Hans Zauner

**Bats are mammals like no other -- airborne, mostly nocturnal, often
hidden away in caves, capable of using echolocation for in-flight
navigation. No two bat species are alike, however. Their diversity of
morphology, life styles and feeding habits is staggering. New bat
genomics research published today in *GigaScience* explores  the
footprints of evolution, to explain how New World Bats adapted to
different food sources.**

![bat genomics
examples](http://gigasciencejournal.com/blog/wp-content/uploads/2020/06/bats-300x294.png){.alignright
.wp-image-3334 .size-medium loading="lazy" decoding="async" width="300"
height="294"
srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2020/06/bats-300x294.png 300w, http://gigasciencejournal.com/blog/wp-content/uploads/2020/06/bats.png 367w"
sizes="(max-width: 300px) 100vw, 300px"}Bats evoke dark fantasies
revolving around vampires, death and disease. These days, actually
fact-based concerns about bats as potential sources of dangerous
coronaviruses add to their shady reputation. However, far from any
movie-inspired popular imaginations of stereotypical blood sucking
vampires, the nearly 1,300 species of bats are adapted to vastly
different habitats and food sources (see [this previous
*GigaScience* article ](https://doi.org/10.1093/gigascience/giy116)on
the cave nectar bat *Eonycteris spelaea,* and our [previous GigaBlog
posting](http://gigasciencejournal.com/blog/release-the-bats-new-halloween-opendata-treat-in-gigadb/)
on bat genomics back in 2013). Some bats feed on fruits, others sip
nectar, some hunt insects, and others are indeed carnivorous -- unique
and fascinating adaptations to sometimes very specialized types of food.
How did this diversity evolve?

To get answers, a team of Mexican scientists, coauthors of [this new
*GigaScience* article](https://doi.org/10.1093/gigascience/giaa059),
looked more closely at one particular group, the New World Leaf-nosed
Bats (*Phyllostomids*), and explored genomic adaptations that could
explain the evolution of different feeding habits.

::: {#attachment_3336 .wp-caption .alignleft style="width: 190px"}
![Another example for bat
genomics](http://gigasciencejournal.com/blog/wp-content/uploads/2020/06/lesser-long-nosed.jpg){.wp-image-3336
.size-full loading="lazy" decoding="async"
aria-describedby="caption-attachment-3336" width="180" height="140"}

The lesser long nosed bat.  
(photo: Wikipedia, C. Schwalbe)
:::

The New World Leaf-nosed Bats are a diverse group, with 216 species in
60 genera in North and South America. One genus within this group is
*Leptonycteris* (the "longed nosed" or agave bats). *Leptonycteris* bats
survive on a diet of nectar and pollen, and, as the authors explain in
an email for GigaBlog, "*they are the most important pollinators of the
agave plants, including the species used for making popular alcoholic
drinks from Mexico, such as tequila and mezcal*." Another Mexican bat,
*Musonycteris harrisoni* (the" Banana bat") has one of the longest faces
of all bats and "*seems to be a bat that wants to be a hummingbird*",
considering its nectar-feeding skills.

And yes, vampires do indeed exist in the bat world. *Desmodus rotundus*
has teeth that are especially adapted to cut into the skin of mammals,
together with other adaptations that allow for the digestion of blood.

## Diverse tastes

Each of these specialized feeding habits comes with adaptations in
morphology, behavior and  physiology. Can we see how evolution acted on
the bats' genomes to enable the utilization of different food types?
That's the question that Luis Eguiarte and colleagues examine in their
new *GigaScience* paper. The authors explain:

*" The evolutionary changes involved in a diet modification by a group
of animals is considered one of the most important events in animal
evolution, given that diet changes open new ecological and physiological
opportunities. In order to take advantage of these new opportunities,
animals evolve new morphologies (such as changes in the head shape, in
the dentition or beak, shape of the wings or limbs, etc.), physiologies
and behaviors."*

*"Some extreme feeding strategies, in particular those that only or
mainly feed on liquids, such as nectar or blood, involve important
physiological challenges. We decided to take advantage of this huge
diversity of diets in the New World leaf-nosed bats to explore the
evolutionary changes in their genomes".*

To obtain a reference for comparative genome analysis, the Mexican
researchers sequenced and assembled the genome of an adult male Lesser
Long-nosed Bat (*Leptonycteris yerbabuenae*) at high quality. They then
got sequence data for four more bat species with different feeding
habits: *Macrotus waterhousii* (an insect feeder ), *Artibeus
jamaicensis* (a fruit-feeder), and two nectar-pollen feeders, *Macrotus
harrisoni* and *Leptonycteris  nivalis*.

