigris) is an iconic snake lineage that is widespread across western North America. This group is composed of several species complexes with unclear species limits, likely the result of ongoing gene flow among nascent lineages. Here I generate reduced representation genomic data and test for a history of reticulation within this group. I demonstrate that all species have undergone hybridization with at least one other lineage, suggesting introgression is widespread in this group. Topologies differ between phylogenies estimated under the multispecies coalescent and multispecies network coalescent methods, indicating that gene flow has obscured phylogenetic relationships within this group. These past introgression events are predominantly restricted to species that co-occur geographically. However, within species that have a history of introgression, this signature is detected regardless of specimen sampling across geography. Overall, my results suggest the accumulation of reproductive isolating barriers occurs slowly in rattlesnakes which likely leads to the difficulty in delimiting species, furthermore, the results of this study have implications for trait evolution in this group.
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Affiliation(s)
- Edward A Myers
- Department of Herpetology, American Museum of Natural History, New York, NY, USA; Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.
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7
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Diet and Feeding Frequency in the Southwestern Speckled Rattlesnake (Crotalus pyrrhus): Ontogenetic, Sexual, Geographic, and Seasonal Variation. J HERPETOL 2021. [DOI: 10.1670/19-144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Schield DR, Perry BW, Adams RH, Card DC, Jezkova T, Pasquesi GIM, Nikolakis ZL, Row K, Meik JM, Smith CF, Mackessy SP, Castoe TA. Allopatric divergence and secondary contact with gene flow: a recurring theme in rattlesnake speciation. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz077] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
The study of recently diverged lineages whose geographical ranges come into contact can provide insight into the early stages of speciation and the potential roles of reproductive isolation in generating and maintaining species. Such insight can also be important for understanding the strategies and challenges for delimiting species within recently diverged species complexes. Here, we use mitochondrial and nuclear genetic data to study population structure, gene flow and demographic history across a geographically widespread rattlesnake clade, the western rattlesnake species complex (Crotalus cerberus, Crotalus viridis, Crotalus oreganus and relatives), which contains multiple lineages with ranges that overlap geographically or contact one another. We find evidence that the evolutionary history of this group does not conform to a bifurcating tree model and that pervasive gene flow has broadly influenced patterns of present-day genetic diversity. Our results suggest that lineage diversity has been shaped largely by drift and divergent selection in isolation, followed by secondary contact, in which reproductive isolating mechanisms appear weak and insufficient to prevent introgression, even between anciently diverged lineages. The complexity of divergence and secondary contact with gene flow among lineages also provides new context for why delimiting species within this complex has been difficult and contentious historically.
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Affiliation(s)
- Drew R Schield
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Blair W Perry
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Richard H Adams
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Daren C Card
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Tereza Jezkova
- Department of Biology, Miami University of Ohio, Oxford, OH, USA
| | | | | | - Kristopher Row
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Jesse M Meik
- Department of Biological Sciences, Tarleton State University, Stephenville, TX, USA
| | - Cara F Smith
- School of Biological Sciences, University of Northern Colorado, Greeley, CO, USA
| | - Stephen P Mackessy
- School of Biological Sciences, University of Northern Colorado, Greeley, CO, USA
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
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Lemos-Espinal JA, Smith GR, Rorabaugh JC. A conservation checklist of the amphibians and reptiles of Sonora, Mexico, with updated species lists. Zookeys 2019; 829:131-160. [PMID: 30914839 PMCID: PMC6422993 DOI: 10.3897/zookeys.829.32146] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 01/28/2019] [Indexed: 11/12/2022] Open
Abstract
Sonora has a rich natural diversity, including reptiles and amphibians. Sonora's location on the United States-Mexico border creates some unique conservation challenges for its wildlife. We compiled a list of the amphibian and reptile species currently known for Sonora, summarized the conservation status of these species, and compared our list of species with known species lists for adjacent states. The herpetofauna of Sonora comprises 200 species of amphibians and reptiles (38 amphibians and 162 reptiles). Overall, Sonora shares the most species with Chihuahua, Sinaloa, and Arizona. Approximately 11% of the amphibian and reptile species are IUCN listed, but 35.5% are placed in a protected category by SEMARNAT, and 32.6% are categorized as high risk by the Environmental Vulnerability Score.
