scholarly journals Is Phylogeographic Congruence Predicted by Historical Habitat Stability, or Ecological Co-associations?

2021 ◽  
Vol 5 (5) ◽  
Author(s):  
Ryan C Garrick ◽  
Chaz Hyseni ◽  
Ísis C Arantes ◽  
Louis G Zachos ◽  
Peter C Zee ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Species Interactions ◽  
Ecological Niche Modeling ◽  
Nuclear Dna ◽  
Abiotic Factors ◽  
Genetic Data ◽  
Phylogeographic Structure ◽  
Biotic Factors ◽  
Effective Population ◽  
Species Responses

Abstract Comparative phylogeographic studies can distinguish between idiosyncratic and community-wide responses to past environmental change. However, to date, the impacts of species interactions have been largely overlooked. Here we used non-genetic data to characterize two competing scenarios about expected levels of congruence among five deadwood-associated (saproxylic) invertebrate species (i.e., a wood-feeding cockroach, termite, and beetle; a predatory centipede, and a detritivorous millipede) from the southern Appalachian Mountains—a globally recognized center of endemism. Under one scenario, abiotic factors primarily drove species’ responses, with predicted congruence based on the spatial overlap of climatically stable habitat areas estimated for each species via ecological niche modeling. The second scenario considered biotic factors to be most influential, with proxies for species interactions used to predict congruence. Analyses of mitochondrial and nuclear DNA sequences focused on four axes of comparison: the number and geographic distribution of distinct spatial-genetic clusters, phylogeographic structure, changes in effective population size, and historical gene flow dynamics. Overall, we found stronger support for the ecological co-associations scenario, suggesting an important influence of biotic factors in constraining or facilitating species’ responses to Pleistocene climatic cycles. However, there was an imperfect fit between predictions and outcomes of genetic data analyses. Thus, while thought-provoking, conclusions remain tentative until additional data on species interactions becomes available. Ultimately, the approaches presented here advance comparative phylogeography by expanding the scope of inferences beyond solely considering abiotic drivers, which we believe is too simplistic. This work also provides conservation-relevant insights into the evolutionary history of a functionally important ecological community.

The roles of possible geographic barriers and geological events on the phylogeographic structure of the Eastern broad toothed field mouse (Apodemus mystacinus)

Mammalia ◽  
2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Gül Olgun Karacan ◽  
Reyhan Çolak ◽  
Ercüment Çolak
Keyword(s):  
Dna Sequences ◽  
Nuclear Dna ◽  
Phylogeographic Structure ◽  
Field Mouse ◽  
Interphotoreceptor Retinoid Binding Protein ◽  
Aegean Islands ◽  
Mitochondrial Data ◽  
D Loop ◽  
Physical Barriers ◽  
First Time

Abstract The Eastern broad toothed field mouse, Apodemus mystacinus, is a rodent species distributed in Turkey, the Middle East, and a few Aegean Islands. The aim of this study is to analyse the phylogeographic structure of A. mystacinus and possible causes of its differentiation, on the basis of mitochondrial and nuclear DNA sequences using a large number of new samples from Turkey. In this context, partial mitochondrial sequences of cytochrome b (Cytb), control region (D-loop) and a nuclear interphotoreceptor retinoid-binding protein (IRBP) gene were used to reveal the geographical differentiation among A. mystacinus populations and the validity of its subspecies. The estimated divergence times revealed that the first separation of A. mystacinus into three distinct groups (subspecies of A. mystacinus: A. m. mystacinus, A. m. smyrnensis, and A. m. euxinus) begun 0.641 Mya. The possible physical barriers in Anatolia such as high mountains and rivers could interrupt the gene flow between A. mystacinus populations. The results of the present study indicated that A. mystacinus might have used the high rocky areas along the Anatolian Diagonal as a dispersal way. Moreover, mitochondrial data in this study suggested for the first time that A. m. rhodius is synonymous with the nominative subspecies A. m. mystacinus.

scholarly journals Measwring and Testing Genetic Differentiation With Ordered Versus Unordered Alleles

Genetics ◽  
1996 ◽  
Vol 144 (3) ◽  
pp. 1237-1245 ◽  
Author(s):  
O Pons ◽  
R J Petit
Keyword(s):  
Dna Sequences ◽  
Nuclear Dna ◽  
Mutation Rates ◽  
Phylogeographic Structure ◽  
Published Data ◽  
Data Set ◽  
Subdivided Populations ◽  
Two Measures ◽  
The Difference ◽  
Single Data

