Comparative mitochondrial phylogeography of two legless lizards (Pygopodidae) from Queensland’s fragmented woodlands

Sclerophyll woodlands and open forests once covered vast areas of eastern Australia, but have been greatly fragmented and reduced in extent since European settlement. The biogeographic and evolutionary history of the biota of eastern Australia’s woodlands also remains poorly known, especially when compared to rainforests to the east, or the arid biome to the west. Here we present an analysis of patterns of mitochondrial genetic diversity in two species of Pygopodid geckos with distributions centred on the Brigalow Belt Bioregion of eastern Queensland. One moderately large and semi-arboreal species, Paradelma orientalis, shows low genetic diversity and no clear geographic structuring across its wide range. In contrast a small and semi-fossorial species, Delma torquata, consists of two moderately divergent clades, one from the ranges and upland of coastal areas of south-east Queensland, and other centred in upland areas further inland. These data point to varying histories of geneflow and refugial persistance in eastern Australia’s vast but now fragmented open woodlands. The Carnarvon Ranges of central Queensland are also highlighted as a zone of persistence for cool and/or wet-adapted taxa, however the evolutionary history and divergence of most outlying populations in these mountains remains unstudied.

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Genetic Diversity of Rice stripe necrosis virus and New Insights into Evolution of the Genus Benyvirus

Viruses ◽

10.3390/v13050737 ◽

2021 ◽

Vol 13 (5) ◽

pp. 737

Author(s):

Issiaka Bagayoko ◽

Marcos Giovanni Celli ◽

Gustavo Romay ◽

Nils Poulicard ◽

Agnès Pinel-Galzi ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Variability ◽

Sierra Leone ◽

Evolutionary History ◽

Molecular Diversity ◽

Genomic Data ◽

Gene Recombination ◽

Necrosis Virus ◽

History Of ◽

Complex Evolutionary History

The rice stripe necrosis virus (RSNV) has been reported to infect rice in several countries in Africa and South America, but limited genomic data are currently publicly available. Here, eleven RSNV genomes were entirely sequenced, including the first corpus of RSNV genomes of African isolates. The genetic variability was differently distributed along the two genomic segments. The segment RNA1, within which clusters of polymorphisms were identified, showed a higher nucleotidic variability than did the beet necrotic yellow vein virus (BNYVV) RNA1 segment. The diversity patterns of both viruses were similar in the RNA2 segment, except for an in-frame insertion of 243 nucleotides located in the RSNV tgbp1 gene. Recombination events were detected into RNA1 and RNA2 segments, in particular in the two most divergent RSNV isolates from Colombia and Sierra Leone. In contrast to BNYVV, the RSNV molecular diversity had a geographical structure with two main RSNV lineages distributed in America and in Africa. Our data on the genetic diversity of RSNV revealed unexpected differences with BNYVV suggesting a complex evolutionary history of the genus Benyvirus.

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Low major histocompatibility complex diversity in the Tasmanian devil predates European settlement and may explain susceptibility to disease epidemics

Biology Letters ◽

10.1098/rsbl.2012.0900 ◽

2013 ◽

Vol 9 (1) ◽

pp. 20120900 ◽

Cited By ~ 36

Author(s):

Katrina Morris ◽

Jeremy J. Austin ◽

Katherine Belov

Keyword(s):

Major Histocompatibility Complex ◽

Tasmanian Devil ◽

Major Histocompatibility ◽

European Settlement ◽

Low Genetic Diversity ◽

Histocompatibility Complex ◽

Devil Facial Tumour Disease ◽

History Of ◽

Mhc Diversity ◽

Disease Epidemics

The Tasmanian devil ( Sarcophilus harrisii ) is at risk of extinction owing to the emergence of a contagious cancer known as devil facial tumour disease (DFTD). The emergence and spread of DFTD has been linked to low genetic diversity in the major histocompatibility complex (MHC). We examined MHC diversity in historical and ancient devils to determine whether loss of diversity is recent or predates European settlement in Australia. Our results reveal no additional diversity in historical Tasmanian samples. Mainland devils had common modern variants plus six new variants that are highly similar to existing alleles. We conclude that low MHC diversity has been a feature of devil populations since at least the Mid-Holocene and could explain their tumultuous history of population crashes.

