Distribution and genetic diversity of Blastocystis subtypes in various mammal and bird species in northeastern China

AbstractUrbanization and associated environmental changes are causing global declines in vertebrate populations. In general, population declines of the magnitudes now detected should lead to reduced effective population sizes for animals living in proximity to humans and disturbed lands. This is cause for concern because effective population sizes set the rate of genetic diversity loss due to genetic drift, the rate of increase in inbreeding, and the efficiency with which selection can act on beneficial alleles. We predicted that the effects of urbanization should decrease effective population size and genetic diversity, and increase population-level genetic differentiation. To test for such patterns, we repurposed and reanalyzed publicly archived genetic data sets for North American birds and mammals. After filtering, we had usable raw genotype data from 85 studies and 41,023 individuals, sampled from 1,008 locations spanning 41 mammal and 25 bird species. We used census-based urban-rural designations, human population density, and the Human Footprint Index as measures of urbanization and habitat disturbance. As predicted, mammals sampled in more disturbed environments had lower effective population sizes and genetic diversity, and were more genetically differentiated from those in more natural environments. There were no consistent relationships detectable for birds. This suggests that, in general, mammal populations living near humans may have less capacity to respond adaptively to further environmental changes, and be more likely to suffer from effects of inbreeding.

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Genetic Diversity and Coexistence of Babesia in Ticks (Acari: Ixodidae) from Northeastern China

Vector-Borne and Zoonotic Diseases ◽

10.1089/vbz.2020.2635 ◽

2020 ◽

Vol 20 (11) ◽

pp. 817-824

Author(s):

Luo-Yuan Xia ◽

Bao-Gui Jiang ◽

Ting-Ting Yuan ◽

Michael von Fricken ◽

Na Jia ◽

...

Keyword(s):

Genetic Diversity ◽

Northeastern China

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Virulence structure and its genetic diversity analyses of Blumeria graminis f. sp. tritici isolates in China

BMC Evolutionary Biology ◽

10.1186/s12862-019-1511-3 ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 3

Author(s):

Xian Xin Wu ◽

Xiao Feng Xu ◽

De Xin Ma ◽

Rong Zhen Chen ◽

Tian Ya Li ◽

...

Keyword(s):

Genetic Diversity ◽

Powdery Mildew ◽

Expressed Sequence Tag ◽

Virulence Gene ◽

Blumeria Graminis ◽

Northeastern China ◽

Gansu Province ◽

Clear Correlation ◽

Wheat Powdery Mildew ◽

Gene Data

Abstract Background Blumeria graminis f. sp. tritici (Bgt), the causal agent of wheat powdery mildew severely affects yield security wheat production in China. Understanding the virulence structure and genetic variations of this pathogen is important for breeding wheat lines resistant to wheat powdery mildew. However, information related to genes controlling resistance remains elusive. This study analyzes the virulence structure and the genetic diversity of pathogenic Bgt populations isolated from northeastern (Liaoning, Heilongjiang) and northwestern (Gansu) China, two representative wheat producing areas, on 37 wheat cultivars each carrying a known powdery mildew resistance (Pm) gene. Results Bgt isolates from northeastern China show higher frequencies of virulence genes than populations from Gansu Province. Many of the known Pm genes failed to provide resistance in this study. However, Pm21 provided 100% resistance to all isolates from all three provinces, obtained during two consecutive years, while Pm13 provided 100% resistance in Gansu. Pm13, Pm16, Pm18, and Pm22 also showed partial resistance in northeastern China, while Pm16, Pm18, Pm22, Pm5 + 6 and Pm2 + 6 +? maintained some resistance in Gansu. Genetic diversity among populations in different regions was detected by cluster analyses using expressed sequence tag-simple sequence repeat (EST-SSR). When the genetic similarity coefficient is relatively high, populations from the same regional origin are mostly clustered into one group while populations from different regions exhibit large genetic differences. Conclusion Pm21 remains the best choice for breeding programs to maintain resistance to Bgt. Only 58% of the isolates tested show a clear correlation between EST-SSR genetic polymorphisms and frequency of virulence gene data.

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Differentiation with drift: a spatio-temporal genetic analysis of Galápagos mockingbird populations ( Mimus spp.)

