I just submitted my four year review and in so doing listed out the students that had published blogs on The Molecular Ecologist. Seventeen students have not only received course credit, but also have a non-peer reviewed publication on their CVs.

Starting a week from today, the next batch of student posts will go live on our new #StudentSciComm post series. Students wrote posts as part of my Evolution and Sci Comm courses this past autumn.

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Posted in blogging, career, chat, community, ecology, evolution, howto, methods, Molecular Ecology, the journal, Science Communication, science publishing | Tagged , , , , , | Leave a comment

Nominations open for the 2020 Molecular Ecology Prize

From the Molecular Ecology Prize Committee:

We are soliciting nominations for the annual Molecular Ecology Prize.

The field of molecular ecology is young and inherently interdisciplinary. As a consequence, research in molecular ecology is not currently represented by a single scientific society, so there is no body that actively promotes the discipline or recognizes its pioneers. The editorial board of the journal Molecular Ecologytherefore created the Molecular Ecology Prize in order to fill this void, and recognize significant contributions to this area of research. The prize selection committee is independent of the journal and its editorial board.

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Revenge of the sex chromosomes

Male (left) and female eastern bluebirds, Sialia sialis. In birds, males are homogametic (with two Z chromosomes) and females are heterogametic (with one Z and one W) — and this means that, all things being equal, he has a slightly longer life expectancy than she does. (Flickr: Vicki DeLoach)

Sex chromosomes are one of evolution’s stranger inventions, when you think about it. Many sexually dimorphic species, including most reptiles and amphibians and lots of plants have sex determination via gene complexes on otherwise conventional chromosomes, or even as a response to environmental variation; and those that do have sex chromosomes don’t all have the same kind.

In mammals, most of us learned in high school biology (or possibly via dusty sitcom jokes), individuals carrying two X chromosomes typically develop as female, while those with one X and one Y chromosome typically develop as male. But, as you find out if you stick around for university-level biology or do the right kind of extracurricular reading, a number of non-mammalian taxa, like birds, do it the other way around, with males carrying two Z chromosomes and females carrying a Z and a W chromosome. It’s a classic evolutionary kluge: there’s more than one way to genetically encode separate features for males and females, and which solution is in use within a given group of species depends largely on the happenstance of their shared ancestry. And, like all kludges, it comes with a downside — recessive deleterious mutations on the X or Z create a genetic burden borne only by XY or ZW individuals — and a paper recently published in Biology Letters finds that, across a wide range of animal taxa, this is indeed the case.

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How to handle the burden of deleterious mutations

Alpine ibex.

With the increasingly pressing matter of populations being threatened by fragmentation and isolation, and with progressively more efficient sequencing technologies and analytical tools at hand, conservation genetics is starting to turn the spotlight on the topic of genetic load. It has become clear that population survival is not only about population sizes and estimates of genetic diversity. Some populations thrive despite extremely low genome-wide diversity, while others go extinct despite seemingly much better prospects.

The buzzword that keeps coming up in recent publications, is purging. Purging is defined as the “increased purifying selection facilitated by inbreeding as it increases the homozygosity of partially recessive deleterious variants” (Hedrick and Garcia-Dorado 2016). In other words, in small populations, where the inbreeding usually increases homozygosity, more of the really nasty stuff [aka highly deleterious mutations] is revealed in homozygous state, which makes it easier for purifying selection to act upon.

The problem is that studies examining bottlenecked natural populations are not conclusive on how much mutational load accumulates in small populations and how much is purged by selection. Remember that in small populations, selection is assumed to be overshadowed by the effects of genetic drift, therefore it is not clear how much power it has for eliminating deleterious mutations.

While some studies found empirical evidence of accumulation of genetic load in a population with low effective population size, for instance in the woolly mammoth (Rogers and Slatkin 2017) and the crested ibis (Feng et al. 2019), others showed that purging of highly deleterious mutations does take place in populations of extremely bottlenecked species, for example in the Channel Island foxes (Robinson et al. 2018) and mountain gorillas (Xue et al. 2015).

The new study by Christine Grossen and colleagues (Grossen et al. 2020) looked at the problem in a beautiful model system of the once near-extinct Alpine ibex. Back at the beginning of the 19th century, there were less than 100 individuals left in a single population in Gran Paradiso, Italy. After recolonizations, the Alpine ibex is now at a census size of 50,000 individuals. Interestingly, the successful recolonized populations were used to found other populations, and thus, the extant populations experienced two to four bottlenecks, which are also well documented in the records.

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How many samples do you need to investigate relationships between genetic make-up & immune function?

When an organism is exposed to a pathogen, what determines their ability to resist or recover from infection? Mounting an effective immune response is a complex dance with multiple partners, changing tempos, and maybe even a costume change or two: An adaptive immune response results from the interplay of the surrounding environment and the specific individual, that individual’s (and sometimes the parents!) history of infection, and the genetic make-up of the individual, just to name a few of the partners. Scientists have been investigating the effects of immunogenetic diversity and genotype on immune system functionality for decades. Among the most studied immune system genes are those of the Major Histocompatibility Complex (MHC), which encode the cell-surface proteins responsible for distinguishing between ‘self’ and ‘non-self’ peptides (Piertney & Oliver 2006). Thus, MHC genes control, in part, an organism’s ability to respond to pathogens through the adaptive immune system. I did my Ph.D. on MHC genes, so I still have a soft spot in my heart for this set of genes; Also, I really love a paper that makes tasty lemonade out of lemons, as a recent paper by Arnaud Gaigher and colleagues (2019) did.

