Gene flow and Population Fitness

Fitness effects of gene flow (both advantageous and deleterious) have garnered plenty of recent press and scientific exploration. At the population level, the concepts and consequences are notoriously familiar. In the context of immigration, they reduce to existing genetic variation, and new variation introduced into the recipient “sink” population, or conversely, homogenizing effects, and loss of overall biodiversity at the species level. Emigration on the other hand (gene flow to a new environment) could result in local adaptation, and eventual speciation, or loss of genomic diversity due to pervasive inbreeding, and eventual extinction. Three recent manuscripts attempt to summarize/study these concepts, and provide neat springboards for future explorations

  • Genetic rescue to the rescue – Whiteley et al. (2015) TREE

Florida panthers (Puma concolor coryi) – poster mammals for population fitness rebounds due to genetic rescue. Image courtesy: http://intra.burltwpsch.org/users/mfilbert/studentwork06-07/goslin/g12/cub.jpg

Genetic Rescue (GR) can be advantageous to small inbred populations in many ways, due to increased genetic diversity introduced into the “sink” population, often increasing fitness of the population, and its ability to evolve adaptively. But the central debate in the efficacy of genetic rescue lies in whether it delivers on its promise above, or results in what’s known as “outbreeding depression” – the overall reduction of genetic diversity (at the species level), leading to more homogenous populations with reduced diversity. Whiteley et al. (2015) in this excellent TREE review assess numerous studies that have measured population fitness in the context of genetic rescue in several taxa. They also provide an excellent review of the state of the science in utilizing genetic rescue for conservation efforts.

GR may not save imperiled populations over the long term (ultimately, sufficient habitat is required for that), but recent results show that GR can buy time by improving their fitness and increasing population sizes in the short term.  

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Posted in adaptation, evolution, genomics, natural history, population genetics, selection, speciation, theory | Tagged , , , , , | Leave a comment

To review or not to review, that is the question

Imagine this scenario. You are industriously working away on your most recent paper (ignoring other pressing data analyses, administrative duties, and grant proposals). You have just begun to get into the zone of intense focus, writing nirvana, when DING!!! a new email appears in your inbox. It is a request to review a paper from Journal X. You immediately ask yourself: to review or not to review?

Deciding whether to accept or decline a request to review a manuscript is a question that we must all frequently ask ourselves. There are two possible actions to this question: agree to review or decline to review. Furthermore, there are two possible logical outcomes to your reasoning process: sound or faulty. This dilemma can be summarized with a two by two matrix (Figure 1) and I discuss each of these scenarios in turn. Continue reading

Posted in career, peer review, science publishing | 3 Comments

Polyploidy can melt the frozen niche

The rabbit hole of asexual reproduction literature is full of weird detours in the evolution of life.

There are asexual lineages that facultatively have sex, asexuals that still need sperm from other species,  and asexuals that steal sperm from other species, among a whole host of flavors of asexual reproduction. These groups, which can be contemporary to ancient in age, are of significant interest to those studying the origin and maintenance of sex. However, one of the main problems in comparing asexual lineages with closely-related sexual species is that asexuals usually have traits, mainly increased ploidy, that confound inferences about reproductive mode.

An interesting paper in the recent edition of PNAS by Mau et al. investigate one of the only systems where disentangling the effects of reproductive mode and ploidy is even possible, the genus Boechera. These perennial plants include widely-spread sexual diploid species, asexual diploids, and asexual triploids. The authors identify specific alleles associated with the creation of apomictic seeds and use these alleles to distinguish between sexual and asexual specimens from across western North America.

Analyses of this distributional data showed comprehensive niche conservatism between sexual and asexual diploids (“the frozen niche”), but niche differentiation between sexual diploids and polyploids.

Our data provide phylogeographic evidence for multiple origins of apomictic cytotypes in Boechera and support a frozen-niche variation model for diploid apomixis niche evolution. Importantly, we provide statistical evidence that ploidy variation, both within and among species, is a stronger driver of niche evolution than reproductive mode.

This is just one aspect of a more complicated evolutionary history that includes multiple bouts of hybridization and transitions between reproductive modes, but Mau and colleagues provide one of the best recent efforts at understanding the mechanism that makes weird asexuals, well, weird.