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2009.0311 ◽

2010 ◽

Vol 365 (1543) ◽

pp. 1127-1138 ◽

Cited By ~ 47

Author(s):

Paquita E. A. Hoeck ◽

Jennifer L. Bollmer ◽

Patricia G. Parker ◽

Lukas F. Keller

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Population Size ◽

Genetic Drift ◽

Bird Species ◽

Effective Population ◽

Island Size ◽

Island Populations ◽

Population Sizes ◽

Spatio Temporal

Small and isolated island populations provide ideal systems to study the effects of limited population size, genetic drift and gene flow on genetic diversity. We assessed genetic diversity within and differentiation among 19 mockingbird populations on 15 Galápagos islands, covering all four endemic species, using 16 microsatellite loci. We tested for signs of drift and gene flow, and used historic specimens to assess genetic change over the last century and to estimate effective population sizes. Within-population genetic diversity and effective population sizes varied substantially among island populations and correlated strongly with island size, suggesting that island size serves as a good predictor for effective population size. Genetic differentiation among populations was pronounced and increased with geographical distance. A century of genetic drift did not change genetic diversity on an archipelago-wide scale, but genetic drift led to loss of genetic diversity in small populations, especially in one of the two remaining populations of the endangered Floreana mockingbird. Unlike in other Galápagos bird species such as the Darwin's finches, gene flow among mockingbird populations was low. The clear pattern of genetically distinct populations reflects the effects of genetic drift and suggests that Galápagos mockingbirds are evolving in relative isolation.

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Phylogenetic Diversity among Low-Virulence Newcastle Disease Viruses from Waterfowl and Shorebirds and Comparison of Genotype Distributions to Those of Poultry-Origin Isolates

Journal of Virology ◽

10.1128/jvi.00843-07 ◽

2007 ◽

Vol 81 (22) ◽

pp. 12641-12653 ◽

Cited By ~ 151

Author(s):

L. Mia Kim ◽

Daniel J. King ◽

Phillip E. Curry ◽

David L. Suarez ◽

David E. Swayne ◽

...

Keyword(s):

Genetic Diversity ◽

Newcastle Disease ◽

Bird Species ◽

The United States ◽

Class Ii ◽

Genomic Diversity ◽

Class I ◽

Diagnostic Tools ◽

Death Time ◽

Matrix Gene

ABSTRACT Low-virulence Newcastle disease viruses (loNDV) are frequently recovered from wild bird species, but little is known about their distribution, genetic diversity, or potential to cause disease in poultry. NDV isolates recovered from cloacal samples of apparently healthy waterfowl and shorebirds (WS) in the United States during 1986 to 2005 were examined for genomic diversity and their potential for virulence (n = 249). In addition 19 loNDV isolates from U.S. live bird markets (LBMs) were analyzed and found to be genetically distinct from NDV used in live vaccines but related to WS-origin NDV. Phylogenetic analysis of the fusion protein identified nine novel genotypes among the class I NDV, and new genomic subgroups were identified among genotypes I and II of the class II viruses. The WS-origin viruses exhibited broad genetic and antigenic diversity, and some WS genotypes displayed a closer phylogenetic relationship to LBM-origin NDV. All NDV were predicted to be lentogenic based upon sequencing of the fusion cleavage site, intracerebral pathogenicity index, or mean death time in embryo assays. The USDA real-time reverse transcription-PCR assay, which targets the matrix gene, identified nearly all of the class II NDV tested but failed to detect class I viruses from both LBM and WS. The close phylogenetic proximity of some WS and LBM loNDV suggests that viral transmission may occur among wild birds and poultry; however, these events may occur unnoticed due to the broad genetic diversity of loNDV, the lentogenic presentation in birds, and the limitations of current rapid diagnostic tools.

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Primer development for amplification of toll-like genes for the assessment of adaptive genetic diversity in vulnerable grassland bird species

Conservation Genetics Resources ◽

10.1007/s12686-017-0690-8 ◽

2017 ◽

Vol 9 (3) ◽

pp. 385-387 ◽

Cited By ~ 2

Author(s):

Alejandro Chávez-Treviño ◽

Ricardo Canales-del-Castillo ◽

Irene Ruvalcaba-Ortega ◽

Diana Reséndez-Pérez ◽

José Ignacio González-Rojas ◽

...

Keyword(s):

Genetic Diversity ◽

Bird Species ◽

Grassland Bird ◽

Adaptive Genetic Diversity

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Genetic Diversity and Coexistence ofBabesiain Ticks (Acari: Ixodidae) from Northeastern China

10.1101/469833 ◽

2018 ◽

Author(s):

Jia-Fu Jiang ◽

Bao-Gui Jiang ◽

Ting-Ting Yuan ◽

Michael Von Fricken ◽

Na Jia ◽

...

