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Li X, Wang X, Zhang D, Huang J, Shi W, Wang J. Historical spread routes of wild walnuts in Central Asia shaped by man-made and nature. FRONTIERS IN PLANT SCIENCE 2024; 15:1394409. [PMID: 38903444 PMCID: PMC11187337 DOI: 10.3389/fpls.2024.1394409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 05/17/2024] [Indexed: 06/22/2024]
Abstract
Walnuts have substantial economic value and are of significant interest being a wild-cultivated species. The study has re-sequenced the entire genome of the wild walnut, aligning it with the walnut reference genome, to identify 2,021,717 single nucleotide polymorphisms (SNPs). These were used to examine the genetics of 130 wild walnut samples collected from three countries. Utilizing structural and principal component analysis, the walnut samples from Central Asia were classified into four populations: Ili ah in Xinjiang (I), Dushanbe region in Tajikistan (II), Sary-Chelek, Arslanbob in Kara-Alma regions of Kyrgyzstan (III), and Kok-Tundy region of Kyrgyzstan (IV). The 4 groups showed large differences in nucleotide diversity, population differentiation, and linkage disequilibrium decay, as well as gene flow among them. The present geographic distribution of these populations does not align with the genetic distribution pattern as the populations of Central Asian wild walnuts have experienced similar population dynamics in the past, i.e., the highest effective population size at ca. 6 Ma, two sharp population declines at 6 and 0.2 Ma, and convergence at ca. 0.2 Ma. The genetic distribution patterns are better explained by human activity, notably through archaeological findings of walnut use and the influence of the Silk Road, rather than by current geographic distributions.
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Affiliation(s)
- Xuerong Li
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Xinjiang Key Lab of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- College of Forestry and Landscape Architecture, Xinjiang Agricultural University, Urumqi, China
| | - Xiyong Wang
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Xinjiang Key Lab of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Turpan Eremophytes Botanic Garden, Chinese Academy of Sciences, Turpan, China
| | - Daoyuan Zhang
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Xinjiang Key Lab of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- College of Forestry and Landscape Architecture, Xinjiang Agricultural University, Urumqi, China
- Turpan Eremophytes Botanic Garden, Chinese Academy of Sciences, Turpan, China
| | - Junhua Huang
- College of Forestry and Landscape Architecture, Xinjiang Agricultural University, Urumqi, China
| | - Wei Shi
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Xinjiang Key Lab of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- College of Forestry and Landscape Architecture, Xinjiang Agricultural University, Urumqi, China
| | - Jiancheng Wang
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Xinjiang Key Lab of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Turpan Eremophytes Botanic Garden, Chinese Academy of Sciences, Turpan, China
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Jiang X, Liu L, Guo H, Liu P, Tian W, Ou F, Ding J, Zhang W, Chang Y. Establishment of Parentage Identification Method for Sea Urchin Strongylocentrotus intermedius Based on SSR-seq Technology. Genes (Basel) 2024; 15:630. [PMID: 38790259 PMCID: PMC11120681 DOI: 10.3390/genes15050630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 05/08/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
To establish a parentage identification method for Strongylocentrotus intermedius, 15 microsatellite loci and simple sequence repeat sequencing (SSR-seq) technology were used to perform SSR sequencing and typing of the validation population with known pedigree information and the simulation population. Cervus v3.0 was used for gene frequency statistics, simulated analysis, and parentage identification analysis. The results showed that, in validation population, using 15 microsatellite loci, the highest success rate of parent pairs identification was 86%, the highest success rate of female parent identification was 93%, and the highest success rate of male parent identification was 90%. The simulated population was analyzed using 12-15 loci, and the identification rate was up to 90%. In cases where accurate parentage was not achieved, individuals could exhibit genetic similarities with 1-3 male or female parents. Individuals identified as lacking a genetic relationship can be selected as parents to prevent inbreeding. This study shows that parent pairs or single parents of most offspring can be identified successfully using these 15 selected loci. The results lay a foundation for the establishment of a parentage identification method for S. intermedius.
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Affiliation(s)
| | | | | | | | | | | | | | - Weijie Zhang
- Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian 116023, China; (X.J.); (Y.C.)
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Jin K, McCoy BM, Goldman EA, Usova V, Tkachev V, Chitsazan AD, Kakebeen A, Jeffery U, Creevy KE, Wills A, Snyder‐Mackler N, Promislow DEL. DNA methylation and chromatin accessibility predict age in the domestic dog. Aging Cell 2024; 23:e14079. [PMID: 38263575 PMCID: PMC11019125 DOI: 10.1111/acel.14079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 01/25/2024] Open
Abstract
Across mammals, the epigenome is highly predictive of chronological age. These "epigenetic clocks," most of which have been built using DNA methylation (DNAm) profiles, have gained traction as biomarkers of aging and organismal health. While the ability of DNAm to predict chronological age has been repeatedly demonstrated, the ability of other epigenetic features to predict age remains unclear. Here, we use two types of epigenetic information-DNAm, and chromatin accessibility as measured by ATAC-seq-to develop age predictors in peripheral blood mononuclear cells sampled from a population of domesticated dogs. We measured DNAm and ATAC-seq profiles for 71 dogs, building separate predictive clocks from each, as well as the combined dataset. We also use fluorescence-assisted cell sorting to quantify major lymphoid populations for each sample. We found that chromatin accessibility can accurately predict chronological age (R2 ATAC = 26%), though less accurately than the DNAm clock (R2 DNAm = 33%), and the clock built from the combined datasets was comparable to both (R2 combined = 29%). We also observed various populations of CD62L+ T cells significantly correlated with dog age. Finally, we found that all three clocks selected features that were in or near at least two protein-coding genes: BAIAP2 and SCARF2, both previously implicated in processes related to cognitive or neurological impairment. Taken together, these results highlight the potential of chromatin accessibility as a complementary epigenetic resource for modeling and investigating biologic age.
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Affiliation(s)
- Kelly Jin
- Department of Laboratory Medicine & PathologyUniversity of WashingtonSeattleWashingtonUSA
| | - Brianah M. McCoy
- Center for Evolution and MedicineArizona State UniversityTempeArizonaUSA
- School of Life SciencesArizona State UniversityTempeArizonaUSA
| | | | - Viktoria Usova
- Department of Laboratory Medicine & PathologyUniversity of WashingtonSeattleWashingtonUSA
| | - Victor Tkachev
- Division of Pediatric Hematology/OncologyBoston Children's HospitalBostonMassachusettsUSA
- Dana Farber Cancer InstituteBostonMassachusettsUSA
- Harvard Medical SchoolBostonMassachusettsUSA
| | - Alex D. Chitsazan
- Department of BiochemistryUniversity of WashingtonSeattleWashingtonUSA
| | - Anneke Kakebeen
- Department of BiochemistryUniversity of WashingtonSeattleWashingtonUSA
| | - Unity Jeffery
- College of Veterinary MedicineTexas A & M UniversityCollege StationTexasUSA
| | - Kate E. Creevy
- College of Veterinary MedicineTexas A & M UniversityCollege StationTexasUSA
| | - Andrea Wills
- Department of BiochemistryUniversity of WashingtonSeattleWashingtonUSA
| | - Noah Snyder‐Mackler
- Center for Evolution and MedicineArizona State UniversityTempeArizonaUSA
- School of Life SciencesArizona State UniversityTempeArizonaUSA
| | - Daniel E. L. Promislow
- Department of Laboratory Medicine & PathologyUniversity of WashingtonSeattleWashingtonUSA
- Department of BiologyUniversity of WashingtonSeattleWashingtonUSA
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Li Z, Wang Q, Lv N, Xu G, Yang X, Zhu B. Genome-wide identification of endogenous retrovirus elements and their active transcription in mink genome. MLIFE 2023; 2:201-208. [PMID: 38817617 PMCID: PMC10989824 DOI: 10.1002/mlf2.12074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 04/12/2023] [Accepted: 05/15/2023] [Indexed: 06/01/2024]
Abstract
Mammalian endogenous retroviruses (ERVs) are ancient retroviruses that have been integrated into genomes. ERVs were believed to be inactive until the discovery of ERV transcription in the mouse genome. However, the transcription level and function of ERV elements in mammalian genomes are not well understood. In this study, we performed the first genome-wide scanning of ERV loci in the American mink (Neogale vison) genome (NeoERV) followed by transcriptomic analysis to detect actively transcribed NeoERV elements. A total of 365,791 NeoERV loci were identified, and161,205 (44%) of these loci were found to be actively transcribed based on transcriptomic data from three types of tissues (amygdala, trachea and lung). More than one third of the actively transcribed NeoERV loci were tissue-specific. Furthermore, some of the active loci were associated with host gene transcription, and the level of NeoERV transcription was positively correlated with that of host genes, specifically when active loci were located in overlapped gene regions. An in-depth analysis of the envelope protein coding env gene showed that, in general, its transcription level was higher than that of NeoERVs, which is believed to be associated with host immunity.
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Affiliation(s)
- Zheng Li
- CAS Key Laboratory of Pathogen Microbiology and ImmunologyInstitute of Microbiology, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Qing Wang
- CAS Key Laboratory of Pathogen Microbiology and ImmunologyInstitute of Microbiology, Chinese Academy of SciencesBeijingChina
- Jiangxi Science and Technology Normal UniversityNanchangChina
| | - Na Lv
- CAS Key Laboratory of Pathogen Microbiology and ImmunologyInstitute of Microbiology, Chinese Academy of SciencesBeijingChina
- Jinan Microecological Biomedicine Shandong LaboratoryJinanChina
| | - Guojin Xu
- CAS Key Laboratory of Pathogen Microbiology and ImmunologyInstitute of Microbiology, Chinese Academy of SciencesBeijingChina
| | - Xuemei Yang
- Beijing Pediatric Research InstituteBeijingChina
| | - Baoli Zhu
- CAS Key Laboratory of Pathogen Microbiology and ImmunologyInstitute of Microbiology, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
- Jinan Microecological Biomedicine Shandong LaboratoryJinanChina
- Department of Pathogenic Biology, School of Basic Medical SciencesSouthwest Medical UniversityLuzhouChina
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5
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Dai C, Feng P. Multiple concordant cytonuclear divergences and potential hybrid speciation within a species complex in Asia. Mol Phylogenet Evol 2023; 180:107709. [PMID: 36657627 DOI: 10.1016/j.ympev.2023.107709] [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: 08/23/2022] [Revised: 12/29/2022] [Accepted: 01/12/2023] [Indexed: 01/19/2023]
Abstract
Various environmental factors impact the distribution, population structure, demography and evolutionary trajectory of a bird species, leading to genetic and morphological divergences between populations across its distribution. The Paradoxornis webbianus species complex is found throughout much of East Asia, where its geographically distinct populations exhibit dramatic morphological variation. This has resulted in a hotly debated taxonomy. This study intended to identify genetic divergence patterns and their underlying contributing factors for this species complex. We collected 243 birds, whose data was combined with those available in GenBank to perform phylogeographic analyses using one mitochondrial and six nuclear loci. Six mitochondrial clades were observed in the species complex, while individual-based Bayesian clustering using nuclear markers showed multiple congruent breaks. Overall, the six molecular lineages could be recognized as independent species under the lineage species concept in view of genetic divergence, clade-specific morphological changes and distribution: P. webbianus, P. w. bulomachus, P. alphonsianus, P. a. ganluoensis, P. brunneus brunneus and P. b. ricketti. The estimated divergence times range from 0.46 to 3.36 million years ago, suggesting it was likely impacted by paleoclimatic changes. Interestingly, P. alphonsianus carries two divergent mitochondrial lineages shared with P. webbianus and P. a. ganluoensis, respectively, and analyses based on nuclear loci found a similar pattern. We discussed the various hypotheses for this pattern and argued that P. alphonsianus was likely the result of hybridization between P. webbianus and P. a. ganluoensis. Further data on genome, transcriptome and breeding ecology are needed to address the hypothesis of hybrid speciation and its underlying mechanisms.
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Affiliation(s)
- Chuanyin Dai
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin 541006, China; Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin 541006, China.
| | - Ping Feng
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin 541006, China; Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin 541006, China
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Yang Y, Lyu M, Liu J, Wu J, Wang Q, Xie T, Li H, Chen R, Sun D, Yang Y, Yao X. Construction of an SNP fingerprinting database and population genetic analysis of 329 cauliflower cultivars. BMC PLANT BIOLOGY 2022; 22:522. [PMID: 36357859 PMCID: PMC9647966 DOI: 10.1186/s12870-022-03920-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 10/31/2022] [Indexed: 06/16/2023]
Abstract
Cauliflower is one of the most important vegetable crops grown worldwide. However, the lack of genetic diversity information and efficient molecular markers hinders efforts to improve cauliflower. This study aims to construct DNA fingerprints for 329 cauliflower cultivars based on SNP markers and the KASP system. After rigorous filtering, a total of 1662 candidate SNPs were obtained from nearly 17.9 million SNP loci. The mean values of PIC, MAF, heterozygosity and gene diversity of these SNPs were 0.389, 0.419, 0.075, and 0.506, respectively. We developed a program for in silico simulations on 153 core germplasm samples to generate ideal SNP marker sets from the candidates. Finally, 41 highly polymorphic KASP markers were selected and applied to identify 329 cauliflower cultivars, mainly collected from the public market. Furthermore, based on the KASP genotyping data, we performed phylogenetic analysis and population structure analysis of the 329 cultivars. As a result, these cultivars could be classified into three major clusters, and the classification patterns were significantly related to their curd solidity and geographical origin. Finally, fingerprints of the 329 cultivars and 2D barcodes with the genetic information of each sample were generated. The fingerprinting database developed in this study provides a practical tool for identifying the authenticity and purity of cauliflower seeds and valuable genetic information about the current cauliflower cultivars.
