Network analyses of the impact of visual habitat structure on behavior, demography, genetic diversity, and gene flow in a metapopulation of collared lizards (Crotaphytus collaris collaris)

2021 ◽  
pp. 131-160
Author(s):  
Amy K. Conley ◽  
Jennifer L. Neuwald ◽  
Alan R. Templeton
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Habitat Structure ◽  
Crotaphytus Collaris ◽  
Network Analyses ◽  
The Impact ◽  
Collared Lizards

scholarly journals 1280. Geospatial Spread of HIV in the Cologne-Bonn Region, Germany: From 2001 to 2016

2018 ◽  
Vol 5 (suppl_1) ◽  
pp. S390-S390
Author(s):  
Melanie Stecher ◽  
Martin Hoenigl ◽  
Anna-Maria Eis-Huebinger ◽  
Clara Lehmann ◽  
Gerd Fätkenheuer ◽  
...  
Keyword(s):  
Gene Flow ◽  
Hiv Transmission ◽  
Viral Gene ◽  
Network Analyses ◽  
Hiv Intervention ◽  
Subtype B ◽  
Geospatial Analyses ◽  
The Impact ◽  
Zip Code ◽  
Hiv 1

Abstract Background Geographical targeting of interventions of hotspots of HIV transmission increases the impact of HIV intervention. We combined molecular epidemiology and geospatial analyses to provide insights into the drivers of HIV transmission and the contribution of geographical hot spots to the rapidly evolving local HIV epidemic of Cologne-Bonn. Methods We included 714 HIV-1-infected ART naïve individuals, followed at the University Hospitals Cologne and Bonn between 2001 and 2016. Phylogenetic and network analyses were performed to infer putative relationships. Assortativity index (AI, i.e., shared attributes) and characteristics of genetically linked individuals were analyzed. The geospatial diffusion of the local epidemic (i.e., viral gene flow) was evaluated using a Slatkin-Maddison approach. Geospatial dispersal of local HIV transmission was determined by calculating the average distance between genetically linked individuals (centroids of 3-digit zip code of residency, ArcGIS®). Results Of 714 sequences, 217 (30.4%) had a putative linkage with at least one other sequence, forming 77 clusters (size range: 2–8). Genetically linked individuals were significantly more likely to live in suburban areas (P = 0.035), <30 years of age (P = 0.013), infected with HIV-1 subtype B (P = 0.002). AI for concurrent area of residency showed that individuals were nonassortative in the network (−0.0026, P = 0.046), indicating that clustering individuals tended to cluster with individuals living in a different zip code. Geospatial analyses revealed that the median distance between genetically linked individuals was 23.4 km, significantly lower than expected (median 39.68 km; P < 0.001) (Figure 1A). Slatkin Maddison analyses revealed increased gene flow originating from Central Cologne toward the surrounding areas (P < 0.001, Figure 1B). Conclusion Phylogeographic analysis suggests that central Cologne may be a significant driver of the regional epidemic. While clustering individuals lived closer than unlinked individuals, they were less likely to be linked to others from their same zip code. This may reflect individuals reaching out of their neighborhoods and social circles to meet new partners. Disclosures All authors: No reported disclosures.

scholarly journals Post-Disturbance Genetic Changes: The Impact of the 2010 Mega-Earthquake and Tsunami on Chilean Sandy Beach Fauna

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Antonio Brante ◽  
Garen Guzmán-Rendón ◽  
Erwin M. Barría ◽  
Marie-Laure Guillemin ◽  
Iván Vera-Escalona ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Adult Survival ◽  
Genetic Changes ◽  
Species Response ◽  
Emerita Analoga ◽  
Mtdna Sequence ◽  
The Impact

Abstract Earthquake/tsunamis can have profound impacts on species and their genetic patterns. It is expected that the magnitude of this impact might depend on the species and the time since the disturbance occurs, nevertheless these assumptions remain mostly unexplored. Here we studied the genetic responses of the crustacean species Emerita analoga, Excirolana hirsuticauda, and Orchestoidea tuberculata to the 27F mega-earthquake/tsunami that occurred in Chile in February 2010. mtDNA sequence analyses revealed a lower haplotype diversity for E. analoga and E. hirsuticauda in impacted areas one month after the 27F, and the opposite for O. tuberculata. Three years after the 27F we observed a recovery in the genetic diversity of E. analoga and E. hirsuticauda and decrease in the genetic diversity in O. tuberculata in 2/3 of sampled areas. Emerita analoga displayed decrease of genetic differentiation and increase in gene flow explained by long-range population expansion. The other two species revealed slight increase in the number of genetic groups, little change in gene flow and no signal of population expansion associated to adult survival, rapid colonization, and capacity to burrow in the sand. Our results reveal that species response to a same disturbance event could be extremely diverse and depending on life-history traits and the magnitude of the effect.

scholarly journals Clinging to survival: Critically Endangered Chapman's pygmy chameleon Rhampholeon chapmanorum persists in shrinking forest patches

Oryx ◽  
2021 ◽  
pp. 1-6
Author(s):  
Krystal A. Tolley ◽  
Colin R. Tilbury ◽  
Jessica M. da Silva ◽  
Gary Brown ◽  
Yankho Chapeta ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Structure ◽  
Satellite Imagery ◽  
Critically Endangered ◽  
Forest Loss ◽  
Mitochondrial Marker ◽  
Forest Patches ◽  
Genetic Diversity And Structure ◽  
The Impact