Abstract Estimates and variances of diversity and differentiation measures in subdivided populations are proposed that can be applied to haplotypes (ordered alleles such as DNA sequences, which may contain a record of their own histories). Hence, two measures of differentiation can be compared for a single data set: one (GST) that makes use only of the allelic frequencies and the other (NST) for which similarities between the haplotypes are taken into account in addition. Tests are proposed to compare NST and GST with zero and with each other. The difference between NST and GST can be caused by several factors, including sampling artefacts, unequal effect of mutation rates and phylogeographic structure. The method presented is applied to a published data set where a nuclear DNA sequence had been determined from individuals of a grasshopper distributed in 24 regions of Europe. Additional insights into the genetic subdivision of these populations are obtained by progressively combining related haplotypes and reanalyzing the data each time.

Multiple Pleistocene refugia in the widespread Patagonian tree Embothrium coccineum (Proteaceae)

2011 ◽  
Vol 59 (4) ◽  
pp. 299 ◽  
Author(s):  
Romina Vidal-Russell ◽  
Cintia P. Souto ◽  
Andrea C. Premoli
Keyword(s):  
Population Size ◽  
Dna Sequences ◽  
Phylogeographic Structure ◽  
Mountain Range ◽  
Pollen Record ◽  
The South ◽  
Effective Population ◽  
The Andes ◽  
Chloroplast Dna Sequences ◽  
The Impact

Embothrium coccineum J.R.Forst. & G.Forst is an endemic tree of the Patagonian temperate forest. The objective of this study is to evaluate the impact of last glaciation events on the genetic structure of this widespread and ecologically tolerant species, to postulate possible refugial areas. Phylogeographic analyses were performed using chloroplast DNA sequences (trnL-trnF spacer and ndhC-trnV spacer) from individuals collected in 34 populations along the total range of the species, and these results were compared with a similar study in Nothofagus. A total of 22 haplotypes were found, three of which were widely distributed while 13 were found at only one location. Historical demography suggests a long period of stable effective population size, decreasing gradually towards the Last Glacial Maximum (LGM), followed by an increase in population size that stabilised 2500 years ago. The phylogeographic analyses reflect recent events of colonisation after the LGM from multiple refugia. In the northern area of its distribution probably the species survived in several pockets within the Andes mountain range and in Cordillera de la Costa in Chile. In the south, it is suggested that Embothrium survived the glacial period at the edge of the glaciers. These findings are in agreement with the fossil pollen record that shows 10 000-year-old grains in the south, suggesting colonisation from nearby areas when ice retreated. Embothrium is a coloniser that naturally occurs as scattered individuals within mixed forests. Hence, the shallow phylogeographic structure reported here reflects a Pleistocene signature highly impacted by drift resulting in the randomly fixation of new variants reducing the cpDNA structure.

Determination of factors involved in the rejection of bananas (Musa acuminata) intended for international commercialization

2020 ◽  
Keyword(s):  
Management Practices ◽  
Abiotic Factors ◽  
Quality Standards ◽  
Musa Acuminata ◽  
P Value ◽  
Biotic Factors ◽  
Significance Level ◽  
Export Sector ◽  
Export System

The banana agro-export sector in Ecuador provides millions of dollars in income for this concept, but with this development, a series of quality standards have been established that must be met to enter the export system. This has contributed to establishing good post-harvest production and management practices that guarantee the optimal production of bananas and plantains. The objective of this study was to determine the factors involved in the rejection of bananas (Musa acuminata) destined for international commercialization. The methodology considered the design modality of non-experimental transactional research, with a quantitative approach. The methodological design was developed in three phases at Finca 6 Hermanas located in the Barraganete sector of the San Juan parish in the Puebloviejo canton of the Los Ríos Province, Ecuador. The results highlight that the main causes for which banana rejection is generated are due to abiotic factors (damage, dry latex, scar, insect damage, broken neck, overgrowth) in a higher percentage of 79.55 % and biotic factors ( twins, diseases, short finger) by 20.45 %. The average rejection was 6 361 fingers and1 269 Kilograms (K) over the 6-week study duration. The analysis of variance turned out to be significant for variable 1 (biotic and abiotic). Ho is rejected; with the criterion of p-value < 0.0001 and F (9; 45) = 2.10., F = 13.17> F critic. In the case of variable (2) “work weeks”, Ho is accepted with the criteria obtained of p-value of 0.7694 and F (5; 45) = 2.4., As F = 0.51 < F critic, it is concludes, that with a significance level of 5% the null hypothesis is accepted. It is concluded that these figures lead to the elaboration of strategies that systemically mitigate the damages, by correcting each one of the causes that cause the deterioration of the banana and increasing the economic gains of the commercialization process.