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Season of birth interacts with measures of inbreeding in multiplex schizophrenia pedigrees: evidence from genetic isolates in Daghestan

Open Medicine ◽

10.2478/s11536-006-0041-8 ◽

2006 ◽

Vol 1 (4) ◽

pp. 392-398

Author(s):

Kazima Bulayeva ◽

John McGrath

Keyword(s):

Genetic Diversity ◽

Family History ◽

Age Of Onset ◽

Population Genetic Study ◽

Season Of Birth ◽

High Genetic Diversity ◽

Low Genetic Diversity ◽

High Prevalence ◽

History Of ◽

Genetic Isolates

AbstractWhile the season-of-birth effect is one of the most consistent epidemiological features of schizophrenia, there is a lack of consistency with respect to the interaction between season of birth and family history of schizophrenia. Apart from family history, measures related to consanguinity can be used as proxy markers of genomic heterogeneity. Thus, these measures may provide an alternate, indirect index of genetic susceptibility. We had the opportunity to explore the interaction between season of birth and measure of consanguinity in well-described genetic isolates in Daghestan, some of which are known for their relatively high prevalence of schizophrenia. Our previous population-genetic study showed Daghestan has an extremely high genetic diversity between the ethnic populations and a low genetic diversity within them. The isolates selected for this study include some with more than 200 and some with less than 100 generations of demographical history since their founding. Based on pedigrees of multiply-affected families, we found that among individuals with schizophrenia, the measure of consanguinity was significantly higher in the parents of those born in winter/spring compared to those born in summer/autumn. Furthermore, compared to summer/autumn born, winter/spring born individuals with schizophrenia had an earlier age-of-onset, and more prominent auditory hallucinations. Our results suggest that the offspring of consanguineous marriages, and thus those with reduced allelic heterogeneity, may be more susceptible to the environmental factor(s) underpinning the season-of-the effect in schizophrenia.

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Evolutionary history and genetic connectivity across highly fragmented populations of an endangered daisy

Heredity ◽

10.1038/s41437-021-00413-0 ◽

2021 ◽

Author(s):

Yael S. Rodger ◽

Alexandra Pavlova ◽

Steve Sinclair ◽

Melinda Pickup ◽

Paul Sunnucks

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Genetic Differentiation ◽

Evolutionary History ◽

Livestock Grazing ◽

Genetic Connectivity ◽

Evolutionary Divergence ◽

Common Component ◽

A Genome ◽

Eastern Australia

AbstractConservation management can be aided by knowledge of genetic diversity and evolutionary history, so that ecological and evolutionary processes can be preserved. The Button Wrinklewort daisy (Rutidosis leptorrhynchoides) was a common component of grassy ecosystems in south-eastern Australia. It is now endangered due to extensive habitat loss and the impacts of livestock grazing, and is currently restricted to a few small populations in two regions >500 km apart, one in Victoria, the other in the Australian Capital Territory and nearby New South Wales (ACT/NSW). Using a genome-wide SNP dataset, we assessed patterns of genetic structure and genetic differentiation of 12 natural diploid populations. We estimated intrapopulation genetic diversity to scope sources for genetic management. Bayesian clustering and principal coordinate analyses showed strong population genetic differentiation between the two regions, and substantial substructure within ACT/NSW. A coalescent tree-building approach implemented in SNAPP indicated evolutionary divergence between the two distant regions. Among the populations screened, the last two known remaining Victorian populations had the highest genetic diversity, despite having among the lowest recent census sizes. A maximum likelihood population tree method implemented in TreeMix suggested little or no recent gene flow except potentially between very close neighbours. Populations that were more genetically distinctive had lower genetic diversity, suggesting that drift in isolation is likely driving population differentiation though loss of diversity, hence re-establishing gene flow among them is desirable. These results provide background knowledge for evidence-based conservation and support genetic rescue within and between regions to elevate genetic diversity and alleviate inbreeding.

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Genetic variation in native and farmed populations of Tambaqui (Colossoma macropomum) in the Brazilian Amazon: regional discrepancies in farming systems

Anais da Academia Brasileira de Ciências ◽

10.1590/0001-376520130007 ◽

2013 ◽

Vol 85 (4) ◽

pp. 1439-1447 ◽

Cited By ~ 8

Author(s):

Jonas Aguiar ◽

Horacio Schneider ◽

Fatima Gomes ◽

Jeferson Carneiro ◽

Simoni Santos ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Dna Sequences ◽

