Estimates of Genetic Differentiation Measured by F ST Do Not Necessarily Require Large Sample Sizes When Using Many SNP Markers

Willing E-M, Dreyer C, Oosterhout C van (2012) Estimates of Genetic Differentiation Measured by F ST Do Not Necessarily Require Large Sample Sizes When Using Many SNP Markers. PLOS ONE, 7, e42649.

Elegido por: Vero R.

Abstract
Population genetic studies provide insights into the evolutionary processes that influence the distribution of sequence variants within and among wild populations. F_ST is among the most widely used measures for genetic differentiation and plays a central role in ecological and evolutionary genetic studies. It is commonly thought that large sample sizes are required in order to precisely infer F_ST and that small sample sizes lead to overestimation of genetic differentiation. Until recently, studies in ecological model organisms incorporated a limited number of genetic markers, but since the emergence of next generation sequencing, the panel size of genetic markers available even in non-reference organisms has rapidly increased. In this study we examine whether a large number of genetic markers can substitute for small sample sizes when estimating F_ST. We tested the behavior of three different estimators that infer F_ST and that are commonly used in population genetic studies. By simulating populations, we assessed the effects of sample size and the number of markers on the various estimates of genetic differentiation. Furthermore, we tested the effect of ascertainment bias on these estimates. We show that the population sample size can be significantly reduced (as small as n = 4–6) when using an appropriate estimator and a large number of bi-allelic genetic markers (k>1,000). Therefore, conservation genetic studies can now obtain almost the same statistical power as studies performed on model organisms using markers developed with next-generation sequencing.

Este artículo se basa en que los estudios genéticos de población proporcionan una visión de los procesos evolutivos que influyen en la distribución de las variantes de secuencia dentro y entre las poblaciones silvestres. Y dentro de los análisis el FST es una de las medidas más utilizadas para la diferenciación genética ya que desempeña un papel central en los estudios genéticos ecológicos y evolutivos. Se piensa comúnmente que se requieren grandes tamaños de muestra con el fin de inferir con precisión los FST y que los tamaños de muestra pequeños conducen a la sobreestimación de la diferenciación genética.  Probado el comportamiento de tres estimadores diferentes que infieren FST (1.-Wright, 2.-Cockerham y Weir, 3.-Reich y colegas) y que se utilizan comúnmente en los estudios de genética de poblaciones. 

Es de mi interes checar este articulo debido a que todos realizaremos este análisis y se nos pueden cruzar problemas a la hora de elegir el estimador o simplemente saber que nos esta arrojando para poder interpretarlo de la manera más adecuada. (Este articulo me lo recomendo Idalia ya que tuvimos unos inconvenientes al determinar los Fst en R y este artículo aclaró unas dudas).

 

Transcriptomes reveal the genetic mechanisms underlying ionic regulatory adaptations to salt in the crab-eating frog.

Seleccionado por: Ruth 

Abstract

The crab-eating frog, Fejervarya cancrivora, is the only frog that lives near seas. It tolerates increasedenvironmental concentrations of sodium, chloride and potassium partly by raising ion and urea levels in its blood plasma. The molecular mechanism of the adaptation remains rarely documented. Herein, we analyze transcriptomes of the crab-eating frog and its closely related saline-intolerant species, F. limnocharis, to explore the molecular basis of adaptations to such extreme environmental conditions. Analyses reveal the potential genetic mechanism underlying the adaptation to salinity for the crabeating frog. Genes in categories associated with ion transport appear to have evolved rapidly in F. cancrivora. Both positively selected and differentially expressed genes exhibit enrichment in the GO category regulation of renal sodium excretion. In this category, the positively selected sites of ANPEP and AVPR2 encode CD13 and V2 receptors, respectively; they fall precisely on conserved domains. More differentially expressed rapidly evolved genes occur in the kidney of F. cancrivora than in F. limnocharis. Four genes involved in the regulation of body fluid levels show signs of positive selection and increased expression. Significant up-regulation occurs in several genes of F. cancrivora associated with renin-angiotensin system and aldosterone-regulated sodium reabsorption pathways, which relate to osmotic regulation.