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Inbreeding and the cougar genome

This week, some of my favorite #scicomm games on Twitter are teaming up with March Mammal Madness to reveal this year’s #2020MMM contestants in my favorite “battle of the fittest.” Specifically, today (2/21/2020) at 12:30 pm EST, Dr. Michelle LaRue (@drmichellelarue) will be dropping an image for her #CougarOrNot science communication game with the big combatant reveal at 2:30 pm EST.

Photo provided by National Parks Service via Wikimedia

The timing is appropriate because the genome of the cougar (Puma concolor; also called mountain lion or puma) was published at the end of last year, providing insights into the divergence between North and South American cougars, as well as some interesting findings regarding genomic diversity that have conservation implications for the puma (Saremi & Supple et al. 2019). Continue reading for some cool cougar insights to prepare you to fill your #2020MMM bracket!

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The crows have eyes — but not only for members of their own species

Two Northwestern crows (Corvus caurinus), or maybe two American crows (Corvus brachyrynchos) — Wikipedia’s caption can’t make up its mind.

If you are a moderately bird-interested person who’s spent much time in Seattle or Vancouver, you’ve probably had a version of the following conversation with a less bird-interested friend or family member from out of town, after one of you spots a midsized black bird perched on the rail of the Burrard Street Bridge or scavenging in Pike Place Market:

The less-bird-interested person: "Hey, a crow!"

You: "Yeah, there’s a different species of crow around here. The Northwestern crow."

The LBIP: "Oh, really? How are they different?"

You: "They’re, uh … slightly smaller?"

The LBIP, skeptically: "So this is one of those?"

The crow: "CRRAAAH"

You: "I … I honestly don’t know."

Anyway, it turns out the distinction between American crows, which are distributed across North America, and the endemic Northwestern crows, is also somewhat tricky for the crows themselves.

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Posted in birds, phylogeography, species delimitation | Tagged | 1 Comment

The brief history of African Americans in Evolutionary Biology, and why that is the case.

Over a decade after the first African American scientist received a PhD in Evolutionary Biology only five others would do the same.
Over a decade after the first African American scientist received a PhD in Evolutionary Biology (broadly defined) only five others would do the same. (Left to Right) Dr. Joseph L. Graves Jr. in 1988 from Wayne State University, Dr. Scott Edwards in 1992 from the University of California-Berkeley, Dr. Tyrone Hays in 1993 from Harvard University, Dr. Colette St Mary in 1994 from the University of California-Santa Barbara, Dr. Paul Turner in 1995 from Michigan State University, and Dr. Charles Richardson (not pictured) in 1999 from Indiana University.

I remember the first day I met a Black faculty member in evolutionary biology. I had just finished my first year of graduate school and was attending the Workshop in Molecular Evolution at Woods Hole biological station. Dr. Scott Edwards, noted ornithologist and member of the National Academy of Sciences, was one of our lecturers for the week. Let me tell you, I had never googled someone faster than when I realized he’d be presenting the lecture on phylogeography. Only a few years out from receiving my B.S. in Botany I found myself thinking “I could do birds, birds are cool!” Don’t get me wrong, I’ve had plenty of amazing mentors who helped foster my interest and practice of science, and by then had shaken off most of the new-grad-student-smell of indecision. In that moment, though, I was struck. Representation, being able to see yourself in someone else and imagine a possible future, has the power to alter the trajectory of any one person’s life. I enjoyed Dr. Edwards’ lecture and got to have a great conversation with him over the workshop’s celebratory lobster dinner, but I ultimately decided I was too much of a plant fanatic to jump ship just then.

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The world through the senses of a pangolin

Source: WikimediaCommons/Shukran8888

Pangolins are bizarre creatures that do not seem to attract a lot of attention, but when they do, they hit the headlines big time. And usually not in a very positive way. After being labeled “the most trafficked mammal you’ve never heard of”, pangolin’s unfortunate reputation has been recently reinforced by the news suggesting that pangolins might be involved in the coronavirus outbreak as an intermediate host.

Since this finding was announced in the form of a press release, let’s not jump to conclusions and let’s wait for the publication that comes out of the peer-review. Nevertheless, this Saturday, February 15, is World Pangolin Day, and thus, it is a good time to do some PR for these fascinating animals.

In 2016, researchers published genome assemblies for two out of eight pangolin species, the Malayan (Manis javanica) and Chinese (M. pentadactyla) pangolins. Choo et al. used whole-genome shotgun sequencing of short-read Illumina libraries to generate 145X and 59X genomes of the Malayan and Chinese pangolins, respectively.

The team, which consisted primarily of researchers from Malaysia, Russia, and the US, focused on looking for loss-of-function genes that have been pseudogenized. Considering that pangolins are toothless creatures with poor eyesight, one can imagine that there’s a lot to find.

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Of microbes and whales

At the end of January, the International Society for Microbial Ecology (ISME) journal put out a list: “Readers’ Choice: The best of The ISME Journal 2019” . I don’t know about you (my fellow scientists also with 35+ chrome tabs open to papers to read), but I often feel behind on reading and worry I missed something during the week’s madness. I am also a list person, so this caught my eye and reminded me of a paper from December about two of my favorite things: microbes and whales.

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Posted in bioinformatics, community ecology, ecology, mammals, microbiology | Tagged , , , | 1 Comment