Abstract The Critically Endangered Chapman's pygmy chameleon Rhampholeon chapmanorum is endemic to the low elevation rainforest of the Malawi Hills in southern Malawi. Much of this forest has been converted to agriculture and it was uncertain whether chameleon populations have persisted. We used current and historical satellite imagery to identify remaining forest patches and assess deforestation. We then surveyed forest patches for the presence of this chameleon, and assessed its genetic diversity and structure. We estimated that 80% of the forest has been destroyed since 1984, although we found extant populations of the chameleon in each of the patches surveyed. Differentiation of genetic structure was strong between populations, suggesting that gene flow has been impaired. Genetic diversity was not low, but this could be the result of a temporal lag as well as lack of sensitivity in the mitochondrial marker used. Overall, the impact of forest loss is assumed to have led to a large demographic decline, with forest fragmentation preventing gene flow.

scholarly journals Effects of Colonization Processes on Genetic Diversity: Differences Between Annual Plants and Tree Species

Genetics ◽  
2000 ◽  
Vol 154 (3) ◽  
pp. 1309-1321 ◽  
Author(s):  
Frédéric Austerlitz ◽  
Stéphanie Mariette ◽  
Nathalie Machon ◽  
Pierre-Henri Gouyon ◽  
Bernard Godelle
Keyword(s):  
Genetic Diversity ◽  
Life Cycle ◽  
Gene Flow ◽  
Tree Species ◽  
Population Diversity ◽  
Pollen Flow ◽  
Nuclear Genes ◽  
Annual Plants ◽  
High Level ◽  
The Impact

Abstract Tree species are striking for their high within-population diversity and low among-population differentiation for nuclear genes. In contrast, annual plants show much more differentiation for nuclear genes but much less diversity than trees. The usual explanation for this difference is that pollen flow, and therefore gene flow, is much higher for trees. This explanation is problematic because it relies on equilibrium hypotheses. Because trees have very recently recolonized temperate areas, they have experienced many foundation events, which usually reduce within-population diversity and increase differentiation. Only extremely high levels of gene flow could counterbalance these successive founder effects. We develop a model to study the impact of life cycle of forest trees, in particular of the length of their juvenile phase, on genetic diversity and differentiation during the glacial period and the following colonization period. We show that both a reasonably high level of pollen flow and the life-cycle characteristics of trees are needed to explain the observed structure of genetic diversity. We also show that gene flow and life cycle both have an impact on maternally inherited cytoplasmic genes, which are characterized both in trees and annual species by much less diversity and much more differentiation than nuclear genes.

scholarly journals Fine-Scale Genetic Diversity of the Brazilian Pantaneiro Horse Breed Adapted To Flooded Regions

2021 ◽  
Author(s):  
Marcelo Bchara Nogueira ◽  
Concepta M Pimentel ◽  
Danielle Assis de Faria ◽  
Sandra Aparecida Oliveria Santos ◽  
Patrícia Ianella ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Variability ◽  
Genetic Distance ◽  
Animal Species ◽  
Principal Component ◽  
Mantel Test ◽  
Sampling Location ◽  
Sampling Strategies ◽  
The Impact

Abstract Among the animal species first introduced in Brazil during the country's discovery, horses (Equus caballus) stand out because of their evolutionary history and relationship with humans. Among the Brazilian horse breeds, the Pantaneiro draws attention due to its adaptative traits. Blood samples of 116 Pantaneiro horses were divided into six populations based on their sampling location, aiming to identify the existence of genetic structure and quantify genetic diversity within and between them. Populations were compared to elucidate genetic variability and differentiation better and assess the impact of Pantanal's natural geographic barriers on gene flow between populations. Data from the GGP Equine BeadChip (Geneseek-Neogen, 65.157 SNPs) was used to assess basic diversity parameters, genetic distance (FST), Principal Component Analysis (PCA) and population structure (ADMIXTURE) for the sampled animals. Mantel Test was also performed to investigate the correlation between the populations' genetic and geographic distances. Results showed high genetic variability in all populations, with elevated levels of admixture in their structure. High levels of admixture make it challenging to establish a racial pattern and, consequently, populations within the breed, being that only one of the populations differentiated itself from the others. No significant correlations between genetic and geographic distances were observed, indicating that environmental barriers did not hinder gene flow between populations. and neither farmers selection practices might have change breed genetic composition signficantly Low genetic distance and similar heterozygosity values were observed among populations, suggesting strong genetic proximity and low differentiation. Thereby, the Pantaneiro breed does not exhibit genetic subpopulations and could be considered, for conservation purposes, a single big population in the Panatnal region. This study will support sampling strategies for National genebank.

scholarly journals The genomic prehistory of peoples speaking Khoisan languages

2020 ◽  
Author(s):  
Brigitte Pakendorf ◽  
Mark Stoneking
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Southern Africa ◽  
Linguistically Diverse ◽  
Indigenous Languages ◽  
Culturally And Linguistically Diverse ◽  
Hunter Gatherers ◽  
Geographic Spread ◽  
Mixed Modes ◽  
The Impact

Abstract Peoples speaking so-called Khoisan languages—that is, indigenous languages of southern Africa that do not belong to the Bantu family—are culturally and linguistically diverse. They comprise herders, hunter-gatherers as well as groups of mixed modes of subsistence, and their languages are classified into three distinct language families. This cultural and linguistic variation is mirrored by extensive genetic diversity. We here review the recent genomics literature and discuss the genetic evidence for a formerly wider geographic spread of peoples with Khoisan-related ancestry, for the deep divergence among populations speaking Khoisan languages overlaid by more recent gene flow among these groups and for the impact of admixture with immigrant food-producers in their prehistory.

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