Mau M., Lovell J.T., Christiane Kiefer, Marcus A. Koch, Olawale M. Aliyu & Timothy F. Sharbel (2015). Hybrid apomicts trapped in the ecological niches of their sexual ancestors, Proceedings of the National Academy of Sciences, 201423447. DOI: http://dx.doi.org/10.1073/pnas.1423447112

Posted in DNA barcoding, natural history, plants | Tagged , , | Leave a comment

The death of the p-value? Probably not.

Image modified from "Death of a Salesman". Image from Wikipedia

Image modified from “Death of a Salesman”. Image from Wikipedia

In February, a social psychology journal, Basic and Applied Social Psychology , made the bold (and extreme) move to ban the use of p-values, F-statistics, T-values, and any other form of Null Hypothesis Testing (NHT) method. This major move generated a lot of buzz in the press and on social media: with some praising the move and others urging that we proceed with caution.

In a recent comment in Nature, Jeffrey Leek and Roger Peng point out this ban is only treating one symptom, while we should really be trying to treat the root cause: problems and errors in judgement during any other stage of experimental design and analysis. Continue reading

Posted in methods, politics, science publishing | Tagged , , | 2 Comments

Sous les mers: cradles or museums of biodiversity?

While thinking about environmental genomics and writing this post on a recent article in Heredity, I interviewed Eric Pante.

Deep sea octocorals in situ, taken with an ROV between 1000 and 3000 meters depth. Image courtesy of NOAA Okeanos Explorer Program, Our Deepwater Backyard: Exploring Atlantic Canyons and Seamounts 2014

Deep sea octocorals in situ, taken with an ROV between 1000 and 3000 meters depth. Image courtesy of NOAA Okeanos Explorer Program, Our Deepwater Backyard: Exploring Atlantic Canyons and Seamounts 2014

Posted in adaptation, bioinformatics, Coevolution, evolution, genomics, interview | Tagged , , , , | Leave a comment

Grasping gorgonians

A recent issue of Heredity focused on the brave new world of environmental genomics. After highlighting the special issue, I started chatting to one of the contributors, Eric Pante and became interested in his work on gorgonians.

Deep sea octocorals in situ, taken with an ROV between 1000 and 3000 meters depth. Image courtesy of NOAA Okeanos Explorer Program, Our Deepwater Backyard: Exploring Atlantic Canyons and Seamounts 2014

Deep sea octocorals in situ, taken with an ROV between 1000 and 3000 meters depth. Image courtesy of NOAA Okeanos Explorer Program, Our Deepwater Backyard: Exploring Atlantic Canyons and Seamounts 2014

Eric and his co-authors explored the extent to which RAD tags can be used to infer phylogeny. This paper arose from a GDR, or Groupement de Recherche (I’ll be posting an interview with Eric to go along with this summary of the Heredity paper, so check back to read more about GDR’s), that facilitated the collaboration of among researchers and labs addressing similar questions.

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Posted in bioinformatics, Coevolution, evolution, genomics, mutation, phylogenetics | Tagged , , , , , | 1 Comment

A few good molecular ecologists: six months and 116 posts later

My usual Wednesday spot on The Molecular Ecologist is primetime real estate: a lot of journal table-of-contents get sent out on Tuesday/Wednesday and whole slew of people are in the office looking at computer screens.

This usually produces a nice readership on Wednesdays, expect for when I drew the unlucky straw for Christmas Eve. On December 24th, I posted a review of the first three months of posts from the five newest contributors to the blog. Since no one probably saw that post and we have just arrived at the end of our six month agreement as contributors, I’ve updated all the data to reflect our full tenure. For good measure, I’m publishing it on a Thursday to steal some of Arun’s fame.

Hopefully this can be used to catch some things you might have missed, see the past and future direction the content, and recognize the unique contributions from each contributor.

