Inferring the geographic origin of a range expansion: Latitudinal and longitudinal coordinates inferred from genomic data in an ABC framework with the program x
-origin

ABSTRACTThe family Tospoviridae, a member of the Bunyavirales order, is constituted of tri-segmented negative-sense single-stranded RNA viruses that infect plants and are also able of replicating in their insect vectors in a persistent manner. The family is composed of a single genus, the Orthotospovirus, whose type species is Tomato spotted wilt virus (TSWV). Previous studies assessing the phylogenetic relationships within this genus were based upon partial genomic sequences, thus resulting in unresolved clades and a poor assessment of the roles of recombination and genome shuffling during mixed infections. Complete genomic data for most Orthotospovirus species are now available at NCBI genome database. In this study we have used 62 complete genomes from 20 species. Our study confirms the existence of four phylogroups (A to D), grouped in two major clades (A-B and C-D), within the genus. We have estimated the split between the two major clades ∼3,100 years ago shortly followed by the split between the A and B phylogroups ∼2,860 years ago. The split between the C and D phylogroups happened more recently, ∼1,465 years ago. Segment reassortment has been shown to be important in the generation of novel viruses. Likewise, within-segment recombination events have been involved in the origin of new viral species. Finally, phylogeographic analyses of representative viruses suggests the Australasian ecozone as the possible origin of the genus, followed by complex patterns of migration, with rapid global spread and numerous reintroduction events.IMPORTANCEMembers of the Orthotospovirus genus infect a large number of plant families, including food crops and ornamentals, resulting in multimillionaire economical losses. Despite this importance, phylogenetic relationships within the genus were established years ago based in partial genomic sequences. A peculiarity of orthotospoviruses is their tri-segmented negative sense genomes, which makes segment reassortment and within-segment recombination, two forms of viral sex, potential evolutionary forces. Using full genomes from all described orthotospovirus species, we revisited their phylogeny and confirmed the existence of four major phylogroups with uneven geographic distribution. We have also shown a pervasive role of sex in the origin of new viral species. Finally, using Bayesian phylogeographic methods, we assessed the possible geographic origin and historical dispersal of representative viruses from the different phylogroups.

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Range Expansion and the Origin of USA300 North American Epidemic Methicillin-Resistant Staphylococcus aureus

mBio ◽

10.1128/mbio.02016-17 ◽

2018 ◽

Vol 9 (1) ◽

Cited By ~ 15

Author(s):

Lavanya Challagundla ◽

Xiao Luo ◽

Isabella A. Tickler ◽

Xavier Didelot ◽

David C. Coleman ◽

...

Keyword(s):

United States ◽

Staphylococcus Aureus ◽

Genetic Variation ◽

Range Expansion ◽

Geographic Origin ◽

The United States ◽

Soft Tissue Infections ◽

Methicillin Resistant ◽

Geographic Spread ◽

Bacterial Clone

ABSTRACT The USA300 North American epidemic (USA300-NAE) clone of methicillin-resistant Staphylococcus aureus has caused a wave of severe skin and soft tissue infections in the United States since it emerged in the early 2000s, but its geographic origin is obscure. Here we use the population genomic signatures expected from the serial founder effects of a geographic range expansion to infer the origin of USA300-NAE and identify polymorphisms associated with its spread. Genome sequences from 357 isolates from 22 U.S. states and territories and seven other countries are compared. We observe two significant signatures of range expansion, including decreases in genetic diversity and increases in derived allele frequency with geographic distance from the Pennsylvania region. These signatures account for approximately half of the core nucleotide variation of this clone, occur genome wide, and are robust to heterogeneity in temporal sampling of isolates, human population density, and recombination detection methods. The potential for positive selection of a gyrA fluoroquinolone resistance allele and several intergenic regions, along with a 2.4 times higher recombination rate in a resistant subclade, is noted. These results are the first to show a pattern of genetic variation that is consistent with a range expansion of an epidemic bacterial clone, and they highlight a rarely considered but potentially common mechanism by which genetic drift may profoundly influence bacterial genetic variation. IMPORTANCE The process of geographic spread of an origin population by a series of smaller populations can result in distinctive patterns of genetic variation. We detect these patterns for the first time with an epidemic bacterial clone and use them to uncover the clone’s geographic origin and variants associated with its spread. We study the USA300 clone of methicillin-resistant Staphylococcus aureus, which was first noticed in the early 2000s and subsequently became the leading cause of skin and soft tissue infections in the United States. The eastern United States is the most likely origin of epidemic USA300. Relatively few variants, which include an antibiotic resistance mutation, have persisted during this clone’s spread. Our study suggests that an early chapter in the genetic history of this epidemic bacterial clone was greatly influenced by random subsampling of isolates during the clone’s geographic spread.