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Affiliation(s)
- Yuyao Yang
- Tianjin Academy of Agricultural Sciences, Tianjin, 300192, China
- College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Mingjie Lyu
- Tianjin Academy of Agricultural Sciences, Tianjin, 300192, China
| | - Jun Liu
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jianjin Wu
- Tianjin Agricultural Development Service Center, Tianjin, 300061, China
| | - Qian Wang
- Tianjin Academy of Agricultural Sciences, Tianjin, 300192, China
| | - Tianyu Xie
- Tianjin Academy of Agricultural Sciences, Tianjin, 300192, China
| | - Haichao Li
- Tianjin Academy of Agricultural Sciences, Tianjin, 300192, China
- College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Rui Chen
- Tianjin Academy of Agricultural Sciences, Tianjin, 300192, China
| | - Deling Sun
- Tianjin Academy of Agricultural Sciences, Tianjin, 300192, China
| | - Yingxia Yang
- Tianjin Academy of Agricultural Sciences, Tianjin, 300192, China.
| | - Xingwei Yao
- Tianjin Academy of Agricultural Sciences, Tianjin, 300192, China.
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vonHoldt BM, Brzeski KE, Aardema ML, Schell CJ, Rutledge LY, Fain SR, Shutt AC, Linderholm A, Murphy WJ. Persistence and expansion of cryptic endangered red wolf genomic ancestry along the American Gulf coast. Mol Ecol 2022; 31:5440-5454. [PMID: 34585803 DOI: 10.1111/mec.16200] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 09/03/2021] [Accepted: 09/22/2021] [Indexed: 12/24/2022]
Abstract
Admixture and introgression play a critical role in adaptation and genetic rescue that has only recently gained a deeper appreciation. Here, we explored the geographical and genomic landscape of cryptic ancestry of the endangered red wolf that persists within the genome of a ubiquitous sister taxon, the coyote, all while the red wolf has been extinct in the wild since the early 1980s. We assessed admixture across 120,621 single nucleotiode polymorphism (SNP) loci genotyped in 293 canid genomes. We found support for increased red wolf ancestry along a west-to-east gradient across the southern United States associated with historical admixture in the past 100 years. Southwestern Louisiana and southeastern Texas, the geographical zone where the last red wolves were known prior to extinction in the wild, contained the highest and oldest levels of red wolf ancestry. Further, given the paucity of inferences based on chromosome types, we compared patterns of ancestry on the X chromosome and autosomes. We additionally aimed to explore the relationship between admixture timing and recombination rate variation to investigate gene flow events. We found that X-linked regions of low recombination rates were depleted of introgression, relative to the autosomes, consistent with the large X effect and enrichment with loci involved in maintaining reproductive isolation. Recombination rate was positively correlated with red wolf ancestry across coyote genomes, consistent with theoretical predictions. The geographical and genomic extent of cryptic red wolf ancestry can provide novel genomic resources for recovery plans targeting the conservation of the endangered red wolf.
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Affiliation(s)
- Bridgett M vonHoldt
- Ecology & Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
| | - Kristin E Brzeski
- College of Forest Resources and Environment Science, Michigan Technological University, Houghton, Michigan, USA
| | - Matthew L Aardema
- Department of Biology, Montclair State University, Montclair, New Jersey, USA.,Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, USA
| | - Christopher J Schell
- Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, California, USA
| | - Linda Y Rutledge
- Biology Department, Trent University, Peterborough, Ontario, Canada
| | - Steven R Fain
- USFWS, Clark R. Bavin National Forensics Laboratory, Ashland, Oregon, USA
| | | | - Anna Linderholm
- Department of Anthropology, Texas A&M University, College Station, Texas, USA
| | - William J Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, USA
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Parker DJ, Jaron KS, Dumas Z, Robinson‐Rechavi M, Schwander T. X chromosomes show relaxed selection and complete somatic dosage compensation across
Timema
stick insect species. J Evol Biol 2022; 35:1734-1750. [PMID: 35933721 PMCID: PMC10087215 DOI: 10.1111/jeb.14075] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 05/06/2022] [Accepted: 07/14/2022] [Indexed: 11/29/2022]
Abstract
Sex chromosomes have evolved repeatedly across the tree of life. As they are present in different copy numbers in males and females, they are expected to experience different selection pressures than the autosomes, with consequences including a faster rate of evolution, increased accumulation of sexually antagonistic alleles and the evolution of dosage compensation. Whether these consequences are general or linked to idiosyncrasies of specific taxa is not clear as relatively few taxa have been studied thus far. Here, we use whole-genome sequencing to identify and characterize the evolution of the X chromosome in five species of Timema stick insects with XX:X0 sex determination. The X chromosome had a similar size (approximately 12% of the genome) and gene content across all five species, suggesting that the X chromosome originated prior to the diversification of the genus. Genes on the X showed evidence of relaxed selection (elevated dN/dS) and a slower evolutionary rate (dN + dS) than genes on the autosomes, likely due to sex-biased mutation rates. Genes on the X also showed almost complete dosage compensation in somatic tissues (heads and legs), but dosage compensation was absent in the reproductive tracts. Contrary to prediction, sex-biased genes showed little enrichment on the X, suggesting that the advantage X-linkage provides to the accumulation of sexually antagonistic alleles is weak. Overall, we found the consequences of X-linkage on gene sequences and expression to be similar across Timema species, showing the characteristics of the X chromosome are surprisingly consistent over 30 million years of evolution.
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Affiliation(s)
- Darren J. Parker
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
- Swiss Institute of Bioinformatics Lausanne Switzerland
- School of Natural Sciences Bangor University Bangor UK
| | - Kamil S. Jaron
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
- Swiss Institute of Bioinformatics Lausanne Switzerland
- School of Biological Sciences Institute of Evolutionary Biology University of Edinburgh Edinburgh UK
| | - Zoé Dumas
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
| | - Marc Robinson‐Rechavi
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
- Swiss Institute of Bioinformatics Lausanne Switzerland
| | - Tanja Schwander
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
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Ni X, Ni Z, Ouma KO, Gao Z. Mutations in PmUFGT3 contribute to color variation of fruit skin in Japanese apricot (Prunus mume Sieb. et Zucc.). BMC PLANT BIOLOGY 2022; 22:304. [PMID: 35751035 PMCID: PMC9229503 DOI: 10.1186/s12870-022-03693-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 06/14/2022] [Indexed: 06/01/2023]
Abstract
BACKGROUND Japanese apricot (Prunus mume Sieb. et Zucc.) is popular for both ornamental and processing value, fruit color affects the processing quality, and red pigmentation is the most obvious phenotype associated with fruit color variation in Japanese apricot, mutations in structural genes in the anthocyanin pathway can disrupt the red pigmentation, while the formation mechanism of the red color trait in Japanese apricot is still unclear. RESULTS: One SNP marker (PmuSNP_27) located within PmUFGT3 gene coding region was found highly polymorphic among 44 different fruit skin color cultivars and relative to anthocyanin biosynthesis in Japanese apricot. Meantime, critical mutations were identified in two alleles of PmUFGT3 in the green-skinned type is inactivated by seven nonsense mutations in the coding region, which leads to seven amino acid substitution, resulting in an inactive UFGT enzyme. Overexpression of the PmUFGT3 allele from red-skinned Japanese apricot in green-skinned fruit lines resulted in greater anthocyanin accumulation in fruit skin. Expression of same allele in an Arabidopsis T-DNA mutant deficient in anthocyanidin activity the accumulation of anthocyanins. In addition, using site-directed mutagenesis, we created a single-base substitution mutation (G to T) of PmUFGT3 isolated from green-skinned cultivar, which caused an E to D amino acid substitution and restored the function of the inactive allele of PmUFGT3 from a green-skinned individual. CONCLUSION This study confirms the function of PmUFGT3, and provides insight into the mechanism underlying fruit color determination in Japanese apricot, and possible approaches towards genetic engineering of fruit color.
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Affiliation(s)
- Xiaopeng Ni
- College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing, 210095 China
| | - Zhaojun Ni
- College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing, 210095 China
| | - Kenneth Omondi Ouma
- College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing, 210095 China
| | - Zhihong Gao
- College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing, 210095 China
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Wang Y, Che M, Zheng Z, Liu J, Ji X, Sun Y, Xin J, Gong W, Na S, Jin Y, Wang S, Zhang S. Animal Models for Postoperative Implant‐Related Spinal Infection. Orthop Surg 2022; 14:1049-1058. [PMID: 35466555 PMCID: PMC9163983 DOI: 10.1111/os.13238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 01/13/2022] [Accepted: 01/19/2022] [Indexed: 12/04/2022] Open
Abstract
Postoperative infections following implant‐related spinal surgery are severe and disastrous complications for both orthopaedic surgeons and patients worldwide. They can cause neurological damage, disability, and death. To better understand the mechanism of these destructive complications and intervene in the process, further research is needed. Therefore, there is an urgent need for efficient, accurate, and easily available animal models to study the pathogenesis of spinal infections and develop new and effective anti‐bacterial methods. In this paper, we provide a general review of the commonly used animal models of postoperative implant‐related spinal infections, describe their advantages and disadvantages, and highlight the significance of correctly choosing the model according to the infection aspect under investigation. These models are valuable tools contributing to the better understanding of postoperative spinal infections and will continue to facilitate the invention of novel preventative and treatment strategies for patients with postoperative spinal infections. However, although they are valid and reproducible in some respects, the current animal models present certain limitations. Future ideal spinal infection animal models may assess the bacterial load of the same animal in real‐time in vivo, and better mimic the human anatomy as well as surgical techniques. Strains other than Staphylococcus aureus account for a large proportion of postoperative spinal infections, and thus, the establishment of models to evaluate other types of microbial infections is expected in the future. Furthermore, novel transgenic models established on advancements in genome editing are also likely to be developed in the future.
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Affiliation(s)
- Yongjie Wang
- Department of Spinal Surgery the First Hospital of Jilin University Changchun China
- Jilin Engineering Research Center for Spine and Spinal Cord Injury Changchun China
| | - Mingxue Che
- Department of Spinal Surgery the First Hospital of Jilin University Changchun China
- Jilin Engineering Research Center for Spine and Spinal Cord Injury Changchun China
| | - Zhi Zheng
- Department of Spinal Surgery the First Hospital of Jilin University Changchun China
- Jilin Engineering Research Center for Spine and Spinal Cord Injury Changchun China
| | - Jun Liu
- Institute of Military Veterinary Science the Academy of Military Medical Science of PLA Changchun China
| | - Xue Ji
- Institute of Military Veterinary Science the Academy of Military Medical Science of PLA Changchun China
| | - Yang Sun
- Institute of Military Veterinary Science the Academy of Military Medical Science of PLA Changchun China
| | - Jingguo Xin
- Department of Spinal Surgery the First Hospital of Jilin University Changchun China
- Jilin Engineering Research Center for Spine and Spinal Cord Injury Changchun China
| | - Weiquan Gong
- Department of Spinal Surgery the First Hospital of Jilin University Changchun China
- Jilin Engineering Research Center for Spine and Spinal Cord Injury Changchun China
| | - Shibo Na
- Department of Spinal Surgery the First Hospital of Jilin University Changchun China
- Jilin Engineering Research Center for Spine and Spinal Cord Injury Changchun China
| | - Yuanzhe Jin
- Department of Spinal Surgery the First Hospital of Jilin University Changchun China
- Jilin Engineering Research Center for Spine and Spinal Cord Injury Changchun China
| | - Shuo Wang
- Department of Ophthalmology the Second Hospital of Jilin University Changchun China
| | - Shaokun Zhang
- Department of Spinal Surgery the First Hospital of Jilin University Changchun China
- Jilin Engineering Research Center for Spine and Spinal Cord Injury Changchun China
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11
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Zou M, Jiang S, Wang F, Zhao L, Zhang C, Bao Y, Chen Y, Xia Z. Feature Compression Applications of Genetic Algorithm. Front Genet 2022; 13:757524. [PMID: 35350241 PMCID: PMC8957834 DOI: 10.3389/fgene.2022.757524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 02/21/2022] [Indexed: 11/13/2022] Open
Abstract
With the rapid development of molecular breeding technology and many new varieties breeding, a method is urgently needed to identify different varieties accurately and quickly. Using this method can not only help farmers feel convenient and efficient in the normal cultivation and breeding process but also protect the interests of breeders, producers and users. In this study, single nucleotide polymorphism (SNP) data of 533 Oryza sativa, 284 Solanum tuberosum and 247 Sus scrofa and 544 Manihot esculenta Crantz were used. The original SNPs were filtered and screened to remove the SNPs with deletion number more than 1% or the homozygous genotype 0/0 and 1/1 number less than 2. The correlation between SNPs were calculated, and the two adjacent SNPs with correlation R2 > 0.95 were retained. The genetic algorithm program was developed to convert the genotype format and randomly combine SNPs to calculate a set of a small number of SNPs which could distinguish all varieties in different species as fingerprint data, using Matlab platform. The successful construction of three sets of fingerprints showed that the method developed in this study was effective in animals and plants. The population structure analysis showed that the genetic algorithm could effectively obtain the core SNPs for constructing fingerprints, and the fingerprint was practical and effective. At present, the two-dimensional code of Manihot esculenta Crantz fingerprint obtained by this method has been applied to field planting. This study provides a novel idea for the Oryza sativa, Solanum tuberosum, Sus scrofa and Manihot esculenta Crantz identification of various species, lays foundation for the cultivation and identification of new varieties, and provides theoretical significance for many other species fingerprints construction.