Keyword(s):

Genetic Diversity ◽

Human Health ◽

Multivariate Logistic Regression Analysis ◽

Northeastern China ◽

Small Scale ◽

Rrna Gene ◽

Ixodes Persulcatus ◽

Health Burden ◽

Human Babesiosis ◽

Babesia Spp

AbstractBackgroundBabesiosis is an emerging zoonosis in humans with significant and increasing health burden in China. A few systematic reports onBabesiaspp. was involved with ticks, especially in the human babesiosis endemic areas.MethodsThe ticks were collected from 30 individual waypoints along 2.0 km transects in two recreational forested areas in Northeastern China. Then we screened them forBabesiaspp. infection by amplifying the partial 18s rRNA gene with subsequent sequencing. Multivariate logistic regression analysis was used to access the association between infections and some related risk factors. The cluster analyses were performed using SaTScan v6.0 Software for identifying the geographic cluster of the positive samples in ticks from each waypoint.ResultsA total ofIxodes persulcatus(n=2380) andHaemaphysalis concinna(n=461) ticks were collected. The 0.97% ofI. persulcatusticks were infected with fiveBabesiaspecies, includingB. bigemina(n=6),B. divergens(n=2),B. microti(n=3),B. venatorum(n=11) and one novel strain HLJ-8. Thirteen (2.92%)H.concinnaticks containedB. bigemina(n=1),B. divergens(n=1), three genetic variants ofBabesiarepresented by HLJ-874 which was closely related toBabesiasp.MA#361-1, and eight otherBabesiavariants represented by HLJ242 which were similar toB.crassa. Each study site had 5~6 differentBabesiaspp. One waypoint was more likely to yieldB.venatorum(relative risk=15.36,P=0.045) than all other waypoints.ConclusionsThere exists a high genetic diversity ofBabesiaspp. across a relatively small sampled region. Further study is needed to understand the risks these variants pose for human health.Author SummaryBabesiosis is the subject of increasing interest as an emerging zoonosis in humans with significant and increasing health burden of the disease at recently. In China, many probably human babesiosis cases who had a history of recent tick bite were found in Lyme endemic area in Northeastern China, where the prevalence of Babesia parasite in the ticks still was far underestimated. In the present study, we conducted a field survey for ticks to identify diversities and complexity of babesia, and then to assess the risk of human babesiosis, by means of a three years longitudinal study that mapped the location of the ticks tested positive for Babesia spp. at two forestry areas with a heavy burden of tick-borne pathogens. We firstly presented the prevalence of Babesia spp. especially the genetic diversities and coexistence of seven Babesia spp. including 2 novel species or variants at one small scale “natural foci” in northeastern China. This work is useful to understand the complexity of Babesia pathogen in China, and how the Babesia perpetuates over the long term in the environment, as well as potential risks for human health.

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Evolutionary history of the Galápagos Rail revealed by ancient mitogenomes and modern samples

10.1101/2020.10.07.326983 ◽

2020 ◽

Author(s):

Jaime A. Chaves ◽

Pedro J. Martinez-Torres ◽

Emiliano A. Depino ◽

Sebastian Espinoza-Ulloa ◽

Jefferson García-Loor ◽

...

Keyword(s):

Genetic Diversity ◽

De Novo ◽

Bird Species ◽

Separate Analysis ◽

Low Genetic Diversity ◽

Lack Of Information ◽

Sister Relationships ◽

Rag 1 ◽

Black Rail ◽

The Impact

AbstractThe biotas of the Galápagos Islands are probably one of the best studied island systems and have provided a broad model of insular species’ origins and evolution. Nevertheless, some Galápagos species remain poorly characterized, such as the Galápagos Rail Laterallus spilonota. This bird species is one of the less explored groups of endemic vertebrates on these islands, due to its elusive behavior, cryptic plumage and restricted distribution. To date there is no genetic assessment of its origins and sister relationships to other taxa, and importantly, there is no data on its current genetic diversity. This lack of information is critical given the adverse fate of island rail species around the world in the recent past. Here we examine the genetics of Galápagos Rails using a combination of mitogenome de novo assembly with multi-locus sequencing (mtDNA+nuDNA) from both modern and historical samples. We show that the Galápagos Rail is part of the ‘American black rail clade’, sister to Black Rail L. jamaicensis, with a colonization of Galápagos dated to 1.2 Mya. The separate analysis of cytb, ND2, and RAG-1 markers demonstrates shallow population structure across sampled islands, possibly due to elevated island connectivity. Additionally, birds sampled from Pinta possessed the lowest levels of genetic diversity, most likely reflecting the impact of past bottlenecks due to habitat loss caused by invasive goats grazing on sensitive habitat. The data presented here highlights the low genetic diversity in this endemic rail species and suggests the use of genetic data (both modern and historical) to guide conservation efforts.

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