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A 3500-year-old leaf from a Pharaonic tomb reveals that New Kingdom Egyptians were cultivating domesticated watermelon

10.1101/642785 ◽

2019 ◽

Cited By ~ 3

Author(s):

Susanne S. Renner ◽

Oscar A. Pérez-Escobar ◽

Martina V. Silber ◽

Mark Nesbitt ◽

Michaela Preick ◽

...

Keyword(s):

South Africa ◽

West Africa ◽

Stop Codon ◽

Citrullus Lanatus ◽

Geographic Origin ◽

Central Africa ◽

Genomic Data ◽

Nile Valley ◽

New Kingdom ◽

Extant Species

AbstractDomestication of the watermelon (Citrullus lanatus) has alternatively been placed in South Africa, the Nile valley, or more recently West Africa, with the oldest archeological evidence coming from Libya and Egypt. The geographic origin and domestication of watermelons has therefore remained unclear. Using extensive nuclear and plastid genomic data from a 3,560-year-oldCitrullusleaf from a mummy’s sarcophagus and skimmed genomes for representatives of the seven extant species ofCitrullus, we show that modern cultivars and the ancient plant uniquely share mutations in a lycopene metabolism gene (LYCB) affecting pulp color and a stop codon in a transcription factor regulating bitter cucurbitacin compounds. This implies that the plant we sequenced had red-fleshed and sweet fruits and that New Kingdom Egyptians were cultivating domesticated watermelons. The genomic data also identify extant Sudanese watermelons with white, sweet pulp as the closest relatives of domesticated watermelons.Significance statementWith some 197.8 million tons in 2017, watermelon,Citrullus lanatus, is among the World’s most important crops, yet its area of origin and domestication have remained unclear, with competing hypotheses favoring South Africa, West Africa, Central Africa, or the Nile valley. We generated extensive nuclear and plastid genomic data from a 3500-year-old leaf from a Pharaonic sarcophagus and performed genome skimming for representatives of all otherCitrullusspecies to compare key genes involved in fruit bitterness and color. White-fleshed, non-bitter melons from southern Sudan are the closest relatives of domesticated watermelon, and the ancient genome shares unique alleles with a red-fleshed, non-bitter domesticated form (but no wild forms), implying that 18thDynasty Egyptians were cultivating domesticated watermelon by 3500 years ago.

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Individual heterozygosity predicts translocation success in threatened desert tortoises

Science ◽

10.1126/science.abb0421 ◽

2020 ◽

Vol 370 (6520) ◽

pp. 1086-1089

Author(s):

Peter A. Scott ◽

Linda J. Allison ◽

Kimberleigh J. Field ◽

Roy C. Averill-Murray ◽

H. Bradley Shaffer

Keyword(s):

Extinction Risk ◽

Empirical Test ◽

Geographic Origin ◽

Genomic Data ◽

Gopherus Agassizii ◽

Species At Risk ◽

Genomic Dataset ◽

New Locations ◽

Related Individuals ◽

Simple Indicator

Anthropogenic environmental modification is placing as many as 1 million species at risk of extinction. One management action for reducing extinction risk is translocation of individuals to locations from which they have disappeared or to new locations where biologists hypothesize they have a good chance of surviving. To maximize this survival probability, the standard practice is to move animals from the closest possible populations that contain presumably related individuals. In an empirical test of this conventional wisdom, we analyzed a genomic dataset for 166 translocated desert tortoises (Gopherus agassizii) that either survived or died over a period of two decades. We used genomic data to infer the geographic origin of translocated tortoises and found that individual heterozygosity predicted tortoise survival, whereas translocation distance or geographic unit of origin did not. Our results suggest a relatively simple indicator of the likelihood of a translocated individual’s survival: heterozygosity.

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