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Affiliation(s)
- Meiling Zou
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China.,Hainan University, Haikou, China
| | | | - Fang Wang
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, China
| | - Long Zhao
- Hainan University, Haikou, China.,Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, China
| | | | | | | | - Zhiqiang Xia
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China.,Hainan University, Haikou, China
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12
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Krofel M, Hatlauf J, Bogdanowicz W, Campbell LAD, Godinho R, Jhala YV, Kitchener AC, Koepfli K, Moehlman P, Senn H, Sillero‐Zubiri C, Viranta S, Werhahn G, Alvares F. Towards resolving taxonomic uncertainties in wolf, dog and jackal lineages of Africa, Eurasia and Australasia. J Zool (1987) 2021. [DOI: 10.1111/jzo.12946] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- M. Krofel
- Biotechnical Faculty University of Ljubljana Ljubljana Slovenia
| | - J. Hatlauf
- University of Natural Resources and Life Sciences Vienna, Department of Integrative Biology and Biodiversity Research Institute of Wildlife Biology and Game Management Vienna Austria
| | - W. Bogdanowicz
- Museum and Institute of Zoology Polish Academy of Sciences Warszawa Poland
| | - L. A. D. Campbell
- Department of Zoology Recanati‐Kaplan Centre; Tubney University of Oxford Wildlife Conservation Research Unit Oxfordshire UK
| | - R. Godinho
- InBIO Laboratório Associado, Campus de Vairão CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos Universidade do Porto Vairão Portugal
- BIOPOLIS Program in Genomics Biodiversity and Land Planning, CIBIO Vairão Portugal
- Departamento de Biologia Faculdade de Ciências Universidade do Porto Porto Portugal
| | - Y. V. Jhala
- Animal Ecology & Conservation Biology Wildlife Institute of India Dehradun India
| | - A. C. Kitchener
- Department of Natural Sciences National Museums Scotland Edinburgh UK
| | - K.‐P. Koepfli
- Smithsonian‐Mason School of Conservation George Mason University Front Royal VA USA
- Smithsonian Conservation Biology Institute Center for Species Survival National Zoological Park Front Royal VA USA
- Computer Technologies Laboratory ITMO University St. Petersburg Russia
| | - P. Moehlman
- IUCN/SSC Equid Specialist Group Tanzania Wildlife Research Institute (TAWIRI) EcoHealth Alliance and The Earth Institute Columbia University Arusha Tanzania
| | - H. Senn
- WildGenes Laboratory Conservation and Science Programmes Royal Zoological Society of Scotland, RZSS Edinburgh UK
| | - C. Sillero‐Zubiri
- Wildlife Conservation Research Unit, Zoology University of Oxford Tubney UK
- IUCN SSC Canid Specialist Group Oxford UK
- Born Free Foundation Horsham UK
| | - S. Viranta
- Faculty of Medicine University of Helsinki Helsinki Finland
| | - G. Werhahn
- IUCN SSC Canid Specialist Group Oxford UK
- Wildlife Conservation Research Unit, Zoology University of Oxford Tubney UK
| | - F. Alvares
- CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos InBIO Laboratório Associado Universidade do Porto Vairão Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning CIBIO Vairão Portugal
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13
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Parker LD, Campana MG, Quinta JD, Cypher B, Rivera I, Fleischer RC, Ralls K, Wilbert TR, Boarman R, Boarman WI, Maldonado JE. An efficient method for simultaneous species, individual, and sex identification via in-solution single nucleotide polymorphism capture from low-quality scat samples. Mol Ecol Resour 2021; 22:1345-1361. [PMID: 34779133 DOI: 10.1111/1755-0998.13552] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/24/2021] [Accepted: 10/27/2021] [Indexed: 12/01/2022]
Abstract
Understanding predator population dynamics is important for conservation management because of the critical roles predators play within ecosystems. Noninvasive genetic sampling methods are useful for the study of predators like canids that can be difficult to capture or directly observe. Here, we introduce the FAECES* method (Fast and Accurate Enrichment of Canid Excrement for Species* and other analyses) which expands the toolbox for canid researchers and conservationists by using in-solution hybridization sequence capture to produce single nucleotide polymorphism (SNP) genotypes for multiple canid species from scat-derived DNA using a single enrichment. We designed a set of hybridization probes to genotype both coyotes (Canis latrans) and kit foxes (Vulpes macrotis) at hundreds of polymorphic SNP loci and we tested the probes on both tissues and field-collected scat samples. We enriched and genotyped by sequencing 52 coyote and 70 kit fox scats collected in and around a conservation easement in the Nevada Mojave Desert. We demonstrate that the FAECES* method produces genotypes capable of differentiating coyotes and kit foxes, identifying individuals and their sex, and estimating genetic diversity and effective population sizes, even using highly degraded, low-quantity DNA extracted from scat. We found that the study area harbours a large and diverse population of kit foxes and a relatively smaller population of coyotes. By replicating our methods in the future, conservationists can assess the impacts of management decisions on canid populations. The method can also be adapted and applied more broadly to enrich and sequence multiple loci from any species of interest using scat or other noninvasive genetic samples.
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Affiliation(s)
- Lillian D Parker
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, District of Columbia, USA.,School of Systems Biology, George Mason University, Fairfax, Virginia, USA
| | - Michael G Campana
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, District of Columbia, USA.,School of Systems Biology, George Mason University, Fairfax, Virginia, USA.,Department of Environmental Science and Policy, George Mason University, Fairfax, Virginia, USA
| | - Jessica D Quinta
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, District of Columbia, USA
| | - Brian Cypher
- Endangered Species Recovery Program, California State University, Turlock, California, USA
| | - Isabel Rivera
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, District of Columbia, USA
| | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, District of Columbia, USA
| | - Katherine Ralls
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, District of Columbia, USA
| | - Tammy R Wilbert
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, District of Columbia, USA
| | - Ryan Boarman
- Conservation Science Research and Consultation, Spring Valley, California, USA
| | - William I Boarman
- Conservation Science Research and Consultation, Spring Valley, California, USA
| | - Jesús E Maldonado
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, District of Columbia, USA.,School of Systems Biology, George Mason University, Fairfax, Virginia, USA.,Department of Environmental Science and Policy, George Mason University, Fairfax, Virginia, USA
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14
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Krzeminska P, Nowacka-Woszuk J, Switonski M. Copy number variation of the SRY gene showed an association with disorders of sex development in Yorkshire Terrier dogs. Anim Genet 2021; 53:152-155. [PMID: 34664728 DOI: 10.1111/age.13147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/04/2021] [Indexed: 11/29/2022]
Abstract
The molecular background of disorders of sex development (DSD) in dogs is poorly understood. Several copies of the SRY genes have been reported in the dog genome. We used droplet digital PCR with the aim of determining variability in SRY copy number and its association with DSD in dogs. Altogether 19 DSD male dogs (XY DSD) of 10 breeds and 87 control dogs of eight breeds were analyzed. Moreover, we performed a comparative analysis of SRY copy number in other canids: wolves (3), red foxes (16), and Chinese raccoon dogs (10). We found that the modal number of SRY copies in dogs, wolves, red foxes, and Chinese raccoon dogs was 3, 3, 1, and 3 respectively. Variability of copy number was only observed in Yorkshire Terriers (two or three copies) and red foxes (one or two copies). An analysis of six DSD Yorkshire Terriers and 38 control males of this breed showed that 50% of the DSD dogs had two copies, while the incidence of this variant was significantly lower in the control dogs (10.5%). Searching for the copy number of the coding and 5'-flanking fragments revealed full concordance with the copy number. These fragments were also sequenced in DSD (19) and control (24) dogs, and no DNA variants were found. We conclude that, in the dog, two or three functional copies of the SRY gene are present, and a smaller number of copies showed an association with the risk of DSD phenotype in Yorkshire Terriers.
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Affiliation(s)
- P Krzeminska
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, Poznan, 60-637, Poland
| | - J Nowacka-Woszuk
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, Poznan, 60-637, Poland
| | - M Switonski
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, Poznan, 60-637, Poland
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15
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Almeida FC, Porzecanski AL, Cracraft JL, Bertelli S. The evolution of tinamous (Palaeognathae: Tinamidae) in light of molecular and combined analyses. Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab080] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
The Neotropical tinamous are of particular interest in our efforts to understand the evolution of modern birds. They inhabit both forested and open environments and, although volant, have limited flight capabilities. Numerous studies have recognized the monophyly of tinamous and their relationships either as sister to the flightless ratites (ostriches, emus and their relatives) or within the ratites themselves. Despite the numerous bird phylogenies published recently, modern investigations of relationships within the tinamous themselves have been limited. Here, we present the first detailed phylogenetic analysis and divergence-date estimation including a significant number of tinamou species, both extant and fossil. The monophyly of most currently recognized polytypic genera is recovered with high support, with the exception of the paraphyletic Nothura and Nothoprocta. The traditional subdivision between those tinamous inhabiting open areas (Nothurinae) and forest environments (Tinaminae) is also confirmed. A temporal calibration of the resultant phylogeny estimates that the basal divergence of crown Tinamidae took place between 31 and 40 Mya.
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Affiliation(s)
- Francisca C Almeida
- Instituto de Ecología, Genética y Evolución (IEGEBA), Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET)/ Universidad de Buenos Aires (UBA), Ciudad Autónoma de Buenos Aires, Argentina
| | - Ana L Porzecanski
- American Museum of Natural History, 200 Central Park West, New York, NY, 10024-5102, USA
| | - Joel L Cracraft
- American Museum of Natural History, 200 Central Park West, New York, NY, 10024-5102, USA
| | - Sara Bertelli
- American Museum of Natural History, 200 Central Park West, New York, NY, 10024-5102, USA
- Fundación Miguel Lillo (FML), Miguel Lillo 251, 4000 San Miguel de Tucumán, Argentina
- Unidad Ejecutora Lillo (UEL) - Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), San Miguel de Tucumán, Tucumán, Argentina
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16
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A global phylogeny of turtles reveals a burst of climate-associated diversification on continental margins. Proc Natl Acad Sci U S A 2021; 118:2012215118. [PMID: 33558231 DOI: 10.1073/pnas.2012215118] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Living turtles are characterized by extraordinarily low species diversity given their age. The clade's extensive fossil record indicates that climate and biogeography may have played important roles in determining their diversity. We investigated this hypothesis by collecting a molecular dataset for 591 individual turtles that, together, represent 80% of all turtle species, including representatives of all families and 98% of genera, and used it to jointly estimate phylogeny and divergence times. We found that the turtle tree is characterized by relatively constant diversification (speciation minus extinction) punctuated by a single threefold increase. We also found that this shift is temporally and geographically associated with newly emerged continental margins that appeared during the Eocene-Oligocene transition about 30 million years before present. In apparent contrast, the fossil record from this time period contains evidence for a major, but regional, extinction event. These seemingly discordant findings appear to be driven by a common global process: global cooling and drying at the time of the Eocene-Oligocene transition. This climatic shift led to aridification that drove extinctions in important fossil-bearing areas, while simultaneously exposing new continental margin habitat that subsequently allowed for a burst of speciation associated with these newly exploitable ecological opportunities.
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17
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Guillen A, Smallwood K, Killick DR. Molecular pathology in the cancer clinic - where are we now and where are we headed? J Small Anim Pract 2021; 62:507-520. [PMID: 33974272 DOI: 10.1111/jsap.13330] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 12/14/2020] [Accepted: 03/04/2021] [Indexed: 11/29/2022]
Abstract
Molecular pathology is a developing sub-microscopic discipline of pathology that studies the effects of molecular variations and mutations on disease processes. The ultimate goal of molecular pathology in cancer is to predict risk, facilitate diagnosis and improve prognostication based on a complete understanding of the biological impact of specific molecular variations, mutations and dysregulations. This knowledge will provide the basis for customised cancer treatment, so-called precision medicine. Rapid developments in genomics have placed this field at the forefront of clinical molecular pathology and there are already a number of well-established genetic tests available for clinical use including PCR of antigen receptor rearrangement and KIT mutational analysis. Moving beyond tests assessing a single gene, there are significant research efforts utilising genomics to predict cancer risk, forecast aggressive behaviour and identify druggable mutations and therapeutic biomarkers. Researchers are also investigating the use of circulating cells and nucleic acid for clinically useful low morbidity genomic assessments. If we are to realise the full potential of molecular pathology and precision medicine there are a number of challenges to overcome. These include developing our understanding of the underlying biology (in particular intra-tumoural heterogeneity), methodological standardisation of assays, provision of adequate infrastructure and production of novel therapeutics backed by high-quality clinical data supporting the precision medicine approach. The era of molecular pathology holds the potential to revolutionise veterinary cancer care, but its impact on clinical practice will depend upon the extent to which the inherent challenges can be overcome.
