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Research Themes
One of my research goals is to understand why some regions are more species-rich than others and why in some regions species possess given traits and why others do not.
Bats, one of the most diverse groups of mammals, are a fascinating model system that provides a huge versatility to explore these questions at different geographic and temporal scales. Bats show a wide range of body sizes, life spans, morphological and ecological adaptations, and life history traits, allowing a diverse mosaic of options to study the drivers of diversification and morphologic specializations.
Detailed updates of my most recent fancy genomic work coming soon!!
Convergence occurs when two or more species develop independently the same traits. Evidence shows that convergent evolution of phenotypic traits and ecological roles is common in nature, but little is known about the genomic and molecular basis of repeated evolutionary changes. The bat genus Myotis provides a promising model system to study the genomic mechanisms underlying repeated ecological adaptation and convergence of phenotypes in natural conditions as the same three foraging strategies have evolved multiple times in this genus.
I have set the phylogenomic basis to study the genomic mechanisms of convergent adaptations in the three ecomorphs that evolved repeatedly in Myotis bats.
Myotis bats have colonized all biogeographic regions and represent 10% of the total species of bats, yet the phenotypic variation among the more than 100 species is restricted to three ecomorphs that have evolved several times. These ecomorphs were described following phenotypic features related with feeding-foraging modalities as gleaners from foliage (‘Myotis’), water surface foragers (‘Leucone’), and aerial insectivores (‘Selysius’). Despite morphological similarities, phylogenetic analyses suggest that these ecomorphs evolved multiple times as clades follow major biogeographic patterns instead of feeding strategies.
I do not receive any commission from the sequencing services I am mentioning. It is just a reference point in case you want to use similar techniques.
I generated whole genome assemblies using long-range (10X Chromium) and short-read (TruSeq) Illumina® data. I used GENEWIZ (NYC) services to build and sequence libraries.
I redesigned a set of capture probes for UCEs that is specific for Myotis bats (using as a reference the previous set of UCEs designed for tetrapods and Myotis genomes). Find the sequences on my GitHub. I purchased myBaits® Custom Target Capture Kits from arbor biosciences.
I have mostly used the Microscopy and Imaging facility at the AMNH to CT-scan specimens from multiple collections.
- Morales AE, Ruedi M, Field K, Carstens (2019) Diversification rates have no effect on the convergent evolution of foraging strategies in the most species-rich genus of bats, Myotis. Evolution: doi.org/10.1111/evo.13849
- Morales AE, Burbrink FT, Segall M, Meza M, Munegowda C, Webala P, Patterson B, Thong VD, Ruedi M, Hiller M, Simmons NB. (In Review) Convergent evolution of bat ecomorphs involves changes in genes with similar functions but not always the same genes.
Watch some videos of the foraging strategies of Myotis bats
Photo source: MerlinTuttle.org. Video source: BBC (YouTube)
Gleaning from foliage
Trawling
Aerial hawking
My third major line of research is understanding how evolutionary forces such as genetic drift, gene flow, and natural selection interact to shape species boundaries, which is a longstanding question in evolutionary biology.
My approach to studying species divergence is through the genic view of speciation. This concept is based on differential adaptation at a genomic level instead of isolation of whole individuals or genomes. Gene flow does not disrupt the independent evolution of lineages. I have shown that genetic exchange can occur during early speciation in Myotis bats from North America and challenged the conventional view of morphology reflecting common ancestry. These findings, supported by innovative bioinformatic toolsI developed (such as PHRAPL), show that accurate estimations of genetic exchange are essential to understanding what genomic regions are or are not exchanged among species and how they may promote or prevent divergence.
The genus Myotis is the most diverse among bats by species number, with more than 100 living species distributed worldwide in a variety of habitats. Of particular interest is the mode of speciation that has produced this speciose clade, a topic complicated by difficulties in determining species boundaries and relationships among terminal clades, even in well-studied North American species such as the Western Long-Eared bats and little brown bats from North America.
Myotis evotis and M. thysanodes have extensive ranges from northwestern US to central Mexico, and may co-occur in part of their distribution. Myotis keenii has a small distribution in coastal areas of the Pacific Northwest, but it may also co-occur with M. evotis and M. thysanodes, especially in the southern part of its distribution. Field observations suggest that the WLE bat species could have hybridized in sympatric zones (T. Dewey pers. comm.)
I do not receive any commission from the sequencing services I am mentioning. It is just a reference point in case you want to use similar techniques. If you are interested in detailed protocols, just ask me.
I designed a set of capture probes to target exons linked to reproduction and immunity in Myotis bats. I purchased myBaits® Custom Target Capture Kits from arbor biosciences and built pre-enrichment TruSeq-like libraries following protocols and indices designed by badDNA@UGA lab. The final pooled libraries were sequenced at the GGBC of University of Georgia using Illumina technologies.
Morales AE*, Fenton MB, Carstens BC, Simmons NB (2021) Comment on “Population genetics reveal Myotis keenii (Keen’s myotis) and Myotis evotis (long-eared myotis) to be a single species”. Canadian Journal of Zoology. 99: 415-422.
Morales AE, Carstens BC (2018) Evidence that Myotis lucifugus ‘subspecies’ are five non-sister species, despite gene flow. Systematic Biology. 67:756–769.
6. Carstens BC, Morales AE, Jackson N, O’Meara BC (2017) Objective choice of Phylogeographic Models. Molecular Phylogenetics and Evolution. 116:136–140.
Morales AE, Jackson N, Dewey T, O’Meara BC, Carstens BC (2017) Speciation with gene flow in North American Myotis bats. Systematic Biology. 66:440–452.
–– New Tool for species delimitation and demographic model selection accounting for gene flow: PHRAPL
Collaborations
Even though most of my research has focused on bats and mammals, one of my main goals has been to understand the evolutionary and ecological processes that promote divergence among lineages, and the skills I have acquired can be applied to almost any system. I have thus collaborated with colleagues from different universities to generate or analyze genetic/genomic data from salamanders, penguins, and ants. I would be happy to expand this list!
- Unisexual Ambystoma salamanders [project led by Rob Denton]
- Megalomyrmex ants [project led by Rachelle Adams]
- Rockhoppers penguins [project led by Herman L. Mays]
– Mays H, Oehler D, Morrison K, Morales AE, Lycans A, …, Weakley L. (In Review) Phylogeography, population structure, gene flow and species delimitation in Rockhopper penguins (Eudyptes chrysocome and Eudyptes moseleyi). Journal of Heredity.
– Denton RD, Morales AE, Gibbs HL (2018) Genome-specific histories of introgression into a polyploid unisexual salamander lineage as revealed using ultraconserved genetic elements.Evolution. 72:1689–1700.