En el  artículo se trata de explicar las adaptaciones genéticas de una ranita a ambientes salobres, mediante la identificación de perfiles de expresión para genes candidatos implicados en la adaptación a estos ambientes. Este artículo es de mi interés dada la naturaleza de mi trabajo, donde planteo estudiar salamandras que aparentemente se han adaptado a ambientes más secos comparadas con sus especies hermanas que habitan en ambientes húmedos y utilizando ahora estas herramientas (transcriptoma) es posible identificar genes candidatos a selección.

Non-adaptive plasticity potentiates rapid adaptive evolution of gene expression in nature

Ghalambor CK, Hoke KL, Ruell EW et al. (2015) Non-adaptive plasticity potentiates rapid adaptive evolution of gene expression in nature. Nature, 525, 372–375.

Seleccionado por: Azalea

Abstract
 Phenotypic plasticity is the capacity for an individual genotype to produce different phenotypes in response to environmental variation¹. Most traits are plastic, but the degree to which plasticity is adaptive or non-adaptive depends on whether environmentally induced phenotypes are closer or further away from the local optimum^{2, 3, 4}. Existing theories make conflicting predictions about whether plasticity constrains or facilitates adaptive evolution^{4, 5, 6, 7, 8, 9, 10, 11, 12}. Debate persists because few empirical studies have tested the relationship between initial plasticity and subsequent adaptive evolution in natural populations. Here we show that the direction of plasticity in gene expression is generally opposite to the direction of adaptive evolution. We experimentally transplanted Trinidadian guppies (Poecilia reticulata) adapted to living with cichlid predators to cichlid-free streams, and tested for evolutionary divergence in brain gene expression patterns after three to four generations. We find 135 transcripts that evolved parallel changes in expression within the replicated introduction populations. These changes are in the same direction exhibited in a native cichlid-free population, suggesting rapid adaptive evolution. We find 89% of these transcripts exhibited non-adaptive plastic changes in expression when the source population was reared in the absence of predators, as they are in the opposite direction to the evolved changes. By contrast, the remaining transcripts exhibiting adaptive plasticity show reduced population divergence. Furthermore, the most plastic transcripts in the source population evolved reduced plasticity in the introduction populations, suggesting strong selection against non-adaptive plasticity. These results support models predicting that adaptive plasticity constrains evolution^{6, 7, 8}, whereas non-adaptive plasticity potentiates evolution by increasing the strength of directional selection^{11, 12}. The role of non-adaptive plasticity in evolution has received relatively little attention; however, our results suggest that it may be an important mechanism that predicts evolutionary responses to new environments.

Quizá debido a la naturaleza de los proyectos que la mayoría de nosotros estamos desarrollando, pocas veces nos preguntamos cómo la plasticidad fenotípica está afectando la trayectoria evolutiva de las especies. Más allá de modelos teóricos, parece que se ha estudiado relativamente poco cómo la plasticidad puede influir en la intensidad de la selección. En el artículo, usando como modelo al pez guppy y un diseño experimental que me pareció muy ingenioso, muestran que la plasticidad, al menos en este caso, NO favorece a una rápida evolución adaptativa. 

Viability of Booby Offspring is Maximized by Having One Young Parent and One Old Parent

Drummond H, Rodríguez C (2015) Viability of Booby Offspring is Maximized by Having One Young Parent and One Old Parent (A Widdig, Ed,). PLOS ONE, 10, e0133213.