scholarly journals Low Nucleotide Diversity in Chimpanzees and Bonobos

Genetics ◽  
2003 ◽  
Vol 164 (4) ◽  
pp. 1511-1518 ◽  
Author(s):  
Ning Yu ◽  
Michael I Jensen-Seaman ◽  
Leona Chemnick ◽  
Judith R Kidd ◽  
Amos S Deinard ◽  
...  
Keyword(s):  
Nucleotide Diversity ◽  
Nuclear Dna ◽  
Demographic History ◽  
Nuclear Genome ◽  
Limited Data ◽  
Effective Population ◽  
East Central ◽  
Dna Diversity ◽  
History Of ◽  
Mtdna Diversity

Abstract Comparison of the levels of nucleotide diversity in humans and apes may provide much insight into the mechanisms of maintenance of DNA polymorphism and the demographic history of these organisms. In the past, abundant mitochondrial DNA (mtDNA) polymorphism data indicated that nucleotide diversity (π) is more than threefold higher in chimpanzees than in humans. Furthermore, it has recently been claimed, on the basis of limited data, that this is also true for nuclear DNA. In this study we sequenced 50 noncoding, nonrepetitive DNA segments randomly chosen from the nuclear genome in 9 bonobos and 17 chimpanzees. Surprisingly, the π value for bonobos is only 0.078%, even somewhat lower than that (0.088%) for humans for the same 50 segments. The π values are 0.092, 0.130, and 0.082% for East, Central, and West African chimpanzees, respectively, and 0.132% for all chimpanzees. These values are similar to or at most only 1.5 times higher than that for humans. The much larger difference in mtDNA diversity than in nuclear DNA diversity between humans and chimpanzees is puzzling. We speculate that it is due mainly to a reduction in effective population size (Ne) in the human lineage after the human-chimpanzee divergence, because a reduction in Ne has a stronger effect on mtDNA diversity than on nuclear DNA diversity.

scholarly journals A phylogenetic estimator of effective population size or mutation rate.

Genetics ◽  
1994 ◽  
Vol 136 (2) ◽  
pp. 685-692 ◽  
Author(s):  
Y X Fu
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Mutation Rate ◽  
Dna Sequences ◽  
High Efficiency ◽  
Minimum Variance ◽  
Population Subdivision ◽  
Effective Population ◽  
Fisher Model ◽  
Mitochondrial Sequences

Abstract A new estimator of the essential parameter theta = 4Ne mu from DNA polymorphism data is developed under the neutral Wright-Fisher model without recombination and population subdivision, where Ne is the effective population size and mu is the mutation rate per locus per generation. The new estimator has a variance only slightly larger than the minimum variance of all possible unbiased estimators of the parameter and is substantially smaller than that of any existing estimator. The high efficiency of the new estimator is achieved by making full use of phylogenetic information in a sample of DNA sequences from a population. An example of estimating theta by the new method is presented using the mitochondrial sequences from an American Indian population.

scholarly journals A New Statistic for Detecting Genetic Differentiation

Genetics ◽  
2000 ◽  
Vol 155 (4) ◽  
pp. 2011-2014 ◽  
Author(s):  
Richard R Hudson
Keyword(s):  
Genetic Differentiation ◽  
Dna Sequences ◽  
Genetic Data ◽  
Island Model ◽  
Wide Range ◽  
Infinite Sites Model ◽  
Parameter Values

Abstract A new statistic for detecting genetic differentiation of subpopulations is described. The statistic can be calculated when genetic data are collected on individuals sampled from two or more localities. It is assumed that haplotypic data are obtained, either in the form of DNA sequences or data on many tightly linked markers. Using a symmetric island model, and assuming an infinite-sites model of mutation, it is found that the new statistic is as powerful or more powerful than previously proposed statistics for a wide range of parameter values.

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