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Affiliation(s)
- A Guillen
- Department of Clinical Science and Services, Royal Veterinary College, Hawkshead Ln, Hatfield, AL9 7TA, UK
| | - K Smallwood
- Department of Small Animal Clinical Science, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Leahurst, Chester High Road, Neston, CH64 7TE, UK
| | - D R Killick
- Department of Small Animal Clinical Science, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Leahurst, Chester High Road, Neston, CH64 7TE, UK
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18
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Lange PNAMJG, Lelieveld G, De Knegt HJ. Diet composition of the golden jackal
Canis aureus
in south‐east Europe – a review. Mamm Rev 2021. [DOI: 10.1111/mam.12235] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Pauline N. A. M. J. G. Lange
- Department of Environmental Sciences, Subdivision Wildlife Ecology and Conservation Wageningen University and Research Postbus 47 Wageningen6700AAthe Netherlands
| | - Glenn Lelieveld
- Zoogdiervereniging Postbus 6531 Nijmegen GA6503the Netherlands
| | - Henjo J. De Knegt
- Department of Environmental Sciences, Subdivision Wildlife Ecology and Conservation Wageningen University and Research Postbus 47 Wageningen6700AAthe Netherlands
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19
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Identification of Echinococcus granulosus Genotypes G1 and G3 by SNPs Genotyping Assays. Pathogens 2021; 10:pathogens10020125. [PMID: 33530642 PMCID: PMC7910869 DOI: 10.3390/pathogens10020125] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/23/2021] [Accepted: 01/24/2021] [Indexed: 11/25/2022] Open
Abstract
Echinococcus granulosus sensu lato (s.l.) is the causative agent of cystic echinococcosis in animals and humans. Different E. granulosuss.l. genotypes exhibit great diversity in their life cycle, host selectivity and pathogenicity. For this reason, the study of genetic variation within Echinococcus species is of importance for their epidemiological implication. We employed two SNP genotyping technologies to distinguish G1 and G3 E. granulosus sensu stricto (s.s.). genotypes. The genotypes of DNA samples (n = 28) extracted from hydatid cysts of different animal species were identified by amplification and sequencing of a fragment of the mitochondrial nad5 gene. Two SYBR green and three TaqMan real time PCR assays were developed for targeting of three nad5 informative positions (SNP758, 1123, and 1380) known to be able to discriminate G1 from G3. Genotyping by SYBR Green PCR based on cycle threshold (Ct) with melting temperature (Tm) analysis and performed on SNP1123 and SNP1380 failed to identify one DNA sample. TaqMan assays for SNP758, 1123 and 1380 effectively confirmed genotype identification obtained by Sanger sequencing. Our results demonstrated that the combination of the three Taqman assays developed in this study represents a valuable and cost effective tool alternative to DNA sequencing for E. granulosus s.s. genotyping.
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20
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Wang Y, Lv H, Xiang X, Yang A, Feng Q, Dai P, Li Y, Jiang X, Liu G, Zhang X. Construction of a SNP Fingerprinting Database and Population Genetic Analysis of Cigar Tobacco Germplasm Resources in China. FRONTIERS IN PLANT SCIENCE 2021; 12:618133. [PMID: 33719288 PMCID: PMC7943628 DOI: 10.3389/fpls.2021.618133] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 01/22/2021] [Indexed: 05/12/2023]
Abstract
Cigar tobacco is an important economic crop that is widely grown around the world. In recent years, varietal identification has become a frequent problem in germplasm preservation collections, which causes considerable inconvenience and uncertainty in the cataloging and preservation of cigar germplasm resources, in the selection of parental lines for breeding, and in the promotion and use of high quality varieties. Therefore, the use of DNA fingerprints to achieve rapid and accurate identification of varieties can play an important role in germplasm identification and property rights disputes. In this study, we used genotyping-by-sequencing (GBS) on 113 cigar tobacco accessions to develop SNP markers. After filtering, 580,942 high-quality SNPs were obtained. We used the 580,942 SNPs to perform principal component analysis (PCA), population structure analysis, and neighbor joining (NJ) cluster analysis on the 113 cigar tobacco accessions. The results showed that the accessions were not completely classified based on their geographical origins, and the genetic backgrounds of these cigar resources are complex and diverse. We further selected from these high-quality SNPs to obtained 163 SNP sites, 133 of which were successfully converted into KASP markers. Finally, 47 core KASP markers and 24 candidate core markers were developed. Using the core markers, we performed variety identification and fingerprinting in 216 cigar germplasm accessions. The results of SNP fingerprinting, 2D barcoding, and genetic analysis of cigar tobacco germplasm in this study provide a scientific basis for screening and identifying high-quality cigar tobacco germplasm, mining important genes, and broadening the basis of cigar tobacco genetics and subsequent breeding work at the molecular level.
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Affiliation(s)
- Yanyan Wang
- Key Laboratory of Tobacco Improvement and Biotechnology, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Hongkun Lv
- Haikou Cigar Research Institute, Hainan Provincial Tobacco Company of China National Tobacco Corporation, Haikou, China
| | - Xiaohua Xiang
- Haikou Cigar Research Institute, Hainan Provincial Tobacco Company of China National Tobacco Corporation, Haikou, China
| | - Aiguo Yang
- Key Laboratory of Tobacco Improvement and Biotechnology, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Quanfu Feng
- Key Laboratory of Tobacco Improvement and Biotechnology, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Peigang Dai
- Key Laboratory of Tobacco Improvement and Biotechnology, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Yuan Li
- Key Laboratory of Tobacco Improvement and Biotechnology, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Xun Jiang
- Key Laboratory of Tobacco Improvement and Biotechnology, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Guoxiang Liu
- Key Laboratory of Tobacco Improvement and Biotechnology, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
- *Correspondence: Guoxiang Liu
| | - Xingwei Zhang
- Key Laboratory of Tobacco Improvement and Biotechnology, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
- Xingwei Zhang
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21
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Chirchir H. Trabecular bone in domestic dogs and wolves: Implications for understanding human self‐domestication. Anat Rec (Hoboken) 2020; 304:31-41. [DOI: 10.1002/ar.24510] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 05/13/2020] [Accepted: 05/13/2020] [Indexed: 12/17/2022]
Affiliation(s)
- Habiba Chirchir
- Department of Biological Sciences Marshall University Huntington West Virginia USA
- Human Origins Program, Department of Anthropology National Museum of Natural History, Smithsonian Institution Washington District of Columbia USA
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22
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Chengetanai S, Tenley JD, Bertelsen MF, Hård T, Bhagwandin A, Haagensen M, Tang CY, Wang VX, Wicinski B, Hof PR, Manger PR, Spocter MA. Brain of the African wild dog. I. Anatomy, architecture, and volumetrics. J Comp Neurol 2020; 528:3245-3261. [PMID: 32720707 DOI: 10.1002/cne.24999] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 07/17/2020] [Accepted: 07/22/2020] [Indexed: 02/05/2023]
Abstract
The African wild dog is endemic to sub-Saharan Africa and belongs to the family Canidae which includes domestic dogs and their closest relatives (i.e., wolves, coyotes, jackals, dingoes, and foxes). The African wild dog is known for its highly social behavior, co-ordinated pack predation, and striking vocal repertoire, but little is known about its brain and whether it differs in any significant way from that of other canids. We employed gross anatomical observation, magnetic resonance imaging, and classical neuroanatomical staining to provide a broad overview of the structure of the African wild dog brain. Our results reveal a mean brain mass of 154.08 g, with an encephalization quotient of 1.73, indicating that the African wild dog has a relatively large brain size. Analysis of the various structures that comprise their brains and their topological inter-relationships, as well as the areas and volumes of the corpus callosum, ventricular system, hippocampus, amygdala, cerebellum and the gyrification index, all reveal that the African wild dog brain is, in general, similar to that of other mammals, and very similar to that of other carnivorans. While at this level of analysis we do not find any striking specializations within the brain of the African wild dog, apart from a relatively large brain size, the observations made indicate that more detailed analyses of specific neural systems, particularly those involved in sensorimotor processing, sociality or cognition, may reveal features that are either unique to this species or shared among the Canidae to the exclusion of other Carnivora.
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Affiliation(s)
- Samson Chengetanai
- School of Anatomical Sciences, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Mads F Bertelsen
- Center for Zoo and Wild Animal Health, Copenhagen Zoo, Fredericksberg, Denmark
| | | | - Adhil Bhagwandin
- School of Anatomical Sciences, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mark Haagensen
- Department of Radiology, University of Witwatersrand-Donald Gordon Medical Centre, Johannesburg, South Africa
| | - Cheuk Y Tang
- Department of Psychiatry, and BioMedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Victoria X Wang
- Department of Psychiatry, and BioMedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Bridget Wicinski
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Patrick R Hof
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,New York Consortium in Evolutionary Primatology, New York, New York, USA
| | - Paul R Manger
- School of Anatomical Sciences, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Muhammad A Spocter
- School of Anatomical Sciences, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Department of Anatomy, Des Moines University, Des Moines, Iowa, USA.,College of Veterinary Medicine, Department of Biomedical Sciences, Iowa State University, Ames, Iowa, USA
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23
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Noonan MJ, Fleming CH, Tucker MA, Kays R, Harrison A, Crofoot MC, Abrahms B, Alberts SC, Ali AH, Altmann J, Antunes PC, Attias N, Belant JL, Beyer DE, Bidner LR, Blaum N, Boone RB, Caillaud D, de Paula RC, de la Torre JA, Dekker J, DePerno CS, Farhadinia M, Fennessy J, Fichtel C, Fischer C, Ford A, Goheen JR, Havmøller RW, Hirsch BT, Hurtado C, Isbell LA, Janssen R, Jeltsch F, Kaczensky P, Kaneko Y, Kappeler P, Katna A, Kauffman M, Koch F, Kulkarni A, LaPoint S, Leimgruber P, Macdonald DW, Markham AC, McMahon L, Mertes K, Moorman CE, Morato RG, Moßbrucker AM, Mourão G, O'Connor D, Oliveira‐Santos LGR, Pastorini J, Patterson BD, Rachlow J, Ranglack DH, Reid N, Scantlebury DM, Scott DM, Selva N, Sergiel A, Songer M, Songsasen N, Stabach JA, Stacy‐Dawes J, Swingen MB, Thompson JJ, Ullmann W, Vanak AT, Thaker M, Wilson JW, Yamazaki K, Yarnell RW, Zieba F, Zwijacz‐Kozica T, Fagan WF, Mueller T, Calabrese JM. Effects of body size on estimation of mammalian area requirements. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2020; 34:1017-1028. [PMID: 32362060 PMCID: PMC7496598 DOI: 10.1111/cobi.13495] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 11/27/2019] [Accepted: 12/24/2019] [Indexed: 06/08/2023]
Abstract
Accurately quantifying species' area requirements is a prerequisite for effective area-based conservation. This typically involves collecting tracking data on species of interest and then conducting home-range analyses. Problematically, autocorrelation in tracking data can result in space needs being severely underestimated. Based on the previous work, we hypothesized the magnitude of underestimation varies with body mass, a relationship that could have serious conservation implications. To evaluate this hypothesis for terrestrial mammals, we estimated home-range areas with global positioning system (GPS) locations from 757 individuals across 61 globally distributed mammalian species with body masses ranging from 0.4 to 4000 kg. We then applied block cross-validation to quantify bias in empirical home-range estimates. Area requirements of mammals <10 kg were underestimated by a mean approximately15%, and species weighing approximately100 kg were underestimated by approximately50% on average. Thus, we found area estimation was subject to autocorrelation-induced bias that was worse for large species. Combined with the fact that extinction risk increases as body mass increases, the allometric scaling of bias we observed suggests the most threatened species are also likely to be those with the least accurate home-range estimates. As a correction, we tested whether data thinning or autocorrelation-informed home-range estimation minimized the scaling effect of autocorrelation on area estimates. Data thinning required an approximately93% data loss to achieve statistical independence with 95% confidence and was, therefore, not a viable solution. In contrast, autocorrelation-informed home-range estimation resulted in consistently accurate estimates irrespective of mass. When relating body mass to home range size, we detected that correcting for autocorrelation resulted in a scaling exponent significantly >1, meaning the scaling of the relationship changed substantially at the upper end of the mass spectrum.
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Affiliation(s)
- Michael J. Noonan
- Smithsonian Conservation Biology InstituteNational Zoological Park1500 Remount RoadFront RoyalVA22630U.S.A.
- Department of BiologyUniversity of MarylandCollege ParkMD20742U.S.A.
| | - Christen H. Fleming
- Smithsonian Conservation Biology InstituteNational Zoological Park1500 Remount RoadFront RoyalVA22630U.S.A.
- Department of BiologyUniversity of MarylandCollege ParkMD20742U.S.A.
| | - Marlee A. Tucker
- Senckenberg Biodiversity and Climate Research CentreSenckenberg Gesellschaft für NaturforschungSenckenberganlage 25Frankfurt (Main)60325Germany
- Department of Biological SciencesGoethe UniversityMax‐von‐Laue‐Straße 9Frankfurt (Main)60438Germany
- Department of Environmental ScienceInstitute for Wetland and Water ResearchRadboud UniversityP.O. Box 9010NijmegenGLNL‐6500The Netherlands
| | - Roland Kays
- North Carolina Museum of Natural SciencesBiodiversity LabRaleighNC27601U.S.A.
- Fisheries, Wildlife, and Conservation Biology Program, College of Natural Resources Campus Box 8001North Carolina State UniversityRaleighNC27695U.S.A.
| | - Autumn‐Lynn Harrison
- Migratory Bird CenterSmithsonian Conservation Biology InstituteWashingtonD.C.20013U.S.A.
| | - Margaret C. Crofoot
- Department of AnthropologyUniversity of California, DavisDavisCA95616U.S.A.
- Smithsonian Tropical Research InstituteBalboa Ancon0843‐03092Republic of Panama
| | - Briana Abrahms
- Environmental Research DivisionNOAA Southwest Fisheries Science CenterMontereyCA93940U.S.A.
| | - Susan C. Alberts
- Departments of Biology and Evolutionary AnthropologyDuke UniversityDurhamNC27708U.S.A.
| | | | - Jeanne Altmann
- Department of Ecology and EvolutionPrinceton University106A Guyot HallPrincetonNJ08544U.S.A.
| | - Pamela Castro Antunes
- Department of EcologyFederal University of Mato Grosso do SulCampo GrandeMS79070–900Brazil
| | - Nina Attias
- Programa de Pós‐Graduaçao em Biologia Animal, Universidade Federal do Mato Grosso do SulCidade UniversitáriaAv. Costa e SilvaCampo GrandeMato Grosso do Sul79070‐900Brazil
| | - Jerrold L. Belant
- Camp Fire Program in Wildlife Conservation, State University of New YorkCollege of Environmental Science and ForestrySyracuseNY13210U.S.A.
| | - Dean E. Beyer
- Michigan Department of Natural Resources1990 U.S. 41 SouthMarquetteMI49855U.S.A.
| | - Laura R. Bidner
- Department of AnthropologyUniversity of California, DavisDavisCA95616U.S.A.