## Getting the bat out of the cave

However, before any of the genomic work could be done, specimen had to
be collected, which required some field work in pitch-dark Mexican
caves. The authors recall the extraordinary outdoor part of the study:

*"Both Mexican Leptonycteris species are pretty common. The individual
that we analyzed in more detail, an adult male L. yerbabuenae, came from
the El Salitre cave, in the state of Morelos, south of Mexico City. Even
if the species is common, the first two hours inside the cave were
frustrating, as we only found other bat species. For Yocelyn, the first
author of the paper, it was her first time in a cave, and she started to
comment on Murphy's law ("If there's any way to do it wrong, we will
find it"). However, to be in the cave was an extraordinary experience,
as it made no difference opening or closing her eyes, and also smelling
the tremendous odor of a tropical cave while listening to the bats'
wings fluttering all around. Fortunately, approximately one hour later,
we found our Leptonycteris!"*

Other samples were donations from researchers of the Zoology Museum
"Alfonso L. Herrera", at the School of Sciences of UNAM university. With
bat samples secured and genomic raw data obtained, the bioinformatic and
phylogenomic work could begin -- a new experience for Eguiarte's lab,
which previously mainly did more traditional population genetic work:

*"This was our pioneering work in mammal genomics, so the adventure
started from getting adequate samples and good, large quantities of very
pure, not degraded and useful DNA for massive sequencing, to learn how
to handle the huge data bases that at first we were not able to manage.
At the end, we learned all this and right now we are even enjoying the
bioinformatic analyses!"*

## Uncovering the footprints of bat evolution

Using their newly generated sequenced bat genomics data, the scientists
undertook a phylogenomic analysis, based on 22,388 gene families, and
looked for footprints of past selection events. Also on the level of
gene families they detected expansions and contractions of genes that
have functions related to different types of diet.

Vampires for example show genomic adaptations that are associated with
feeding on blood, such as coagulation mechanisms. In the genomes of
nectar feeders, on the other hand, genes that have to do with
metabolizing sugary liquids showed up prominently.

::: {#attachment_3335 .wp-caption .alignright style="width: 310px"}
![](http://gigasciencejournal.com/blog/wp-content/uploads/2020/06/Desmo-Flug-01-300x249.jpg){.size-medium
.wp-image-3335 loading="lazy" decoding="async"
aria-describedby="caption-attachment-3335" width="300" height="249"
srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2020/06/Desmo-Flug-01-300x249.jpg 300w, http://gigasciencejournal.com/blog/wp-content/uploads/2020/06/Desmo-Flug-01-768x638.jpg 768w, http://gigasciencejournal.com/blog/wp-content/uploads/2020/06/Desmo-Flug-01.jpg 1024w"
sizes="(max-width: 300px) 100vw, 300px"}

The vampire bat, Desmodus rotundus. (image: Wikipedia, U. Schmidt )
:::

Feeding mainly on nectar comes with another huge challenge: This
particular diet is awfully sweet-- way too much sugar for a usual
mammalian metabolism. How do the specialized bats cope? The genomic
results provide a clue: The species that feed on nectar (*M. harrisoni,
L. nivalis*, and* L. yerbabuenae*) show signatures of positive selection
for genes involved in insulin secretion, calcium and iron storage. Luis
Eguiarte explains:

*"The nectar feeding bats share a group of positively selected genes
that help them to avoid the adverse effects of high blood sugar levels.
These genes are of potential relevance to humans and may help in future
studies involving nutrient mal-absorption and metabolism disorders
including diabetes, hyper- glycemia, and obesity in our populations.
Some of the selected genes in nectar feeding bats were directly involved
in sugar metabolism, that accounts for almost all their diet (as nectar
is basically sugar and water), as well as lipids metabolism genes, as
these bats have to make lipids from the energy obtained from sugars. We
also found selective signals in iron metabolism genes, an element that
is seldom present in nectar and pollen and thus became a very precious
nutrient to nectar feeding bats."*

There's also a bigger ecological picture that Eguiarte's lab is
interested in: Bats from the genus *Leptonycteris* pollinate agaves and
related plants. The coevolution between agaves and bats is the topic of
another recent paper from their lab ( [Flores-Abreu et
al.)](https://doi.org/10.1016/j.ympev.2019.01.004) and the insight from
comparative genomics will be helpful to better understand "*the
fascinating love story between pollinator and plant*", as Eguiarte calls
it.