Abstract
It is widely expected that the quality of offspring will vary with the age of their parents and
that this variation should influence animals’ choice of mates. However, theoretical predictions
for age effects are contradictory and, to our knowledge, we do not know for any wild
animal how the quality of offspring is affected by both parents’ ages across their lifespans,
or whether mothers’ and fathers’ ages interact. We tackled this question using long-term
data on a highly philopatric, insular population of the blue-footed booby (Sula nebouxii). In
this species extra-pair paternity is most common in pairs of two young parents or two old
parents, implying that these age combinations might prejudice offspring quality. Analysis of
the viability of 3,361 offspring of parents up to 21 years old revealed that fledglings with two
young parents or two old parents were least likely to become breeders, whereas fledglings
with one young parent and one old parent were most likely to do so. For young parents of
either sex, offspring viability increased with age of the other parent; for very old parents, it
decreased. These effects could be mediated by parents flexibly modifying their investment
in offspring in response to their own and their partners´ ages, but evidence for this was lacking.
In 5,343 breeding attempts, although mothers’ and fathers’ ages independently affected
four heavily care-dependent breeding traits at the clutch and nestling stages, their interaction
did not affect any trait. The effects of parental age combinations on viability could also
be mediated by genes: fledglings with one young parent and one old parent could benefit
from greater heterozygosity or better genes. 


Seleccionado por: Verónica G

Yo estoy enfocada un poco más en el área de la conducta, por lo que me interesa revisar este artículo ya que es una de las bases de mi proyecto y dado que soy inexperta en el área de molecular y genómica quiero ver si me dan ideas o comentarios
Este artículo habla sobre el efecto en la viabilidad de las crías de pajaros bobos al combinarse las edades parentales.
A mi me interesa saber si el combinar las edades de los padres puede incrementar la Heterocigosis de las crías y si las hembras incurren en
copulas extra pareja para incrementar dicha heterocigosis.
Es un artículo que a mi parecer es bastante interesante aunque no habla tanto de molecular, espero les guste.

Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol

Elbrecht V, Leese F (2015) Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol. PLOS ONE, 10, e0130324.

Seleccionado por: Nancy


Abstract

Metabarcoding is an emerging genetic tool to rapidly assess biodiversity in ecosystems. It
involves high-throughput sequencing of a standard gene from an environmental sample
and comparison to a reference database. However, no consensus has emerged regarding
laboratory pipelines to screen species diversity and infer species abundances from environmental
samples. In particular, the effect of primer bias and the detection limit for specimens
with a low biomass has not been systematically examined, when processing samples in
bulk. We developed and tested a DNA metabarcoding protocol that utilises the standard cytochrome
c oxidase subunit I (COI) barcoding fragment to detect freshwater macroinvertebrate
taxa. DNA was extracted in bulk, amplified in a single PCR step, and purified, and the
libraries were directly sequenced in two independent MiSeq runs (300-bp paired-end
reads). Specifically, we assessed the influence of specimen biomass on sequence read
abundance by sequencing 31 specimens of a stonefly species with known haplotypes spanning
three orders of magnitude in biomass (experiment I). Then, we tested the recovery of
52 different freshwater invertebrate taxa of similar biomass using the same standard barcoding
primers (experiment II). Each experiment was replicated ten times to maximise statistical
power. The results of both experiments were consistent across replicates. We found
a distinct positive correlation between species biomass and resulting numbers of MiSeq
reads. Furthermore, we reliably recovered 83% of the 52 taxa used to test primer bias. However,
sequence abundance varied by four orders of magnitudes between taxa despite the
use of similar amounts of biomass. Our metabarcoding approach yielded reliable results for
high-throughput assessments. However, the results indicated that primer efficiency is highly
species-specific, which would prevent straightforward assessments of species abundance
and biomass in a sample. Thus, PCR-based metabarcoding assessments of biodiversity
should rely on presence-absence metrics.


Elegí este artículo porque me viene de perlas ahora que estoy en medio del establecimiento de un buen diseño de protocolo a seguir, para la parte experimental de mi proyecto de investigación. 1) Saber si la cantidad de ADN afecta en la diversidad en la comunidad de insectos. 2) Saber si realizar la extracción con nitrógeno líquido o TissueLyser afecta de alguna manera esta diversidad. Esto y otros puntos espero discutir con ustedes.

Utilizing RADseq data for phylogenetic analysis of challenging taxonomic groups: A case study in Carex sect. Racemosae

Massatti R, Reznicek AA, Knowles LL (2016) Utilizing RADseq data for phylogenetic analysis of challenging taxonomic groups: A case study in Carex sect. Racemosae. American Journal of Botany, 103, 337–347.