- Mpala Research CentreNanyuki555–104000Kenya
| | - Niels Blaum
- University of Potsdam, Plant Ecology and Nature ConservationAm Mühlenberg 3Potsdam14476Germany
| | - Randall B. Boone
- Natural Resource Ecology LaboratoryColorado State UniversityFort CollinsCO80523U.S.A.
- Department of Ecosystem Science and SustainabilityColorado State UniversityFort CollinsCO80523U.S.A.
| | - Damien Caillaud
- Department of AnthropologyUniversity of California, DavisDavisCA95616U.S.A.
| | - Rogerio Cunha de Paula
- National Research Center for Carnivores ConservationChico Mendes Institute for the Conservation of BiodiversityEstrada Municipal Hisaichi Takebayashi 8600AtibaiaSP12952‐011Brazil
| | - J. Antonio de la Torre
- Instituto de Ecología, Universidad Nacional Autónoma de Mexico and CONACyTCiudad UniversitariaMexicoD.F.04318Mexico
| | - Jasja Dekker
- Jasja Dekker DierecologieEnkhuizenstraat 26ArnhemWZ6843The Netherlands
| | - Christopher S. DePerno
- Fisheries, Wildlife, and Conservation Biology Program, College of Natural Resources Campus Box 8001North Carolina State UniversityRaleighNC27695U.S.A.
| | - Mohammad Farhadinia
- Wildlife Conservation Research Unit, Department of ZoologyUniversity of OxfordTubney House, OxfordshireOxfordOX13 5QLU.K.
- Future4Leopards FoundationTehranIran
| | | | - Claudia Fichtel
- German Primate CenterBehavioral Ecology & Sociobiology UnitKellnerweg 4Göttingen37077Germany
| | - Christina Fischer
- Restoration Ecology, Department of Ecology and Ecosystem ManagementTechnische Universität MünchenEmil‐Ramann‐Straße 6Freising85354Germany
| | - Adam Ford
- The Irving K. Barber School of Arts and Sciences, Unit 2: BiologyThe University of British ColumbiaOkanagan Campus, SCI 109, 1177 Research RoadKelownaBCV1V 1V7Canada
| | - Jacob R. Goheen
- Department of Zoology and PhysiologyUniversity of WyomingLaramieWY82071U.S.A.
| | | | - Ben T. Hirsch
- Zoology and Ecology, College of Science and EngineeringJames Cook UniversityTownsvilleQLD4811Australia
| | - Cindy Hurtado
- Museo de Historia NaturalUniversidad Nacional Mayor de San MarcosLima15072Peru
- Department of Forest Resources ManagementThe University of British ColumbiaVancouverBCV6T 1Z4Canada
| | - Lynne A. Isbell
- Department of AnthropologyUniversity of California, DavisDavisCA95616U.S.A.
- Mpala Research CentreNanyuki555–104000Kenya
| | - René Janssen
- Bionet NatuuronderzoekValderstraat 39Stein6171ELThe Netherlands
| | - Florian Jeltsch
- University of Potsdam, Plant Ecology and Nature ConservationAm Mühlenberg 3Potsdam14476Germany
| | - Petra Kaczensky
- Norwegian Institute for Nature Research — NINASluppenTrondheimNO‐7485Norway
- Research Institute of Wildlife Ecology, University of Veterinary MedicineSavoyenstraße 1ViennaA‐1160Austria
| | - Yayoi Kaneko
- Tokyo University of Agriculture and TechnologyTokyo183–8509Japan
| | - Peter Kappeler
- German Primate CenterBehavioral Ecology & Sociobiology UnitKellnerweg 4Göttingen37077Germany
| | - Anjan Katna
- Ashoka Trust for Research in Ecology and the Environment (ATREE)BangaloreKarnataka560064India
- Manipal Academy of Higher EducationManipalKarnataka576104India
| | - Matthew Kauffman
- U.S. Geological Survey, Wyoming Cooperative Fish and Wildlife Research Unit, Department of Zoology and PhysiologyUniversity of WyomingLaramieWY82071U.S.A.
| | - Flavia Koch
- German Primate CenterBehavioral Ecology & Sociobiology UnitKellnerweg 4Göttingen37077Germany
| | - Abhijeet Kulkarni
- Ashoka Trust for Research in Ecology and the Environment (ATREE)BangaloreKarnataka560064India
| | - Scott LaPoint
- Max Planck Institute for OrnithologyVogelwarte RadolfzellAm Obstberg 1RadolfzellD‐78315Germany
- Black Rock Forest65 Reservoir RoadCornwallNY12518U.S.A.
| | - Peter Leimgruber
- Smithsonian Conservation Biology InstituteNational Zoological Park1500 Remount RoadFront RoyalVA22630U.S.A.
| | - David W. Macdonald
- Wildlife Conservation Research Unit, Department of ZoologyUniversity of OxfordTubney House, OxfordshireOxfordOX13 5QLU.K.
| | | | - Laura McMahon
- Office of Applied ScienceDepartment of Natural ResourcesRhinelanderWI54501U.S.A.
| | - Katherine Mertes
- Smithsonian Conservation Biology InstituteNational Zoological Park1500 Remount RoadFront RoyalVA22630U.S.A.
| | - Christopher E. Moorman
- Fisheries, Wildlife, and Conservation Biology Program, College of Natural Resources Campus Box 8001North Carolina State UniversityRaleighNC27695U.S.A.
| | - Ronaldo G. Morato
- National Research Center for Carnivores ConservationChico Mendes Institute for the Conservation of BiodiversityEstrada Municipal Hisaichi Takebayashi 8600AtibaiaSP12952‐011Brazil
- Institute for the Conservation of Neotropical Carnivores – Pró‐CarnívorosAtibaiaSao Paulo12945‐010Brazil
| | | | - Guilherme Mourão
- Embrapa PantanalRua 21 de setembro 1880Corumb´aMS79320–900Brazil
| | - David O'Connor
- Department of Biological SciencesGoethe UniversityMax‐von‐Laue‐Straße 9Frankfurt (Main)60438Germany
- San Diego Zoo Institute of Conservation Research15600 San Pasqual Valley RoadEscondidoCA92027U.S.A.
- National Geographic Partners1145 17th Street NWWashingtonD.C.20036U.S.A.
| | | | - Jennifer Pastorini
- Centre for Conservation and Research26/7 C2 Road, KodigahawewaJulpallamaTissamaharama82600Sri Lanka
- Anthropologisches InstitutUniversität ZürichWinterthurerstrasse 190Zurich8057Switzerland
| | - Bruce D. Patterson
- Integrative Research CenterField Museum of Natural HistoryChicagoIL60605U.S.A.
| | - Janet Rachlow
- Department of Fish and Wildlife SciencesUniversity of Idaho875 Perimeter Drive MS 1136MoscowID83844‐1136U.S.A.
| | - Dustin H. Ranglack
- Department of BiologyUniversity of Nebraska at KearneyKearneyNE68849U.S.A.
| | - Neil Reid
- Institute for Global Food Security (IGFS), School of Biological SciencesQueen's University BelfastBelfastBT9 5DLU.K.
| | - David M. Scantlebury
- School of Biological SciencesQueen's University Belfast19 Chlorine GardensBelfastNorthern IrelandBT9 5DLU.K.
| | - Dawn M. Scott
- School of Life SciencesKeele UniversityKeeleStaffordshireST5 5BGU.K.
| | - Nuria Selva
- Institute of Nature ConservationPolish Academy of SciencesMickiewicza 33Krakow31–120Poland
| | - Agnieszka Sergiel
- Institute of Nature ConservationPolish Academy of SciencesMickiewicza 33Krakow31–120Poland
| | - Melissa Songer
- Smithsonian Conservation Biology InstituteNational Zoological Park1500 Remount RoadFront RoyalVA22630U.S.A.
| | - Nucharin Songsasen
- Smithsonian Conservation Biology InstituteNational Zoological Park1500 Remount RoadFront RoyalVA22630U.S.A.
| | - Jared A. Stabach
- Smithsonian Conservation Biology InstituteNational Zoological Park1500 Remount RoadFront RoyalVA22630U.S.A.
| | - Jenna Stacy‐Dawes
- San Diego Zoo Institute of Conservation Research15600 San Pasqual Valley RoadEscondidoCA92027U.S.A.
| | - Morgan B. Swingen
- Fisheries, Wildlife, and Conservation Biology Program, College of Natural Resources Campus Box 8001North Carolina State UniversityRaleighNC27695U.S.A.
- 1854 Treaty Authority4428 Haines RoadDuluthMN55811U.S.A.
| | - Jeffrey J. Thompson
- Asociación Guyra Paraguay – CONACYTParque Ecológico Asunción VerdeAsuncion1101Paraguay
- Instituto SaiteCoronel Felix Cabrera 166Asuncion1101Paraguay
| | - Wiebke Ullmann
- University of Potsdam, Plant Ecology and Nature ConservationAm Mühlenberg 3Potsdam14476Germany
| | - Abi Tamim Vanak
- Ashoka Trust for Research in Ecology and the Environment (ATREE)BangaloreKarnataka560064India
- Wellcome Trust/DBT India AllianceHyderabad500034India
- School of Life SciencesUniversity of KwaZulu‐NatalWestvilleDurban4041South Africa
| | - Maria Thaker
- Centre for Ecological SciencesIndian Institute of ScienceBangalore560012India
| | - John W. Wilson
- Department of Zoology & EntomologyUniversity of PretoriaPretoria0002South Africa
| | - Koji Yamazaki
- Ibaraki Nature MuseumZoological Laboratory700 OsakiBando‐cityIbaraki306–0622Japan
- Forest Ecology LaboratoryDepartment of Forest ScienceTokyo University of Agriculture1‐1‐1 SakuragaokaSetagaya‐KuTokyo156–8502Japan
| | - Richard W. Yarnell
- School of Animal, Rural and Environmental SciencesNottingham Trent UniversityBrackenhurst CampusSouthwellNG25 0QFU.K.
| | - Filip Zieba
- Tatra National ParkKúznice 1Zakopane34–500Poland
| | | | - William F. Fagan
- Department of BiologyUniversity of MarylandCollege ParkMD20742U.S.A.
| | - Thomas Mueller
- Senckenberg Biodiversity and Climate Research CentreSenckenberg Gesellschaft für NaturforschungSenckenberganlage 25Frankfurt (Main)60325Germany
- Department of Biological SciencesGoethe UniversityMax‐von‐Laue‐Straße 9Frankfurt (Main)60438Germany
| | - Justin M. Calabrese
- Smithsonian Conservation Biology InstituteNational Zoological Park1500 Remount RoadFront RoyalVA22630U.S.A.
- Department of BiologyUniversity of MarylandCollege ParkMD20742U.S.A.
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Hansen Wheat C, van der Bijl W, Wheat CW. Morphology does not covary with predicted behavioral correlations of the domestication syndrome in dogs. Evol Lett 2020; 4:189-199. [PMID: 32547780 PMCID: PMC7293089 DOI: 10.1002/evl3.168] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 02/14/2020] [Accepted: 02/19/2020] [Indexed: 01/05/2023] Open
Abstract
Domesticated animals display suites of altered morphological, behavioral, and physiological traits compared to their wild ancestors, a phenomenon known as the domestication syndrome (DS). Because these alterations are observed to co-occur across a wide range of present day domesticates, the traits within the DS are assumed to covary within species and a single developmental mechanism has been hypothesized to cause the observed co-occurrence. However, due to the lack of formal testing it is currently not well-resolved if the traits within DS actually covary. Here, we test the hypothesis that the presence of the classic morphological domestication traits white pigmentation, floppy ears, and curly tails predict the strength of behavioral correlations in support of the DS in 78 dog breeds. Contrary to the expectations of covariation among DS traits, we found that morphological traits did not covary among themselves, nor did they predict the strength of behavioral correlations among dog breeds. Further, the number of morphological traits in a breed did not predict the strength of behavioral correlations. Our results thus contrast with the hypothesis that the DS arises due to a shared underlying mechanism, but more importantly, questions if the morphological traits embedded in the DS are actual domestication traits or postdomestication improvement traits. For dogs, it seems highly likely that strong selection for breed specific morphological traits only happened recently and in relation to breed formation. Present day dogs therefore have limited bearing of the initial selection pressures applied during domestication and we should reevaluate our expectations of the DS accordingly.