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Posted in blogging, Molecular Ecology views, Uncategorized | 1 Comment

Quantifying risks of consanguineous mating in humans

The efficacy of selection in purging a deleterious mutation from a randomly mating population depends on numerous factors, including dominance effects of alleles – see my previous posts. Simplistically, most new mutations are expected to be heterozygotic, and be purged less effectively if they are recessive, than dominant alleles in homozygotes. In other words, recessive mutations segregate at higher frequencies (in heterozygotes), than dominant mutant homozygotes, especially so for Mendelian traits.

In inbreeding populations, thus, there’s a greater reduction of population fitness due to the accumulation of deleterious alleles in homozygotes, a phenomenon commonly termed “inbreeding depression”. Modern humans are a classic example of repeated non-random, consanguineous mating, resulting in localized population structure. Understanding the effects of non-random mating on the accumulation of recessive deleterious mutations is of great interest to disease genetics, anthropology, and the social sciences at large.

A Hutterite family – Image courtesy: National Geographic Channel – http://channel.nationalgeographic.com/american-colony-meet-the-hutterites/galleries/barnburners/at/king-colony-family-portrait-54169/

In a recent publication, Gao et al. (2015) attempt to quantify the fitness effects of deleterious (particularly autosomal, recessive lethal – i.e. inviable homozygote) mutations, using a founder population of Hutterites with well documented pedigrees, since 1950. The Hutterites are a small community of South Dakotans founded by 64 ancestors in the 18th-19th centuries, that migrated over to the United States and established 3 communal farms, and have since married consanguineously.

In short, Gao et al. (2015) (a) simulated Mendelian inheritance at 14 autosomal recessive disease genes along small and large pedigrees of the Hutterite population, (b) quantified loss or manifestation of mutant alleles (that were present in the founder population), and (c) use a Bayesian approach for point estimates (and intervals) of the number of autosomal recessive lethal mutations in a haploid human genome. Their study finds that 57% of recessive mutations from the founding population were lost prior to 1950 (after which extensive disease and pedigree records exist), 19% of the surviving alleles were present in homozygotes, and that 8.1% of the founder alleles will be expected to manifest in the present generation. This is also equivalent to 0.29 recessive deleterious mutant alleles on an average per haploid human genome. More importantly,

(this study) suggests that the risk of autosomal recessive disorders that manifest after birth should be increased by 0.29/16 = 1.8% in offspring of first-cousin couples (assuming no difference in environmental factors).

Here’s some recent press coverage on this study: http://www.sciencedaily.com/releases/2015/04/150408100522.htm

http://www.nature.com/news/genomes-carry-a-heavy-burden-1.17304

Reference:

Gao, Z., Waggoner, D., Stephens, M., Ober, C. & Przeworski, M. Genetics 199, 1243–1254(2015). DOI: http://dx.doi.org/10.1534/genetics.114.173351

Posted in genomics, mutation, pedigree, population genetics, selection, societal structure | Tagged , , , , | Leave a comment

A mammoth bottleneck prior to extinction

Woolly mammoth

Here’s to back-to-back posts on extinct mammalian genomes!

Woolly mammoth genomes are all the rage. How do I know? Just check out the new book, pre-print, and paper that were recently published.

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Posted in conservation, genomics, next generation sequencing, Paleogenomics, population genetics | Tagged , , | Leave a comment

Extinct and extant Equus genomes reveal speciation with gene flow despite chromosome number variation

Painting of a stallion in Louis XVI's menagerie at Versailles by Nicolas Marechal, 1793. Photo from  WIkipedia.

Painting of a quagga stallion by Nicolas Marechal, 1793. Photo from Wikipedia.

In their recent PNAS paper*, Hákon et al. generate full genome sequence data for each living species of asses and zebras, thus completing the set of genomes available for all extant species in the genus Equus (genomes for the donkey and horse have been published previously- see references below). The authors also collected full genome data for the quagga (Equus quagga quagga), a subspecies of the plains zebra that lived in South Africa until being driven to extinction in the 19th century. The last captive individual died in an Amsterdam zoo in 1883. In 1984, the quagga was the first extinct species to have its DNA sequenced. Hákon et al. used the Equus genome sequences to search for loci under selection, reconstruct demographic history, and measure gene flow among diverging lineages. Continue reading

Posted in genomics, speciation | 1 Comment