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Affiliation(s)
- Julio A Lemos-Espinal
- Laboratorio de Ecología-UBIPRO, FES Iztacala UNAM, Avenida los Barrios 1, Los Reyes Iztacala, Tlalnepantla, edo. de Mexico, 54090, Mexico Universidad Nacional Autónoma de México Tlalnepantla Mexico
| | - Geoffrey R Smith
- Department of Biology, Denison University, Granville, Ohio 43023, USA Denison University Granville United States of America
| | - James C Rorabaugh
- P.O. Box 31, Saint David, Arizona 85630, USA Unaffilaited Phoenix United States of America
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10
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Castellanos AA, Huntley JW, Voelker G, Lawing AM. Environmental filtering improves ecological niche models across multiple scales. Methods Ecol Evol 2019. [DOI: 10.1111/2041-210x.13142] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Adrian A. Castellanos
- Department of Wildlife and Fisheries SciencesTexas A&M University College Station Texas
| | - Jerry W. Huntley
- Department of Wildlife and Fisheries SciencesTexas A&M University College Station Texas
- Department of OrnithologyAmerican Museum of Natural History New York City New York
| | - Gary Voelker
- Department of Wildlife and Fisheries SciencesTexas A&M University College Station Texas
| | - A. Michelle Lawing
- Department of Ecosystem Science and ManagementTexas A&M University College Station Texas
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11
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DNA barcodes from snake venom: a broadly applicable method for extraction of DNA from snake venoms. Biotechniques 2018; 65:339-345. [PMID: 30477329 DOI: 10.2144/btn-2018-0096] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
DNA barcoding is a simple technique used to develop a large-scale system of classification that is broadly applicable across a wide variety of taxa. DNA-based analysis of snake venoms can provide a system of classification independent of currently accepted taxonomic relationships by generating DNA barcodes specific to each venom sample. DNA purification from dried snake venoms has previously required large amounts of starting material, has resulted in low yields and inconsistent amplification, and was possible with front-fanged snakes only. Here, we present a modified DNA extraction protocol applied to venoms of both front- and rear-fanged snakes that requires significantly less starting material (1 mg) and yields sufficient amounts of DNA for successful PCR amplification of regions commonly used for DNA barcoding. [Formula: see text].
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12
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Schield DR, Adams RH, Card DC, Corbin AB, Jezkova T, Hales NR, Meik JM, Perry BW, Spencer CL, Smith LL, García GC, Bouzid NM, Strickland JL, Parkinson CL, Borja M, Castañeda-Gaytán G, Bryson RW, Flores-Villela OA, Mackessy SP, Castoe TA. Cryptic genetic diversity, population structure, and gene flow in the Mojave rattlesnake (Crotalus scutulatus). Mol Phylogenet Evol 2018; 127:669-681. [DOI: 10.1016/j.ympev.2018.06.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 05/30/2018] [Accepted: 06/06/2018] [Indexed: 10/28/2022]
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13
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Affiliation(s)
| | - Jesse M. Meik
- Department of Biological Sciences, Tarleton State University, Stephenville, TX USA
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14
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Alternative methods of phylogenetic inference for the Patagonian lizard group Liolaemus elongatus-kriegi (Iguania: Liolaemini) based on mitochondrial and nuclear markers. Mol Phylogenet Evol 2018; 120:158-169. [DOI: 10.1016/j.ympev.2017.11.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 11/07/2017] [Accepted: 11/27/2017] [Indexed: 11/18/2022]
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15
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Meik JM, Schaack S, Flores-Villela O, Streicher JW. Integrative taxonomy at the nexus of population divergence and speciation in insular speckled rattlesnakes. J NAT HIST 2018. [DOI: 10.1080/00222933.2018.1429689] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Jesse M. Meik
- Department of Biological Sciences, Tarleton State University, Stephenville, TX, USA
| | - Sarah Schaack
- Department of Biology, Reed College, Portland, OR, USA
| | - Oscar Flores-Villela
- Museo de Zoología, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
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16
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Book Reviews. COPEIA 2017. [DOI: 10.1643/ot-17-687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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17
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Zhang S, Wang Z. Inferring Passenger Denial Behavior of Taxi Drivers from Large-Scale Taxi Traces. PLoS One 2016; 11:e0165597. [PMID: 27812121 PMCID: PMC5094781 DOI: 10.1371/journal.pone.0165597] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Accepted: 10/16/2016] [Indexed: 11/18/2022] Open
Abstract
How to understand individual human actions is a fundamental question to modern science, which drives and incurs many social, technological, racial, religious and economic phenomena. Human dynamics tries to reveal the temporal pattern and internal mechanism of human actions in letter or electronic communications, from the perspective of continuous interactions among friends or acquaintances. For interactions between stranger to stranger, taxi industry provide fruitful phenomina and evidence to investigate the action decisions. In fact, one striking disturbing events commonly reported in taxi industry is passenger refusing or denial, whose reasons vary, including skin color, blind passenger, being a foreigner or too close destination, religion reasons and anti specific nationality, so that complaints about taxi passenger refusing have to be concerned and processed carefully by local governments. But more universal factors for this phenomena are of great significance, which might be fulfilled by big data research to obtain novel insights in this question. In this paper, we demonstrate the big data analytics application in revealing novel insights from massive taxi trace data, which, for the first time, validates the passengers denial in taxi industry and estimates the denial ratio in Beijing city. We first quantify the income differentiation facts among taxi drivers. Then we find out that choosing the drop-off places also contributes to the high income for taxi drivers, compared to the previous explanation of mobility intelligence. Moreover, we propose the pick-up, drop-off and grid diversity concepts and related diversity analysis suggest that, high income taxi drivers will deny passengers in some situations, so as to choose the passengers' destination they prefer. Finally we design an estimation method for denial ratio and infer that high income taxi drivers will deny passengers with 8.52% likelihood in Beijing. Our work exhibits the power of big data analysis in revealing some dark side investigation.