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Affiliation(s)
| | - Wouter van der Bijl
- Department of ZoologyStockholm UniversityStockholmSE‐10961Sweden
- Department of Zoology and Biodiversity Research CentreUniversity of British ColumbiaVancouverBCV6T 1Z4Canada
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25
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Ghorbani F, Aliabadian M, Zhang R, Irestedt M, Hao Y, Sundev G, Lei F, Ma M, Olsson U, Alström P. Densely sampled phylogenetic analyses of the Lesser Short‐toed Lark (
Alaudala rufescens
) — Sand Lark (
A. raytal
) species complex (Aves, Passeriformes) reveal cryptic diversity. ZOOL SCR 2020. [DOI: 10.1111/zsc.12422] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Fatemeh Ghorbani
- Department of Biology Faculty of Science Ferdowsi University of Mashhad Mashhad Iran
| | - Mansour Aliabadian
- Department of Biology Faculty of Science Ferdowsi University of Mashhad Mashhad Iran
- Zoological Innovations Research Department Institute of Applied Zoology Faculty of Science Ferdowsi University of Mashhad Mashhad Iran
| | - Ruiying Zhang
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Martin Irestedt
- Department of Bioinformatics and Genetics Swedish Museum of Natural History Stockholm Sweden
| | - Yan Hao
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Gombobaatar Sundev
- National University of Mongolia and Mongolian Ornithological Society Ulaanbaatar Mongolia
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Ming Ma
- Xinjiang Institute of Ecology and Geography Chinese Academy of Sciences Xinjiang China
| | - Urban Olsson
- Systematics and Biodiversity Department of Biology and Environmental Sciences University of Gothenburg Göteborg Sweden
- Gothenburg Global Biodiversity Centre Gothenburg Sweden
| | - Per Alström
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
- Animal Ecology Department of Ecology and Genetics Evolutionary Biology Centre Uppsala University Uppsala Sweden
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26
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Chen L, Li J, Yang G. A comparative review of intelectins. Scand J Immunol 2020; 92:e12882. [PMID: 32243627 DOI: 10.1111/sji.12882] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 03/23/2020] [Accepted: 03/24/2020] [Indexed: 12/20/2022]
Abstract
Intelectin (ITLN) is a new type of glycan-binding lectin. It has been demonstrated to agglutinate bacteria probably due to its carbohydrate-binding capacity, suggesting its role in an innate immune response. It is involved not only in many physiological processes but also in some human diseases such as asthma, heart disease, inflammatory bowel disease, chronic obstructive pulmonary disease and cancer. Up to now, intelectin orthologs have been identified in placozoans, urochordatas, cephalochordates and several vertebrates, such as cyclostomata, fish, amphibians and mammals. Although the sequences of intelectins in different species are conserved, their expression patterns, quaternary structures and functions differ considerably among and within species. We summarize the evolution of the intelectin gene family, the tissue distribution, structure and functions of intelectins. We conclude that intelectin plays a role in innate immune response and there are still potential functions of intelectin awaiting discovery.
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Affiliation(s)
- Lei Chen
- Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Jinyi Li
- Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Guiwen Yang
- Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, China
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27
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Functional morphology of the jaw adductor muscles in the Canidae. Anat Rec (Hoboken) 2020; 303:2878-2903. [DOI: 10.1002/ar.24391] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 01/18/2020] [Accepted: 01/25/2020] [Indexed: 12/17/2022]
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28
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Olsson U, Alström P. A comprehensive phylogeny and taxonomic evaluation of the waxbills (Aves: Estrildidae). Mol Phylogenet Evol 2020; 146:106757. [PMID: 32028027 DOI: 10.1016/j.ympev.2020.106757] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 12/23/2019] [Accepted: 01/28/2020] [Indexed: 11/24/2022]
Abstract
We present a revised taxonomy of Estrildidae based on the first time-calibrated phylogeny of the family Estrildidae estimated from a data set including the majority of the species, and all genera except the monospecific Paludipasser, using two mitochondrial and five nuclear markers. We find that most differences in current taxonomy reflect alternative opinions among authors regarding inclusiveness of genera, which are usually not in conflict with the phylogeny. The most notable exception is the current circumscriptions of the genera Neochmia, Nesocharis and Taeniopygia, which are incompatible with the phylogeny. Estrildidae is subdivided into six well supported subclades, which we propose be recognized as the subfamilies Amandavinae, Erythrurinae, Estrildinae, Lagonostictinae, Lonchurinae and Poephilinae.
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Affiliation(s)
- Urban Olsson
- Department of Biology and Environmental Science, University of Gothenburg, Box 463, SE-405 30 Gothenburg, Sweden; Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Gothenburg, Sweden.
| | - Per Alström
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36, Uppsala, Sweden; Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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29
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Hagen IJ, Lien S, Billing AM, Elgvin TO, Trier C, Niskanen AK, Tarka M, Slate J, Sætre G, Jensen H. A genome‐wide linkage map for the house sparrow (Passer domesticus) provides insights into the evolutionary history of the avian genome. Mol Ecol Resour 2020; 20:544-559. [DOI: 10.1111/1755-0998.13134] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 11/07/2019] [Accepted: 12/10/2019] [Indexed: 01/18/2023]
Affiliation(s)
- Ingerid J. Hagen
- Centre for Biodiversity Dynamics Department of Biology Norwegian University of Science and Technology Trondheim Norway
- Norwegian Institute for Nature Research (NINA) Trondheim Norway
| | - Sigbjørn Lien
- Centre for Integrative Genetics Department of Animal and Aquacultural Sciences Faculty of Biosciences Norwegian University of Life Sciences Ås Norway
| | - Anna M. Billing
- Centre for Biodiversity Dynamics Department of Biology Norwegian University of Science and Technology Trondheim Norway
| | - Tore O. Elgvin
- Centre for Ecological and Evolutionary Synthesis Department of Biology University of Oslo Oslo Norway
| | - Cassandra Trier
- Centre for Ecological and Evolutionary Synthesis Department of Biology University of Oslo Oslo Norway
| | - Alina K. Niskanen
- Centre for Biodiversity Dynamics Department of Biology Norwegian University of Science and Technology Trondheim Norway
- Ecology and Genetics Research Unit University of Oulu Oulu Finland
| | - Maja Tarka
- Centre for Biodiversity Dynamics Department of Biology Norwegian University of Science and Technology Trondheim Norway
- Department of Biology Lund University Lund Sweden
| | - Jon Slate
- Department of Animal and Plant Sciences University of Sheffield Western Bank Sheffield UK
| | - Glenn‐Peter Sætre
- Centre for Ecological and Evolutionary Synthesis Department of Biology University of Oslo Oslo Norway
| | - Henrik Jensen
- Centre for Biodiversity Dynamics Department of Biology Norwegian University of Science and Technology Trondheim Norway
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30
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Jagannathan V, Drögemüller C, Leeb T. A comprehensive biomedical variant catalogue based on whole genome sequences of 582 dogs and eight wolves. Anim Genet 2019; 50:695-704. [PMID: 31486122 PMCID: PMC6842318 DOI: 10.1111/age.12834] [Citation(s) in RCA: 135] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/21/2019] [Indexed: 12/16/2022]
Abstract
The domestic dog serves as an excellent model to investigate the genetic basis of disease. More than 400 heritable traits analogous to human diseases have been described in dogs. To further canine medical genetics research, we established the Dog Biomedical Variant Database Consortium (DBVDC) and present a comprehensive list of functionally annotated genome variants that were identified with whole genome sequencing of 582 dogs from 126 breeds and eight wolves. The genomes used in the study have a minimum coverage of 10× and an average coverage of ~24×. In total, we identified 23 133 692 single-nucleotide variants (SNVs) and 10 048 038 short indels, including 93% undescribed variants. On average, each individual dog genome carried ∼4.1 million single-nucleotide and ~1.4 million short-indel variants with respect to the reference genome assembly. About 2% of the variants were located in coding regions of annotated genes and loci. Variant effect classification showed 247 141 SNVs and 99 562 short indels having moderate or high impact on 11 267 protein-coding genes. On average, each genome contained heterozygous loss-of-function variants in 30 potentially embryonic lethal genes and 97 genes associated with developmental disorders. More than 50 inherited disorders and traits have been unravelled using the DBVDC variant catalogue, enabling genetic testing for breeding and diagnostics. This resource of annotated variants and their corresponding genotype frequencies constitutes a highly useful tool for the identification of potential variants causative for rare inherited disorders in dogs.
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Affiliation(s)
- V Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - C Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - T Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
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31
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Garamszegi LZ, Temrin H, Kubinyi E, Miklósi Á, Kolm N. The role of common ancestry and gene flow in the evolution of human-directed play behaviour in dogs. J Evol Biol 2019; 33:318-328. [PMID: 31705702 DOI: 10.1111/jeb.13567] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 11/04/2019] [Indexed: 11/29/2022]
Abstract
Among-population variance of phenotypic traits is of high relevance for understanding evolutionary mechanisms that operate in relatively short timescales, but various sources of nonindependence, such as common ancestry and gene flow, can hamper the interpretations. In this comparative analysis of 138 dog breeds, we demonstrate how such confounders can independently shape the evolution of a behavioural trait (human-directed play behaviour from the Dog Mentality Assessment project). We combined information on genetic relatedness and haplotype sharing to reflect common ancestry and gene flow, respectively, and entered these into a phylogenetic mixed model to partition the among-breed variance of human-directed play behaviour while also accounting for within-breed variance. We found that 75% of the among-breed variance was explained by overall genetic relatedness among breeds, whereas 15% could be attributed to haplotype sharing that arises from gene flow. Therefore, most of the differences in human-directed play behaviour among breeds have likely been caused by constraints of common ancestry as a likely consequence of past selection regimes. On the other hand, gene flow caused by crosses among breeds has played a minor, but not negligible role. Our study serves as an example of an analytical approach that can be applied to comparative situations where the effects of shared origin and gene flow require quantification and appropriate statistical control in a within-species/among-population framework. Altogether, our results suggest that the evolutionary history of dog breeds has left remarkable signatures on the among-breed variation of a behavioural phenotype.
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Affiliation(s)
- László Zsolt Garamszegi
- Centre for Ecological Research, Institute of Ecology and Botany, Vácrátót, Hungary.,MTA-ELTE Theoretical Biology and Evolutionary Ecology Research Group, Department of Plant Systematics, Ecology and Theoretical Biology, Eötvös Loránd University, Budapest, Hungary.,Department of Evolutionary Ecology, Estación Biológica de Doñana-CSIC, Seville, Spain
| | - Hans Temrin
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Enikő Kubinyi
- Department of Ethology, Eötvös Loránd University, Budapest, Hungary
| | - Ádám Miklósi
- Department of Ethology, Eötvös Loránd University, Budapest, Hungary.,MTA-ELTE Comparative Ethology Research Group, Budapest, Hungary
| | - Niclas Kolm
- Department of Zoology, Stockholm University, Stockholm, Sweden
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Gao X, Li Y, Adetula AA, Wu Y, Chen H. Analysis of new retrogenes provides insight into dog adaptive evolution. Ecol Evol 2019; 9:11185-11197. [PMID: 31641464 PMCID: PMC6802060 DOI: 10.1002/ece3.5620] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 08/07/2019] [Accepted: 08/08/2019] [Indexed: 01/01/2023] Open
Abstract
The origin and subsequent evolution of new genes have been considered as an important source of genetic and phenotypic diversity in organisms. Dog breeds show great phenotypic diversity for morphological, physiological, and behavioral traits. However, the contributions of newly originated retrogenes, which provide important genetic bases for dog species differentiation and adaptive traits, are largely unknown. Here, we analyzed the dog genome to identify new RNA-based duplications and comprehensively investigated their origin, evolution, functions in adaptive traits, and gene movement processes. First, we totally identified 3,025 retrocopies including 476 intact retrogenes, 2,518 retropseudogenes, and 31 chimerical retrogenes. Second, selective pressure along with ESTs expression analysis showed that most of the intact retrogenes were significantly under stronger purifying selection and subjected to more functional constraints when compared to retropseudogenes. Furthermore, a large number of retrocopies and chimerical retrogenes that occurred approximately 22 million years ago implied a burst of retrotransposition in the dog genome after the divergence time between dog and its closely related species red fox. Interestingly, GO and pathway analyses showed that new retrogenes had expanded in glutathione biosynthetic/metabolic process which likely provided important genetic basis for dogs' adaptation to scavenge human waste dumps. Finally, consistent with the results in human and mouse, a significant excess of functional retrogenes movement on and off the X chromosome in the dog confirmed a general pattern of gene movement process in mammals which was likely driven by natural selection or sexual antagonism. Together, these results increase our understanding that new retrogenes can reshape the dog genome and provide further exploration of the molecular mechanisms underlying the dogs' adaptive evolution.
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Affiliation(s)
- Xiang Gao
- Center LaboratoryRenmin Hospital of Wuhan UniversityWuhanChina
| | - Yan Li
- Department of Infectious DiseasesZhongnan Hospital of Wuhan UniversityWuhanChina
| | - Adeyinka A. Adetula
- Key Laboratory of Agricultural Animal Genetics, Breeding, and ReproductionHuazhong Agricultural UniversityWuhanChina
| | - Yu Wu
- Oilfield Community D-1-902WuhanChina
| | - Hong Chen
- Department of Scientific ResearchRenmin Hospital of Wuhan UniversityWuhanChina
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33
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Mariotti F, Magi GE, Gavazza A, Vincenzetti S, Komissarov A, Shneider A, Venanzi FM. p62/SQSTM1 expression in canine mammary tumours: Evolutionary notes. Vet Comp Oncol 2019; 17:570-577. [PMID: 31332942 DOI: 10.1111/vco.12523] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 07/09/2019] [Accepted: 07/11/2019] [Indexed: 12/30/2022]
Abstract
Recent studies highlighted the role of autophagy as a cardinal regulatory system for homeostasis and cancer-related signalling pathways. In this context, the deregulated expression of p62 - Sequestosome1 (p62/SQSTM1) - a protein acting both as an autophagy receptor and signalling hub, has been associated with tumour development and chronic inflammation. Multiple clinical studies test drugs targeting autophagy, and even more research is on the way to clinical trials. However, no comparative investigations have been carried out to identify adequate preclinical models to assess p62-based medicine. In veterinary oncology the role of p62 in cancer-related pathways has been largely ignored. We compared p62 sequences in multiple organisms and found that canine p62 significantly diverges from the humans and from other animals sequences. Then, we chart by immunohistochemistry the expression levels of p62 in canine mammary tumours. A total of 66 tumours and 10 non-neoplastic mammary samples were examined. The expression of p62 was higher in normal tissue and adenomas than carcinomas, with lowest levels of p62 protein detected in high grade carcinomas. In all cases examined the tumour stroma appeared to be p62-negative. Taken together our results would suggest that in dogs the association between p62 expression and cancer cells overturns that reported in human breast carcinoma, where p62 accumulates in malignant cells as compared to normal epithelium. Thus, at least in canine mammary tumours, p62 should be not considered a tumour-rejection antigen for an anti-cancer immunotherapy.
