Inbreeding and the cougar genome

Posted on 21 Feb, 2020 by Kathleen Grogan

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!

Continue reading →
Posted in conservation, genomics, mammals | Tagged , , , , | Leave a comment

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

Posted on 20 Feb, 2020 by Jeremy Yoder
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.

Continue reading →
Posted in birds, phylogeography, species delimitation | Tagged | 1 Comment

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

Posted on 17 Feb, 2020 by R Shawn Abrahams
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.


Update, 11 June 2020: This post has been edited to clarify attributions.

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. At 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. Still, I ultimately decided I was too much of a plant fanatic to jump ship just then.

Continue reading →
Posted in evolution, Science History | Tagged , , | 1 Comment

The world through the senses of a pangolin

Posted on 14 Feb, 2020 by Patrícia Chrzanová Pečnerová
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.

Continue reading →
Posted in ecology, evolution, genomics, mammals, RNAseq, transcriptomics | Tagged , , | Leave a comment

Of microbes and whales

Posted on 10 Feb, 2020 by Kelle Freel

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.

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

Microbial mutualists parted ways with this host plant — multiple times

Posted on 6 Feb, 2020 by Jeremy Yoder
Acmispon strigosus, the Californian wild legume at the center of the study. (CalPhotos: Wynn Anderson)

Mutually beneficial interactions between species provide key services and resources for most ecological communities. Maintaining traits that benefit a separate, unrelated species requires a potentially delicate balance of costs and benefits, but most species that host mutualists are equipped to prevent them from taking advantage of the interaction. That doesn’t mean that mutualists never walk away from mutualism — as seen in a new study of the bacteria that fix nitrogen for one native California wildflower, mutualists may go their own way pretty frequently.

Continue reading →
Posted in evolution, microbiology, phylogenetics, plants | Tagged , , | Leave a comment

One Thousand Plant Transcriptomes and Not a Single to Spare

Posted on 3 Feb, 2020 by R Shawn Abrahams
The diversity of form and physiology within Viridiplantae. ( One Thousand Plant Transcriptomes Initiative 2019, Figure 1)

What is the weight of a transcriptome? How about a thousand? Every day new sequencing machines are purring away, base pair by base pair, producing novel insights into the genomes of our favorite organisms. As technology improves, costs come down, and opportunities for “Big data” to have an impact on the most non-model of non-model species occur more often. Soon, even the darkest corners of the Eukaryotic branch of life, thought left only to the most artisanal of biological research, will benefit from proximity to annotated genomic data. Towards the end of 2019, the One Thousand Plant Transcriptome Initiative (1KP), a consortium of almost 200 researchers from around the world, released their capstone paper in the Journal Nature. In that paper, they detail the summary analyses of transcriptome data from 1,124 species across Archaeplastida (Green Plants, Glaucophytes, and Red Algae), spanning over a billion years of evolutionary time

Continue reading →
Posted in phylogenetics, plants, RNAseq, transcriptomics | Tagged , , | Leave a comment

The genomic & physiological basis of high altitude adaptation in North American deer mice

Posted on 31 Jan, 2020 by Kathleen Grogan

In biology, there are many ways to solve evolutionary ‘challenges’ so it always amazes me when organisms solve them in similar ways. And I love a good paper that adds to our attempts to dissect multi-trait adaptations. Recently, Schweizer et al. 2019 examined the genetic and physiological basis of high altitude adaptation in North American deer mice (Peromyscus maniculatus) by combining population genetics with physiological experiments.

The authors genotyped highland (Mt. Evans, CO – 4350 meters above sea level) and lowland (Lincoln, NE – 430 meters above sea level) mice and identified SNPs that exhibit extreme allele frequency changes in the highland population. Among the top SNPs were several in EPAS1, a gene that encodes the O2-sensitive subunit of hypoxia inducible factor 2 (HIF-2). HIF-2 is one of a critical family of transcription factors that are responsible for ensuring that O2 supply matches O2 demand, and transcription factors are exactly where you might expect to find the genetic basis of multi-trait adaptations, because they regulate the expression of many genes and potentially many traits. Thus, changes in the expression or binding capacity of a transcription factor can simultaneously affect many phenotypes. Sampling across a wide range of deer mice populations in the Southwest (see figure below) showed an EPAS1 allelic frequency distribution that positively correlates with altitude distribution.

Continue reading →
Posted in adaptation, association genetics, evolution, genomics, mammals, population genetics, RNAseq, Uncategorized | Leave a comment

Beetles' diversity was driven by coevolution with plants — and a little help from some microbial friends

Posted on 21 Jan, 2020 by Jeremy Yoder
A green immigrant leaf weevil, Polydrusus sericeus, one of tens of thousands of species in the family Curculionidae (Flickr, Dann Thrombs)

Beetles have long had a special place, if not in the heart of the Creator, in the imaginations of evolutionary biologists. They’re widely considered the most diverse single clade of animals, something upwards of 400,000 species that share a common ancestor — when the explosive diversification of that ancient lineage began, how it proceeded, and what caused it have been the subject of a lot of research. Many of those questions are addressed in a paper published in Proceedings of the National Academy of Sciences last month, which uses an unprecedented genomic dataset to figure out when beetles began their epic diversification, and tests one major hypothesis for the reason behind that diversification.

Continue reading →
Posted in insects, next generation sequencing, phylogenetics, plants, RNAseq | Tagged , , | 1 Comment

Molecular ecology highlights at the American Naturalist 2020 meeting

Posted on 15 Jan, 2020 by Jeremy Yoder
A great blue heron keeps watch over the dunes of Asilomar State Beach.

Even-numbered years are distinguished by Olympic Games (summer or winter), U.S. Congressional elections, and the American Society of Naturalists biennial meeting at Asilomar, a retreat center embedded in a California state park near the northern tip of the Monterey Peninsula. AmNat2020, which took place over the first weekend of the decade, featured the full range of biological research represented by the American Society of Naturalists and the U.S. scientific journal with the longest continuous publication history, but genetic and genomic data were key to many of the meeting’s highlights.

Continue reading →
Posted in community, conferences, evolution, genomics | Tagged | 1 Comment