Amazon Basin ◽

Farming Systems ◽

Wild Populations ◽

The West ◽

Colossoma Macropomum ◽

Breeding Stock ◽

History Of

The tambaqui, Colossoma macropomum, is the most popular fish species used for aquaculture in Brazil but there is no study comparing genetic variation among native and farmed populations of this species. In the present study, we analyzed DNA sequences of the mitochondrial DNA to evaluate the genetic diversity among two wild populations, a fry-producing breeding stock, and a sample of fish farm stocks, all from the region of Santarém, in the west of the Brazilian state of Pará. Similar levels of genetic diversity were found in all the samples and surprisingly the breeding stock showed expressive representation of the genetic diversity registered on wild populations. These results contrast considerably with those of the previous study of farmed stocks in the states of Amapá, Pará, Piauí, and Rondônia, which recorded only two haplotypes, indicating a long history of endogamy in the breeding stocks used to produce fry. The results of the two studies show two distinct scenarios of tambaqui farming in the Amazon basin, which must be better evaluated in order to guarantee the successful expansion of this activity in the region, and the rest of Brazil, given that the tambaqui and its hybrids are now farmed throughout the country.

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SARS-Like Coronaviruses in Horseshoe Bats (Rhinolophus spp.) in Russia, 2020

Viruses ◽

10.3390/v14010113 ◽

2022 ◽

Vol 14 (1) ◽

pp. 113

Author(s):

Sergey Alkhovsky ◽

Sergey Lenshin ◽

Alexey Romashin ◽

Tatyana Vishnevskaya ◽

Oleg Vyshemirsky ◽

...

Keyword(s):

Genetic Diversity ◽

Evolutionary History ◽

Structural Proteins ◽

Rt Pcr ◽

Phylogenetic Lineage ◽

History Of ◽

Horseshoe Bats ◽

Regions Of Russia ◽

Nonstructural Genes

We found and genetically described two novel SARS-like coronaviruses in feces and oral swabs of the greater (R. ferrumequinum) and the lesser (R. hipposideros) horseshoe bats in southern regions of Russia. The viruses, named Khosta-1 and Khosta-2, together with related viruses from Bulgaria and Kenya, form a separate phylogenetic lineage. We found evidence of recombination events in the evolutionary history of Khosta-1, which involved the acquisition of the structural proteins S, E, and M, as well as the nonstructural genes ORF3, ORF6, ORF7a, and ORF7b, from a virus that is related to the Kenyan isolate BtKY72. The examination of bats by RT-PCR revealed that 62.5% of the greater horseshoe bats in one of the caves were positive for Khosta-1 virus, while its overall prevalence was 14%. The prevalence of Khosta-2 was 1.75%. Our results show that SARS-like coronaviruses circulate in horseshoe bats in the region, and we provide new data on their genetic diversity.

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A test statistic to quantify treelikeness in phylogenetics

10.1101/2021.02.16.431544 ◽

2021 ◽

Author(s):

Caitlin Cherryh ◽

Bui Quang Minh ◽

Rob Lanfear

Keyword(s):

Evolutionary History ◽

Incomplete Lineage Sorting ◽

Phylogenetic Analyses ◽

Phylogenetic Network ◽

Parametric Bootstrap ◽

Lineage Sorting ◽

Test Statistic ◽

Sequence Alignments ◽

Wide Range ◽

History Of

AbstractMost phylogenetic analyses assume that the evolutionary history of an alignment (either that of a single locus, or of multiple concatenated loci) can be described by a single bifurcating tree, the so-called the treelikeness assumption. Treelikeness can be violated by biological events such as recombination, introgression, or incomplete lineage sorting, and by systematic errors in phylogenetic analyses. The incorrect assumption of treelikeness may then mislead phylogenetic inferences. To quantify and test for treelikeness in alignments, we develop a test statistic which we call the tree proportion. This statistic quantifies the proportion of the edge weights in a phylogenetic network that are represented in a bifurcating phylogenetic tree of the same alignment. We extend this statistic to a statistical test of treelikeness using a parametric bootstrap. We use extensive simulations to compare tree proportion to a range of related approaches. We show that tree proportion successfully identifies non-treelikeness in a wide range of simulation scenarios, and discuss its strengths and weaknesses compared to other approaches. The power of the tree-proportion test to reject non-treelike alignments can be lower than some other approaches, but these approaches tend to be limited in their scope and/or the ease with which they can be interpreted. Our recommendation is to test treelikeness of sequence alignments with both tree proportion and mosaic methods such as 3Seq. The scripts necessary to replicate this study are available at https://github.com/caitlinch/treelikeness

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No Evidence of Low Genetic Diversity Despite High Levels of Inbreeding and Poor Genetic Connectivity Among Tetrastigma loheri (Vitaceae) Populations in Remaining Forest Areas in Cebu, Philippines

Systematic Botany ◽

10.1600/036364421x16370109698614 ◽

2021 ◽

Vol 46 (4) ◽

pp. 951-961

Author(s):

Jasper John A. Obico ◽

Hemres Alburo ◽

Julie F. Barcelona ◽

Marie Hale ◽

Lisa Paguntalan ◽

...