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Affiliation(s)
- Francesca Mariotti
- School of Biosciences and Veterinary Medicine, University of Camerino, Italy
| | - Gian Enrico Magi
- School of Biosciences and Veterinary Medicine, University of Camerino, Italy
| | - Alessandra Gavazza
- School of Biosciences and Veterinary Medicine, University of Camerino, Italy
| | - Silvia Vincenzetti
- School of Biosciences and Veterinary Medicine, University of Camerino, Italy
| | | | - Alex Shneider
- CureLab Oncology. Inc. Dedham Boston, Massachusetts.,Department of Molecular Biology, Ariel University, Ariel, Israel.,Sechenov First Moscow State Medical University, Moscow, Russia
| | - Franco Maria Venanzi
- CureLab Oncology. Inc. Dedham Boston, Massachusetts.,Sechenov First Moscow State Medical University, Moscow, Russia
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Barrowclough GF, Groth JG, Mauck WM, Blair ME. Phylogeography and species limits in the red-shouldered hawk ( Buteo lineatus): Characterization of the Northern Florida Suture Zone in birds. Ecol Evol 2019; 9:6245-6258. [PMID: 31236218 PMCID: PMC6580285 DOI: 10.1002/ece3.5190] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 03/28/2019] [Accepted: 03/29/2019] [Indexed: 11/22/2022] Open
Abstract
The North American red-shouldered hawk, Buteo lineatus, is comprised of two widely allopatric eastern and western populations with an additional well-marked subspecies in the Florida peninsula. The two eastern populations meet in northern Florida, the location of a well-known suture zone in many nonavian organisms. We sequenced the complete mitochondrial ND2 gene and two nuclear introns to investigate its genetic population structure and species status. No mitochondrial haplotypes were shared between the eastern and western populations, and genetic variance among 14 populations was 0.42; almost all of this (0.40) was distributed among the three regions. A clade of haplotypes very common in the Florida peninsula decreased in frequency elsewhere and, when modeled as a hybrid zone, had an estimated width of 1,158 km with a center near Ocala, FL. Ecological niche modeling suggests the western, eastern, and Florida peninsula populations were geographically isolated during the last glacial maximum. We consider these to represent three phylogenetic species. A coalescent analysis incorporating incomplete lineage sorting and gene tree uncertainty also suggested the divergence between the western and eastern populations is consistent with species-level divergence. With the addition of this hawk, four avian species are now known to hybridize along the Gulf Coast of the United States in or near the Northern Florida Suture Zone. The widths of these avian zones vary substantially (176-1,158 km) and appear to reflect magnitude of gene flow, rather than extent of genetic differentiation. None of these birds was suggested as possible exemplars in the original description of the suture zone. Of the six species that were so identified, three have been surveyed to date, but none of those was found to be genetically differentiated.
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Affiliation(s)
| | - Jeff G. Groth
- Department of OrnithologyAmerican Museum of Natural HistoryNew YorkNew York
| | - William M. Mauck
- Department of OrnithologyAmerican Museum of Natural HistoryNew YorkNew York
- New York Genome CenterNew YorkNew York
| | - Mary E. Blair
- Center for Biodiversity and ConservationAmerican Museum of Natural HistoryNew YorkNew York
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Ehrhart EJ, Wong S, Richter K, Zismann V, Grimes C, Hendricks W, Khanna C. Polymerase chain reaction for antigen receptor rearrangement: Benchmarking performance of a lymphoid clonality assay in diverse canine sample types. J Vet Intern Med 2019; 33:1392-1402. [PMID: 30939225 PMCID: PMC6524097 DOI: 10.1111/jvim.15485] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 03/06/2019] [Indexed: 01/24/2023] Open
Abstract
Background Polymerase chain reaction for antigen receptor rearrangement (PARR) is a molecular diagnostic tool used for discrimination of lymphoid malignancies in dogs from benign processes. Assay variations have been described and are commercially available, but performance metrics are not uniformly reported. Objectives To describe performance (accuracy, sensitivity, specificity) and rigorous benchmarking of a PARR protocol (ePARR) in clinically relevant samples. Animals One hundred eighty‐one client‐owned dogs. Methods Lymphoma and benign tissues representative of the clinical spectrum with gold standard histopathologic and immunohistochemical diagnoses were collected. Assay development and benchmarking were performed on fresh frozen (FF) tissue, formalin‐fixed paraffin‐embedded (FFPE) tissue, flow cytometry pellets, and air‐dried fine‐needle aspirates (FNA). Assay performance was determined for FFPE from 56 dogs (18 B‐cell lymphoma, 24 T‐cell lymphoma, and 14 non‐lymphoma), 80 frozen flow cytometry pellets (66 B‐cell lymphoma, 14 T‐cell lymphoma, 0 non‐lymphoma), and 41 air‐dried FNA slides (23 lymphoma, 18 non‐lymphoma). Results For discrimination of lymphoma versus non‐lymphoma, ePARR had 92% and 92% sensitivity and specificity on FFPE with 92% accuracy, 85% sensitivity from flow cytometry pellets (non‐lymphoma was not evaluated to calculate specificity) with 85% accuracy, and 100% and 100% sensitivity and specificity for FNA with 100% accuracy. Stringent quality control criteria decreased assay success rate without significant performance improvement. Performance metrics were lower in most cases for discrimination of B‐ or T‐cell versus non‐B‐ or non‐T‐cell samples than for lymphoma versus non‐lymphoma. Conclusions and Clinical Importance These benchmarking data facilitate effective interpretation and application of PARR assays in multiple sample types.
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Affiliation(s)
- E J Ehrhart
- Ethos Discovery, San Diego, California.,Ethos Veterinary Health, Woburn, Massachusetts
| | - Shukmei Wong
- Integrated Cancer Genomics Division, The Translational Genomics Research Institute (TGen), Phoenix, Arizona
| | - Keith Richter
- Ethos Discovery, San Diego, California.,Ethos Veterinary Health, Woburn, Massachusetts
| | - Victoria Zismann
- Integrated Cancer Genomics Division, The Translational Genomics Research Institute (TGen), Phoenix, Arizona
| | - Carolyn Grimes
- Ethos Discovery, San Diego, California.,Ethos Veterinary Health, Woburn, Massachusetts
| | - William Hendricks
- Integrated Cancer Genomics Division, The Translational Genomics Research Institute (TGen), Phoenix, Arizona
| | - Chand Khanna
- Ethos Discovery, San Diego, California.,Ethos Veterinary Health, Woburn, Massachusetts
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Qiao J, Luo Z, Gu Z, Zhang Y, Zhang X, Ma X. Identification of a Novel Specific Cucurbitadienol Synthase Allele in Siraitia grosvenorii Correlates with High Catalytic Efficiency. Molecules 2019; 24:E627. [PMID: 30754652 PMCID: PMC6384864 DOI: 10.3390/molecules24030627] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 01/20/2019] [Accepted: 01/24/2019] [Indexed: 01/17/2023] Open
Abstract
Mogrosides, the main bioactive compounds isolated from the fruits of Siraitia grosvenorii, are a group of cucurbitane-type triterpenoid glycosides that exhibit a wide range of notable biological activities and are commercially available worldwide as natural sweeteners. However, the extraction cost is high due to their relatively low contents in plants. Therefore, molecular breeding needs to be achieved when conventional plant breeding can hardly improve the quality so far. In this study, the levels of 21 active mogrosides and two precursors in 15 S. grosvenorii varieties were determined by HPLC-MS/MS and GC-MS, respectively. The results showed that the variations in mogroside V content may be caused by the accumulation of cucurbitadienol. Furthermore, a total of four wild-type cucurbitadienol synthase protein variants (50R573L, 50C573L, 50R573Q, and 50C573Q) based on two missense mutation single nucleotide polymorphism (SNP) sites were discovered. An in vitro enzyme reaction analysis indicated that 50R573L had the highest activity, with a specific activity of 10.24 nmol min-1 mg-1. In addition, a site-directed mutant, namely, 50K573L, showed a 33% enhancement of catalytic efficiency compared to wild-type 50R573L. Our findings identify a novel cucurbitadienol synthase allele correlates with high catalytic efficiency. These results are valuable for the molecular breeding of luohanguo.
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Affiliation(s)
- Jing Qiao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China.
| | - Zuliang Luo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China.
| | - Zhe Gu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China.
| | | | - Xindan Zhang
- Guilin GFS Monk Fruit Corp., Guilin 541006, China.
| | - Xiaojun Ma
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China.
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DeCandia AL, Brzeski KE, Heppenheimer E, Caro CV, Camenisch G, Wandeler P, Driscoll C, vonHoldt BM. Urban colonization through multiple genetic lenses: The city-fox phenomenon revisited. Ecol Evol 2019; 9:2046-2060. [PMID: 30847091 PMCID: PMC6392345 DOI: 10.1002/ece3.4898] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 12/11/2018] [Accepted: 12/13/2018] [Indexed: 12/31/2022] Open
Abstract
Urbanization is driving environmental change on a global scale, creating novel environments for wildlife to colonize. Through a combination of stochastic and selective processes, urbanization is also driving evolutionary change. For instance, difficulty in traversing human-modified landscapes may isolate newly established populations from rural sources, while novel selective pressures, such as altered disease risk, toxicant exposure, and light pollution, may further diverge populations through local adaptation. Assessing the evolutionary consequences of urban colonization and the processes underlying them is a principle aim of urban evolutionary ecology. In the present study, we revisited the genetic effects of urbanization on red foxes (Vulpes vulpes) that colonized Zurich, Switzerland. Through use of genome-wide single nucleotide polymorphisms and microsatellite markers linked to the major histocompatibility complex (MHC), we expanded upon a previous neutral microsatellite study to assess population structure, characterize patterns of genetic diversity, and detect outliers associated with urbanization. Our results indicated the presence of one large evolutionary cluster, with substructure evident between geographic sampling areas. In urban foxes, we observed patterns of neutral and functional diversity consistent with founder events and reported increased differentiation between populations separated by natural and anthropogenic barriers. We additionally reported evidence of selection acting on MHC-linked markers and identified outlier loci with putative gene functions related to energy metabolism, behavior, and immunity. We concluded that demographic processes primarily drove patterns of diversity, with outlier tests providing preliminary evidence of possible urban adaptation. This study contributes to our overall understanding of urban colonization ecology and emphasizes the value of combining datasets when examining evolutionary change in an increasingly urban world.
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Affiliation(s)
- Alexandra L. DeCandia
- Department of Ecology and Evolutionary BiologyPrinceton UniversityPrincetonNew Jersey
| | - Kristin E. Brzeski
- Department of Ecology and Evolutionary BiologyPrinceton UniversityPrincetonNew Jersey
- School of Forest Resources and Environmental ScienceMichigan Technological UniversityHoughtonMichigan
| | | | - Catherine V. Caro
- Department of Ecology and Evolutionary BiologyPrinceton UniversityPrincetonNew Jersey
| | - Glauco Camenisch
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurichSwitzerland
| | | | - Carlos Driscoll
- Laboratory of Comparative Behavioral GenomicsNational Institute on Alcohol Abuse and Alcoholism, National Institutes of HealthRockvilleMaryland
| | - Bridgett M. vonHoldt
- Department of Ecology and Evolutionary BiologyPrinceton UniversityPrincetonNew Jersey
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Ramírez-Barrera SM, Hernández-Baños BE, Jaramillo-Correa JP, Klicka J. Deep divergence of Red-crowned Ant Tanager ( Habia rubica: Cardinalidae), a multilocus phylogenetic analysis with emphasis in Mesoamerica. PeerJ 2018; 6:e5496. [PMID: 30225165 PMCID: PMC6139011 DOI: 10.7717/peerj.5496] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 07/31/2018] [Indexed: 11/20/2022] Open
Abstract
Many neotropical species have a complex history of diversification as a result of the influence of geographical, ecological, climatic, and geological factors that determine the distribution of populations within a lineage. Phylogeography identifies such populations, determines their geographic distributions, and quantifies the degree of genetic divergence. In this work we explored the genetic structure of Habia rubica populations, a polytypic taxon with 17 subspecies described, in order to obtain hypotheses about their evolutionary history and processes of diversification. We undertook multilocus analyses using sequences of five molecular markers (ND2, ACOI-I9, MUSK, FGB-I5 and ODC), and sampling from across the species’ distribution range, an area encompassing from Central Mexico throughout much of South America. With these data, we obtained a robust phylogenetic hypothesis, a species delimitation analysis, and estimates of divergence times for these lineages. The phylogenetic hypothesis of concatenated molecular markers shows that H. rubica can be divided in three main clades: the first includes Mexican Pacific coast populations, the second is formed by population from east of Mexico to Panama and the third comprises the South American populations. Within these clades we recognize seven principal phylogroups whose limits have a clear correspondence with important geographical discontinuities including the Isthmus of Tehuantepec in southern Mexico, the Talamanca Cordillera, and the Isthmus of Panama in North America. In South America, we observed a marked separation of two phylogroups that include the populations that inhabit mesic forests in western and central South America (Amazon Forest) and those inhabiting the seasonal forest from the eastern and northern regions of the South America (Atlantic Forest). These areas are separated by an intervening dry vegetation “diagonal” (Chaco, Cerrado and Caatinga). The geographic and genetic structure of these phylogroups describes a history of diversification more active and complex in the northern distribution of this species, producing at least seven well-supported lineages that could be considered species.