Seleccionado por: Daniel

Abstract

PREMISE OF THE STUDY: Relationships among closely related and recently diverged taxa can be especially difficult to resolve. Here we use both Sanger sequencing and next-generation RADseq data sets to estimate phylogenetic relationships among species of Carex section Racemosae (Cyperaceae), a clade largely restricted to high latitudes and elevations. Interest in relationships among these taxa derives from questions about the species’ biogeographic histories and possible links between diversification and Pleistocene glaciations.

METHODS: A combination of approaches and molecular markers were used to estimate relationships among Carex species within sect. Racemosae and taxa from closely related sections. Nuclear and chloroplast loci generated by Sanger sequencing were analyzed with *BEAST, and SNP data from RADseq loci were analyzed as a concatenated data set using maximum likelihood and as independent loci using SVDquartets.

KEY RESULTS: Sanger sequencing data sets resolved relationships among taxa at intermediate phylogenetic depths (albeit with low levels of support). Only the RADseq data resolved relationships with strong support at all phylogenetic depths. Moreover, different methods and data partitions of the RADseq data resulted in nearly identical topologies. Carex sect. Racemosae is a strongly supported clade, although a handful of species were found to group with closely related sections. Herbarium specimens up to 35 yr old successfully produced informative RADseq data.

CONCLUSIONS: Despite the short read lengths of RADseq data, they nevertheless resolved relationships that Sanger sequencing data did not. Resolution of the phylogenetic relationships among recently and rapidly diversifying taxa within sect. Racemosae clades suggest a role for the Pleistocene glaciations in clade diversification.

 

En este artículo Massati et al demuestran que sí es posible utilizar ratos RADseq para estudios filogeográficos, incluso en grupos cuyas relaciones incluyen diferentes profundidades temporales y donde hay falta de resolución con secuenciación Sanger y caracteres morfológicos ambiguos.

The domestication of Amazonia before European conquest

Seleccionado por: Idalia

Clement CR, Denevan WM, Heckenberger MJ et al. (2015) The domestication of Amazonia before European conquest. Proc. R. Soc. B, 282, 20150813.

Abstract
During the twentieth century, Amazonia was widely regarded as relatively pristine nature, little impacted by human history. This view remains popular despite mounting evidence of substantial human influence over millennial scales across the region. Here, we review the evidence of an anthropogenic Amazonia in response to claims of sparse populations across broad portions of the region. Amazonia was a major centre of crop domestication, with at least 83 native species containing populations domesticated to some degree. Plant domestication occurs in domesticated landscapes, including highly modified Amazonian dark earths (ADEs) associated with large settled populations and that may cover greater than 0.1% of the region. Populations and food production expanded rapidly within land management systems in the mid-Holocene, and complex societies expanded in resource-rich areas creating domesticated landscapes with profound impacts on local and regional ecology. ADE food production projections support estimates of at least eight million people in 1492. By this time, highly diverse regional systems had developed across Amazonia where subsistence resources were created with plant and landscape domestication, including earthworks. This review argues that the Amazonian anthrome was no less socio-culturally diverse or populous than other tropical forested areas of the world prior to European conquest.

Durante el simposio de Domesticación, al que asistimos Azalea y yo en julio,  Charles Clement se presentó con dos charlas, una sobre la domesticación de Theobroma cacao y otra sobre Domesticación del paisaje. La segunda fue la que más me impresionó. Pues habló sobre la influencia que tienen las poblaciones y actividades humanas no sólo sobre los recursos sino sobre el paisaje.

La zona de estudio de Charle Clement es el Amazonas, esta región del mundo suele ser concebida como una lugar virgen y prístino, a pesar de la creciente evidencia de la influencia que tuvieron y tienen los nativos sobre este sitio. En esta revisión los autores indican que los recursos y el paisaje del Amazonas no están menos afectados, que otras zonas del mundo. por las actividades socio-culturales. Cuando hablamos de recursos domesticados debemos pensar en un gradiente que incluye al recurso y la modificación del sitio que lo resguarda; y aunque no sea tan evidente, la escala de cambio que se ocasiona a los ecosistemas a lo largo del tiempo, puede llegar a ser de grandes proporciones.