Keyword(s):

Genetic Diversity ◽

Habitat Fragmentation ◽

Tropical Forests ◽

Forest Cover ◽

Genetic Connectivity ◽

Philippine Island ◽

Low Genetic Diversity ◽

History Of ◽

Gap Data ◽

The Impact

Abstract— Little is known about the effects of habitat fragmentation on the patterns of genetic diversity and genetic connectivity of species in the remaining tropical forests of Southeast Asia. This is particularly evident in Cebu, a Philippine island that has a long history of deforestation and has lost nearly all of its forest cover. To begin filling this gap, data from 13 microsatellite loci developed for Tetrastigma loheri (Vitaceae), a common vine species in Philippine forests, were used to study patterns of genetic diversity and genetic connectivity for the four largest of the remaining forest areas in Cebu. Evidence of relatively high levels of inbreeding was found in all four areas, despite no evidence of low genetic diversity. The four areas are genetically differentiated, suggesting low genetic connectivity. The presence of inbreeding and low genetic connectivity in a commonly encountered species such as T. loheri in Cebu suggests that the impact of habitat fragmentation is likely greater on rare plant species with more restricted distributions in Cebu. Conservation recommendations for the remaining forest areas in Cebu include the establishment of steppingstone corridors between nearby areas to improve the movement of pollinators and seed dispersers among them.

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Evolution of the U.S. Biological Select AgentRathayibacter toxicus

mBio ◽

10.1128/mbio.01280-18 ◽

2018 ◽

Vol 9 (4) ◽

Cited By ~ 6

Author(s):

Edward W. Davis ◽

Javier F. Tabima ◽

Alexandra J. Weisberg ◽

Lucas Dantas Lopes ◽

Michele S. Wiseman ◽

...

Keyword(s):

Genetic Diversity ◽

Adaptive Immune System ◽

The United States ◽

Genomic Diversity ◽

Data Set ◽

Important Species ◽

Content Type ◽

Low Genetic Diversity ◽

History Of ◽

Short Palindromic Repeat

ABSTRACTRathayibacter toxicusis a species of Gram-positive, corynetoxin-producing bacteria that causes annual ryegrass toxicity, a disease often fatal to grazing animals. A phylogenomic approach was employed to model the evolution ofR. toxicusto explain the low genetic diversity observed among isolates collected during a 30-year period of sampling in three regions of Australia, gain insight into the taxonomy ofRathayibacter, and provide a framework for studying these bacteria. Analyses of a data set of more than 100 sequencedRathayibactergenomes indicated thatRathayibacterforms nine species-level groups.R. toxicusis the most genetically distant, and evidence suggested that this species experienced a dramatic event in its evolution. Its genome is significantly reduced in size but is colinear to those of sister species. Moreover,R. toxicushas low intergroup genomic diversity and almost no intragroup genomic diversity between ecologically separated isolates.R. toxicusis the only species of the genus that encodes a clustered regularly interspaced short palindromic repeat (CRISPR) locus and that is known to host a bacteriophage parasite. The spacers, which represent a chronological history of infections, were characterized for information on past events. We propose a three-stage process that emphasizes the importance of the bacteriophage and CRISPR in the genome reduction and low genetic diversity of theR. toxicusspecies.IMPORTANCERathayibacter toxicusis a toxin-producing species found in Australia and is often fatal to grazing animals. The threat of introduction of the species into the United States led to its inclusion in the Federal Select Agent Program, which makesR. toxicusa highly regulated species. This work provides novel insights into the evolution ofR. toxicus.R. toxicusis the only species in the genus to have acquired a CRISPR adaptive immune system to protect against bacteriophages. Results suggest that coexistence with the bacteriophage NCPPB3778 led to the massive shrinkage of theR. toxicusgenome, species divergence, and the maintenance of low genetic diversity in extant bacterial groups. This work contributes to an understanding of the evolution and ecology of an agriculturally important species of bacteria.

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