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Affiliation(s)
- Sandra M Ramírez-Barrera
- Departamento de Biología Evolutiva, Facultad de Ciencias, Museo de Zoología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Blanca E Hernández-Baños
- Departamento de Biología Evolutiva, Facultad de Ciencias, Museo de Zoología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Juan P Jaramillo-Correa
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - John Klicka
- Department of Biology and Burke Museum of Natural History and Culture, University of Washington, Seatle, WA, United States of America
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Racocetra crispa (Glomeromycotina) delimited by integrative evidence based on morphology, long continuous nuclear rDNA sequencing and phylogeny. Mycol Prog 2018. [DOI: 10.1007/s11557-018-1410-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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40
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Malenfant RM, Davis CS, Richardson ES, Lunn NJ, Coltman DW. Heritability of body size in the polar bears of Western Hudson Bay. Mol Ecol Resour 2018; 18:854-866. [DOI: 10.1111/1755-0998.12889] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 03/23/2018] [Accepted: 03/29/2018] [Indexed: 12/16/2022]
Affiliation(s)
- René M. Malenfant
- Department of Biology University of New Brunswick Fredericton NB Canada
- Department of Biological Sciences University of Alberta Edmonton Alberta Canada
| | - Corey S. Davis
- Department of Biological Sciences University of Alberta Edmonton Alberta Canada
| | - Evan S. Richardson
- Wildlife Research Division Science and Technology Branch Environment and Climate Change Canada Winnipeg MB Canada
| | - Nicholas J. Lunn
- Wildlife Research Division Science and Technology Branch Environment and Climate Change Canada University of Alberta Edmonton AB Canada
| | - David W. Coltman
- Department of Biological Sciences University of Alberta Edmonton Alberta Canada
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Koparde P, Mehta P, Reddy S, Ramakrishnan U, Mukherjee S, Robin VV. The critically endangered forest owlet Heteroglaux blewitti is nested within the currently recognized Athene clade: A century-old debate addressed. PLoS One 2018; 13:e0192359. [PMID: 29401484 PMCID: PMC5798823 DOI: 10.1371/journal.pone.0192359] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 01/21/2018] [Indexed: 11/23/2022] Open
Abstract
Range-restricted species generally have specific niche requirements and may often have unique evolutionary histories. Unfortunately, many of these species severely lack basic research, resulting in poor conservation strategies. The phylogenetic relationship of the Critically Endangered Forest Owlet Heteroglaux blewitti has been the subject of a century-old debate. The current classifications based on non-phylogenetic comparisons of morphology place the small owls of Asia into three genera, namely, Athene, Glaucidium, and Heteroglaux. Based on morphological and anatomical data, H. blewitti has been alternatively hypothesized to belong within Athene, Glaucidium, or its own monotypic genus Heteroglaux. To test these competing hypotheses, we sequenced six loci (~4300 bp data) and performed phylogenetic analyses of owlets. Mitochondrial and nuclear trees were not congruent in their placement of H. blewitti. However, both mitochondrial and nuclear combined datasets showed strong statistical support with high maximum likelihood bootstrap (>/ = 90) and Bayesian posterior probability values (>/ = 0.98) for H. blewitti being nested in the currently recognized Athene group, but not sister to Indian A. brama. The divergence of H. blewitti from its sister taxa was between 4.3 and 5.7 Ma coinciding with a period of drastic climatic changes in the Indian subcontinent. This study presented the first genetic analysis of H. blewitti, a Critically Endangered species, and addressed the long debate on the relationships of the Athene-Heteroglaux-Glaucidium complex. We recommend further studies with more data and complete taxon sampling to understand the biogeography of Indian Athene species.
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Affiliation(s)
- Pankaj Koparde
- Division of Conservation Biology, Sálim Ali Centre for Ornithology & Natural History, Coimbatore, Tamil Nadu, India
- Manipal Academy of Higher Education, Madhav Nagar, Manipal, Karnataka, India
- Indian Institute of Science Education and Research, Tirupati, Andhra Pradesh, India
- * E-mail:
| | - Prachi Mehta
- Wildlife Research and Conservation Society, Pune, Maharashtra, India
| | - Sushma Reddy
- Loyola University, Chicago, Illinois, United States of America
| | - Uma Ramakrishnan
- National Centre for Biological Science, TIFR, Bangalore, Karnataka, India
| | - Shomita Mukherjee
- Division of Conservation Biology, Sálim Ali Centre for Ornithology & Natural History, Coimbatore, Tamil Nadu, India
| | - V. V. Robin
- Indian Institute of Science Education and Research, Tirupati, Andhra Pradesh, India
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42
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Ye J, Niu X, Yang Y, Wang S, Xu Q, Yuan X, Yu H, Wang Y, Wang S, Feng Y, Wei X. Divergent Hd1, Ghd7, and DTH7 Alleles Control Heading Date and Yield Potential of Japonica Rice in Northeast China. FRONTIERS IN PLANT SCIENCE 2018; 9:35. [PMID: 29434613 PMCID: PMC5790996 DOI: 10.3389/fpls.2018.00035] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 01/09/2018] [Indexed: 05/04/2023]
Abstract
The heading date is a vital factor in achieving a full rice yield. Cultivars with particular flowering behaviors have been artificially selected to survive in the long-day and low-temperature conditions of Northeast China. To dissect the genetic mechanism responsible for heading date in rice populations from Northeast China, association mapping was performed to identify major controlling loci. A genome-wide association study (GWAS) identified three genetic loci, Hd1, Ghd7, and DTH7, using general and mixed linear models. The three genes were sequenced to analyze natural variations and identify their functions. Loss-of-function alleles of these genes contributed to early rice heading dates in the northern regions of Northeast China, while functional alleles promoted late rice heading dates in the southern regions of Northeast China. Selecting environmentally appropriate allele combinations in new varieties is recommended during breeding. Introducing the early indica rice's genetic background into Northeast japonica rice is a reasonable strategy for improving genetic diversity.
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Affiliation(s)
- Jing Ye
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
- College of Agronomy, Shenyang Agricultural University, Shenyang, China
| | - Xiaojun Niu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Yaolong Yang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Shan Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Qun Xu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Xiaoping Yuan
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Hanyong Yu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Yiping Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Shu Wang
- College of Agronomy, Shenyang Agricultural University, Shenyang, China
- *Correspondence: Xinghua Wei, Yue Feng, Shu Wang,
| | - Yue Feng
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
- *Correspondence: Xinghua Wei, Yue Feng, Shu Wang,
| | - Xinghua Wei
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
- *Correspondence: Xinghua Wei, Yue Feng, Shu Wang,
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Thomson RC, Spinks PQ, Shaffer HB. Molecular phylogeny and divergence of the map turtles (Emydidae: Graptemys). Mol Phylogenet Evol 2017; 121:61-70. [PMID: 29242165 DOI: 10.1016/j.ympev.2017.11.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 10/13/2017] [Accepted: 11/27/2017] [Indexed: 11/30/2022]
Abstract
The map turtles (genus Graptemys) comprise a morphologically diverse clade that forms a major component of the southeastern US hotspot of chelonian diversity. Map turtles have experienced both recent and rapid diversification resulting in long-standing uncertainty regarding species boundaries and phylogenetic relationships within the genus as well as timing of their divergence. We present a phylogeny for the group that includes geographically representative sampling for all described species and subspecies. We make use of an empirical prior on rates of molecular evolution to estimate divergence times with a molecular clock under a coalescent framework. Together, the phylogeny and divergence time estimates suggest that diversification has been both more recent and more rapid than has so far been suspected. We provide a well-supported evolutionary framework for Graptemys that is necessary for understanding map turtle diversity, biogeography, and for conservation of this threatened clade of turtles.
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Affiliation(s)
- Robert C Thomson
- Department of Biology, University of Hawai'i, Honolulu, HI 96822, USA.
| | - Phillip Q Spinks
- Department of Ecology and Evolutionary Biology, and La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA
| | - H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, and La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA
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44
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Discovery and validation of species–specific diagnostic SNP markers for the endangered San Diego fairy shrimp (Branchinecta sandiegonensis) and the versatile fairy shrimp (Branchinecta lindahli). CONSERV GENET RESOUR 2017. [DOI: 10.1007/s12686-017-0912-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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45
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Campana MG. BaitsTools: Software for hybridization capture bait design. Mol Ecol Resour 2017; 18:356-361. [PMID: 28941033 DOI: 10.1111/1755-0998.12721] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 09/12/2017] [Accepted: 09/14/2017] [Indexed: 12/01/2022]
Abstract
Nucleic acid hybridization capture is a principal technology in molecular ecology and genomics. Bait design, however, is a nontrivial task and few resources currently exist to automate the process. Here, I present baitstools, an open-source, user-friendly software package to facilitate the design of nucleic acid baits for hybridization capture.
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Affiliation(s)
- Michael G Campana
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, Washington, DC, USA
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Wickramasinghe N, Robin VV, Ramakrishnan U, Reddy S, Seneviratne SS. Non-sister Sri Lankan white-eyes (genus Zosterops) are a result of independent colonizations. PLoS One 2017; 12:e0181441. [PMID: 28792950 PMCID: PMC5549887 DOI: 10.1371/journal.pone.0181441] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 07/02/2017] [Indexed: 11/18/2022] Open
Abstract
Co-occurrence of closely related taxa on islands could be attributed to sympatric speciation or multiple colonization. Sympatric speciation is considered to be rare in small islands, however multiple colonizations are known to be common in both oceanic and continental islands. In this study we investigated the phylogenetic relatedness and means of origin of the two sympatrically co-occurring Zosterops white-eyes, the endemic Zosterops ceylonensis and its widespread regional congener Z. palpebrosus, in the island of Sri Lanka. Sri Lanka is a continental island in the Indian continental shelf of the Northern Indian Ocean. Our multivariate morphometric analyses confirmed the phenotypic distinctness of the two species. Maximum Likelihood and Bayesian phylogenetic analyses with ~2000bp from two mitochondrial (ND2 and ND3) and one nuclear (TGF) gene indicated that they are phylogenetically distinct, and not sister to each other. The two subspecies of the peninsula India; Z. p. egregius of Sri Lanka and India and Z. p. nilgiriensis of Western Ghats (India) clustered within the Z. palpebrosus clade having a common ancestor. In contrast, the divergence of the endemic Z. ceylonensis appears to be much deeper and is basal to the other Zosterops white-eyes. Therefore we conclude that the two Zosterops species originated in the island through independent colonizations from different ancestral lineages, and not through island speciation or multiple colonization from the same continental ancestral population. Despite high endemism, Sri Lankan biodiversity is long considered to be a subset of southern India. This study on a speciose group with high dispersal ability and rapid diversification rate provide evidence for the contribution of multiple colonizations in shaping Sri Lanka’s biodiversity. It also highlights the complex biogeographic patterns of the South Asian region, reflected even in highly vagile groups such as birds.
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Affiliation(s)
- Nelum Wickramasinghe
- Avian Evolution Node, Department of Zoology and Environment Sciences, Faculty of Science, University of Colombo, Colombo, Sri Lanka
- National Center for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - V. V. Robin
- National Center for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Uma Ramakrishnan
- National Center for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Sushma Reddy
- Biology Department, Loyola University Chicago, Chicago, Illinois, United States of America
| | - Sampath S. Seneviratne
- Avian Evolution Node, Department of Zoology and Environment Sciences, Faculty of Science, University of Colombo, Colombo, Sri Lanka
- * E-mail:
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47
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Villanueva‐Cañas JL, Rech GE, Cara MAR, González J. Beyond
SNP
s: how to detect selection on transposable element insertions. Methods Ecol Evol 2017. [DOI: 10.1111/2041-210x.12781] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
| | - Gabriel E. Rech
- Institute of Evolutionary Biology (CSIC‐Universitat Pompeu Fabra) Barcelona Spain
| | - Maria Angeles Rodriguez Cara
- Ecoanthropology and Ethnobiology Laboratory, UMR 7206, CNRS/MNHN/Universite Paris 7 Museum National d'HistoireNaturelle F‐75116 Paris France
| | - Josefa González
- Institute of Evolutionary Biology (CSIC‐Universitat Pompeu Fabra) Barcelona Spain
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48
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Fernando SW, Peterson AT, Li SH. Reconstructing the geographic origin of the New World jays. NEOTROPICAL BIODIVERSITY 2017. [DOI: 10.1080/23766808.2017.1296751] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Affiliation(s)
- Sumudu W. Fernando
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
| | - A. Townsend Peterson
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
| | - Shou-Hsien Li
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
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49
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Hung CM, Drovetski SV, Zink RM. Matching loci surveyed to questions asked in phylogeography. Proc Biol Sci 2016; 283:20152340. [PMID: 26962145 DOI: 10.1098/rspb.2015.2340] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Although mitochondrial DNA (mtDNA) has long been used for assessing genetic variation within and between populations, its workhorse role in phylogeography has been criticized owing to its single-locus nature. The only choice for testing mtDNA results is to survey nuclear loci, which brings into contrast the difference in locus effective size and coalescence times. Thus, it remains unclear how erroneous mtDNA-based estimates of species history might be, especially for evolutionary events in the recent past. To test the robustness of mtDNA and nuclear sequences in phylogeography, we provide one of the largest paired comparisons of summary statistics and demographic parameters estimated from mitochondrial, five Z-linked and 10 autosomal genes of 30 avian species co-distributed in the Caucasus and Europe. The results suggest that mtDNA is robust in estimating inter-population divergence but not in intra-population diversity, which is sensitive to population size change. Here, we provide empirical evidence showing that mtDNA was more likely to detect population divergence than any other single locus owing to its smaller Ne and thus faster coalescent time. Therefore, at least in birds, numerous studies that have based their inferences of phylogeographic patterns solely on mtDNA should not be readily dismissed.
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Affiliation(s)
- Chih-Ming Hung
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Sergei V Drovetski
- Division of Birds, National Museum of Natural History, Smithsonian Institution, Washington, DC 20004, USA
| | - Robert M Zink
- Bell Museum and Department of Ecology, Evolution and Behavior, University of Minnesota, St Paul, MN, USA
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50
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Population expansion, current and past gene flow in Gould’s petrel: implications for conservation. CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0886-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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