*"This new study in GigaScience is our first contribution to the
evolutionary genomics of Mexican animals and we hope in the future to
have other relevant and original contributions, in particular including
other nectar feeding animals".*

PS.

At *GigaScience*, we recently got bat genomics expertise on board. We
are pleased to announce that [Emma Teeling (University College
Dublin)](https://people.ucd.ie/emma.teeling) has joined our [Editorial
Board](https://academic.oup.com/gigascience/pages/Editorial_Board).  As
one of the Founding Directors of the [Bat1K
project](https://bat1k.ucd.ie/), aiming to produce high quality genomes
of all living bat species to uncover the genes and genetic mechanisms
behind their unusual adaptations, stay turned for many more exciting
insights on bat genomics to be revealed. If you wish to learn more about
the importance of bat genomics, don't miss her TED talk:

### **References**

Gutiérrez-Guerrero YT, Ibarra-Laclette E, Martínez Del Río C, et al.
Genomic consequences of dietary diversification and parallel evolution
due to nectarivory in leaf-nosed bats. *Gigascience*.
2020;**9**(6):giaa059.
doi:[10.1093/gigascience/giaa059](https://doi.org/10.1093/gigascience/giaa059)

**Data in
GigaDB:** [http](http://dx.doi.org/10.5524/100746)[://dx.doi.org/10.5524/100746](http://dx.doi.org/10.5524/100746)

The post [Nectar, fruits, and blood. A genomic view on the feeding
habits of
bats.](http://gigasciencejournal.com/blog/bat-genomics/){rel="nofollow"}
appeared first on
[GigaBlog](http://gigasciencejournal.com/blog){rel="nofollow"}.


<b>
 Bats are mammals like no other – airborne, mostly nocturnal, often hidden away in caves, capable of using echolocation for in-flight navigation. No two bat species are alike, however. Their diversity of morphology, life styles and feeding habits is staggering. New bat genomics research published today in
 <em>
  GigaScience
 </em>
 explores
</b>

Nectar, fruits, and blood. A genomic view on the feeding habits of bats.

University of Glasgow

Roderic Page

Notes on fonts in trying decipher some bat names (and sort out some
synonyms). It can be difficult to tell \"œ\" (o + e) from \"æ\" (a + e)
in some texts. For example, BHL page
[35549499](http://biodiversitylibrary.org/page/35549499) has
\"Chœrephon\":  
  
![Chœrephon](http://lh3.ggpht.com/-mc6_mW0N1MQ/UhuHQD0nIpI/AAAAAAAADAE/O0s50ZB9ZiI/Ch%25253Frephon.png?imgmax=800 "Chœrephon.png"){border="0"
width="400" height="113" style="float:left;"}

[*Chœrephon*]{style="font-family:Times;font-size:72px;"}

  
Here is the name on BHL
[37695497](http://biodiversitylibrary.org/page/37695497) (Catalogue of
the Chiroptera in the collection of the British Museum):  
  
![Chærephon](http://lh5.ggpht.com/-CZRa5c49EK8/UhuHR57en2I/AAAAAAAADAM/hSa95RcJfeE/Ch%2525C3%2525A6rephon.png?imgmax=800 "Chærephon.png"){border="0"
width="400" height="107" style="float:left;"}

[*Chærephon*]{style="font-family:Times;font-size:72px;"}

  
This genus of bats is named for \"Χαιρεφῶν, Aristophanes, Aves, 1296,
1564.\" according to Dobson 1874 ([On the Asiatic species of
Molossi](http://biostor.org/reference/129456)), but is regarded as
having been amended by Dobson 1878 to Chærephon. It took some time
squinting at the BHL scan to see that Dobson 1878 and Dobson 1874 did
actually write the name differently. Why does this matter? Well, the
GBIF classification has both \"Choerephon\" and \"Chaerephon\" in its
list of bat genera in the family Molossidae, and it can have one or
other, but not both.  
  


Notes on fonts in trying decipher some bat names (and sort out some synonyms). It can be difficult to tell "œ" (o + e) from "æ" (a + e) in some texts.