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Affiliation(s)
- Sihai Zhang
- Key Laboratory of Wireless-Optical Communications, Chinese Academy of Sciences, University of Science and Technology of China, Hefei, Anhui, 230017, China
- * E-mail:
| | - Zhiyang Wang
- Key Laboratory of Wireless-Optical Communications, Chinese Academy of Sciences, University of Science and Technology of China, Hefei, Anhui, 230017, China
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18
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Aguilar C, Wood PL, Belk MC, Duff MH, Sites JW. Different roads lead to Rome: Integrative taxonomic approaches lead to the discovery of two new lizard lineages in theLiolaemus montanusgroup (Squamata: Liolaemidae). Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12890] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Cesar Aguilar
- Department of Biology and M. L. Bean Life Science Museum; Brigham Young University (BYU); Provo UT 84602 USA
- Departamento de Herpetologia; Museo de Historia Natural de San Marcos (MUSM); Av. Arenales 1256, Jesus Maria Lima Peru
- Facultad de Ciencias Biologicas; Instituto de Ciencias Biologicas Antonio Raimondi; Universidad Nacional Mayor de San Marcos; Lima Peru
| | - Perry L. Wood
- Department of Biology and M. L. Bean Life Science Museum; Brigham Young University (BYU); Provo UT 84602 USA
| | - Mark C. Belk
- Department of Biology and M. L. Bean Life Science Museum; Brigham Young University (BYU); Provo UT 84602 USA
| | - Mike H. Duff
- Department of Biology and M. L. Bean Life Science Museum; Brigham Young University (BYU); Provo UT 84602 USA
| | - Jack W. Sites
- Department of Biology and M. L. Bean Life Science Museum; Brigham Young University (BYU); Provo UT 84602 USA
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19
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Burns M, Starrett J, Derkarabetian S, Richart CH, Cabrero A, Hedin M. Comparative performance of double‐digest
RAD
sequencing across divergent arachnid lineages. Mol Ecol Resour 2016; 17:418-430. [DOI: 10.1111/1755-0998.12575] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 06/23/2016] [Indexed: 11/28/2022]
Affiliation(s)
- Mercedes Burns
- Department of Biology San Diego State University 5500 Campanile Drive San Diego CA 92182 USA
| | - James Starrett
- Department of Biology San Diego State University 5500 Campanile Drive San Diego CA 92182 USA
| | - Shahan Derkarabetian
- Department of Biology San Diego State University 5500 Campanile Drive San Diego CA 92182 USA
- Department of Biology University of California 900 University Avenue Riverside CA 92521 USA
| | - Casey H. Richart
- Department of Biology San Diego State University 5500 Campanile Drive San Diego CA 92182 USA
- Department of Biology University of California 900 University Avenue Riverside CA 92521 USA
| | - Allan Cabrero
- Department of Biology San Diego State University 5500 Campanile Drive San Diego CA 92182 USA
| | - Marshal Hedin
- Department of Biology San Diego State University 5500 Campanile Drive San Diego CA 92182 USA
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20
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Lawing AM, Polly PD, Hews DK, Martins EP. Including Fossils in Phylogenetic Climate Reconstructions: A Deep Time Perspective on the Climatic Niche Evolution and Diversification of Spiny Lizards (Sceloporus). Am Nat 2016; 188:133-48. [PMID: 27420780 DOI: 10.1086/687202] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Fossils and other paleontological information can improve phylogenetic comparative method estimates of phenotypic evolution and generate hypotheses related to species diversification. Here, we use fossil information to calibrate ancestral reconstructions of suitable climate for Sceloporus lizards in North America. Integrating data from the fossil record, general circulation models of paleoclimate during the Miocene, climate envelope modeling, and phylogenetic comparative methods provides a geographically and temporally explicit species distribution model of Sceloporus-suitable habitat through time. We provide evidence to support the historic biogeographic hypothesis of Sceloporus diversification in warm North American deserts and suggest a relatively recent Sceloporus invasion into Mexico around 6 Ma. We use a physiological model to map extinction risk. We suggest that the number of hours of restriction to a thermal refuge limited Sceloporus from inhabiting Mexico until the climate cooled enough to provide suitable habitat at approximately 6 Ma. If the future climate returns to the hotter climates of the past, Mexico, the place of highest modern Sceloporus richness, will no longer provide suitable habitats for Sceloporus to survive and reproduce.
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21
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Diversity-dependent cladogenesis throughout western Mexico: Evolutionary biogeography of rattlesnakes (Viperidae: Crotalinae: Crotalus and Sistrurus). Mol Phylogenet Evol 2016; 97:145-154. [DOI: 10.1016/j.ympev.2015.12.020] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 12/15/2015] [Accepted: 12/30/2015] [Indexed: 11/22/2022]
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