Bat names, ligatures, and fonts

Continuing the theme of the [failings of the GBIF
classification](http://iphylo.blogspot.com/2013/06/more-gbif-fail.html)
I\'ve been playing further with cluster maps to visualise the problem
(see [this earlier post for an
introduction](http://iphylo.blogspot.co.uk/2012/06/visualising-differences-between.html)).  
  
Browsing through bats in GBIF I keep finding the same species appearing
more than once, albeit in different genera. As discussed in the [gibbon
example](http://iphylo.blogspot.com/2013/06/gibbons-and-gbif-good-grief-what-mess.html),
GBIF merges several competing classifications for mammals, and these
often don\'t agree on the \"accepted name\" for a species. In the
absence of a decent database of taxonomic synonyms, GBIF ends up
duplicating species, and each duplicate is often associated with
different occurence data. If you are trying to get the distribution for
a species this can be a disaster.  
  
To get a sense of the scale of the problem I put together a simple tool
to create cluster maps. The code is on
[github](https://github.com/rdmpage/cluster-map)) and there is a live
service at <http://iphylo.org/~rpage/cluster-map/>. The service takes a
simple tab-delimited file that lists sets and their members, computes
the overlap between the sets, calls Graphviz to layout a graph in SVG,
then draws in the members of each cluster (phew).  
  
The input file looks something like this:  

    Molossops    aequatorianus
    Chaerephon   aloysiisabaudiae
    Tadarida  aloysiisabaudiae
    Chaerephon    ansorgei
    Tadarida  ansorgei
    Molossus  ater
    Mormopterus   petrophilus
    Sauromys   petrophilus

  
  
What can we do with this tool? Well, I created a quick list of all the
species of bat in the family Molossidae according to GBIF. The sets are
the bat genera, the members are the species (you can see the file
[here](https://github.com/rdmpage/cluster-map/blob/master/examples/clusters.txt)).
I then ran this through the cluster map, and got something like this
(this is only part of the cluster map):  
  
![Bats](http://lh4.ggpht.com/-yX2f7U5J3Ew/UguXr3UxOaI/AAAAAAAAC-Q/3_TiV9T8GaM/bats.png?imgmax=800 "bats.png"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="460" height="156"}  
  
(now can you see why I call these \"papaya plots\"?). Note that there
are species names (i.e., specific epithets) in common to more than one
genus. Some of these may be perfectly OK (it\'s not unusual for the same
epithet to be used in different species, e.g. \"major\", etc.). But in
many cases these bat species turn out to be **the same species**, just
in different genera in different classifications. For example, GBIF has
both *Cynomops greenhalli* and *Molossops greenhalli*. These are the
same thing. Species in the genus *Mormopterus* may also occur in other
genera. In some cases the issue is competing classifications, sometimes
it is conflict over whether a species is a species or merely a
subspecies, and some generic conflicts are because some genera are
relegated to subgeneric status in some classifications. In short, it\'s
an unholy mess.  
  
Does this matter? Well, consider [*Mormopterus
petrophilus*](http://uat.gbif.org/species/2433054) and [*Sauromys
petrophilus*](http://uat.gbif.org/species/7261924), which GBIF both
regard as valid species (they\'re the same thing). Here are the
distributions for the two different names in GBIF:  
  

::: {style="text-align:center"}
![Mormopterus](http://lh3.ggpht.com/-pgzN8DbEp9E/UguXs4NsUZI/AAAAAAAAC-Y/RjWMq3rRMCU/Mormopterus.png?imgmax=800 "Mormopterus.png"){border="0"
width="200"
height="225"}![Sauromys](http://lh3.ggpht.com/-UJFjx_kCd_Q/UguXtvsVlSI/AAAAAAAAC-g/oZDLjmI8loI/sauromys.png?imgmax=800 "sauromys.png"){border="0"
width="200" height="225"}
:::

  
  
Depending on which name you use you\'ll get a very different picture of
the distribution of this bat.  
  
The next step is to figure out how to fix this. Is there a way we can
automate fixing the GBIF classification so that it is not riddled with
spurious duplicates like these?  
  


Continuing the theme of the failings of the GBIF classification I've been playing further with cluster maps to visualise the problem (see this earlier post for an introduction).Browsing through bats in GBIF I keep finding the same species appearing more than once, albeit in different genera.

Messages de Rogue Scholar

Nectar, fruits, and blood. A genomic view on the feeding habits of bats.

Bat names, ligatures, and fonts

Cluster maps, papaya plots, and the trouble with GBIF taxonomy